Starting phenix.refine on Mon May 20 17:17:05 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2jcl.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2jcl/2jcl.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/2jcl/2jcl.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2jcl/2jcl.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2jcl.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2jcl.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 None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 9180 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4576 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 262} Chain: "B" Number of atoms: 4579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 4579 Classifications: {'peptide': 277} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Unusual residues: {'SO4': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 3.12, per 1000 atoms: 0.34 Number of scatterers: 9180 At special positions: 0 Unit cell: (95.93, 103.26, 121.49, 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 29 16.00 O 832 8.00 N 756 7.00 C 3022 6.00 H 4541 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: 5.15 Conformation dependent library (CDL) restraints added in 733.8 milliseconds 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Time building geometry restraints manager: 4.87 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: 4535 1.15 - 1.32: 823 1.32 - 1.49: 2124 1.49 - 1.66: 1795 1.66 - 1.83: 42 Bond restraints: 9319 Sorted by residual: bond pdb=" C ASP B2197 " pdb=" N ILE B2198 " ideal model delta sigma weight residual 1.332 1.503 -0.171 1.36e-02 5.41e+03 1.58e+02 bond pdb=" NE1 TRP B2088 " pdb=" HE1 TRP B2088 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE1 TRP A1249 " pdb=" HE1 TRP A1249 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS B2209 " pdb=" HE2 HIS B2209 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS B2319 " pdb=" H HIS B2319 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9314 not shown) Histogram of bond angle deviations from ideal: 93.01 - 104.72: 202 104.72 - 116.43: 11723 116.43 - 128.14: 4848 128.14 - 139.85: 68 139.85 - 151.56: 1 Bond angle restraints: 16842 Sorted by residual: angle pdb=" O ILE B2198 " pdb=" C ILE B2198 " pdb=" N SER B2199 " ideal model delta sigma weight residual 122.57 95.30 27.27 1.25e+00 6.40e-01 4.76e+02 angle pdb=" C ILE B2198 " pdb=" N SER B2199 " pdb=" CA SER B2199 " ideal model delta sigma weight residual 120.82 151.56 -30.74 1.50e+00 4.44e-01 4.20e+02 angle pdb=" CA ILE B2198 " pdb=" C ILE B2198 " pdb=" N SER B2199 " ideal model delta sigma weight residual 116.60 139.06 -22.46 1.45e+00 4.76e-01 2.40e+02 angle pdb=" O ASP B2197 " pdb=" C ASP B2197 " pdb=" N ILE B2198 " ideal model delta sigma weight residual 122.59 112.14 10.45 1.33e+00 5.65e-01 6.17e+01 angle pdb=" N GLN B2357 " pdb=" CA GLN B2357 " pdb=" C GLN B2357 " ideal model delta sigma weight residual 108.86 119.47 -10.61 1.41e+00 5.03e-01 5.67e+01 ... (remaining 16837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3762 17.65 - 35.30: 408 35.30 - 52.95: 154 52.95 - 70.60: 43 70.60 - 88.25: 16 Dihedral angle restraints: 4383 sinusoidal: 2288 harmonic: 2095 Sorted by residual: dihedral pdb=" CA ASP B2197 " pdb=" C ASP B2197 " pdb=" N ILE B2198 " pdb=" CA ILE B2198 " ideal model delta harmonic sigma weight residual -180.00 -148.71 -31.29 0 