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/2etc.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2etc/2etc.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2etc.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2etc.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2etc/2etc.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2etc/2etc.mtz" } 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 None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 7817 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 3938 Classifications: {'peptide': 252} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 240} Chain: "B" Number of atoms: 3879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3879 Inner-chain residues flagged as termini: ['pdbres="LYS B 201 "', 'pdbres="GLY B 204 "'] Classifications: {'peptide': 248} Modifications used: {'COO': 2, 'NH3': 2} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 235} Chain breaks: 1 Time building chain proxies: 1.41, per 1000 atoms: 0.18 Number of scatterers: 7817 At special positions: 0 Unit cell: (39.514, 95.862, 164.504, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 O 742 8.00 N 678 7.00 C 2473 6.00 H 3898 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 206 " distance=2.05 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 206 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.94 Conformation dependent library (CDL) restraints added in 244.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3886 1.15 - 1.31: 685 1.31 - 1.48: 1547 1.48 - 1.65: 1739 1.65 - 1.81: 36 Bond restraints: 7893 Sorted by residual: bond pdb=" N PRO A 72 " pdb=" CD PRO A 72 " ideal model delta sigma weight residual 1.474 1.622 -0.148 1.40e-02 5.10e+03 1.12e+02 bond pdb=" NH1 ARG A 77 " pdb="HH12 ARG A 77 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLY A 131 " pdb=" H GLY A 131 " 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 305 " pdb=" H GLU B 305 " 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 B 294 " pdb="HE22 GLN B 294 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 7888 not shown) Histogram of bond angle deviations from ideal: 86.59 - 96.08: 6 96.08 - 105.56: 171 105.56 - 115.04: 9916 115.04 - 124.52: 3984 124.52 - 134.00: 212 Bond angle restraints: 14289 Sorted by residual: angle pdb=" C GLU A 211 " pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " ideal model delta sigma weight residual 110.42 86.59 23.83 1.99e+00 2.53e-01 1.43e+02 angle pdb=" N PRO A 72 " pdb=" CA PRO A 72 " pdb=" CB PRO A 72 " ideal model delta sigma weight residual 102.60 113.11 -10.51 1.10e+00 8.26e-01 9.13e+01 angle pdb=" N GLN B 200 " pdb=" CA GLN B 200 " pdb=" C GLN B 200 " ideal model delta sigma weight residual 111.56 123.12 -11.56 1.43e+00 4.89e-01 6.53e+01 angle pdb=" N LEU B 212 " pdb=" CA LEU B 212 " pdb=" CB LEU B 212 " ideal model delta sigma weight residual 111.11 132.49 -21.38 2.74e+00 1.33e-01 6.09e+01 angle pdb=" N GLU B 211 " pdb=" CA GLU B 211 " pdb=" C GLU B 211 " ideal model delta sigma weight residual 113.72 125.22 -11.50 1.52e+00 4.33e-01 5.73e+01 ... (remaining 14284 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 3278 17.87 - 35.74: 277 35.74 - 53.61: 111 53.61 - 71.48: 31 71.48 - 