Starting phenix.refine on Mon May 20 17:16:28 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.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=False 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/4yei/4yei.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.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 { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 9333 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "B" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "C" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Time building chain proxies: 1.66, per 1000 atoms: 0.18 Number of scatterers: 9333 At special positions: 0 Unit cell: (110.36, 115.96, 164.12, 90, 90, 90) Space group: I 2 2 2 (No. 23) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 966 8.00 N 909 7.00 C 2865 6.00 H 4584 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: 2.65 Conformation dependent library (CDL) restraints added in 324.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Time building geometry restraints manager: 2.98 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: 4581 1.15 - 1.32: 1124 1.32 - 1.49: 1726 1.49 - 1.66: 1935 1.66 - 1.84: 15 Bond restraints: 9381 Sorted by residual: bond pdb=" N GLU A 44 " pdb=" H GLU A 44 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ARG A 186 " pdb=" H ARG A 186 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 210 " pdb=" H ALA A 210 " 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 177 " pdb=" H LEU B 177 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 228 " pdb=" H ALA A 228 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9376 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 223 105.44 - 112.60: 10348 112.60 - 119.75: 2632 119.75 - 126.90: 3592 126.90 - 134.06: 50 Bond angle restraints: 16845 Sorted by residual: angle pdb=" N LEU A 233 " pdb=" CA LEU A 233 " pdb=" C LEU A 233 " ideal model delta sigma weight residual 110.80 119.87 -9.07 2.13e+00 2.20e-01 1.81e+01 angle pdb=" N THR B 209 " pdb=" CA THR B 209 " pdb=" C THR B 209 " ideal model delta sigma weight residual 113.88 119.07 -5.19 1.23e+00 6.61e-01 1.78e+01 angle pdb=" N SER A 211 " pdb=" CA SER A 211 " pdb=" CB SER A 211 " ideal model delta sigma weight residual 110.06 116.02 -5.96 1.51e+00 4.39e-01 1.56e+01 angle pdb=" CG ARG A 191 " pdb=" CD ARG A 191 " pdb=" NE ARG A 191 " ideal model delta sigma weight residual 112.00 103.57 8.43 2.20e+00 2.07e-01 1.47e+01 angle pdb=" CA ALA C 210 " pdb=" C ALA C 210 " pdb=" O ALA C 210 " ideal model delta sigma weight residual 121.47 117.12 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 16840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 3987 15.79 - 31.57: 244 31.57 - 47.36: 121 47.36 - 63.15: 23 63.15 - 78.93: 8 Dihedral angle restraints: 4383 sinusoidal: 2373 harmonic: 2010 Sorted by residual: dihedral pdb=" C ASP A 218 " pdb=" N ASP A 218 " pdb=" CA ASP A 218 " pdb=" CB ASP A 218 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N ALA A 234 " pdb=" CA ALA A 234 " ideal model delta harmonic sigma weight residual -180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" C VAL C 205 " pdb=" N VAL C 205 " pdb=" CA VAL C 205 " pdb=" CB VAL C 205 " ideal model delta harmonic sigma weight residual -122.00 -130.88 8.88 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 559 0.093 - 0.186: 157 0.186 - 0.278: 32 0.278 - 0.371: 16 0.371 - 0.464: 1 Chirality restraints: 765 Sorted by residual: chirality