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/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=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2a8z.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/2a8z.pdb" 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" } 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: 0.00s 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: 2.02, per 1000 atoms: 0.32 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: 3.25 Conformation dependent library (CDL) restraints added in 391.0 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Time building geometry restraints manager: 3.11 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.242945 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 0.2293 0.2492 0.0199 0.002 0.5 1.4 0.0 3.9 0 0.125 0.2257 0.2489 0.0232 0.002 0.5 2.1 0.0 3.6 0 0.250 0.2197 0.2490 0.0293 0.003 0.5 1.9 0.0 4.5 0 0.500 0.2124 0.2490 0.0366 0.004 0.6 2.9 0.0 4.2 0 1.000 0.2050 0.2498 0.0448 0.005 0.7 4.6 0.0 5.1 0 2.000 0.2011 0.2506 0.0495 0.007 0.8 6.1 0.0 4.5 0 3.000 0.1978 0.2517 0.0538 0.009 0.9 7.0 0.0 4.8 0 4.000 0.1955 0.2521 0.0566 0.010 1.0 8.3 0.0 5.7 0 5.000 0.1929 0.2528 0.0599 0.012 1.1 9.7 0.0 5.4 0 6.000 0.1918 0.2539 0.0622 0.013 1.2 11.0 0.0 6.3 0 7.000 0.1901 0.2552 0.0651 0.014 1.2 13.2 0.0 6.6 0 8.000 0.1884 0.2570 0.0686 0.015 1.3 13.1 0.0 6.9 0 9.000 0.1870 0.2563 0.0693 0.017 1.4 14.5 0.2 7.2 0 10.000 0.1923 0.2540 0.0617 0.012 1.1 10.5 0.0 6.0 0 6.621 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2293 0.2492 0.0199 0.002 0.5 1.4 0.0 3.9 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.93 24.92 1.99 0.478 47.025 0.238 0.063 22.90 24.84 1.94 1.377 47.069 0.007 0.062 22.41 24.77 2.36 1.586 47.075 0.030 0.060 21.65 24.68 3.03 2.750 47.126 0.119 0.055 20.60 24.79 4.18 5.792 47.615 0.238 0.050 20.32 24.86 4.55 6.934 47.892 0.356 0.049 20.13 24.93 4.80 7.766 48.104 0.475 0.048 20.01 24.99 4.98 8.393 48.270 0.594 0.047 19.86 25.07 5.21 9.195 48.504 0.713 0.046 19.80 25.13 5.33 9.600 48.612 0.832 0.046 19.54 25.30 5.76 11.204 49.109 0.950 0.045 19.46 25.36 5.90 11.730 49.264 1.069 0.045 19.41 25.41 6.01 12.200 49.403 1.188 0.044 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.119 Accepted refinement result: 21.65 24.68 3.03 2.750 47.126 0.119 0.055 Individual atomic B min max mean iso aniso Overall: 18.96 82.21 47.27 2.77 3245 0 Protein: 18.96 82.21 47.27 2.77 3245 0 Chain A: 18.96 82.21 47.27 N/A 3245 0 Histogram: Values Number of atoms 18.96 - 25.29 3 25.29 - 31.61 130 31.61 - 37.94 525 37.94 - 44.26 643 44.26 - 50.59 768 50.59 - 56.91 635 56.91 - 63.24 338 63.24 - 69.56 123 69.56 - 75.88 53 75.88 - 82.21 27 =========================== Idealize ADP of riding H ========================== r_work=0.2165 r_free=0.2468 r_work=0.2145 r_free=0.2464 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2145 r_free= 0.2464 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.054394 | | target function (ls_wunit_k1) not normalized (work): 