Starting phenix.refine on Mon May 20 17:17:05 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1wl3.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1wl3/1wl3.mtz" } 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 { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 8905 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4443 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 270} Chain: "B" Number of atoms: 4462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4462 Classifications: {'peptide': 278} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 271} Time building chain proxies: 2.95, per 1000 atoms: 0.33 Number of scatterers: 8905 At special positions: 0 Unit cell: (149.548, 149.548, 68.031, 90, 90, 90) Space group: P 4 21 2 (No. 90) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 O 823 8.00 N 729 7.00 C 2831 6.00 H 4498 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 5.49 Conformation dependent library (CDL) restraints added in 490.2 milliseconds 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Time building geometry restraints manager: 4.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 4496 1.15 - 1.31: 769 1.31 - 1.48: 1661 1.48 - 1.64: 2002 1.64 - 1.81: 46 Bond restraints: 8974 Sorted by residual: bond pdb=" N GLY B 56 " pdb=" H GLY B 56 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 22 " pdb=" H GLN A 22 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG B 88 " pdb=" HE ARG B 88 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU A 144 " pdb=" H LEU A 144 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS B 118 " pdb=" HE2 HIS B 118 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8969 not shown) Histogram of bond angle deviations from ideal: 97.16 - 104.54: 115 104.54 - 111.91: 10297 111.91 - 119.29: 2244 119.29 - 126.66: 3608 126.66 - 134.03: 30 Bond angle restraints: 16294 Sorted by residual: angle pdb=" N LEU B 38 " pdb=" CA LEU B 38 " pdb=" C LEU B 38 " ideal model delta sigma weight residual 111.11 124.42 -13.31 1.20e+00 6.94e-01 1.23e+02 angle pdb=" N GLU B 14 " pdb=" CA GLU B 14 " pdb=" C GLU B 14 " ideal model delta sigma weight residual 112.23 102.63 9.60 1.26e+00 6.30e-01 5.81e+01 angle pdb=" N ARG B 286 " pdb=" CA ARG B 286 " pdb=" C ARG B 286 " ideal model delta sigma weight residual 112.87 104.22 8.65 1.20e+00 6.94e-01 5.20e+01 angle pdb=" N ARG A 286 " pdb=" CA ARG A 286 " pdb=" C ARG A 286 " ideal model delta sigma weight residual 110.80 125.14 -14.34 2.13e+00 2.20e-01 4.53e+01 angle pdb=" N GLY B 168 " pdb=" CA GLY B 168 " pdb=" C GLY B 168 " ideal model delta sigma weight residual 112.83 120.50 -7.67 1.22e+00 6.72e-01 3.96e+01 ... (remaining 16289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.89: 3699 15.89 - 31.78: 227 31.78 - 47.67: 111 47.67 - 63.56: 81 63.56 - 79.45: 14 Dihedral angle restraints: 4132 sinusoidal: 2289 harmonic: 1843 Sorted by residual: dihedral pdb=" C ASP A 287 " pdb=" N ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual -122.60 -131.21 8.61 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CA ASP A 287 " pdb=" CB ASP A 287 " ideal model delta harmonic sigma weight residual 122.80 131.25 -8.45 0 2.50e+00 1.60e-01 1.14e+01 dihedral pdb=" CG ARG A 243 " pdb=" CD ARG A 243 " pdb=" NE ARG A 243 " pdb=" CZ ARG A 243 " ideal model delta sinusoidal sigma weight residual -180.00 -137.85 -42.15 2 1.50e+01 4.44e-03 9.61e+00 ... (remaining 4129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 495 0.097 - 0.194: 152 0.194 - 0.291: 22 0.291 - 0.388: 1 0.388 - 0.485: 3 Chirality restraints: 673 Sorted by residual: chirality pdb=" CA