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/1w60.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1w60/1w60.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/1w60/1w60.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1w60/1w60.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1w60.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1w60.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: 7874 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Chain: "B" Number of atoms: 3937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 3937 Classifications: {'peptide': 255} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 247} Time building chain proxies: 2.48, per 1000 atoms: 0.31 Number of scatterers: 7874 At special positions: 0 Unit cell: (82.892, 82.892, 70.859, 90, 90, 120) Space group: P 3 (No. 143) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 786 8.00 N 644 7.00 C 2466 6.00 H 3946 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: 4.60 Conformation dependent library (CDL) restraints added in 723.7 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Time building geometry restraints manager: 3.84 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: 3934 1.15 - 1.32: 712 1.32 - 1.49: 1460 1.49 - 1.66: 1768 1.66 - 1.83: 52 Bond restraints: 7926 Sorted by residual: bond pdb=" NE1 TRP B 28 " pdb=" CE2 TRP B 28 " ideal model delta sigma weight residual 1.370 1.483 -0.113 1.10e-02 8.26e+03 1.06e+02 bond pdb=" N SER A 112 " pdb=" H SER A 112 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" ND2 ASN B 107 " pdb="HD22 ASN B 107 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLN B 131 " pdb=" H GLN B 131 " 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 B 6 " pdb=" H LEU B 6 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7921 not shown) Histogram of bond angle deviations from ideal: 97.88 - 105.14: 87 105.14 - 112.40: 9571 112.40 - 119.66: 1859 119.66 - 126.92: 2837 126.92 - 134.18: 20 Bond angle restraints: 14374 Sorted by residual: angle pdb=" N ASP B 232 " pdb=" CA ASP B 232 " pdb=" CB ASP B 232 " ideal model delta sigma weight residual 114.17 108.16 6.01 1.14e+00 7.69e-01 2.78e+01 angle pdb=" CD ARG A 64 " pdb=" NE ARG A 64 " pdb=" CZ ARG A 64 " ideal model delta sigma weight residual 124.40 117.23 7.17 1.40e+00 5.10e-01 2.62e+01 angle pdb=" N PRO B 234 " pdb=" CA PRO B 234 " pdb=" CB PRO B 234 " ideal model delta sigma weight residual 103.31 107.82 -4.51 8.90e-01 1.26e+00 2.57e+01 angle pdb=" CD ARG A 61 " pdb=" NE ARG A 61 " pdb=" CZ ARG A 61 " ideal model delta sigma weight residual 124.40 117.32 7.08 1.40e+00 5.10e-01 2.56e+01 angle pdb=" N PRO B 202 " pdb=" CA PRO B 202 " pdb=" CB PRO B 202 " ideal model delta sigma weight residual 103.19 107.64 -4.45 9.00e-01 1.23e+00 2.45e+01 ... (remaining 14369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 3107 17.84 - 35.68: 335 35.68 - 53.52: 181 53.52 - 71.37: 70 71.37 - 89.21: 19 Dihedral angle restraints: 3712 sinusoidal: 2056 harmonic: 1656 Sorted by residual: dihedral pdb=" CA ASP A 122 " pdb=" C ASP A 122 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " ideal model delta harmonic sigma weight residual -180.00 -162.23 -17.77 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASN A 95 " pdb=" C ASN A 95 " pdb=" N ALA A 96 " pdb=" CA ALA A 96 " ideal model delta harmonic sigma weight residual -180.00 -162.99 -17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA ASP B 122 " pdb=" C ASP B 122 " pdb=" N VAL B 123 " pdb=" CA VAL B 123 " ideal model delta harmonic sigma weight residual -180.00 -163.34 -16.66 