5.00e+00 4.00e-02 3.92e+01 dihedral pdb=" N HIS B2280 " pdb=" C HIS B2280 " pdb=" CA HIS B2280 " pdb=" CB HIS B2280 " ideal model delta harmonic sigma weight residual 122.80 108.29 14.51 0 2.50e+00 1.60e-01 3.37e+01 dihedral pdb=" C GLU A1192 " pdb=" N GLU A1192 " pdb=" CA GLU A1192 " pdb=" CB GLU A1192 " ideal model delta harmonic sigma weight residual -122.60 -135.18 12.58 0 2.50e+00 1.60e-01 2.53e+01 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 502 0.111 - 0.221: 143 0.221 - 0.332: 21 0.332 - 0.442: 5 0.442 - 0.553: 1 Chirality restraints: 672 Sorted by residual: chirality pdb=" CA ASN B2293 " pdb=" N ASN B2293 " pdb=" C ASN B2293 " pdb=" CB ASN B2293 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.64e+00 chirality pdb=" CA GLN B2357 " pdb=" N GLN B2357 " pdb=" C GLN B2357 " pdb=" CB GLN B2357 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" CA GLU A1192 " pdb=" N GLU A1192 " pdb=" C GLU A1192 " pdb=" CB GLU A1192 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.83e+00 ... (remaining 669 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B2198 " 0.047 2.00e-02 2.50e+03 7.37e-02 5.43e+01 pdb=" C ILE B2198 " -0.127 2.00e-02 2.50e+03 pdb=" O ILE B2198 " 0.037 2.00e-02 2.50e+03 pdb=" N SER B2199 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B2197 " -0.040 2.00e-02 2.50e+03 7.13e-02 5.08e+01 pdb=" C ASP B2197 " 0.123 2.00e-02 2.50e+03 pdb=" O ASP B2197 " -0.045 2.00e-02 2.50e+03 pdb=" N ILE B2198 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1092 " -0.016 2.00e-02 2.50e+03 1.76e-02 9.34e+00 pdb=" CG PHE A1092 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE A1092 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A1092 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A1092 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A1092 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A1092 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A1092 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 PHE A1092 " -0.017 2.00e-02 2.50e+03 pdb=" HE1 PHE A1092 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A1092 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A1092 " -0.006 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 67 1.62 - 2.37: 3379 2.37 - 3.11: 29973 3.11 - 3.86: 43584 3.86 - 4.60: 67311 Warning: very small nonbonded interaction distances. Nonbonded interactions: 144314 Sorted by model distance: nonbonded pdb="HD11 ILE B2283 " pdb=" HE1 MET B2354 " model vdw 0.877 2.440 nonbonded pdb=" H GLU B2192 " pdb=" HG3 GLU B2192 " model vdw 1.263 2.270 nonbonded pdb=" HA LEU B2178 " pdb="HD23 LEU B2178 " model vdw 1.305 2.440 nonbonded pdb=" H ILE B2302 " pdb="HG13 ILE B2302 " model vdw 1.339 2.270 nonbonded pdb=" HB3 ASP B2197 " pdb=" HG3 MET B2200 " model vdw 1.346 2.440 ... (remaining 144309 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 29 15.96 2 O 832 7.97 1 N 756 6.97 1 C 3022 5.97 2 H 4541 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: 4541 of 9180 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 9180 n_use_u_iso = 9180 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 = 9180 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (9180 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 9180 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 = "2jcl_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4541 occupancy sum: 4541.00 (% of total atoms 49.50) Rotatable: count: 1174 occupancy sum: 1174.00 (% of total atoms 12.80) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.29 - 25.82 A, n_refl.