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/2ogu.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.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/2ogu.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2ogu.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2ogu/2ogu.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: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3448 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3448 Classifications: {'peptide': 221} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Time building chain proxies: 1.27, per 1000 atoms: 0.37 Number of scatterers: 3448 At special positions: 0 Unit cell: (165.889, 165.889, 82.223, 90, 90, 120) Space group: R 3 2 :H (No. 155) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 338 8.00 N 305 7.00 C 1069 6.00 H 1729 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: 2.24 Conformation dependent library (CDL) restraints added in 414.6 milliseconds 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 406 Time building geometry restraints manager: 1.96 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: 1726 1.15 - 1.31: 311 1.31 - 1.48: 654 1.48 - 1.65: 767 1.65 - 1.82: 11 Bond restraints: 3469 Sorted by residual: bond pdb=" CD GLU A 325 " pdb=" OE1 GLU A 325 " ideal model delta sigma weight residual 1.249 1.413 -0.164 1.90e-02 2.77e+03 7.49e+01 bond pdb=" N SER A 273 " pdb=" H SER A 273 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N SER A 235 " pdb=" H SER A 235 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG A 329 " pdb="HH22 ARG A 329 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASN A 174 " pdb=" H ASN A 174 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 3464 not shown) Histogram of bond angle deviations from ideal: 96.85 - 107.61: 528 107.61 - 118.37: 4323 118.37 - 129.13: 1425 129.13 - 139.89: 9 139.89 - 150.65: 1 Bond angle restraints: 6286 Sorted by residual: angle pdb=" CB ARG A 213 " pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " ideal model delta sigma weight residual 111.30 150.65 -39.35 2.30e+00 1.89e-01 2.93e+02 angle pdb=" CG ARG A 213 " pdb=" CD ARG A 213 " pdb=" NE ARG A 213 " ideal model delta sigma weight residual 112.00 134.35 -22.35 2.20e+00 2.07e-01 1.03e+02 angle pdb=" N ASP A 202 " pdb=" CA ASP A 202 " pdb=" C ASP A 202 " ideal model delta sigma weight residual 107.32 118.69 -11.37 1.65e+00 3.67e-01 4.75e+01 angle pdb=" N THR A 127 " pdb=" CA THR A 127 " pdb=" C THR A 127 " ideal model delta sigma weight residual 112.68 104.82 7.86 1.33e+00 5.65e-01 3.50e+01 angle pdb=" C VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta sigma weight residual 110.52 101.59 8.93 1.57e+00 4.06e-01 3.24e+01 ... (remaining 6281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 1348 17.94 - 35.89: 149 35.89 - 53.83: 71 53.83 - 71.77: 28 71.77 - 89.72: 2 Dihedral angle restraints: 1598 sinusoidal: 909 harmonic: 689 Sorted by residual: dihedral pdb=" C THR A 261 " pdb=" N THR A 261 " pdb=" CA THR A 261 " pdb=" CB THR A 261 " ideal model delta harmonic sigma weight residual -122.00 -133.67 11.67 0 2.50e+00 1.60e-01 2.18e+01 dihedral pdb=" C VAL A 265 " pdb=" N VAL A 265 " pdb=" CA VAL A 265 " pdb=" CB VAL A 265 " ideal model delta harmonic sigma weight residual -122.00 -111.17 -10.83 0 2.50e+00 1.60e-01 1.88e+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 122.80 132.91 -10.11 0 2.50e+00 1.60e-01 1.64e+01 ... (remaining 1595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 197 0.092 - 0.183: 58 0.183 - 0.275: 13 0.275 - 0.366: 2 