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/1x24.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1x24/1x24.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/1x24/1x24.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1x24/1x24.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1x24.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1x24.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 "B TYR 53": "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: 4962 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2481 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Chain: "B" Number of atoms: 2481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 2481 Classifications: {'peptide': 152} Modifications used: {'COO': 1, 'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 144} Time building chain proxies: 1.00, per 1000 atoms: 0.20 Number of scatterers: 4962 At special positions: 0 Unit cell: (146.891, 146.891, 146.891, 90, 90, 90) Space group: I 21 3 (No. 199) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 434 8.00 N 424 7.00 C 1580 6.00 H 2510 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 104 " distance=2.01 Simple disulfide: pdb=" SG CYS B 49 " - pdb=" SG CYS B 104 " distance=2.02 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: 1.11 Conformation dependent library (CDL) restraints added in 209.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Time building geometry restraints manager: 1.30 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: 2506 1.15 - 1.32: 455 1.32 - 1.50: 983 1.50 - 1.67: 1052 1.67 - 1.84: 20 Bond restraints: 5016 Sorted by residual: bond pdb=" N GLY B 73 " pdb=" H GLY B 73 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N TYR A 14 " pdb=" H TYR A 14 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ILE A 45 " pdb=" H ILE A 45 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE A 160 " pdb=" H PHE A 160 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG A 153 " pdb=" HE ARG A 153 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 5011 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.19: 382 107.19 - 113.90: 5754 113.90 - 120.62: 1661 120.62 - 127.33: 1294 127.33 - 134.05: 19 Bond angle restraints: 9110 Sorted by residual: angle pdb=" N ARG B 93 " pdb=" CA ARG B 93 " pdb=" C ARG B 93 " ideal model delta sigma weight residual 111.40 103.59 7.81 1.22e+00 6.72e-01 4.10e+01 angle pdb=" C GLU B 95 " pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta sigma weight residual 119.84 127.73 -7.89 1.25e+00 6.40e-01 3.99e+01 angle pdb=" N ARG A 93 " pdb=" CA ARG A 93 " pdb=" C ARG A 93 " ideal model delta sigma weight residual 111.40 103.82 7.58 1.22e+00 6.72e-01 3.86e+01 angle pdb=" C GLU A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta sigma weight residual 119.84 127.01 -7.17 1.25e+00 6.40e-01 3.29e+01 angle pdb=" N LYS A 91 " pdb=" CA LYS A 91 " pdb=" C LYS A 91 " ideal model delta sigma weight residual 110.80 120.32 -9.52 2.13e+00 2.20e-01 2.00e+01 ... (remaining 9105 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.13: 2041 15.13 - 30.26: 170 30.26 - 45.39: 74 45.39 - 60.52: 51 60.52 - 75.65: 6 Dihedral angle restraints: 2342 sinusoidal: 1294 harmonic: 1048 Sorted by residual: dihedral pdb=" CB CYS B 49 " pdb=" SG CYS B 49 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual 93.00 59.98 33.02 1 1.00e+01 1.00e-02 1.55e+01 dihedral pdb=" N LEU A 158 " pdb=" CA LEU A 158 " pdb=" CB LEU A 158 " pdb=" CG LEU A 158 " ideal model delta sinusoidal sigma weight residual -60.00 -117.55 57.55 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" N VAL B 12 " pdb=" CA VAL B 12 " pdb=" CB VAL B 12 " pdb=" CG1 VAL B 12 " ideal model delta sinusoidal sigma weight residual 60.00 3.29 56.71 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2339 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.065: 177 0.065 - 0.129: 129 0.129 - 0.193: 56 0.193 - 0.257: 12 0.257 - 0.322: 6 Chirality restraints: 380 Sorted by residual: chirality pdb=" CA LYS A 91 " pdb=" N LYS A 91 " pdb=" C LYS A 91 " pdb=" CB LYS A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ILE B 100 " pdb=" N ILE B 100 " pdb=" C ILE B 100 " pdb=" CB ILE B 100 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA LYS B 91 " pdb=" N LYS B 91 " pdb=" C LYS B 91 " pdb=" CB LYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 377 not shown) Planarity restraints: 718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 14 " -0.055 2.00e-02 2.50e+03 2.08e-02 1.30e+01 pdb=" CG TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR B 14 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 14 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 