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/2a8z.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2a8z/2a8z.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/2a8z/2a8z.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/2a8z/2a8z.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2a8z.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2a8z.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: 6280 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 6280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 6280 Classifications: {'peptide': 404} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 388} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N THR A 217 " occ=0.50 ... (12 atoms not shown) pdb="HG23 THR A 217 " occ=0.00 residue: pdb=" N TYR A 381 " occ=0.60 ... (19 atoms not shown) pdb=" HH TYR A 381 " occ=0.00 Time building chain proxies: 1.22, per 1000 atoms: 0.19 Number of scatterers: 6280 At special positions: 0 Unit cell: (77.779, 77.779, 149.634, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 O 612 8.00 N 555 7.00 C 2066 6.00 H 3035 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 339 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 199.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Time building geometry restraints manager: 1.82 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: 3035 1.15 - 1.32: 568 1.32 - 1.49: 1477 1.49 - 1.66: 1273 1.66 - 1.84: 22 Bond restraints: 6375 Sorted by residual: bond pdb=" N THR A 403 " pdb=" H THR A 403 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 228 " pdb=" H VAL A 228 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 89 " pdb=" H MET A 89 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN A 276 " pdb="HE21 GLN A 276 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N SER A 232 " pdb=" H SER A 232 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6370 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.02: 217 106.02 - 113.10: 6605 113.10 - 120.19: 2340 120.19 - 127.27: 2193 127.27 - 134.35: 34 Bond angle restraints: 11389 Sorted by residual: angle pdb=" N ASP A 73 " pdb=" CA ASP A 73 " pdb=" C ASP A 73 " ideal model delta sigma weight residual 110.35 119.54 -9.19 1.40e+00 5.10e-01 4.31e+01 angle pdb=" N LEU A 49 " pdb=" CA LEU A 49 " pdb=" C LEU A 49 " ideal model delta sigma weight residual 114.75 107.29 7.46 1.26e+00 6.30e-01 3.50e+01 angle pdb=" N GLN A 47 " pdb=" CA GLN A 47 " pdb=" C GLN A 47 " ideal model delta sigma weight residual 113.50 107.61 5.89 1.23e+00 6.61e-01 2.30e+01 angle pdb=" N ASN A 320 " pdb=" CA ASN A 320 " pdb=" C ASN A 320 " ideal model delta sigma weight residual 108.69 116.64 -7.95 1.77e+00 3.19e-01 2.02e+01 angle pdb=" CA PHE A 404 " pdb=" C PHE A 404 " pdb=" O PHE A 404 " ideal model delta sigma weight residual 121.00 134.22 -13.22 3.00e+00 1.11e-01 1.94e+01 ... (remaining 11384 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 2647 16.41 - 32.81: 248 32.81 - 49.22: 116 49.22 - 65.63: 50 65.63 - 82.03: 9 Dihedral angle restraints: 3070 sinusoidal: 1572 harmonic: 1498 Sorted by residual: dihedral pdb=" CA PRO A 141 " pdb=" C PRO A 141 " pdb=" N ALA A 142 " pdb=" CA ALA A 142 " ideal model delta harmonic sigma weight residual 180.00 158.17 21.83 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ALA A 142 " pdb=" C ALA A 142 " pdb=" N PRO A 143 " pdb=" CA PRO A 143 " ideal model delta harmonic sigma weight residual 180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TRP A 277 " pdb=" C TRP A 277 " pdb=" N TYR A 278 " pdb=" CA TYR A 278 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 3067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 273 0.066 - 0.133: 106 0.133 - 0.199: 54 0.199 - 0.265: 12 0.265 - 0.332: 3 Chirality restraints: 448 Sorted by residual: chirality pdb=" CA TRP A 124 " pdb=" N TRP A 124 " pdb=" C TRP A 124 " pdb=" CB TRP A 124 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TRP A 249 " pdb=" N TRP A 249 " pdb=" C TRP A 249 " pdb=" CB TRP A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA PHE A 364 " pdb=" N PHE A 364 " pdb=" C PHE A 364 " pdb=" CB PHE A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 445 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 37 " -0.002 2.00e-02 2.50e+03 1.04e-02 3.24e+00 pdb=" CG PHE A 37 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 37 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 37 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 37 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 37 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 37 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 37 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 37 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE A 37 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 37 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 312 " -0.011 2.00e-02 2.50e+03 9.92e-03 2.95e+00 pdb=" CG PHE A 312 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 312 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 312 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 312 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 312 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE A 312 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 PHE A 312 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE A 312 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 124 " 0.013 2.00e-02 2.50e+03 7.84e-03 2.46e+00 pdb=" CG TRP A 124 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 124 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 124 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 124 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 124 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 124 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 124 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP A 124 " 0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 124 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 124 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 124 " 0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 124 " -0.004 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 0.96 - 1.69: 59 1.69 - 2.42: 2680 2.42 - 3.14: 20671 3.14 - 3.87: 30286 3.87 - 4.60: 45948 Warning: very small nonbonded interaction distances. Nonbonded interactions: 99644 Sorted by model distance: nonbonded pdb=" HG1 THR A 217 " pdb="HD22 ASN A 28 " model vdw sym.op. 0.960 2.100 -x+1,-x+y,-z+1/3 nonbonded pdb="HD22 ASN A 28 " pdb=" HG1 THR A 217 " model vdw sym.op. 0.960 2.100 -x+1,-x+y+1,-z+1/3 nonbonded pdb=" ND2 ASN A 28 " pdb=" HG1 THR A 217 " model vdw sym.op. 1.028 2.600 -x+1,-x+y+1,-z+1/3 nonbonded pdb=" HG1 THR A 217 " pdb=" ND2 ASN A 28 " model vdw sym.op. 1.028 2.600 -x+1,-x+y,-z+1/3 nonbonded pdb=" HB3 PHE A 149 " pdb=" HE3 MET A 175 " model vdw 1.257 2.440 ... (remaining 99639 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 12 15.96 2 O 612 7.97 1 N 555 6.97 1 C 2066 5.97 2 H 3035 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: 3035 of 6280 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6280 n_use_u_iso = 6280 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 = 6280 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6280 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 6280 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 = "2a8z_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3035 occupancy sum: 3035.00 (% of total atoms 48.91) Rotatable: count: 691 occupancy sum: 691.00 (% of total atoms 11.14) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.20 - 12.00 A, n_refl.