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/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=True 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 { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s 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: 2.58, per 1000 atoms: 0.33 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: 4.51 Conformation dependent library (CDL) restraints added in 840.9 milliseconds 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Time building geometry restraints manager: 3.90 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.372657 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 0.2466 0.2724 0.0259 0.002 0.5 2.3 0.0 4.9 0 0.125 0.2414 0.2700 0.0286 0.003 0.5 2.4 0.0 5.1 0 0.250 0.2353 0.2669 0.0316 0.003 0.5 2.4 0.0 5.1 0 0.500 0.2276 0.2668 0.0392 0.004 0.6 2.3 0.0 5.8 0 1.000 0.2202 0.2682 0.0480 0.005 0.7 2.6 0.0 5.8 0 2.000 0.2155 0.2707 0.0552 0.007 0.8 4.1 0.2 6.5 0 3.000 0.2121 0.2706 0.0585 0.009 0.9 4.9 0.2 7.4 0 4.000 0.2091 0.2717 0.0625 0.010 1.0 5.8 0.2 7.6 0 5.000 0.2069 0.2723 0.0654 0.012 1.1 5.9 0.4 9.0 0 6.000 0.2054 0.2747 0.0693 0.013 1.2 6.3 0.4 8.8 0 7.000 0.2037 0.2746 0.0709 0.014 1.2 6.5 0.6 9.0 0 8.000 0.2024 0.2752 0.0728 0.015 1.3 7.4 0.8 10.4 0 9.000 0.2009 0.2749 0.0740 0.017 1.4 7.7 1.0 10.6 0 10.000 0.2046 0.2737 0.0691 0.013 1.2 6.4 0.6 8.8 0 7.186 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2466 0.2724 0.0259 0.002 0.5 2.3 0.0 4.9 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.66 27.24 2.59 0.184 40.818 0.301 0.068 24.41 27.08 2.67 1.116 40.852 0.009 0.067 23.95 26.99 3.04 1.311 40.842 0.038 0.064 22.83 26.55 3.72 3.134 40.913 0.151 0.058 21.62 26.27 4.65 6.452 41.593 0.301 0.052 21.25 26.27 5.02 7.990 42.054 0.452 0.051 21.06 26.22 5.16 8.738 42.292 0.603 0.050 20.85 26.26 5.41 9.883 42.654 0.753 0.049 20.80 26.28 5.48 10.213 42.734 0.904 0.049 20.41 26.28 5.87 12.348 43.457 1.054 0.047 20.35 26.31 5.96 12.827 43.592 1.205 0.047 20.30 26.33 6.03 13.226 43.703 1.356 0.047 20.30 26.55 6.25 15.368 44.363 1.506 0.046 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.603 Accepted refinement result: 21.06 26.22 5.16 8.738 42.292 0.603 0.050 Individual atomic B min max mean iso aniso Overall: 25.90 90.82 43.83 8.25 3919 0 Protein: 25.90 90.82 43.83 8.25 3919 0 Chain A: 25.90 87.87 44.12 N/A 1976 0 Chain B: 26.34 90.82 43.53 N/A 1943 0 Histogram: Values Number of atoms 25.90 - 32.39 509 32.39 - 38.88 1050 38.88 - 45.38 916 45.38 - 51.87 602 51.87 - 58.36 383 58.36 - 64.85 235 64.85 - 71.35 117 71.35 - 77.84 71 77.84 - 84.33 31 84.33 - 90.82 5 =========================== Idealize ADP of riding H ========================== r_work=0.2106 r_free=0.2622 r_work=0.2079 r_free=0.2618 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.2079 r_free= 0.2618 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ls_wunit_k1) (work): 0.048675 | | target function (ls_wunit_k1) not normalized (work): 523.890622 | | target function (ls_wunit_k1) not normalized (free): 92.013458 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2134 0.2079 0.2618 n_refl.: 11936 re-set all scales: r(all,work,free)=0.4027 0.4021 0.4080 n_refl.: 11936 remove outliers: r(all,work,free)=0.4027 0.4021 0.4080 n_refl.: 11936 overall B=0.19 to atoms: r(all,work,free)=0.4034 0.4028 0.4087 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2130 0.2075 0.2618 n_refl.: 11936 remove outliers: r(all,work,free)=0.2130 0.2075 0.2618 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 0.3242 507.000 460.956 1.183 1.039 0.370 15.606-12.533 99.01 92 8 0.1930 614.496 605.276 1.165 1.037 0.372 12.531-10.071 98.91 168 14 0.1721 656.416 646.131 1.165 1.035 0.390 10.061-8.090 99.71 322 26 0.1561 645.262 652.599 1.168 1.028 0.400 8.076-6.488 100.00 590 71 0.1791 448.381 442.964 1.062 1.021 0.400 6.485-5.210 100.00 1131 128 0.2187 335.259 324.292 0.919 1.010 0.396 5.208-4.183 99.96 2124 230 0.1848 401.694 391.350 0.949 0.995 0.369 4.182-3.358 99.96 4019 440 0.2141 319.523 308.223 1.073 0.971 0.148 3.358-3.102 99.68 2234 243 0.2587 212.855 198.814 1.047 0.948 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0716 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.725724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.066378 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 0.1993 0.2584 0.0591 0.002 0.5 2.7 0.0 4.4 0 0.125 0.1943 0.2574 0.0631 0.003 0.5 2.3 0.0 4.9 0 0.250 0.1901 0.2570 0.0668 0.005 0.6 1.9 0.0 5.6 0 0.500 0.1885 0.2580 0.0695 0.009 0.9 3.2 0.0 5.3 0 1.000 0.1813 0.2612 0.0799 0.014 1.2 7.0 0.0 8.8 0 2.000 0.1788 0.2634 0.0846 0.019 1.4 8.7 0.0 10.9 0 3.000 0.1765 0.2664 0.0900 0.023 1.7 10.1 0.6 11.8 0 4.000 0.1750 0.2672 0.0922 0.027 1.9 11.7 0.6 12.5 0 5.000 0.1737 0.2677 0.0940 0.030 2.1 12.9 0.8 13.9 0 6.000 0.1727 0.2695 0.0968 0.033 2.3 13.1 1.0 14.8 0 7.000 0.1717 0.2702 0.0985 0.036 2.4 14.0 1.0 16.2 0 8.000 0.1709 0.2692 0.0983 0.039 2.6 14.1 1.0 15.5 0 9.000 0.1701 0.2698 0.0997 0.041 2.7 15.4 1.2 16.9 0 10.000 0.1816 0.2608 0.0792 0.014 1.1 6.9 0.0 8.3 0 1.863 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1993 0.2584 0.0591 0.002 0.5 2.7 0.0 4.4 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.93 25.84 5.91 8.631 48.298 0.066 5.858 22.80 26.02 3.22 6.953 52.073 0.002 5.909 21.66 25.31 3.66 7.343 50.291 0.008 5.879 20.11 25.13 5.03 8.433 48.131 0.033 5.839 19.62 25.09 5.47 9.203 48.168 0.066 5.825 19.37 25.17 5.80 9.755 48.295 0.100 5.820 19.23 25.24 6.02 10.195 48.444 0.133 5.818 19.12 25.29 6.18 10.640 48.623 0.166 5.817 19.05 25.35 6.30 10.995 48.746 0.199 5.816 19.00 25.40 6.40 11.317 48.858 0.232 5.816 18.96 25.44 6.48 11.590 48.950 0.266 5.816 18.94 25.48 6.55 11.809 49.023 0.299 5.816 19.00 25.53 6.53 11.401 48.814 0.332 5.819 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.066 Accepted refinement result: 19.62 25.09 5.47 9.203 48.168 0.066 5.825 Individual atomic B min max mean iso aniso Overall: 21.09 97.56 43.76 7.89 3919 0 