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 402 0.037 - 0.075: 108 0.075 - 0.112: 81 0.112 - 0.149: 23 0.149 - 0.187: 22 Chirality restraints: 636 Sorted by residual: chirality pdb=" CB THR B 219 " pdb=" CA THR B 219 " pdb=" OG1 THR B 219 " pdb=" CG2 THR B 219 " both_signs ideal model delta sigma weight residual False 2.55 2.74 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CB THR A 219 " pdb=" CA THR A 219 " pdb=" OG1 THR A 219 " pdb=" CG2 THR A 219 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 8.13e-01 chirality pdb=" CB THR B 73 " pdb=" CA THR B 73 " pdb=" OG1 THR B 73 " pdb=" CG2 THR B 73 " both_signs ideal model delta sigma weight residual False 2.55 2.73 -0.18 2.00e-01 2.50e+01 7.95e-01 ... (remaining 633 not shown) Planarity restraints: 1186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 239 " -0.113 2.00e-02 2.50e+03 4.19e-02 5.26e+01 pdb=" CG TYR B 239 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 239 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 239 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR B 239 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 239 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 239 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 239 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR B 239 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 TYR B 239 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR B 239 " -0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR B 239 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 246 " -0.035 2.00e-02 2.50e+03 1.72e-02 6.67e+00 pdb=" CG HIS B 246 " 0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS B 246 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS B 246 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 246 " -0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS B 246 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS B 246 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 HIS B 246 " 0.013 2.00e-02 2.50e+03 pdb=" HE1 HIS B 246 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 246 " 0.034 2.00e-02 2.50e+03 1.68e-02 6.34e+00 pdb=" CG HIS A 246 " -0.015 2.00e-02 2.50e+03 pdb=" ND1 HIS A 246 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 246 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS A 246 " 0.006 2.00e-02 2.50e+03 pdb=" NE2 HIS A 246 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 HIS A 246 " -0.021 2.00e-02 2.50e+03 pdb=" HD2 HIS A 246 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS A 246 " 0.017 2.00e-02 2.50e+03 ... (remaining 1183 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.67: 63 1.67 - 2.40: 3135 2.40 - 3.13: 24071 3.13 - 3.87: 33793 3.87 - 4.60: 51974 Warning: very small nonbonded interaction distances. Nonbonded interactions: 113036 Sorted by model distance: nonbonded pdb=" O LEU B 182 " pdb=" HG SER B 183 " model vdw 0.936 1.850 nonbonded pdb=" HB2 GLN B 184 " pdb="HG11 VAL B 195 " model vdw 1.002 2.440 nonbonded pdb="HG13 VAL A 188 " pdb=" HB2 ALA B 252 " model vdw sym.op. 1.043 2.440 -x+y+1,-x+1,z nonbonded pdb="HG13 VAL B 195 " pdb=" H THR B 196 " model vdw 1.203 2.270 nonbonded pdb=" HG2 PRO B 140 " pdb=" HG3 GLU B 193 " model vdw 1.204 2.440 ... (remaining 113031 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 32 15.96 2 O 786 7.97 1 N 644 6.97 1 C 2466 5.97 2 H 3946 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: 3946 of 7874 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7874 n_use_u_iso = 7874 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 = 7874 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7874 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7874 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 = "1w60_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3946 occupancy sum: 3946.00 (% of total atoms 50.11) Rotatable: count: 1214 occupancy sum: 1214.00 (% of total atoms 15.42) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.14 - 25.21 A, n_refl.