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/4yei.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.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/4yei.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.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 Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 9333 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "B" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "C" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Time building chain proxies: 2.95, per 1000 atoms: 0.32 Number of scatterers: 9333 At special positions: 0 Unit cell: (110.36, 115.96, 164.12, 90, 90, 90) Space group: I 2 2 2 (No. 23) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 966 8.00 N 909 7.00 C 2865 6.00 H 4584 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: 5.82 Conformation dependent library (CDL) restraints added in 862.8 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Time building geometry restraints manager: 4.71 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: 4581 1.15 - 1.32: 1124 1.32 - 1.49: 1726 1.49 - 1.66: 1935 1.66 - 1.84: 15 Bond restraints: 9381 Sorted by residual: bond pdb=" N GLU A 44 " pdb=" H GLU A 44 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ARG A 186 " pdb=" H ARG A 186 " 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 210 " pdb=" H ALA A 210 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU B 177 " pdb=" H LEU B 177 " 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 228 " pdb=" H ALA A 228 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9376 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 223 105.44 - 112.60: 10348 112.60 - 119.75: 2632 119.75 - 126.90: 3592 126.90 - 134.06: 50 Bond angle restraints: 16845 Sorted by residual: angle pdb=" N LEU A 233 " pdb=" CA LEU A 233 " pdb=" C LEU A 233 " ideal model delta sigma weight residual 110.80 119.87 -9.07 2.13e+00 2.20e-01 1.81e+01 angle pdb=" N THR B 209 " pdb=" CA THR B 209 " pdb=" C THR B 209 " ideal model delta sigma weight residual 113.88 119.07 -5.19 1.23e+00 6.61e-01 1.78e+01 angle pdb=" N SER A 211 " pdb=" CA SER A 211 " pdb=" CB SER A 211 " ideal model delta sigma weight residual 110.06 116.02 -5.96 1.51e+00 4.39e-01 1.56e+01 angle pdb=" CG ARG A 191 " pdb=" CD ARG A 191 " pdb=" NE ARG A 191 " ideal model delta sigma weight residual 112.00 103.57 8.43 2.20e+00 2.07e-01 1.47e+01 angle pdb=" CA ALA C 210 " pdb=" C ALA C 210 " pdb=" O ALA C 210 " ideal model delta sigma weight residual 121.47 117.12 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 16840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 3987 15.79 - 31.57: 244 31.57 - 47.36: 121 47.36 - 63.15: 23 63.15 - 78.93: 8 Dihedral angle restraints: 4383 sinusoidal: 2373 harmonic: 2010 Sorted by residual: dihedral pdb=" C ASP A 218 " pdb=" N ASP A 218 " pdb=" CA ASP A 218 " pdb=" CB ASP A 218 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N ALA A 234 " pdb=" CA ALA A 234 " ideal model delta harmonic sigma weight residual -180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" C VAL C 205 " pdb=" N VAL C 205 " pdb=" CA VAL C 205 " pdb=" CB VAL C 205 " ideal model delta harmonic sigma weight residual -122.00 -130.88 8.88 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 559 0.093 - 0.186: 157 0.186 - 0.278: 32 0.278 - 0.371: 16 0.371 - 0.464: 1 Chirality restraints: 765 Sorted by residual: chirality pdb=" CA ARG A 208 " pdb=" N ARG A 208 " pdb=" C ARG A 208 " pdb=" CB ARG A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA MET B 171 " pdb=" N MET B 171 " pdb=" C MET B 171 " pdb=" CB MET B 171 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU A 109 " pdb=" N GLU A 109 " pdb=" C GLU A 109 " pdb=" CB GLU A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 762 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 208 " 0.046 9.50e-02 1.11e+02 3.78e-02 2.72e+01 pdb=" NE ARG A 208 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 208 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 208 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 208 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 208 " 0.058 2.00e-02 2.50e+03 pdb="HH12 ARG A 208 " -0.020 2.00e-02 2.50e+03 pdb="HH21 ARG A 208 " 0.056 2.00e-02 2.50e+03 pdb="HH22 ARG A 208 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.022 2.00e-02 2.50e+03 2.61e-02 2.05e+01 pdb=" CG TYR A 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 59 " -0.005 2.00e-02 2.50e+03 2.61e-02 2.05e+01 pdb=" CG TYR C 59 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 59 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 59 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 59 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 59 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 59 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TYR C 59 " -0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR C 59 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 TYR C 59 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 TYR C 59 " -0.049 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 1.27 - 1.94: 322 1.94 - 2.60: 9707 2.60 - 3.27: 30939 3.27 - 3.93: 40839 3.93 - 4.60: 59795 Nonbonded interactions: 141602 Sorted by model distance: nonbonded pdb=" HE1 HIS A 198 " pdb=" HB3 ALA A 234 " model vdw sym.op. 1.270 2.270 x,-y+2,-z+2 nonbonded pdb=" HD3 ARG A 208 " pdb=" O ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 nonbonded pdb=" O ARG A 208 " pdb=" HD3 ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 nonbonded pdb=" HB3 ALA B 234 " pdb=" HE ARG C 216 " model vdw sym.op. 1.398 2.270 x,-y+2,-z+2 nonbonded pdb=" OXT ALA B 234 " pdb="HH21 ARG C 216 " model vdw sym.op. 1.425 1.850 x,-y+2,-z+2 ... (remaining 141597 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 9 15.91 1 O 966 7.97 1 N 909 6.97 1 C 2865 5.97 1 H 4584 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: 4584 of 9333 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 9333 n_use_u_iso = 4587 n_use_u_aniso = 4746 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 = 9333 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (9333 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4587 aniso = 4746) 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 = "4yei_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4584 occupancy sum: 4584.00 (% of total atoms 49.12) Rotatable: count: 1419 occupancy sum: 1419.00 (% of total atoms 15.20) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4648 r_free= 0.3724 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.850734 | | target function (ml) not normalized (work): 82845.930745 | | target function (ml) not normalized (free): 4160.088940 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 37.43 - 5.64 0.98 3160 150 0.4377 0.4107 7.9301 7.1801| | 2: 5.64 - 4.48 0.97 3007 139 0.4270 0.3140 6.6996 6.8358| | 3: 4.48 - 3.91 0.98 2977 158 0.4835 0.3449 6.4646 6.5718| | 4: 3.91 - 3.55 0.98 2949 176 0.5523 0.4277 6.238 6.2191| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 37.43 - 5.64 3160 150 0.58 44.13 0.74 0.59 276018.49| | 2: 5.64 - 4.48 3007 139 0.64 40.12 1.64 0.84 146839.46| | 3: 4.48 - 3.91 2977 158 0.77 28.52 1.84 0.98 70891.22| | 4: 3.91 - 3.55 2949 176 0.73 33.00 2.00 1.01 48173.76| |alpha: min = 0.59 max = 1.01 mean = 0.85| |beta: min = 48173.76 max = 276018.49 mean = 137837.