=8335 (all), 4.73 % free)-------------| | | | r_work= 0.3129 r_free= 0.3533 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.773695 | | target function (ml) not normalized (work): 45848.910197 | | target function (ml) not normalized (free): 2283.639130 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 12.00 - 4.56 0.92 2698 109 0.3333 0.3782 5.9894 6.0293| | 2: 4.56 - 3.65 0.94 2624 139 0.2857 0.3234 5.8247 5.8395| | 3: 3.65 - 3.20 0.95 2619 146 0.3197 0.3629 5.5004 5.5806| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 12.00 - 4.56 2698 109 0.66 38.31 0.93 0.31 29425.10| | 2: 4.56 - 3.65 2624 139 0.72 33.68 1.09 0.35 19121.17| | 3: 3.65 - 3.20 2619 146 0.70 35.58 1.04 0.38 11437.88| |alpha: min = 0.31 max = 0.38 mean = 0.35| |beta: min = 11437.88 max = 29425.10 mean = 20087.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.69| |phase err.(work): min = 0.00 max = 89.93 mean = 35.88| |phase err.(test): min = 0.00 max = 88.66 mean = 35.84| |-----------------------------------------------------------------------------| ----------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 : 0.008 0.100 3340 Z= 0.493 Angle : 1.367 13.217 4535 Z= 0.896 Chirality : 0.089 0.332 448 Planarity : 0.003 0.010 602 Dihedral : 17.613 81.511 1181 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.71 % Favored : 91.54 % Rotamer: Outliers : 7.81 % Allowed : 9.31 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.33), residues: 402 helix: -2.91 (0.26), residues: 192 sheet: -2.64 (0.92), residues: 22 loop : -2.13 (0.39), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 337 TYR 0.020 0.003 TYR A 148 PHE 0.022 0.003 PHE A 312 TRP 0.021 0.003 TRP A 124 HIS 0.007 0.001 HIS A 302 Individual atomic B min max mean iso aniso Overall: 3.85 57.10 26.96 0.66 3245 0 Protein: 3.85 57.10 26.96 0.66 3245 0 Chain A: 3.85 57.10 26.96 N/A 3245 0 Histogram: Values Number of atoms 3.85 - 9.18 8 9.18 - 14.50 371 14.50 - 19.83 524 19.83 - 25.15 498 25.15 - 30.48 647 30.48 - 35.80 648 35.80 - 41.12 295 41.12 - 46.45 151 46.45 - 51.78 45 51.78 - 57.10 58 |-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: 3.20 - 12.00 A, n_refl.=8335 (all), 4.73 % free)-------------| | | | r_work= 0.3129 r_free= 0.3533 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 5.773695 | | target function (ml) not normalized (work): 45848.910197 | | target function (ml) not normalized (free): 2283.639130 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3148 0.3129 0.3533 n_refl.: 8335 re-set all scales: r(all,work,free)=0.3148 0.3129 0.3533 n_refl.: 8335 remove outliers: r(all,work,free)=0.3147 0.3129 0.3533 n_refl.: 8334 overall B=20.11 to atoms: r(all,work,free)=0.3412 0.3391 0.3856 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2140 0.2121 0.2526 n_refl.: 8334 remove outliers: r(all,work,free)=0.2140 0.2121 0.2526 n_refl.: 8334 ======================== 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 11.998-10.364 91.74 96 4 0.2061 1018.156 981.806 1.016 0.997 0.326 10.272-9.295 90.91 94 6 0.2047 877.570 847.545 1.057 0.990 0.359 9.288-8.400 90.37 120 2 0.1824 902.743 893.544 1.038 0.994 0.356 8.393-7.595 91.10 165 9 0.1960 807.576 781.668 1.078 0.999 0.358 7.592-6.868 91.57 220 8 0.2401 650.279 625.385 1.016 0.993 0.373 6.866-6.210 91.74 299 12 0.2710 553.846 521.628 1.012 0.995 0.366 6.206-5.619 92.63 386 16 0.2364 540.376 514.119 0.988 0.997 0.350 5.613-5.076 92.87 551 22 0.2135 562.783 547.919 0.993 0.996 0.335 5.075-4.591 93.18 709 29 0.1919 622.367 608.134 0.994 0.999 0.298 4.589-4.150 93.71 986 42 0.1839 661.715 646.053 1.033 