Starting phenix.refine on Mon May 20 17:17:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2yhj.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2yhj/2yhj.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2yhj.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2yhj.pdb" } 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: 8784 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain: "B" Number of atoms: 4392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4392 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 277} Time building chain proxies: 2.80, per 1000 atoms: 0.32 Number of scatterers: 8784 At special positions: 0 Unit cell: (159.697, 159.697, 159.697, 90, 90, 90) Space group: P 21 3 (No. 198) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 904 8.00 N 728 7.00 C 2814 6.00 H 4334 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: 5.08 Conformation dependent library (CDL) restraints added in 930.0 milliseconds 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Time building geometry restraints manager: 4.23 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: 4332 1.15 - 1.31: 765 1.31 - 1.48: 1860 1.48 - 1.64: 1909 1.64 - 1.81: 6 Bond restraints: 8872 Sorted by residual: bond pdb=" N VAL A 100 " pdb=" H VAL A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N LYS B 46 " pdb=" H LYS B 46 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN B 140 " pdb="HE22 GLN B 140 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASP B 292 " pdb=" H ASP B 292 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 253 " pdb=" H ILE A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8867 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.43: 162 104.43 - 111.82: 9279 111.82 - 119.21: 2643 119.21 - 126.60: 3803 126.60 - 133.99: 71 Bond angle restraints: 15958 Sorted by residual: angle pdb=" N LEU B 37 " pdb=" CA LEU B 37 " pdb=" C LEU B 37 " ideal model delta sigma weight residual 110.14 119.17 -9.03 1.47e+00 4.63e-01 3.78e+01 angle pdb=" N VAL B 89 " pdb=" CA VAL B 89 " pdb=" CB VAL B 89 " ideal model delta sigma weight residual 111.00 117.48 -6.48 1.14e+00 7.69e-01 3.23e+01 angle pdb=" N ILE A 108 " pdb=" CA ILE A 108 " pdb=" C ILE A 108 " ideal model delta sigma weight residual 110.53 115.72 -5.19 9.40e-01 1.13e+00 3.04e+01 angle pdb=" C GLU A 181 " pdb=" N THR A 182 " pdb=" CA THR A 182 " ideal model delta sigma weight residual 120.31 128.30 -7.99 1.52e+00 4.33e-01 2.76e+01 angle pdb=" N ILE A 289 " pdb=" CA ILE A 289 " pdb=" C ILE A 289 " ideal model delta sigma weight residual 108.27 115.35 -7.08 1.37e+00 5.33e-01 2.67e+01 ... (remaining 15953 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 3781 17.72 - 35.43: 252 35.43 - 53.15: 113 53.15 - 70.87: 53 70.87 - 88.58: 11 Dihedral angle restraints: 4210 sinusoidal: 2252 harmonic: 1958 Sorted by residual: dihedral pdb=" C THR B 212 " pdb=" N THR B 212 " pdb=" CA THR B 212 " pdb=" CB THR B 212 " ideal model delta harmonic sigma weight residual -122.00 -135.87 13.87 0 2.50e+00 1.60e-01 3.08e+01 dihedral pdb=" C GLU B 184 " pdb=" N GLU B 184 " pdb=" CA GLU B 184 " pdb=" CB GLU B 184 " ideal model delta harmonic sigma weight residual -122.60 -135.02 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" C ASN B 86 " pdb=" N ASN B 86 " pdb=" CA ASN B 86 " pdb=" CB ASN B 86 " ideal model delta harmonic sigma weight residual -122.60 -134.99 12.39 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 4207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 495 0.107 - 0.213: 154 0.213 - 