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/1u9o.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u9o/1u9o.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/1u9o/1u9o.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u9o/1u9o.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u9o.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u9o.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 GLU 180": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 5976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain: "B" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Time building chain proxies: 1.10, per 1000 atoms: 0.18 Number of scatterers: 5976 At special positions: 0 Unit cell: (140.5, 140.5, 76.69, 90, 90, 120) Space group: R 3 :H (No. 146) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 586 8.00 N 520 7.00 C 1908 6.00 H 2954 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: 1.46 Conformation dependent library (CDL) restraints added in 194.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Time building geometry restraints manager: 1.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2954 1.16 - 1.33: 935 1.33 - 1.51: 1032 1.51 - 1.69: 1101 1.69 - 1.86: 16 Bond restraints: 6038 Sorted by residual: bond pdb=" N SER A 131 " pdb=" H SER A 131 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH1 ARG A 122 " pdb="HH11 ARG A 122 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ALA A 95 " pdb=" H ALA A 95 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG B 78 " pdb="HH22 ARG B 78 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 191 " pdb=" H GLN A 191 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6033 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.85: 324 106.85 - 113.67: 6801 113.67 - 120.49: 2030 120.49 - 127.31: 1705 127.31 - 134.13: 30 Bond angle restraints: 10890 Sorted by residual: angle pdb=" N LEU B 36 " pdb=" CA LEU B 36 " pdb=" C LEU B 36 " ideal model delta sigma weight residual 114.56 103.25 11.31 1.27e+00 6.20e-01 7.92e+01 angle pdb=" N VAL B 109 " pdb=" CA VAL B 109 " pdb=" C VAL B 109 " ideal model delta sigma weight residual 110.30 103.58 6.72 9.70e-01 1.06e+00 4.81e+01 angle pdb=" N ARG B 159 " pdb=" CA ARG B 159 " pdb=" C ARG B 159 " ideal model delta sigma weight residual 112.92 104.87 8.05 1.23e+00 6.61e-01 4.29e+01 angle pdb=" N VAL A 47 " pdb=" CA VAL A 47 " pdb=" C VAL A 47 " ideal model delta sigma weight residual 111.05 103.32 7.73 1.25e+00 6.40e-01 3.83e+01 angle pdb=" N LEU A 90 " pdb=" CA LEU A 90 " pdb=" C LEU A 90 " ideal model delta sigma weight residual 114.39 106.42 7.97 1.45e+00 4.76e-01 3.02e+01 ... (remaining 10885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 2583 18.01 - 36.02: 171 36.02 - 54.02: 65 54.02 - 72.03: 23 72.03 - 90.04: 4 Dihedral angle restraints: 2846 sinusoidal: 1524 harmonic: 1322 Sorted by residual: dihedral pdb=" CB GLU B 180 " pdb=" CG GLU B 180 " pdb=" CD GLU B 180 " pdb=" OE1 GLU B 180 " ideal model delta sinusoidal sigma weight residual 0.00 90.04 -90.04 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU B 26 " pdb=" CG GLU B 26 " pdb=" CD GLU B 26 " pdb=" OE1 GLU B 26 " ideal model delta sinusoidal sigma weight residual 0.00 -88.21 88.21 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" N ASP B 96 " pdb=" CA ASP B 96 " pdb=" CB ASP B 96 " pdb=" CG ASP B 96 " ideal model delta sinusoidal sigma weight residual -180.00 -120.07 -59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 283 0.065 - 0.129: 133 0.129 - 0.194: 50 0.194 - 0.258: 13 0.258 - 0.323: 5 