431.892105 | | target function (ls_wunit_k1) not normalized (free): 30.157868 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2159 0.2145 0.2464 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3468 0.3450 0.3847 n_refl.: 8334 remove outliers: r(all,work,free)=0.3468 0.3450 0.3847 n_refl.: 8334 overall B=-6.92 to atoms: r(all,work,free)=0.3345 0.3329 0.3701 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2154 0.2140 0.2452 n_refl.: 8334 remove outliers: r(all,work,free)=0.2154 0.2140 0.2452 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 0.2104 717.043 694.172 1.135 0.995 0.335 10.272-9.295 91.74 94 6 0.2161 618.034 602.467 1.175 0.988 0.364 9.288-8.400 91.04 120 2 0.1881 635.763 627.211 1.137 0.992 0.366 8.393-7.595 91.58 165 9 0.1999 568.741 554.370 1.176 0.997 0.369 7.592-6.868 92.31 220 8 0.2397 457.963 441.915 1.085 0.991 0.372 6.866-6.210 92.28 299 12 0.2478 390.050 371.009 1.063 0.994 0.375 6.206-5.619 93.06 386 16 0.2365 380.564 366.770 1.047 0.995 0.378 5.613-5.076 93.02 551 22 0.2196 396.344 387.558 1.015 0.995 0.350 5.075-4.591 93.42 709 29 0.1905 438.306 430.460 1.011 0.998 0.334 4.589-4.150 93.88 986 42 0.1842 466.017 457.048 1.038 0.997 0.307 4.148-3.753 94.07 1277 72 0.2019 397.568 389.429 1.055 1.005 0.268 3.750-3.393 94.60 1743 97 0.2201 324.160 311.403 1.085 1.008 0.172 3.392-3.201 94.94 1294 75 0.2633 251.710 238.255 1.042 1.010 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=1.7031 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.680933 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.051104 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 0.2048 0.2472 0.0424 0.002 0.5 2.9 0.0 1.8 0 0.125 0.1990 0.2492 0.0501 0.004 0.5 2.7 0.0 2.4 0 0.250 0.1944 0.2512 0.0568 0.006 0.7 3.7 0.0 3.3 0 0.500 0.1885 0.2540 0.0655 0.010 1.0 6.7 0.0 4.5 0 1.000 0.1820 0.2604 0.0785 0.017 1.4 12.3 0.2 7.2 0 2.000 0.1781 0.2605 0.0825 0.023 1.8 16.4 0.7 8.7 0 3.000 0.1744 0.2610 0.0866 0.028 2.1 19.6 1.0 9.0 0 4.000 0.1718 0.2635 0.0918 0.033 2.3 22.5 1.2 10.2 0 5.000 0.1695 0.2634 0.0938 0.037 2.6 24.2 1.5 10.8 0 6.000 0.1676 0.2642 0.0966 0.041 2.8 25.5 1.7 11.7 0 7.000 0.1662 0.2638 0.0976 0.044 3.0 28.8 1.7 13.2 1 8.000 0.1649 0.2632 0.0984 0.047 3.2 33.1 2.0 13.5 1 9.000 0.1638 0.2645 0.1007 0.050 3.3 35.4 2.2 14.7 1 10.000 0.1859 0.2567 0.0708 0.013 1.1 8.8 0.2 5.7 0 1.340 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2048 0.2472 0.0424 0.002 0.5 2.9 0.0 1.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.48 24.72 4.24 6.993 45.057 0.051 5.968 22.13 25.08 2.95 7.342 46.076 0.002 6.017 21.05 24.77 3.72 7.118 45.093 0.006 5.980 20.12 24.83 4.70 7.290 45.048 0.026 5.955 19.07 25.05 5.98 8.638 45.399 0.051 5.931 18.87 25.20 6.33 9.090 45.517 0.077 5.929 18.72 25.31 6.59 9.514 45.680 0.102 5.928 18.64 25.40 6.76 9.783 45.781 0.128 5.928 18.55 25.51 6.96 10.179 45.940 0.153 5.928 18.51 25.55 7.04 10.354 46.003 0.179 5.928 18.44 25.64 7.20 10.761 46.158 0.204 5.928 18.41 25.68 7.27 10.943 46.223 0.230 