Protein: 21.09 97.56 43.76 7.89 3919 0 Chain A: 21.09 97.56 44.11 N/A 1976 0 Chain B: 21.53 96.00 43.40 N/A 1943 0 Histogram: Values Number of atoms 21.09 - 28.73 314 28.73 - 36.38 993 36.38 - 44.03 945 44.03 - 51.68 760 51.68 - 59.32 437 59.32 - 66.97 225 66.97 - 74.62 130 74.62 - 82.27 73 82.27 - 89.92 33 89.92 - 97.56 9 =========================== Idealize ADP of riding H ========================== r_work=0.1962 r_free=0.2509 r_work=0.1966 r_free=0.2506 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.1966 r_free= 0.2506 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.824131 | | target function (ml) not normalized (work): 62685.118676 | | target function (ml) not normalized (free): 7046.957016 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2020 0.1966 0.2506 n_refl.: 11936 re-set all scales: r(all,work,free)=0.3938 0.3932 0.3994 n_refl.: 11936 remove outliers: r(all,work,free)=0.3938 0.3932 0.3994 n_refl.: 11936 overall B=0.39 to atoms: r(all,work,free)=0.3954 0.3949 0.4009 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2017 0.1963 0.2499 n_refl.: 11936 remove outliers: r(all,work,free)=0.2017 0.1963 0.2499 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 0.3116 507.000 467.851 1.225 1.059 0.379 15.606-12.533 99.01 92 8 0.1922 614.496 602.425 1.162 1.057 0.377 12.531-10.071 98.91 168 14 0.1732 656.416 645.348 1.109 1.054 0.377 10.061-8.090 99.71 322 26 0.1516 645.262 648.950 1.133 1.045 0.390 8.076-6.488 100.00 590 71 0.1771 448.381 440.363 1.033 1.035 0.389 6.485-5.210 100.00 1131 128 0.2124 335.259 323.228 0.913 1.019 0.389 5.208-4.183 99.96 2124 230 0.1678 401.694 390.829 0.948 0.996 0.348 4.182-3.358 99.96 4019 440 0.2001 319.523 307.238 1.088 0.959 0.137 3.358-3.102 99.68 2234 243 0.2494 212.855 196.662 1.063 0.926 0.089 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.1520 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1963 r_free=0.2499 After: r_work=0.1963 r_free=0.2500 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.913001 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.063136 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 0.1963 0.2500 0.0537 0.002 0.5 2.7 0.0 4.4 0 0.125 0.1958 0.2498 0.0540 0.003 0.5 2.7 0.0 4.4 0 0.250 0.1930 0.2496 0.0566 0.005 0.6 2.7 0.0 4.6 0 0.500 0.1823 0.2507 0.0684 0.011 1.2 4.5 0.0 4.6 0 1.000 0.1771 0.2530 0.0759 0.014 1.6 7.9 0.0 5.8 0 2.000 0.1735 0.2557 0.0821 0.019 2.0 11.0 0.0 6.9 0 3.000 0.1722 0.2559 0.0837 0.021 2.1 9.9 0.0 6.2 0 4.000 0.1725 0.2579 0.0854 0.024 2.2 15.5 0.4 10.9 0 5.000 0.1704 0.2573 0.0870 0.029 2.3 14.3 0.6 10.2 0 6.000 0.1694 0.2578 0.0884 0.032 2.5 15.4 0.6 11.1 0 7.000 0.1684 0.2585 0.0901 0.033 2.7 16.3 0.6 11.8 0 8.000 0.1678 0.2592 0.0914 0.035 2.9 17.9 0.6 13.0 0 9.000 0.1669 0.2595 0.0926 0.037 3.1 18.2 0.6 13.7 0 10.000 0.1769 0.2537 0.0767 0.015 1.6 9.1 0.0 5.8 0 1.957 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1958 0.2498 0.0540 0.003 0.5 2.7 0.0 4.4 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.58 