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA VAL B 109 " pdb=" N VAL B 109 " pdb=" C VAL B 109 " pdb=" CB VAL B 109 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA TYR B 62 " pdb=" N TYR B 62 " pdb=" C TYR B 62 " pdb=" CB TYR B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 481 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 148 " 0.157 2.00e-02 2.50e+03 6.20e-02 1.15e+02 pdb=" CG TYR A 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 148 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 148 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 148 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 148 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 148 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 148 " 0.109 2.00e-02 2.50e+03 pdb=" HD1 TYR A 148 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 148 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR A 148 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 148 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 141 " 0.107 2.00e-02 2.50e+03 3.96e-02 4.70e+01 pdb=" CG PHE A 141 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 141 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE A 141 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 PHE A 141 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 141 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 141 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 138 " -0.105 2.00e-02 2.50e+03 3.17e-02 4.02e+01 pdb=" CG TRP B 138 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 138 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 138 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP B 138 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 138 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 138 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 138 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 138 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 138 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP B 138 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TRP B 138 " -0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP B 138 " 0.031 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 138 " -0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 138 " 0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP B 138 " -0.021 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.88: 245 1.88 - 2.56: 5793 2.56 - 3.24: 19194 3.24 - 3.92: 24770 3.92 - 4.60: 37824 Nonbonded interactions: 87826 Sorted by model distance: nonbonded pdb=" HE3 MET B 178 " pdb="HD22 LEU B 203 " model vdw 1.201 2.440 nonbonded pdb=" H ALA B 127 " pdb=" H ARG B 128 " model vdw 1.227 2.100 nonbonded pdb=" O GLN B 125 " pdb=" H ALA B 127 " model vdw 1.252 1.850 nonbonded pdb=" H LEU B 36 " pdb=" H LEU B 37 " model vdw 1.342 2.100 nonbonded pdb=" HG3 ARG A 40 " pdb="HH11 ARG A 40 " model vdw 1.436 2.270 ... (remaining 87821 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 8 15.96 2 O 586 7.97 1 N 520 6.97 1 C 1908 5.97 2 H 2954 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: 2954 of 5976 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 5976 n_use_u_iso = 5976 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 = 5976 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (5976 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 5976 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 { nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1u9o_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2954 