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.82 mean = 36.58| |phase err.(test): min = 0.00 max = 89.91 mean = 35.81| |-----------------------------------------------------------------------------| ----------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 : 0.017 0.091 4797 Z= 1.131 Angle : 1.564 10.417 6522 Z= 0.950 Chirality : 0.097 0.464 765 Planarity : 0.008 0.044 900 Dihedral : 14.850 78.933 1683 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.49 % Allowed : 5.94 % Favored : 92.57 % 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: -1.82 (0.25), residues: 639 helix: -0.76 (0.52), residues: 93 sheet: None (None), residues: 0 loop : -1.42 (0.19), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 208 TYR 0.030 0.009 TYR C 30 PHE 0.030 0.007 PHE B 225 TRP 0.026 0.009 TRP C 207 HIS 0.015 0.004 HIS A 198 Individual atomic B min max mean iso aniso Overall: 49.64 289.79 106.35 4.55 4749 0 Protein: 49.64 289.79 106.35 4.55 4749 0 Chain A: 49.64 180.30 105.91 N/A 1583 0 Chain B: 56.85 174.83 98.34 N/A 1583 0 Chain C: 58.38 289.79 114.82 N/A 1583 0 Histogram: Values Number of atoms 49.64 - 73.66 630 73.66 - 97.67 1454 97.67 - 121.69 1256 121.69 - 145.70 892 145.70 - 169.72 426 169.72 - 193.73 50 193.73 - 217.74 22 217.74 - 241.76 11 241.76 - 265.77 5 265.77 - 289.79 3 |-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: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4648 r_free= 0.3724 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.850734 | | target function (ml) not normalized (work): 82845.930745 | | target function (ml) not normalized (free): 4160.088940 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 7.9863 percent. r_work = 0.5447 r_free = 0.4722 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5420 0.5447 0.4722 n_refl.: 12716 re-set all scales: r(all,work,free)=0.5420 0.5447 0.4722 n_refl.: 12716 remove outliers: r(all,work,free)=0.5326 0.5350 0.4722 n_refl.: 12706 overall B=-19.52 to atoms: r(all,work,free)=0.4761 0.4780 0.4317 n_refl.: 12706 bulk-solvent and scaling: r(all,work,free)=0.2831 0.2821 0.3031 n_refl.: 12706 remove outliers: r(all,work,free)=0.2830 0.2820 0.3031 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2361 2888.741 2836.860 1.377 1.103 0.425 17.650-14.285 98.02 94 5 0.1437 3045.471 3027.032 1.043 1.100 0.372 14.282-11.568 95.90 180 7 0.1422 3015.142 2972.767 1.162 1.084 0.366 11.530-9.354 97.49 335 14 0.2123 1633.314 1609.041 1.151 1.071 0.367 9.349-7.570 98.64 624 29 0.2492 1223.678 1175.786 0.914 1.049 0.311 7.566-6.123 98.85 1143 56 0.2819 950.581 897.392 0.914 1.017 0.268 6.123-4.955 97.48 2111 97 0.3017 843.953 800.215 1.013 0.964 0.260 4.954-4.009 97.40 3921 193 0.2745 1174.560 1150.097 1.226 0.888 0.193 4.009-3.554 97.79 3579 218 0.3563 708.485 625.652 1.175 0.814 0.156 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0608 b_overall=6.4247 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 13.358920 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.141170 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 0.2904 