0.320: 30 0.320 - 0.427: 15 0.427 - 0.533: 6 Chirality restraints: 700 Sorted by residual: chirality pdb=" CA GLU B 184 " pdb=" N GLU B 184 " pdb=" C GLU B 184 " pdb=" CB GLU B 184 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" CA ASN B 86 " pdb=" N ASN B 86 " pdb=" C ASN B 86 " pdb=" CB ASN B 86 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.73e+00 chirality pdb=" CA ASN A 86 " pdb=" N ASN A 86 " pdb=" C ASN A 86 " pdb=" CB ASN A 86 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.28e+00 ... (remaining 697 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 61 " -0.013 2.00e-02 2.50e+03 3.89e-02 2.26e+01 pdb=" CD GLN B 61 " -0.051 2.00e-02 2.50e+03 pdb=" OE1 GLN B 61 " 0.052 2.00e-02 2.50e+03 pdb=" NE2 GLN B 61 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN B 61 " 0.050 2.00e-02 2.50e+03 pdb="HE22 GLN B 61 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 264 " -0.005 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 264 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 264 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 264 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 264 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 264 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR B 264 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR B 264 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR B 264 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR B 264 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 130 " 0.014 2.00e-02 2.50e+03 2.57e-02 1.99e+01 pdb=" CG TYR B 130 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR B 130 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR B 130 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR B 130 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 130 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR B 130 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 130 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR B 130 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 TYR B 130 " -0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR B 130 " 0.041 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 26 1.64 - 2.38: 2855 2.38 - 3.12: 27212 3.12 - 3.86: 38333 3.86 - 4.60: 59693 Warning: very small nonbonded interaction distances. Nonbonded interactions: 128119 Sorted by model distance: nonbonded pdb="HH12 ARG A 227 " pdb=" HB2 PRO A 311 " model vdw 0.896 2.270 nonbonded pdb="HH12 ARG B 227 " pdb=" HB2 PRO B 311 " model vdw 0.922 2.270 nonbonded pdb=" HE2 LYS B 257 " pdb=" HA LYS B 283 " model vdw 1.020 2.440 nonbonded pdb=" HE2 LYS A 257 " pdb=" HA LYS A 283 " model vdw 1.026 2.440 nonbonded pdb="HD21 ASN A 36 " pdb=" HE2 LYS B 283 " model vdw 1.089 2.270 ... (remaining 128114 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 4 15.91 1 O 904 7.97 1 N 728 6.97 1 C 2814 5.97 1 H 4334 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: 4334 of 8784 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8784 n_use_u_iso = 8784 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 = 8784 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8784 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8784 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 = "2yhj_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4334 occupancy sum: 4334.00 (% of total atoms 49.51) Rotatable: count: 1252 occupancy sum: 1252.00 (% of total atoms 14.30) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11707 (all), 4.74 % free)------------| | | | r_work= 