LEU B 38 " pdb=" N LEU B 38 " pdb=" C LEU B 38 " pdb=" CB LEU B 38 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA ASP A 287 " pdb=" N ASP A 287 " pdb=" C ASP A 287 " pdb=" CB ASP A 287 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA ARG A 286 " pdb=" N ARG A 286 " pdb=" C ARG A 286 " pdb=" CB ARG A 286 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.93e+00 ... (remaining 670 not shown) Planarity restraints: 1313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 171 " -0.140 2.00e-02 2.50e+03 5.27e-02 8.34e+01 pdb=" CG PHE A 171 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 171 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 171 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 171 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 171 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE A 171 " 0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE A 171 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 171 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 171 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 251 " 0.084 2.00e-02 2.50e+03 2.57e-02 2.63e+01 pdb=" CG TRP B 251 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 251 " -0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP B 251 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP B 251 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP B 251 " -0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 251 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 251 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 251 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP B 251 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP B 251 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 251 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 251 " 0.024 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 251 " 0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP B 251 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 11 " 0.072 2.00e-02 2.50e+03 2.68e-02 2.16e+01 pdb=" CG TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 11 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 11 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 11 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 11 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 11 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 11 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR A 11 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 11 " -0.031 2.00e-02 2.50e+03 pdb=" HE1 TYR A 11 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 11 " 0.005 2.00e-02 2.50e+03 ... (remaining 1310 not shown) Histogram of nonbonded interaction distances: 1.03 - 1.75: 107 1.75 - 2.46: 5136 2.46 - 3.17: 29832 3.17 - 3.89: 39137 3.89 - 4.60: 59445 Nonbonded interactions: 133657 Sorted by model distance: nonbonded pdb=" HD2 PHE A 171 " pdb=" HA2 GLY A 197 " model vdw 1.033 2.270 nonbonded pdb=" HH TYR B 11 " pdb=" HG2 LYS B 15 " model vdw sym.op. 1.245 2.270 -y+1,-x+1,-z+1 nonbonded pdb=" HE3 LYS A 93 " pdb="HH22 ARG B 259 " model vdw sym.op. 1.356 2.270 y+1/2,-x+1/2,z nonbonded pdb=" O LEU A 170 " pdb=" H LEU A 173 " model vdw 1.370 1.850 nonbonded pdb=" H GLU A 157 " pdb=" HG3 GLU A 157 " model vdw 1.448 2.270 ... (remaining 133652 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: 5 Type Number sf(0) Gaussians S 24 15.91 1 O 823 7.97 1 N 729 6.97 1 C 2831 5.97 1 H 4498 1.00 1 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 ===================== Setting occupancies to: 1.000: selected atoms: 4498 of 8905 