=18668 (all), 5.14 % free)------------| | | | r_work= 0.3574 r_free= 0.4506 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 6.005759 | | target function (ml) not normalized (work): 106349.971859 | | target function (ml) not normalized (free): 5850.706034 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.82 - 6.27 0.96 2609 121 0.5460 0.6039 6.8079 7.0011| | 2: 6.27 - 4.99 1.00 2567 134 0.2965 0.4098 6.2482 6.2459| | 3: 4.99 - 4.36 1.00 2539 145 0.2829 0.3788 6.0268 6.1824| | 4: 4.36 - 3.96 1.00 2505 152 0.3257 0.4046 5.8953 5.9435| | 5: 3.96 - 3.68 1.00 2528 131 0.3404 0.4589 5.7793 5.8925| | 6: 3.68 - 3.46 1.00 2500 143 0.3408 0.4654 5.693 5.8233| | 7: 3.46 - 3.29 0.98 2460 134 0.3280 0.4313 5.5433 5.6874| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.82 - 6.27 2609 121 0.28 68.42 0.66 0.21 181754.43| | 2: 6.27 - 4.99 2567 134 0.53 49.33 1.03 0.40 83819.95| | 3: 4.99 - 4.36 2539 145 0.79 26.89 1.22 0.53 30673.89| | 4: 4.36 - 3.96 2505 152 0.82 25.11 1.35 0.59 23718.81| | 5: 3.96 - 3.68 2528 131 0.79 27.45 1.39 0.61 20566.81| | 6: 3.68 - 3.46 2500 143 0.77 29.89 1.34 0.59 18379.46| | 7: 3.46 - 3.29 2460 134 0.71 34.66 1.26 0.54 15754.19| |alpha: min = 0.21 max = 0.61 mean = 0.49| |beta: min = 15754.19 max = 181754.43 mean = 54402.34| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 89.99 mean = 37.59| |phase err.(test): min = 0.00 max = 89.97 mean = 36.22| |-----------------------------------------------------------------------------| ----------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 : 0.016 0.171 4778 Z= 0.914 Angle : 1.720 30.745 6478 Z= 1.107 Chirality : 0.105 0.553 672 Planarity : 0.006 0.074 810 Dihedral : 18.634 88.252 1734 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 22.79 Ramachandran Plot: Outliers : 2.91 % Allowed : 10.55 % Favored : 86.55 % Rotamer: Outliers : 11.69 % Allowed : 14.92 % Favored : 73.39 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -4.17 (0.30), residues: 550 helix: -4.08 (0.23), residues: 171 sheet: -1.10 (0.46), residues: 102 loop : -2.50 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B2202 TYR 0.021 0.004 TYR B2251 PHE 0.041 0.004 PHE A1092 TRP 0.028 0.005 TRP B2195 HIS 0.008 0.003 HIS A1280 Individual atomic B min max mean iso aniso Overall: 13.23 125.66 36.40 1.07 4639 0 Protein: 13.23 96.11 36.04 1.07 4614 0 Other: 75.33 125.66 102.20 N/A 25 0 Chain A: 14.29 96.11 37.07 N/A 2307 0 Chain B: 13.23 125.66 35.73 N/A 2332 0 Histogram: Values Number of atoms 13.23 - 24.47 986 24.47 - 35.72 1683 35.72 - 46.96 899 46.96 - 58.20 780 58.20 - 69.44 154 69.44 - 80.69 49 80.69 - 91.93 53 91.93 - 103.17 25 103.17 - 114.42 5 114.42 - 125.66 5 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18668 (all), 5.14 % free)------------| | | | r_work= 0.3574 r_free= 0.4506 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 6.005759 | | target function (ml) not normalized (work): 106349.971859 | | target function (ml) not normalized (free): 5850.706034 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3624 0.3574 0.4506 n_refl.: 18668 re-set all scales: r(all,work,free)=0.3624 0.3574 0.4506 n_refl.: 18668 remove outliers: r(all,work,free)=0.3577 0.3525 0.4501 n_refl.: 18638 overall B=9.12 to atoms: r(all,work,free)=0.3890 0.3834 0.4867 n_refl.: 18638 bulk-solvent and scaling: r(all,work,free)=0.2080 0.2057 0.2502 n_refl.: 18638 remove outliers: r(all,work,free)=0.2076 0.2053 0.2492 n_refl.: 18632 ======================== 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 25.815-15.025 50.00 90 6 0.6251 63.748 40.141 0.096 1.038 0.433 14.999-13.060 76.79 85 1 0.6539 531.218 497.411 0.821 1.041 0.400 12.994-11.375 88.62 138 10 0.2683 977.054 929.700 1.098 1.037 0.394 11.369-9.901 99.22 240 13 0.1734 1062.997 1045.100 1.163 1.034 0.392 9.883-8.622 100.00 356 16 0.1658 1073.143 1054.776 1.123 1.031 0.389 8.618-7.507 99.82 546 20 0.1852 778.443 761.941 1.087 1.026 0.415 7.504-6.535 100.00 806 36 0.2240 611.718 592.471 1.024 1.020 0.410 6.532-5.692 100.00 1192 64 0.2011 610.109 588.519 1.005 1.013 0.376 5.690-4.954 99.95 1802 91 0.1944 639.590 618.957 0.948 1.002 0.359 4.954-4.314 100.00 2679 154 0.1716 728.361 712.094 1.005 0.988 0.341 4.314-3.756 100.00 4069 230 0.1848 628.274 609.098 1.067 0.970 0.251 3.756-3.291 98.98 5671 317 0.2536 453.064 424.909 1.060 0.947 0.166 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9563 b_overall=-3.3287 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.111469 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.288037 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 0.2257 0.2559 0.0302 0.003 0.6 6.0 0.2 8.9 0 0.125 0.2217 0.2540 0.0323 0.003 0.6 6.3 0.2 8.9 0 0.250 0.2166 0.2520 0.0354 0.003 0.6 6.3 0.2 8.9 0 0.500 0.2108 0.2487 0.0379 0.004 0.7 7.0 0.2 9.3 0 1.000 0.2038 0.2468 0.0430 0.006 0.8 8.8 0.2 9.9 0 2.000 0.2004 0.2472 0.0468 0.007 0.9 10.5 0.2 10.3 0 3.000 0.1977 0.2464 0.0487 0.009 0.9 11.7 0.2 10.3 0 4.000 0.1956 0.2462 0.0505 0.010 1.0 13.0 0.2 10.7 0 5.000 0.1941 0.2464 0.0523 0.011 1.1 14.4 0.2 11.1 0 6.000 0.1927 0.2460 0.0533 0.013 1.2 15.9 0.2 11.5 0 7.000 0.1911 0.2455 0.0544 0.014 1.3 16.5 0.2 11.7 0 8.000 0.1901 0.2453 0.0552 0.015 1.3 17.2 0.2 11.7 0 9.000 0.1893 0.2459 0.0566 0.016 1.4 18.0 0.2 11.9 0 10.000 0.1906 0.2458 0.0552 0.015 1.3 17.2 0.2 11.5 0 8.556 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2257 0.2559 0.0302 0.003 0.6 6.0 0.2 8.9 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.57 25.59 3.02 0.767 45.293 0.288 0.061 22.55 25.41 2.86 1.635 45.426 0.009 0.060 22.25 25.31 3.06 1.813 45.475 0.036 0.059 21.61 25.16 3.55 2.837 45.572 0.144 0.056 20.75 24.84 4.09 5.994 46.060 0.288 0.051 20.42 24.82 4.40 7.524 46.461 0.432 0.050 20.24 24.79 4.55 8.542 46.729 0.576 0.049 20.12 24.77 4.65 9.358 46.948 0.720 0.048 20.04 24.77 4.72 9.943 47.097 0.864 0.048 19.84 24.69 4.85 11.455 47.587 1.008 0.047 19.78 24.67 4.89 11.987 47.724 1.152 0.047 19.72 24.69 4.97 12.573 47.892 1.296 0.047 19.68 24.69 5.01 12.932 47.981 1.440 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: 1.152 Accepted refinement result: 19.78 24.67 4.89 11.987 47.724 1.152 0.047 Individual atomic B min max mean iso aniso Overall: 18.79 131.48 50.33 11.40 4639 0 Protein: 18.79 124.89 50.00 11.41 4614 0 Other: 79.60 131.48 111.11 N/A 25 0 Chain A: 20.13 124.89 51.13 N/A 2307 0 Chain B: 18.79 131.48 49.54 N/A 2332 0 Histogram: Values Number of atoms 18.79 - 30.06 433 30.06 - 41.33 1168 41.33 - 52.60 1263 52.60 - 63.87 877 63.87 - 75.13 500 75.13 - 86.40 203 86.40 - 97.67 103 97.67 - 108.94 52 108.94 - 120.21 31 120.21 - 131.48 9 =========================== Idealize ADP of riding