pdb=" CA ARG A 208 " pdb=" N ARG A 208 " pdb=" C ARG A 208 " pdb=" CB ARG A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA MET B 171 " pdb=" N MET B 171 " pdb=" C MET B 171 " pdb=" CB MET B 171 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU A 109 " pdb=" N GLU A 109 " pdb=" C GLU A 109 " pdb=" CB GLU A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 762 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 208 " 0.046 9.50e-02 1.11e+02 3.78e-02 2.72e+01 pdb=" NE ARG A 208 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 208 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 208 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 208 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 208 " 0.058 2.00e-02 2.50e+03 pdb="HH12 ARG A 208 " -0.020 2.00e-02 2.50e+03 pdb="HH21 ARG A 208 " 0.056 2.00e-02 2.50e+03 pdb="HH22 ARG A 208 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.022 2.00e-02 2.50e+03 2.61e-02 2.05e+01 pdb=" CG TYR A 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 59 " -0.005 2.00e-02 2.50e+03 2.61e-02 2.05e+01 pdb=" CG TYR C 59 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 59 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 59 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 59 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 59 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 59 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TYR C 59 " -0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR C 59 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 TYR C 59 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 TYR C 59 " -0.049 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 322 1.94 - 2.60: 9707 2.60 - 3.27: 30939 3.27 - 3.93: 40839 3.93 - 4.60: 59795 Nonbonded interactions: 141602 Sorted by model distance: nonbonded pdb=" HE1 HIS A 198 " pdb=" HB3 ALA A 234 " model vdw sym.op. 1.270 2.270 x,-y+2,-z+2 nonbonded pdb=" HD3 ARG A 208 " pdb=" O ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 nonbonded pdb=" O ARG A 208 " pdb=" HD3 ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 nonbonded pdb=" HB3 ALA B 234 " pdb=" HE ARG C 216 " model vdw sym.op. 1.398 2.270 x,-y+2,-z+2 nonbonded pdb=" OXT ALA B 234 " pdb="HH21 ARG C 216 " model vdw sym.op. 1.425 1.850 x,-y+2,-z+2 ... (remaining 141597 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 9 15.91 1 O 966 7.97 1 N 909 6.97 1 C 2865 5.97 1 H 4584 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: 4584 of 9333 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 9333 n_use_u_iso = 4587 n_use_u_aniso = 4746 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 = 9333 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (9333 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4587 aniso = 4746) 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 { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "4yei_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4584 occupancy sum: 4584.00 (% of total atoms 49.12) Rotatable: count: 1419 occupancy sum: 1419.00 (% of total atoms 15.20) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4648 r_free= 0.3724 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.850734 | | target function (ml) not normalized (work): 82845.930745 | | target function (ml) not normalized (free): 4160.088940 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 37.43 - 5.64 0.98 3160 150 0.4377 0.4107 7.9301 7.1801| | 2: 5.64 - 4.48 0.97 3007 139 0.4270 0.3140 6.6996 6.8358| | 3: 4.48 - 3.91 0.98 2977 158 0.4835 0.3449 6.4646 6.5718| | 4: 3.91 - 3.55 0.98 2949 176 0.5523 0.4277 6.238 6.2191| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 37.43 - 5.64 3160 150 0.58 44.13 0.74 0.59 276018.49| | 2: 5.64 - 4.48 3007 139 0.64 40.12 1.64 0.84 146839.46| | 3: 4.48 - 3.91 2977 158 0.77 28.52 1.84 0.98 70891.22| | 4: 3.91 - 3.55 2949 176 0.73 33.00 2.00 1.01 48173.76| |alpha: min = 0.59 max = 1.01 mean = 0.85| |beta: min = 48173.76 max = 276018.49 mean = 137837.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.82 mean = 36.58| |phase err.(test): min = 0.00 max = 89.91 mean = 35.81| |-----------------------------------------------------------------------------| ----------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 : 0.017 0.091 4797 Z= 1.131 Angle : 1.564 10.417 6522 Z= 0.950 Chirality : 0.097 0.464 765 Planarity : 0.008 0.044 900 Dihedral : 14.850 78.933 1683 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.49 % Allowed : 5.94 % Favored : 92.57 % 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: -1.82 (0.25), residues: 639 helix: -0.76 (0.52), residues: 93 sheet: None (None), residues: 0 loop : -1.42 (0.19), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 208 TYR 0.030 0.009 TYR C 30 PHE 0.030 0.007 PHE B 225 TRP 0.026 0.009 TRP C 207 HIS 0.015 0.004 HIS A 198 Individual atomic B min max mean iso aniso Overall: 49.64 289.79 106.35 4.55 4749 0 Protein: 49.64 289.79 106.35 4.55 4749 0 Chain A: 49.64 180.30 105.91 N/A 1583 0 Chain B: 56.85 174.83 98.34 N/A 1583 0 Chain C: 58.38 289.79 114.82 N/A 1583 0 Histogram: Values Number of atoms 49.64 - 73.66 630 73.66 - 97.67 1454 97.67 - 121.69 1256 121.69 - 145.70 892 145.70 - 169.72 426 169.72 - 193.73 50 193.73 - 217.74 22 217.74 - 241.76 11 241.76 - 265.77 5 265.77 - 289.79 3 |-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: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4648 r_free= 0.3724 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.850734 | | target function (ml) not normalized (work): 82845.930745 | | target function (ml) not normalized (free): 4160.088940 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 7.9863 percent. r_work = 0.5447 r_free = 0.4722 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5420 0.5447 0.4722 n_refl.: 12716 re-set all scales: r(all,work,free)=0.5420 0.5447 0.4722 n_refl.: 12716 remove outliers: r(all,work,free)=0.5326 0.5350 0.4722 n_refl.: 12706 overall B=-19.52 to atoms: r(all,work,free)=0.4761 0.4780 0.4317 n_refl.: 12706 bulk-solvent and scaling: r(all,work,free)=0.2831 0.2821 0.3031 n_refl.: 12706 remove outliers: r(all,work,free)=0.2830 0.2820 0.3031 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2361 2888.741 2836.860 1.377 1.103 0.425 17.650-14.285 98.02 94 5 0.1437 3045.471 3027.032 1.043 1.100 0.372 14.282-11.568 95.90 180 7 0.1422 3015.142 2972.767 1.162 1.084 0.366 11.530-9.354 97.49 335 14 0.2123 1633.314 1609.041 1.151 1.071 0.367 9.349-7.570 98.64 624 29 0.2492 1223.678 1175.786 0.914 1.049 0.311 7.566-6.123 98.85 1143 56 0.2819 950.581 897.392 0.914 1.017 0.268 6.123-4.955 97.48 2111 97 0.3017 843.953 800.215 1.013 0.964 0.260 4.954-4.009 97.40 3921 193 0.2745 1174.560 1150.097 1.226 0.888 0.193 4.009-3.554 97.79 3579 218 0.3563 708.485 625.652 1.175 0.814 0.156 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0608 b_overall=6.4247 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.905868 