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/1fb5.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.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/1fb5/1fb5.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1fb5/1fb5.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1fb5.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 Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 5100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 5082 Classifications: {'peptide': 320} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 306} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Classifications: {'peptide': 1} Modifications used: {'NH3': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.21 Number of scatterers: 5100 At special positions: 0 Unit cell: (184.7, 184.7, 184.7, 90, 90, 90) Space group: P 43 3 2 (No. 212) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 11 16.00 O 476 8.00 N 427 7.00 C 1617 6.00 H 2569 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: 1.33 Conformation dependent library (CDL) restraints added in 156.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 602 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 565 1.05 - 1.25: 2357 1.25 - 1.44: 743 1.44 - 1.64: 1466 1.64 - 1.83: 20 Bond restraints: 5151 Sorted by residual: bond pdb=" NH2 ARG A 94 " pdb="HH22 ARG A 94 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" ND1 HIS A 117 " pdb=" HD1 HIS A 117 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA A 253 " pdb=" H ALA A 253 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 HIS A 168 " pdb=" HE2 HIS A 168 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LYS A 275 " pdb=" H LYS A 275 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 5146 not shown) Histogram of bond angle deviations from ideal: 98.23 - 105.38: 128 105.38 - 112.52: 5958 112.52 - 119.66: 1333 119.66 - 126.80: 1893 126.80 - 133.95: 34 Bond angle restraints: 9346 Sorted by residual: angle pdb=" N ALA A 280 " pdb=" CA ALA A 280 " pdb=" C ALA A 280 " ideal model delta sigma weight residual 113.38 99.63 13.75 1.23e+00 6.61e-01 1.25e+02 angle pdb=" N GLN A 279 " pdb=" CA GLN A 279 " pdb=" C GLN A 279 " ideal model delta sigma weight residual 114.09 99.75 14.34 1.55e+00 4.16e-01 8.56e+01 angle pdb=" N GLN A 145 " pdb=" CA GLN A 145 " pdb=" C GLN A 145 " ideal model delta sigma weight residual 110.97 101.49 9.48 1.09e+00 8.42e-01 7.57e+01 angle pdb=" N LEU A 186 " pdb=" CA LEU A 186 " pdb=" C LEU A 186 " ideal model delta sigma weight residual 113.72 103.13 10.59 1.30e+00 5.92e-01 6.64e+01 angle pdb=" N ALA A 253 " pdb=" CA ALA A 253 " pdb=" C ALA A 253 " ideal model delta sigma weight residual 113.41 104.47 8.94 1.22e+00 6.72e-01 5.37e+01 ... (remaining 9341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 2174 22.04 - 44.07: 165 44.07 - 66.11: 60 66.11 - 88.14: 7 88.14 - 110.18: 2 Dihedral angle restraints: 2408 sinusoidal: 1323 harmonic: 1085 Sorted by residual: dihedral pdb=" CG NVA A 900 " pdb=" CA NVA A 900 " pdb=" CB NVA A 900 " pdb=" HA NVA A 900 " ideal model delta sinusoidal sigma weight residual -62.82 47.36 -110.18 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" N GLN A 348 " pdb=" C GLN A 348 " pdb=" CA GLN A 348 " pdb=" CB GLN A 348 " ideal model delta harmonic sigma weight residual 122.80 114.22 8.58 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" CG ARG A 40 " pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " ideal model delta sinusoidal sigma weight residual -90.00 -43.56 -46.44 2 1.50e+01 4.44e-03 1.12e+01 ... (remaining 2405 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.077: 