89.35: 13 Dihedral angle restraints: 3710 sinusoidal: 2042 harmonic: 1668 Sorted by residual: dihedral pdb=" C GLU A 211 " pdb=" N GLU A 211 " pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " ideal model delta harmonic sigma weight residual -122.60 -100.22 -22.38 0 2.50e+00 1.60e-01 8.01e+01 dihedral pdb=" N LEU B 212 " pdb=" C LEU B 212 " pdb=" CA LEU B 212 " pdb=" CB LEU B 212 " ideal model delta harmonic sigma weight residual 122.80 142.47 -19.67 0 2.50e+00 1.60e-01 6.19e+01 dihedral pdb=" CA GLN B 200 " pdb=" C GLN B 200 " pdb=" N LYS B 201 " pdb=" CA LYS B 201 " ideal model delta harmonic sigma weight residual 180.00 146.17 33.83 0 5.00e+00 4.00e-02 4.58e+01 ... (remaining 3707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 554 0.117 - 0.233: 51 0.233 - 0.350: 6 0.350 - 0.467: 2 0.467 - 0.583: 1 Chirality restraints: 614 Sorted by residual: chirality pdb=" CA LEU B 212 " pdb=" N LEU B 212 " pdb=" C LEU B 212 " pdb=" CB LEU B 212 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.50e+00 chirality pdb=" CA LYS B 201 " pdb=" N LYS B 201 " pdb=" C LYS B 201 " pdb=" CB LYS B 201 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.01e+00 chirality pdb=" CA GLU A 71 " pdb=" N GLU A 71 " pdb=" C GLU A 71 " pdb=" CB GLU A 71 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 611 not shown) Planarity restraints: 1182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 71 " -0.067 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO A 72 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 158 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C THR B 158 " -0.032 2.00e-02 2.50e+03 pdb=" O THR B 158 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 159 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 251 " -0.022 2.00e-02 2.50e+03 1.21e-02 3.29e+00 pdb=" CG HIS B 251 " 0.002 2.00e-02 2.50e+03 pdb=" ND1 HIS B 251 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS B 251 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS B 251 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 251 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 HIS B 251 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 HIS B 251 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 HIS B 251 " -0.012 2.00e-02 2.50e+03 ... (remaining 1179 not shown) Histogram of nonbonded interaction distances: 0.55 - 1.36: 14 1.36 - 2.17: 740 2.17 - 2.98: 21023 2.98 - 3.79: 35765 3.79 - 4.60: 57039 Warning: very small nonbonded interaction distances. Nonbonded interactions: 114581 Sorted by model distance: nonbonded pdb=" HE1 PHE B 198 " pdb=" HB2 CYS B 206 " model vdw 0.547 2.270 nonbonded pdb=" HZ PHE B 198 " pdb=" SG CYS B 206 " model vdw 0.669 2.850 nonbonded pdb=" CE1 PHE B 198 " pdb=" HB2 CYS B 206 " model vdw 0.810 2.970 nonbonded pdb=" HA CYS B 195 " pdb=" HE2 PHE B 198 " model vdw 0.883 2.270 nonbonded pdb=" CE1 PHE B 198 " pdb=" CB CYS B 206 " model vdw 1.146 3.450 ... (remaining 114576 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 26 15.96 2 O 742 7.97 1 N 678 6.97 1 C 2473 5.97 2 H 3898 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: 3898 of 7817 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7817 n_use_u_iso = 7817 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 = 7817 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7817 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7817 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 = "2etc_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3898 occupancy sum: 3898.00 (% of total atoms 49.98) Rotatable: count: 1095 occupancy sum: 1095.00 (% of total atoms 14.04) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 47.93 A, n_refl.