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.141170 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 0.2907 0.3181 0.0274 0.002 0.4 0.2 0.0 0.2 0 0.125 0.2838 0.3156 0.0319 0.002 0.5 0.3 0.0 0.2 0 0.250 0.2739 0.3140 0.0401 0.002 0.5 0.4 0.0 0.4 0 0.500 0.2662 0.3125 0.0463 0.003 0.6 1.3 0.0 0.8 0 1.000 0.2610 0.3098 0.0487 0.005 0.8 2.8 0.0 1.1 0 2.000 0.2577 0.3081 0.0504 0.007 1.0 2.7 0.0 1.3 0 3.000 0.2551 0.3070 0.0519 0.009 1.2 4.3 0.0 1.5 0 4.000 0.2408 0.3162 0.0754 0.009 1.0 12.3 2.8 6.6 0 5.000 0.2383 0.3194 0.0812 0.010 1.1 18.3 4.9 7.4 0 6.000 0.2360 0.3145 0.0785 0.011 1.2 17.7 4.9 7.0 0 7.000 0.2335 0.3151 0.0817 0.012 1.3 20.7 6.9 8.5 0 8.000 0.2321 0.3163 0.0842 0.013 1.4 24.5 7.4 11.0 0 9.000 0.2307 0.3159 0.0852 0.014 1.4 26.6 7.8 11.7 0 10.000 0.2369 0.3166 0.0797 0.010 1.1 17.5 4.5 7.0 0 6.453 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2907 0.3181 0.0274 0.002 0.4 0.2 0.0 0.2 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 29.07 31.81 2.74 3.255 86.699 0.141 0.086 28.93 31.67 2.74 3.525 86.939 0.004 0.085 28.65 31.54 2.90 3.579 86.943 0.018 0.084 27.36 31.00 3.63 6.066 87.566 0.071 0.075 26.76 30.75 3.99 7.180 87.734 0.141 0.072 26.45 30.63 4.18 8.091 87.931 0.212 0.070 26.26 30.56 4.30 8.784 88.095 0.282 0.069 26.04 30.49 4.45 9.683 88.393 0.353 0.068 25.75 30.41 4.66 10.978 88.873 0.424 0.066 25.65 30.40 4.75 11.517 89.026 0.494 0.066 25.56 30.37 4.81 12.010 89.169 0.565 0.065 25.47 30.36 4.89 12.548 89.337 0.635 0.065 25.44 30.35 4.91 12.762 89.383 0.706 0.065 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.706 Accepted refinement result: 25.44 30.35 4.91 12.762 89.383 0.706 0.065 Individual atomic B min max mean iso aniso Overall: 26.71 265.26 92.10 12.12 4749 0 Protein: 26.71 265.26 92.10 12.12 4749 0 Chain A: 26.71 167.43 91.04 N/A 1583 0 Chain B: 32.93 162.15 84.98 N/A 1583 0 Chain C: 37.15 265.26 100.29 N/A 1583 0 Histogram: Values Number of atoms 26.71 - 50.56 250 50.56 - 74.42 1219 74.42 - 98.27 1451 98.27 - 122.13 1042 122.13 - 145.98 632 145.98 - 169.84 115 169.84 - 193.70 21 193.70 - 217.55 11 217.55 - 241.41 5 241.41 - 265.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.2544 r_free=0.3035 r_work=0.2509 r_free=0.3012 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2509 r_free= 0.3012 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ls_wunit_k1) (work): 0.062748 | | target function (ls_wunit_k1) not normalized (work): 758.125881 | | target function (ls_wunit_k1) not normalized (free): 54.995954 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2533 0.2509 0.3012 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4841 0.4855 0.4484 n_refl.: 12705 remove outliers: r(all,work,free)=0.4841 0.4855 0.4484 n_refl.: 12705 overall B=0.59 to atoms: r(all,work,free)=0.4858 0.4873 0.4495 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2513 0.2487 0.3014 n_refl.: 12705 remove outliers: r(all,work,free)=0.2513 0.2487 0.3014 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2368 1602.772 1593.236 1.284 1.093 0.430 17.650-14.285 98.02 94 5 0.1548 1689.731 1670.272 1.063 1.092 0.385 14.282-11.568 95.90 180 7 0.1394 1672.904 1657.194 1.173 1.076 0.375 11.530-9.354 97.49 335 14 0.2051 906.218 896.548 1.141 1.065 0.369 9.349-7.570 98.64 624 29 0.2380 678.938 656.297 0.891 1.044 0.299 7.566-6.123 98.85 1143 56 0.2620 527.415 505.233 0.896 1.015 0.268 6.123-4.955 97.48 2111 97 0.2683 468.254 451.982 1.008 0.968 