0.3159 0.0255 0.001 0.4 0.3 0.0 0.2 0 0.125 0.2842 0.3158 0.0315 0.002 0.4 0.2 0.0 0.2 0 0.250 0.2749 0.3157 0.0409 0.002 0.5 0.2 0.0 0.4 0 0.500 0.2649 0.3151 0.0502 0.003 0.6 1.2 0.0 0.6 0 1.000 0.2549 0.3164 0.0615 0.005 0.7 2.6 0.0 1.9 0 2.000 0.2502 0.3202 0.0700 0.006 0.8 4.5 0.0 3.6 0 3.000 0.2465 0.3199 0.0733 0.008 0.9 6.1 0.0 4.2 0 4.000 0.2429 0.3167 0.0738 0.009 1.0 6.9 0.2 6.2 0 5.000 0.2399 0.3169 0.0770 0.010 1.1 9.2 0.2 7.0 0 6.000 0.2376 0.3173 0.0798 0.011 1.2 12.7 0.3 8.5 0 7.000 0.2358 0.3145 0.0787 0.012 1.3 13.6 0.5 8.5 0 8.000 0.2342 0.3157 0.0815 0.013 1.4 16.2 0.5 9.8 0 9.000 0.2330 0.3149 0.0819 0.014 1.4 16.9 0.5 10.0 0 10.000 0.2386 0.3157 0.0771 0.011 1.2 10.1 0.2 7.2 0 6.679 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2842 0.3158 0.0315 0.002 0.4 0.2 0.0 0.2 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 28.42 31.58 3.15 3.255 86.699 0.141 0.082 28.30 31.59 3.29 3.527 86.940 0.004 0.081 28.03 31.47 3.43 3.577 86.944 0.018 0.079 26.80 30.91 4.11 6.001 87.563 0.071 0.071 26.18 30.54 4.36 7.131 87.730 0.141 0.068 25.88 30.39 4.52 8.058 87.927 0.212 0.066 25.70 30.29 4.59 8.767 88.097 0.282 0.065 25.48 30.19 4.71 9.638 88.384 0.353 0.064 25.20 30.05 4.86 10.904 88.850 0.424 0.063 25.10 30.03 4.92 11.366 88.980 0.494 0.062 25.02 30.00 4.98 11.842 89.114 0.565 0.062 24.96 29.97 5.01 12.228 89.220 0.635 0.062 24.90 29.95 5.05 12.598 89.325 0.706 0.061 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.706 Accepted refinement result: 24.90 29.95 5.05 12.598 89.325 0.706 0.061 Individual atomic B min max mean iso aniso Overall: 25.45 265.26 91.99 11.98 4749 0 Protein: 25.45 265.26 91.99 11.98 4749 0 Chain A: 25.45 169.25 90.78 N/A 1583 0 Chain B: 32.93 163.17 84.79 N/A 1583 0 Chain C: 35.83 265.26 100.41 N/A 1583 0 Histogram: Values Number of atoms 25.45 - 49.43 218 49.43 - 73.41 1194 73.41 - 97.39 1453 97.39 - 121.37 1071 121.37 - 145.35 646 145.35 - 169.34 125 169.34 - 193.32 23 193.32 - 217.30 11 217.30 - 241.28 5 241.28 - 265.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.2490 r_free=0.2995 r_work=0.2457 r_free=0.2971 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2457 r_free= 0.2971 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ls_wunit_k1) (work): 0.059579 | | target function (ls_wunit_k1) not normalized (work): 719.828062 | | target function (ls_wunit_k1) not normalized (free): 53.517272 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2482 0.2457 0.2971 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4822 0.4839 0.4433 n_refl.: 12705 remove outliers: r(all,work,free)=0.4822 0.4839 0.4433 n_refl.: 12705 overall B=-0.05 to atoms: r(all,work,free)=0.4821 0.4838 0.4432 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2463 0.2437 0.2980 n_refl.: 12705 remove outliers: r(all,work,free)=0.2463 0.2437 0.2980 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2264 1601.237 1598.269 1.330 1.079 0.430 17.650-14.285 98.02 94 5 0.1536 1688.113 1666.979 1.067 1.078 0.380 14.282-11.568 95.90 180 7 0.1369 1671.302 1652.393 1.169 1.064 0.365 11.530-9.354 97.49 335 14 0.2004 905.350 895.139 1.153 1.053 0.360 9.349-7.570 98.64 624 29 0.2344 678.288 658.082 0.909 1.035 0.300 7.566-6.123 98.85 1143 56 0.2564 526.910 507.035 0.904 1.008 0.260 6.123-4.955 97.48 2111 97 0.2626 467.805 451.883 1.015 0.965 0.250 4.954-4.009 97.40 3921 193 0.2199 651.062 645.812 1.233 0.903 0.170 4.009-3.554 97.79 3579 218 0.3143 392.716 360.400 1.225 0.844 0.130 