occupancy sum: 2954.00 (% of total atoms 49.43) Rotatable: count: 874 occupancy sum: 874.00 (% of total atoms 14.63) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.3147 r_free= 0.3639 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 7.003758 | | target function (ml) not normalized (work): 54657.324350 | | target function (ml) not normalized (free): 2915.597919 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.48 - 4.76 0.96 2554 135 0.3296 0.3883 7.6147 7.643| | 2: 4.76 - 3.79 1.00 2644 139 0.3008 0.3414 7.0188 7.1475| | 3: 3.79 - 3.31 0.98 2606 137 0.3026 0.3485 6.3898 6.4985| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.48 - 4.76 2554 135 0.56 48.14 0.92 0.54 844097.77| | 2: 4.76 - 3.79 2644 139 0.62 43.00 1.24 0.73 373205.76| | 3: 3.79 - 3.31 2606 137 0.74 33.70 1.14 0.78 84339.63| |alpha: min = 0.54 max = 0.78 mean = 0.68| |beta: min = 84339.63 max = 844097.77 mean = 430852.23| |figures of merit: min = 0.01 max = 0.99 mean = 0.64| |phase err.(work): min = 6.22 max = 89.62 mean = 41.58| |phase err.(test): min = 8.18 max = 87.95 mean = 39.39| |-----------------------------------------------------------------------------| ----------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 0.071 3084 Z= 0.595 Angle : 1.426 11.305 4206 Z= 0.952 Chirality : 0.088 0.323 484 Planarity : 0.009 0.069 552 Dihedral : 15.917 90.038 1102 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 29.65 Ramachandran Plot: Outliers : 5.73 % Allowed : 20.83 % Favored : 73.44 % Rotamer: Outliers : 7.05 % Allowed : 6.41 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -7.23 (0.24), residues: 384 helix: -4.48 (0.16), residues: 286 sheet: None (None), residues: 0 loop : -4.93 (0.41), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 181 TYR 0.129 0.017 TYR A 148 PHE 0.065 0.014 PHE A 141 TRP 0.072 0.010 TRP B 138 HIS 0.003 0.001 HIS B 169 Individual atomic B min max mean iso aniso Overall: 6.35 60.00 50.91 1.57 3022 0 Protein: 6.35 60.00 50.91 1.57 3022 0 Chain A: 6.35 60.00 49.62 N/A 1511 0 Chain B: 25.19 60.00 52.21 N/A 1511 0 Histogram: Values Number of atoms 6.35 - 11.71 1 11.71 - 17.08 1 17.08 - 22.45 0 22.45 - 27.81 5 27.81 - 33.18 12 33.18 - 38.54 109 38.54 - 43.91 375 43.91 - 49.27 750 49.27 - 54.64 743 54.64 - 60.00 1026 |-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: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.3147 r_free= 0.3639 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 7.003758 | | target function (ml) not normalized (work): 54657.324350 | | target function (ml) not normalized (free): 2915.597919 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3173 0.3147 0.3639 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3173 0.3147 0.3639 n_refl.: 8215 remove outliers: r(all,work,free)=0.3173 0.3147 0.3639 n_refl.: 8215 overall B=19.06 to atoms: r(all,work,free)=0.3688 0.3662 0.4130 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2244 0.2218 0.2725 n_refl.: 8215 remove outliers: r(all,work,free)=0.2244 0.2218 0.2725 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.2140 2101.007 1985.849 1.061 1.015 0.363 12.667-10.628 93.40 94 5 0.1444 2797.724 2757.347 1.135 1.012 0.357 10.620-8.919 89.94 153 8 0.1314 2794.309 2744.774 1.125 1.010 0.351 8.899-7.465 94.10 272 15 0.1747 2026.099 1969.520 1.129 1.007 0.343 7.459-6.262 96.09 468 24 0.2320 1345.638 1277.552 1.060 1.002 0.320 6.257-5.249 97.47 805 43 0.2137 1120.292 1077.800 0.933 0.996 0.267 5.246-4.401 98.85 1382 73 0.2029 1249.575 1192.160 0.988 0.986 0.235 4.399-3.690 99.80 2346 