Starting phenix.refine on Mon May 20 17:17:05 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/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=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/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 { ramachandran_plot_restraints { enabled = True } 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: 0.01s 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: 2.24, per 1000 atoms: 0.37 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: 3.40 Conformation dependent library (CDL) restraints added in 575.9 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Time building geometry restraints manager: 3.18 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.281603 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 0.2292 0.2729 0.0437 0.004 0.8 9.5 0.5 7.1 0 0.125 0.2283 0.2722 0.0439 0.004 0.8 9.9 0.5 7.1 0 0.250 0.2268 0.2713 0.0445 0.005 0.8 10.6 0.5 7.1 0 0.500 0.2238 0.2717 0.0479 0.005 0.8 10.7 0.5 7.1 0 1.000 0.2190 0.2714 0.0524 0.006 0.9 11.6 0.5 7.1 0 2.000 0.2149 0.2713 0.0564 0.008 0.9 12.1 0.5 7.1 0 3.000 0.2112 0.2731 0.0618 0.009 1.0 12.7 0.5 7.1 0 4.000 0.2083 0.2737 0.0653 0.010 1.1 13.9 0.5 7.1 0 5.000 0.2058 0.2746 0.0689 0.011 1.2 16.1 0.5 7.1 0 6.000 0.2036 0.2751 0.0714 0.012 1.2 16.6 0.5 7.1 0 7.000 0.2018 0.2752 0.0734 0.014 1.3 17.6 0.8 7.1 0 8.000 0.2001 0.2747 0.0747 0.014 1.3 18.8 0.8 7.4 0 9.000 0.1988 0.2756 0.0768 0.015 1.4 19.3 0.8 7.7 0 10.000 0.1999 0.2748 0.0749 0.014 1.4 18.9 0.8 7.4 0 9.141 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2292 0.2729 0.0437 0.004 0.8 9.5 0.5 7.1 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.92 27.29 4.37 1.120 69.771 0.258 0.058 22.98 27.31 4.33 1.776 69.843 0.008 0.058 22.59 27.25 4.66 1.826 69.901 0.032 0.056 21.62 27.13 5.51 3.334 70.189 0.129 0.052 20.44 27.20 6.76 7.239 71.143 0.258 0.047 20.13 27.27 7.14 8.626 71.564 0.387 0.045 19.78 27.23 7.46 10.301 72.208 0.516 0.044 19.63 27.27 7.64 11.192 72.499 0.645 0.043 19.52 27.29 7.77 11.897 72.729 0.774 0.043 19.44 27.32 7.88 12.474 72.916 0.903 0.043 19.38 27.34 7.96 12.959 73.072 1.032 0.042 19.27 27.37 8.10 13.788 73.369 1.161 0.042 19.02 27.40 8.38 15.593 74.079 1.290 0.041 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: 21.62 27.13 5.51 3.334 70.189 0.129 0.052 Individual atomic B min max mean iso aniso Overall: 43.89 92.07 70.80 3.06 3022 0 Protein: 43.89 92.07 70.80 3.06 3022 0 Chain A: 43.89 91.64 69.19 N/A 1511 0 Chain B: 50.52 92.07 72.41 N/A 1511 0 Histogram: Values Number of atoms 43.89 - 48.71 3 48.71 - 53.53 28 53.53 - 58.35 158 58.35 - 63.16 382 63.16 - 67.98 646 67.98 - 72.80 646 72.80 - 77.62 492 77.62 - 82.43 334 82.43 - 87.25 243 87.25 - 92.07 90 =========================== Idealize ADP of riding H ========================== r_work=0.2162 r_free=0.2713 r_work=0.2144 r_free=0.2719 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2144 r_free= 0.2719 coordinate error (max.-lik. estimate): 0.52 A | | | | normalized target function (ls_wunit_k1) (work): 0.050945 | | target function (ls_wunit_k1) not normalized (work): 397.573695 | | target function (ls_wunit_k1) not normalized (free): 34.432243 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2174 0.2144 0.2719 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3649 0.3625 0.4073 n_refl.: 8215 remove outliers: r(all,work,free)=0.3649 0.3625 0.4073 n_refl.: 8215 overall B=0.00 to atoms: r(all,work,free)=0.3649 0.3625 0.4073 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2166 0.2135 0.2711 n_refl.: 8215 remove outliers: r(all,work,free)=0.2166 0.2135 