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.1321 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.651094 wxc_scale = 0.029 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.035454 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 0.2540 0.3062 0.0522 0.001 0.4 0.6 0.0 0.2 0 0.011 0.2465 0.3026 0.0561 0.001 0.4 0.5 0.0 0.0 0 0.032 0.2400 0.2992 0.0592 0.001 0.4 0.3 0.0 0.0 0 0.064 0.2365 0.2982 0.0616 0.001 0.4 0.3 0.0 0.2 0 0.097 0.2344 0.2967 0.0623 0.002 0.4 0.4 0.0 0.4 0 0.129 0.2325 0.2955 0.0630 0.002 0.5 0.8 0.0 0.4 0 0.161 0.2317 0.2944 0.0626 0.002 0.5 0.6 0.0 0.4 0 0.193 0.2305 0.2963 0.0658 0.002 0.5 0.8 0.0 0.6 0 0.225 0.2358 0.2973 0.0615 0.001 0.4 0.3 0.0 0.2 0 0.107 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2317 0.2944 0.0626 0.002 0.5 0.6 0.0 0.4 0 0.193 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.17 29.44 6.26 16.056 101.240 0.035 6.502 26.49 30.78 4.29 14.113 106.220 0.001 6.580 26.34 30.76 4.43 14.018 106.810 0.004 6.570 24.54 29.68 5.14 15.459 103.023 0.018 6.515 23.90 29.38 5.47 16.275 102.132 0.035 6.493 23.35 28.94 5.59 16.525 101.730 0.053 6.477 23.17 28.97 5.80 16.916 101.886 0.071 6.471 23.02 28.98 5.96 17.177 101.888 0.089 6.467 22.92 28.94 6.02 17.445 101.986 0.106 6.464 22.85 28.94 6.08 17.507 101.844 0.124 6.463 22.79 28.93 6.13 17.708 101.942 0.142 6.461 22.75 28.91 6.17 17.886 102.029 0.160 6.460 22.71 28.91 6.21 18.051 102.112 0.177 6.459 max suggested for this run: 20.25 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.053 Accepted refinement result: 23.35 28.94 5.59 16.525 101.730 0.053 6.477 Individual atomic B min max mean iso aniso Overall: 28.71 260.22 92.90 11.35 4749 0 Protein: 28.71 260.22 92.90 11.35 4749 0 Chain A: 28.71 170.00 90.70 N/A 1583 0 Chain B: 36.58 165.22 85.80 N/A 1583 0 Chain C: 39.95 260.22 102.21 N/A 1583 0 Histogram: Values Number of atoms 28.71 - 51.86 202 51.86 - 75.01 1309 75.01 - 98.16 1425 98.16 - 121.31 935 121.31 - 144.46 642 144.46 - 167.61 189 167.61 - 190.76 28 190.76 - 213.91 11 213.91 - 237.06 5 237.06 - 260.22 3 =========================== Idealize ADP of riding H ========================== r_work=0.2335 r_free=0.2894 r_work=0.2345 r_free=0.2890 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2345 r_free= 0.2890 coordinate error (max.-lik. estimate): 0.61 A | | | | normalized target function (ml) (work): 6.477290 | | target function (ml) not normalized (work): 78258.613014 | | target function (ml) not normalized (free): 4126.363728 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2371 0.2345 0.2890 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4797 0.4815 0.4393 n_refl.: 12705 remove outliers: r(all,work,free)=0.4797 0.4815 0.4393 n_refl.: 12705 overall B=1.24 to atoms: r(all,work,free)=0.4837 0.4855 0.4421 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2348 0.2321 0.2880 n_refl.: 12705 remove outliers: r(all,work,free)=0.2348 0.2321 0.2880 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2279 1601.237 1605.787 1.213 1.158 0.430 17.650-14.285 98.02 94 5 0.1318 1688.113 1676.147 0.962 1.154 0.380 14.282-11.568 95.90 180 7 0.1282 1671.302 1651.658 1.056 1.134 0.364 11.530-9.354 97.49 335 14 0.1768 905.350 892.610 1.061 1.117 0.359 9.349-7.570 98.64 624 29 0.2144 678.288 656.041 0.862 1.087 0.299 7.566-6.123 98.85 1143 56 0.2461 526.910 503.803 0.869 1.044 0.250 6.123-4.955 97.48 2111 97 0.2611 467.805 444.691 1.022 0.975 0.247 4.954-4.009 97.40 3921 193 0.2054 651.062 638.812 1.245 0.875 0.157 4.009-3.554 