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/1fp9.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fp9/1fp9.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fp9.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fp9.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 7982 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7982 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 38, 'TRANS': 461} Time building chain proxies: 2.45, per 1000 atoms: 0.31 Number of scatterers: 7982 At special positions: 0 Unit cell: (104.913, 52.445, 104.908, 90, 96.42, 90) Space group: C 1 2 1 (No. 5) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 707 8.00 N 703 7.00 C 2641 6.00 H 3920 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.11 Conformation dependent library (CDL) restraints added in 651.5 milliseconds 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 910 Time building geometry restraints manager: 4.10 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: 3919 1.15 - 1.32: 661 1.32 - 1.48: 1834 1.48 - 1.65: 1688 1.65 - 1.82: 21 Bond restraints: 8123 Sorted by residual: bond pdb=" NH1 ARG A 84 " pdb="HH11 ARG A 84 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG A 476 " pdb="HH22 ARG A 476 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N THR A 399 " pdb=" H THR A 399 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG A 279 " pdb="HH22 ARG A 279 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE1 TRP A 159 " pdb=" HE1 TRP A 159 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 8118 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.96: 414 106.96 - 113.72: 8838 113.72 - 120.48: 2791 120.48 - 127.23: 2538 127.23 - 133.99: 74 Bond angle restraints: 14655 Sorted by residual: angle pdb=" OE1 GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 122.60 112.79 9.81 1.00e+00 1.00e+00 9.63e+01 angle pdb=" N THR A 391 " pdb=" CA THR A 391 " pdb=" C THR A 391 " ideal model delta sigma weight residual 111.36 102.64 8.72 1.09e+00 8.42e-01 6.40e+01 angle pdb=" CG GLN A 27 " pdb=" CD GLN A 27 " pdb=" NE2 GLN A 27 " ideal model delta sigma weight residual 116.40 126.40 -10.00 1.50e+00 4.44e-01 4.44e+01 angle pdb=" N GLY A 21 " pdb=" CA GLY A 21 " pdb=" C GLY A 21 " ideal model delta sigma weight residual 114.90 124.70 -9.80 1.54e+00 4.22e-01 4.05e+01 angle pdb=" N GLY A 114 " pdb=" CA GLY A 114 " pdb=" C GLY A 114 " ideal model delta sigma weight residual 114.67 108.55 6.12 1.10e+00 8.26e-01 3.10e+01 ... (remaining 14650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.82: 3435 14.82 - 29.65: 193 29.65 - 44.47: 97 44.47 - 59.29: 91 59.29 - 74.12: 23 Dihedral angle restraints: 3839 sinusoidal: 2018 harmonic: 1821 Sorted by residual: dihedral pdb=" CG ARG A 84 " pdb=" CD ARG A 84 " pdb=" NE ARG A 84 " pdb=" CZ ARG A 84 " ideal model delta sinusoidal sigma weight residual 180.00 136.22 43.78 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" N GLU A 180 " pdb=" CA GLU A 180 " pdb=" CB GLU A 180 " pdb=" CG GLU A 180 " ideal model delta sinusoidal sigma weight residual 180.00 -129.53 -50.47 3 1.50e+01 4.44e-03 8.90e+00 dihedral pdb=" CA ARG A 296 " pdb=" CB ARG A 296 " pdb=" CG ARG A 296 " pdb=" CD ARG A 296 " ideal model delta sinusoidal sigma weight residual 60.00 109.93 -49.93 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 3836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 255 0.056 - 0.112: 233 0.112 - 0.168: 47 0.168 - 0.224: 23 0.224 - 0.280: 6 Chirality restraints: 564 Sorted by residual: chirality pdb=" CA PRO A 469 " pdb=" N PRO A 469 " pdb=" C PRO A 469 " pdb=" CB PRO A 469 " both_signs ideal model delta sigma weight residual False 2.72 2.44 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA VAL A 349 " pdb=" N VAL A 349 " pdb=" C VAL A 349 " pdb=" CB VAL A 349 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA VAL A 182 " pdb=" N VAL A 182 " pdb=" C VAL A 182 " pdb=" CB VAL A 182 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 561 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.051 2.00e-02 2.50e+03 2.06e-02 1.27e+01 pdb=" CG TYR A 141 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.051 2.00e-02 2.50e+03 1.96e-02 1.15e+01 pdb=" CG TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 192 " 0.052 2.00e-02 2.50e+03 1.93e-02 1.11e+01 pdb=" CG PHE A 192 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 192 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 192 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 192 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 192 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 192 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 192 " -0.018 2.00e-02 2.50e+03 pdb=" HD2 PHE A 192 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 192 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE A 192 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 192 " 0.017 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 1.28 - 1.94: 410 1.94 - 2.61: 9016 2.61 - 3.27: 26771 3.27 - 3.94: 35377 3.94 - 4.60: 53388 Nonbonded interactions: 124962 Sorted by model distance: nonbonded pdb=" O PRO A 215 " pdb="HH22 ARG A 279 " model vdw 1.279 1.850 nonbonded pdb=" HG2 ARG A 75 " pdb=" HD3 PRO A 76 " model vdw 1.320 2.440 nonbonded pdb=" HB3 GLN A 27 " pdb="HH21 ARG A 30 " model vdw 1.321 2.270 nonbonded pdb=" HG3 GLU A 334 " pdb=" HD3 PRO A 336 " model vdw 1.355 2.440 nonbonded pdb="HH22 ARG A 291 " pdb=" HE1 HIS A 394 " model vdw 1.358 2.100 ... (remaining 124957 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 11 15.96 2 O 707 7.97 1 N 703 6.97 1 C 2641 5.97 2 H 3920 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: 3920 of 7982 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 7982 n_use_u_iso = 7982 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 = 7982 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (7982 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 7982 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 = "1fp9_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3920 occupancy sum: 3920.00 (% of total atoms 49.11) Rotatable: count: 903 occupancy sum: 903.00 (% of total atoms 11.31) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 52.13 A, n_refl.=10132 (all), 10.01 % free)------------| | | | r_work= 0.4298 r_free= 0.5329 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.559026 | | target function (ml) not normalized (work): 50687.195951 | | target function (ml) not normalized (free): 5601.206097 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 52.13 - 5.93 0.97 1355 151 0.4603 0.4878 6.2066 6.1554| | 2: 5.93 - 4.71 0.96 1323 147 0.3547 0.4794 5.7546 5.7028| | 3: 4.71 - 4.11 0.96 1288 144 0.4084 0.5271 5.5696 5.4451| | 4: 4.11 - 3.74 0.96 1288 143 0.4551 0.5640 5.5142 5.619| | 5: 3.74 - 