=11944 (all), 9.83 % free)------------| | | | r_work= 0.4152 r_free= 0.4183 coordinate error (max.-lik. estimate): 0.21 A | | | | normalized target function (ml) (work): 5.788779 | | target function (ml) not normalized (work): 62345.151786 | | target function (ml) not normalized (free): 6853.282930 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.93 - 6.20 0.99 1452 152 0.4913 0.4827 6.5785 6.4828| | 2: 6.20 - 4.92 1.00 1344 159 0.3477 0.4135 5.9528 6.0241| | 3: 4.92 - 4.30 1.00 1358 142 0.3410 0.3231 5.9315 6.0023| | 4: 4.30 - 3.91 1.00 1323 158 0.4012 0.3773 5.8529 5.8753| | 5: 3.91 - 3.63 1.00 1336 129 0.4251 0.4218 5.6811 5.7238| | 6: 3.63 - 3.41 1.00 1340 144 0.4436 0.4587 5.556 5.6799| | 7: 3.41 - 3.24 1.00 1296 151 0.4236 0.4325 5.3674 5.3844| | 8: 3.24 - 3.10 0.99 1321 139 0.4326 0.4646 5.3014 5.4684| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 47.93 - 6.20 1452 152 0.54 46.98 0.74 0.28 68465.19| | 2: 6.20 - 4.92 1344 159 0.57 45.88 0.99 0.36 38528.75| | 3: 4.92 - 4.30 1358 142 0.75 30.74 1.25 0.45 21394.54| | 4: 4.30 - 3.91 1323 158 0.76 29.99 1.45 0.54 18158.20| | 5: 3.91 - 3.63 1336 129 0.77 28.93 1.53 0.59 14688.26| | 6: 3.63 - 3.41 1340 144 0.74 32.09 1.56 0.59 12264.07| | 7: 3.41 - 3.24 1296 151 0.70 35.03 1.56 0.58 10484.99| | 8: 3.24 - 3.10 1321 139 0.63 41.21 1.49 0.56 9962.42| |alpha: min = 0.28 max = 0.59 mean = 0.49| |beta: min = 9962.42 max = 68465.19 mean = 24798.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.91 mean = 36.47| |phase err.(test): min = 0.00 max = 89.94 mean = 35.09| |-----------------------------------------------------------------------------| ----------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 : 0.007 0.148 3995 Z= 0.481 Angle : 1.418 23.826 5414 Z= 0.895 Chirality : 0.079 0.583 614 Planarity : 0.004 0.093 707 Dihedral : 17.234 89.351 1485 Min Nonbonded Distance : 1.146 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.61 % Allowed : 3.85 % Favored : 95.55 % Rotamer: Outliers : 6.71 % Allowed : 6.71 % Favored : 86.57 % Cbeta Deviations : 1.28 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -2.92 (0.31), residues: 494 helix: -2.07 (0.24), residues: 294 sheet: None (None), residues: 0 loop : -1.46 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 197 TYR 0.011 0.002 TYR A 208 PHE 0.010 0.001 PHE A 199 TRP 0.011 0.002 TRP A 223 HIS 0.004 0.001 HIS A 251 Individual atomic B min max mean iso aniso Overall: 30.90 56.89 40.89 0.26 3919 0 Protein: 30.90 56.89 40.89 0.26 3919 0 Chain A: 30.90 56.89 41.00 N/A 1976 0 Chain B: 31.34 56.45 40.78 N/A 1943 0 Histogram: Values Number of atoms 30.90 - 33.50 134 33.50 - 36.10 780 36.10 - 38.70 556 38.70 - 41.30 642 41.30 - 43.90 680 43.90 - 46.49 563 46.49 - 49.09 322 49.09 - 51.69 135 51.69 - 54.29 47 54.29 - 56.89 60 |-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: 3.10 - 47.93 A, n_refl.