0.366 - 0.458: 1 Chirality restraints: 271 Sorted by residual: 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 5.24e+00 chirality pdb=" CA THR A 261 " pdb=" N THR A 261 " pdb=" C THR A 261 " pdb=" CB THR A 261 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 268 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " 0.012 2.00e-02 2.50e+03 1.08e-02 3.52e+00 pdb=" CG PHE A 232 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 232 " -0.005 2.00e-02 2.50e+03 pdb=" HD2 PHE A 232 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 PHE A 232 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 232 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 232 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 333 " -0.019 2.00e-02 2.50e+03 1.07e-02 3.44e+00 pdb=" CG TYR A 333 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 333 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 333 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 333 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 333 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 333 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 333 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 333 " 0.008 2.00e-02 2.50e+03 pdb=" HD2 TYR A 333 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TYR A 333 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 TYR A 333 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 247 " -0.002 2.00e-02 2.50e+03 7.99e-03 1.92e+00 pdb=" CG TYR A 247 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 247 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 247 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 247 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 247 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 247 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 247 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 TYR A 247 " -0.001 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 1.12 - 1.82: 110 1.82 - 2.51: 2893 2.51 - 3.21: 10969 3.21 - 3.90: 14997 3.90 - 4.60: 22785 Nonbonded interactions: 51754 Sorted by model distance: nonbonded pdb="HH11 ARG A 262 " pdb=" HB ILE A 304 " model vdw sym.op. 1.119 2.270 -x+2,-x+y+1,-z+1 nonbonded pdb=" HB3 SER A 126 " pdb=" HD1 PHE A 232 " model vdw sym.op. 1.225 2.270 -x+2,-x+y+1,-z+1 nonbonded pdb="HD22 LEU A 330 " pdb="HD11 ILE A 334 " model vdw 1.269 2.440 nonbonded pdb=" HB3 ASP A 202 " pdb="HG23 VAL A 205 " model vdw 1.288 2.440 nonbonded pdb=" HG3 GLU A 133 " pdb=" HG SER A 240 " model vdw sym.op. 1.307 2.270 -x+2,-x+y+1,-z+1 ... (remaining 51749 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 7 15.96 2 O 338 7.97 1 N 305 6.97 1 C 1069 5.97 2 H 1729 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: 1729 of 3448 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3448 n_use_u_iso = 3448 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 = 3448 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3448 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3448 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 = "2ogu_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1729 occupancy sum: 1729.00 (% of total atoms 50.22) Rotatable: count: 500 occupancy sum: 500.00 (% of total atoms 14.52) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.23 - 28.61 A, n_refl.