3.47 0.96 1281 142 0.4754 0.5967 5.4726 5.2661| | 6: 3.47 - 3.26 0.97 1282 142 0.4418 0.5860 5.2538 5.3947| | 7: 3.26 - 3.10 0.97 1301 145 0.4200 0.5257 5.1055 5.0481| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 52.13 - 5.93 1355 151 0.16 77.62 0.60 0.03 59863.03| | 2: 5.93 - 4.71 1323 147 0.58 46.10 1.30 0.17 26644.58| | 3: 4.71 - 4.11 1288 144 0.83 24.31 1.53 0.26 9202.68| | 4: 4.11 - 3.74 1288 143 0.82 25.71 1.67 0.28 8178.16| | 5: 3.74 - 3.47 1281 142 0.80 27.27 1.71 0.29 7239.08| | 6: 3.47 - 3.26 1282 142 0.77 30.37 1.60 0.27 6252.41| | 7: 3.26 - 3.10 1301 145 0.73 33.46 1.45 0.23 4577.34| |alpha: min = 0.03 max = 0.29 mean = 0.22| |beta: min = 4577.34 max = 59863.03 mean = 17766.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.67| |phase err.(work): min = 0.00 max = 90.00 mean = 38.16| |phase err.(test): min = 0.00 max = 89.99 mean = 38.55| |-----------------------------------------------------------------------------| ----------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 : 0.005 0.046 4203 Z= 0.321 Angle : 1.249 9.998 5718 Z= 0.861 Chirality : 0.082 0.280 564 Planarity : 0.005 0.040 750 Dihedral : 14.688 74.118 1524 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 28.95 Ramachandran Plot: Outliers : 1.81 % Allowed : 12.25 % Favored : 85.94 % Rotamer: Outliers : 2.24 % Allowed : 2.24 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.15 (0.30), residues: 498 helix: -4.21 (0.20), residues: 229 sheet: -1.62 (0.66), residues: 60 loop : -2.83 (0.38), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 279 TYR 0.043 0.007 TYR A 141 PHE 0.032 0.005 PHE A 192 TRP 0.033 0.006 TRP A 159 HIS 0.002 0.000 HIS A 384 Individual atomic B min max mean iso aniso Overall: 12.70 77.70 33.40 2.74 4062 0 Protein: 12.70 77.70 33.40 2.74 4062 0 Chain A: 12.70 77.70 33.40 N/A 4062 0 Histogram: Values Number of atoms 12.70 - 19.20 560 19.20 - 25.70 851 25.70 - 32.20 919 32.20 - 38.70 595 38.70 - 45.20 378 45.20 - 51.70 244 51.70 - 58.20 183 58.20 - 64.70 129 64.70 - 71.20 85 71.20 - 77.70 118 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10132 (all), 10.01 % free)------------| | | | r_work= 0.4298 r_free= 0.5329 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 5.559026 | | target function (ml) not normalized (work): 50687.195951 | | target function (ml) not normalized (free): 5601.206097 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4407 0.4298 0.5329 n_refl.: 10132 re-set all scales: r(all,work,free)=0.4407 0.4298 0.5329 n_refl.: 10132 remove outliers: r(all,work,free)=0.4160 0.4027 0.5329 n_refl.: 10127 overall B=3.30 to atoms: r(all,work,free)=0.4309 0.4168 0.5513 n_refl.: 10127 bulk-solvent and scaling: r(all,work,free)=0.2399 0.2398 0.2416 n_refl.: 10127 remove outliers: r(all,work,free)=0.2397 0.2397 0.2400 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2450 1487.728 1446.815 1.051 1.275 0.404 14.763-11.705 97.09 91 9 0.1774 1550.646 1541.206 0.930 1.260 0.398 11.688-9.266 96.82 191 22 0.1307 1812.092 1781.536 0.927 1.236 0.395 9.245-7.329 97.77 355 40 0.1746 1351.329 1327.100 0.906 1.200 0.392 7.324-5.801 97.35 727 80 0.2319 959.455 924.737 0.843 1.146 0.389 5.796-4.593 96.03 1414 157 0.2081 1149.827 1113.607 0.910 1.055 0.352 4.593-3.637 95.90 2818 313 0.2376 1063.229 1016.166 1.121 0.912 0.295 3.636-3.100 96.41 3429 381 0.2953 729.417 669.032 1.293 0.739 0.111 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.8055 