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8905 n_use_u_iso = 8905 n_use_u_aniso = 0 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 = 8905 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8905 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8905 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (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 { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1wl3_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4498 occupancy sum: 4498.00 (% of total atoms 50.51) Rotatable: count: 1300 occupancy sum: 1300.00 (% of total atoms 14.60) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 41.75 A, n_refl.=9579 (all), 5.31 % free)-------------| | | | r_work= 0.4622 r_free= 0.4889 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 3.693737 | | target function (ml) not normalized (work): 33502.195647 | | target function (ml) not normalized (free): 2005.039620 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.75 - 5.55 0.98 2477 144 0.4989 0.4770 4.495 5.1259| | 2: 5.55 - 4.41 0.96 2311 121 0.3871 0.4311 3.6506 3.6312| | 3: 4.41 - 3.85 0.93 2220 112 0.4708 0.5130 3.3519 3.4414| | 4: 3.85 - 3.50 0.88 2062 132 0.4868 0.5658 3.1476 3.3492| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 41.75 - 5.55 2477 144 0.45 54.77 0.83 0.03 995.04| | 2: 5.55 - 4.41 2311 121 0.46 55.10 1.34 0.02 444.27| | 3: 4.41 - 3.85 2220 112 0.63 41.12 1.62 0.03 154.61| | 4: 3.85 - 3.50 2062 132 0.56 47.24 1.53 0.03 126.03| |alpha: min = 0.02 max = 0.03 mean = 0.03| |beta: min = 126.03 max = 995.04 mean = 451.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.52| |phase err.(work): min = 0.00 max = 89.98 mean = 49.80| |phase err.(test): min = 0.00 max = 89.87 mean = 48.86| |-----------------------------------------------------------------------------| ----------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 : 0.005 0.085 4476 Z= 0.328 Angle : 1.323 14.340 6012 Z= 0.928 Chirality : 0.095 0.485 673 Planarity : 0.005 0.053 772 Dihedral : 15.841 79.450 1703 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 2.36 % Allowed : 5.26 % Favored : 92.38 % Rotamer: Outliers : 3.40 % Allowed : 7.43 % Favored : 89.17 % 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: -4.05 (0.27), residues: 551 helix: -2.44 (0.18), residues: 445 sheet: None (None), residues: 0 loop : -2.62 (0.54), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 161 TYR 0.056 0.011 TYR A 11 PHE 0.085 0.007 PHE A 171 TRP 0.056 0.008 TRP B 251 HIS 0.001 0.000 HIS B 118 Individual atomic B min max mean iso aniso Overall: 21.36 100.34 56.13 1.48 4407 0 Protein: 21.36 100.34 56.13 1.48 4407 0 Chain A: 24.53 91.36 59.78 N/A 2198 0 Chain B: 21.36 100.34 52.50 N/A 2209 0 Histogram: Values Number of atoms 21.36 - 29.26 126 29.26 - 37.16 321 37.16 - 45.05 629 45.05 - 52.95 817 52.95 - 60.85 833 60.85 - 68.75 769 68.75 - 76.65 497 76.65 - 84.54 290 84.54 - 92.44 121 92.44 - 100.34 4 |-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 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9579 (all), 5.31 % free)-------------| | | | r_work= 0.4622 r_free= 0.4889 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 3.693737 | | target function (ml) not normalized (work): 33502.195647 | | target function (ml) not normalized (free): 2005.039620 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4642 0.4622 0.4889 n_refl.: 9579 re-set all scales: r(all,work,free)=0.4642 0.4622 0.4889 n_refl.: 9579 remove outliers: r(all,work,free)=0.4621 0.4602 0.4849 n_refl.: 9561 overall B=23.46 to atoms: r(all,work,free)=0.5303 0.5276 0.5612 