123 0.2350 936.813 886.466 1.076 0.973 0.119 3.688-3.311 97.83 2189 115 0.2945 565.805 509.627 1.024 0.960 0.041 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=1.0130 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.358659 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.258016 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 0.2296 0.2730 0.0434 0.003 0.5 5.5 2.3 6.7 0 0.125 0.2274 0.2736 0.0462 0.003 0.5 5.4 2.6 6.7 0 0.250 0.2246 0.2729 0.0483 0.003 0.6 6.4 2.9 6.7 0 0.500 0.2204 0.2733 0.0528 0.004 0.6 7.7 2.9 6.7 0 1.000 0.2149 0.2754 0.0605 0.005 0.7 9.5 3.4 7.1 0 2.000 0.2106 0.2757 0.0651 0.007 0.8 11.6 3.9 7.1 0 3.000 0.2073 0.2772 0.0700 0.008 0.9 13.1 4.2 7.1 0 4.000 0.2046 0.2767 0.0721 0.009 1.0 15.6 4.4 7.1 0 5.000 0.2024 0.2770 0.0746 0.010 1.1 17.8 5.5 7.1 0 6.000 0.2011 0.2770 0.0759 0.012 1.2 19.6 5.5 7.4 0 7.000 0.1992 0.2764 0.0772 0.013 1.2 20.1 6.0 7.4 0 8.000 0.1980 0.2769 0.0789 0.014 1.3 20.9 6.0 7.4 0 9.000 0.1967 0.2757 0.0790 0.015 1.4 22.8 6.2 7.7 0 10.000 0.1984 0.2763 0.0779 0.013 1.3 20.6 6.2 7.4 0 8.679 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2296 0.2730 0.0434 0.003 0.5 5.5 2.3 6.7 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.96 27.30 4.34 1.120 69.771 0.258 0.058 23.03 27.36 4.34 1.761 69.844 0.008 0.059 22.62 27.30 4.68 1.816 69.905 0.032 0.057 21.65 27.16 5.52 3.316 70.208 0.129 0.052 20.49 27.21 6.72 7.111 71.113 0.258 0.047 20.13 27.25 7.13 8.641 71.615 0.387 0.046 19.78 27.22 7.44 10.248 72.225 0.516 0.044 19.64 27.26 7.62 11.129 72.514 0.645 0.044 19.53 27.30 7.77 11.832 72.743 0.774 0.043 19.45 27.33 7.88 12.404 72.930 0.903 0.043 19.31 27.34 8.03 13.356 73.276 1.032 0.042 19.23 27.36 8.13 13.981 73.491 1.161 0.042 19.21 27.38 8.17 14.153 73.532 1.290 0.042 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.129 Accepted refinement result: 21.65 27.16 5.52 3.316 70.208 0.129 0.052 Individual atomic B min max mean iso aniso Overall: 44.02 92.60 70.84 3.04 3022 0 Protein: 44.02 92.60 70.84 3.04 3022 0 Chain A: 44.02 90.91 69.23 N/A 1511 0 Chain B: 48.42 92.60 72.44 N/A 1511 0 Histogram: Values Number of atoms 44.02 - 48.88 5 48.88 - 53.74 32 53.74 - 58.60 168 58.60 - 63.45 395 63.45 - 68.31 657 68.31 - 73.17 640 73.17 - 78.03 477 78.03 - 82.88 349 82.88 - 87.74 228 87.74 - 92.60 71 =========================== Idealize ADP of riding H ========================== r_work=0.2165 r_free=0.2716 r_work=0.2147 r_free=0.2717 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2147 r_free= 0.2717 coordinate error (max.-lik. estimate): 0.54 A | | | | normalized target function (ls_wunit_k1) (work): 0.051361 | | target function (ls_wunit_k1) not normalized (work): 400.823067 | | target function (ls_wunit_k1) not normalized (free): 34.295521 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2177 0.2147 0.2717 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3659 0.3636 0.4066 n_refl.: 8215 remove outliers: r(all,work,free)=0.3659 0.3636 0.4066 n_refl.: 8215 overall B=0.00 to atoms: r(all,work,free)=0.3659 0.3636 0.4066 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2169 0.2139 0.2704 n_refl.: 8215 remove outliers: r(all,work,free)=0.2169 0.2139 0.2704 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.2097 1235.230 1175.362 1.095 1.028 0.370 12.667-10.628 93.40 94 5 0.1524 1644.847 1619.600 1.161 1.024 0.370 10.620-8.919 89.94 153 8 0.1260 1642.839 1620.013 1.133 1.021 0.351 8.899-7.465 94.10 272 15 0.1671 1191.190 1165.664 1.134 1.016 0.347 7.459-6.262 96.09 468 24 0.2157 791.132 760.651 1.075 1.009 0.340 