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.771758 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.301602 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 0.1990 0.2734 0.0744 0.013 1.3 20.9 0.2 3.7 0 6.886 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.90 27.34 7.44 1.968 36.488 0.302 0.047 20.31 27.36 7.05 3.984 37.015 0.009 0.049 19.87 27.36 7.49 3.915 36.963 0.038 0.047 18.82 27.45 8.62 4.368 36.872 0.151 0.042 18.24 27.58 9.34 5.277 36.933 0.302 0.040 17.90 27.67 9.76 6.248 37.136 0.452 0.038 17.72 27.73 10.01 6.903 37.266 0.603 0.038 17.60 27.78 10.18 7.424 37.378 0.754 0.037 17.51 27.81 10.31 7.854 37.477 0.905 0.037 17.43 27.85 10.42 8.256 37.576 1.056 0.036 17.36 27.89 10.54 8.725 37.703 1.206 0.036 17.30 27.93 10.63 9.100 37.803 1.357 0.036 17.11 28.05 10.94 10.375 38.220 1.508 0.035 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.038 Accepted refinement result: 19.87 27.36 7.49 3.915 36.963 0.038 0.047 Individual atomic B min max mean iso aniso Overall: 18.84 82.28 37.64 2.50 4062 0 Protein: 18.84 82.28 37.64 2.50 4062 0 Chain A: 18.84 82.28 37.64 N/A 4062 0 Histogram: Values Number of atoms 18.84 - 25.18 376 25.18 - 31.53 1149 31.53 - 37.87 1031 37.87 - 44.22 562 44.22 - 50.56 369 50.56 - 56.90 197 56.90 - 63.25 151 63.25 - 69.59 88 69.59 - 75.93 78 75.93 - 82.28 61 =========================== Idealize ADP of riding H ========================== r_work=0.1987 r_free=0.2736 r_work=0.1986 r_free=0.2725 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.1986 r_free= 0.2725 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ls_wunit_k1) (work): 0.047268 | | target function (ls_wunit_k1) not normalized (work): 430.707019 | | target function (ls_wunit_k1) not normalized (free): 94.951970 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2060 0.1986 0.2725 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4213 0.4040 0.5537 n_refl.: 10125 remove outliers: r(all,work,free)=0.4213 0.4040 0.5537 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4213 0.4040 0.5537 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2056 0.1981 0.2735 n_refl.: 10125 remove outliers: r(all,work,free)=0.2056 0.1981 0.2735 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2135 812.052 791.308 1.156 1.218 0.408 14.763-11.705 97.09 91 9 0.1242 846.395 850.044 1.023 1.207 0.407 11.688-9.266 96.82 191 22 0.1075 989.100 971.725 0.991 1.187 0.400 9.245-7.329 97.77 355 40 0.1425 737.601 728.042 0.964 1.157 0.400 7.324-5.801 97.35 727 80 0.1904 523.703 513.480 0.896 1.112 0.400 5.796-4.593 96.03 1414 157 0.1717 627.614 618.914 0.949 1.037 0.370 4.593-3.637 95.90 2818 313 0.1954 580.346 568.900 1.138 0.917 0.280 3.636-3.100 96.41 3429 381 0.2471 398.140 377.743 1.315 0.773 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.5264 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.929785 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.082505 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 0.2211 0.2673 0.0462 0.003 0.5 4.0 0.0 2.5 0 0.125 0.2165 0.2685 0.0520 0.004 0.6 5.3 0.0 2.7 0 0.250 0.2101 0.2721 0.0619 0.006 0.8 8.8 0.0 3.5 0 0.500 0.2034 0.2782 0.0748 0.010 1.0 14.2 0.0 5.5 0 1.000 0.1952 0.2834 0.0881 0.018 1.5 23.9 0.2 7.5 0 2.000 0.1897 0.2871 0.0974 0.024 1.9 30.3 0.4 12.2 0 3.000 0.1864 0.2883 0.1019 0.029 2.3 34.7 0.8 14.0 0 4.000 0.1837 0.2911 0.1074 0.034 2.6 39.5 