0.998 0.261 4.148-3.753 93.94 1277 72 0.2027 564.522 549.387 1.068 1.005 0.194 3.750-3.393 94.50 1743 97 0.2146 460.286 441.696 1.126 1.007 0.141 3.392-3.201 94.81 1294 75 0.2541 357.412 335.983 1.120 1.008 0.057 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-5.6730 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.334248 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237597 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 0.2349 0.2530 0.0181 0.002 0.4 1.9 0.0 3.0 0 0.125 0.2265 0.2489 0.0224 0.002 0.5 1.9 0.0 3.9 0 0.250 0.2209 0.2502 0.0293 0.003 0.5 1.8 0.0 3.6 0 0.500 0.2127 0.2518 0.0390 0.003 0.5 2.9 0.0 3.9 0 1.000 0.2045 0.2519 0.0474 0.005 0.7 4.3 0.2 4.5 0 2.000 0.2002 0.2517 0.0516 0.007 0.8 5.6 0.2 4.5 0 3.000 0.1969 0.2533 0.0564 0.008 0.9 8.1 0.7 5.1 0 4.000 0.1949 0.2537 0.0588 0.010 1.0 9.2 1.0 4.8 0 5.000 0.1927 0.2548 0.0621 0.011 1.1 11.0 1.2 5.1 0 6.000 0.1909 0.2563 0.0655 0.013 1.2 12.7 1.2 6.0 0 7.000 0.1890 0.2567 0.0677 0.014 1.2 13.9 1.7 6.3 0 8.000 0.1875 0.2577 0.0702 0.015 1.3 14.6 1.7 7.2 0 9.000 0.1862 0.2560 0.0698 0.016 1.4 16.1 1.7 7.8 0 10.000 0.1916 0.2555 0.0639 0.012 1.1 12.1 1.2 6.0 0 6.667 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2349 0.2530 0.0181 0.002 0.4 1.9 0.0 3.0 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.49 25.30 1.81 0.478 47.025 0.238 0.065 23.44 25.25 1.81 1.377 47.073 0.007 0.065 22.96 25.14 2.19 1.596 47.085 0.030 0.062 22.13 25.10 2.97 2.935 47.178 0.119 0.058 21.14 25.33 4.19 5.824 47.661 0.238 0.052 20.81 25.42 4.61 7.087 47.995 0.356 0.051 20.63 25.49 4.86 7.926 48.220 0.475 0.050 20.44 25.56 5.12 8.833 48.492 0.594 0.049 20.35 25.62 5.26 9.350 48.633 0.713 0.048 20.04 25.79 5.75 11.014 49.181 0.832 0.047 19.96 25.87 5.91 11.551 49.337 0.950 0.047 19.86 25.98 6.12 12.300 49.574 1.069 0.046 19.78 26.06 6.28 12.882 49.754 1.188 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: 0.119 Accepted refinement result: 22.13 25.10 2.97 2.935 47.178 0.119 0.058 Individual atomic B min max mean iso aniso Overall: 18.96 83.26 47.37 2.93 3245 0 Protein: 18.96 83.26 47.37 2.93 3245 0 Chain A: 18.96 83.26 47.37 N/A 3245 0 Histogram: Values Number of atoms 18.96 - 25.39 4 25.39 - 31.82 136 31.82 - 38.25 527 38.25 - 44.68 655 44.68 - 51.11 800 51.11 - 57.54 627 57.54 - 63.97 309 63.97 - 70.40 115 70.40 - 76.83 56 76.83 - 83.26 16 =========================== Idealize ADP of riding H ========================== r_work=0.2213 r_free=0.2510 r_work=0.2193 r_free=0.2508 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2193 r_free= 0.2508 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.056423 | | target function (ls_wunit_k1) not normalized (work): 448.001439 | | target function (ls_wunit_k1) not normalized (free): 30.560592 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2207 0.2193 0.2508 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3515 0.3499 0.3857 n_refl.: 8334 remove outliers: r(all,work,free)=0.3515 0.3499 0.3857 n_refl.: 8334 overall B=-6.74 to atoms: r(all,work,free)=0.3397 0.3382 0.3710 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2201 0.2187 0.2506 n_refl.: 8334 remove outliers: r(all,work,free)=0.2201 0.2187 0.2506 n_refl.: 8334 ======================== 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 11.998-10.364 92.59 96 4 0.2044 717.931 698.006 1.146 0.995 0.335 10.272-9.295 91.74 94 6 0.2165 618.800 601.528 1.174 0.989 0.355 9.288-8.400 91.04 120 2 0.1900 636.550 626.265 1.133 0.992 0.361 8.393-7.595 91.58 165 9 0.1990 569.445 556.406 1.178 0.996 0.363 7.592-6.868 92.31 220 8 0.2360 458.531 444.509 1.092 0.991 0.371 6.866-6.210 92.28 299 12 0.2491 390.533 371.312 1.066 0.993 0.371 6.206-5.619 93.06 386 16 0.2392 381.035 367.132 1.046 0.995 