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/1jkt.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1jkt/1jkt.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/1jkt/1jkt.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1jkt/1jkt.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1jkt.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1jkt.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 "A PHE 104": "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: 8966 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4483 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Chain: "B" Number of atoms: 4483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4483 Classifications: {'peptide': 276} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264} Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 8966 At special positions: 0 Unit cell: (58.37, 58.37, 212.61, 90, 90, 90) Space group: P 41 (No. 76) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 850 8.00 N 744 7.00 C 2876 6.00 H 4488 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: 2.29 Conformation dependent library (CDL) restraints added in 321.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Time building geometry restraints manager: 2.61 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: 4486 1.16 - 1.34: 1456 1.34 - 1.52: 2031 1.52 - 1.70: 1071 1.70 - 1.89: 14 Bond restraints: 9058 Sorted by residual: bond pdb=" N PHE A 162 " pdb=" H PHE A 162 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLN A 38 " pdb=" H GLN A 38 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLU B 192 " pdb=" H GLU B 192 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN A 271 " pdb="HE22 GLN A 271 " 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 A 111 " pdb=" H LEU A 111 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9053 not shown) Histogram of bond angle deviations from ideal: 94.75 - 102.61: 90 102.61 - 110.47: 9016 110.47 - 118.34: 3303 118.34 - 126.20: 3941 126.20 - 134.06: 78 Bond angle restraints: 16428 Sorted by residual: angle pdb=" N LEU B 196 " pdb=" CA LEU B 196 " pdb=" C LEU B 196 " ideal model delta sigma weight residual 113.18 99.40 13.78 1.21e+00 6.83e-01 1.30e+02 angle pdb=" N PHE B 183 " pdb=" CA PHE B 183 " pdb=" C PHE B 183 " ideal model delta sigma weight residual 112.87 125.82 -12.95 1.20e+00 6.94e-01 1.16e+02 angle pdb=" N PHE A 178 " pdb=" CA PHE A 178 " pdb=" C PHE A 178 " ideal model delta sigma weight residual 110.17 126.12 -15.95 1.51e+00 4.39e-01 1.12e+02 angle pdb=" N LEU A 196 " pdb=" CA LEU A 196 " pdb=" C LEU A 196 " ideal model delta sigma weight residual 113.18 100.49 12.69 1.21e+00 6.83e-01 1.10e+02 angle pdb=" N PHE B 104 " pdb=" CA PHE B 104 " pdb=" C PHE B 104 " ideal model delta sigma weight residual 113.97 101.08 12.89 1.28e+00 6.10e-01 1.01e+02 ... (remaining 16423 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 3662 17.98 - 35.97: 340 35.97 - 53.95: 149 53.95 - 71.94: 58 71.94 - 89.92: 17 Dihedral angle restraints: 4226 sinusoidal: 2310 harmonic: 1916 Sorted by residual: dihedral pdb=" N THR B 180 " pdb=" C THR B 180 " pdb=" CA THR B 180 " pdb=" CB THR B 180 " ideal model delta harmonic sigma weight residual 123.40 133.58 -10.18 0 2.50e+00 1.60e-01 1.66e+01 dihedral pdb=" C THR B 180 " pdb=" N THR B 180 " pdb=" CA THR B 180 " pdb=" CB THR B 180 " ideal model delta harmonic sigma weight residual -122.00 -132.09 10.09 0 2.50e+00 1.60e-01 1.63e+01 dihedral pdb=" C LYS A 175 " pdb=" N LYS A 175 " pdb=" CA LYS A 175 " pdb=" CB LYS A 175 " ideal model delta harmonic sigma weight residual -122.60 -132.24 9.64 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 4223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 524 0.131 - 0.262: 137 0.262 - 0.393: 16 0.393 - 0.524: 6 0.524 - 0.655: 3 Chirality restraints: 686 Sorted by residual: chirality pdb=" CA LYS A 175 " pdb=" N LYS A 175 " pdb=" C LYS A 175 " pdb=" CB LYS A 175 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA THR B 180 " pdb=" N THR B 180 " pdb=" C THR B 180 " pdb=" CB THR B 180 " both_signs ideal model delta sigma weight residual False 2.53 1.92 0.61 2.00e-01 2.50e+01 9.27e+00 chirality pdb=" CA GLU A 192 " pdb=" N GLU A 192 " pdb=" C GLU A 192 " pdb=" CB GLU A 192 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.34e+00 ... (remaining 683 not shown) Planarity restraints: 1326 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 234 " 0.133 2.00e-02 2.50e+03 5.31e-02 8.47e+01 pdb=" CG TYR A 234 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 234 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 234 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 234 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR A 234 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 234 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 234 " 0.094 2.00e-02 2.50e+03 pdb=" HD1 TYR A 234 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR A 234 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 TYR A 234 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 TYR A 234 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 191 " 0.113 2.00e-02 2.50e+03 4.82e-02 6.98e+01 pdb=" CG TYR B 191 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 191 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 191 " -0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR B 191 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR B 191 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 191 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 191 " 0.099 2.00e-02 2.50e+03 pdb=" HD1 TYR B 191 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 TYR B 191 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 191 " -0.023 2.00e-02 2.50e+03 pdb=" HE2 TYR B 191 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 208 " 0.113 2.00e-02 2.50e+03 4.57e-02 6.26e+01 pdb=" CG TYR A 208 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR A 208 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 208 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 208 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 208 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 208 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 208 " 0.085 2.00e-02 2.50e+03 pdb=" HD1 TYR A 208 " -0.032 2.00e-02 2.50e+03 pdb=" HD2 TYR A 208 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 208 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR A 208 " -0.009 2.00e-02 2.50e+03 ... (remaining 1323 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.54: 133 1.54 - 2.31: 2854 2.31 - 3.07: 28771 3.07 - 3.84: 38164 3.84 - 4.60: 61883 Warning: very small nonbonded