H ========================== r_work=0.1978 r_free=0.2467 r_work=0.1953 r_free=0.2463 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18632 (all), 5.14 % free)------------| | | | r_work= 0.1953 r_free= 0.2463 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ls_wunit_k1) (work): 0.045648 | | target function (ls_wunit_k1) not normalized (work): 806.780022 | | target function (ls_wunit_k1) not normalized (free): 64.344625 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1980 0.1953 0.2463 n_refl.: 18632 re-set all scales: r(all,work,free)=0.3895 0.3837 0.4895 n_refl.: 18632 remove outliers: r(all,work,free)=0.3895 0.3837 0.4895 n_refl.: 18632 overall B=-1.02 to atoms: r(all,work,free)=0.3857 0.3799 0.4853 n_refl.: 18632 bulk-solvent and scaling: r(all,work,free)=0.1979 0.1953 0.2463 n_refl.: 18632 remove outliers: r(all,work,free)=0.1979 0.1952 0.2463 n_refl.: 18631 ======================== 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 25.815-15.025 50.00 90 6 0.6147 38.985 27.029 0.081 1.011 0.411 14.999-13.060 75.89 84 1 0.6231 328.100 324.452 0.868 1.015 0.395 12.994-11.375 88.62 138 10 0.2523 597.510 582.234 1.113 1.013 0.391 11.369-9.901 99.22 240 13 0.1761 650.068 642.753 1.181 1.012 0.393 9.883-8.622 100.00 356 16 0.1654 656.272 648.946 1.132 1.010 0.395 8.618-7.507 99.82 546 20 0.1863 476.051 470.311 1.078 1.008 0.402 7.504-6.535 100.00 806 36 0.2094 374.092 364.910 1.004 1.005 0.402 6.532-5.692 100.00 1192 64 0.1939 373.108 364.123 0.985 1.001 0.383 5.690-4.954 99.95 1802 91 0.1876 391.136 382.151 0.914 0.996 0.353 4.954-4.314 100.00 2679 154 0.1604 445.424 438.700 0.979 0.989 0.344 4.314-3.756 100.00 4069 230 0.1801 384.216 375.250 1.026 0.980 0.264 3.756-3.291 98.98 5671 317 0.2338 277.068 264.905 1.024 0.968 0.153 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.5689 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.225302 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.050532 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 0.1890 0.2410 0.0521 0.003 0.5 5.0 0.0 6.7 0 0.125 0.1852 0.2422 0.0570 0.004 0.6 5.7 0.0 7.7 0 0.250 0.1823 0.2418 0.0595 0.006 0.7 7.6 0.0 8.5 0 0.500 0.1791 0.2422 0.0631 0.010 0.9 10.1 0.0 9.1 0 1.000 0.1763 0.2417 0.0654 0.016 1.3 13.2 0.2 10.1 0 2.000 0.1745 0.2419 0.0674 0.021 1.6 14.9 0.2 10.5 0 3.000 0.1733 0.2425 0.0693 0.025 1.8 16.9 0.2 11.9 0 4.000 0.1721 0.2424 0.0703 0.028 2.0 18.6 0.2 13.1 0 5.000 0.1712 0.2418 0.0706 0.032 2.2 20.1 0.2 13.9 0 6.000 0.1705 0.2408 0.0703 0.035 2.4 22.0 0.2 14.7 0 7.000 0.1702 0.2408 0.0706 0.037 2.6 22.6 0.5 16.1 0 8.000 0.1698 0.2408 0.0710 0.040 2.7 23.8 0.5 16.7 0 9.000 0.1696 0.2409 0.0713 0.042 2.9 25.2 0.5 17.1 0 10.000 0.1770 0.2410 0.0640 0.014 1.1 11.7 0.2 9.5 0 1.613 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1890 0.2410 0.0521 0.003 0.5 5.0 0.0 6.7 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.90 24.10 5.21 11.158 55.127 0.051 5.882 21.44 24.10 2.66 9.392 59.404 0.002 5.946 20.75 23.84 3.09 9.513 57.867 0.006 5.927 19.57 23.71 4.14 10.752 55.378 0.025 5.889 19.02 23.81 4.79 11.419 54.526 0.051 5.872 18.85 23.88 5.03 11.890 54.411 0.076 5.867 18.78 23.86 5.08 12.367 54.602 0.101 5.865 18.71 23.89 5.19 12.674 54.662 0.126 5.862 18.65 23.91 5.26 12.948 54.733 0.152 5.861 18.61 23.92 5.31 13.198 54.815 0.177 5.859 18.58 23.92 5.35 13.424 54.891 0.202 5.858 18.55 23.93 5.38 13.627 54.962 0.227 