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2595 0.2579 0.2869 n_refl.: 9561 remove outliers: r(all,work,free)=0.2595 0.2579 0.2869 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.4381 1220.303 1224.065 1.165 1.112 0.405 16.951-13.495 94.17 95 2 0.3095 1758.562 1726.307 0.965 1.108 0.377 13.466-10.728 99.01 188 12 0.2313 2173.838 2118.815 1.052 1.095 0.368 10.715-8.517 98.92 348 19 0.1972 2052.862 2022.519 1.059 1.081 0.351 8.515-6.766 98.37 689 37 0.2427 1366.340 1306.911 0.994 1.051 0.326 6.761-5.374 96.29 1294 80 0.2758 856.308 812.122 0.876 1.007 0.279 5.373-4.268 96.39 2549 123 0.2287 952.347 913.140 0.992 0.935 0.223 4.267-3.500 89.96 3807 225 0.2939 675.635 628.033 1.221 0.844 0.129 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-0.4189 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.551948 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.168723 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2539 0.2781 0.0243 0.002 0.5 1.6 0.0 2.3 0 0.125 0.2486 0.2778 0.0293 0.002 0.5 1.9 0.0 2.3 0 0.250 0.2403 0.2776 0.0373 0.003 0.5 2.1 0.0 2.3 0 0.500 0.2329 0.2781 0.0452 0.004 0.6 3.4 0.0 2.3 0 1.000 0.2247 0.2843 0.0596 0.005 0.7 4.4 0.0 2.1 0 2.000 0.2205 0.2865 0.0660 0.007 0.8 5.6 0.0 2.8 0 3.000 0.2180 0.2905 0.0726 0.008 0.9 7.8 0.0 3.2 0 4.000 0.2163 0.2925 0.0763 0.010 1.0 8.9 0.0 3.4 0 5.000 0.2146 0.2944 0.0799 0.011 1.1 9.6 0.0 4.2 0 6.000 0.2128 0.2958 0.0830 0.012 1.2 10.8 0.0 4.2 0 7.000 0.2116 0.2966 0.0850 0.014 1.3 12.7 0.0 4.7 0 8.000 0.2103 0.2977 0.0875 0.015 1.3 13.1 0.0 4.9 0 9.000 0.2091 0.2965 0.0873 0.016 1.4 14.8 0.0 5.3 0 10.000 0.2141 0.2960 0.0819 0.011 1.1 10.0 0.0 4.2 0 6.276 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2539 0.2781 0.0243 0.002 0.5 1.6 0.0 2.3 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.39 27.81 2.43 1.044 79.246 0.169 0.073 25.39 27.62 2.23 2.179 79.344 0.005 0.073 24.99 27.66 2.67 2.356 79.407 0.021 0.070 23.66 27.82 4.15 5.161 79.876 0.084 0.063 23.07 27.96 4.89 6.883 80.276 0.169 0.060 22.79 28.01 5.22 8.000 80.562 0.253 0.059 22.56 28.09 5.53 8.969 80.839 0.337 0.058 22.23 28.18 5.95 10.520 81.371 0.422 0.056 22.11 28.23 6.11 11.177 81.556 0.506 0.056 22.02 28.25 6.23 11.768 81.727 0.591 0.055 21.86 28.32 6.46 12.712 82.039 0.675 0.055 21.79 28.36 6.57 13.175 82.172 0.759 0.054 21.69 28.42 6.73 13.892 82.397 0.844 0.054 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.005 Accepted refinement result: 25.39 27.62 2.23 2.179 79.344 0.005 0.073 Individual atomic B min max mean iso aniso Overall: 50.62 120.96 79.79 1.50 4407 0 Protein: 50.62 120.96 79.79 1.50 4407 0 Chain A: 53.44 112.53 83.28 N/A 2198 0 Chain B: 50.62 120.96 76.31 N/A 2209 0 Histogram: Values Number of atoms 50.62 - 57.65 173 57.65 - 64.69 414 64.69 - 71.72 740 71.72 - 78.75 836 78.75 - 85.79 816 85.79 - 92.82 637 92.82 - 99.85 440 99.85 - 106.89 246 106.89 - 113.92 101 113.92 - 120.96 4 =========================== Idealize ADP of riding H ========================== r_work=0.2539 r_free=0.2762 r_work=0.2527 r_free=0.2756 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2527 r_free= 0.2756 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ls_wunit_k1) (work): 0.072113 | | target function (ls_wunit_k1) not normalized (work): 652.913240 | | target function (ls_wunit_k1) not normalized (free): 43.338696 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2540 0.2527 0.2756 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5274 0.5246 0.5616 n_refl.: 9561 remove outliers: r(all,work,free)=0.5274 0.5246 0.5616 n_refl.: 9561 overall B=1.39 to atoms: r(all,work,free)=0.5317 0.5288 0.5660 