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/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=False secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/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 { 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: 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: 1.57, per 1000 atoms: 0.17 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: 2.57 Conformation dependent library (CDL) restraints added in 292.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Time building geometry restraints manager: 2.90 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: 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 { 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 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.456310 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 0.2246 0.2558 0.0312 0.003 0.6 5.0 2.0 8.7 0 0.125 0.2218 0.2548 0.0330 0.003 0.6 5.2 1.8 8.5 0 0.250 0.2165 0.2517 0.0352 0.003 0.6 5.6 1.6 8.5 0 0.500 0.2098 0.2489 0.0390 0.004 0.6 6.8 1.8 8.7 0 1.000 0.2029 0.2486 0.0457 0.006 0.8 8.3 1.8 9.7 0 2.000 0.1989 0.2485 0.0495 0.007 0.9 10.5 2.4 9.7 0 3.000 0.1967 0.2479 0.0512 0.009 0.9 12.1 2.5 10.3 0 4.000 0.1949 0.2472 0.0523 0.010 1.0 13.6 2.7 10.9 0 5.000 0.1935 0.2480 0.0545 0.011 1.1 14.7 3.1 10.9 0 6.000 0.1920 0.2465 0.0545 0.013 1.2 15.7 3.1 10.9 0 7.000 0.1906 0.2464 0.0559 0.014 1.2 16.8 3.3 11.5 0 8.000 0.1895 0.2468 0.0573 0.015 1.3 17.7 3.3 11.5 0 9.000 0.1888 0.2467 0.0579 0.016 1.4 17.8 3.1 11.5 0 10.000 0.1899 0.2462 0.0563 0.015 1.3 17.3 3.3 11.5 0 8.728 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2218 0.2548 0.0330 0.003 0.6 5.2 1.8 8.5 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.18 25.48 3.30 0.767 45.293 0.288 0.058 22.16 25.34 3.18 1.638 45.427 0.009 0.058 21.88 25.24 3.37 1.762 45.466 0.036 0.057 21.25 25.05 3.80 2.813 45.593 0.144 0.054 20.45 24.78 4.34 5.677 46.022 0.288 0.050 20.15 24.70 4.56 7.050 46.367 0.432 0.048 19.99 24.72 4.73 7.890 46.562 0.576 0.048 19.89 24.71 4.83 8.541 46.721 0.720 0.047 19.81 24.71 4.89 9.065 46.854 0.864 0.047 19.76 24.71 4.95 9.484 46.960 1.008 0.047 19.66 24.70 5.04 10.199 47.169 1.152 0.046 19.52 24.66 5.14 11.362 47.530 1.296 0.045 19.44 24.65 5.22 12.142 47.776 1.440 0.045 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.440 Accepted refinement result: 19.44 24.65 5.22 12.142 47.776 1.440 0.045 Individual atomic B min max mean iso aniso Overall: 18.56 133.51 50.43 11.50 4639 0 Protein: 18.56 127.65 50.10 11.51 4614 0 Other: 79.45 133.51 111.65 N/A 25 0 Chain A: 18.56 127.65 51.28 N/A 2307 0 Chain B: 18.74 133.51 49.59 N/A 2332 0 Histogram: Values Number of atoms 18.56 - 30.05 445 30.05 - 41.55 1173 41.55 - 53.04 1252 53.04 - 64.54 911 64.54 - 76.03 480 76.03 - 87.53 188 87.53 - 99.02 108 99.02 - 110.52 49 110.52 - 122.01 26 122.01 - 133.51 7 =========================== Idealize ADP of riding H ========================== r_work=0.1944 r_free=0.2465 r_work=0.1921 r_free=0.2468 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18632 (all), 5.14 % free)------------| | | | r_work= 0.1921 r_free= 0.2468 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.044029 | | target function (ls_wunit_k1) not normalized (work): 778.175072 | | target function (ls_wunit_k1) not normalized (free): 64.069885 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1949 0.1921 0.2468 n_refl.: 18632 re-set all scales: r(all,work,free)=0.3887 0.3828 0.4897 n_refl.: 18632 remove outliers: r(all,work,free)=0.3887 0.3828 0.4897 n_refl.: 18632 overall B=-1.19 to atoms: r(all,work,free)=0.3842 0.3784 0.4848 n_refl.: 18632 bulk-solvent and scaling: r(all,work,free)=0.1949 0.1920 0.2464 n_refl.: 18632 remove outliers: r(all,work,free)=0.1948 0.1919 0.2464 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 0.6160 38.914 26.943 0.084 1.014 0.411 14.999-13.060 75.89 84 1 0.6158 327.500 327.096 0.916 1.017 0.397 12.994-11.375 88.62 138 10 0.2444 596.419 580.337 1.167 1.015 0.394 11.369-9.901 99.22 240 13 0.1690 648.881 640.451 1.228 1.013 0.395 9.883-8.622 100.00 356 16 0.1581 655.074 649.050 1.176 1.011 0.396 8.618-7.507 99.82 546 20 0.1809 475.182 470.973 1.118 1.009 0.396 7.504-6.535 100.00 806 36 0.2083 373.409 364.201 1.041 1.005 0.392 6.532-5.692 100.00 1192 64 0.1905 372.426 364.303 1.018 1.001 0.373 5.690-4.954 99.95 1802 91 0.1855 390.422 381.039 0.953 0.995 0.354 4.954-4.314 100.00 2679 154 0.1569 444.610 438.025 1.019 0.987 0.345 4.314-3.756 100.00 4069 230 0.1758 383.514 375.061 1.069 0.976 0.265 3.756-3.291 98.98 5671 317 0.2325 276.562 264.627 1.065 0.962 0.164 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.2728 ============================ 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 = 3.272792 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.051300 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 0.1877 0.2395 0.0518 0.003 0.6 4.8 1.3 6.9 0 0.125 0.1835 0.2385 0.0549 0.004 0.6 5.2 1.3 7.7 0 0.250 0.1807 0.2399 0.0592 0.006 0.7 7.1 1.5 8.3 0 0.500 0.1782 0.2408 0.0626 0.010 0.9 10.4 1.8 8.9 0 1.000 0.1754 0.2415 0.0661 0.016 1.3 13.4 2.0 9.3 0 2.000 0.1740 0.2420 0.0680 0.021 1.6 16.5 2.2 10.7 0 3.000 0.1727 0.2421 0.0694 0.024 1.8 18.0 2.4 11.1 0 4.000 0.1719 0.2423 0.0704 0.028 2.1 20.5 2.4 12.5 0 5.000 0.1710 0.2426 0.0716 0.031 2.2 22.0 2.4 13.1 0 6.000 0.1705 0.2425 0.0721 0.034 2.5 23.1 2.4 14.1 0 7.000 0.1698 0.2419 0.0722 0.037 2.6 24.3 2.4 13.3 0 8.000 0.1695 0.2426 0.0731 0.040 2.8 25.6 2.5 14.7 0 9.000 0.1691 0.2425 0.0734 0.043 2.9 26.8 2.4 14.9 0 10.000 0.1764 0.2423 0.0659 0.014 1.2 12.5 2.2 9.3 0 1.636 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1877 0.2395 0.0518 0.003 0.6 4.8 1.3 6.9 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.77 23.95 5.18 11.224 55.064 0.051 5.875 21.29 23.96 2.67 9.428 59.296 0.002 5.938 20.60 23.73 3.13 9.541 57.752 0.006 5.920 19.48 23.47 4.00 10.698 55.303 0.026 5.882 18.92 23.60 4.68 11.369 54.489 0.051 5.865 18.75 23.64 4.88 11.863 54.390 0.077 5.859 18.68 23.68 5.00 12.348 54.581 0.103 5.858 18.60 23.71 5.11 12.670 54.637 0.128 5.855 18.55 23.71 5.16 12.954 54.703 0.154 5.853 18.51 23.72 5.22 13.210 54.775 0.180 5.852 18.47 23.76 5.28 13.438 54.841 0.205 5.851 18.45 23.76 5.32 13.646 54.906 0.231 5.850 18.43 23.78 5.35 13.832 54.966 0.257 5.850 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.026 