5.928 18.38 25.72 7.34 11.161 46.301 0.256 5.928 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 21.05 24.77 3.72 7.118 45.093 0.006 5.980 Individual atomic B min max mean iso aniso Overall: 21.09 74.25 40.42 1.68 3245 0 Protein: 21.09 74.25 40.42 1.68 3245 0 Chain A: 21.09 74.25 40.42 N/A 3245 0 Histogram: Values Number of atoms 21.09 - 26.41 150 26.41 - 31.72 475 31.72 - 37.04 644 37.04 - 42.36 676 42.36 - 47.67 630 47.67 - 52.99 355 52.99 - 58.30 179 58.30 - 63.62 72 63.62 - 68.93 45 68.93 - 74.25 19 =========================== Idealize ADP of riding H ========================== r_work=0.2105 r_free=0.2477 r_work=0.2112 r_free=0.2479 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2112 r_free= 0.2479 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.982570 | | target function (ml) not normalized (work): 47501.607572 | | target function (ml) not normalized (free): 2394.300125 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2129 0.2112 0.2479 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3338 0.3318 0.3753 n_refl.: 8334 remove outliers: r(all,work,free)=0.3338 0.3318 0.3753 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3338 0.3318 0.3753 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2127 0.2110 0.2474 n_refl.: 8334 remove outliers: r(all,work,free)=0.2127 0.2110 0.2474 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 0.1992 717.043 697.733 1.138 0.998 0.340 10.272-9.295 91.74 94 6 0.2011 618.034 604.130 1.165 0.991 0.367 9.288-8.400 91.04 120 2 0.1794 635.763 631.058 1.139 0.995 0.370 8.393-7.595 91.58 165 9 0.1856 568.741 555.668 1.179 0.999 0.380 7.592-6.868 92.31 220 8 0.2292 457.963 444.216 1.089 0.993 0.382 6.866-6.210 92.28 299 12 0.2350 390.050 372.004 1.068 0.995 0.383 6.206-5.619 93.06 386 16 0.2267 380.564 365.174 1.042 0.996 0.380 5.613-5.076 93.02 551 22 0.2141 396.344 388.100 1.021 0.994 0.360 5.075-4.591 93.42 709 29 0.1898 438.306 430.123 1.014 0.997 0.340 4.589-4.150 93.88 986 42 0.1800 466.017 456.980 1.033 0.995 0.300 4.148-3.753 94.07 1277 72 0.2046 397.568 387.723 1.055 1.001 0.290 3.750-3.393 94.60 1743 97 0.2197 324.160 310.251 1.088 1.003 0.180 3.392-3.201 94.94 1294 75 0.2656 251.710 236.779 1.052 1.003 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=1.6480 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2110 r_free=0.2474 After: r_work=0.2111 r_free=0.2474 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.600138 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.048700 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 0.2111 0.2475 0.0364 0.002 0.5 2.9 0.0 1.8 0 0.125 0.2103 0.2473 0.0370 0.003 0.5 3.0 0.0 1.8 0 0.250 0.2037 0.2476 0.0440 0.009 0.7 4.3 0.0 2.1 0 0.500 0.1934 0.2503 0.0569 0.014 1.4 9.1 0.0 3.0 0 1.000 0.1886 0.2544 0.0658 0.018 1.6 13.2 0.2 5.4 0 2.000 0.1836 0.2552 0.0716 0.024 2.0 18.5 1.2 6.6 0 3.000 0.1805 0.2596 0.0791 0.029 2.4 25.0 1.5 7.8 0 4.000 0.1772 0.2612 0.0840 0.033 2.8 29.3 1.5 9.3 0 5.000 0.1748 0.2616 0.0868 0.036 3.0 32.5 1.7 10.2 0 6.000 0.1714 0.2626 0.0912 0.043 3.6 35.0 2.0 9.9 1 7.000 0.1699 0.2624 0.0925 0.046 3.8 35.8 2.0 9.6 1 8.000 0.1687 0.2633 0.0946 0.050 4.0 40.4 2.0 10.5 2 9.000 0.1675 0.2638 0.0963 0.053 4.3 42.2 2.0 11.1 4 10.000 0.1908 0.2524 0.0616 0.015 1.6 12.7 0.0 3.3 0 1.300 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2111 0.2475 0.0364 0.002 0.5 2.9 0.0 1.