254 0.077 - 0.153: 94 0.153 - 0.229: 35 0.229 - 0.306: 10 0.306 - 0.382: 4 Chirality restraints: 397 Sorted by residual: chirality pdb=" CA TRP A 298 " pdb=" N TRP A 298 " pdb=" C TRP A 298 " pdb=" CB TRP A 298 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CA ASN A 329 " pdb=" N ASN A 329 " pdb=" C ASN A 329 " pdb=" CB ASN A 329 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ALA A 280 " pdb=" N ALA A 280 " pdb=" C ALA A 280 " pdb=" CB ALA A 280 " both_signs ideal model delta sigma weight residual False 2.48 2.80 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 394 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 298 " -0.117 2.00e-02 2.50e+03 3.53e-02 5.00e+01 pdb=" CG TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 298 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP A 298 " 0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP A 298 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 298 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 298 " 0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 298 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 298 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 298 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP A 298 " 0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP A 298 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP A 298 " 0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 298 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 298 " 0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP A 298 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 193 " -0.080 2.00e-02 2.50e+03 2.41e-02 2.33e+01 pdb=" CG TRP A 193 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 193 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 193 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 193 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 193 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 193 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 193 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 193 " 0.023 2.00e-02 2.50e+03 pdb=" HE1 TRP A 193 " -0.007 2.00e-02 2.50e+03 pdb=" HE3 TRP A 193 " 0.025 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 193 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 193 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 193 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 317 " 0.057 2.00e-02 2.50e+03 2.24e-02 1.51e+01 pdb=" CG TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 317 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 317 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 317 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 317 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 317 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 317 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 TYR A 317 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR A 317 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TYR A 317 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 317 " -0.008 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 0.68 - 1.47: 38 1.47 - 2.25: 1195 2.25 - 3.03: 16091 3.03 - 3.82: 24076 3.82 - 4.60: 38651 Warning: very small nonbonded interaction distances. Nonbonded interactions: 80051 Sorted by model distance: nonbonded pdb=" HB3 ARG A 40 " pdb="HH11 ARG A 40 " model vdw 0.684 2.270 nonbonded pdb=" HG2 GLU A 87 " pdb=" HD1 HIS A 117 " model vdw 0.725 2.270 nonbonded pdb="HD13 ILE A 116 " pdb=" HB3 LEU A 124 " model vdw 0.838 2.440 nonbonded pdb=" HA ILE A 116 " pdb="HG21 VAL A 120 " model vdw 0.941 2.440 nonbonded pdb=" OE2 GLU A 122 " pdb=" HB3 PRO A 305 " model vdw sym.op. 0.998 2.620 z,x,y ... (remaining 80046 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 15.91 1 O 476 7.97 1 N 427 6.97 1 C 1617 5.97 1 H 2569 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: 2569 of 5100 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 5100 n_use_u_iso = 5100 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 = 5100 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (5100 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 5100 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 = "1fb5_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2569 occupancy sum: 2569.00 (% of total atoms 50.55) Rotatable: count: 751 occupancy sum: 751.00 (% of total atoms 14.78) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.3934 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 7.070147 | | target function (ml) not normalized (work): 91155.402602 | | target function (ml) not normalized (free): 4891.182011 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2727 155 0.4383 0.4389 7.8547 7.6803| | 2: 5.98 - 4.75 0.97 2600 136 0.3400 0.3210 7.1228 7.1545| | 3: 4.75 - 4.15 0.98 2607 127 0.3675 0.3564 6.9337 6.9672| | 4: 4.15 - 3.77 0.95 2474 131 0.3917 0.3663 6.7408 6.855| | 5: 3.77 - 3.50 0.96 2485 141 0.4190 0.4058 6.6251 6.7013| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2727 155 0.56 45.31 0.74 0.54 772694.27| | 2: 5.98 - 4.75 2600 136 0.62 41.75 1.31 0.69 464297.85| | 3: 4.75 - 4.15 2607 127 0.77 28.66 1.48 0.80 250471.84| | 4: 4.15 - 3.77 2474 131 0.82 24.66 1.52 0.86 130060.96| | 5: 3.77 - 3.50 2485 141 0.79 27.72 1.54 0.87 102817.37| |alpha: min = 0.54 max = 0.87 mean = 0.75| |beta: min = 102817.37 max = 772694.27 mean = 352483.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 33.87| |phase err.(test): min = 0.00 max = 89.68 mean = 32.98| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.067 2582 Z= 0.581 Angle : 1.670 14.337 3492 Z= 1.077 Chirality : 0.099 0.382 397 Planarity : 0.008 0.083 441 Dihedral : 17.955 87.743 961 Min Nonbonded Distance : 1.472 Molprobity Statistics. All-atom Clashscore : 64.94 Ramachandran Plot: Outliers : 7.86 % Allowed : 20.75 % Favored : 71.38 % Rotamer: Outliers : 16.73 % Allowed : 15.64 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -6.37 (0.33), residues: 318 helix: -4.89 (0.20), residues: 119 sheet: -2.43 (0.57), residues: 57 loop : -4.35 (0.40), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 94 TYR 0.047 0.010 TYR A 317 PHE 0.031 0.012 PHE A 65 TRP 0.080 0.015 TRP A 298 HIS 0.003 0.001 HIS A 182 Individual atomic B min max mean iso aniso Overall: 9.34 143.19 50.12 1.69 2531 0 Protein: 9.34 143.19 50.12 1.69 2531 0 Chain A: 9.34 143.19 50.12 N/A 2531 0 Histogram: Values Number of atoms 9.34 - 22.73 309 22.73 - 36.11 663 36.11 - 49.50 541 49.50 - 62.88 410 62.88 - 76.27 277 76.27 - 89.65 96 89.65 - 103.03 41 103.03 - 116.42 41 116.42 - 129.81 78 129.81 - 143.19 75 |-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: 3.50 - 55.69 A, n_refl.