0.367 5.613-5.076 93.02 551 22 0.2254 396.835 389.097 1.017 0.994 0.350 5.075-4.591 93.42 709 29 0.1940 438.849 430.490 1.011 0.997 0.333 4.589-4.150 93.88 986 42 0.1886 466.595 458.017 1.038 0.997 0.317 4.148-3.753 94.07 1277 72 0.2077 398.061 389.849 1.054 1.005 0.272 3.750-3.393 94.60 1743 97 0.2299 324.561 311.007 1.086 1.008 0.183 3.392-3.201 94.94 1294 75 0.2681 252.022 238.557 1.046 1.010 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=1.6599 ============================ 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 = 2.805321 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.052700 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 0.2044 0.2479 0.0434 0.002 0.5 1.8 0.0 2.4 0 0.125 0.1991 0.2491 0.0500 0.003 0.5 3.7 0.0 2.4 0 0.250 0.1941 0.2504 0.0563 0.006 0.7 5.1 0.5 3.3 0 0.500 0.1889 0.2546 0.0657 0.010 0.9 6.8 1.2 4.5 0 1.000 0.1834 0.2631 0.0796 0.016 1.4 12.7 1.5 5.7 0 2.000 0.1792 0.2654 0.0862 0.022 1.7 17.2 2.0 8.1 0 3.000 0.1754 0.2664 0.0910 0.027 2.0 20.9 2.5 8.1 0 4.000 0.1731 0.2658 0.0926 0.031 2.3 21.8 3.0 9.0 0 5.000 0.1707 0.2669 0.0963 0.035 2.5 26.0 3.7 10.2 0 6.000 0.1690 0.2673 0.0982 0.038 2.7 28.7 4.0 11.7 0 7.000 0.1674 0.2678 0.1004 0.042 2.9 28.7 3.7 10.5 0 8.000 0.1664 0.2678 0.1014 0.045 3.1 31.2 4.2 14.7 1 9.000 0.1650 0.2673 0.1022 0.048 3.2 29.9 3.7 11.7 1 10.000 0.1863 0.2579 0.0716 0.012 1.1 8.8 1.5 4.8 0 1.403 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2044 0.2479 0.0434 0.002 0.5 1.8 0.0 2.4 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.44 24.79 4.34 7.037 45.323 0.053 5.969 22.13 25.35 3.22 7.371 46.284 0.002 6.021 21.02 24.88 3.86 7.137 45.329 0.007 5.983 20.11 24.92 4.81 7.355 45.274 0.026 5.958 19.37 25.02 5.65 8.220 45.336 0.053 5.941 18.98 25.26 6.28 9.053 45.607 0.079 5.935 18.83 25.35 6.52 9.460 45.779 0.105 5.934 18.70 25.48 6.78 9.916 45.976 0.132 5.934 18.63 25.54 6.91 10.213 46.096 0.158 5.933 18.58 25.62 7.04 10.476 46.200 0.184 5.934 18.52 25.70 7.18 10.779 46.318 0.211 5.934 18.50 25.73 7.22 10.900 46.362 0.237 5.934 18.47 25.77 7.30 11.098 46.435 0.263 5.934 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.007 Accepted refinement result: 21.02 24.88 3.86 7.137 45.329 0.007 5.983 Individual atomic B min max mean iso aniso Overall: 20.98 74.73 40.64 1.74 3245 0 Protein: 20.98 74.73 40.64 1.74 3245 0 Chain A: 20.98 74.73 40.64 N/A 3245 0 Histogram: Values Number of atoms 20.98 - 26.36 147 26.36 - 31.73 464 31.73 - 37.11 650 37.11 - 42.48 680 42.48 - 47.85 625 47.85 - 53.23 367 53.23 - 58.60 177 58.60 - 63.98 70 63.98 - 69.35 46 69.35 - 74.73 19 =========================== Idealize ADP of riding H ========================== r_work=0.2102 r_free=0.2488 r_work=0.2109 r_free=0.2492 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2109 r_free= 0.2492 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.985734 | | target function (ml) not normalized (work): 47526.729897 | | target function (ml) not normalized (free): 2394.106453 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2127 0.2109 0.2492 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3342 0.3323 0.3738 n_refl.: 8334 remove outliers: r(all,work,free)=0.3342 0.3323 0.3738 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3342 0.3323 0.3738 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2124 0.2106 0.2498 n_refl.: 8334 remove outliers: r(all,work,free)=0.2124 0.2106 0.2498 n_refl.: 8334 ======================== 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 11.998-10.364 92.59 96 4 0.1993 717.931 696.568 1.107 0.999 0.340 10.272-9.295 91.74 94 6 0.1983 618.800 605.601 1.134 0.992 0.365 9.288-8.400 91.04 120 2 0.1761 636.550 631.035 1.103 0.995 0.368 8.393-7.595 91.58 165 9 0.1839 569.445 