0.249 4.954-4.009 97.40 3921 193 0.2263 651.686 646.254 1.236 0.900 0.179 4.009-3.554 97.79 3579 218 0.3170 393.092 359.238 1.233 0.834 0.129 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.2294 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.528721 wxc_scale = 0.025 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.034844 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 0.2605 0.3130 0.0526 0.001 0.4 1.3 0.0 0.2 0 0.009 0.2509 0.3066 0.0557 0.001 0.4 0.5 0.0 0.2 0 0.026 0.2428 0.3013 0.0585 0.001 0.4 0.5 0.0 0.2 0 0.053 0.2391 0.3006 0.0615 0.001 0.4 0.4 0.0 0.2 0 0.079 0.2363 0.2999 0.0636 0.001 0.4 0.5 0.0 0.4 0 0.106 0.2347 0.2985 0.0638 0.002 0.4 0.5 0.0 0.4 0 0.132 0.2335 0.2967 0.0632 0.002 0.4 0.5 0.0 0.4 0 0.159 0.2327 0.2963 0.0636 0.002 0.5 0.8 0.0 0.4 0 0.185 0.2381 0.2978 0.0597 0.001 0.4 0.5 0.0 0.2 0 0.088 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2327 0.2963 0.0636 0.002 0.5 0.8 0.0 0.4 0 0.185 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.27 29.63 6.36 16.123 102.025 0.035 6.500 26.50 30.88 4.38 14.205 107.017 0.001 6.577 26.63 30.99 4.36 14.576 107.899 0.004 6.572 24.46 29.59 5.12 15.510 103.747 0.017 6.509 23.84 29.27 5.42 16.349 102.870 0.035 6.487 23.29 29.00 5.71 16.539 102.161 0.052 6.475 23.15 29.00 5.85 16.907 102.476 0.070 6.468 23.01 29.02 6.01 17.081 102.354 0.087 6.466 22.93 29.04 6.11 17.314 102.462 0.105 6.463 22.86 29.04 6.18 17.535 102.567 0.122 6.461 22.80 29.05 6.25 17.733 102.666 0.139 6.459 22.75 29.03 6.28 17.912 102.755 0.157 6.458 22.72 29.03 6.31 18.080 102.835 0.174 6.457 max suggested for this run: 20.41 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.052 Accepted refinement result: 23.29 29.00 5.71 16.539 102.161 0.052 6.475 Individual atomic B min max mean iso aniso Overall: 28.72 260.86 92.96 10.90 4749 0 Protein: 28.72 260.86 92.96 10.90 4749 0 Chain A: 28.72 163.78 90.98 N/A 1583 0 Chain B: 37.42 164.10 86.02 N/A 1583 0 Chain C: 38.14 260.86 101.89 N/A 1583 0 Histogram: Values Number of atoms 28.72 - 51.93 190 51.93 - 75.14 1300 75.14 - 98.36 1440 98.36 - 121.57 968 121.57 - 144.79 649 144.79 - 168.00 163 168.00 - 191.21 20 191.21 - 214.43 11 214.43 - 237.64 5 237.64 - 260.86 3 =========================== Idealize ADP of riding H ========================== r_work=0.2329 r_free=0.2900 r_work=0.2335 r_free=0.2894 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2335 r_free= 0.2894 coordinate error (max.-lik. estimate): 0.59 A | | | | normalized target function (ml) (work): 6.474721 | | target function (ml) not normalized (work): 78227.575646 | | target function (ml) not normalized (free): 4124.697979 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2363 0.2335 0.2894 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4813 0.4830 0.4422 n_refl.: 12705 remove outliers: r(all,work,free)=0.4813 0.4830 0.4422 n_refl.: 12705 overall B=1.10 to atoms: r(all,work,free)=0.4848 0.4865 0.4446 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2340 0.2313 0.2873 n_refl.: 12705 remove outliers: r(all,work,free)=0.2340 0.2313 0.2873 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2195 1602.772 1615.825 1.228 1.139 0.430 17.650-14.285 98.02 94 5 0.1298 1689.731 1687.192 1.017 1.136 0.390 14.282-11.568 95.90 180 7 0.1296 1672.904 1648.732 1.094 1.117 0.369 11.530-9.354 97.49 335 14 0.1761 906.218 893.376 1.084 1.101 0.359 9.349-7.570 98.64 624 29 0.2182 678.938 658.135 0.874 1.074 0.299 7.566-6.123 98.85 1143 56 