Starting phenix.refine on Mon May 20 17:17:06 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/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=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/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 { 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 "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s 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: 2.74, per 1000 atoms: 0.31 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: 5.16 Conformation dependent library (CDL) restraints added in 911.4 milliseconds 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Time building geometry restraints manager: 4.72 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.112093 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 0.2881 0.3650 0.0769 0.004 0.9 22.5 2.6 12.6 0 0.125 0.2869 0.3651 0.0782 0.005 1.0 24.0 1.8 13.2 0 0.250 0.2829 0.3670 0.0841 0.005 0.9 19.0 1.6 11.2 0 0.500 0.2745 0.3688 0.0943 0.006 1.0 20.9 1.6 12.6 0 1.000 0.2624 0.3689 0.1065 0.008 1.1 28.9 1.8 14.2 0 2.000 0.2541 0.3669 0.1128 0.010 1.2 37.7 2.4 15.7 0 3.000 0.2479 0.3673 0.1194 0.012 1.4 39.7 1.8 17.3 0 4.000 0.2432 0.3657 0.1225 0.013 1.5 45.7 1.8 18.3 0 5.000 0.2392 0.3655 0.1263 0.015 1.6 50.8 2.6 18.5 0 6.000 0.2361 0.3655 0.1294 0.016 1.7 53.8 2.4 19.3 0 7.000 0.2335 0.3645 0.1310 0.018 1.8 58.4 3.1 19.5 0 8.000 0.2305 0.3661 0.1356 0.019 1.9 61.0 2.9 19.9 0 9.000 0.2279 0.3671 0.1391 0.021 2.0 63.6 2.9 20.1 0 10.000 0.2388 0.3665 0.1277 0.015 1.6 50.3 2.2 18.9 0 6.056 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2335 0.3645 0.1310 0.018 1.8 58.4 3.1 19.5 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.35 36.45 13.10 2.945 72.831 0.206 0.067 23.26 36.48 13.22 3.425 73.180 0.006 0.066 22.78 36.47 13.69 3.569 73.242 0.026 0.064 21.78 36.50 14.72 4.979 73.532 0.103 0.059 21.24 36.51 15.27 6.608 73.956 0.206 0.056 20.95 36.53 15.57 7.772 74.280 0.310 0.055 20.61 36.50 15.90 9.279 74.844 0.413 0.053 20.46 36.53 16.07 10.083 75.090 0.516 0.053 20.35 36.54 16.18 10.746 75.291 0.619 0.052 20.27 36.54 16.27 11.311 75.461 0.723 0.052 20.21 36.56 16.35 11.774 75.603 0.826 0.051 20.14 36.57 16.44 12.268 75.763 0.929 0.051 20.04 36.60 16.56 12.919 75.985 1.032 0.051 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: 23.26 36.48 13.22 3.425 73.180 0.006 0.066 Individual atomic B min max mean iso aniso Overall: 44.07 111.29 73.28 2.24 4478 0 Protein: 44.07 111.29 73.28 2.24 4478 0 Chain A: 44.07 111.29 73.17 N/A 2239 0 Chain B: 50.53 110.15 73.39 N/A 2239 0 Histogram: Values Number of atoms 44.07 - 50.79 6 50.79 - 57.51 10 57.51 - 64.24 74 64.24 - 70.96 2116 70.96 - 77.68 1464 77.68 - 84.40 355 84.40 - 91.12 243 91.12 - 97.84 94 97.84 - 104.57 68 104.57 - 111.29 48 =========================== Idealize ADP of riding H ========================== r_work=0.2326 r_free=0.3648 r_work=0.2333 r_free=0.3641 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2333 r_free= 0.3641 coordinate error (max.