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.11 24.75 3.64 5.857 44.327 0.049 5.984 21.81 24.78 2.98 6.055 44.407 0.001 6.007 21.17 24.72 3.55 5.963 44.358 0.006 5.985 20.37 24.76 4.39 6.220 44.319 0.024 5.961 19.35 25.00 5.65 7.536 44.621 0.049 5.938 19.10 25.15 6.04 8.143 44.842 0.073 5.935 18.95 25.25 6.30 8.646 45.030 0.097 5.934 18.81 25.34 6.53 9.226 45.241 0.122 5.933 18.73 25.42 6.69 9.613 45.372 0.146 5.932 18.68 25.49 6.81 9.940 45.481 0.170 5.933 18.63 25.54 6.91 10.228 45.575 0.195 5.932 18.59 25.61 7.02 10.525 45.671 0.219 5.932 18.56 25.65 7.09 10.725 45.734 0.243 5.933 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.006 Accepted refinement result: 21.17 24.72 3.55 5.963 44.358 0.006 5.985 Individual atomic B min max mean iso aniso Overall: 20.75 72.31 40.48 1.66 3245 0 Protein: 20.75 72.31 40.48 1.66 3245 0 Chain A: 20.75 72.31 40.48 N/A 3245 0 Histogram: Values Number of atoms 20.75 - 25.91 63 25.91 - 31.06 406 31.06 - 36.22 682 36.22 - 41.37 698 41.37 - 46.53 669 46.53 - 51.69 367 51.69 - 56.84 199 56.84 - 62.00 81 62.00 - 67.16 55 67.16 - 72.31 25 =========================== Idealize ADP of riding H ========================== r_work=0.2117 r_free=0.2472 r_work=0.2117 r_free=0.2473 ----------X-ray data---------- |--(resolution: 3.20 - 12.00 A, n_refl.=8334 (all), 4.73 % free)-------------| | | | r_work= 0.2117 r_free= 0.2473 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.985223 | | target function (ml) not normalized (work): 47522.673085 | | target function (ml) not normalized (free): 2395.118273 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2066 0.2385 6.1432 6.2824| | 2: 4.56 - 3.65 0.94 2624 139 0.1959 0.2181 6.0075 6.0786| | 3: 3.65 - 3.20 0.95 2619 146 0.2438 0.2976 5.8002 5.9275| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 22.26 1.00 0.88 34292.03| | 2: 4.56 - 3.65 2624 139 0.85 21.33 1.00 0.88 27474.73| | 3: 3.65 - 3.20 2619 146 0.79 27.92 1.00 0.87 21938.08| |alpha: min = 0.87 max = 0.88 mean = 0.87| |beta: min = 21938.08 max = 34292.03 mean = 27964.12| |figures of merit: min = 0.00 max = 1.00 mean = 0.82| |phase err.(work): min = 0.00 max = 89.98 mean = 23.82| |phase err.(test): min = 0.00 max = 89.47 mean = 23.58| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2134 0.2117 0.2473 n_refl.: 8334 re-set all scales: r(all,work,free)=0.3348 0.3329 0.3759 n_refl.: 8334 remove outliers: r(all,work,free)=0.3348 0.3329 0.3759 n_refl.: 8334 overall B=0.00 to atoms: r(all,work,free)=0.3348 0.3329 0.3759 n_refl.: 8334 bulk-solvent and scaling: r(all,work,free)=0.2133 0.2117 0.2472 n_refl.: 8334 remove outliers: r(all,work,free)=0.2133 