Accepted refinement result: 19.48 23.47 4.00 10.698 55.303 0.026 5.882 Individual atomic B min max mean iso aniso Overall: 18.89 127.31 49.71 7.45 4639 0 Protein: 18.89 121.45 49.41 7.43 4614 0 Other: 73.26 127.31 105.54 N/A 25 0 Chain A: 21.19 121.45 50.58 N/A 2307 0 Chain B: 18.89 127.31 48.86 N/A 2332 0 Histogram: Values Number of atoms 18.89 - 29.73 178 29.73 - 40.58 1367 40.58 - 51.42 1371 51.42 - 62.26 865 62.26 - 73.10 479 73.10 - 83.94 174 83.94 - 94.79 107 94.79 - 105.63 49 105.63 - 116.47 39 116.47 - 127.31 10 =========================== Idealize ADP of riding H ========================== r_work=0.1948 r_free=0.2347 r_work=0.1962 r_free=0.2350 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.29 - 25.82 A, n_refl.=18631 (all), 5.14 % free)------------| | | | r_work= 0.1962 r_free= 0.2350 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 5.886251 | | target function (ml) not normalized (work): 104027.716122 | | target function (ml) not normalized (free): 5739.639634 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1982 0.1962 0.2350 n_refl.: 18631 re-set all scales: r(all,work,free)=0.3896 0.3839 0.4886 n_refl.: 18631 remove outliers: r(all,work,free)=0.3896 0.3839 0.4886 n_refl.: 18631 overall B=-0.56 to atoms: r(all,work,free)=0.3875 0.3819 0.4862 n_refl.: 18631 bulk-solvent and scaling: r(all,work,free)=0.1979 0.1959 0.2345 n_refl.: 18631 remove outliers: r(all,work,free)=0.1978 0.1958 0.2345 n_refl.: 18630 ======================== 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 0.6135 38.914 26.490 0.086 0.909 0.411 14.999-13.060 75.00 83 1 0.5709 330.686 341.645 1.069 0.913 0.399 12.994-11.375 88.62 138 10 0.2239 596.419 587.667 1.307 0.910 0.399 11.369-9.901 99.22 240 13 0.1546 648.881 643.699 1.365 0.908 0.399 9.883-8.622 100.00 356 16 0.1502 655.074 649.520 1.303 0.906 0.401 8.618-7.507 99.82 546 20 0.1682 475.182 474.478 1.251 0.904 0.411 7.504-6.535 100.00 806 36 0.1995 373.409 363.838 1.166 0.900 0.411 6.532-5.692 100.00 1192 64 0.1912 372.426 362.758 1.130 0.895 0.391 5.690-4.954 99.95 1802 91 0.1824 390.422 379.889 1.050 0.888 0.372 4.954-4.314 100.00 2679 154 0.1624 444.610 436.049 1.105 0.879 0.352 4.314-3.756 100.00 4069 230 0.1848 383.514 372.701 1.167 0.867 0.272 3.756-3.291 98.98 5671 317 0.2451 276.562 260.520 1.150 0.852 0.162 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9580 b_overall=-1.9367 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1958 r_free=0.2345 After: r_work=0.1959 r_free=0.2345 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.111794 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.048552 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 0.1959 0.2345 0.0386 0.003 0.6 5.1 1.3 6.7 0 0.125 0.1953 0.2344 0.0391 0.003 0.6 5.1 1.3 6.7 0 0.250 0.1912 0.2327 0.0415 0.008 0.7 6.1 1.3 6.7 0 0.500 0.1846 0.2315 0.0469 0.014 1.2 9.7 1.3 7.3 0 1.000 0.1807 0.2334 0.0527 0.017 1.5 15.0 1.6 8.7 0 2.000 0.1783 0.2359 0.0576 0.021 2.0 20.5 1.8 10.1 0 3.000 0.1763 0.2370 0.0608 0.028 2.6 23.7 2.4 11.7 0 4.000 0.1753 0.2379 0.0627 0.031 2.8 24.0 2.7 11.9 0 5.000 0.1743 0.2364 0.0621 0.032 2.9 23.4 2.4 10.7 0 6.000 0.1735 0.2383 0.0648 0.036 3.2 26.4 2.7 