557.335 1.138 1.000 0.369 7.592-6.868 92.31 220 8 0.2308 458.531 444.573 1.056 0.994 0.370 6.866-6.210 92.28 299 12 0.2394 390.533 371.779 1.035 0.995 0.376 6.206-5.619 93.06 386 16 0.2289 381.035 364.827 1.015 0.996 0.377 5.613-5.076 93.02 551 22 0.2133 396.835 389.278 0.988 0.995 0.350 5.075-4.591 93.42 709 29 0.1910 438.849 430.353 0.983 0.997 0.330 4.589-4.150 93.88 986 42 0.1796 466.595 457.417 1.007 0.995 0.305 4.148-3.753 94.07 1277 72 0.2040 398.061 387.876 1.028 1.001 0.300 3.750-3.393 94.60 1743 97 0.2194 324.561 310.657 1.062 1.002 0.190 3.392-3.201 94.94 1294 75 0.2620 252.022 237.674 1.028 1.002 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.2362 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2106 r_free=0.2498 After: r_work=0.2107 r_free=0.2498 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.678954 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.050439 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 0.2107 0.2501 0.0394 0.002 0.5 2.1 0.0 2.4 0 0.125 0.2099 0.2496 0.0398 0.003 0.5 1.9 0.0 2.4 0 0.250 0.2044 0.2506 0.0463 0.008 0.7 3.5 0.0 2.7 0 0.500 0.1938 0.2517 0.0579 0.014 1.4 8.9 0.5 3.6 0 1.000 0.1891 0.2547 0.0656 0.018 1.7 15.0 1.2 4.8 0 2.000 0.1845 0.2560 0.0716 0.023 2.0 17.2 1.7 6.3 0 3.000 0.1815 0.2576 0.0761 0.026 2.2 22.0 2.0 7.2 0 4.000 0.1777 0.2616 0.0838 0.031 2.7 29.9 2.5 9.0 0 5.000 0.1742 0.2614 0.0872 0.038 3.3 34.9 2.7 9.6 0 6.000 0.1738 0.2624 0.0887 0.040 3.2 35.0 3.0 10.2 0 7.000 0.1702 0.2631 0.0929 0.045 3.7 38.7 3.7 10.2 1 8.000 0.1687 0.2628 0.0941 0.049 3.9 40.8 3.7 10.8 3 9.000 0.1679 0.2650 0.0971 0.051 4.1 43.0 4.0 12.9 4 10.000 0.1919 0.2537 0.0618 0.014 1.5 12.1 1.0 3.6 0 1.339 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2099 0.2496 0.0398 0.003 0.5 1.9 0.0 2.4 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.99 24.96 3.98 5.899 44.576 0.050 5.985 21.68 24.96 3.28 6.051 44.619 0.002 6.008 21.00 24.97 3.97 5.925 44.569 0.006 5.985 20.38 25.00 4.62 6.225 44.531 0.025 5.966 19.34 25.22 5.88 7.594 44.773 0.050 5.944 19.10 25.37 6.27 8.186 45.003 0.076 5.941 18.92 25.49 6.56 8.766 45.234 0.101 5.940 18.82 25.56 6.75 9.225 45.406 0.126 5.939 18.75 25.64 6.89 9.574 45.530 0.151 5.939 18.70 25.70 7.01 9.890 45.640 0.177 5.939 18.63 25.78 7.15 10.314 45.782 0.202 5.939 18.61 25.83 7.22 10.515 45.848 0.227 5.939 18.57 25.87 7.30 10.780 45.934 0.252 5.939 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.002 Accepted refinement result: 21.68 24.96 3.28 6.051 44.619 0.002 6.008 Individual atomic B min max mean iso aniso Overall: 24.42 69.73 40.72 0.88 3245 0 Protein: 24.42 69.73 40.72 0.88 3245 0 Chain A: 24.42 69.73 40.72 N/A 3245 0 Histogram: Values Number of atoms 24.42 - 28.95 248 28.95 - 33.48 515 33.48 - 38.01 575 38.01 - 42.54 612 42.54 - 47.07 601 47.07 - 51.60 336 51.60 - 56.13 192 56.13 - 60.66 71 60.66 - 65.20 54 65.20 - 69.73 41 =========================== Idealize ADP of riding H ========================== r_work=0.2168 r_free=0.2496 r_work=0.2174 r_free=0.2496 ----------X-ray data---------- |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2174 r_free= 0.2496 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 6.009769 | | target function (ml) not normalized (work): 47717.562324 | | target function (ml) not normalized (free): 2396.029990 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 12.00 - 4.56 0.92 2697 109 0.2103 0.2493 6.1646 6.3042| | 2: 4.56 - 3.65 0.94 2624 139 0.2014 0.2162 6.0352 6.0754| | 3: 3.65 - 3.20 0.95 2619 146 0.2530 0.2952 5.8249 5.9205| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 12.00 - 4.56 2697 109 0.83 23.05 1.00 0.90 36573.07| | 2: 4.56 - 3.65 2624 139 0.85 21.65 1.00 0.90 28257.21| | 3: 3.65 - 3.20 2619 146 0.79 27.79 1.00 0.89 21862.03| |alpha: min = 0.89 max = 0.90 mean = 0.90| |beta: min = 21862.03 max = 36573.07 mean = 28972.