0.5891 r_free= 0.4411 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.177790 | | target function (ml) not normalized (work): 46590.717736 | | target function (ml) not normalized (free): 2297.685890 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 65.20 - 6.35 1.00 2869 154 0.5470 0.4516 5.0219 4.6882| | 2: 6.35 - 5.04 1.00 2777 143 0.5707 0.3865 4.0914 4.1453| | 3: 5.04 - 4.40 1.00 2783 123 0.6252 0.4330 3.9538 4.0152| | 4: 4.40 - 4.00 0.99 2723 135 0.6724 0.5113 3.6055 3.6227| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 65.20 - 6.35 2869 154 0.51 50.27 0.85 0.03 2262.31| | 2: 6.35 - 5.04 2777 143 0.43 57.38 2.00 0.04 1473.91| | 3: 5.04 - 4.40 2783 123 0.59 44.81 2.34 0.05 841.25| | 4: 4.40 - 4.00 2723 135 0.61 43.53 2.67 0.06 378.44| |alpha: min = 0.03 max = 0.06 mean = 0.04| |beta: min = 378.44 max = 2262.31 mean = 1251.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.54| |phase err.(work): min = 0.00 max = 89.88 mean = 49.03| |phase err.(test): min = 0.00 max = 89.64 mean = 49.15| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.113 4538 Z= 0.608 Angle : 1.541 9.034 6170 Z= 1.009 Chirality : 0.123 0.533 700 Planarity : 0.007 0.028 792 Dihedral : 15.468 88.583 1622 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.22 % Allowed : 6.83 % Favored : 88.96 % Cbeta Deviations : 2.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.32), residues: 566 helix: -0.38 (0.69), residues: 42 sheet: 0.26 (0.29), residues: 286 loop : -0.96 (0.35), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG A 116 TYR 0.045 0.007 TYR B 264 PHE 0.018 0.005 PHE B 316 TRP 0.046 0.009 TRP A 162 HIS 0.008 0.002 HIS A 146 Individual atomic B min max mean iso aniso Overall: 34.09 300.00 115.49 16.58 4450 0 Protein: 34.09 300.00 115.49 16.58 4450 0 Chain A: 34.09 300.00 113.10 N/A 2225 0 Chain B: 38.50 300.00 117.88 N/A 2225 0 Histogram: Values Number of atoms 34.09 - 60.68 195 60.68 - 87.27 913 87.27 - 113.86 1318 113.86 - 140.45 1013 140.45 - 167.04 585 167.04 - 193.64 250 193.64 - 220.23 97 220.23 - 246.82 41 246.82 - 273.41 14 273.41 - 300.00 24 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11707 (all), 4.74 % free)------------| | | | r_work= 0.5891 r_free= 0.4411 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.177790 | | target function (ml) not normalized (work): 46590.717736 | | target function (ml) not normalized (free): 2297.685890 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5850 0.5891 0.4411 n_refl.: 11707 re-set all scales: r(all,work,free)=0.5850 0.5891 0.4411 n_refl.: 11707 remove outliers: r(all,work,free)=0.5853 0.5894 0.4411 n_refl.: 11703 overall B=1.75 to atoms: r(all,work,free)=0.5901 0.5942 0.4442 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.3020 0.2998 0.3469 n_refl.: 11703 remove outliers: r(all,work,free)=0.3020 0.2998 0.3469 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3727 4797.975 4480.474 1.327 1.203 0.370 20.447-16.215 100.00 96 3 0.3168 3372.726 3174.597 1.053 1.189 0.340 16.132-12.745 100.00 194 11 0.2772 3266.441 3051.447 1.121 1.171 0.329 12.705-10.080 100.00 377 16 0.2682 3068.794 2812.929 1.067 1.142 0.309 10.040-7.926 100.00 749 47 0.2594 2378.704 2226.653 1.035 1.095 0.278 7.906-6.254 99.81 1487 80 0.3015 1468.580 1345.750 1.035 1.018 0.228 6.249-4.933 100.00 3011 157 0.3075 1268.682 1121.341 1.068 0.895 0.177 4.931-4.001 99.68 5136 240 0.3089 1069.236 942.207 1.427 0.716 0.137 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=7.8620 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.051422 