0.2478 527.415 503.975 0.882 1.035 0.255 6.123-4.955 97.48 2111 97 0.2621 468.254 444.592 1.014 0.973 0.238 4.954-4.009 97.40 3921 193 0.2037 651.686 639.467 1.239 0.881 0.168 4.009-3.554 97.79 3579 218 0.3021 393.092 356.392 1.282 0.790 0.127 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.4244 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2313 r_free=0.2873 After: r_work=0.2313 r_free=0.2872 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.995297 wxc_scale = 0.043 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.033697 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 0.2321 0.2876 0.0555 0.002 0.5 0.6 0.0 0.4 0 0.017 0.2318 0.2876 0.0558 0.002 0.5 0.6 0.0 0.4 0 0.051 0.2314 0.2877 0.0562 0.002 0.5 0.6 0.0 0.4 0 0.102 0.2312 0.2876 0.0565 0.002 0.5 0.6 0.0 0.4 0 0.153 0.2310 0.2875 0.0565 0.002 0.5 0.6 0.0 0.4 0 0.204 0.2308 0.2872 0.0564 0.002 0.5 0.6 0.0 0.4 0 0.255 0.2302 0.2869 0.0567 0.003 0.5 0.6 0.0 0.4 0 0.306 0.2297 0.2867 0.0570 0.003 0.5 0.6 0.0 0.4 0 0.357 0.2312 0.2877 0.0565 0.002 0.5 0.6 0.0 0.4 0 0.170 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2297 0.2867 0.0570 0.003 0.5 0.6 0.0 0.4 0 0.357 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.97 28.67 5.70 15.730 103.438 0.034 6.476 27.99 31.73 3.74 14.402 111.348 0.001 6.611 26.68 31.14 4.47 13.641 109.872 0.004 6.578 24.31 29.32 5.01 15.035 104.713 0.017 6.516 23.47 28.90 5.43 15.660 103.971 0.034 6.489 22.74 28.41 5.67 16.062 103.605 0.051 6.464 22.49 28.24 5.74 16.539 103.620 0.067 6.456 22.31 28.31 5.99 17.062 103.669 0.084 6.450 22.25 28.31 6.06 17.297 103.714 0.101 6.448 22.19 28.32 6.12 17.516 103.827 0.118 6.446 22.15 28.31 6.16 17.696 103.928 0.135 6.445 22.12 28.31 6.20 17.863 104.025 0.152 6.444 22.09 28.30 6.22 18.010 104.110 0.168 6.443 max suggested for this run: 20.69 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.067 Accepted refinement result: 22.49 28.24 5.74 16.539 103.620 0.067 6.456 Individual atomic B min max mean iso aniso Overall: 28.01 256.96 94.42 12.94 4749 0 Protein: 28.01 256.96 94.42 12.94 4749 0 Chain A: 28.01 181.66 91.34 N/A 1583 0 Chain B: 36.76 176.30 87.48 N/A 1583 0 Chain C: 41.54 256.96 104.44 N/A 1583 0 Histogram: Values Number of atoms 28.01 - 50.90 159 50.90 - 73.80 1159 73.80 - 96.69 1517 96.69 - 119.59 919 119.59 - 142.48 640 142.48 - 165.38 278 165.38 - 188.27 58 188.27 - 211.17 11 211.17 - 234.06 5 234.06 - 256.96 3 =========================== Idealize ADP of riding H ========================== r_work=0.2249 r_free=0.2824 r_work=0.2246 r_free=0.2821 ----------X-ray data---------- |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2246 r_free= 0.2821 coordinate error (max.-lik. estimate): 0.57 A | | | | normalized target function (ml) (work): 6.454515 | | target function (ml) not normalized (work): 77983.448165 | | target function (ml) not normalized (free): 4116.778616 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.24 - 5.63 0.98 3159 150 0.2075 0.2540 6.6175 6.7969| | 2: 5.63 - 4.48 0.97 3003 139 0.2081 0.2603 6.4721 6.6596| | 3: 4.48 - 3.91 0.98 2973 158 0.2095 0.2602 6.4472 6.6913| | 4: 3.91 - 3.55 0.98 2947 176 0.3109 0.3955 6.2693 6.3315| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.24 - 5.63 3159 150 0.75 29.60 1.00 1.00 112153.93| | 2: 5.63 - 4.48 3003 139 0.70 34.81 1.04 1.00 96514.94| | 3: 4.48 - 3.91 2973 158 0.74 31.45 0.97 0.93 82615.85| | 4: 3.91 - 3.55 2947 176 0.61 42.92 0.98 0.79 70456.65| |alpha: min = 0.79 max = 1.00 mean = 0.93| |beta: min = 70456.65 max = 112153.93 mean = 90827.