=13583 (all), 5.08 % free)------------| | | | r_work= 0.3934 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 7.070147 | | target function (ml) not normalized (work): 91155.402602 | | target function (ml) not normalized (free): 4891.182011 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3926 0.3934 0.3841 n_refl.: 13583 re-set all scales: r(all,work,free)=0.3926 0.3934 0.3841 n_refl.: 13583 remove outliers: r(all,work,free)=0.3925 0.3933 0.3841 n_refl.: 13580 overall B=7.43 to atoms: r(all,work,free)=0.4217 0.4227 0.4091 n_refl.: 13580 bulk-solvent and scaling: r(all,work,free)=0.2182 0.2162 0.2544 n_refl.: 13580 remove outliers: r(all,work,free)=0.2181 0.2161 0.2544 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5432 2167.891 1699.946 1.237 1.215 0.394 19.362-15.234 92.45 91 7 0.4008 2001.516 1851.844 0.999 1.207 0.352 15.182-11.849 95.91 195 16 0.2182 2357.622 2247.797 1.016 1.196 0.346 11.824-9.235 95.44 396 23 0.1342 2602.458 2571.289 0.979 1.173 0.344 9.223-7.200 96.44 830 38 0.1832 1876.452 1853.962 0.974 1.135 0.330 7.195-5.615 96.35 1675 92 0.2488 1247.522 1185.861 0.934 1.073 0.276 5.612-4.379 97.24 3486 178 0.1919 1353.373 1301.390 0.987 0.969 0.222 4.378-3.502 95.73 6123 328 0.2280 1060.465 1008.484 1.225 0.812 0.131 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0575 b_overall=4.7221 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.046051 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254008 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2402 0.2684 0.0282 0.003 0.7 11.0 4.1 15.3 0 0.125 0.2371 0.2670 0.0299 0.003 0.7 10.8 4.4 15.6 0 0.250 0.2316 0.2629 0.0312 0.003 0.7 12.6 4.7 16.0 0 0.500 0.2248 0.2594 0.0346 0.004 0.7 15.9 5.0 16.4 0 1.000 0.2192 0.2559 0.0367 0.005 0.8 19.8 5.7 17.1 0 2.000 0.2155 0.2537 0.0382 0.007 0.9 25.3 6.0 18.2 0 3.000 0.2125 0.2522 0.0397 0.008 1.0 29.4 6.0 18.9 0 4.000 0.2102 0.2502 0.0399 0.010 1.1 32.4 6.3 21.1 0 5.000 0.2090 0.2494 0.0404 0.011 1.2 33.2 6.3 21.1 0 6.000 0.2072 0.2491 0.0419 0.012 1.3 35.3 6.3 22.9 0 7.000 0.2060 0.2484 0.0424 0.013 1.3 36.5 6.6 23.6 0 8.000 0.2049 0.2476 0.0426 0.014 1.4 37.1 6.9 24.4 0 9.000 0.2038 0.2473 0.0435 0.015 1.5 39.0 6.9 24.7 0 10.000 0.2043 0.2473 0.0431 0.015 1.4 38.1 6.9 24.7 0 9.523 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2248 0.2594 0.0346 0.004 0.7 15.9 5.0 16.4 0 1.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.48 25.94 3.46 1.196 57.300 0.254 0.063 22.54 25.74 3.19 2.583 57.523 0.008 0.063 22.35 25.62 3.27 2.690 57.600 0.032 0.062 21.85 25.38 3.53 3.079 57.697 0.127 0.060 21.19 25.02 3.83 5.567 58.196 0.254 0.057 20.96 24.97 4.01 6.375 58.349 0.381 0.056 20.75 24.91 4.16 7.356 58.623 0.508 0.055 20.62 24.87 4.25 8.140 58.837 0.635 0.054 20.54 24.84 4.30 8.667 58.967 0.762 0.054 20.47 24.83 4.36 9.142 59.087 0.889 0.054 20.42 24.79 4.38 9.535 59.177 1.016 0.053 20.35 24.77 4.42 10.087 59.336 1.143 0.053 20.30 24.75 4.45 10.543 59.465 1.270 0.053 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 1.270 Accepted refinement result: 20.30 24.75 4.45 10.543 59.465 1.270 0.053 Individual atomic B min max mean iso aniso Overall: 12.82 166.61 61.91 9.70 2531 0 Protein: 12.82 166.61 61.91 9.70 2531 0 Chain A: 12.82 166.61 61.91 N/A 2531 0 Histogram: Values Number of atoms 12.82 - 28.20 152 28.20 - 43.58 606 43.58 - 58.96 622 58.96 - 74.34 526 74.34 - 89.72 254 89.72 - 105.10 136 105.10 - 120.47 65 120.47 - 135.85 69 135.85 - 151.23 75 151.23 - 166.61 26 =========================== Idealize ADP of riding H ========================== r_work=0.2030 r_free=0.2475 r_work=0.2009 r_free=0.2454 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2009 r_free= 0.2454 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.051781 | | target function (ls_wunit_k1) not normalized (work): 667.407916 | | target function (ls_wunit_k1) not normalized (free): 54.931697 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2009 0.2454 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4247 0.4255 0.4150 n_refl.: 13579 remove outliers: r(all,work,free)=0.4247 0.4255 0.4150 n_refl.: 13579 overall B=0.00 to atoms: r(all,work,free)=0.4247 