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2550 0.2537 0.2784 n_refl.: 9561 remove outliers: r(all,work,free)=0.2550 0.2537 0.2784 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.3841 515.631 511.416 1.350 1.023 0.410 16.951-13.495 94.17 95 2 0.2770 743.070 739.480 1.032 1.025 0.366 13.466-10.728 99.01 188 12 0.2225 918.542 905.294 1.127 1.019 0.356 10.715-8.517 98.92 348 19 0.1837 867.424 858.012 1.133 1.016 0.349 8.515-6.766 98.37 689 37 0.2286 577.339 557.133 1.049 1.005 0.348 6.761-5.374 96.29 1294 80 0.2742 361.828 344.374 0.915 0.991 0.297 5.373-4.268 96.39 2549 123 0.2296 402.408 384.906 0.954 0.966 0.226 4.267-3.500 89.96 3807 225 0.2941 285.485 265.611 1.087 0.941 0.133 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.2527 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.236039 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.044284 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2587 0.2787 0.0200 0.002 0.4 1.0 0.0 1.7 0 0.007 0.2540 0.2782 0.0242 0.002 0.4 1.1 0.0 1.9 0 0.022 0.2476 0.2754 0.0278 0.002 0.4 1.3 0.0 1.9 0 0.044 0.2429 0.2741 0.0312 0.002 0.4 1.5 0.0 2.1 0 0.066 0.2395 0.2760 0.0365 0.002 0.4 1.9 0.0 2.1 0 0.088 0.2368 0.2770 0.0403 0.002 0.4 2.0 0.0 1.9 0 0.110 0.2349 0.2769 0.0420 0.002 0.5 2.5 0.0 1.9 0 0.132 0.2333 0.2774 0.0441 0.003 0.5 2.8 0.0 1.9 0 0.154 0.2414 0.2776 0.0362 0.002 0.4 1.9 0.0 1.9 0 0.073 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2587 0.2787 0.0200 0.002 0.4 1.0 0.0 1.7 0 0.007 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.87 27.87 2.00 11.426 88.913 0.044 6.188 26.38 28.15 1.76 11.706 89.729 0.001 6.198 25.37 27.77 2.41 11.569 88.900 0.006 6.168 23.66 27.83 4.17 12.246 90.153 0.022 6.110 23.16 27.94 4.78 13.538 90.857 0.044 6.096 23.13 27.97 4.84 13.438 90.674 0.066 6.096 22.99 28.03 5.04 14.063 90.958 0.089 6.092 22.89 28.07 5.18 14.624 91.196 0.111 6.090 22.87 28.11 5.24 14.836 91.270 0.133 6.090 22.80 28.13 5.33 15.301 91.456 0.155 6.088 22.78 28.16 5.39 15.568 91.556 0.177 6.088 22.73 28.20 5.48 15.984 91.713 0.199 6.087 22.71 28.23 5.52 16.226 91.799 0.221 6.086 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 25.37 27.77 2.41 11.569 88.900 0.006 6.168 Individual atomic B min max mean iso aniso Overall: 53.41 123.95 81.16 2.33 4407 0 Protein: 53.41 123.95 81.16 2.33 4407 0 Chain A: 54.83 113.51 84.55 N/A 2198 0 Chain B: 53.41 123.95 77.78 N/A 2209 0 Histogram: Values Number of atoms 53.41 - 60.46 166 60.46 - 67.52 523 67.52 - 74.57 815 74.57 - 81.62 845 81.62 - 88.68 826 88.68 - 95.73 602 95.73 - 102.78 370 102.78 - 109.84 216 109.84 - 116.89 40 116.89 - 123.95 4 =========================== Idealize ADP of riding H ========================== r_work=0.2537 r_free=0.2777 r_work=0.2532 r_free=0.2776 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2532 r_free= 0.2776 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.166630 | | target function (ml) not normalized (work): 55832.666633 | | target function (ml) not normalized (free): 3160.645297 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2545 0.2532 0.2776 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5322 0.5295 0.5652 n_refl.: 9561 remove outliers: r(all,work,free)=0.5322 0.5295 0.5652 n_refl.: 9561 overall B=0.81 to atoms: r(all,work,free)=0.5347 0.5320 0.5678 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2544 0.2529 0.2808 n_refl.: 9561 remove outliers: r(all,work,free)=0.2544 0.2529 0.2808 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.3986 515.631 529.718 1.381 1.036 0.420 16.951-13.495 94.17 95 2 0.2765 743.070 743.331 1.031 1.037 0.371 13.466-10.728 99.01 188 12 0.2247 918.542 903.729 1.107 1.031 0.359 10.715-8.517 98.92 348 19 0.1902 867.424 853.706 1.103 1.025 0.349 8.515-6.766 98.37 689 37 0.2307 577.339 556.365 1.034 1.012 0.349 6.761-5.374 96.29 1294 80 0.2812 361.828 343.487 0.915 0.993 0.298 5.373-4.268 96.39 2549 123 0.2303 402.408 384.297 0.961 0.960 0.228 4.267-3.500 89.96 3807 225 0.2844 285.485 266.147 1.103 0.925 0.135 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.1478 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1102 Ramachandran restraints generated. 