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.94 mean = 24.15| |phase err.(test): min = 0.00 max = 87.33 mean = 23.92| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2189 0.2174 0.2496 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3385 0.3367 0.3749 n_refl.: 8334 remove outliers: r(all,work,free)=0.3385 0.3367 0.3749 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3385 0.3367 0.3749 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2189 0.2174 0.2493 n_refl.: 8334 remove outliers: r(all,work,free)=0.2189 0.2174 0.2493 n_refl.: 8334 ======================== 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 11.998-10.364 92.59 96 4 0.2022 717.931 697.903 1.089 0.997 0.330 10.272-9.295 91.74 94 6 0.2009 618.800 605.322 1.129 0.990 0.365 9.288-8.400 91.04 120 2 0.1772 636.550 631.248 1.107 0.994 0.373 8.393-7.595 91.58 165 9 0.1855 569.445 556.480 1.138 0.998 0.376 7.592-6.868 92.31 220 8 0.2346 458.531 443.542 1.062 0.993 0.385 6.866-6.210 92.28 299 12 0.2442 390.533 370.406 1.034 0.994 0.385 6.206-5.619 93.06 386 16 0.2330 381.035 364.643 1.014 0.995 0.384 5.613-5.076 93.02 551 22 0.2196 396.835 388.537 0.985 0.994 0.350 5.075-4.591 93.42 709 29 0.1961 438.849 430.130 0.985 0.997 0.340 4.589-4.150 93.88 986 42 0.1854 466.595 457.012 1.007 0.995 0.305 4.148-3.753 94.07 1277 72 0.2114 398.061 387.279 1.028 1.002 0.300 3.750-3.393 94.60 1743 97 0.2289 324.561 309.814 1.061 1.003 0.190 3.392-3.201 94.94 1294 75 0.2737 252.022 236.302 1.022 1.004 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=1.2994 ================= 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 : 0.3129 0.3533 0.008 1.367 3.9 57.1 27.0 0 0.000 1_bss: 0.2121 0.2526 0.008 1.367 24.0 77.2 47.1 0 0.000 1_settarget: 0.2121 0.2526 0.008 1.367 24.0 77.2 47.1 0 0.000 1_weight: 0.2121 0.2526 0.008 1.367 24.0 77.2 47.1 0 0.000 1_xyzrec: 0.2349 0.2530 0.002 0.444 24.0 77.2 47.1 0 0.198 1_adp: 0.2213 0.2510 0.002 0.444 19.0 83.3 47.4 0 0.198 1_regHadp: 0.2193 0.2508 0.002 0.444 19.0 83.3 47.4 0 0.198 2_bss: 0.2187 0.2506 0.002 0.444 12.2 76.5 40.6 0 0.198 2_settarget: 0.2187 0.2506 0.002 0.444 12.2 76.5 40.6 0 0.198 2_updatecdl: 0.2187 0.2506 0.002 0.526 12.2 76.5 40.6 0 0.198 2_weight: 0.2187 0.2506 0.002 0.526 12.2 76.5 40.6 0 0.198 2_xyzrec: 0.2044 0.2479 0.002 0.451 12.2 76.5 40.6 0 0.195 2_adp: 0.2102 0.2488 0.002 0.451 21.0 74.7 40.6 0 0.195 2_regHadp: 0.2109 0.2492 0.002 0.451 21.0 74.7 40.6 0 0.195 3_bss: 0.2106 0.2498 0.002 0.451 21.0 74.7 40.6 0 0.195 3_settarget: 0.2106 0.2498 0.002 0.451 21.0 74.7 40.6 0 0.195 3_updatecdl: 0.2106 0.2498 0.002 0.477 21.0 74.7 40.6 0 0.195 3_setrh: 0.2107 0.2498 0.002 0.477 21.0 74.7 40.6 0 0.195 3_weight: 0.2107 0.2498 0.002 0.477 21.0 74.7 40.6 0 0.195 3_xyzrec: 0.2099 0.2496 0.003 0.466 21.0 74.7 40.6 0 0.195 3_adp: 0.2168 0.2496 0.003 0.466 24.4 69.7 40.7 0 0.195 3_regHadp: 0.2174 0.2496 0.003 0.466 24.4 69.7 40.7 0 0.195 end: 0.2174 0.2493 0.003 0.466 24.4 69.7 40.7 0 0.195 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2a8z_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/2a8z_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 8.5600 Refinement macro-cycles (run) : 227.6600 Write final files (write_after_run_outputs) : 23.3100 Total : 259.5300 Total CPU time: 4.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:32:19 PDT -0700 (1716251539.44 s) Start R-work = 0.2121, R-free = 0.2526 Final R-work = 0.2174, R-free = 0.2493 =============================================================================== Job complete usr+sys time: 306.78 seconds wall clock time: 16 minutes 22.85 seconds (982.85 seconds total)