0.4255 0.4150 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2044 0.2021 0.2464 n_refl.: 13579 remove outliers: r(all,work,free)=0.2044 0.2021 0.2464 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5292 1179.964 956.011 1.123 1.158 0.384 19.362-15.234 92.45 91 7 0.3591 1089.408 1037.097 1.026 1.153 0.351 15.182-11.849 95.91 195 16 0.2085 1283.233 1234.911 1.065 1.146 0.340 11.824-9.235 95.44 396 23 0.1404 1416.495 1406.346 1.034 1.128 0.335 9.223-7.200 96.44 830 38 0.1851 1021.336 1012.241 1.039 1.100 0.330 7.195-5.615 96.35 1675 92 0.2362 679.015 649.283 0.978 1.051 0.280 5.612-4.379 97.24 3486 178 0.1746 736.629 713.896 1.002 0.971 0.220 4.378-3.502 95.73 6123 328 0.2094 577.202 551.888 1.200 0.849 0.129 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.2719 ============================ 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 = 4.555591 wxc_scale = 0.031 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.059045 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2171 0.2527 0.0356 0.002 0.6 9.2 4.4 13.8 0 0.014 0.2152 0.2510 0.0358 0.002 0.6 9.0 4.4 14.2 0 0.043 0.2121 0.2478 0.0357 0.002 0.6 9.0 4.1 13.8 0 0.085 0.2091 0.2455 0.0364 0.002 0.6 10.2 3.8 14.5 0 0.128 0.2063 0.2448 0.0385 0.003 0.6 11.0 4.1 15.3 0 0.170 0.2035 0.2433 0.0398 0.003 0.6 12.0 3.8 16.7 0 0.213 0.2018 0.2418 0.0399 0.003 0.6 12.9 3.8 16.7 0 0.256 0.2007 0.2407 0.0400 0.004 0.7 13.7 3.8 17.1 0 0.298 0.2070 0.2445 0.0375 0.002 0.6 10.6 3.8 14.9 0 0.142 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2121 0.2478 0.0357 0.002 0.6 9.0 4.1 13.8 0 0.085 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.21 24.78 3.57 11.971 68.875 0.059 6.619 23.29 25.38 2.09 11.576 72.247 0.002 6.673 22.70 25.04 2.34 11.735 70.846 0.007 6.655 21.71 24.65 2.94 12.411 68.963 0.030 6.620 21.30 24.50 3.20 12.840 68.666 0.059 6.604 21.09 24.49 3.40 13.198 68.753 0.089 6.596 20.95 24.49 3.54 13.564 68.910 0.118 6.591 20.86 24.50 3.64 13.893 69.044 0.148 6.588 20.79 24.51 3.73 14.208 69.170 0.177 6.586 20.74 24.52 3.78 14.513 69.294 0.207 6.584 20.69 24.53 3.83 14.798 69.415 0.236 6.583 20.65 24.54 3.89 15.102 69.538 0.266 6.582 20.63 24.55 3.92 15.326 69.620 0.295 6.581 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.089 Accepted refinement result: 21.09 24.49 3.40 13.198 68.753 0.089 6.596 Individual atomic B min max mean iso aniso Overall: 16.28 166.69 61.67 10.51 2531 0 Protein: 16.28 166.69 61.67 10.51 2531 0 Chain A: 16.28 166.69 61.67 N/A 2531 0 Histogram: Values Number of atoms 16.28 - 31.32 198 31.32 - 46.36 761 46.36 - 61.40 619 61.40 - 76.44 376 76.44 - 91.49 209 91.49 - 106.53 124 106.53 - 121.57 70 121.57 - 136.61 69 136.61 - 151.65 68 151.65 - 166.69 37 =========================== Idealize ADP of riding H ========================== r_work=0.2109 r_free=0.2449 r_work=0.2115 r_free=0.2458 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2115 r_free= 0.2458 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 6.596702 | | target function (ml) not normalized (work): 85024.893655 | | target function (ml) not normalized (free): 4620.160321 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2133 0.2115 0.2458 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4219 0.4228 0.4097 n_refl.: 13579 remove outliers: r(all,work,free)=0.4219 0.4228 0.4097 n_refl.: 13579 overall B=3.58 to atoms: r(all,work,free)=0.4366 0.4376 0.4230 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2114 0.2096 0.2438 n_refl.: 13579 remove outliers: r(all,work,free)=0.2114 0.2096 0.2438 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5031 1179.964 982.461 1.339 