24.98 5.40 8.485 48.360 0.063 5.823 22.49 25.64 3.15 7.368 51.682 0.002 5.900 21.93 25.22 3.29 7.558 50.824 0.008 5.886 20.03 24.72 4.69 8.122 48.085 0.032 5.830 19.55 24.96 5.42 8.516 48.308 0.063 5.821 19.41 24.97 5.56 8.752 48.220 0.095 5.818 19.28 25.03 5.75 9.093 48.117 0.126 5.815 18.80 25.03 6.23 10.312 48.220 0.158 5.805 18.60 25.08 6.48 11.142 48.493 0.189 5.802 18.45 25.30 6.84 12.167 48.782 0.221 5.803 18.40 25.36 6.96 12.602 48.947 0.253 5.804 18.37 25.42 7.05 12.994 49.092 0.284 5.804 18.34 25.48 7.15 13.348 49.220 0.316 5.805 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: 20.03 24.72 4.69 8.122 48.085 0.032 5.830 Individual atomic B min max mean iso aniso Overall: 19.45 97.59 43.60 5.54 3919 0 Protein: 19.45 97.59 43.60 5.54 3919 0 Chain A: 20.65 97.58 44.00 N/A 1976 0 Chain B: 19.45 97.59 43.20 N/A 1943 0 Histogram: Values Number of atoms 19.45 - 27.27 129 27.27 - 35.08 949 35.08 - 42.90 1091 42.90 - 50.71 826 50.71 - 58.52 452 58.52 - 66.34 236 66.34 - 74.15 119 74.15 - 81.97 76 81.97 - 89.78 34 89.78 - 97.59 7 =========================== Idealize ADP of riding H ========================== r_work=0.2003 r_free=0.2472 r_work=0.2009 r_free=0.2472 ----------X-ray data---------- |--(resolution: 3.10 - 29.79 A, n_refl.=11936 (all), 9.83 % free)------------| | | | r_work= 0.2009 r_free= 0.2472 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ml) (work): 5.831746 | | target function (ml) not normalized (work): 62767.081081 | | target function (ml) not normalized (free): 7036.418466 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1845 0.2312 6.1833 6.3383| | 2: 6.19 - 4.92 1.00 1344 158 0.2036 0.2251 5.8781 5.9538| | 3: 4.92 - 4.30 1.00 1355 145 0.1673 0.2019 5.8522 6.0348| | 4: 4.30 - 3.91 1.00 1321 156 0.1843 0.2301 5.8776 6.0639| | 5: 3.91 - 3.63 1.00 1335 128 0.1990 0.2430 5.8339 6.0213| | 6: 3.63 - 3.41 1.00 1341 144 0.2250 0.3067 5.7578 6.0399| | 7: 3.41 - 3.24 1.00 1293 151 0.2427 0.2944 5.6566 5.7161| | 8: 3.24 - 3.10 0.99 1320 139 0.2662 0.3235 5.5751 5.8107| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.83 21.23 1.00 0.95 36054.54| | 2: 6.19 - 4.92 1344 158 0.80 25.11 1.01 0.96 25932.79| | 3: 4.92 - 4.30 1355 145 0.86 19.22 0.99 0.97 21577.34| | 4: 4.30 - 3.91 1321 156 0.84 21.68 1.03 0.98 22829.92| | 5: 3.91 - 3.63 1335 128 0.84 22.66 1.02 0.96 22823.87| | 6: 3.63 - 3.41 1341 144 0.80 26.61 0.96 0.93 21339.38| | 7: 3.41 - 3.24 1293 151 0.75 31.27 1.00 0.91 19073.55| | 8: 3.24 - 3.10 1320 139 0.69 36.04 0.96 0.89 18058.84| |alpha: min = 0.89 max = 0.98 mean = 0.94| |beta: min = 18058.84 max = 36054.54 mean = 23623.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.80| |phase err.(work): min = 0.00 max = 89.99 mean = 25.39| |phase err.