interaction distances. Nonbonded interactions: 131805 Sorted by model distance: nonbonded pdb=" HA LYS A 276 " pdb=" HZ2 LYS A 276 " model vdw 0.775 2.270 nonbonded pdb="HD12 LEU B 218 " pdb=" H GLY B 219 " model vdw 0.996 2.270 nonbonded pdb=" H ASN A 75 " pdb="HD22 ASN A 75 " model vdw 1.050 2.100 nonbonded pdb=" O THR A 225 " pdb=" H ASN A 228 " model vdw 1.052 1.850 nonbonded pdb=" HA ILE A 252 " pdb="HD12 LEU A 255 " model vdw 1.091 2.440 ... (remaining 131800 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 15.91 1 O 850 7.97 1 N 744 6.97 1 C 2876 5.97 1 H 4488 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: 4488 of 8966 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 8966 n_use_u_iso = 8966 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 = 8966 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (8966 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 8966 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 = "1jkt_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4488 occupancy sum: 4488.00 (% of total atoms 50.10) Rotatable: count: 1226 occupancy sum: 1226.00 (% of total atoms 13.68) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.49 - 19.81 A, n_refl.=8549 (all), 10.56 % free)-------------| | | | r_work= 0.3487 r_free= 0.4112 coordinate error (max.-lik. estimate): 0.89 A | | | | normalized target function (ml) (work): 3.958556 | | target function (ml) not normalized (work): 30267.121761 | | target function (ml) not normalized (free): 3647.010734 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.81 - 6.29 0.98 1324 168 0.3612 0.4250 4.6265 4.6744| | 2: 6.28 - 5.01 0.95 1261 150 0.3316 0.4130 4.1035 4.1876| | 3: 5.01 - 4.38 0.96 1313 141 0.3048 0.3765 3.9593 4.1225| | 4: 4.38 - 3.99 0.96 1271 167 0.3456 0.3921 3.8353 3.8742| | 5: 3.99 - 3.70 0.94 1269 134 0.3597 0.4227 3.6703 3.736| | 6: 3.70 - 3.49 0.90 1208 143 0.4145 0.4423 3.5068 3.5292| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.81 - 6.29 1324 168 0.57 47.00 1.03 0.05 2494.09| | 2: 6.28 - 5.01 1261 150 0.48 53.95 0.88 0.04 1381.54| | 3: 5.01 - 4.38 1313 141 0.60 44.72 1.05 0.04 742.67| | 4: 4.38 - 3.99 1271 167 0.59 45.77 1.00 0.04 612.41| | 5: 3.99 - 3.70 1269 134 0.52 51.28 1.02 0.04 452.69| | 6: 3.70 - 3.49 1208 143 0.47 55.01 0.99 0.03 305.83| |alpha: min = 0.03 max = 0.05 mean = 0.04| |beta: min = 305.83 max = 2494.09 mean = 1012.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.54| |phase err.(work): min = 0.00 max = 89.95 mean = 49.53| |phase err.(test): min = 1.00 max = 89.86 mean = 50.50| |-----------------------------------------------------------------------------| ----------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 0.095 4570 Z= 0.588 Angle : 1.826 19.340 6174 Z= 1.153 Chirality : 0.125 0.655 686 Planarity : 0.009 0.101 798 Dihedral : 19.361 89.293 1728 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 92.65 Ramachandran Plot: Outliers : 16.42 % Allowed : 22.45 % Favored : 61.13 % Rotamer: Outliers : 17.07 % Allowed : 17.07 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -7.21 (0.23), residues: 548 helix: -5.22 (0.15), residues: 172 sheet: -2.89 (0.79), residues: 47 loop : -5.13 (0.22), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 48 TYR 0.108 0.023 TYR A 234 PHE 0.052 0.011 PHE B 251 TRP 0.043 0.007 TRP B 201 HIS 