=11944 (all), 9.83 % free)------------| | | | r_work= 0.4152 r_free= 0.4183 coordinate error (max.-lik. estimate): 0.21 A | | | | normalized target function (ml) (work): 5.788779 | | target function (ml) not normalized (work): 62345.151786 | | target function (ml) not normalized (free): 6853.282930 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4155 0.4152 0.4183 n_refl.: 11944 re-set all scales: r(all,work,free)=0.4155 0.4152 0.4183 n_refl.: 11944 remove outliers: r(all,work,free)=0.4126 0.4124 0.4147 n_refl.: 11936 overall B=0.00 to atoms: r(all,work,free)=0.4126 0.4124 0.4147 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2404 0.2372 0.2694 n_refl.: 11936 remove outliers: r(all,work,free)=0.2404 0.2372 0.2694 n_refl.: 11936 ======================== 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 29.785-15.677 93.20 83 13 0.2885 774.675 701.593 1.443 1.027 0.390 15.606-12.533 99.01 92 8 0.1861 938.923 899.555 1.293 1.026 0.390 12.531-10.071 98.91 168 14 0.1665 1002.975 989.849 1.245 1.024 0.396 10.061-8.090 99.71 322 26 0.1634 985.933 979.849 1.231 1.019 0.403 8.076-6.488 100.00 590 71 0.2035 685.107 665.424 1.107 1.014 0.406 6.485-5.210 100.00 1131 128 0.2405 512.261 488.859 0.945 1.007 0.401 5.208-4.183 99.96 2124 230 0.2130 613.771 592.712 0.969 0.997 0.390 4.182-3.358 99.96 4019 440 0.2555 488.218 465.924 1.056 0.981 0.188 3.358-3.102 99.68 2234 243 0.2976 325.233 300.282 1.021 0.965 0.120 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.9374 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.444842 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.301282 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 0.2447 0.2727 0.0280 0.002 0.5 2.0 1.0 5.3 0 0.125 0.2398 0.2708 0.0310 0.002 0.5 1.8 0.8 5.3 0 0.250 0.2336 0.2696 0.0360 0.003 0.5 1.9 0.8 5.3 0 0.500 0.2259 0.2706 0.0447 0.003 0.6 2.7 1.2 5.8 0 1.000 0.2184 0.2725 0.0540 0.005 0.7 2.9 1.0 6.2 0 2.000 0.2141 0.2719 0.0578 0.007 0.8 3.6 1.0 6.7 0 3.000 0.2107 0.2720 0.0613 0.009 0.9 4.4 1.2 7.9 0 4.000 0.2079 0.2732 0.0653 0.010 1.0 5.8 1.2 7.9 0 5.000 0.2059 0.2748 0.0689 0.011 1.1 6.7 1.2 9.0 0 6.000 0.2042 0.2748 0.0706 0.013 1.1 7.2 1.2 8.8 0 7.000 0.2027 0.2758 0.0731 0.014 1.2 7.9 1.4 10.0 0 8.000 0.2011 0.2762 0.0750 0.015 1.3 8.2 1.4 10.9 0 9.000 0.1999 0.2770 0.0771 0.016 1.4 9.1 1.4 11.6 0 10.000 0.2039 0.2744 0.0705 0.013 1.2 7.2 1.2 8.3 0 7.222 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2398 0.2708 0.0310 0.002 0.5 1.8 0.8 5.3 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.98 27.08 3.10 0.184 40.818 0.301 0.064 23.75 26.96 3.20 1.109 40.857 0.009 0.063 23.29 26.82 3.54 1.307 40.853 0.038 0.060 21.59 26.18 4.58 4.594 41.154 0.151 0.052 20.93 26.02 5.09 6.548 41.678 0.301 0.049 20.65 26.00 5.35 7.660 41.990 0.452 0.048 20.49 26.02 5.53 8.430 42.210 0.603 0.047 20.30 25.96 5.66 9.328 42.503 0.753 0.046 20.22 25.97 5.75 9.809 42.643 0.904 0.046 19.90 25.93 6.03 11.617 43.261 1.054 0.044 19.86 25.97 6.11 11.979 43.355 1.205 0.044 19.80 25.98 6.18 12.458 43.500 1.356 0.044 19.76 25.99 6.23 12.814 43.603 1.506 0.044 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.753 Accepted refinement result: 20.30 