6.257-5.249 97.47 805 43 0.2191 658.646 635.514 0.945 0.999 0.280 5.246-4.401 98.85 1382 73 0.1938 734.654 702.900 0.987 0.985 0.260 4.399-3.690 99.80 2346 123 0.2221 550.774 525.278 1.056 0.965 0.120 3.688-3.311 97.83 2189 115 0.2870 332.650 302.805 1.011 0.945 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.2552 ============================ 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 = 4.282822 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.056718 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 0.2102 0.2677 0.0575 0.002 0.4 4.0 1.8 4.2 0 0.125 0.2058 0.2680 0.0622 0.003 0.5 4.4 3.1 6.1 0 0.250 0.2009 0.2654 0.0644 0.004 0.6 6.9 3.4 6.7 0 0.500 0.1966 0.2688 0.0722 0.008 0.8 10.6 4.2 7.1 0 1.000 0.1914 0.2713 0.0800 0.013 1.2 19.3 5.2 9.0 0 2.000 0.1886 0.2724 0.0839 0.018 1.4 22.6 5.7 9.3 0 3.000 0.1863 0.2727 0.0864 0.022 1.7 26.6 6.8 12.2 0 4.000 0.1851 0.2723 0.0872 0.026 1.9 29.5 8.1 14.1 0 5.000 0.1839 0.2734 0.0895 0.030 2.1 30.5 8.3 15.1 0 6.000 0.1826 0.2743 0.0917 0.033 2.3 33.0 9.6 15.1 0 7.000 0.1821 0.2751 0.0931 0.036 2.5 34.8 10.2 15.7 0 8.000 0.1810 0.2761 0.0950 0.039 2.7 35.2 10.2 17.3 0 9.000 0.1803 0.2766 0.0963 0.041 2.8 36.0 10.2 17.3 0 10.000 0.1912 0.2721 0.0809 0.014 1.2 19.3 5.2 9.0 0 2.141 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2102 0.2677 0.0575 0.002 0.4 4.0 1.8 4.2 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.02 26.77 5.75 10.189 77.751 0.057 6.441 22.47 27.07 4.60 8.866 79.805 0.002 6.473 21.31 26.67 5.36 10.390 77.609 0.007 6.443 21.02 26.77 5.75 10.189 77.751 0.028 6.441 20.37 26.56 6.19 11.236 77.244 0.057 6.417 19.57 26.15 6.58 12.542 78.173 0.085 6.386 19.46 26.19 6.72 12.923 78.456 0.113 6.384 19.38 26.21 6.83 13.332 78.708 0.142 6.382 19.39 26.27 6.89 13.384 78.720 0.170 6.382 19.35 26.29 6.95 13.649 78.862 0.199 6.382 19.33 26.32 6.99 13.836 78.953 0.227 6.381 19.29 26.33 7.04 14.105 79.086 0.255 6.381 19.28 26.35 7.07 14.270 79.161 0.284 6.380 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.007 Accepted refinement result: 21.31 26.67 5.36 10.390 77.609 0.007 6.443 Individual atomic B min max mean iso aniso Overall: 47.14 92.63 70.55 2.24 3022 0 Protein: 47.14 92.63 70.55 2.24 3022 0 Chain A: 47.14 91.33 68.90 N/A 1511 0 Chain B: 52.82 92.63 72.21 N/A 1511 0 Histogram: Values Number of atoms 47.14 - 51.69 3 51.69 - 56.24 62 56.24 - 60.79 280 60.79 - 65.34 520 65.34 - 69.88 657 69.88 - 74.43 581 74.43 - 78.98 405 78.98 - 83.53 268 83.53 - 88.08 176 88.08 - 92.63 70 =========================== Idealize ADP of riding H ========================== r_work=0.2131 r_free=0.2667 r_work=0.2135 r_free=0.2665 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2135 r_free= 0.2665 coordinate error (max.-lik. estimate): 0.52 A | | | | normalized target function (ml) (work): 6.443060 | | target function (ml) not normalized (work): 50281.638384 | | target function (ml) not normalized (free): 2710.291640 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2163 0.2135 0.2665 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3662 0.3637 0.4090 n_refl.: 8215 remove outliers: r(all,work,free)=0.3662 0.3637 0.4090 n_refl.: 8215 overall B=1.13 to atoms: r(all,work,free)=0.3699 0.3675 0.4127 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2160 0.2132 0.2663 n_refl.: 8215 remove outliers: r(all,work,free)=0.2160 0.2132 0.2663 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.1921 1235.230 1185.709 1.122 1.014 0.370 12.667-10.628 93.40 94 5 0.1382 1644.847 1626.045 1.188 1.011 0.369 10.620-8.919 89.94 153 8 