0.003 0.001 HIS A 131 Individual atomic B min max mean iso aniso Overall: 0.00 77.44 33.73 4.15 4478 0 Protein: 0.00 77.44 33.73 4.15 4478 0 Chain A: 0.00 77.44 33.35 N/A 2239 0 Chain B: 0.00 73.79 34.12 N/A 2239 0 Histogram: Values Number of atoms 0.00 - 7.74 79 7.74 - 15.49 0 15.49 - 23.23 10 23.23 - 30.98 2024 30.98 - 38.72 1429 38.72 - 46.46 430 46.46 - 54.21 303 54.21 - 61.95 94 61.95 - 69.70 64 69.70 - 77.44 45 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8549 (all), 10.56 % free)-------------| | | | r_work= 0.3487 r_free= 0.4112 coordinate error (max.-lik. estimate): 0.89 A | | | | normalized target function (ml) (work): 3.958556 | | target function (ml) not normalized (work): 30267.121761 | | target function (ml) not normalized (free): 3647.010734 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3553 0.3487 0.4112 n_refl.: 8549 re-set all scales: r(all,work,free)=0.3553 0.3487 0.4112 n_refl.: 8549 remove outliers: r(all,work,free)=0.3545 0.3478 0.4112 n_refl.: 8544 overall B=38.85 to atoms: r(all,work,free)=0.3940 0.3881 0.4443 n_refl.: 8544 bulk-solvent and scaling: r(all,work,free)=0.2857 0.2765 0.3621 n_refl.: 8544 remove outliers: r(all,work,free)=0.2855 0.2765 0.3607 n_refl.: 8543 ======================== 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 19.814-13.883 97.98 87 10 0.3174 1300.952 1107.908 1.348 0.971 0.356 13.859-11.604 100.00 90 12 0.2176 1680.008 1539.871 1.266 0.975 0.329 11.577-9.718 99.43 156 19 0.2370 1643.853 1535.873 1.342 0.979 0.321 9.700-8.140 99.66 262 33 0.2802 1318.742 1207.528 1.320 0.987 0.303 8.117-6.812 97.25 444 52 0.2708 923.512 849.358 1.079 0.998 0.251 6.812-5.705 94.76 721 93 0.2876 655.291 593.315 0.810 1.015 0.163 5.702-4.776 94.99 1247 137 0.2640 640.119 588.984 0.813 1.037 0.090 4.775-3.999 95.66 2113 265 0.2666 608.046 548.501 1.025 1.066 0.054 3.998-3.486 92.23 2521 281 0.3081 415.289 367.051 1.160 1.112 0.045 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.8814 b_overall=-15.0006 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.401486 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.206479 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 0.2908 0.3694 0.0786 0.004 0.8 14.2 5.8 11.8 0 0.125 0.2851 0.3675 0.0825 0.004 0.8 19.0 6.6 12.2 0 0.250 0.2811 0.3697 0.0886 0.004 0.8 16.1 6.4 12.2 0 0.500 0.2720 0.3694 0.0974 0.005 0.9 19.6 6.6 13.0 0 1.000 0.2600 0.3700 0.1100 0.007 1.0 28.9 8.4 13.6 0 2.000 0.2523 0.3682 0.1158 0.010 1.2 36.8 9.3 14.2 0 3.000 0.2462 0.3674 0.1213 0.011 1.3 44.4 9.3 16.5 0 4.000 0.2412 0.3665 0.1253 0.013 1.4 50.6 10.6 17.5 0 5.000 0.2380 0.3660 0.1280 0.014 1.5 51.2 11.5 18.3 0 6.000 0.2342 0.3651 0.1309 0.016 1.6 56.8 12.4 19.5 0 7.000 0.2318 0.3648 0.1331 0.017 1.7 60.1 12.6 19.7 0 8.000 0.2290 0.3662 0.1372 0.019 1.9 63.4 13.9 20.1 0 9.000 0.2266 0.3679 0.1414 0.020 2.0 67.9 14.4 20.9 0 10.000 0.2348 0.3663 0.1315 0.016 1.6 56.2 12.2 19.7 0 6.701 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2318 0.3648 0.1331 0.017 1.7 60.1 12.6 19.7 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.18 36.48 13.31 2.945 72.831 0.206 0.065 23.11 36.48 13.37 3.429 73.178 0.006 0.065 22.65 36.48 13.84 3.570 73.238 0.026 0.063 21.66 36.49 14.83 4.954 73.513 0.103 0.058 21.13 36.53 15.41 6.506 73.903 0.206 0.055 20.84 36.54 15.70 7.632 74.215 0.310 0.054 20.52 36.51 