5.857 18.53 23.93 5.40 13.818 55.028 0.253 5.857 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.025 Accepted refinement result: 19.57 23.71 4.14 10.752 55.378 0.025 5.889 Individual atomic B min max mean iso aniso Overall: 19.07 125.46 49.81 7.55 4639 0 Protein: 19.07 118.88 49.51 7.54 4614 0 Other: 73.59 125.46 105.34 N/A 25 0 Chain A: 22.68 118.88 50.50 N/A 2307 0 Chain B: 19.07 125.46 49.13 N/A 2332 0 Histogram: Values Number of atoms 19.07 - 29.71 158 29.71 - 40.35 1351 40.35 - 50.99 1353 50.99 - 61.62 883 61.62 - 72.26 482 72.26 - 82.90 192 82.90 - 93.54 105 93.54 - 104.18 59 104.18 - 114.82 43 114.82 - 125.46 13 =========================== Idealize ADP of riding H ========================== r_work=0.1957 r_free=0.2371 r_work=0.1971 r_free=0.2372 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18631 (all), 5.14 % free)------------| | | | r_work= 0.1971 r_free= 0.2372 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 5.892924 | | target function (ml) not normalized (work): 104145.645321 | | target function (ml) not normalized (free): 5746.972515 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1993 0.1971 0.2372 n_refl.: 18631 re-set all scales: r(all,work,free)=0.3905 0.3849 0.4887 n_refl.: 18631 remove outliers: r(all,work,free)=0.3905 0.3849 0.4887 n_refl.: 18631 overall B=-0.65 to atoms: r(all,work,free)=0.3881 0.3825 0.4859 n_refl.: 18631 bulk-solvent and scaling: r(all,work,free)=0.1989 0.1968 0.2364 n_refl.: 18631 remove outliers: r(all,work,free)=0.1989 0.1968 0.2364 n_refl.: 18631 ======================== 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 25.815-15.025 50.00 90 6 0.6172 38.985 26.590 0.074 1.032 0.406 14.999-13.060 75.89 84 1 0.5850 328.100 342.650 0.900 1.036 0.390 12.994-11.375 88.62 138 10 0.2303 597.510 589.603 1.134 1.033 0.392 11.369-9.901 99.22 240 13 0.1577 650.068 645.060 1.202 1.030 0.397 9.883-8.622 100.00 356 16 0.1534 656.272 650.012 1.157 1.027 0.401 8.618-7.507 99.82 546 20 0.1734 476.051 473.852 1.108 1.023 0.411 7.504-6.535 100.00 806 36 0.1970 374.092 365.144 1.034 1.018 0.411 6.532-5.692 100.00 1192 64 0.1906 373.108 363.418 1.004 1.011 0.392 5.690-4.954 99.95 1802 91 0.1827 391.136 380.825 0.932 1.001 0.362 4.954-4.314 100.00 2679 154 0.1619 445.424 436.686 0.990 0.988 0.353 4.314-3.756 100.00 4069 230 0.1864 384.216 373.381 1.048 0.972 0.272 3.756-3.291 98.98 5671 317 0.2461 277.068 260.857 1.038 0.950 0.172 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-2.2654 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1100 Ramachandran restraints generated. 550 Oldfield, 0 Emsley, 550 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1968 r_free=0.2364 After: r_work=0.1968 r_free=0.2364 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.063833 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.047675 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 0.1968 0.2362 0.0395 0.003 0.5 5.0 0.0 6.7 0 0.125 0.1962 0.2360 0.0397 0.003 0.5 5.1 0.0 6.7 0 0.250 0.1924 0.2346 0.0422 0.008 0.7 5.9 0.0 6.9 0 0.500 0.1848 0.2337 0.0489 0.015 1.3 9.9 0.0 7.5 0 1.000 0.1808 0.2361 0.0553 0.018 1.7 15.8 0.0 9.1 0 2.000 0.1785 0.2376 0.0592 0.023 2.0 19.7 0.5 10.1 0 3.000 0.1778 0.2379 0.0601 0.025 2.1 19.5 0.4 10.9 0 4.000 0.1771 0.2379 0.0608 0.028 2.3 19.7 0.5 11.3 0 5.000 0.1747 0.2384 0.0638 0.033 2.8 23.3 0.9 11.3 0 6.000 0.1743 0.2411 0.0668 0.037 3.0 26.7 1.1 