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.153546 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 0.3021 0.3532 0.0512 0.002 0.5 1.3 0.0 2.6 0 0.125 0.2980 0.3529 0.0549 0.002 0.5 1.5 0.0 2.6 0 0.250 0.2917 0.3525 0.0608 0.003 0.5 1.7 0.0 2.8 0 0.500 0.2850 0.3534 0.0683 0.003 0.6 2.3 0.0 2.6 0 1.000 0.2788 0.3550 0.0762 0.005 0.7 3.5 0.0 3.6 0 2.000 0.2751 0.3573 0.0822 0.007 0.8 5.2 0.0 3.2 0 3.000 0.2728 0.3562 0.0834 0.008 0.9 5.4 0.0 3.8 0 4.000 0.2709 0.3568 0.0859 0.009 1.0 7.4 0.0 5.0 0 5.000 0.2694 0.3562 0.0868 0.011 1.1 8.5 0.0 6.0 0 6.000 0.2677 0.3576 0.0899 0.012 1.2 9.5 0.0 6.4 0 7.000 0.2660 0.3563 0.0903 0.013 1.2 10.9 0.0 7.6 0 8.000 0.2652 0.3575 0.0922 0.014 1.3 11.7 0.0 8.6 0 9.000 0.2641 0.3582 0.0941 0.016 1.4 13.6 0.0 10.0 0 10.000 0.2668 0.3564 0.0896 0.013 1.2 10.5 0.0 8.2 0 7.526 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2917 0.3525 0.0608 0.003 0.5 1.7 0.0 2.8 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.17 35.25 6.08 11.856 115.379 0.154 0.107 29.48 33.88 4.40 15.585 119.791 0.005 0.109 29.26 33.83 4.58 15.540 119.709 0.019 0.108 28.55 33.73 5.18 15.667 119.486 0.077 0.103 27.90 33.73 5.82 16.068 119.289 0.154 0.100 27.48 33.77 6.28 16.614 119.195 0.230 0.097 27.22 33.84 6.62 17.105 119.139 0.307 0.096 27.01 33.91 6.90 17.647 119.152 0.384 0.095 26.88 34.00 7.12 18.060 119.147 0.461 0.094 26.77 34.09 7.32 18.458 119.171 0.537 0.093 26.69 34.19 7.50 18.860 119.219 0.614 0.093 26.58 34.26 7.68 19.533 119.419 0.691 0.092 26.51 34.33 7.82 20.005 119.528 0.768 0.092 max suggested for this run: 23.08 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.154 Accepted refinement result: 27.90 33.73 5.82 16.068 119.289 0.154 0.100 Individual atomic B min max mean iso aniso Overall: 31.97 296.75 124.96 12.93 4450 0 Protein: 31.97 296.75 124.96 12.93 4450 0 Chain A: 31.97 296.75 122.72 N/A 2225 0 Chain B: 50.35 296.75 127.19 N/A 2225 0 Histogram: Values Number of atoms 31.97 - 58.45 9 58.45 - 84.93 317 84.93 - 111.40 1368 111.40 - 137.88 1476 137.88 - 164.36 809 164.36 - 190.84 288 190.84 - 217.31 103 217.31 - 243.79 42 243.79 - 270.27 15 270.27 - 296.75 23 =========================== Idealize ADP of riding H ========================== r_work=0.2790 r_free=0.3373 r_work=0.2782 r_free=0.3379 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2782 r_free= 0.3379 coordinate error (max.-lik. estimate): 0.67 A | | | | normalized target function (ls_wunit_k1) (work): 0.099181 | | target function (ls_wunit_k1) not normalized (work): 1105.673995 | | target function (ls_wunit_k1) not normalized (free): 79.898995 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2810 0.2782 0.3379 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6085 0.6123 0.4618 n_refl.: 11703 remove outliers: r(all,work,free)=0.6085 0.6123 0.4618 n_refl.: 11703 overall B=-0.83 to atoms: r(all,work,free)=0.6063 0.6102 0.4602 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2815 0.2787 0.3375 n_refl.: 11703 remove outliers: r(all,work,free)=0.2815 0.2787 0.3375 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3479 1677.484 1575.771 1.339 1.064 0.370 20.447-16.215 100.00 96 3 0.2988 1179.183 1125.947 1.037 1.060 0.335 16.132-12.745 100.00 194 11 0.2494 1142.024 1088.590 1.097 1.053 0.324 12.705-10.080 100.00 377 16 0.2403 1072.922 1011.601 1.083 1.043 0.321 10.040-7.926 100.00 749 47 0.2271 831.650 795.300 1.017 1.026 0.271 7.906-6.254 99.81 1487 80 0.2636 513.450 482.025 0.979 0.998 0.221 6.249-4.933 100.00 3011 157 0.2804 443.561 399.181 0.967 0.953 