=6717 (all), 4.75 % free)-------------| | | | r_work= 0.4624 r_free= 0.5099 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.058324 | | target function (ml) not normalized (work): 38761.159679 | | target function (ml) not normalized (free): 1913.185558 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 28.61 - 4.07 0.94 3212 159 0.4154 0.4599 6.5974 6.5063| | 2: 4.07 - 3.23 0.96 3186 160 0.6033 0.6527 5.5149 5.4918| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 28.61 - 4.07 3212 159 0.43 57.03 0.98 0.24 84005.03| | 2: 4.07 - 3.23 3186 160 0.53 49.94 1.93 0.59 9836.65| |alpha: min = 0.24 max = 0.59 mean = 0.42| |beta: min = 9836.65 max = 84005.03 mean = 47071.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.48| |phase err.(work): min = 0.00 max = 89.90 mean = 53.50| |phase err.(test): min = 2.39 max = 89.71 mean = 55.64| |-----------------------------------------------------------------------------| ----------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 : 0.013 0.164 1740 Z= 0.742 Angle : 1.793 39.348 2349 Z= 1.075 Chirality : 0.093 0.458 271 Planarity : 0.004 0.014 311 Dihedral : 20.776 89.715 667 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 3.20 % Allowed : 14.61 % Favored : 82.19 % Rotamer: Outliers : 20.63 % Allowed : 14.81 % Favored : 64.55 % Cbeta Deviations : 1.48 % 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: -5.26 (0.44), residues: 219 helix: -4.53 (0.27), residues: 89 sheet: -0.37 (0.86), residues: 42 loop : -3.82 (0.47), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 329 TYR 0.014 0.004 TYR A 247 PHE 0.020 0.003 PHE A 232 TRP 0.005 0.002 TRP A 123 HIS 0.003 0.001 HIS A 193 Individual atomic B min max mean iso aniso Overall: 91.32 163.00 123.43 0.77 1719 0 Protein: 91.32 163.00 123.43 0.77 1719 0 Chain A: 91.32 163.00 123.43 N/A 1719 0 Histogram: Values Number of atoms 91.32 - 98.49 108 98.49 - 105.66 221 105.66 - 112.82 174 112.82 - 119.99 133 119.99 - 127.16 184 127.16 - 134.33 354 134.33 - 141.50 450 141.50 - 148.66 70 148.66 - 155.83 17 155.83 - 163.00 8 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1 = 5 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6717 (all), 4.75 % free)-------------| | | | r_work= 0.4624 r_free= 0.5099 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.058324 | | target function (ml) not normalized (work): 38761.159679 | | target function (ml) not normalized (free): 1913.185558 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4647 0.4624 0.5099 n_refl.: 6717 re-set all scales: r(all,work,free)=0.4647 0.4624 0.5099 n_refl.: 6717 remove outliers: r(all,work,free)=0.4639 0.4616 0.5099 n_refl.: 6712 overall B=-12.08 to atoms: r(all,work,free)=0.4399 0.4379 0.4756 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2973 0.2966 0.3135 n_refl.: 6712 remove outliers: r(all,work,free)=0.2973 0.2966 0.3135 n_refl.: 6712 ======================== 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 28.612-12.706 81.97 93 7 0.2705 2116.694 2050.380 1.316 0.964 0.337 12.682-10.260 91.59 95 3 0.1550 2500.151 2446.970 1.254 0.968 0.328 10.240-8.268 91.43 185 7 0.1279 2215.464 2168.706 1.217 0.969 0.301 8.239-6.652 93.16 358 10 0.2218 1353.840 1317.902 1.163 0.975 0.286 6.641-5.360 94.83 677 38 0.3037 820.100 772.991 0.955 0.983 0.240 5.359-4.320 95.50 1280 57 0.2894 759.011 710.060 0.881 0.992 0.160 4.319-3.481 96.04 2452 119 0.3937 427.822 388.084 0.990 1.009 0.052 3.480-3.231 96.10 1253 78 0.4479 240.887 203.131 1.029 1.019 0.026 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9878 b_overall=2.3997 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.037561 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.163194 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3098 0.3314 0.0216 0.003 0.6 11.1 0.0 