15.99 9.056 74.745 0.413 0.053 20.38 36.52 16.14 9.827 74.977 0.516 0.052 20.28 36.52 16.24 10.451 75.166 0.619 0.051 20.20 36.53 16.33 10.983 75.323 0.723 0.051 20.14 36.53 16.39 11.420 75.455 0.826 0.051 20.07 36.54 16.47 11.872 75.599 0.929 0.051 19.97 36.55 16.57 12.595 75.848 1.032 0.050 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 23.11 36.48 13.37 3.429 73.178 0.006 0.065 Individual atomic B min max mean iso aniso Overall: 43.76 111.29 73.28 2.24 4478 0 Protein: 43.76 111.29 73.28 2.24 4478 0 Chain A: 43.76 111.29 73.16 N/A 2239 0 Chain B: 48.57 110.54 73.39 N/A 2239 0 Histogram: Values Number of atoms 43.76 - 50.52 5 50.52 - 57.27 8 57.27 - 64.02 61 64.02 - 70.77 2076 70.77 - 77.53 1501 77.53 - 84.28 375 84.28 - 91.03 241 91.03 - 97.78 94 97.78 - 104.53 68 104.53 - 111.29 49 =========================== Idealize ADP of riding H ========================== r_work=0.2311 r_free=0.3648 r_work=0.2319 r_free=0.3642 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2319 r_free= 0.3642 coordinate error (max.-lik. estimate): 0.85 A | | | | normalized target function (ls_wunit_k1) (work): 0.065165 | | target function (ls_wunit_k1) not normalized (work): 497.923947 | | target function (ls_wunit_k1) not normalized (free): 148.686811 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2463 0.2319 0.3642 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3658 0.3574 0.4366 n_refl.: 8543 remove outliers: r(all,work,free)=0.3658 0.3574 0.4366 n_refl.: 8543 overall B=-2.27 to atoms: r(all,work,free)=0.3608 0.3521 0.4333 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2442 0.2299 0.3615 n_refl.: 8543 remove outliers: r(all,work,free)=0.2442 0.2299 0.3615 n_refl.: 8543 ======================== 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 19.814-13.883 97.98 87 10 0.2427 722.288 652.161 1.491 0.962 0.372 13.859-11.604 100.00 90 12 0.1726 932.739 885.245 1.426 0.965 0.355 11.577-9.718 99.43 156 19 0.1896 912.666 874.201 1.355 0.967 0.307 9.700-8.140 99.66 262 33 0.2005 732.164 697.484 1.357 0.973 0.292 8.117-6.812 97.25 444 52 0.2092 512.733 490.415 1.117 0.981 0.253 6.812-5.705 94.76 721 93 0.2425 363.817 342.501 0.859 0.993 0.183 5.702-4.776 94.99 1247 137 0.2292 355.394 337.490 0.810 1.008 0.070 4.775-3.999 95.66 2113 265 0.2245 337.587 318.402 1.025 1.028 0.041 3.998-3.486 92.23 2521 281 0.2661 230.568 214.493 1.151 1.061 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-10.2202 ============================ 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 = 7.565630 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.094172 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 0.2687 0.3650 0.0963 0.003 0.7 14.4 6.4 15.0 0 0.125 0.2681 0.3656 0.0975 0.004 0.8 13.8 5.8 15.0 0 0.250 0.2622 0.3656 0.1034 0.004 0.8 17.3 6.0 15.7 0 0.500 0.2564 0.3648 0.1084 0.006 0.9 25.0 6.9 16.1 0 1.000 0.2501 0.3643 0.1142 0.011 1.3 35.7 8.6 18.7 0 2.000 0.2453 0.3635 0.1183 0.015 1.6 47.0 9.7 19.5 0 3.000 0.2427 0.3630 0.1203 0.019 1.8 52.1 10.6 19.5 0 4.000 0.2379 0.3628 0.1248 0.022 1.9 55.5 11.3 20.1 0 5.000 0.2370 0.3630 0.1260 0.026 2.1 59.1 11.7 19.9 0 6.000 0.2391 0.3691 0.1299 0.025 2.3 71.3 17.9 27.2 0 7.000 0.2375 0.3701 0.1325 0.027 2.4 75.0 17.9 28.9 0 8.000 0.2357 0.3709 0.1352 0.029 2.6 79.8 18.1 29.3 0 9.000 0.2315 0.3641 0.1327 0.036 2.7 70.7 12.0 20.7 0 10.000 0.2475 0.3652 0.1177 0.015 1.6 50.1 11.7 21.5 0 3.783 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2379 0.3628 0.1248 0.022 1.9 55.5 11.3 20.1 0 5.