0.2711 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 0.2107 1234.367 1171.209 1.052 1.022 0.360 12.667-10.628 93.40 94 5 0.1477 1643.698 1619.726 1.136 1.019 0.354 10.620-8.919 89.94 153 8 0.1282 1641.691 1619.324 1.141 1.016 0.349 8.899-7.465 94.10 272 15 0.1709 1190.358 1165.497 1.145 1.012 0.347 7.459-6.262 96.09 468 24 0.2191 790.579 758.617 1.092 1.005 0.340 6.257-5.249 97.47 805 43 0.2159 658.185 634.102 0.951 0.997 0.280 5.246-4.401 98.85 1382 73 0.1933 734.141 702.858 0.988 0.985 0.250 4.399-3.690 99.80 2346 123 0.2205 550.389 525.292 1.064 0.968 0.120 3.688-3.311 97.83 2189 115 0.2871 332.417 302.645 1.009 0.950 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.9247 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.183922 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.055541 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 0.2120 0.2662 0.0542 0.002 0.5 4.0 0.3 6.1 0 0.125 0.2073 0.2650 0.0577 0.003 0.5 5.0 0.3 6.1 0 0.250 0.2027 0.2655 0.0628 0.005 0.6 6.0 0.3 6.7 0 0.500 0.1972 0.2658 0.0685 0.008 0.8 9.9 0.3 7.7 0 1.000 0.1916 0.2707 0.0791 0.014 1.2 13.7 0.3 9.6 0 2.000 0.1886 0.2714 0.0829 0.018 1.5 18.8 0.8 12.8 0 3.000 0.1862 0.2705 0.0843 0.023 1.7 23.5 1.0 14.4 0 4.000 0.1845 0.2720 0.0876 0.026 1.9 25.5 1.0 16.0 0 5.000 0.1833 0.2734 0.0901 0.030 2.1 28.3 1.6 17.3 0 6.000 0.1828 0.2742 0.0914 0.033 2.3 30.5 1.8 17.9 0 7.000 0.1823 0.2761 0.0938 0.036 2.5 32.5 2.3 18.6 0 8.000 0.1815 0.2770 0.0955 0.039 2.7 34.0 2.3 18.6 0 9.000 0.1811 0.2787 0.0977 0.042 2.8 34.8 3.1 18.9 0 10.000 0.1915 0.2714 0.0799 0.014 1.2 14.6 0.3 9.0 0 2.092 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2120 0.2662 0.0542 0.002 0.5 4.0 0.3 6.1 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.20 26.62 5.42 10.188 77.714 0.056 6.445 22.64 27.02 4.38 8.703 79.950 0.002 6.477 21.46 26.51 5.04 10.372 77.589 0.007 6.446 21.20 26.62 5.42 10.188 77.714 0.028 6.445 20.47 26.37 5.90 11.290 77.229 0.056 6.418 19.66 25.94 6.28 12.537 78.249 0.083 6.388 19.52 25.99 6.47 12.999 78.589 0.111 6.384 19.45 26.04 6.59 13.335 78.793 0.139 6.383 19.40 26.06 6.66 13.710 78.999 0.167 6.382 19.36 26.08 6.72 14.053 79.171 0.194 6.381 19.41 26.15 6.74 13.900 79.082 0.222 6.382 19.38 26.17 6.78 14.145 79.200 0.250 6.382 19.38 26.18 6.80 14.260 79.251 0.278 6.382 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.056 Accepted refinement result: 20.47 26.37 5.90 11.290 77.229 0.056 6.418 Individual atomic B min max mean iso aniso Overall: 43.26 102.14 69.84 5.02 3022 0 Protein: 43.26 102.14 69.84 5.02 3022 0 Chain A: 43.26 98.13 68.00 N/A 1511 0 Chain B: 48.13 102.14 71.67 N/A 1511 0 Histogram: Values Number of atoms 43.26 - 49.15 25 49.15 - 55.04 173 55.04 - 60.93 441 60.93 - 66.82 652 66.82 - 72.70 649 72.70 - 78.59 457 78.59 - 84.48 302 84.48 - 90.37 194 90.37 - 96.26 105 96.26 - 102.14 24 =========================== Idealize ADP of riding H ========================== r_work=0.2047 r_free=0.2637 r_work=0.2042 r_free=0.2635 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2042 r_free= 0.2635 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ml) (work): 6.415762 | | target function (ml) not normalized (work): 50068.608567 | | target function (ml) not normalized (free): 2706.574036 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2074 0.2042 0.2635 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3576 0.3551 0.4010 n_refl.: 8215 remove outliers: r(all,work,free)=0.3576 0.3551 0.4010 n_refl.: 8215 overall B=1.21 to atoms: r(all,work,free)=0.3617 0.3592 0.4049 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2069 0.2038 