18.0 0 0.125 0.3072 0.3313 0.0242 0.003 0.6 9.9 0.0 18.0 0 0.250 0.3027 0.3275 0.0248 0.004 0.6 10.5 0.0 18.0 0 0.500 0.2961 0.3314 0.0353 0.005 0.7 10.8 0.0 18.0 0 1.000 0.2879 0.3306 0.0427 0.007 0.8 16.0 0.0 20.6 0 2.000 0.2828 0.3310 0.0482 0.008 0.9 20.4 0.0 20.6 0 3.000 0.2790 0.3297 0.0507 0.010 1.0 22.1 0.0 19.6 0 4.000 0.2764 0.3301 0.0537 0.012 1.2 24.5 0.0 20.1 0 5.000 0.2744 0.3319 0.0574 0.013 1.3 26.8 0.0 20.6 0 6.000 0.2720 0.3333 0.0613 0.015 1.4 29.4 0.0 20.6 0 7.000 0.2702 0.3354 0.0652 0.017 1.5 31.2 0.0 21.2 0 8.000 0.2688 0.3331 0.0642 0.018 1.5 31.8 0.0 21.7 0 9.000 0.2677 0.3276 0.0599 0.020 1.6 32.3 0.0 21.7 0 10.000 0.2729 0.3315 0.0586 0.015 1.3 28.3 0.0 20.6 0 6.519 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.3072 0.3313 0.0242 0.003 0.6 9.9 0.0 18.0 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 30.72 33.13 2.42 0.548 111.307 0.163 0.088 30.65 33.18 2.53 1.660 111.361 0.005 0.087 30.18 32.92 2.74 1.829 111.397 0.020 0.084 29.32 32.48 3.15 3.362 111.645 0.082 0.080 27.95 31.97 4.02 8.284 112.966 0.163 0.073 27.63 31.85 4.22 9.911 113.446 0.245 0.071 27.43 31.80 4.37 11.125 113.803 0.326 0.070 27.29 31.75 4.46 12.028 114.063 0.408 0.069 27.08 31.74 4.66 13.255 114.492 0.490 0.068 26.94 31.76 4.82 14.159 114.795 0.571 0.067 26.66 31.77 5.11 15.866 115.419 0.653 0.066 26.47 31.80 5.33 17.273 115.916 0.734 0.065 26.41 31.80 5.39 17.830 116.087 0.816 0.065 max suggested for this run: 22.26 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.490 Accepted refinement result: 27.08 31.74 4.66 13.255 114.492 0.490 0.068 Individual atomic B min max mean iso aniso Overall: 74.92 173.83 117.75 11.12 1719 0 Protein: 74.92 173.83 117.75 11.12 1719 0 Chain A: 74.92 173.83 117.75 N/A 1719 0 Histogram: Values Number of atoms 74.92 - 84.82 56 84.82 - 94.71 136 94.71 - 104.60 180 104.60 - 114.49 305 114.49 - 124.38 476 124.38 - 134.27 283 134.27 - 144.16 171 144.16 - 154.05 82 154.05 - 163.94 22 163.94 - 173.83 8 =========================== Idealize ADP of riding H ========================== r_work=0.2708 r_free=0.3174 r_work=0.2677 r_free=0.3156 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6712 (all), 4.75 % free)-------------| | | | r_work= 0.2677 r_free= 0.3156 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.066661 | | target function (ls_wunit_k1) not normalized (work): 426.162422 | | target function (ls_wunit_k1) not normalized (free): 30.021406 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2698 0.2677 0.3156 n_refl.: 6712 re-set all scales: r(all,work,free)=0.4375 0.4349 0.4920 n_refl.: 6712 remove outliers: r(all,work,free)=0.4375 0.4349 0.4920 n_refl.: 6712 overall B=-0.33 to atoms: r(all,work,free)=0.4369 0.4342 0.4911 n_refl.: 6712 bulk-solvent and scaling: r(all,work,free)=0.2694 0.2673 0.3142 n_refl.: 6712 remove outliers: r(all,work,free)=0.2693 0.2672 0.3142 n_refl.: 6711 ======================== 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 28.612-12.706 81.97 93 7 0.2622 1254.542 1211.368 1.171 0.975 0.328 12.682-10.260 91.59 95 3 0.1449 1481.812 1448.067 1.140 0.978 0.310 10.240-8.268 91.00 185 7 0.1087 1313.082 1290.863 1.142 0.978 0.305 8.239-6.652 93.64 358 10 0.1833 802.406 792.662 1.087 0.981 0.290 6.641-5.360 94.83 677 38 0.2670 486.064 467.547 0.907 0.986 0.231 5.359-4.320 95.50 1280 57 0.2585 449.857 429.960 0.846 0.990 0.151 4.319-3.481 96.04 2451 119 0.3575 253.409 235.710 0.986 1.000 0.044 3.480-3.231 96.10 1253 78 0.4321 142.771 122.500 1.040 1.004 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-0.5628 