0.171 4.931-4.001 99.68 5136 240 0.3044 373.830 334.012 1.136 0.886 0.101 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-2.8665 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.493356 wxc_scale = 0.026 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.074719 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 0.2870 0.3375 0.0505 0.002 0.4 1.3 0.0 2.4 0 0.022 0.2839 0.3352 0.0513 0.002 0.4 1.4 0.0 2.4 0 0.067 0.2816 0.3361 0.0545 0.002 0.4 1.4 0.0 2.4 0 0.133 0.2805 0.3399 0.0594 0.002 0.4 2.2 0.0 2.2 0 0.200 0.2788 0.3392 0.0604 0.002 0.5 2.1 0.0 2.2 0 0.267 0.2779 0.3406 0.0627 0.003 0.5 2.4 0.0 2.4 0 0.333 0.2775 0.3411 0.0637 0.003 0.5 2.7 0.0 2.2 0 0.400 0.2766 0.3421 0.0655 0.003 0.5 3.1 0.0 2.2 0 0.467 0.2798 0.3390 0.0592 0.002 0.4 2.1 0.0 2.2 0 0.222 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2839 0.3352 0.0513 0.002 0.4 1.4 0.0 2.4 0 0.067 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 28.39 33.52 5.13 20.028 135.447 0.075 6.492 31.62 33.98 2.37 17.823 144.020 0.002 6.515 31.31 33.97 2.66 17.642 144.667 0.009 6.505 29.53 33.79 4.26 18.581 141.473 0.037 6.476 28.42 34.09 5.67 20.283 139.654 0.075 6.465 27.89 33.92 6.03 20.325 138.113 0.112 6.463 27.68 33.89 6.21 20.808 137.814 0.149 6.462 27.57 33.87 6.30 21.036 137.627 0.187 6.463 27.47 33.90 6.43 21.454 137.823 0.224 6.462 27.42 33.85 6.43 21.627 137.846 0.262 6.462 27.36 33.90 6.54 21.975 138.044 0.299 6.461 27.32 33.90 6.58 22.129 138.097 0.336 6.461 27.29 33.92 6.63 22.340 138.207 0.374 6.461 max suggested for this run: 27.09 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.037 Accepted refinement result: 29.53 33.79 4.26 18.581 141.473 0.037 6.476 Individual atomic B min max mean iso aniso Overall: 66.97 303.77 136.02 12.25 4450 0 Protein: 66.97 303.77 136.02 12.25 4450 0 Chain A: 66.97 303.77 133.60 N/A 2225 0 Chain B: 73.68 290.92 138.45 N/A 2225 0 Histogram: Values Number of atoms 66.97 - 90.65 204 90.65 - 114.33 989 114.33 - 138.01 1314 138.01 - 161.69 1119 161.69 - 185.37 535 185.37 - 209.05 181 209.05 - 232.73 60 232.73 - 256.41 21 256.41 - 280.09 9 280.09 - 303.77 18 =========================== Idealize ADP of riding H ========================== r_work=0.2953 r_free=0.3379 r_work=0.2970 r_free=0.3405 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2970 r_free= 0.3405 coordinate error (max.-lik. estimate): 0.57 A | | | | normalized target function (ml) (work): 6.478038 | | target function (ml) not normalized (work): 72217.162915 | | target function (ml) not normalized (free): 3628.320994 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2991 0.2970 0.3405 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6393 0.6430 0.4854 n_refl.: 11703 remove outliers: r(all,work,free)=0.6393 0.6430 0.4854 n_refl.: 11703 overall B=-17.01 to atoms: r(all,work,free)=0.5958 0.5998 0.4502 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2958 0.2937 0.3394 n_refl.: 11703 remove outliers: r(all,work,free)=0.2958 0.2937 0.3394 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3543 1468.430 1361.096 1.405 1.091 0.372 20.447-16.215 100.00 96 3 0.3022 1032.230 983.909 1.100 1.085 0.340 16.132-12.745 100.00 194 11 0.2591 999.701 942.234 1.149 1.076 0.330 12.705-10.080 100.00 377 16 0.2487 939.211 874.924 1.132 1.063 0.331 10.040-7.926 100.00 749 47 0.2375 728.007 687.232 1.070 1.040 0.285 7.906-6.254 99.81 1487 80 0.2957 449.462 407.882 1.024 1.004 0.230 6.249-4.933 100.00 3011 157 0.3046 388.283 340.664 0.981 0.945 0.173 4.931-4.001 99.68 5136 240 0.3110 327.242 287.481 1.135 0.858 0.112 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=7.3472 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1132 Ramachandran restraints generated. 