=9258 (all), 4.80 % free)-------------| | | | r_work= 0.3127 r_free= 0.3555 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.213664 | | target function (ml) not normalized (work): 54767.234476 | | target function (ml) not normalized (free): 2756.138780 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.21 - 4.53 0.98 2961 131 0.3221 0.3675 6.7019 6.6358| | 2: 4.52 - 3.60 0.98 2955 140 0.3038 0.3318 6.2193 6.2826| | 3: 3.60 - 3.14 0.97 2898 173 0.3059 0.3697 5.709 5.8225| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.21 - 4.53 2961 131 0.65 40.73 0.91 0.65 115062.26| | 2: 4.52 - 3.60 2955 140 0.68 38.46 1.23 0.87 57473.34| | 3: 3.60 - 3.14 2898 173 0.73 34.32 1.19 0.95 19014.54| |alpha: min = 0.65 max = 0.95 mean = 0.83| |beta: min = 19014.54 max = 115062.26 mean = 64174.86| |figures of merit: min = 0.00 max = 0.99 mean = 0.68| |phase err.(work): min = 0.00 max = 89.90 mean = 37.86| |phase err.(test): min = 0.00 max = 88.83 mean = 37.54| |-----------------------------------------------------------------------------| ----------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 : 0.007 0.113 3980 Z= 0.444 Angle : 1.399 7.165 5378 Z= 0.912 Chirality : 0.058 0.187 636 Planarity : 0.003 0.044 692 Dihedral : 23.356 87.623 1492 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 2.96 % Allowed : 6.32 % Favored : 90.71 % Rotamer: Outliers : 23.77 % Allowed : 18.39 % Favored : 57.85 % 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: -3.75 (0.31), residues: 506 helix: -2.40 (0.42), residues: 82 sheet: -1.98 (0.30), residues: 252 loop : -2.98 (0.35), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 61 TYR 0.086 0.005 TYR B 239 PHE 0.018 0.001 PHE B 103 TRP 0.020 0.004 TRP B 28 HIS 0.002 0.001 HIS B 246 Individual atomic B min max mean iso aniso Overall: 2.00 149.48 50.67 9.35 3928 0 Protein: 2.00 149.48 50.67 9.35 3928 0 Chain A: 2.00 149.40 50.68 N/A 1964 0 Chain B: 3.06 149.48 50.65 N/A 1964 0 Histogram: Values Number of atoms 2.00 - 16.75 88 16.75 - 31.50 624 31.50 - 46.24 1249 46.24 - 60.99 942 60.99 - 75.74 488 75.74 - 90.49 299 90.49 - 105.24 135 105.24 - 119.98 34 119.98 - 134.73 25 134.73 - 149.48 44 |-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: 3.14 - 25.21 A, n_refl.=9258 (all), 4.80 % free)-------------| | | | r_work= 0.3127 r_free= 0.3555 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 6.213664 | | target function (ml) not normalized (work): 54767.234476 | | target function (ml) not normalized (free): 2756.138780 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3149 0.3127 0.3555 n_refl.: 9258 re-set all scales: r(all,work,free)=0.3149 0.3127 0.3555 n_refl.: 9258 remove outliers: r(all,work,free)=0.3148 0.3126 0.3555 n_refl.: 9255 overall B=5.77 to atoms: r(all,work,free)=0.3305 0.3283 0.3719 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2347 0.2324 0.2782 n_refl.: 9255 remove outliers: r(all,work,free)=0.2347 0.2324 0.2782 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.2240 720.927 692.011 1.575 1.004 0.382 13.182-10.771 92.52 92 7 0.2328 728.577 659.686 1.354 1.009 0.372 10.742-8.763 94.15 183 10 0.1786 646.556 624.296 1.235 1.006 0.367 8.709-7.139 97.85 350 14 0.1955 566.962 549.169 1.218 1.006 0.361 7.120-5.819 