97.79 3579 218 0.3045 392.716 355.381 1.308 0.774 0.117 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.4803 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2321 r_free=0.2880 After: r_work=0.2321 r_free=0.2880 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.918567 wxc_scale = 0.074 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.033435 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 0.2327 0.2882 0.0555 0.002 0.5 0.6 0.0 0.4 0 0.029 0.2323 0.2881 0.0558 0.002 0.5 0.6 0.0 0.4 0 0.087 0.2321 0.2880 0.0560 0.002 0.5 0.6 0.0 0.4 0 0.174 0.2316 0.2878 0.0562 0.002 0.5 0.6 0.0 0.4 0 0.261 0.2309 0.2877 0.0568 0.003 0.5 0.6 0.0 0.4 0 0.347 0.2289 0.2873 0.0584 0.005 0.6 0.6 0.0 0.4 0 0.434 0.2273 0.2864 0.0591 0.006 0.7 1.0 0.0 0.4 0 0.521 0.2253 0.2853 0.0600 0.008 0.9 1.4 0.0 0.4 0 0.608 0.2315 0.2877 0.0562 0.002 0.5 0.6 0.0 0.4 0 0.290 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2253 0.2853 0.0600 0.008 0.9 1.4 0.0 0.4 0 0.608 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.53 28.53 6.00 15.900 103.506 0.033 6.464 27.15 31.19 4.04 14.432 110.462 0.001 6.592 26.19 30.81 4.62 13.749 110.071 0.004 6.565 24.06 29.17 5.11 15.203 105.328 0.017 6.511 22.97 28.58 5.60 15.976 103.605 0.033 6.476 22.34 28.35 6.01 16.276 103.213 0.050 6.456 22.29 28.39 6.10 16.402 103.115 0.067 6.454 21.93 28.17 6.24 16.985 103.557 0.084 6.442 21.87 28.19 6.32 17.375 103.574 0.100 6.440 21.82 28.17 6.35 17.595 103.683 0.117 6.438 21.78 28.16 6.38 17.772 103.785 0.134 6.436 21.75 28.17 6.42 17.930 103.879 0.150 6.435 21.73 28.18 6.45 18.071 103.963 0.167 6.434 max suggested for this run: 20.70 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.033 Accepted refinement result: 22.97 28.58 5.60 15.976 103.605 0.033 6.476 Individual atomic B min max mean iso aniso Overall: 38.34 256.46 94.34 9.16 4749 0 Protein: 38.34 256.46 94.34 9.16 4749 0 Chain A: 38.34 170.21 91.11 N/A 1583 0 Chain B: 43.73 167.34 87.03 N/A 1583 0 Chain C: 44.27 256.46 104.88 N/A 1583 0 Histogram: Values Number of atoms 38.34 - 60.16 367 60.16 - 81.97 1550 81.97 - 103.78 1277 103.78 - 125.59 787 125.59 - 147.40 543 147.40 - 169.21 176 169.21 - 191.02 33 191.02 - 212.84 9 212.84 - 234.65 4 234.65 - 256.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.2297 r_free=0.2858 r_work=0.2309 r_free=0.2859 ----------X-ray data---------- |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2309 r_free= 0.2859 coordinate error (max.-lik. estimate): 0.56 A | | | | normalized target function (ml) (work): 6.479208 | | target function (ml) not normalized (work): 78281.785587 | | target function (ml) not normalized (free): 4130.224156 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.24 - 5.63 0.98 3159 150 0.2050 0.2547 6.6169 6.8063| | 2: 5.63 - 4.48 0.97 3003 139 0.2144 0.2620 6.5026 6.6806| | 3: 4.48 - 3.91 0.98 2973 158 0.2218 0.2688 6.4947 6.745| | 4: 3.91 - 3.55 0.98 2947 176 0.3260 0.4001 6.2922 6.335| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.24 - 5.63 3159 150 0.76 29.29 0.99 1.01 111195.28| | 2: 5.63 - 4.48 3003 139 0.70 34.75 1.04 1.01 99057.03| | 3: 4.48 - 3.91 2973 158 0.74 31.61 0.97 0.94 85382.11| | 4: 3.91 - 3.55 2947 176 0.61 42.91 0.99 0.81 70170.53| |alpha: min = 0.81 max = 1.01 mean = 0.94| |beta: min = 70170.53 max = 111195.28 mean = 91819.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.70| |phase err.(work): min = 0.00 max = 89.97 mean = 34.54| |phase err.