25.96 5.66 9.328 42.503 0.753 0.046 Individual atomic B min max mean iso aniso Overall: 25.90 95.65 44.25 8.90 3919 0 Protein: 25.90 95.65 44.25 8.90 3919 0 Chain A: 25.90 93.27 44.59 N/A 1976 0 Chain B: 26.34 95.65 43.91 N/A 1943 0 Histogram: Values Number of atoms 25.90 - 32.87 598 32.87 - 39.85 1077 39.85 - 46.82 913 46.82 - 53.80 578 53.80 - 60.77 351 60.77 - 67.75 219 67.75 - 74.72 113 74.72 - 81.70 48 81.70 - 88.67 19 88.67 - 95.65 3 =========================== Idealize ADP of riding H ========================== r_work=0.2030 r_free=0.2596 r_work=0.2007 r_free=0.2589 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.2007 r_free= 0.2589 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ls_wunit_k1) (work): 0.045117 | | target function (ls_wunit_k1) not normalized (work): 485.596227 | | target function (ls_wunit_k1) not normalized (free): 90.519737 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2067 0.2007 0.2589 n_refl.: 11936 re-set all scales: r(all,work,free)=0.4006 0.4000 0.4066 n_refl.: 11936 remove outliers: r(all,work,free)=0.4006 0.4000 0.4066 n_refl.: 11936 overall B=0.30 to atoms: r(all,work,free)=0.4019 0.4012 0.4077 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2067 0.2008 0.2594 n_refl.: 11936 remove outliers: r(all,work,free)=0.2067 0.2008 0.2594 n_refl.: 11936 ======================== 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 29.785-15.677 93.20 83 13 0.3090 503.709 468.694 1.361 1.037 0.389 15.606-12.533 99.01 92 8 0.1930 610.507 601.099 1.240 1.035 0.387 12.531-10.071 98.91 168 14 0.1644 652.155 644.311 1.164 1.033 0.388 10.061-8.090 99.71 322 26 0.1495 641.074 648.365 1.165 1.026 0.390 8.076-6.488 100.00 590 71 0.1747 445.470 439.655 1.056 1.018 0.390 6.485-5.210 100.00 1131 128 0.2107 333.083 323.189 0.915 1.008 0.389 5.208-4.183 99.96 2124 230 0.1761 399.086 390.379 0.946 0.992 0.359 4.182-3.358 99.96 4019 440 0.2080 317.449 307.274 1.075 0.968 0.141 3.358-3.102 99.68 2234 243 0.2539 211.473 198.209 1.052 0.946 0.099 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.1148 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.824616 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.067732 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 0.1951 0.2570 0.0619 0.002 0.5 2.2 1.4 4.9 0 0.125 0.1911 0.2567 0.0655 0.003 0.5 2.4 1.0 5.6 0 0.250 0.1872 0.2580 0.0709 0.005 0.6 2.4 0.8 6.2 0 0.500 0.1829 0.2593 0.0764 0.008 0.8 4.1 1.0 7.4 0 1.000 0.1804 0.2582 0.0778 0.015 1.2 5.1 0.8 6.2 0 2.000 0.1769 0.2651 0.0881 0.019 1.4 10.9 1.6 11.3 0 3.000 0.1746 0.2669 0.0923 0.023 1.7 11.8 1.8 12.5 0 4.000 0.1731 0.2683 0.0952 0.026 1.9 12.2 2.2 13.7 0 5.000 0.1718 0.2688 0.0969 0.030 2.1 12.7 2.4 14.4 0 6.000 0.1706 0.2693 0.0987 0.032 2.3 14.6 2.8 15.0 0 7.000 0.1697 0.2701 0.1004 0.035 2.4 16.3 2.8 15.3 0 8.000 0.1688 0.2710 0.1021 0.038 2.6 16.9 2.8 16.2 0 9.000 0.1682 0.2709 0.1028 0.041 2.7 16.9 2.8 16.7 0 10.000 0.1792 0.2605 0.0813 0.013 1.1 8.1 1.0 7.4 0 1.912 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1911 0.2567 0.0655 0.003 0.5 2.4 1.0 5.6 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.11 25.67 6.55 8.996 48.831 0.068 5.823 22.01 26.21 4.20 7.128 52.726 0.002 5.873 20.84 25.49 4.65 7.367 51.027 0.008 