98.85 652 33 0.2417 394.630 369.156 1.076 1.002 0.357 5.810-4.742 98.41 1191 49 0.2078 477.646 452.627 0.970 0.997 0.284 4.737-3.861 98.48 2221 114 0.2121 429.398 408.632 1.018 0.988 0.203 3.860-3.143 97.34 4027 214 0.2781 247.845 230.388 1.027 0.974 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.8102 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.331053 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.207977 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 0.2314 0.2750 0.0436 0.004 0.7 5.8 2.0 21.3 0 0.125 0.2294 0.2741 0.0447 0.004 0.7 5.8 2.0 21.3 0 0.250 0.2177 0.2729 0.0552 0.003 0.6 3.6 1.6 15.7 0 0.500 0.2087 0.2716 0.0628 0.004 0.6 3.7 2.0 16.6 0 1.000 0.1991 0.2753 0.0762 0.005 0.7 5.7 2.2 17.3 0 2.000 0.1937 0.2743 0.0806 0.006 0.8 8.1 2.0 17.9 0 3.000 0.1901 0.2735 0.0835 0.008 0.9 9.3 2.0 19.3 0 4.000 0.1865 0.2735 0.0870 0.009 1.0 10.7 2.0 20.6 0 5.000 0.1841 0.2736 0.0894 0.010 1.1 11.3 2.0 21.3 0 6.000 0.1826 0.2723 0.0898 0.011 1.1 12.1 2.0 21.7 0 7.000 0.1803 0.2730 0.0928 0.012 1.2 13.0 2.0 22.6 0 8.000 0.1790 0.2723 0.0933 0.013 1.3 12.4 2.4 22.9 0 9.000 0.1773 0.2728 0.0955 0.014 1.4 14.0 2.4 23.3 0 10.000 0.1809 0.2724 0.0915 0.012 1.2 12.7 2.0 22.4 0 7.666 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2177 0.2729 0.0552 0.003 0.6 3.6 1.6 15.7 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.77 27.29 5.52 6.626 55.231 0.208 0.056 22.78 28.02 5.25 6.190 55.932 0.006 0.060 22.53 27.99 5.46 6.117 55.896 0.026 0.059 21.70 27.86 6.16 6.325 55.860 0.104 0.055 20.98 27.76 6.78 7.131 55.923 0.208 0.051 20.54 27.70 7.15 7.933 56.012 0.312 0.049 20.23 27.66 7.43 8.765 56.195 0.416 0.048 19.97 27.65 7.68 9.709 56.464 0.520 0.046 19.81 27.66 7.85 10.307 56.585 0.624 0.046 19.68 27.67 7.99 10.832 56.697 0.728 0.045 19.59 27.67 8.08 11.263 56.789 0.832 0.045 19.45 27.67 8.23 11.994 57.020 0.936 0.044 19.36 27.67 8.32 12.476 57.150 1.040 0.044 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.026 Accepted refinement result: 22.53 27.99 5.46 6.117 55.896 0.026 0.059 Individual atomic B min max mean iso aniso Overall: 23.39 153.19 57.77 5.43 3928 0 Protein: 23.39 153.19 57.77 5.43 3928 0 Chain A: 23.39 153.19 57.76 N/A 1964 0 Chain B: 25.03 152.37 57.78 N/A 1964 0 Histogram: Values Number of atoms 23.39 - 36.37 261 36.37 - 49.35 1398 49.35 - 62.33 1082 62.33 - 75.31 535 75.31 - 88.29 310 88.29 - 101.27 204 101.27 - 114.25 52 114.25 - 127.23 25 127.23 - 140.21 23 140.21 - 153.19 38 =========================== Idealize ADP of riding H ========================== r_work=0.2253 r_free=0.2799 r_work=0.2256 r_free=0.2790 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2256 r_free= 0.2790 coordinate error (max.-lik. estimate): 0.52 A | | | | normalized target function (ls_wunit_k1) (work): 0.058875 | | target function (ls_wunit_k1) not normalized (work): 518.748036 | | target function (ls_wunit_k1) not normalized (free): 44.681229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2281 0.2256 0.2790 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3354 0.3331 0.3789 n_refl.: 9255 remove outliers: r(all,work,free)=0.3354 0.3331 0.3789 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3354 0.3331 0.3789 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2276 0.2252 0.2767 n_refl.: 9255 remove outliers: r(all,work,free)=0.2276 0.2252 0.2767 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.2029 534.080 517.555 1.440 1.028 0.374 13.182-10.771 91.67 92 7 0.2052 539.747 506.039 1.315 1.030 0.368 10.742-8.763 94.15 183 10 0.1551 478.984 462.512 1.207 1.025 0.363 8.709-7.139 97.85 350 14 0.1694 