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.79 36.28 12.48 10.525 78.416 0.094 6.081 24.05 36.30 12.25 10.877 78.893 0.003 6.084 23.78 36.28 12.50 10.546 78.396 0.012 6.081 23.76 36.28 12.52 10.582 78.370 0.047 6.080 23.56 36.25 12.70 11.003 78.104 0.094 6.074 22.81 36.21 13.41 12.689 78.515 0.141 6.057 22.68 36.22 13.54 13.063 78.834 0.188 6.055 22.58 36.22 13.64 13.518 79.129 0.235 6.053 22.51 36.23 13.73 13.987 79.378 0.283 6.052 22.50 36.35 13.85 13.825 79.222 0.330 6.055 22.47 36.35 13.88 14.028 79.336 0.377 6.054 22.44 36.35 13.91 14.206 79.432 0.424 6.054 22.43 36.35 13.92 14.363 79.513 0.471 6.054 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.012 Accepted refinement result: 23.78 36.28 12.50 10.546 78.396 0.012 6.081 Individual atomic B min max mean iso aniso Overall: 41.84 108.20 70.97 2.12 4478 0 Protein: 41.84 108.20 70.97 2.12 4478 0 Chain A: 41.84 107.95 70.87 N/A 2239 0 Chain B: 48.89 108.20 71.06 N/A 2239 0 Histogram: Values Number of atoms 41.84 - 48.48 4 48.48 - 55.11 8 55.11 - 61.75 62 61.75 - 68.39 2046 68.39 - 75.02 1504 75.02 - 81.66 391 81.66 - 88.29 242 88.29 - 94.93 105 94.93 - 101.56 68 101.56 - 108.20 48 =========================== Idealize ADP of riding H ========================== r_work=0.2378 r_free=0.3628 r_work=0.2378 r_free=0.3628 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2378 r_free= 0.3628 coordinate error (max.-lik. estimate): 0.80 A | | | | normalized target function (ml) (work): 6.080475 | | target function (ml) not normalized (work): 46460.906504 | | target function (ml) not normalized (free): 5630.699509 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2511 0.2378 0.3628 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3570 0.3477 0.4349 n_refl.: 8543 remove outliers: r(all,work,free)=0.3570 0.3477 0.4349 n_refl.: 8543 overall B=-8.23 to atoms: r(all,work,free)=0.3394 0.3293 0.4250 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2474 0.2340 0.3604 n_refl.: 8543 remove outliers: r(all,work,free)=0.2474 0.2340 0.3604 n_refl.: 8543 ======================== 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 19.814-13.883 97.98 87 10 0.2463 722.288 647.216 1.709 0.978 0.378 13.859-11.604 100.00 90 12 0.1731 932.739 880.552 1.555 0.978 0.355 11.577-9.718 99.43 156 19 0.1837 912.666 867.080 1.491 0.978 0.316 9.700-8.140 99.66 262 33 0.1922 732.164 695.115 1.518 0.982 0.308 8.117-6.812 97.25 444 52 0.2310 512.733 483.102 1.251 0.985 0.249 6.812-5.705 94.76 721 93 0.2704 363.817 334.500 0.979 0.991 0.201 5.702-4.776 94.99 1247 137 0.2439 355.394 331.422 0.876 0.997 0.079 4.775-3.999 95.66 2113 265 0.2289 337.587 312.265 1.031 1.005 0.016 3.998-3.486 92.23 2521 281 0.2513 230.568 210.341 1.109 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=3.2004 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2340 r_free=0.3604 After: r_work=0.2343 r_free=0.3604 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.162396 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.129137 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 0.2498 0.3595 0.1097 0.013 1.5 55.1 12.0 19.5 0 0.125 0.2491 0.3594 0.1103 0.013 1.5 54.9 12.2 19.9 0 