-lik. estimate): 0.84 A | | | | normalized target function (ls_wunit_k1) (work): 0.066289 | | target function (ls_wunit_k1) not normalized (work): 506.517276 | | target function (ls_wunit_k1) not normalized (free): 148.361473 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2474 0.2333 0.3641 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3666 0.3582 0.4373 n_refl.: 8543 remove outliers: r(all,work,free)=0.3666 0.3582 0.4373 n_refl.: 8543 overall B=-2.28 to atoms: r(all,work,free)=0.3615 0.3528 0.4339 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2458 0.2316 0.3619 n_refl.: 8543 remove outliers: r(all,work,free)=0.2458 0.2316 0.3619 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 0.2508 721.746 653.217 1.449 0.962 0.366 13.859-11.604 100.00 90 12 0.1739 932.040 883.579 1.419 0.965 0.351 11.577-9.718 99.43 156 19 0.1913 911.982 872.837 1.361 0.967 0.307 9.700-8.140 99.66 262 33 0.2044 731.615 696.804 1.366 0.973 0.292 8.117-6.812 97.25 444 52 0.2112 512.349 490.275 1.107 0.981 0.243 6.812-5.705 94.76 721 93 0.2451 363.544 341.945 0.864 0.993 0.183 5.702-4.776 94.99 1247 137 0.2313 355.127 336.340 0.814 1.009 0.076 4.775-3.999 95.66 2113 265 0.2252 337.334 317.936 1.024 1.029 0.030 3.998-3.486 92.23 2521 281 0.2668 230.395 213.975 1.150 1.063 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-10.2760 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 7.523289 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.095992 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 0.2629 0.3654 0.1025 0.005 0.9 22.1 1.8 18.9 0 0.125 0.2636 0.3649 0.1014 0.004 0.8 17.1 1.6 15.4 0 0.250 0.2583 0.3657 0.1074 0.005 0.9 23.1 1.6 18.3 0 0.500 0.2556 0.3655 0.1099 0.007 1.0 26.5 1.6 17.7 0 1.000 0.2521 0.3658 0.1138 0.011 1.3 33.0 1.5 18.5 0 2.000 0.2467 0.3655 0.1189 0.014 1.5 41.4 1.8 19.5 0 3.000 0.2423 0.3628 0.1205 0.018 1.8 48.4 1.8 19.5 0 4.000 0.2401 0.3624 0.1222 0.022 2.0 52.0 2.2 19.7 0 5.000 0.2383 0.3622 0.1239 0.025 2.1 55.9 2.6 20.1 0 6.000 0.2393 0.3698 0.1306 0.025 2.3 63.5 3.6 26.4 0 7.000 0.2348 0.3630 0.1282 0.031 2.4 61.2 2.9 20.5 0 8.000 0.2335 0.3632 0.1297 0.033 2.5 63.2 3.1 20.7 0 9.000 0.2350 0.3734 0.1384 0.032 2.8 80.9 4.7 29.5 0 10.000 0.2444 0.3634 0.1189 0.018 1.7 47.0 1.8 18.9 0 3.762 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2383 0.3622 0.1239 0.025 2.1 55.9 2.6 20.1 0 6.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.83 36.22 12.39 10.526 78.406 0.096 6.079 24.08 36.25 12.17 10.883 78.872 0.003 6.082 23.82 36.22 12.41 10.545 78.386 0.012 6.078 23.70 36.22 12.51 10.731 78.254 0.048 6.075 23.41 36.23 12.82 11.511 77.852 0.096 6.068 22.82 36.23 13.41 12.662 78.553 0.144 6.055 22.69 36.24 13.54 13.041 78.858 0.192 6.053 22.60 36.24 13.65 13.481 79.137 0.240 6.051 22.53 36.25 13.72 13.922 79.372 0.288 6.050 22.48 36.26 13.78 14.334 79.567 0.336 6.049 22.51 36.38 13.87 13.992 79.344 0.384 6.052 22.49 36.38 13.89 14.148 79.429 0.432 6.052 22.47 36.39 13.92 14.303 79.511 0.480 6.052 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: 