14.1 0 7.000 0.1736 0.2420 0.0683 0.040 3.3 29.4 1.6 15.5 1 8.000 0.1732 0.2417 0.0685 0.043 3.5 29.7 1.6 16.5 1 9.000 0.1724 0.2415 0.0691 0.044 3.7 31.6 1.6 16.5 1 10.000 0.1826 0.2353 0.0527 0.014 1.5 15.9 0.0 8.5 0 1.532 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1968 0.2362 0.0395 0.003 0.5 5.0 0.0 6.7 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.68 23.62 3.95 9.159 54.490 0.048 5.893 22.00 24.19 2.19 8.209 58.122 0.001 5.964 21.53 24.11 2.59 8.759 56.960 0.006 5.954 19.65 23.55 3.90 9.126 54.269 0.024 5.891 19.48 23.54 4.06 9.405 54.208 0.048 5.885 19.31 23.54 4.23 9.817 54.010 0.072 5.879 19.13 23.49 4.36 10.349 53.854 0.095 5.872 18.97 23.53 4.56 11.151 53.908 0.119 5.865 18.92 23.53 4.60 11.341 54.017 0.143 5.863 18.87 23.54 4.67 11.591 54.148 0.167 5.862 18.84 23.57 4.73 11.758 54.230 0.191 5.861 18.81 23.58 4.77 11.919 54.310 0.215 5.860 18.80 23.60 4.81 12.028 54.361 0.238 5.860 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.095 Accepted refinement result: 19.13 23.49 4.36 10.349 53.854 0.095 5.872 Individual atomic B min max mean iso aniso Overall: 17.03 122.58 47.90 8.68 4639 0 Protein: 17.03 122.58 47.60 8.66 4614 0 Other: 69.64 119.81 103.11 N/A 25 0 Chain A: 18.50 122.58 48.68 N/A 2307 0 Chain B: 17.03 119.81 47.13 N/A 2332 0 Histogram: Values Number of atoms 17.03 - 27.59 254 27.59 - 38.14 1243 38.14 - 48.70 1313 48.70 - 59.25 874 59.25 - 69.81 489 69.81 - 80.36 218 80.36 - 90.92 113 90.92 - 101.47 68 101.47 - 112.03 45 112.03 - 122.58 22 =========================== Idealize ADP of riding H ========================== r_work=0.1913 r_free=0.2349 r_work=0.1908 r_free=0.2350 ----------X-ray data---------- |--(resolution: 3.29 - 25.82 A, n_refl.=18631 (all), 5.14 % free)------------| | | | r_work= 0.1908 r_free= 0.2350 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.870170 | | target function (ml) not normalized (work): 103743.518797 | | target function (ml) not normalized (free): 5740.227555 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.82 - 6.27 0.95 2574 119 0.1895 0.1847 6.085 6.1783| | 2: 6.27 - 4.99 1.00 2567 134 0.1810 0.2417 5.874 5.9763| | 3: 4.99 - 4.36 1.00 2539 145 0.1567 0.1866 5.8931 6.0752| | 4: 4.36 - 3.96 1.00 2505 152 0.1720 0.2279 5.8943 5.9965| | 5: 3.96 - 3.68 1.00 2528 131 0.1963 0.2495 5.8391 5.9774| | 6: 3.68 - 3.46 1.00 2500 143 0.2211 0.2924 5.8108 5.9411| | 7: 3.46 - 3.29 0.98 2460 134 0.2613 0.3275 5.6854 5.8149| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.82 - 6.27 2574 119 0.85 19.86 1.00 0.96 23661.32| | 2: 6.27 - 4.99 2567 134 0.86 20.20 1.00 0.94 22962.97| | 3: 4.99 - 4.36 2539 145 0.89 17.51 1.00 0.93 22576.12| | 4: 4.36 - 3.96 2505 152 0.88 18.30 1.02 0.93 22052.33| | 5: 3.96 - 3.68 2528 131 0.85 21.91 1.00 0.94 22269.62| | 6: 3.68 - 3.46 2500 143 0.82 25.48 1.03 0.89 21100.34| | 7: 3.46 - 3.29 2460 134 0.77 29.96 0.92 0.80 18992.96| |alpha: min = 0.80 max = 0.96 mean = 0.91| |beta: min = 18992.96 max = 23661.32 mean = 21964.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.84| |phase err.