(test): min = 0.00 max = 88.17 mean = 23.95| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2056 0.2009 0.2472 n_refl.: 11936 re-set all scales: r(all,work,free)=0.3948 0.3943 0.3993 n_refl.: 11936 remove outliers: r(all,work,free)=0.3948 0.3943 0.3993 n_refl.: 11936 overall B=0.68 to atoms: r(all,work,free)=0.3976 0.3972 0.4019 n_refl.: 11936 bulk-solvent and scaling: r(all,work,free)=0.2048 0.2002 0.2467 n_refl.: 11936 remove outliers: r(all,work,free)=0.2048 0.2002 0.2467 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 0.3115 507.000 466.663 1.184 1.090 0.379 15.606-12.533 99.01 92 8 0.1908 614.496 601.773 1.128 1.086 0.377 12.531-10.071 98.91 168 14 0.1722 656.416 644.781 1.078 1.080 0.377 10.061-8.090 99.71 322 26 0.1524 645.262 648.190 1.102 1.069 0.386 8.076-6.488 100.00 590 71 0.1777 448.381 440.002 1.012 1.052 0.386 6.485-5.210 100.00 1131 128 0.2157 335.259 323.229 0.904 1.028 0.385 5.208-4.183 99.96 2124 230 0.1722 401.694 391.080 0.951 0.991 0.337 4.182-3.358 99.96 4019 440 0.2044 319.523 307.352 1.118 0.934 0.152 3.358-3.102 99.68 2234 243 0.2570 212.855 196.735 1.113 0.882 0.108 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.2609 ================= 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_updatephipsi: 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: 0.2466 0.2724 0.002 0.521 30.9 56.9 40.9 0 0.161 1_adp: 0.2106 0.2622 0.002 0.521 25.9 90.8 43.8 0 0.161 1_regHadp: 0.2079 0.2618 0.002 0.521 25.9 90.8 43.8 0 0.161 2_bss: 0.2075 0.2618 0.002 0.521 26.1 91.0 44.0 0 0.161 2_settarget: 0.2075 0.2618 0.002 0.521 26.1 91.0 44.0 0 0.161 2_updatephipsi: 0.2075 0.2618 0.002 0.521 26.1 91.0 44.0 0 0.161 2_updatecdl: 0.2075 0.2618 0.002 0.546 26.1 91.0 44.0 0 0.161 2_weight: 0.2075 0.2618 0.002 0.546 26.1 91.0 44.0 0 0.161 2_xyzrec: 0.1993 0.2584 0.002 0.489 26.1 91.0 44.0 0 0.186 2_adp: 0.1962 0.2509 0.002 0.489 21.1 97.6 43.8 0 0.186 2_regHadp: 0.1966 0.2506 0.002 0.489 21.1 97.6 43.8 0 0.186 3_bss: 0.1963 0.2499 0.002 0.489 21.5 98.0 44.1 0 0.186 3_settarget: 0.1963 0.2499 0.002 0.489 21.5 98.0 44.1 0 0.186 3_updatephipsi: 0.1963 0.2499 0.002 0.489 21.5 98.0 44.1 0 0.186 3_updatecdl: 0.1963 0.2499 0.002 0.510 21.5 98.0 44.1 0 0.186 3_setrh: 0.1963 0.2500 0.002 0.510 21.5 98.0 44.1 0 0.186 3_weight: 0.1963 0.2500 0.002 0.510 21.5 98.0 44.1 0 0.186 3_xyzrec: 0.1958 0.2498 0.003 0.500 21.5 98.0 44.1 0 0.186 3_adp: 0.2003 0.2472 0.003 0.500 19.5 97.6 43.6 0 0.186 3_regHadp: 0.2009 0.2472 0.003 0.500 19.5 97.6 43.6 0 0.186 end: 0.2002 0.2467 0.003 0.500 20.1 98.3 44.3 0 0.186 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2etc_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2etc_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 11.4300 Refinement macro-cycles (run) : 326.8500 Write final files (write_after_run_outputs) : 17.1700 Total : 355.4500 Total CPU time: 6.66 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:32 PDT -0700 (1716251732.92 s) Start R-work = 0.2372, R-free = 0.2694 Final R-work = 0.2002, R-free = 0.2467 =============================================================================== Job complete usr+sys time: 418.96 seconds wall clock time: 18 minutes 49.48 seconds (1129.48 seconds total)