0.250 0.2482 0.3596 0.1114 0.013 1.5 55.1 12.0 20.1 0 0.500 0.2435 0.3609 0.1174 0.013 1.6 56.9 11.7 19.7 0 1.000 0.2404 0.3608 0.1204 0.013 1.7 58.2 11.1 19.7 0 2.000 0.2375 0.3606 0.1230 0.015 1.9 58.0 11.1 19.9 0 3.000 0.2353 0.3606 0.1254 0.019 1.9 56.9 11.5 20.1 0 4.000 0.2347 0.3608 0.1261 0.020 2.0 57.9 11.3 19.9 0 5.000 0.2339 0.3607 0.1268 0.021 2.1 60.3 11.1 20.1 0 6.000 0.2328 0.3610 0.1283 0.024 2.1 61.2 11.3 20.3 0 7.000 0.2310 0.3616 0.1306 0.029 2.4 65.0 11.9 20.7 0 8.000 0.2294 0.3619 0.1325 0.032 2.5 67.8 11.9 20.7 0 9.000 0.2276 0.3624 0.1348 0.038 2.8 71.0 12.4 20.9 0 10.000 0.2352 0.3606 0.1254 0.019 1.9 57.0 11.5 20.1 0 4.081 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2498 0.3595 0.1097 0.013 1.5 55.1 12.0 19.5 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.98 35.95 10.97 10.192 69.915 0.129 6.105 25.07 35.90 10.83 10.455 69.916 0.004 6.105 24.95 35.95 11.00 10.215 69.894 0.016 6.104 24.69 35.92 11.23 10.453 69.737 0.065 6.098 23.55 35.99 12.45 12.222 70.392 0.129 6.074 23.32 36.05 12.73 12.886 70.862 0.194 6.071 23.23 36.13 12.90 13.364 70.983 0.258 6.072 23.15 36.15 13.00 13.829 71.232 0.323 6.070 23.09 36.16 13.08 14.211 71.421 0.387 6.069 23.04 36.18 13.14 14.544 71.576 0.452 6.069 23.00 36.19 13.18 14.826 71.702 0.517 6.068 22.97 36.20 13.23 15.163 71.847 0.581 6.068 22.91 36.21 13.30 15.732 72.079 0.646 6.066 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.016 Accepted refinement result: 24.95 35.95 11.00 10.215 69.894 0.016 6.104 Individual atomic B min max mean iso aniso Overall: 33.94 99.90 62.69 2.04 4478 0 Protein: 33.94 99.90 62.69 2.04 4478 0 Chain A: 33.94 99.76 62.61 N/A 2239 0 Chain B: 42.60 99.90 62.77 N/A 2239 0 Histogram: Values Number of atoms 33.94 - 40.53 3 40.53 - 47.13 9 47.13 - 53.73 85 53.73 - 60.32 2085 60.32 - 66.92 1463 66.92 - 73.52 379 73.52 - 80.11 236 80.11 - 86.71 103 86.71 - 93.31 69 93.31 - 99.90 46 =========================== Idealize ADP of riding H ========================== r_work=0.2495 r_free=0.3595 r_work=0.2495 r_free=0.3595 ----------X-ray data---------- |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2495 r_free= 0.3595 coordinate error (max.-lik. estimate): 0.75 A | | | | normalized target function (ml) (work): 6.104098 | | target function (ml) not normalized (work): 46641.409277 | | target function (ml) not normalized (free): 5635.368831 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.81 - 6.29 0.98 1321 168 0.2279 0.3243 6.6113 6.7093| | 2: 6.28 - 5.01 0.95 1261 149 0.2700 0.3576 6.2594 6.346| | 3: 5.01 - 4.38 0.96 1313 141 0.2385 0.3752 6.1706 6.4073| | 4: 4.38 - 3.99 0.95 1270 167 0.2525 0.3784 6.0303 6.169| | 5: 3.99 - 3.70 0.94 1269 134 0.2651 0.3817 5.8642 6.0261| | 6: 3.70 - 3.49 0.90 1207 143 0.2803 0.3974 5.6442 5.7449| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.81 - 6.29 1321 168 0.73 33.62 1.00 0.75 140032.78| | 2: 6.28 - 5.01 1261 149 0.60 44.53 0.98 0.70 92397.94| | 3: 5.01 - 4.38 1313 141 0.70 36.58 1.01 0.66 62845.88| | 4: 4.38 - 3.99 1270 167 0.68 38.13 0.99 0.70 51997.80| | 5: 3.99 - 3.70 1269 134 0.63 42.49 1.02 0.65 37537.12| | 6: 3.70 - 3.49 1207 143 0.63 42.13 0.97 0.61 22910.05| |alpha: min = 0.61 max = 0.75 mean = 0.68| |beta: min = 22910.05 max = 140032.78 mean = 68752.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 89.79 mean = 39.50| |phase err.