0.1175 1642.839 1629.028 1.178 1.010 0.353 8.899-7.465 94.10 272 15 0.1519 1191.190 1171.949 1.191 1.006 0.350 7.459-6.262 96.09 468 24 0.2121 791.132 759.774 1.124 1.002 0.348 6.257-5.249 97.47 805 43 0.2321 658.646 631.606 1.009 0.996 0.297 5.246-4.401 98.85 1382 73 0.1970 734.654 701.068 1.009 0.987 0.247 4.399-3.690 99.80 2346 123 0.2246 550.774 522.504 1.064 0.975 0.128 3.688-3.311 97.83 2189 115 0.2816 332.650 303.671 1.020 0.962 0.039 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.0877 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2132 r_free=0.2663 After: r_work=0.2132 r_free=0.2663 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.179959 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.052813 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 0.2132 0.2666 0.0533 0.002 0.4 4.7 1.6 4.5 0 0.125 0.2126 0.2662 0.0537 0.003 0.4 4.9 1.6 4.5 0 0.250 0.2098 0.2661 0.0563 0.006 0.6 4.9 1.8 4.8 0 0.500 0.2017 0.2680 0.0663 0.010 1.1 10.6 3.4 4.5 0 1.000 0.1970 0.2709 0.0740 0.016 1.6 16.1 3.9 5.1 0 2.000 0.1934 0.2729 0.0794 0.020 1.9 24.1 5.5 7.7 0 3.000 0.1913 0.2739 0.0826 0.024 2.2 25.1 5.2 7.1 0 4.000 0.1896 0.2750 0.0854 0.026 2.4 28.3 5.5 8.3 0 5.000 0.1883 0.2762 0.0879 0.027 2.5 30.7 7.0 9.9 0 6.000 0.1879 0.2785 0.0906 0.031 2.8 34.7 8.1 11.9 0 7.000 0.1869 0.2789 0.0920 0.033 2.9 34.2 8.1 11.9 0 8.000 0.1852 0.2790 0.0938 0.038 3.2 37.7 7.8 11.5 0 9.000 0.1844 0.2788 0.0944 0.039 3.3 36.3 8.1 12.2 0 10.000 0.1966 0.2719 0.0753 0.017 1.7 16.6 3.9 5.1 0 2.090 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2132 0.2666 0.0533 0.002 0.4 4.7 1.6 4.5 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.32 26.66 5.33 10.031 78.532 0.053 6.443 21.79 26.63 4.83 10.135 78.500 0.002 6.455 21.32 26.66 5.33 10.031 78.532 0.007 6.443 21.32 26.66 5.33 10.031 78.532 0.026 6.443 20.80 26.55 5.75 10.645 78.197 0.053 6.427 19.68 26.07 6.39 12.429 78.986 0.079 6.388 19.59 26.15 6.56 12.839 79.267 0.106 6.386 19.57 26.21 6.64 13.043 79.370 0.132 6.386 19.55 26.25 6.70 13.236 79.469 0.158 6.385 19.51 26.28 6.76 13.516 79.618 0.185 6.384 19.48 26.30 6.83 13.787 79.754 0.211 6.384 19.46 26.33 6.87 13.984 79.846 0.238 6.383 19.44 26.35 6.91 14.169 79.931 0.264 6.383 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.053 Accepted refinement result: 20.80 26.55 5.75 10.645 78.197 0.053 6.427 Individual atomic B min max mean iso aniso Overall: 46.45 97.12 71.02 3.62 3022 0 Protein: 46.45 97.12 71.02 3.62 3022 0 Chain A: 46.45 95.50 69.24 N/A 1511 0 Chain B: 48.95 97.12 72.81 N/A 1511 0 Histogram: Values Number of atoms 46.45 - 51.51 16 51.51 - 56.58 118 56.58 - 61.65 351 61.65 - 66.71 596 66.71 - 71.78 644 71.78 - 76.85 518 76.85 - 81.92 337 81.92 - 86.98 249 86.98 - 92.05 139 92.05 - 97.12 54 =========================== Idealize ADP of riding H ========================== r_work=0.2080 r_free=0.2655 r_work=0.2077 r_free=0.2654 ----------X-ray data---------- |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2077 r_free= 0.2654 coordinate error (max.-lik. estimate): 0.52 A | | | | normalized target function (ml) (work): 6.425410 | | target function (ml) not normalized (work): 50143.899394 | | target function (ml) not normalized (free): 2708.251271 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.48 - 4.76 0.96 2554 135 0.1891 0.2477 6.751 6.879| | 2: 4.76 - 3.79 1.00 2644 139 0.2028 0.2571 6.4564 6.6832| | 3: 3.79 - 3.31 0.98 2606 137 0.2617 0.3232 6.0748 6.209| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.48 - 4.76 2554 135 0.83 24.39 1.00 0.90 140077.97| | 2: 4.76 - 3.79 2644 139 0.81 26.44 1.00 0.89 90973.83| | 3: 3.79 - 3.31 2606 137 0.73 33.88 0.98 0.83 48344.65| |alpha: min = 0.83 max = 0.90 mean = 0.87| |beta: min = 48344.65 max = 140077.97 mean = 92808.83| |figures of merit: min = 0.01 max = 1.00 mean = 0.79| |phase err.