(test): min = 0.00 max = 89.63 mean = 35.01| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2336 0.2309 0.2859 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4851 0.4870 0.4404 n_refl.: 12705 remove outliers: r(all,work,free)=0.4851 0.4870 0.4404 n_refl.: 12705 overall B=-0.06 to atoms: r(all,work,free)=0.4849 0.4869 0.4403 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2325 0.2298 0.2857 n_refl.: 12705 remove outliers: r(all,work,free)=0.2325 0.2298 0.2857 n_refl.: 12705 ======================== 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 32.244-17.658 90.00 95 4 0.2236 1601.237 1605.713 1.160 1.206 0.430 17.650-14.285 98.02 94 5 0.1294 1688.113 1678.847 0.918 1.201 0.380 14.282-11.568 95.90 180 7 0.1237 1671.302 1649.186 1.013 1.177 0.365 11.530-9.354 97.49 335 14 0.1683 905.350 893.217 1.028 1.156 0.360 9.349-7.570 98.64 624 29 0.2092 678.288 655.896 0.835 1.119 0.300 7.566-6.123 98.85 1143 56 0.2417 526.910 504.638 0.854 1.066 0.247 6.123-4.955 97.48 2111 97 0.2580 467.805 445.773 1.024 0.982 0.240 4.954-4.009 97.40 3921 193 0.2029 651.062 640.312 1.269 0.859 0.160 4.009-3.554 97.79 3579 218 0.3071 392.716 356.292 1.397 0.734 0.110 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.1625 ================= 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 : 0.4648 0.3724 0.017 1.564 49.6 289.8 106.4 0 0.000 1_bss: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_settarget: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_updatephipsi: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_weight: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_xyzrec: 0.2842 0.3158 0.002 0.445 30.1 270.3 86.8 0 0.163 1_adp: 0.2490 0.2995 0.002 0.445 25.4 265.3 92.0 0 0.163 1_regHadp: 0.2457 0.2971 0.002 0.445 25.4 265.3 92.0 0 0.163 2_bss: 0.2437 0.2980 0.002 0.445 25.4 265.2 91.9 0 0.163 2_settarget: 0.2437 0.2980 0.002 0.445 25.4 265.2 91.9 0 0.163 2_updatephipsi: 0.2437 0.2980 0.002 0.445 25.4 265.2 91.9 0 0.163 2_updatecdl: 0.2437 0.2980 0.002 0.463 25.4 265.2 91.9 0 0.163 2_weight: 0.2437 0.2980 0.002 0.463 25.4 265.2 91.9 0 0.163 2_xyzrec: 0.2317 0.2944 0.002 0.470 25.4 265.2 91.9 0 0.211 2_adp: 0.2335 0.2894 0.002 0.470 28.7 260.2 92.9 0 0.211 2_regHadp: 0.2345 0.2890 0.002 0.470 28.7 260.2 92.9 0 0.211 3_bss: 0.2321 0.2880 0.002 0.470 30.0 261.5 94.1 0 0.211 3_settarget: 0.2321 0.2880 0.002 0.470 30.0 261.5 94.1 0 0.211 3_updatephipsi: 0.2321 0.2880 0.002 0.470 30.0 261.5 94.1 0 0.211 3_updatecdl: 0.2321 0.2880 0.002 0.485 30.0 261.5 94.1 0 0.211 3_setrh: 0.2321 0.2880 0.002 0.485 30.0 261.5 94.1 0 0.211 3_weight: 0.2321 0.2880 0.002 0.485 30.0 261.5 94.1 0 0.211 3_xyzrec: 0.2253 0.2853 0.008 0.890 30.0 261.5 94.1 0 0.220 3_adp: 0.2297 0.2858 0.008 0.890 38.3 256.5 94.3 0 0.220 3_regHadp: 0.2309 0.2859 0.008 0.890 38.3 256.5 94.3 0 0.220 end: 0.2298 0.2857 0.008 0.890 38.3 256.4 94.3 0 0.220 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/4yei_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/4yei_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 13.5100 Refinement macro-cycles (run) : 323.1800 Write final files (write_after_run_outputs) : 19.7100 Total : 356.4000 Total CPU time: 6.76 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:36:11 PDT -0700 (1716251771.95 s) Start R-work = 0.2820, R-free = 0.3031 Final R-work = 0.2298, R-free = 0.2857 =============================================================================== Job complete usr+sys time: 428.18 seconds wall clock time: 19 minutes 31.95 seconds (1171.95 seconds total)