12.1 1 7.000 0.1730 0.2384 0.0654 0.039 3.4 27.4 3.1 12.5 1 8.000 0.1728 0.2400 0.0672 0.043 3.7 33.3 3.8 16.5 2 9.000 0.1720 0.2396 0.0675 0.045 3.9 32.9 3.6 15.3 2 10.000 0.1813 0.2339 0.0526 0.016 1.7 15.7 1.6 8.3 0 1.556 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1959 0.2345 0.0386 0.003 0.6 5.1 1.3 6.7 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.59 23.45 3.86 9.110 54.509 0.049 5.887 21.88 24.07 2.18 8.204 58.059 0.001 5.957 21.44 23.91 2.47 8.739 56.968 0.006 5.947 19.54 23.39 3.84 9.098 54.291 0.024 5.884 19.39 23.36 3.97 9.352 54.246 0.049 5.878 19.21 23.33 4.12 9.783 54.044 0.073 5.872 19.03 23.29 4.26 10.334 53.894 0.097 5.864 18.87 23.31 4.44 11.146 53.963 0.121 5.857 18.82 23.33 4.51 11.311 54.059 0.146 5.856 18.78 23.35 4.58 11.477 54.151 0.170 5.855 18.73 23.39 4.66 11.704 54.264 0.194 5.854 18.70 23.40 4.71 11.905 54.360 0.218 5.853 18.68 23.41 4.74 12.037 54.417 0.243 5.853 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.097 Accepted refinement result: 19.03 23.29 4.26 10.334 53.894 0.097 5.864 Individual atomic B min max mean iso aniso Overall: 17.98 125.91 47.94 8.63 4639 0 Protein: 17.98 125.91 47.64 8.61 4614 0 Other: 67.83 121.75 103.32 N/A 25 0 Chain A: 19.61 125.91 48.82 N/A 2307 0 Chain B: 17.98 121.75 47.06 N/A 2332 0 Histogram: Values Number of atoms 17.98 - 28.77 332 28.77 - 39.56 1347 39.56 - 50.36 1296 50.36 - 61.15 815 61.15 - 71.94 448 71.94 - 82.74 180 82.74 - 93.53 117 93.53 - 104.32 53 104.32 - 115.12 32 115.12 - 125.91 19 =========================== Idealize ADP of riding H ========================== r_work=0.1903 r_free=0.2329 r_work=0.1899 r_free=0.2330 ----------X-ray data---------- |--(resolution: 3.29 - 25.82 A, n_refl.=18630 (all), 5.14 % free)------------| | | | r_work= 0.1899 r_free= 0.2330 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.862740 | | target function (ml) not normalized (work): 103606.339510 | | target function (ml) not normalized (free): 5734.160780 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.82 - 6.27 0.95 2573 119 0.1868 0.1837 6.067 6.1454| | 2: 6.27 - 4.99 1.00 2567 134 0.1809 0.2418 5.8698 5.9816| | 3: 4.99 - 4.36 1.00 2539 145 0.1569 0.1884 5.8867 6.0683| | 4: 4.36 - 3.96 1.00 2505 152 0.1702 0.2276 5.8869 6.0068| | 5: 3.96 - 3.68 1.00 2528 131 0.1950 0.2408 5.8293 5.9466| | 6: 3.68 - 3.46 1.00 2500 143 0.2189 0.2867 5.8037 5.9407| | 7: 3.46 - 3.29 0.98 2460 134 0.2633 0.3243 5.6868 5.8199| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2573 119 0.85 19.39 1.01 0.97 22347.48| | 2: 6.27 - 4.99 2567 134 0.86 19.93 1.00 0.94 22419.73| | 3: 4.99 - 4.36 2539 145 0.89 17.44 1.00 0.93 22394.80| | 4: 4.36 - 3.96 2505 152 0.88 18.26 1.02 0.94 22039.68| | 5: 3.96 - 3.68 2528 131 0.85 21.74 1.00 0.95 21967.96| | 6: 3.68 - 3.46 2500 143 0.82 25.30 1.03 0.90 20837.27| | 7: 3.46 - 3.29 2460 134 0.77 30.05 0.92 0.80 18880.64| |alpha: min = 0.80 max = 0.97 mean = 0.92| |beta: min = 18880.64 max = 22419.73 mean = 21570.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.68| |phase err.(test): min = 0.00 max = 88.90 mean = 21.