0.2634 n_refl.: 8215 remove outliers: r(all,work,free)=0.2069 0.2038 0.2634 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 0.1961 1234.367 1182.660 1.126 1.017 0.369 12.667-10.628 93.40 94 5 0.1421 1643.698 1626.656 1.158 1.014 0.358 10.620-8.919 89.94 153 8 0.1242 1641.691 1621.913 1.166 1.013 0.355 8.899-7.465 94.10 272 15 0.1514 1190.358 1168.246 1.185 1.009 0.354 7.459-6.262 96.09 468 24 0.2105 790.579 759.900 1.108 1.005 0.335 6.257-5.249 97.47 805 43 0.2232 658.185 631.203 1.004 0.998 0.297 5.246-4.401 98.85 1382 73 0.1869 734.141 702.143 1.006 0.989 0.257 4.399-3.690 99.80 2346 123 0.2083 550.389 525.066 1.060 0.977 0.118 3.688-3.311 97.83 2189 115 0.2664 332.417 304.942 1.007 0.964 0.039 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.4493 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2038 r_free=0.2634 After: r_work=0.2038 r_free=0.2634 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.325303 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.051495 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 0.2039 0.2637 0.0598 0.002 0.5 4.2 0.3 6.1 0 0.125 0.2035 0.2642 0.0608 0.003 0.5 4.2 0.3 6.1 0 0.250 0.2009 0.2641 0.0632 0.006 0.6 5.2 0.3 6.1 0 0.500 0.1939 0.2654 0.0715 0.011 1.1 7.5 0.3 5.4 0 1.000 0.1895 0.2678 0.0784 0.014 1.4 13.6 1.0 5.1 0 2.000 0.1872 0.2695 0.0823 0.018 1.7 17.4 1.3 6.1 0 3.000 0.1845 0.2696 0.0850 0.023 2.1 21.8 1.3 6.7 0 4.000 0.1828 0.2724 0.0896 0.026 2.4 25.6 2.3 8.0 0 5.000 0.1819 0.2717 0.0898 0.027 2.4 24.6 2.3 8.3 0 6.000 0.1798 0.2721 0.0923 0.030 2.6 30.0 2.1 11.2 0 7.000 0.1791 0.2723 0.0932 0.032 2.7 29.6 2.6 11.5 0 8.000 0.1774 0.2716 0.0942 0.035 3.0 30.7 3.6 11.5 0 9.000 0.1771 0.2734 0.0963 0.037 3.1 33.0 2.9 13.8 0 10.000 0.1891 0.2675 0.0784 0.014 1.5 14.6 1.0 5.8 0 2.163 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2039 0.2637 0.0598 0.002 0.5 4.2 0.3 6.1 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.39 26.37 5.98 10.480 77.846 0.051 6.414 22.37 26.71 4.34 8.426 80.516 0.002 6.459 20.90 26.19 5.28 10.463 77.734 0.006 6.423 20.39 26.37 5.98 10.480 77.846 0.026 6.414 20.39 26.37 5.98 10.481 77.845 0.051 6.414 20.07 26.32 6.25 11.189 77.483 0.077 6.404 19.22 25.87 6.65 13.128 78.161 0.103 6.377 19.22 25.98 6.76 13.092 78.109 0.129 6.378 19.13 26.00 6.87 13.396 78.340 0.154 6.376 19.07 26.02 6.95 13.631 78.491 0.180 6.376 19.04 26.05 7.01 13.804 78.591 0.206 6.375 19.03 26.07 7.04 13.859 78.618 0.232 6.375 19.00 26.08 7.08 13.996 78.694 0.257 6.375 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: 20.90 26.19 5.28 10.463 77.734 0.006 6.423 Individual atomic B min max mean iso aniso Overall: 48.00 103.70 70.83 3.20 3022 0 Protein: 48.00 103.70 70.83 3.20 3022 0 Chain A: 48.00 100.05 68.95 N/A 1511 0 Chain B: 51.73 103.70 72.71 N/A 1511 0 Histogram: Values Number of atoms 48.00 - 53.57 44 53.57 - 59.14 277 59.14 - 64.71 580 64.71 - 70.28 702 70.28 - 75.85 569 75.85 - 81.42 386 81.42 - 86.99 237 86.99 - 92.56 123 92.56 - 98.13 89 98.13 - 103.70 15 =========================== Idealize ADP of riding H ========================== r_work=0.2090 r_free=0.2619 r_work=0.2096 r_free=0.2617 ----------X-ray data---------- |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2096 r_free= 0.2617 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 6.424737 | | target function (ml) not normalized (work): 50138.649205 | | target function (ml) not normalized (free): 2704.607041 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1904 0.2476 6.7572 6.8843| | 2: 4.76 - 3.79 1.00 2644 139 0.2044 0.2528 6.4562 6.6739| | 3: 3.79 - 3.31 0.98 2606 137 0.2660 0.3116 6.067 6.1865| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 24.61 1.00 0.90 141938.04| | 2: 4.76 - 3.79 2644 139 0.82 26.01 1.01 0.90 88832.37| | 3: 3.79 - 3.31 2606 137 0.75 32.33 0.98 0.85 44725.52| |alpha: min = 0.85 max = 0.90 mean = 0.88| |beta: min = 44725.52 max = 141938.04 mean = 91483.50| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.71 mean = 27.66| |phase err.