1.175 0.409 19.362-15.234 92.45 91 7 0.3649 1089.408 1023.392 1.027 1.170 0.359 15.182-11.849 95.91 195 16 0.2103 1283.233 1230.771 1.091 1.162 0.353 11.824-9.235 95.44 396 23 0.1496 1416.495 1404.277 1.042 1.143 0.340 9.223-7.200 96.44 830 38 0.2039 1021.336 1004.697 1.046 1.113 0.335 7.195-5.615 96.35 1675 92 0.2599 679.015 641.480 1.004 1.061 0.293 5.612-4.379 97.24 3486 178 0.1918 736.629 707.829 0.986 0.976 0.212 4.378-3.502 95.73 6123 328 0.2033 577.202 549.263 1.190 0.846 0.132 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.2568 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2096 r_free=0.2438 After: r_work=0.2096 r_free=0.2438 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.353171 wxc_scale = 0.030 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.053796 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2099 0.2438 0.0339 0.002 0.6 9.8 3.8 13.8 0 0.013 0.2098 0.2438 0.0340 0.002 0.6 9.6 3.8 13.8 0 0.039 0.2097 0.2438 0.0341 0.002 0.6 9.6 3.8 13.8 0 0.077 0.2096 0.2438 0.0342 0.002 0.6 9.6 3.8 13.8 0 0.116 0.2095 0.2436 0.0342 0.002 0.6 9.8 3.8 13.8 0 0.154 0.2094 0.2436 0.0342 0.002 0.6 9.8 3.8 13.8 0 0.193 0.2092 0.2434 0.0341 0.003 0.6 9.4 3.8 13.8 0 0.232 0.2091 0.2434 0.0343 0.003 0.6 9.8 3.8 13.8 0 0.270 0.2096 0.2438 0.0342 0.002 0.6 9.6 3.8 13.8 0 0.129 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2092 0.2434 0.0341 0.003 0.6 9.4 3.8 13.8 0 0.232 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.92 24.34 3.41 12.277 71.885 0.054 6.596 23.57 25.45 1.88 11.339 75.574 0.002 6.670 23.39 25.38 1.99 11.843 74.893 0.007 6.669 21.41 24.42 3.01 12.275 71.402 0.027 6.611 20.94 24.29 3.36 12.432 71.581 0.054 6.595 20.90 24.31 3.41 12.409 71.752 0.081 6.595 20.79 24.32 3.53 12.830 71.494 0.108 6.590 20.78 24.38 3.60 13.019 71.400 0.134 6.590 20.72 24.40 3.68 13.312 71.299 0.161 6.587 20.62 24.41 3.79 13.738 71.213 0.188 6.584 20.49 24.35 3.87 14.312 71.272 0.215 6.579 20.50 24.45 3.94 14.398 71.197 0.242 6.580 20.49 24.46 3.96 14.476 71.236 0.269 6.580 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.054 Accepted refinement result: 20.94 24.29 3.36 12.432 71.581 0.054 6.595 Individual atomic B min max mean iso aniso Overall: 20.99 170.15 64.63 10.04 2531 0 Protein: 20.99 170.15 64.63 10.04 2531 0 Chain A: 20.99 170.15 64.63 N/A 2531 0 Histogram: Values Number of atoms 20.99 - 35.91 242 35.91 - 50.82 795 50.82 - 65.74 603 65.74 - 80.66 339 80.66 - 95.57 192 95.57 - 110.49 118 110.49 - 125.40 70 125.40 - 140.32 67 140.32 - 155.24 68 155.24 - 170.15 37 =========================== Idealize ADP of riding H ========================== r_work=0.2094 r_free=0.2429 r_work=0.2094 r_free=0.2429 ----------X-ray data---------- |--(resolution: 3.50 - 55.69 A, n_refl.=13579 (all), 5.08 % free)------------| | | | r_work= 0.2094 r_free= 0.2429 coordinate error (max.-lik. estimate): 0.44 A | | | | normalized target function (ml) (work): 6.595088 | | target function (ml) not normalized (work): 85004.091737 | | target function (ml) not normalized (free): 4619.964565 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 55.69 - 5.99 0.96 2723 155 0.2268 0.2622 7.0132 7.1228| | 2: 5.98 - 4.75 0.97 2600 136 0.2178 0.2188 6.678 6.711| | 3: 4.75 - 4.15 0.98 2607 127 0.1736 0.2192 6.5294 6.6447| | 4: 4.15 - 3.77 0.95 2474 131 0.1968 0.2273 6.4195 6.5288| | 5: 3.77 - 3.50 0.96 2485 141 0.2316 0.2832 6.294 6.412| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 55.69 - 5.99 2723 155 0.80 24.73 1.00 0.93 196017.34| | 2: 5.98 - 4.75 2600 136 0.80 26.17 1.00 0.94 137031.21| | 3: 4.75 - 4.15 2607 127 0.87 19.77 1.00 0.94 93420.03| | 4: 4.15 - 3.77 2474 131 0.86 20.54 1.01 0.92 64937.44| | 5: 3.77 - 3.50 2485 141 0.84 22.89 0.97 0.89 51705.36| |alpha: min = 0.89 max = 0.94 mean = 0.92| |beta: min = 51705.36 max = 196017.34 mean = 110382.