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1921 0.1899 0.2330 n_refl.: 18630 re-set all scales: r(all,work,free)=0.3798 0.3741 0.4794 n_refl.: 18630 remove outliers: r(all,work,free)=0.3798 0.3741 0.4794 n_refl.: 18630 overall B=-0.24 to atoms: r(all,work,free)=0.3789 0.3733 0.4784 n_refl.: 18630 bulk-solvent and scaling: r(all,work,free)=0.1921 0.1899 0.2328 n_refl.: 18630 remove outliers: r(all,work,free)=0.1921 0.1899 0.2328 n_refl.: 18630 ======================== 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 0.6139 38.914 26.508 0.078 1.017 0.411 14.999-13.060 75.00 83 1 0.5701 330.686 345.682 0.970 1.021 0.398 12.994-11.375 88.62 138 10 0.2242 596.419 587.911 1.173 1.019 0.397 11.369-9.901 99.22 240 13 0.1545 648.881 643.703 1.228 1.017 0.399 9.883-8.622 100.00 356 16 0.1494 655.074 649.677 1.173 1.015 0.401 8.618-7.507 99.82 546 20 0.1689 475.182 474.818 1.119 1.012 0.401 7.504-6.535 100.00 806 36 0.1982 373.409 363.466 1.039 1.008 0.401 6.532-5.692 100.00 1192 64 0.1867 372.426 363.054 1.008 1.003 0.391 5.690-4.954 99.95 1802 91 0.1782 390.422 380.254 0.930 0.997 0.371 4.954-4.314 100.00 2679 154 0.1563 444.610 436.518 0.976 0.988 0.361 4.314-3.756 100.00 4069 230 0.1754 383.514 373.380 1.029 0.976 0.281 3.756-3.291 98.98 5671 317 0.2375 276.562 261.029 1.003 0.961 0.161 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.8529 ================= 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_weight: 0.2053 0.2492 0.016 1.720 22.4 134.8 45.5 0 0.000 1_xyzrec: 0.2218 0.2548 0.003 0.585 22.4 134.8 45.5 0 0.182 1_adp: 0.1944 0.2465 0.003 0.585 18.6 133.5 50.4 0 0.182 1_regHadp: 0.1921 0.2468 0.003 0.585 18.6 133.5 50.4 0 0.182 2_bss: 0.1919 0.2464 0.003 0.585 17.4 132.3 49.2 0 0.182 2_settarget: 0.1919 0.2464 0.003 0.585 17.4 132.3 49.2 0 0.182 2_updatecdl: 0.1919 0.2464 0.003 0.665 17.4 132.3 49.2 0 0.182 2_weight: 0.1919 0.2464 0.003 0.665 17.4 132.3 49.2 0 0.182 2_xyzrec: 0.1877 0.2395 0.003 0.569 17.4 132.3 49.2 0 0.229 2_adp: 0.1948 0.2347 0.003 0.569 18.9 127.3 49.7 0 0.229 2_regHadp: 0.1962 0.2350 0.003 0.569 18.9 127.3 49.7 0 0.229 3_bss: 0.1958 0.2345 0.003 0.569 18.3 126.8 49.2 0 0.229 3_settarget: 0.1958 0.2345 0.003 0.569 18.3 126.8 49.2 0 0.229 3_updatecdl: 0.1958 0.2345 0.003 0.598 18.3 126.8 49.2 0 0.229 3_setrh: 0.1959 0.2345 0.003 0.598 18.3 126.8 49.2 0 0.229 3_weight: 0.1959 0.2345 0.003 0.598 18.3 126.8 49.2 0 0.229 3_xyzrec: 0.1959 0.2345 0.003 0.574 18.3 126.8 49.2 0 0.229 3_adp: 0.1903 0.2329 0.003 0.574 18.0 125.9 47.9 0 0.229 3_regHadp: 0.1899 0.2330 0.003 0.574 18.0 125.9 47.9 0 0.229 end: 0.1899 0.2328 0.003 0.574 17.7 125.7 47.7 0 0.229 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2jcl_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2jcl_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 12.1000 Refinement macro-cycles (run) : 349.1900 Write final files (write_after_run_outputs) : 20.7600 Total : 382.0500 Total CPU time: 6.88 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:40 PDT -0700 (1716251740.72 s) Start R-work = 0.2053, R-free = 0.2492 Final R-work = 0.1899, R-free = 0.2328 =============================================================================== Job complete usr+sys time: 438.13 seconds wall clock time: 19 minutes 39.38 seconds (1179.38 seconds total)