23.82 36.22 12.41 10.545 78.386 0.012 6.078 Individual atomic B min max mean iso aniso Overall: 42.10 107.81 70.96 2.13 4478 0 Protein: 42.10 107.81 70.96 2.13 4478 0 Chain A: 42.10 107.81 70.86 N/A 2239 0 Chain B: 50.36 107.74 71.05 N/A 2239 0 Histogram: Values Number of atoms 42.10 - 48.67 5 48.67 - 55.24 9 55.24 - 61.81 67 61.81 - 68.38 2044 68.38 - 74.95 1484 74.95 - 81.52 405 81.52 - 88.09 239 88.09 - 94.66 106 94.66 - 101.23 66 101.23 - 107.81 53 =========================== Idealize ADP of riding H ========================== r_work=0.2382 r_free=0.3622 r_work=0.2381 r_free=0.3622 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2381 r_free= 0.3622 coordinate error (max.-lik. estimate): 0.79 A | | | | normalized target function (ml) (work): 6.078045 | | target function (ml) not normalized (work): 46442.342771 | | target function (ml) not normalized (free): 5630.031335 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2512 0.2381 0.3622 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3558 0.3466 0.4335 n_refl.: 8543 remove outliers: r(all,work,free)=0.3558 0.3466 0.4335 n_refl.: 8543 overall B=-7.34 to atoms: r(all,work,free)=0.3401 0.3301 0.4243 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2473 0.2343 0.3577 n_refl.: 8543 remove outliers: r(all,work,free)=0.2473 0.2343 0.3577 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 0.2424 721.746 654.832 1.855 0.977 0.393 13.859-11.604 100.00 90 12 0.1759 932.040 880.284 1.503 0.978 0.344 11.577-9.718 99.43 156 19 0.1863 911.982 868.104 1.493 0.978 0.315 9.700-8.140 99.66 262 33 0.1960 731.615 694.995 1.499 0.981 0.297 8.117-6.812 97.25 444 52 0.2336 512.349 481.459 1.264 0.985 0.259 6.812-5.705 94.76 721 93 0.2713 363.544 333.978 0.979 0.991 0.199 5.702-4.776 94.99 1247 137 0.2435 355.127 330.752 0.875 0.997 0.079 4.775-3.999 95.66 2113 265 0.2278 337.334 312.035 1.038 1.005 0.021 3.998-3.486 92.23 2521 281 0.2508 230.395 210.169 1.117 1.022 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=2.8534 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1096 Ramachandran restraints generated. 548 Oldfield, 0 Emsley, 548 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2343 r_free=0.3577 After: r_work=0.2345 r_free=0.3578 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 8.162979 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.123871 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 0.2551 0.3579 0.1028 0.014 1.5 47.1 1.6 17.9 0 0.125 0.2533 0.3573 0.1041 0.012 1.5 52.0 2.2 19.1 0 0.250 0.2521 0.3577 0.1056 0.012 1.5 52.1 2.2 19.1 0 0.500 0.2481 0.3583 0.1102 0.013 1.6 56.2 2.6 18.7 0 1.000 0.2425 0.3585 0.1160 0.013 1.7 57.5 2.6 19.9 0 2.000 0.2402 0.3593 0.1191 0.014 1.8 59.4 2.4 19.7 0 3.000 0.2375 0.3589 0.1214 0.017 2.0 59.1 2.2 20.1 0 4.000 0.2357 0.3586 0.1229 0.020 2.1 57.8 2.4 20.5 0 5.000 0.2346 0.3593 0.1247 0.022 2.2 60.1 2.4 20.1 0 6.000 0.2334 0.3596 0.1263 0.024 2.3 60.6 2.4 20.3 0 7.000 0.2320 0.3600 0.1280 0.027 2.4 62.0 2.4 20.5 0 8.000 0.2302 0.3603 0.1301 0.031 2.6 