(test): min = 0.00 max = 89.09 mean = 21.72| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1932 0.1908 0.2350 n_refl.: 18631 re-set all scales: r(all,work,free)=0.3805 0.3749 0.4790 n_refl.: 18631 remove outliers: r(all,work,free)=0.3805 0.3749 0.4790 n_refl.: 18631 overall B=-0.27 to atoms: r(all,work,free)=0.3795 0.3739 0.4778 n_refl.: 18631 bulk-solvent and scaling: r(all,work,free)=0.1931 0.1908 0.2348 n_refl.: 18631 remove outliers: r(all,work,free)=0.1931 0.1908 0.2348 n_refl.: 18631 ======================== 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 25.815-15.025 50.00 90 6 0.6191 38.985 26.531 0.078 1.021 0.411 14.999-13.060 75.89 84 1 0.5766 328.100 342.613 0.943 1.026 0.397 12.994-11.375 88.62 138 10 0.2312 597.510 589.067 1.154 1.022 0.394 11.369-9.901 99.22 240 13 0.1585 650.068 644.803 1.218 1.020 0.397 9.883-8.622 100.00 356 16 0.1527 656.272 650.256 1.171 1.018 0.400 8.618-7.507 99.82 546 20 0.1722 476.051 474.308 1.120 1.015 0.410 7.504-6.535 100.00 806 36 0.1956 374.092 364.942 1.040 1.011 0.411 6.532-5.692 100.00 1192 64 0.1871 373.108 363.649 1.005 1.006 0.391 5.690-4.954 99.95 1802 91 0.1787 391.136 381.165 0.930 0.999 0.371 4.954-4.314 100.00 2679 154 0.1562 445.424 437.137 0.976 0.989 0.351 4.314-3.756 100.00 4069 230 0.1772 384.216 373.981 1.031 0.976 0.281 3.756-3.291 98.98 5671 317 0.2379 277.068 261.443 1.007 0.959 0.171 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.9551 ================= 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 : 0.3574 0.4506 0.016 1.720 13.2 125.7 36.4 0 0.000 1_bss: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_settarget: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_updatephipsi: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_weight: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_xyzrec: 0.2257 0.2559 0.003 0.580 22.4 134.8 45.5 0 0.193 1_adp: 0.1978 0.2467 0.003 0.580 18.8 131.5 50.3 0 0.193 1_regHadp: 0.1953 0.2463 0.003 0.580 18.8 131.5 50.3 0 0.193 2_bss: 0.1952 0.2463 0.003 0.580 17.8 130.5 49.3 0 0.193 2_settarget: 0.1952 0.2463 0.003 0.580 17.8 130.5 49.3 0 0.193 2_updatephipsi: 0.1952 0.2463 0.003 0.580 17.8 130.5 49.3 0 0.193 2_updatecdl: 0.1952 0.2463 0.003 0.625 17.8 130.5 49.3 0 0.193 2_weight: 0.1952 0.2463 0.003 0.625 17.8 130.5 49.3 0 0.193 2_xyzrec: 0.1890 0.2410 0.003 0.530 17.8 130.5 49.3 0 0.235 2_adp: 0.1957 0.2371 0.003 0.530 19.1 125.5 49.8 0 0.235 2_regHadp: 0.1971 0.2372 0.003 0.530 19.1 125.5 49.8 0 0.235 3_bss: 0.1968 0.2364 0.003 0.530 18.4 124.8 49.2 0 0.235 3_settarget: 0.1968 0.2364 0.003 0.530 18.4 124.8 49.2 0 0.235 3_updatephipsi: 0.1968 0.2364 0.003 0.530 18.4 124.8 49.2 0 0.235 3_updatecdl: 0.1968 0.2364 0.003 0.555 18.4 124.8 49.2 0 0.235 3_setrh: 0.1968 0.2364 0.003 0.555 18.4 124.8 49.2 0 0.234 3_weight: 0.1968 0.2364 0.003 0.555 18.4 124.8 49.2 0 0.234 3_xyzrec: 0.1968 0.2362 0.003 0.542 18.4 124.8 49.2 0 0.235 3_adp: 0.1913 0.2349 0.003 0.542 17.0 122.6 47.9 0 0.235 3_regHadp: 0.1908 0.2350 0.003 0.542 17.0 122.6 47.9 0 0.235 end: 0.1908 0.2348 0.003 0.542 16.8 122.3 47.6 0 0.235 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2jcl_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2jcl_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 13.3200 Refinement macro-cycles (run) : 347.0200 Write final files (write_after_run_outputs) : 20.4800 Total : 380.8200 Total CPU time: 7.17 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:36:28 PDT -0700 (1716251788.13 s) Start R-work = 0.2053, R-free = 0.2492 Final R-work = 0.1908, R-free = 0.2348 =============================================================================== Job complete usr+sys time: 452.81 seconds wall clock time: 19 minutes 47.83 seconds (1187.83 seconds total)