420.019 410.508 1.195 1.021 0.360 7.120-5.819 98.85 652 33 0.2176 292.352 279.321 1.062 1.012 0.350 5.810-4.742 98.41 1191 49 0.1884 353.852 338.364 0.985 0.998 0.310 4.737-3.861 98.48 2221 114 0.2061 318.109 304.395 1.036 0.977 0.240 3.860-3.143 97.34 4027 214 0.2891 183.610 170.138 1.065 0.944 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.4758 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.652903 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.056857 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 0.2185 0.2762 0.0577 0.003 0.5 4.7 1.2 11.2 0 0.125 0.2108 0.2758 0.0650 0.003 0.6 5.7 1.2 12.1 0 0.250 0.2039 0.2764 0.0725 0.006 0.7 6.7 1.2 14.3 0 0.500 0.1971 0.2791 0.0820 0.009 0.9 9.4 1.2 18.2 0 1.000 0.1888 0.2766 0.0878 0.015 1.4 12.4 1.6 20.9 0 2.000 0.1843 0.2742 0.0899 0.021 1.7 15.6 2.0 22.4 0 3.000 0.1814 0.2735 0.0920 0.025 1.9 15.5 2.0 24.0 0 4.000 0.1784 0.2753 0.0969 0.030 2.2 18.8 2.4 25.6 0 5.000 0.1756 0.2759 0.1003 0.034 2.5 22.2 2.8 26.5 0 6.000 0.1736 0.2785 0.1049 0.037 2.7 23.2 3.0 27.6 0 7.000 0.1716 0.2810 0.1094 0.041 2.9 25.7 4.0 27.6 0 8.000 0.1704 0.2818 0.1114 0.044 3.1 26.2 4.2 28.3 1 9.000 0.1694 0.2827 0.1134 0.047 3.3 28.2 4.3 27.6 1 10.000 0.1897 0.2768 0.0871 0.014 1.3 12.4 1.6 20.6 0 1.826 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2185 0.2762 0.0577 0.003 0.5 4.7 1.2 11.2 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.85 27.62 5.77 9.237 62.685 0.057 5.666 23.73 29.40 5.67 9.310 65.635 0.002 5.719 22.49 28.86 6.38 9.739 63.805 0.007 5.687 21.47 27.70 6.23 9.476 62.454 0.028 5.655 20.96 27.68 6.72 10.189 62.129 0.057 5.640 20.26 27.62 7.36 11.479 62.510 0.085 5.621 20.08 27.61 7.53 11.919 62.777 0.114 5.615 19.91 27.62 7.71 12.481 63.060 0.142 5.611 19.86 27.61 7.75 12.709 63.173 0.171 5.610 19.79 27.62 7.83 13.073 63.333 0.199 5.608 19.74 27.62 7.87 13.342 63.447 0.227 5.606 19.70 27.63 7.92 13.615 63.558 0.256 5.605 19.67 27.63 7.97 13.854 63.651 0.284 5.604 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.002 Accepted refinement result: 23.73 29.40 5.67 9.310 65.635 0.002 5.719 Individual atomic B min max mean iso aniso Overall: 35.01 148.19 63.68 4.48 3928 0 Protein: 35.01 148.19 63.68 4.48 3928 0 Chain A: 35.01 148.19 63.61 N/A 1964 0 Chain B: 37.16 147.37 63.76 N/A 1964 0 Histogram: Values Number of atoms 35.01 - 46.33 222 46.33 - 57.65 1543 57.65 - 68.96 1121 68.96 - 80.28 549 80.28 - 91.60 248 91.60 - 102.92 115 102.92 - 114.24 37 114.24 - 125.56 31 125.56 - 136.88 28 136.88 - 148.19 34 =========================== Idealize ADP of riding H ========================== r_work=0.2373 r_free=0.2940 r_work=0.2386 r_free=0.2944 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2386 r_free= 0.2944 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ml) (work): 5.724274 | | target function (ml) not normalized (work): 50436.581019 | | target function (ml) not normalized (free): 2579.832483 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2412 0.2386 0.2944 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3704 0.3681 0.4130 n_refl.: 9255 remove outliers: r(all,work,free)=0.3704 0.3681 0.4130 n_refl.: 9255 overall B=-1.05 to atoms: r(all,work,free)=0.3669 0.3646 0.4095 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2375 0.2349 0.2891 n_refl.: 9255 remove outliers: r(all,work,free)=0.2375 0.2349 0.2891 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.2021 534.080 515.130 1.231 1.130 0.379 13.182-10.771 91.67 92 7 0.1912 539.747 509.379 1.125 1.123 0.368 10.742-8.763 94.15 183 10 0.1515 478.984 461.756 1.049 1.109 0.360 8.709-7.139 97.85 350 14 0.1763 