1.4 15.5 0 5.000 0.1810 0.2920 0.1110 0.039 2.8 42.5 1.8 17.2 0 6.000 0.1795 0.2945 0.1150 0.043 3.1 46.9 1.8 18.5 0 7.000 0.1774 0.2972 0.1197 0.047 3.3 51.3 2.6 19.0 0 8.000 0.1759 0.2992 0.1233 0.050 3.5 55.1 2.8 19.5 1 9.000 0.1747 0.3002 0.1256 0.054 3.7 59.0 3.6 20.4 2 10.000 0.1989 0.2810 0.0821 0.014 1.3 19.7 0.0 6.5 0 1.465 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2211 0.2673 0.0462 0.003 0.5 4.0 0.0 2.5 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.11 26.73 4.62 5.767 41.288 0.083 6.368 23.07 27.17 4.11 6.363 42.568 0.002 6.398 21.94 26.77 4.83 6.029 41.178 0.010 6.360 21.47 26.86 5.39 6.331 41.027 0.041 6.346 20.36 27.39 7.03 8.549 41.225 0.083 6.315 20.09 27.56 7.48 9.366 41.582 0.124 6.310 19.90 27.73 7.82 10.153 41.880 0.165 6.307 19.78 27.85 8.07 10.844 42.120 0.206 6.305 19.69 27.96 8.26 11.444 42.317 0.248 6.304 19.62 28.05 8.43 11.968 42.483 0.289 6.303 19.57 28.12 8.54 12.399 42.618 0.330 6.303 19.53 28.18 8.64 12.784 42.736 0.371 6.303 19.50 28.22 8.72 13.123 42.839 0.413 6.302 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.010 Accepted refinement result: 21.94 26.77 4.83 6.029 41.178 0.010 6.360 Individual atomic B min max mean iso aniso Overall: 15.72 83.14 37.42 2.57 4062 0 Protein: 15.72 83.14 37.42 2.57 4062 0 Chain A: 15.72 83.14 37.42 N/A 4062 0 Histogram: Values Number of atoms 15.72 - 22.46 110 22.46 - 29.21 961 29.21 - 35.95 1234 35.95 - 42.69 722 42.69 - 49.43 443 49.43 - 56.17 227 56.17 - 62.91 155 62.91 - 69.66 95 69.66 - 76.40 69 76.40 - 83.14 46 =========================== Idealize ADP of riding H ========================== r_work=0.2194 r_free=0.2677 r_work=0.2193 r_free=0.2678 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.2193 r_free= 0.2678 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ml) (work): 6.359175 | | target function (ml) not normalized (work): 57944.798680 | | target function (ml) not normalized (free): 6565.272307 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2242 0.2193 0.2678 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4265 0.4102 0.5544 n_refl.: 10125 remove outliers: r(all,work,free)=0.4265 0.4102 0.5544 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4265 0.4102 0.5544 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2274 0.2224 0.2715 n_refl.: 10125 remove outliers: r(all,work,free)=0.2274 0.2224 0.2715 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2074 812.052 809.062 1.445 1.021 0.410 14.763-11.705 97.09 91 9 0.1263 846.395 857.414 1.233 1.020 0.408 11.688-9.266 96.82 191 22 0.1101 989.100 983.444 1.184 1.016 0.407 9.245-7.329 97.77 355 40 0.1493 737.601 735.442 1.128 1.009 0.403 7.324-5.801 97.35 727 80 0.2085 523.703 513.904 1.009 0.999 0.400 5.796-4.593 96.03 1414 157 0.1885 627.614 614.182 0.990 0.983 0.400 4.593-3.637 95.90 2818 313 0.2257 580.346 558.299 1.052 0.955 0.290 3.636-3.100 96.41 3429 381 0.2798 398.140 367.982 1.053 0.925 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.9029 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2224 r_free=0.2715 After: r_work=0.2224 r_free=0.2714 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.059280 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.083437 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 0.2224 0.2716 0.0491 0.002 0.5 4.3 0.0 2.5 0 0.125 0.2219 0.2717 0.0498 0.003 0.5 4.1 0.0 2.5 0 0.250 0.2179 0.2723 0.0544 0.007 0.6 4.8 