5.844 19.19 25.03 5.83 8.540 48.778 0.034 5.804 18.72 24.96 6.24 9.299 48.736 0.068 5.791 18.49 24.97 6.48 9.864 48.858 0.102 5.787 18.37 25.02 6.65 10.277 48.958 0.135 5.785 18.29 25.06 6.77 10.633 49.067 0.169 5.785 18.24 25.10 6.85 10.930 49.162 0.203 5.785 18.21 25.12 6.92 11.180 49.244 0.237 5.785 18.16 25.15 6.99 11.529 49.378 0.271 5.784 18.13 25.17 7.04 11.756 49.455 0.305 5.784 18.12 25.20 7.09 11.942 49.517 0.339 5.784 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.034 Accepted refinement result: 19.19 25.03 5.83 8.540 48.778 0.034 5.804 Individual atomic B min max mean iso aniso Overall: 22.64 94.65 44.44 6.05 3919 0 Protein: 22.64 94.65 44.44 6.05 3919 0 Chain A: 23.49 94.65 44.89 N/A 1976 0 Chain B: 22.64 90.95 43.99 N/A 1943 0 Histogram: Values Number of atoms 22.64 - 29.84 237 29.84 - 37.04 943 37.04 - 44.24 998 44.24 - 51.44 805 51.44 - 58.65 471 58.65 - 65.85 250 65.85 - 73.05 124 73.05 - 80.25 66 80.25 - 87.45 20 87.45 - 94.65 5 =========================== Idealize ADP of riding H ========================== r_work=0.1919 r_free=0.2503 r_work=0.1928 r_free=0.2502 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.1928 r_free= 0.2502 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 5.804608 | | target function (ml) not normalized (work): 62474.998637 | | target function (ml) not normalized (free): 7030.420626 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1986 0.1928 0.2502 n_refl.: 11936 re-set all scales: r(all,work,free)=0.3972 0.3964 0.4053 n_refl.: 11936 remove outliers: r(all,work,free)=0.3972 0.3964 0.4053 n_refl.: 11936 overall B=0.01 to atoms: r(all,work,free)=0.3973 0.3964 0.4054 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.1977 0.1919 0.2487 n_refl.: 11936 remove outliers: r(all,work,free)=0.1977 0.1919 0.2487 n_refl.: 11936 ======================== 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 29.785-15.677 93.20 83 13 0.3020 503.709 469.614 1.237 1.062 0.380 15.606-12.533 99.01 92 8 0.1696 610.507 598.043 1.170 1.060 0.381 12.531-10.071 98.91 168 14 0.1595 652.155 641.758 1.116 1.056 0.383 10.061-8.090 99.71 322 26 0.1487 641.074 643.934 1.135 1.046 0.395 8.076-6.488 100.00 590 71 0.1710 445.470 437.199 1.039 1.034 0.400 6.485-5.210 100.00 1131 128 0.2030 333.083 321.768 0.920 1.017 0.400 5.208-4.183 99.96 2124 230 0.1628 399.086 389.141 0.952 0.991 0.340 4.182-3.358 99.96 4019 440 0.1977 317.449 305.383 1.094 0.950 0.175 3.358-3.102 99.68 2234 243 0.2499 211.473 195.504 1.092 0.913 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0040 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1919 r_free=0.2487 After: r_work=0.1920 r_free=0.2488 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.923661 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.064421 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 0.1922 0.2489 0.0567 0.003 0.5 2.6 1.2 5.6 0 0.125 0.1919 0.2490 0.0571 0.003 0.5 2.6 1.2 5.6 0 0.250 0.1906 0.2496 0.0591 0.004 0.6 2.4 1.2 5.8 0 0.500 0.1840 0.2512 0.0672 0.012 0.9 4.1 1.0 6.2 0 1.000 0.1770 0.2546 0.0775 0.014 1.5 9.2 0.8 7.2 0 2.000 0.1745 0.2568 0.0824 0.018 2.0 13.4 1.0 7.6 0 3.000 0.1736 0.2555 0.0819 0.022 1.9 12.6 0.8 9.0 0 4.000 0.1720 0.2562 0.0842 0.025 2.2 15.4 1.0 9.5 0 5.000 