420.019 408.901 1.058 1.091 0.354 7.120-5.819 98.85 652 33 0.2401 292.352 275.444 0.942 1.060 0.332 5.810-4.742 98.41 1191 49 0.2018 353.852 336.394 0.965 1.016 0.313 4.737-3.861 98.48 2221 114 0.2170 318.109 303.115 1.077 0.947 0.233 3.860-3.143 97.34 4027 214 0.2963 183.610 168.877 1.236 0.843 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0393 b_overall=0.3585 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2349 r_free=0.2891 After: r_work=0.2349 r_free=0.2891 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.591475 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049304 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 0.2348 0.2889 0.0542 0.002 0.5 4.8 1.2 11.2 0 0.125 0.2340 0.2885 0.0545 0.003 0.5 4.7 1.2 11.2 0 0.250 0.2283 0.2872 0.0589 0.008 0.7 5.3 1.2 11.0 0 0.500 0.2162 0.2870 0.0708 0.013 1.4 10.7 1.2 11.7 0 1.000 0.2079 0.2856 0.0777 0.017 1.7 19.7 1.4 15.5 0 2.000 0.2011 0.2852 0.0841 0.024 2.4 24.6 1.6 16.6 0 3.000 0.1971 0.2841 0.0870 0.029 2.7 30.2 2.2 19.3 0 4.000 0.1950 0.2845 0.0895 0.031 3.0 32.1 2.4 20.4 0 5.000 0.1931 0.2865 0.0934 0.034 3.2 32.1 3.0 23.1 0 6.000 0.1893 0.2849 0.0956 0.040 3.5 35.6 3.2 23.3 0 7.000 0.1872 0.2857 0.0984 0.044 3.8 38.9 3.2 24.9 1 8.000 0.1854 0.2847 0.0993 0.048 4.0 39.2 3.2 24.4 2 9.000 0.1842 0.2847 0.1006 0.049 4.2 40.0 3.6 25.8 2 10.000 0.2077 0.2870 0.0794 0.018 1.9 19.9 1.4 15.0 0 1.796 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2340 0.2885 0.0545 0.003 0.5 4.7 1.2 11.2 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.40 28.85 5.45 9.658 68.389 0.049 5.713 24.73 30.61 5.88 8.257 73.638 0.001 5.742 23.09 28.88 5.79 9.611 68.301 0.006 5.703 22.74 28.76 6.02 9.891 68.167 0.025 5.693 21.02 28.01 6.98 11.539 68.725 0.049 5.638 20.70 27.92 7.22 12.411 69.220 0.074 5.628 20.49 27.87 7.38 13.279 69.619 0.099 5.622 20.36 27.84 7.48 14.063 69.939 0.123 5.619 20.58 27.77 7.19 13.589 69.727 0.148 5.622 20.53 27.74 7.21 13.905 69.860 0.173 5.621 20.50 27.73 7.23 14.171 69.969 0.197 5.620 20.47 27.73 7.26 14.395 70.060 0.222 5.619 20.44 27.73 7.29 14.586 70.135 0.247 5.618 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: 23.09 28.88 5.79 9.611 68.301 0.006 5.703 Individual atomic B min max mean iso aniso Overall: 40.74 146.20 62.46 3.45 3928 0 Protein: 40.74 146.20 62.46 3.45 3928 0 Chain A: 40.74 146.20 62.39 N/A 1964 0 Chain B: 40.76 145.49 62.53 N/A 1964 0 Histogram: Values Number of atoms 40.74 - 51.29 905 51.29 - 61.83 1508 61.83 - 72.38 750 72.38 - 82.92 395 82.92 - 93.47 170 93.47 - 104.01 80 104.01 - 114.56 31 114.56 - 125.10 29 125.10 - 135.65 27 135.65 - 146.20 33 =========================== Idealize ADP of riding H ========================== r_work=0.2309 r_free=0.2888 r_work=0.2306 r_free=0.2888 ----------X-ray data---------- |--(resolution: 3.14 - 25.21 A, n_refl.=9255 (all), 4.80 % free)-------------| | | | r_work= 0.2306 r_free= 0.2888 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ml) (work): 5.702655 | | target function (ml) not normalized (work): 50246.089833 | | target function (ml) not normalized (free): 2575.030492 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.21 - 4.53 0.98 2958 131 0.1949 0.2478 5.9082 6.0121| | 2: 4.52 - 3.60 0.98 2955 140 0.2403 0.2875 5.7568 5.9102| | 3: 3.60 - 3.14 0.97 2898 173 0.2967 0.3559 5.4376 5.5493| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.21 - 4.53 2958 131 0.85 23.28 1.00 0.99 25789.47| | 2: 4.52 - 3.60 2955 140 0.80 27.27 1.01 0.96 18052.20| | 3: 3.60 - 3.14 2898 173 0.72 34.97 0.98 0.91 10960.53| |alpha: min = 0.91 max = 0.99 mean = 0.96| |beta: min = 10960.53 max = 25789.47 mean = 18317.23| |figures of merit: min = 0.01 max = 1.00 mean = 0.79| |phase err.