65.1 2.6 21.1 0 9.000 0.2283 0.3603 0.1320 0.035 2.8 67.5 2.6 21.3 0 10.000 0.2374 0.3588 0.1215 0.017 2.0 58.9 2.4 19.9 0 4.081 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2533 0.3573 0.1041 0.012 1.5 52.0 2.2 19.1 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.33 35.73 10.41 10.191 70.797 0.124 6.106 25.41 35.68 10.26 10.446 70.806 0.004 6.106 25.29 35.73 10.44 10.213 70.776 0.015 6.105 25.02 35.72 10.69 10.434 70.630 0.062 6.100 23.78 35.76 11.98 12.276 71.437 0.124 6.073 23.58 35.81 12.23 12.873 71.805 0.186 6.070 23.50 35.93 12.43 13.338 71.934 0.248 6.070 23.42 35.95 12.53 13.809 72.186 0.310 6.069 23.36 35.96 12.60 14.210 72.382 0.372 6.068 23.31 35.98 12.67 14.587 72.557 0.434 6.067 23.24 35.99 12.75 15.217 72.830 0.495 6.065 23.21 36.00 12.79 15.521 72.955 0.557 6.065 23.19 36.01 12.82 15.672 73.017 0.619 6.064 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.015 Accepted refinement result: 25.29 35.73 10.44 10.213 70.776 0.015 6.105 Individual atomic B min max mean iso aniso Overall: 35.09 100.53 63.58 2.04 4478 0 Protein: 35.09 100.53 63.58 2.04 4478 0 Chain A: 35.09 100.53 63.50 N/A 2239 0 Chain B: 44.70 100.28 63.65 N/A 2239 0 Histogram: Values Number of atoms 35.09 - 41.64 4 41.64 - 48.18 10 48.18 - 54.72 97 54.72 - 61.27 2096 61.27 - 67.81 1432 67.81 - 74.35 385 74.35 - 80.90 236 80.90 - 87.44 103 87.44 - 93.98 65 93.98 - 100.53 50 =========================== Idealize ADP of riding H ========================== r_work=0.2529 r_free=0.3573 r_work=0.2529 r_free=0.3574 ----------X-ray data---------- |--(resolution: 3.49 - 19.81 A, n_refl.=8543 (all), 10.56 % free)-------------| | | | r_work= 0.2529 r_free= 0.3574 coordinate error (max.-lik. estimate): 0.75 A | | | | normalized target function (ml) (work): 6.105488 | | target function (ml) not normalized (work): 46652.033406 | | target function (ml) not normalized (free): 5631.535162 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2325 0.3207 6.6211 6.7113| | 2: 6.28 - 5.01 0.95 1261 149 0.2724 0.3489 6.2577 6.3362| | 3: 5.01 - 4.38 0.96 1313 141 0.2412 0.3766 6.1721 6.4067| | 4: 4.38 - 3.99 0.95 1270 167 0.2550 0.3804 6.0303 6.1635| | 5: 3.99 - 3.70 0.94 1269 134 0.2687 0.3832 5.8624 6.0271| | 6: 3.70 - 3.49 0.90 1207 143 0.2843 0.3941 5.6444 5.7319| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 33.55 1.01 0.76 139762.14| | 2: 6.28 - 5.01 1261 149 0.61 44.29 0.97 0.70 91599.62| | 3: 5.01 - 4.38 1313 141 0.71 36.36 1.01 0.67 62149.49| | 4: 4.38 - 3.99 1270 167 0.69 37.85 0.98 0.71 51429.46| | 5: 3.99 - 3.70 1269 134 0.63 42.19 1.02 0.66 37071.12| | 6: 3.70 - 3.49 1207 143 0.64 41.28 0.97 0.62 22038.86| |alpha: min = 0.62 max = 0.76 mean = 0.69| |beta: min = 22038.86 max = 139762.14 mean = 68144.84| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 89.79 mean = 39.17| |phase err.