0.2117 0.2472 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 0.2003 717.043 698.496 1.136 0.999 0.340 10.272-9.295 91.74 94 6 0.2020 618.034 604.413 1.164 0.992 0.367 9.288-8.400 91.04 120 2 0.1801 635.763 631.300 1.138 0.995 0.370 8.393-7.595 91.58 165 9 0.1851 568.741 556.797 1.180 1.000 0.377 7.592-6.868 92.31 220 8 0.2315 457.963 443.833 1.090 0.994 0.383 6.866-6.210 92.28 299 12 0.2372 390.050 371.426 1.066 0.995 0.383 6.206-5.619 93.06 386 16 0.2276 380.564 364.925 1.043 0.996 0.383 5.613-5.076 93.02 551 22 0.2156 396.344 387.834 1.020 0.995 0.360 5.075-4.591 93.42 709 29 0.1905 438.306 430.157 1.016 0.997 0.340 4.589-4.150 93.88 986 42 0.1808 466.017 456.705 1.035 0.995 0.300 4.148-3.753 94.07 1277 72 0.2052 397.568 387.516 1.058 1.000 0.300 3.750-3.393 94.60 1743 97 0.2196 324.160 310.007 1.092 1.002 0.190 3.392-3.201 94.94 1294 75 0.2657 251.710 236.543 1.055 1.001 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=1.5341 ================= 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_updatephipsi: 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: 0.2293 0.2492 0.002 0.480 24.0 77.2 47.1 0 0.167 1_adp: 0.2165 0.2468 0.002 0.480 19.0 82.2 47.3 0 0.167 1_regHadp: 0.2145 0.2464 0.002 0.480 19.0 82.2 47.3 0 0.167 2_bss: 0.2140 0.2452 0.002 0.480 12.0 75.3 40.3 0 0.167 2_settarget: 0.2140 0.2452 0.002 0.480 12.0 75.3 40.3 0 0.167 2_updatephipsi: 0.2140 0.2452 0.002 0.480 12.0 75.3 40.3 0 0.167 2_updatecdl: 0.2140 0.2452 0.002 0.508 12.0 75.3 40.3 0 0.167 2_weight: 0.2140 0.2452 0.002 0.508 12.0 75.3 40.3 0 0.167 2_xyzrec: 0.2048 0.2472 0.002 0.468 12.0 75.3 40.3 0 0.202 2_adp: 0.2105 0.2477 0.002 0.468 21.1 74.3 40.4 0 0.202 2_regHadp: 0.2112 0.2479 0.002 0.468 21.1 74.3 40.4 0 0.202 3_bss: 0.2110 0.2474 0.002 0.468 21.1 74.3 40.4 0 0.202 3_settarget: 0.2110 0.2474 0.002 0.468 21.1 74.3 40.4 0 0.202 3_updatephipsi: 0.2110 0.2474 0.002 0.468 21.1 74.3 40.4 0 0.202 3_updatecdl: 0.2110 0.2474 0.002 0.477 21.1 74.3 40.4 0 0.202 3_setrh: 0.2111 0.2474 0.002 0.477 21.1 74.3 40.4 0 0.202 3_weight: 0.2111 0.2474 0.002 0.477 21.1 74.3 40.4 0 0.202 3_xyzrec: 0.2111 0.2475 0.002 0.472 21.1 74.3 40.4 0 0.202 3_adp: 0.2117 0.2472 0.002 0.472 20.7 72.3 40.5 0 0.202 3_regHadp: 0.2117 0.2473 0.002 0.472 20.7 72.3 40.5 0 0.202 end: 0.2117 0.2472 0.002 0.472 20.7 72.3 40.5 0 0.202 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2a8z_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/2a8z_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 9.3000 Refinement macro-cycles (run) : 237.8800 Write final files (write_after_run_outputs) : 24.4900 Total : 271.6700 Total CPU time: 5.16 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:33:57 PDT -0700 (1716251637.31 s) Start R-work = 0.2121, R-free = 0.2526 Final R-work = 0.2117, R-free = 0.2472 =============================================================================== Job complete usr+sys time: 330.59 seconds wall clock time: 17 minutes 16.83 seconds (1036.83 seconds total)