551 Oldfield, 0 Emsley, 551 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2529 r_free=0.2808 After: r_work=0.2529 r_free=0.2807 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.370858 wxc_scale = 0.021 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.045490 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2528 0.2805 0.0277 0.002 0.4 1.1 0.0 1.7 0 0.007 0.2527 0.2805 0.0278 0.002 0.4 1.1 0.0 1.7 0 0.022 0.2526 0.2805 0.0279 0.002 0.4 1.1 0.0 1.7 0 0.043 0.2525 0.2806 0.0282 0.002 0.4 1.1 0.0 1.7 0 0.065 0.2522 0.2804 0.0282 0.002 0.4 1.1 0.0 1.7 0 0.087 0.2520 0.2802 0.0282 0.002 0.4 1.1 0.0 1.7 0 0.108 0.2515 0.2799 0.0285 0.002 0.4 1.2 0.0 1.7 0 0.130 0.2511 0.2795 0.0284 0.003 0.4 1.2 0.0 1.7 0 0.152 0.2523 0.2803 0.0279 0.002 0.4 1.1 0.0 1.7 0 0.072 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2523 0.2803 0.0279 0.002 0.4 1.1 0.0 1.7 0 0.072 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.23 28.03 2.79 11.688 89.906 0.045 6.172 26.21 28.53 2.32 11.914 90.536 0.001 6.202 25.19 28.02 2.83 11.712 89.893 0.006 6.171 24.40 28.06 3.66 12.068 89.807 0.023 6.145 22.99 28.09 5.10 13.166 91.188 0.045 6.101 22.86 28.17 5.31 13.623 91.375 0.068 6.097 22.72 28.23 5.51 14.199 91.674 0.091 6.094 22.64 28.28 5.64 14.654 91.891 0.114 6.092 22.57 28.32 5.76 15.121 92.102 0.136 6.090 22.53 28.35 5.82 15.457 92.246 0.159 6.089 22.49 28.40 5.91 15.810 92.394 0.182 6.088 22.46 28.43 5.98 16.108 92.514 0.205 6.088 22.43 28.48 6.05 16.414 92.633 0.227 6.087 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 25.19 28.02 2.83 11.712 89.893 0.006 6.171 Individual atomic B min max mean iso aniso Overall: 54.17 125.06 81.94 2.41 4407 0 Protein: 54.17 125.06 81.94 2.41 4407 0 Chain A: 55.82 114.60 85.31 N/A 2198 0 Chain B: 54.17 125.06 78.59 N/A 2209 0 Histogram: Values Number of atoms 54.17 - 61.26 152 61.26 - 68.34 530 68.34 - 75.43 829 75.43 - 82.52 853 82.52 - 89.61 825 89.61 - 96.70 610 96.70 - 103.79 358 103.79 - 110.88 214 110.88 - 117.97 32 117.97 - 125.06 4 =========================== Idealize ADP of riding H ========================== r_work=0.2519 r_free=0.2802 r_work=0.2518 r_free=0.2802 ----------X-ray data---------- |--(resolution: 3.50 - 41.75 A, n_refl.=9561 (all), 5.30 % free)-------------| | | | r_work= 0.2518 r_free= 0.2802 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.170553 | | target function (ml) not normalized (work): 55868.184634 | | target function (ml) not normalized (free): 3167.323900 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 41.75 - 5.55 0.97 2463 143 0.2447 0.2797 6.5517 6.6455| | 2: 5.55 - 4.41 0.96 2310 121 0.2336 0.2546 6.1985 6.2218| | 3: 4.41 - 3.85 0.93 2220 112 0.2531 0.3052 6.0288 6.1557| | 4: 3.85 - 3.50 0.88 2061 131 0.3016 0.2891 5.8365 5.9141| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 41.75 - 5.55 2463 143 0.72 31.85 1.00 0.94 86447.90| | 2: 5.55 - 4.41 2310 121 0.76 29.44 1.00 0.98 50187.44| | 3: 4.41 - 3.85 2220 112 0.79 27.09 1.06 0.96 27718.35| | 4: 3.85 - 3.50 2061 131 0.76 29.88 0.93 0.89 19040.63| |alpha: min = 0.89 max = 0.98 mean = 0.95| |beta: min = 19040.63 max = 86447.90 mean = 47452.