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.70| |phase err.(work): min = 0.00 max = 90.00 mean = 34.60| |phase err.(test): min = 0.00 max = 89.08 mean = 35.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2274 0.2246 0.2821 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4817 0.4836 0.4411 n_refl.: 12705 remove outliers: r(all,work,free)=0.4817 0.4836 0.4411 n_refl.: 12705 overall B=0.12 to atoms: r(all,work,free)=0.4821 0.4840 0.4414 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2266 0.2238 0.2823 n_refl.: 12705 remove outliers: r(all,work,free)=0.2266 0.2238 0.2823 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2219 1602.772 1614.804 1.207 1.162 0.430 17.650-14.285 98.02 94 5 0.1292 1689.731 1685.993 0.958 1.159 0.380 14.282-11.568 95.90 180 7 0.1282 1672.904 1648.484 1.040 1.138 0.360 11.530-9.354 97.49 335 14 0.1762 906.218 892.081 1.050 1.121 0.350 9.349-7.570 98.64 624 29 0.2157 678.938 656.989 0.863 1.091 0.300 7.566-6.123 98.85 1143 56 0.2419 527.415 504.176 0.878 1.047 0.250 6.123-4.955 97.48 2111 97 0.2537 468.254 444.155 1.021 0.978 0.230 4.954-4.009 97.40 3921 193 0.1934 651.686 638.388 1.243 0.877 0.160 4.009-3.554 97.79 3579 218 0.2932 393.092 357.817 1.311 0.776 0.120 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0475 ================= 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 : 0.4648 0.3724 0.017 1.564 49.6 289.8 106.4 0 0.000 1_bss: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_settarget: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_weight: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_xyzrec: 0.2907 0.3181 0.002 0.441 30.1 270.3 86.8 0 0.151 1_adp: 0.2544 0.3035 0.002 0.441 26.7 265.3 92.1 0 0.151 1_regHadp: 0.2509 0.3012 0.002 0.441 26.7 265.3 92.1 0 0.151 2_bss: 0.2487 0.3014 0.002 0.441 27.3 265.9 92.7 0 0.151 2_settarget: 0.2487 0.3014 0.002 0.441 27.3 265.9 92.7 0 0.151 2_updatecdl: 0.2487 0.3014 0.002 0.484 27.3 265.9 92.7 0 0.151 2_weight: 0.2487 0.3014 0.002 0.484 27.3 265.9 92.7 0 0.151 2_xyzrec: 0.2327 0.2963 0.002 0.459 27.3 265.9 92.7 0 0.222 2_adp: 0.2329 0.2900 0.002 0.459 28.7 260.9 93.0 0 0.222 2_regHadp: 0.2335 0.2894 0.002 0.459 28.7 260.9 93.0 0 0.222 3_bss: 0.2313 0.2873 0.002 0.459 29.8 262.0 94.1 0 0.222 3_settarget: 0.2313 0.2873 0.002 0.459 29.8 262.0 94.1 0 0.222 3_updatecdl: 0.2313 0.2873 0.002 0.519 29.8 262.0 94.1 0 0.222 3_setrh: 0.2313 0.2872 0.002 0.519 29.8 262.0 94.1 0 0.222 3_weight: 0.2313 0.2872 0.002 0.519 29.8 262.0 94.1 0 0.222 3_xyzrec: 0.2297 0.2867 0.003 0.538 29.8 262.0 94.1 0 0.224 3_adp: 0.2249 0.2824 0.003 0.538 28.0 257.0 94.4 0 0.224 3_regHadp: 0.2246 0.2821 0.003 0.538 28.0 257.0 94.4 0 0.224 end: 0.2238 0.2823 0.003 0.538 28.1 257.1 94.5 0 0.224 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/4yei_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/4yei_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 13.2500 Refinement macro-cycles (run) : 332.6900 Write final files (write_after_run_outputs) : 18.8600 Total : 364.8000 Total CPU time: 6.66 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:27 PDT -0700 (1716251727.66 s) Start R-work = 0.2820, R-free = 0.3031 Final R-work = 0.2238, R-free = 0.2823 =============================================================================== Job complete usr+sys time: 420.37 seconds wall clock time: 19 minutes 21.91 seconds (1161.91 seconds total)