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.994224 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.028794 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2653 0.3161 0.0508 0.003 0.5 7.0 0.0 15.9 0 0.125 0.2606 0.3117 0.0510 0.004 0.6 9.0 0.0 15.9 0 0.250 0.2554 0.3117 0.0563 0.005 0.7 14.0 0.0 18.0 0 0.500 0.2508 0.3165 0.0657 0.009 1.0 21.0 0.0 16.9 0 1.000 0.2456 0.3186 0.0730 0.014 1.4 28.3 0.0 16.9 0 2.000 0.2420 0.3195 0.0775 0.019 1.7 35.8 0.0 20.6 0 3.000 0.2409 0.3225 0.0816 0.024 2.0 41.1 0.0 21.7 0 4.000 0.2395 0.3211 0.0816 0.028 2.3 42.8 0.0 22.2 0 5.000 0.2376 0.3204 0.0828 0.032 2.5 47.2 2.3 21.2 0 6.000 0.2361 0.3190 0.0829 0.035 2.7 48.4 2.7 21.2 0 7.000 0.2353 0.3198 0.0845 0.038 2.9 52.7 3.2 23.3 0 8.000 0.2340 0.3178 0.0838 0.041 3.1 54.2 3.7 24.3 0 9.000 0.2333 0.3175 0.0842 0.044 3.3 58.3 3.7 25.4 0 10.000 0.2456 0.3184 0.0729 0.014 1.3 27.1 0.0 16.9 0 1.997 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2653 0.3161 0.0508 0.003 0.5 7.0 0.0 15.9 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.53 31.61 5.08 18.687 129.825 0.029 6.183 30.54 34.79 4.25 12.993 137.909 0.001 6.236 29.69 33.82 4.13 13.795 136.831 0.004 6.214 27.97 32.52 4.56 16.737 134.115 0.014 6.173 27.02 31.72 4.70 17.313 133.117 0.029 6.147 26.54 31.24 4.70 17.793 132.763 0.043 6.134 26.31 31.08 4.77 18.243 132.864 0.058 6.126 26.16 31.03 4.88 18.672 133.032 0.072 6.121 26.09 30.99 4.91 19.232 133.444 0.086 6.117 26.03 30.94 4.91 19.807 133.801 0.101 6.113 25.99 30.92 4.93 20.384 134.117 0.115 6.110 25.96 30.89 4.93 20.943 134.393 0.130 6.108 25.75 30.63 4.88 20.335 133.747 0.144 6.105 max suggested for this run: 25.97 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.144 Accepted refinement result: 25.75 30.63 4.88 20.335 133.747 0.144 6.105 Individual atomic B min max mean iso aniso Overall: 70.29 194.09 125.29 19.32 1719 0 Protein: 70.29 194.09 125.29 19.32 1719 0 Chain A: 70.29 194.09 125.29 N/A 1719 0 Histogram: Values Number of atoms 70.29 - 82.67 27 82.67 - 95.05 91 95.05 - 107.43 239 107.43 - 119.81 397 119.81 - 132.19 367 132.19 - 144.57 280 144.57 - 156.95 156 156.95 - 169.33 96 169.33 - 181.71 53 181.71 - 194.09 13 =========================== Idealize ADP of riding H ========================== r_work=0.2575 r_free=0.3063 r_work=0.2580 r_free=0.3064 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.23 - 28.61 A, n_refl.=6711 (all), 4.75 % free)-------------| | | | r_work= 0.2580 r_free= 0.3064 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 6.103161 | | target function (ml) not normalized (work): 39011.408094 | | target function (ml) not normalized (free): 1978.421937 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2602 0.2580 0.3064 n_refl.: 6711 re-set all scales: r(all,work,free)=0.4449 0.4421 0.5061 n_refl.: 6711 remove outliers: r(all,work,free)=0.4449 0.4421 0.5061 n_refl.: 6711 overall B=-12.45 to atoms: r(all,work,free)=0.4174 0.4149 0.4703 n_refl.: 6711 bulk-solvent and scaling: r(all,work,free)=0.2572 0.2551 0.3037 n_refl.: 6711 remove outliers: r(all,work,free)=0.2572 0.2551 0.3037 n_refl.: 6711 ======================== 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 28.612-12.706 81.97 93 7 0.2660 1254.542 1216.056 1.418 0.892 0.327 12.682-10.260 91.59 95 3 0.1342 1481.812 1450.340 1.383 0.894 0.318 10.240-8.268 91.00 185 7 0.1103 1313.082 1286.153 1.350 0.893 0.299 8.239-6.652 93.64 358 10 0.1895 802.406 788.230 1.272 0.895 0.286 6.641-5.360 94.83 677 38 0.2657 486.064 463.809 1.076 0.898 0.241 5.359-4.320 95.50 1280 57 0.2677 449.857 426.664 0.956 0.899 0.138 4.319-3.481 96.04 2451 119 0.3123 253.409 237.020 1.085 0.905 0.030 3.480-3.231 96.10 1253 78 0.3867 142.771 124.108 1.177 0.906 0.013 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9878 b_overall=2.4735 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 438 Ramachandran restraints generated. 