(work): min = 0.00 max = 89.41 mean = 28.25| |phase err.(test): min = 0.00 max = 88.50 mean = 27.10| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2107 0.2077 0.2654 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3643 0.3617 0.4097 n_refl.: 8215 remove outliers: r(all,work,free)=0.3643 0.3617 0.4097 n_refl.: 8215 overall B=0.00 to atoms: r(all,work,free)=0.3643 0.3617 0.4097 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2105 0.2074 0.2660 n_refl.: 8215 remove outliers: r(all,work,free)=0.2105 0.2074 0.2660 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.1923 1235.230 1184.071 1.109 1.024 0.370 12.667-10.628 93.40 94 5 0.1398 1644.847 1624.665 1.145 1.020 0.360 10.620-8.919 89.94 153 8 0.1165 1642.839 1628.485 1.161 1.018 0.354 8.899-7.465 94.10 272 15 0.1503 1191.190 1171.346 1.177 1.013 0.350 7.459-6.262 96.09 468 24 0.2095 791.132 760.225 1.114 1.006 0.350 6.257-5.249 97.47 805 43 0.2287 658.646 631.685 1.003 0.997 0.300 5.246-4.401 98.85 1382 73 0.1920 734.654 701.686 1.002 0.983 0.250 4.399-3.690 99.80 2346 123 0.2156 550.774 523.253 1.059 0.964 0.130 3.688-3.311 97.83 2189 115 0.2708 332.650 304.713 1.018 0.945 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.0597 ================= 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 : 0.3147 0.3639 0.010 1.426 6.3 60.0 50.9 0 0.000 1_bss: 0.2218 0.2725 0.010 1.426 25.4 79.1 70.0 0 0.000 1_settarget: 0.2218 0.2725 0.010 1.426 25.4 79.1 70.0 0 0.000 1_weight: 0.2218 0.2725 0.010 1.426 25.4 79.1 70.0 0 0.000 1_xyzrec: 0.2296 0.2730 0.003 0.535 25.4 79.1 70.0 0 0.147 1_adp: 0.2165 0.2716 0.003 0.535 44.0 92.6 70.8 0 0.147 1_regHadp: 0.2147 0.2717 0.003 0.535 44.0 92.6 70.8 0 0.147 2_bss: 0.2139 0.2704 0.003 0.535 44.0 92.6 70.8 0 0.147 2_settarget: 0.2139 0.2704 0.003 0.535 44.0 92.6 70.8 0 0.147 2_updatecdl: 0.2139 0.2704 0.003 0.603 44.0 92.6 70.8 0 0.147 2_weight: 0.2139 0.2704 0.003 0.603 44.0 92.6 70.8 0 0.147 2_xyzrec: 0.2102 0.2677 0.002 0.422 44.0 92.6 70.8 0 0.218 2_adp: 0.2131 0.2667 0.002 0.422 47.1 92.6 70.6 0 0.218 2_regHadp: 0.2135 0.2665 0.002 0.422 47.1 92.6 70.6 0 0.218 3_bss: 0.2132 0.2663 0.002 0.422 48.3 93.8 71.7 0 0.218 3_settarget: 0.2132 0.2663 0.002 0.422 48.3 93.8 71.7 0 0.218 3_updatecdl: 0.2132 0.2663 0.002 0.488 48.3 93.8 71.7 0 0.218 3_setrh: 0.2132 0.2663 0.002 0.488 48.3 93.8 71.7 0 0.217 3_weight: 0.2132 0.2663 0.002 0.488 48.3 93.8 71.7 0 0.217 3_xyzrec: 0.2132 0.2666 0.002 0.438 48.3 93.8 71.7 0 0.217 3_adp: 0.2080 0.2655 0.002 0.438 46.4 97.1 71.0 0 0.217 3_regHadp: 0.2077 0.2654 0.002 0.438 46.4 97.1 71.0 0 0.217 end: 0.2074 0.2660 0.002 0.438 46.4 97.1 71.0 0 0.217 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1u9o_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1u9o_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3400 Refinement macro-cycles (run) : 215.8600 Write final files (write_after_run_outputs) : 22.9700 Total : 245.1700 Total CPU time: 4.47 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:31:33 PDT -0700 (1716251493.68 s) Start R-work = 0.2218, R-free = 0.2725 Final R-work = 0.2074, R-free = 0.2660 =============================================================================== Job complete usr+sys time: 291.36 seconds wall clock time: 15 minutes 41.65 seconds (941.65 seconds total)