0.0 2.5 0 0.500 0.2069 0.2746 0.0677 0.015 1.3 11.7 0.0 2.2 0 1.000 0.1998 0.2834 0.0836 0.018 2.0 26.8 0.2 4.5 0 2.000 0.1977 0.2839 0.0861 0.020 2.1 26.2 0.2 5.5 0 3.000 0.1918 0.2883 0.0965 0.030 3.0 35.8 0.4 5.2 0 4.000 0.1924 0.2870 0.0946 0.028 2.7 33.5 0.4 8.5 0 5.000 0.1876 0.2957 0.1081 0.037 3.7 47.6 2.0 11.7 1 6.000 0.1863 0.2888 0.1026 0.042 3.7 40.0 0.8 6.0 0 7.000 0.1843 0.2960 0.1117 0.044 4.1 51.6 2.2 12.5 2 8.000 0.1833 0.2977 0.1144 0.047 4.3 56.1 2.8 14.2 3 9.000 0.1823 0.2990 0.1167 0.051 4.6 58.0 3.4 15.2 4 10.000 0.2027 0.2790 0.0763 0.016 1.7 18.5 0.2 3.0 0 1.530 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2219 0.2717 0.0498 0.003 0.5 4.1 0.0 2.5 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.19 27.17 4.98 5.746 41.073 0.083 6.370 23.58 27.82 4.23 6.293 42.630 0.003 6.415 22.19 27.18 5.00 5.788 41.044 0.010 6.371 21.73 27.29 5.56 6.226 40.835 0.042 6.356 20.63 27.86 7.24 8.516 40.719 0.083 6.328 20.36 28.07 7.71 9.318 41.106 0.125 6.323 20.19 28.24 8.05 10.070 41.414 0.167 6.321 20.07 28.38 8.31 10.748 41.662 0.209 6.319 19.99 28.50 8.51 11.345 41.866 0.250 6.319 19.93 28.60 8.67 11.848 42.032 0.292 6.318 19.89 28.69 8.80 12.296 42.175 0.334 6.318 19.85 28.75 8.90 12.692 42.299 0.375 6.318 19.83 28.80 8.98 13.036 42.405 0.417 6.318 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.010 Accepted refinement result: 22.19 27.18 5.00 5.788 41.044 0.010 6.371 Individual atomic B min max mean iso aniso Overall: 16.10 83.29 37.37 2.55 4062 0 Protein: 16.10 83.29 37.37 2.55 4062 0 Chain A: 16.10 83.29 37.37 N/A 4062 0 Histogram: Values Number of atoms 16.10 - 22.82 133 22.82 - 29.54 996 29.54 - 36.26 1242 36.26 - 42.98 674 42.98 - 49.69 449 49.69 - 56.41 216 56.41 - 63.13 154 63.13 - 69.85 90 69.85 - 76.57 68 76.57 - 83.29 40 =========================== Idealize ADP of riding H ========================== r_work=0.2219 r_free=0.2718 r_work=0.2219 r_free=0.2718 ----------X-ray data---------- |--(resolution: 3.10 - 52.13 A, n_refl.=10125 (all), 10.00 % free)------------| | | | r_work= 0.2219 r_free= 0.2718 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ml) (work): 6.370515 | | target function (ml) not normalized (work): 58048.131158 | | target function (ml) not normalized (free): 6577.119455 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 52.13 - 5.93 0.97 1352 151 0.1638 0.1959 6.3464 6.515| | 2: 5.93 - 4.71 0.96 1323 147 0.1905 0.2424 6.3991 6.5097| | 3: 4.71 - 4.11 0.96 1288 144 0.2084 0.2244 6.5128 6.5434| | 4: 4.11 - 3.74 0.96 1286 142 0.2287 0.3079 6.4629 6.7175| | 5: 3.74 - 3.47 0.96 1281 142 0.2694 0.3132 6.4553 6.4784| | 6: 3.47 - 3.26 0.97 1281 142 0.2630 0.3464 6.2914 6.5107| | 7: 3.26 - 3.10 0.97 1301 145 0.2990 0.3711 6.1288 6.1782| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 52.13 - 5.93 1352 151 0.88 17.73 0.99 0.97 55044.19| | 2: 5.93 - 4.71 1323 147 0.86 20.80 1.00 0.93 63853.11| | 3: 4.71 - 4.11 1288 144 0.86 21.78 1.02 0.90 69798.19| | 4: 4.11 - 3.74 1286 142 0.82 25.35 0.99 0.91 77481.61| | 5: 3.74 - 3.47 1281 142 0.78 29.23 1.06 0.92 75396.01| | 6: 3.47 - 3.26 1281 142 0.73 33.54 1.03 0.86 66310.61| | 7: 3.26 - 3.10 1301 145 0.71 35.57 0.90 0.71 45623.22| |alpha: min = 0.71 max = 0.97 mean = 0.89| |beta: min = 45623.22 max = 77481.61 mean = 64675.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.91 mean = 26.21| |phase err.