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.83| |phase err.(work): min = 0.00 max = 89.89 mean = 22.86| |phase err.(test): min = 0.00 max = 89.40 mean = 22.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2112 0.2094 0.2429 n_refl.: 13579 re-set all scales: r(all,work,free)=0.4337 0.4347 0.4203 n_refl.: 13579 remove outliers: r(all,work,free)=0.4337 0.4347 0.4203 n_refl.: 13579 overall B=1.25 to atoms: r(all,work,free)=0.4389 0.4399 0.4250 n_refl.: 13579 bulk-solvent and scaling: r(all,work,free)=0.2114 0.2096 0.2427 n_refl.: 13579 remove outliers: r(all,work,free)=0.2114 0.2096 0.2427 n_refl.: 13579 ======================== 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 55.689-19.469 89.38 93 8 0.5027 1179.964 984.081 1.357 1.165 0.410 19.362-15.234 92.45 91 7 0.3623 1089.408 1027.480 1.012 1.160 0.354 15.182-11.849 95.91 195 16 0.2122 1283.233 1232.415 1.071 1.154 0.343 11.824-9.235 95.44 396 23 0.1500 1416.495 1404.860 1.050 1.135 0.339 9.223-7.200 96.44 830 38 0.2039 1021.336 1005.157 1.058 1.106 0.338 7.195-5.615 96.35 1675 92 0.2607 679.015 641.494 1.018 1.057 0.298 5.612-4.379 97.24 3486 178 0.1917 736.629 707.468 0.994 0.976 0.217 4.378-3.502 95.73 6123 328 0.2031 577.202 549.012 1.193 0.852 0.131 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.6442 ================= 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 : 0.3934 0.3841 0.010 1.670 9.3 143.2 50.1 0 0.000 1_bss: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_settarget: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_weight: 0.2161 0.2544 0.010 1.670 16.8 150.6 57.6 0 0.000 1_xyzrec: 0.2248 0.2594 0.004 0.740 16.8 150.6 57.6 0 0.206 1_adp: 0.2030 0.2475 0.004 0.740 12.8 166.6 61.9 0 0.206 1_regHadp: 0.2009 0.2454 0.004 0.740 12.8 166.6 61.9 0 0.206 2_bss: 0.2021 0.2464 0.004 0.740 12.8 166.6 61.9 0 0.206 2_settarget: 0.2021 0.2464 0.004 0.740 12.8 166.6 61.9 0 0.206 2_updatecdl: 0.2021 0.2464 0.004 0.793 12.8 166.6 61.9 0 0.206 2_weight: 0.2021 0.2464 0.004 0.793 12.8 166.6 61.9 0 0.206 2_xyzrec: 0.2121 0.2478 0.002 0.581 12.8 166.6 61.9 0 0.276 2_adp: 0.2109 0.2449 0.002 0.581 16.3 166.7 61.7 0 0.276 2_regHadp: 0.2115 0.2458 0.002 0.581 16.3 166.7 61.7 0 0.276 3_bss: 0.2096 0.2438 0.002 0.581 19.9 170.3 65.2 0 0.276 3_settarget: 0.2096 0.2438 0.002 0.581 19.9 170.3 65.2 0 0.276 3_updatecdl: 0.2096 0.2438 0.002 0.628 19.9 170.3 65.2 0 0.276 3_setrh: 0.2096 0.2438 0.002 0.628 19.9 170.3 65.2 0 0.276 3_weight: 0.2096 0.2438 0.002 0.628 19.9 170.3 65.2 0 0.276 3_xyzrec: 0.2092 0.2434 0.003 0.600 19.9 170.3 65.2 0 0.276 3_adp: 0.2094 0.2429 0.003 0.600 21.0 170.2 64.6 0 0.276 3_regHadp: 0.2094 0.2429 0.003 0.600 21.0 170.2 64.6 0 0.276 end: 0.2096 0.2427 0.003 0.600 22.2 171.4 65.9 0 0.276 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1fb5_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1fb5_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.2500 Refinement macro-cycles (run) : 297.9200 Write final files (write_after_run_outputs) : 23.4300 Total : 326.6000 Total CPU time: 5.88 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:35:15 PDT -0700 (1716251715.68 s) Start R-work = 0.2161, R-free = 0.2544 Final R-work = 0.2096, R-free = 0.2427 =============================================================================== Job complete usr+sys time: 375.26 seconds wall clock time: 19 minutes 11.65 seconds (1151.65 seconds total)