219 Oldfield, 0 Emsley, 219 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2551 r_free=0.3037 After: r_work=0.2551 r_free=0.3037 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.695161 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.030757 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2551 0.3031 0.0479 0.003 0.6 7.0 0.0 15.3 0 0.125 0.2548 0.3034 0.0486 0.003 0.6 7.0 0.0 15.3 0 0.250 0.2524 0.2999 0.0475 0.005 0.6 9.3 0.0 14.8 0 0.500 0.2443 0.2978 0.0535 0.012 1.2 19.5 0.0 16.4 0 1.000 0.2398 0.2990 0.0592 0.014 1.5 26.8 0.0 14.8 0 2.000 0.2362 0.3003 0.0641 0.021 2.0 35.2 0.9 16.4 0 3.000 0.2345 0.3022 0.0678 0.024 2.3 39.9 0.9 18.0 0 4.000 0.2323 0.3035 0.0712 0.028 2.6 44.3 0.9 18.5 0 5.000 0.2310 0.3061 0.0751 0.030 2.8 46.9 0.9 19.0 0 6.000 0.2302 0.3058 0.0755 0.032 2.9 46.3 0.9 19.6 0 7.000 0.2293 0.3093 0.0800 0.034 3.1 53.3 0.5 21.7 0 8.000 0.2296 0.3125 0.0829 0.036 3.3 60.9 0.9 22.2 0 9.000 0.2263 0.3043 0.0779 0.043 3.7 58.8 1.4 22.2 0 10.000 0.2389 0.2986 0.0597 0.015 1.6 26.5 0.5 15.3 0 2.348 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2551 0.3031 0.0479 0.003 0.6 7.0 0.0 15.3 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.51 30.31 4.79 22.680 125.907 0.031 6.113 31.90 35.84 3.94 16.070 138.037 0.001 6.230 30.59 34.58 3.99 15.920 136.119 0.004 6.213 28.11 32.72 4.61 17.846 131.860 0.015 6.173 26.91 31.59 4.68 18.718 129.871 0.031 6.143 26.34 31.31 4.98 19.146 129.116 0.046 6.128 26.07 31.26 5.19 19.468 129.137 0.062 6.120 25.72 30.94 5.22 19.542 128.593 0.077 6.111 25.57 30.95 5.38 19.748 128.696 0.092 6.107 25.37 30.92 5.55 20.154 128.376 0.108 6.102 25.29 30.96 5.67 20.385 128.674 0.123 6.100 25.19 30.89 5.71 20.803 128.283 0.138 6.097 25.13 30.91 5.78 21.020 128.489 0.154 6.096 max suggested for this run: 25.18 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.138 Accepted refinement result: 25.19 30.89 5.71 20.803 128.283 0.138 6.097 Individual atomic B min max mean iso aniso Overall: 53.90 191.98 117.60 19.24 1719 0 Protein: 53.90 191.98 117.60 19.24 1719 0 Chain A: 53.90 191.98 117.60 N/A 1719 0 Histogram: Values Number of atoms 53.90 - 67.71 9 67.71 - 81.52 56 81.52 - 95.32 213 95.32 - 109.13 361 109.13 - 122.94 431 122.94 - 136.75 321 136.75 - 150.56 177 150.56 - 164.36 100 164.36 - 178.17 41 178.17 - 191.98 10 =========================== Idealize ADP of riding H ========================== r_work=0.2519 r_free=0.3089 r_work=0.2519 r_free=0.3089 ----------X-ray data---------- |--(resolution: 3.23 - 28.61 A, n_refl.=6711 (all), 4.75 % free)-------------| | | | r_work= 0.2519 r_free= 0.3089 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 6.097691 | | target function (ml) not normalized (work): 38976.439755 | | target function (ml) not normalized (free): 1984.964288 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 28.61 - 4.07 0.94 3209 159 0.2311 0.2805 6.5274 6.6254| | 2: 4.07 - 3.23 0.96 3183 160 0.3145 0.3900 5.6645 5.822| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 28.61 - 4.07 3209 159 0.74 31.71 1.00 0.90 86016.04| | 2: 4.07 - 3.23 3183 160 0.62 42.38 1.06 0.93 19447.71| |alpha: min = 0.90 max = 0.93 mean = 0.91| |beta: min = 19447.71 max = 86016.04 mean = 52867.