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.76| |phase err.(work): min = 0.00 max = 89.93 mean = 29.62| |phase err.(test): min = 0.00 max = 89.44 mean = 29.67| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2534 0.2518 0.2802 n_refl.: 9561 re-set all scales: r(all,work,free)=0.5345 0.5318 0.5677 n_refl.: 9561 remove outliers: r(all,work,free)=0.5345 0.5318 0.5677 n_refl.: 9561 overall B=-0.24 to atoms: r(all,work,free)=0.5338 0.5310 0.5670 n_refl.: 9561 bulk-solvent and scaling: r(all,work,free)=0.2540 0.2525 0.2797 n_refl.: 9561 remove outliers: r(all,work,free)=0.2540 0.2525 0.2797 n_refl.: 9561 ======================== 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 41.747-17.006 86.11 84 9 0.4000 515.631 524.932 1.405 1.014 0.420 16.951-13.495 94.17 95 2 0.2826 743.070 740.523 1.042 1.017 0.370 13.466-10.728 99.01 188 12 0.2247 918.542 903.005 1.156 1.012 0.370 10.715-8.517 98.92 348 19 0.1897 867.424 859.609 1.133 1.010 0.350 8.515-6.766 98.37 689 37 0.2310 577.339 558.901 1.054 1.001 0.350 6.761-5.374 96.29 1294 80 0.2806 361.828 339.340 0.913 0.990 0.301 5.373-4.268 96.39 2549 123 0.2297 402.408 383.215 0.957 0.970 0.241 4.267-3.500 89.96 3807 225 0.2835 285.485 266.989 1.077 0.952 0.131 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.5485 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4622 0.4889 0.005 1.323 21.4 100.3 56.1 0 0.000 1_bss: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_settarget: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_updatephipsi: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_weight: 0.2579 0.2869 0.005 1.323 44.8 123.8 79.6 0 0.000 1_xyzrec: 0.2539 0.2781 0.002 0.461 44.8 123.8 79.6 0 0.172 1_adp: 0.2539 0.2762 0.002 0.461 50.6 121.0 79.8 0 0.172 1_regHadp: 0.2527 0.2756 0.002 0.461 50.6 121.0 79.8 0 0.172 2_bss: 0.2537 0.2784 0.002 0.461 52.0 122.3 81.2 0 0.172 2_settarget: 0.2537 0.2784 0.002 0.461 52.0 122.3 81.2 0 0.172 2_updatephipsi: 0.2537 0.2784 0.002 0.461 52.0 122.3 81.2 0 0.172 2_updatecdl: 0.2537 0.2784 0.002 0.509 52.0 122.3 81.2 0 0.172 2_weight: 0.2537 0.2784 0.002 0.509 52.0 122.3 81.2 0 0.172 2_xyzrec: 0.2587 0.2787 0.002 0.361 52.0 122.3 81.2 0 0.222 2_adp: 0.2537 0.2777 0.002 0.361 53.4 123.9 81.2 0 0.222 2_regHadp: 0.2532 0.2776 0.002 0.361 53.4 123.9 81.2 0 0.222 3_bss: 0.2529 0.2808 0.002 0.361 54.2 124.8 82.0 0 0.222 3_settarget: 0.2529 0.2808 0.002 0.361 54.2 124.8 82.0 0 0.222 3_updatephipsi: 0.2529 0.2808 0.002 0.361 54.2 124.8 82.0 0 0.222 3_updatecdl: 0.2529 0.2808 0.002 0.376 54.2 124.8 82.0 0 0.222 3_setrh: 0.2529 0.2807 0.002 0.376 54.2 124.8 82.0 0 0.222 3_weight: 0.2529 0.2807 0.002 0.376 54.2 124.8 82.0 0 0.222 3_xyzrec: 0.2523 0.2803 0.002 0.353 54.2 124.8 82.0 0 0.223 3_adp: 0.2519 0.2802 0.002 0.353 54.2 125.1 81.9 0 0.223 3_regHadp: 0.2518 0.2802 0.002 0.353 54.2 125.1 81.9 0 0.223 end: 0.2525 0.2797 0.002 0.353 53.9 124.8 81.7 0 0.223 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1wl3_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1wl3_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 12.7500 Refinement macro-cycles (run) : 311.6500 Write final files (write_after_run_outputs) : 17.0600 Total : 341.4600 Total CPU time: 6.50 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:30 PDT -0700 (1716251730.37 s) Start R-work = 0.2579, R-free = 0.2869 Final R-work = 0.2525, R-free = 0.2797 =============================================================================== Job complete usr+sys time: 407.10 seconds wall clock time: 18 minutes 44.93 seconds (1124.93 seconds total)