0.1696 0.2567 0.0871 0.030 2.7 15.9 1.0 7.9 0 6.000 0.1682 0.2605 0.0923 0.031 3.0 18.6 2.0 9.7 0 7.000 0.1685 0.2632 0.0948 0.033 3.3 23.3 2.2 14.6 0 8.000 0.1679 0.2557 0.0878 0.040 3.1 15.2 1.6 7.6 1 9.000 0.1672 0.2559 0.0887 0.043 3.3 15.5 1.6 8.1 1 10.000 0.1777 0.2541 0.0764 0.013 1.5 9.9 0.8 7.4 0 1.962 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1922 0.2489 0.0567 0.003 0.5 2.6 1.2 5.6 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.22 24.89 5.67 7.707 48.679 0.064 5.805 22.10 26.11 4.00 6.621 51.811 0.002 5.883 21.58 25.66 4.07 6.962 51.066 0.008 5.870 19.24 24.75 5.51 7.693 48.558 0.032 5.802 19.04 24.84 5.80 7.918 48.586 0.064 5.799 18.59 24.79 6.20 8.734 48.480 0.097 5.786 18.14 24.76 6.62 10.102 48.782 0.129 5.776 18.11 24.86 6.75 10.264 48.817 0.161 5.777 18.05 24.91 6.86 10.600 48.950 0.193 5.776 18.02 24.95 6.93 10.800 49.026 0.225 5.777 17.98 24.98 6.99 10.991 49.100 0.258 5.777 17.94 25.02 7.07 11.292 49.219 0.290 5.776 17.94 25.04 7.10 11.324 49.229 0.322 5.777 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.032 Accepted refinement result: 19.24 24.75 5.51 7.693 48.558 0.032 5.802 Individual atomic B min max mean iso aniso Overall: 20.63 95.34 44.21 5.52 3919 0 Protein: 20.63 95.34 44.21 5.52 3919 0 Chain A: 22.35 95.34 44.68 N/A 1976 0 Chain B: 20.63 90.24 43.73 N/A 1943 0 Histogram: Values Number of atoms 20.63 - 28.10 116 28.10 - 35.57 886 35.57 - 43.04 1044 43.04 - 50.52 886 50.52 - 57.99 509 57.99 - 65.46 248 65.46 - 72.93 139 72.93 - 80.40 65 80.40 - 87.87 21 87.87 - 95.34 5 =========================== Idealize ADP of riding H ========================== r_work=0.1924 r_free=0.2475 r_work=0.1925 r_free=0.2474 ----------X-ray data---------- |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.1925 r_free= 0.2474 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 5.802420 | | target function (ml) not normalized (work): 62451.449707 | | target function (ml) not normalized (free): 7024.692986 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.79 - 6.19 0.99 1454 152 0.1768 0.2265 6.1442 6.3157| | 2: 6.19 - 4.92 1.00 1344 158 0.1917 0.2327 5.8455 5.9578| | 3: 4.92 - 4.30 1.00 1355 145 0.1587 0.1977 5.8153 6.0138| | 4: 4.30 - 3.91 1.00 1321 156 0.1757 0.2220 5.8375 6.0164| | 5: 3.91 - 3.63 1.00 1335 128 0.1944 0.2519 5.8077 6.0255| | 6: 3.63 - 3.41 1.00 1341 144 0.2123 0.3111 5.729 6.0444| | 7: 3.41 - 3.24 1.00 1293 151 0.2372 0.2967 5.6472 5.7214| | 8: 3.24 - 3.10 0.99 1320 139 0.2580 0.3277 5.555 5.8073| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.79 - 6.19 1454 152 0.84 20.84 1.00 0.95 34505.51| | 2: 6.19 - 4.92 1344 158 0.81 24.86 1.00 0.97 25358.29| | 3: 4.92 - 4.30 1355 145 0.87 19.09 0.99 0.98 21198.88| | 4: 4.30 - 3.91 1321 156 0.84 21.56 1.03 0.99 22137.19| | 5: 3.91 - 3.63 1335 128 0.84 22.58 1.02 0.97 22420.73| | 6: 3.63 - 3.41 1341 144 0.79 26.80 0.96 0.93 21293.15| | 7: 3.41 - 3.24 1293 151 0.74 31.61 0.99 0.91 19230.25| | 8: 3.24 - 3.10 1320 139 0.69 36.31 0.97 0.90 17882.68| |alpha: min = 0.90 max = 0.99 mean = 0.95| |beta: min = 17882.68 max = 34505.51 mean = 23151.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.99 mean = 25.36| |phase err.