(test): min = 0.08 max = 87.21 mean = 41.54| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2611 0.2495 0.3595 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3493 0.3404 0.4248 n_refl.: 8543 remove outliers: r(all,work,free)=0.3493 0.3404 0.4248 n_refl.: 8543 overall B=0.61 to atoms: r(all,work,free)=0.3504 0.3416 0.4255 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2603 0.2489 0.3569 n_refl.: 8543 remove outliers: r(all,work,free)=0.2603 0.2489 0.3569 n_refl.: 8543 ======================== 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 19.814-13.883 97.98 87 10 0.2500 845.541 762.452 2.074 0.854 0.390 13.859-11.604 100.00 90 12 0.1761 1091.904 1037.465 1.708 0.856 0.340 11.577-9.718 99.43 156 19 0.1967 1068.406 1012.641 1.710 0.856 0.315 9.700-8.140 99.66 262 33 0.2097 857.103 812.275 1.724 0.859 0.299 8.117-6.812 97.25 444 52 0.2424 600.227 563.127 1.474 0.862 0.279 6.812-5.705 94.76 721 93 0.2847 425.900 390.887 1.076 0.868 0.179 5.702-4.776 94.99 1247 137 0.2563 416.039 387.175 1.011 0.875 0.098 4.775-3.999 95.66 2113 265 0.2451 395.193 363.083 1.193 0.882 0.060 3.998-3.486 92.23 2521 281 0.2706 269.913 244.662 1.266 0.898 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=2.7450 ================= 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 : 0.3487 0.4112 0.010 1.826 0.0 77.4 33.7 0 0.000 1_bss: 0.2765 0.3607 0.010 1.826 38.8 116.3 72.6 0 0.000 1_settarget: 0.2765 0.3607 0.010 1.826 38.8 116.3 72.6 0 0.000 1_weight: 0.2765 0.3607 0.010 1.826 38.8 116.3 72.6 0 0.000 1_xyzrec: 0.2318 0.3648 0.017 1.741 38.8 116.3 72.6 0 0.369 1_adp: 0.2311 0.3648 0.017 1.741 43.8 111.3 73.3 0 0.369 1_regHadp: 0.2319 0.3642 0.017 1.741 43.8 111.3 73.3 0 0.369 2_bss: 0.2299 0.3615 0.017 1.741 41.5 109.0 71.0 0 0.369 2_settarget: 0.2299 0.3615 0.017 1.741 41.5 109.0 71.0 0 0.369 2_updatecdl: 0.2299 0.3615 0.017 1.785 41.5 109.0 71.0 0 0.369 2_weight: 0.2299 0.3615 0.017 1.785 41.5 109.0 71.0 0 0.369 2_xyzrec: 0.2379 0.3628 0.022 1.937 41.5 109.0 71.0 0 0.396 2_adp: 0.2378 0.3628 0.022 1.937 41.8 108.2 71.0 0 0.396 2_regHadp: 0.2378 0.3628 0.022 1.937 41.8 108.2 71.0 0 0.396 3_bss: 0.2340 0.3604 0.022 1.937 33.6 100.0 62.7 0 0.396 3_settarget: 0.2340 0.3604 0.022 1.937 33.6 100.0 62.7 0 0.396 3_updatecdl: 0.2340 0.3604 0.022 1.952 33.6 100.0 62.7 0 0.396 3_setrh: 0.2343 0.3604 0.022 1.952 33.6 100.0 62.7 0 0.396 3_weight: 0.2343 0.3604 0.022 1.952 33.6 100.0 62.7 0 0.396 3_xyzrec: 0.2498 0.3595 0.013 1.451 33.6 100.0 62.7 0 0.392 3_adp: 0.2495 0.3595 0.013 1.451 33.9 99.9 62.7 0 0.392 3_regHadp: 0.2495 0.3595 0.013 1.451 33.9 99.9 62.7 0 0.392 end: 0.2489 0.3569 0.013 1.451 34.5 100.5 63.3 0 0.392 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1jkt_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1jkt_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 12.9600 Refinement macro-cycles (run) : 288.1100 Write final files (write_after_run_outputs) : 26.1200 Total : 327.1900 Total CPU time: 5.98 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:21 PDT -0700 (1716251661.71 s) Start R-work = 0.2765, R-free = 0.3607 Final R-work = 0.2489, R-free = 0.3569 =============================================================================== Job complete usr+sys time: 384.33 seconds wall clock time: 18 minutes 21.14 seconds (1101.14 seconds total)