566 Oldfield, 0 Emsley, 566 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2937 r_free=0.3394 After: r_work=0.2936 r_free=0.3394 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.997384 wxc_scale = 0.025 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.081492 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 0.2936 0.3394 0.0457 0.001 0.4 1.4 0.0 2.4 0 0.020 0.2936 0.3394 0.0458 0.002 0.4 1.4 0.0 2.4 0 0.059 0.2935 0.3394 0.0459 0.002 0.4 1.4 0.0 2.4 0 0.118 0.2934 0.3395 0.0461 0.002 0.4 1.4 0.0 2.4 0 0.177 0.2933 0.3394 0.0462 0.002 0.4 1.4 0.0 2.4 0 0.236 0.2932 0.3394 0.0462 0.002 0.4 1.4 0.0 2.2 0 0.295 0.2928 0.3392 0.0465 0.003 0.4 1.4 0.0 2.2 0 0.354 0.2924 0.3391 0.0467 0.003 0.4 1.3 0.0 2.2 0 0.414 0.2934 0.3395 0.0461 0.002 0.4 1.4 0.0 2.4 0 0.197 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2924 0.3391 0.0467 0.003 0.4 1.3 0.0 2.2 0 0.414 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.24 33.91 4.67 21.279 132.006 0.081 6.343 31.37 34.21 2.84 17.690 140.021 0.002 6.380 30.64 34.13 3.49 17.440 139.435 0.010 6.370 28.40 33.98 5.59 19.337 136.397 0.041 6.336 27.79 34.09 6.31 21.188 134.882 0.081 6.324 27.74 34.00 6.27 21.575 134.044 0.122 6.322 27.69 34.07 6.38 22.036 134.088 0.163 6.320 27.64 34.08 6.44 22.408 134.268 0.204 6.319 27.63 34.10 6.47 22.591 134.365 0.244 6.318 27.58 34.14 6.56 22.878 134.572 0.285 6.318 27.55 34.18 6.63 23.049 134.687 0.326 6.317 27.51 34.21 6.70 23.303 134.869 0.367 6.317 27.48 34.24 6.75 23.531 135.022 0.407 6.316 max suggested for this run: 26.40 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.041 Accepted refinement result: 28.40 33.98 5.59 19.337 136.397 0.041 6.336 Individual atomic B min max mean iso aniso Overall: 64.30 281.75 127.68 11.70 4450 0 Protein: 64.30 281.75 127.68 11.70 4450 0 Chain A: 64.44 281.75 125.84 N/A 2225 0 Chain B: 64.30 268.91 129.51 N/A 2225 0 Histogram: Values Number of atoms 64.30 - 86.05 301 86.05 - 107.79 1045 107.79 - 129.54 1138 129.54 - 151.28 1039 151.28 - 173.03 541 173.03 - 194.77 243 194.77 - 216.52 92 216.52 - 238.26 26 238.26 - 260.01 7 260.01 - 281.75 18 =========================== Idealize ADP of riding H ========================== r_work=0.2840 r_free=0.3398 r_work=0.2833 r_free=0.3400 ----------X-ray data---------- |--(resolution: 4.00 - 65.20 A, n_refl.=11703 (all), 4.74 % free)------------| | | | r_work= 0.2833 r_free= 0.3400 coordinate error (max.-lik. estimate): 0.58 A | | | | normalized target function (ml) (work): 6.337585 | | target function (ml) not normalized (work): 70651.400081 | | target function (ml) not normalized (free): 3556.761607 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 65.20 - 6.35 1.00 2866 154 0.2622 0.3224 6.8007 6.8179| | 2: 6.35 - 5.04 1.00 2776 143 0.2969 0.3381 6.306 6.3801| | 3: 5.04 - 4.40 1.00 2783 123 0.2915 0.3535 6.2467 6.3369| | 4: 4.40 - 4.00 0.99 2723 135 0.3070 0.3713 5.9753 6.0371| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 65.20 - 6.35 2866 154 0.77 29.06 0.97 0.83 121570.79| | 2: 6.35 - 5.04 2776 143 0.64 40.89 1.04 0.83 91474.33| | 3: 5.04 - 4.40 2783 123 0.72 34.79 1.09 0.83 65387.14| | 4: 4.40 - 4.00 2723 135 0.66 39.20 1.04 0.83 43884.92| |alpha: min = 0.83 max = 0.83 mean = 0.83| |beta: min = 43884.92 max = 121570.79 mean = 81075.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.70| |phase err.