(test): min = 0.00 max = 85.40 mean = 26.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2123 0.2096 0.2617 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3636 0.3613 0.4043 n_refl.: 8215 remove outliers: r(all,work,free)=0.3636 0.3613 0.4043 n_refl.: 8215 overall B=1.15 to atoms: r(all,work,free)=0.3675 0.3651 0.4081 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2121 0.2094 0.2614 n_refl.: 8215 remove outliers: r(all,work,free)=0.2121 0.2094 0.2614 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 0.1961 1234.367 1182.781 1.110 1.026 0.370 12.667-10.628 93.40 94 5 0.1423 1643.698 1626.922 1.161 1.023 0.365 10.620-8.919 89.94 153 8 0.1265 1641.691 1622.511 1.157 1.021 0.359 8.899-7.465 94.10 272 15 0.1527 1190.358 1167.477 1.175 1.016 0.358 7.459-6.262 96.09 468 24 0.2126 790.579 760.094 1.119 1.010 0.358 6.257-5.249 97.47 805 43 0.2269 658.185 630.193 1.002 1.002 0.297 5.246-4.401 98.85 1382 73 0.1920 734.141 701.065 1.002 0.990 0.247 4.399-3.690 99.80 2346 123 0.2170 550.389 523.768 1.067 0.974 0.118 3.688-3.311 97.83 2189 115 0.2754 332.417 303.867 1.022 0.958 0.049 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.1534 ================= 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_updatephipsi: 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: 0.2292 0.2729 0.004 0.764 25.4 79.1 70.0 0 0.118 1_adp: 0.2162 0.2713 0.004 0.764 43.9 92.1 70.8 0 0.118 1_regHadp: 0.2144 0.2719 0.004 0.764 43.9 92.1 70.8 0 0.118 2_bss: 0.2135 0.2711 0.004 0.764 43.9 92.1 70.8 0 0.118 2_settarget: 0.2135 0.2711 0.004 0.764 43.9 92.1 70.8 0 0.118 2_updatephipsi: 0.2135 0.2711 0.004 0.764 43.9 92.1 70.8 0 0.118 2_updatecdl: 0.2135 0.2711 0.005 0.823 43.9 92.1 70.8 0 0.118 2_weight: 0.2135 0.2711 0.005 0.823 43.9 92.1 70.8 0 0.118 2_xyzrec: 0.2120 0.2662 0.002 0.478 43.9 92.1 70.8 0 0.214 2_adp: 0.2047 0.2637 0.002 0.478 43.3 102.1 69.8 0 0.214 2_regHadp: 0.2042 0.2635 0.002 0.478 43.3 102.1 69.8 0 0.214 3_bss: 0.2038 0.2634 0.002 0.478 44.5 103.4 71.0 0 0.214 3_settarget: 0.2038 0.2634 0.002 0.478 44.5 103.4 71.0 0 0.214 3_updatephipsi: 0.2038 0.2634 0.002 0.478 44.5 103.4 71.0 0 0.214 3_updatecdl: 0.2038 0.2634 0.002 0.512 44.5 103.4 71.0 0 0.214 3_setrh: 0.2038 0.2634 0.002 0.512 44.5 103.4 71.0 0 0.214 3_weight: 0.2038 0.2634 0.002 0.512 44.5 103.4 71.0 0 0.214 3_xyzrec: 0.2039 0.2637 0.002 0.471 44.5 103.4 71.0 0 0.214 3_adp: 0.2090 0.2619 0.002 0.471 48.0 103.7 70.8 0 0.214 3_regHadp: 0.2096 0.2617 0.002 0.471 48.0 103.7 70.8 0 0.214 end: 0.2094 0.2614 0.002 0.471 49.1 104.8 72.0 0 0.214 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1u9o_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1u9o_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 9.0800 Refinement macro-cycles (run) : 242.0400 Write final files (write_after_run_outputs) : 23.8900 Total : 275.0100 Total CPU time: 5.22 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:33:26 PDT -0700 (1716251606.33 s) Start R-work = 0.2218, R-free = 0.2725 Final R-work = 0.2094, R-free = 0.2614 =============================================================================== Job complete usr+sys time: 336.32 seconds wall clock time: 16 minutes 58.16 seconds (1018.16 seconds total)