(work): min = 0.00 max = 88.93 mean = 28.47| |phase err.(test): min = 5.78 max = 86.87 mean = 29.81| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2334 0.2306 0.2888 n_refl.: 9255 re-set all scales: r(all,work,free)=0.3647 0.3623 0.4095 n_refl.: 9255 remove outliers: r(all,work,free)=0.3647 0.3623 0.4095 n_refl.: 9255 overall B=0.00 to atoms: r(all,work,free)=0.3647 0.3623 0.4095 n_refl.: 9255 bulk-solvent and scaling: r(all,work,free)=0.2335 0.2308 0.2888 n_refl.: 9255 remove outliers: r(all,work,free)=0.2335 0.2308 0.2888 n_refl.: 9255 ======================== 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 25.215-13.182 84.48 95 3 0.1994 534.080 515.012 1.237 1.120 0.379 13.182-10.771 91.67 92 7 0.1865 539.747 510.140 1.128 1.114 0.366 10.742-8.763 94.15 183 10 0.1486 478.984 462.282 1.053 1.101 0.357 8.709-7.139 97.85 350 14 0.1738 420.019 409.252 1.062 1.085 0.353 7.120-5.819 98.85 652 33 0.2361 292.352 276.070 0.956 1.056 0.340 5.810-4.742 98.41 1191 49 0.1997 353.852 336.502 0.968 1.014 0.320 4.737-3.861 98.48 2221 114 0.2127 318.109 303.382 1.070 0.951 0.230 3.860-3.143 97.34 4027 214 0.2908 183.610 169.269 1.220 0.854 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0393 b_overall=0.3661 ================= 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 : 0.3127 0.3555 0.007 1.399 2.0 149.5 50.7 0 0.000 1_bss: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_settarget: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_updatephipsi: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_weight: 0.2324 0.2782 0.007 1.399 7.8 155.3 56.4 0 0.000 1_xyzrec: 0.2177 0.2729 0.003 0.570 7.8 155.3 56.4 0 0.168 1_adp: 0.2253 0.2799 0.003 0.570 23.4 153.2 57.8 0 0.168 1_regHadp: 0.2256 0.2790 0.003 0.570 23.4 153.2 57.8 0 0.168 2_bss: 0.2252 0.2767 0.003 0.570 23.4 153.2 57.8 0 0.168 2_settarget: 0.2252 0.2767 0.003 0.570 23.4 153.2 57.8 0 0.168 2_updatephipsi: 0.2252 0.2767 0.003 0.570 23.4 153.2 57.8 0 0.168 2_updatecdl: 0.2252 0.2767 0.003 0.611 23.4 153.2 57.8 0 0.168 2_weight: 0.2252 0.2767 0.003 0.611 23.4 153.2 57.8 0 0.168 2_xyzrec: 0.2185 0.2762 0.003 0.505 23.4 153.2 57.8 0 0.247 2_adp: 0.2373 0.2940 0.003 0.505 35.0 148.2 63.7 0 0.247 2_regHadp: 0.2386 0.2944 0.003 0.505 35.0 148.2 63.7 0 0.247 3_bss: 0.2349 0.2891 0.003 0.505 34.0 147.1 62.6 0 0.247 3_settarget: 0.2349 0.2891 0.003 0.505 34.0 147.1 62.6 0 0.247 3_updatephipsi: 0.2349 0.2891 0.003 0.505 34.0 147.1 62.6 0 0.247 3_updatecdl: 0.2349 0.2891 0.003 0.526 34.0 147.1 62.6 0 0.247 3_setrh: 0.2349 0.2891 0.003 0.526 34.0 147.1 62.6 0 0.247 3_weight: 0.2349 0.2891 0.003 0.526 34.0 147.1 62.6 0 0.247 3_xyzrec: 0.2340 0.2885 0.003 0.513 34.0 147.1 62.6 0 0.248 3_adp: 0.2309 0.2888 0.003 0.513 40.7 146.2 62.5 0 0.248 3_regHadp: 0.2306 0.2888 0.003 0.513 40.7 146.2 62.5 0 0.248 end: 0.2308 0.2888 0.003 0.513 40.7 146.2 62.5 0 0.248 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1w60_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1w60_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 11.4100 Refinement macro-cycles (run) : 274.6500 Write final files (write_after_run_outputs) : 22.1300 Total : 308.1900 Total CPU time: 5.87 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:58 PDT -0700 (1716251698.33 s) Start R-work = 0.2324, R-free = 0.2782 Final R-work = 0.2308, R-free = 0.2888 =============================================================================== Job complete usr+sys time: 370.66 seconds wall clock time: 18 minutes 13.79 seconds (1093.79 seconds total)