(work): min = 0.00 max = 90.00 mean = 35.91| |phase err.(test): min = 0.00 max = 89.56 mean = 36.22| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2860 0.2833 0.3400 n_refl.: 11703 re-set all scales: r(all,work,free)=0.6170 0.6206 0.4676 n_refl.: 11703 remove outliers: r(all,work,free)=0.6170 0.6206 0.4676 n_refl.: 11703 overall B=-0.13 to atoms: r(all,work,free)=0.6166 0.6203 0.4674 n_refl.: 11703 bulk-solvent and scaling: r(all,work,free)=0.2833 0.2805 0.3398 n_refl.: 11703 remove outliers: r(all,work,free)=0.2833 0.2805 0.3398 n_refl.: 11703 ======================== 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 65.196-20.791 100.00 98 1 0.3540 1468.430 1363.398 1.188 1.179 0.370 20.447-16.215 100.00 96 3 0.3014 1032.230 983.580 0.945 1.166 0.335 16.132-12.745 100.00 194 11 0.2612 999.701 938.123 1.012 1.150 0.327 12.705-10.080 100.00 377 16 0.2424 939.211 878.252 1.007 1.124 0.320 10.040-7.926 100.00 749 47 0.2294 728.007 690.802 0.995 1.083 0.280 7.906-6.254 99.81 1487 80 0.2748 449.462 415.412 0.995 1.016 0.220 6.249-4.933 100.00 3011 157 0.2909 388.283 346.749 1.046 0.909 0.170 4.931-4.001 99.68 5136 240 0.2948 327.242 292.519 1.369 0.752 0.110 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.3486 ================= 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 : 0.5891 0.4411 0.010 1.541 34.1 300.0 115.5 0 0.000 1_bss: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_settarget: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_updatephipsi: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_weight: 0.2998 0.3469 0.010 1.541 35.8 301.7 117.2 0 0.000 1_xyzrec: 0.2917 0.3525 0.003 0.502 35.8 301.7 117.2 0 0.193 1_adp: 0.2790 0.3373 0.003 0.502 32.0 296.7 125.0 0 0.193 1_regHadp: 0.2782 0.3379 0.003 0.502 32.0 296.7 125.0 0 0.193 2_bss: 0.2787 0.3375 0.003 0.502 31.1 295.9 124.1 0 0.193 2_settarget: 0.2787 0.3375 0.003 0.502 31.1 295.9 124.1 0 0.193 2_updatephipsi: 0.2787 0.3375 0.003 0.502 31.1 295.9 124.1 0 0.193 2_updatecdl: 0.2787 0.3375 0.003 0.542 31.1 295.9 124.1 0 0.193 2_weight: 0.2787 0.3375 0.003 0.542 31.1 295.9 124.1 0 0.193 2_xyzrec: 0.2839 0.3352 0.002 0.375 31.1 295.9 124.1 0 0.242 2_adp: 0.2953 0.3379 0.002 0.375 67.0 303.8 136.0 0 0.242 2_regHadp: 0.2970 0.3405 0.002 0.375 67.0 303.8 136.0 0 0.242 3_bss: 0.2937 0.3394 0.002 0.375 50.0 286.8 119.0 0 0.242 3_settarget: 0.2937 0.3394 0.002 0.375 50.0 286.8 119.0 0 0.242 3_updatephipsi: 0.2937 0.3394 0.002 0.375 50.0 286.8 119.0 0 0.242 3_updatecdl: 0.2937 0.3394 0.002 0.395 50.0 286.8 119.0 0 0.242 3_setrh: 0.2936 0.3394 0.002 0.395 50.0 286.8 119.0 0 0.242 3_weight: 0.2936 0.3394 0.002 0.395 50.0 286.8 119.0 0 0.242 3_xyzrec: 0.2924 0.3391 0.003 0.401 50.0 286.8 119.0 0 0.244 3_adp: 0.2840 0.3398 0.003 0.401 64.3 281.8 127.7 0 0.244 3_regHadp: 0.2833 0.3400 0.003 0.401 64.3 281.8 127.7 0 0.244 end: 0.2805 0.3398 0.003 0.401 64.2 281.6 127.5 0 0.244 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2yhj_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2yhj_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 12.4300 Refinement macro-cycles (run) : 323.8200 Write final files (write_after_run_outputs) : 17.8600 Total : 354.1100 Total CPU time: 6.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:36:13 PDT -0700 (1716251773.34 s) Start R-work = 0.2998, R-free = 0.3469 Final R-work = 0.2805, R-free = 0.3398 =============================================================================== Job complete usr+sys time: 425.94 seconds wall clock time: 19 minutes 31.04 seconds (1171.04 seconds total)