(test): min = 0.00 max = 89.57 mean = 23.89| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1981 0.1925 0.2474 n_refl.: 11936 re-set all scales: r(all,work,free)=0.3965 0.3957 0.4039 n_refl.: 11936 remove outliers: r(all,work,free)=0.3965 0.3957 0.4039 n_refl.: 11936 overall B=-0.26 to atoms: r(all,work,free)=0.3954 0.3946 0.4028 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.1981 0.1926 0.2474 n_refl.: 11936 remove outliers: r(all,work,free)=0.1981 0.1926 0.2474 n_refl.: 11936 ======================== 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 29.785-15.677 93.20 83 13 0.3021 503.709 465.295 1.244 1.064 0.380 15.606-12.533 99.01 92 8 0.1715 610.507 592.855 1.178 1.062 0.381 12.531-10.071 98.91 168 14 0.1603 652.155 636.134 1.121 1.057 0.383 10.061-8.090 99.71 322 26 0.1502 641.074 639.606 1.133 1.048 0.386 8.076-6.488 100.00 590 71 0.1734 445.470 434.815 1.036 1.035 0.386 6.485-5.210 100.00 1131 128 0.2056 333.083 320.574 0.918 1.018 0.384 5.208-4.183 99.96 2124 230 0.1632 399.086 389.163 0.964 0.990 0.341 4.182-3.358 99.96 4019 440 0.1978 317.449 307.275 1.113 0.949 0.186 3.358-3.102 99.68 2234 243 0.2504 211.473 197.581 1.112 0.910 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.7234 ================= 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 : 0.4152 0.4183 0.007 1.418 30.9 56.9 40.9 0 0.000 1_bss: 0.2372 0.2694 0.007 1.418 30.9 56.9 40.9 0 0.000 1_settarget: 0.2372 0.2694 0.007 1.418 30.9 56.9 40.9 0 0.000 1_weight: 0.2372 0.2694 0.007 1.418 30.9 56.9 40.9 0 0.000 1_xyzrec: 0.2398 0.2708 0.002 0.514 30.9 56.9 40.9 0 0.152 1_adp: 0.2030 0.2596 0.002 0.514 25.9 95.6 44.3 0 0.152 1_regHadp: 0.2007 0.2589 0.002 0.514 25.9 95.6 44.3 0 0.152 2_bss: 0.2008 0.2594 0.002 0.514 26.2 95.9 44.5 0 0.152 2_settarget: 0.2008 0.2594 0.002 0.514 26.2 95.9 44.5 0 0.152 2_updatecdl: 0.2008 0.2594 0.002 0.556 26.2 95.9 44.5 0 0.152 2_weight: 0.2008 0.2594 0.002 0.556 26.2 95.9 44.5 0 0.152 2_xyzrec: 0.1911 0.2567 0.003 0.527 26.2 95.9 44.5 0 0.206 2_adp: 0.1919 0.2503 0.003 0.527 22.6 94.7 44.4 0 0.206 2_regHadp: 0.1928 0.2502 0.003 0.527 22.6 94.7 44.4 0 0.206 3_bss: 0.1919 0.2487 0.003 0.527 22.6 94.7 44.5 0 0.206 3_settarget: 0.1919 0.2487 0.003 0.527 22.6 94.7 44.5 0 0.206 3_updatecdl: 0.1919 0.2487 0.003 0.542 22.6 94.7 44.5 0 0.206 3_setrh: 0.1920 0.2488 0.003 0.542 22.6 94.7 44.5 0 0.205 3_weight: 0.1920 0.2488 0.003 0.542 22.6 94.7 44.5 0 0.205 3_xyzrec: 0.1922 0.2489 0.003 0.524 22.6 94.7 44.5 0 0.205 3_adp: 0.1924 0.2475 0.003 0.524 20.6 95.3 44.2 0 0.205 3_regHadp: 0.1925 0.2474 0.003 0.524 20.6 95.3 44.2 0 0.205 end: 0.1926 0.2474 0.003 0.524 20.4 95.1 43.9 0 0.205 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2etc_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2etc_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 10.5700 Refinement macro-cycles (run) : 314.8700 Write final files (write_after_run_outputs) : 26.8700 Total : 352.3100 Total CPU time: 6.39 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:36 PDT -0700 (1716251676.45 s) Start R-work = 0.2372, R-free = 0.2694 Final R-work = 0.1926, R-free = 0.2474 =============================================================================== Job complete usr+sys time: 412.92 seconds wall clock time: 18 minutes 39.51 seconds (1119.51 seconds total)