(test): min = 0.00 max = 89.77 mean = 26.83| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2269 0.2219 0.2718 n_refl.: 10125 re-set all scales: r(all,work,free)=0.4262 0.4098 0.5543 n_refl.: 10125 remove outliers: r(all,work,free)=0.4262 0.4098 0.5543 n_refl.: 10125 overall B=0.00 to atoms: r(all,work,free)=0.4262 0.4098 0.5543 n_refl.: 10125 bulk-solvent and scaling: r(all,work,free)=0.2229 0.2180 0.2668 n_refl.: 10125 remove outliers: r(all,work,free)=0.2229 0.2180 0.2668 n_refl.: 10125 ======================== 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 52.125-14.829 89.91 87 11 0.2056 812.052 801.035 1.232 1.211 0.410 14.763-11.705 97.09 91 9 0.1292 846.395 849.422 1.064 1.199 0.409 11.688-9.266 96.82 191 22 0.1103 989.100 974.471 1.036 1.180 0.409 9.245-7.329 97.77 355 40 0.1472 737.601 729.726 1.004 1.151 0.408 7.324-5.801 97.35 727 80 0.2055 523.703 511.801 0.931 1.107 0.407 5.796-4.593 96.03 1414 157 0.1865 627.614 614.766 0.964 1.034 0.400 4.593-3.637 95.90 2818 313 0.2223 580.346 559.809 1.121 0.917 0.310 3.636-3.100 96.41 3429 381 0.2708 398.140 370.737 1.283 0.778 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.0557 ================= 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 : 0.4298 0.5329 0.005 1.249 12.7 77.7 33.4 0 0.000 1_bss: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_settarget: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_updatephipsi: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_weight: 0.2397 0.2400 0.005 1.249 16.0 81.0 36.7 0 0.000 1_xyzrec: 0.1990 0.2734 0.013 1.257 16.0 81.0 36.7 0 0.259 1_adp: 0.1987 0.2736 0.013 1.257 18.8 82.3 37.6 0 0.259 1_regHadp: 0.1986 0.2725 0.013 1.257 18.8 82.3 37.6 0 0.259 2_bss: 0.1981 0.2735 0.013 1.257 18.8 82.3 37.6 0 0.259 2_settarget: 0.1981 0.2735 0.013 1.257 18.8 82.3 37.6 0 0.259 2_updatephipsi: 0.1981 0.2735 0.013 1.257 18.8 82.3 37.6 0 0.259 2_updatecdl: 0.1981 0.2735 0.013 1.287 18.8 82.3 37.6 0 0.259 2_weight: 0.1981 0.2735 0.013 1.287 18.8 82.3 37.6 0 0.259 2_xyzrec: 0.2211 0.2673 0.003 0.524 18.8 82.3 37.6 0 0.243 2_adp: 0.2194 0.2677 0.003 0.524 15.7 83.1 37.4 0 0.243 2_regHadp: 0.2193 0.2678 0.003 0.524 15.7 83.1 37.4 0 0.243 3_bss: 0.2224 0.2715 0.003 0.524 15.7 83.1 37.4 0 0.243 3_settarget: 0.2224 0.2715 0.003 0.524 15.7 83.1 37.4 0 0.243 3_updatephipsi: 0.2224 0.2715 0.003 0.524 15.7 83.1 37.4 0 0.243 3_updatecdl: 0.2224 0.2715 0.003 0.544 15.7 83.1 37.4 0 0.243 3_setrh: 0.2224 0.2714 0.003 0.544 15.7 83.1 37.4 0 0.242 3_weight: 0.2224 0.2714 0.003 0.544 15.7 83.1 37.4 0 0.242 3_xyzrec: 0.2219 0.2717 0.003 0.516 15.7 83.1 37.4 0 0.243 3_adp: 0.2219 0.2718 0.003 0.516 16.1 83.3 37.4 0 0.243 3_regHadp: 0.2219 0.2718 0.003 0.516 16.1 83.3 37.4 0 0.243 end: 0.2180 0.2668 0.003 0.516 16.1 83.3 37.4 0 0.243 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1fp9_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1fp9_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 11.6900 Refinement macro-cycles (run) : 323.4200 Write final files (write_after_run_outputs) : 22.6900 Total : 357.8000 Total CPU time: 6.69 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:14 PDT -0700 (1716251714.14 s) Start R-work = 0.2397, R-free = 0.2400 Final R-work = 0.2180, R-free = 0.2668 =============================================================================== Job complete usr+sys time: 418.78 seconds wall clock time: 18 minutes 28.63 seconds (1108.63 seconds total)