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.93 mean = 37.02| |phase err.(test): min = 0.00 max = 89.79 mean = 39.83| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2544 0.2519 0.3089 n_refl.: 6711 re-set all scales: r(all,work,free)=0.4252 0.4225 0.4855 n_refl.: 6711 remove outliers: r(all,work,free)=0.4252 0.4225 0.4855 n_refl.: 6711 overall B=-2.12 to atoms: r(all,work,free)=0.4206 0.4179 0.4792 n_refl.: 6711 bulk-solvent and scaling: r(all,work,free)=0.2528 0.2502 0.3081 n_refl.: 6711 remove outliers: r(all,work,free)=0.2528 0.2502 0.3081 n_refl.: 6711 ======================== 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 28.612-12.706 81.97 93 7 0.2668 1254.542 1216.473 1.360 0.890 0.329 12.682-10.260 91.59 95 3 0.1336 1481.812 1446.890 1.325 0.892 0.321 10.240-8.268 91.00 185 7 0.1110 1313.082 1286.300 1.276 0.892 0.292 8.239-6.652 93.64 358 10 0.1933 802.406 789.653 1.185 0.894 0.257 6.641-5.360 94.83 677 38 0.2646 486.064 464.921 1.033 0.898 0.234 5.359-4.320 95.50 1280 57 0.2631 449.857 427.179 0.924 0.900 0.133 4.319-3.481 96.04 2451 119 0.3010 253.409 238.657 1.082 0.908 0.025 3.480-3.231 96.10 1253 78 0.3677 142.771 125.721 1.193 0.910 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-1.7642 ================= 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 : 0.4624 0.5099 0.013 1.793 91.3 163.0 123.4 0 0.000 1_bss: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_settarget: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_updatephipsi: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_weight: 0.2966 0.3135 0.013 1.793 79.2 150.9 111.4 0 0.000 1_xyzrec: 0.3072 0.3313 0.003 0.635 79.2 150.9 111.4 0 0.180 1_adp: 0.2708 0.3174 0.003 0.635 74.9 173.8 117.7 0 0.180 1_regHadp: 0.2677 0.3156 0.003 0.635 74.9 173.8 117.7 0 0.180 2_bss: 0.2672 0.3142 0.003 0.635 74.6 173.5 117.4 0 0.180 2_settarget: 0.2672 0.3142 0.003 0.635 74.6 173.5 117.4 0 0.180 2_updatephipsi: 0.2672 0.3142 0.003 0.635 74.6 173.5 117.4 0 0.180 2_updatecdl: 0.2672 0.3142 0.003 0.683 74.6 173.5 117.4 0 0.180 2_weight: 0.2672 0.3142 0.003 0.683 74.6 173.5 117.4 0 0.180 2_xyzrec: 0.2653 0.3161 0.003 0.544 74.6 173.5 117.4 0 0.222 2_adp: 0.2575 0.3063 0.003 0.544 70.3 194.1 125.3 0 0.222 2_regHadp: 0.2580 0.3064 0.003 0.544 70.3 194.1 125.3 0 0.222 3_bss: 0.2551 0.3037 0.003 0.544 57.8 181.6 112.8 0 0.222 3_settarget: 0.2551 0.3037 0.003 0.544 57.8 181.6 112.8 0 0.222 3_updatephipsi: 0.2551 0.3037 0.003 0.544 57.8 181.6 112.8 0 0.222 3_updatecdl: 0.2551 0.3037 0.003 0.586 57.8 181.6 112.8 0 0.222 3_setrh: 0.2551 0.3037 0.003 0.586 57.8 181.6 112.8 0 0.222 3_weight: 0.2551 0.3037 0.003 0.586 57.8 181.6 112.8 0 0.222 3_xyzrec: 0.2551 0.3031 0.003 0.555 57.8 181.6 112.8 0 0.223 3_adp: 0.2519 0.3089 0.003 0.555 53.9 192.0 117.6 0 0.223 3_regHadp: 0.2519 0.3089 0.003 0.555 53.9 192.0 117.6 0 0.223 end: 0.2502 0.3081 0.003 0.555 51.8 189.9 115.5 0 0.223 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2ogu_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2ogu_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0400 Refinement macro-cycles (run) : 170.0900 Write final files (write_after_run_outputs) : 19.2500 Total : 194.3800 Total CPU time: 3.73 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:31:29 PDT -0700 (1716251489.09 s) Start R-work = 0.2966, R-free = 0.3135 Final R-work = 0.2502, R-free = 0.3081 =============================================================================== Job complete usr+sys time: 242.99 seconds wall clock time: 14 minutes 53.62 seconds (893.62 seconds total)