(test): min = 0.09 max = 88.66 mean = 41.21| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2639 0.2529 0.3574 n_refl.: 8543 re-set all scales: r(all,work,free)=0.3521 0.3436 0.4245 n_refl.: 8543 remove outliers: r(all,work,free)=0.3521 0.3436 0.4245 n_refl.: 8543 overall B=0.00 to atoms: r(all,work,free)=0.3521 0.3436 0.4245 n_refl.: 8543 bulk-solvent and scaling: r(all,work,free)=0.2634 0.2524 0.3560 n_refl.: 8543 remove outliers: r(all,work,free)=0.2634 0.2524 0.3560 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 0.2499 837.653 752.526 1.832 0.981 0.390 13.859-11.604 100.00 90 12 0.1902 1081.718 1020.393 1.562 0.983 0.353 11.577-9.718 99.43 156 19 0.2032 1058.439 1003.109 1.516 0.983 0.318 9.700-8.140 99.66 262 33 0.2182 849.107 801.905 1.540 0.985 0.310 8.117-6.812 97.25 444 52 0.2453 594.628 557.266 1.294 0.989 0.280 6.812-5.705 94.76 721 93 0.2883 421.926 387.154 0.910 0.994 0.150 5.702-4.776 94.99 1247 137 0.2580 412.158 383.319 0.890 1.000 0.099 4.775-3.999 95.66 2113 265 0.2469 391.507 359.922 1.055 1.007 0.060 3.998-3.486 92.23 2521 281 0.2742 267.395 242.775 1.124 1.022 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=2.2230 ================= 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_updatephipsi: 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: 0.2335 0.3645 0.018 1.786 38.8 116.3 72.6 0 0.348 1_adp: 0.2326 0.3648 0.018 1.786 44.1 111.3 73.3 0 0.348 1_regHadp: 0.2333 0.3641 0.018 1.786 44.1 111.3 73.3 0 0.348 2_bss: 0.2316 0.3619 0.018 1.786 41.8 109.0 71.0 0 0.348 2_settarget: 0.2316 0.3619 0.018 1.786 41.8 109.0 71.0 0 0.348 2_updatephipsi: 0.2316 0.3619 0.018 1.786 41.8 109.0 71.0 0 0.348 2_updatecdl: 0.2316 0.3619 0.018 1.811 41.8 109.0 71.0 0 0.348 2_weight: 0.2316 0.3619 0.018 1.811 41.8 109.0 71.0 0 0.348 2_xyzrec: 0.2383 0.3622 0.025 2.108 41.8 109.0 71.0 0 0.382 2_adp: 0.2382 0.3622 0.025 2.108 42.1 107.8 71.0 0 0.382 2_regHadp: 0.2381 0.3622 0.025 2.108 42.1 107.8 71.0 0 0.382 3_bss: 0.2343 0.3577 0.025 2.108 34.8 100.5 63.6 0 0.382 3_settarget: 0.2343 0.3577 0.025 2.108 34.8 100.5 63.6 0 0.382 3_updatephipsi: 0.2343 0.3577 0.025 2.108 34.8 100.5 63.6 0 0.382 3_updatecdl: 0.2343 0.3577 0.025 2.123 34.8 100.5 63.6 0 0.382 3_setrh: 0.2345 0.3578 0.025 2.123 34.8 100.5 63.6 0 0.382 3_weight: 0.2345 0.3578 0.025 2.123 34.8 100.5 63.6 0 0.382 3_xyzrec: 0.2533 0.3573 0.012 1.516 34.8 100.5 63.6 0 0.380 3_adp: 0.2529 0.3573 0.012 1.516 35.1 100.5 63.6 0 0.380 3_regHadp: 0.2529 0.3574 0.012 1.516 35.1 100.5 63.6 0 0.380 end: 0.2524 0.3560 0.012 1.516 35.1 100.5 63.6 0 0.380 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1jkt_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1jkt_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 13.5400 Refinement macro-cycles (run) : 308.7000 Write final files (write_after_run_outputs) : 15.8600 Total : 338.1000 Total CPU time: 6.45 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:32 PDT -0700 (1716251732.70 s) Start R-work = 0.2765, R-free = 0.3607 Final R-work = 0.2524, R-free = 0.3560 =============================================================================== Job complete usr+sys time: 403.27 seconds wall clock time: 18 minutes 45.97 seconds (1125.97 seconds total)