14 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR B 14 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 14 " -0.028 2.00e-02 2.50e+03 pdb=" HD1 TYR B 14 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 TYR B 14 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR B 14 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR B 14 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 14 " 0.053 2.00e-02 2.50e+03 2.01e-02 1.21e+01 pdb=" CG TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 14 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 14 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 14 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 14 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 14 " 0.027 2.00e-02 2.50e+03 pdb=" HD1 TYR A 14 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 TYR A 14 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 TYR A 14 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 TYR A 14 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 70 " 0.053 2.00e-02 2.50e+03 1.96e-02 1.16e+01 pdb=" CG PHE B 70 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE B 70 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 70 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE B 70 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 70 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 70 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE B 70 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE B 70 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE B 70 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE B 70 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 70 " 0.019 2.00e-02 2.50e+03 ... (remaining 715 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 95 1.80 - 2.50: 3928 2.50 - 3.20: 15943 3.20 - 3.90: 21818 3.90 - 4.60: 33020 Nonbonded interactions: 74804 Sorted by model distance: nonbonded pdb=" HB3 CYS B 104 " pdb=" H VAL B 105 " model vdw 1.099 2.270 nonbonded pdb="HD11 ILE A 34 " pdb="HG22 VAL A 58 " model vdw 1.159 2.440 nonbonded pdb="HD11 ILE B 34 " pdb="HG22 VAL B 58 " model vdw 1.174 2.440 nonbonded pdb=" HE2 MET A 156 " pdb=" HE2 MET B 156 " model vdw 1.336 2.440 nonbonded pdb=" OE1 GLU A 127 " pdb=" H GLU A 127 " model vdw 1.401 1.850 ... (remaining 74799 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 14 15.96 2 O 434 7.97 1 N 424 6.97 1 C 1580 5.97 2 H 2510 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: 2510 of 4962 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4962 n_use_u_iso = 4962 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 = 4962 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4962 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4962 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 = "1x24_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2510 occupancy sum: 2510.00 (% of total atoms 50.58) Rotatable: count: 700 occupancy sum: 700.00 (% of total atoms 14.11) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.10 - 25.19 A, n_refl.=9450 (all), 10.31 % free)-------------| | | | r_work= 0.3217 r_free= 0.3511 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 3.705103 | | target function (ml) not normalized (work): 31404.451511 | | target function (ml) not normalized (free): 3715.470795 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.19 - 5.92 0.99 1279 156 0.3984 0.4374 4.5731 4.6595| | 2: 5.91 - 4.71 1.00 1245 142 0.2750 0.3052 4.1105 4.2067| | 3: 4.70 - 4.12 1.00 1230 149 0.2995 0.3165 3.9373 3.9737| | 4: 4.11 - 3.74 0.99 1195 141 0.3075 0.3413 3.6254 3.7264| | 5: 3.74 - 3.47 0.99 1236 140 0.2850 0.3008 3.3831 3.5066| | 6: 3.47 - 3.27 0.98 1167 145 0.2752 0.2989 3.1427 3.2223| | 7: 3.27 - 3.10 0.90 1124 101 0.3715 0.4011 3.037 3.1246| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.19 - 5.92 1279 156 0.60 43.52 0.86 0.02 1484.45| | 2: 5.91 - 4.71 1245 142 0.54 48.68 1.00 0.02 1282.82| | 3: 4.70 - 4.12 1230 149 0.68 37.31 1.29 0.03 685.00| | 4: 4.11 - 3.74 1195 141 0.66 39.30 1.28 0.03 455.35| | 5: 3.74 - 3.47 1236 140 0.73 33.45 1.21 0.03 224.54| | 6: 3.47 - 3.27 1167 145 0.72 34.52 1.11 0.02 131.69| | 7: 3.27 - 3.10 1124 101 0.65 40.46 0.93 0.02 103.07| |alpha: min = 0.02 max = 0.03 mean = 0.02| |beta: min = 103.07 max = 1484.45 mean = 640.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.65| |phase err.(work): min = 0.00 max = 89.99 mean = 39.67| |phase err.(test): min = 0.00 max = 89.17 mean = 39.22| |-----------------------------------------------------------------------------| ----------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 : 0.009 0.077 2506 Z= 0.578 Angle : 1.390 9.518 3390 Z= 0.917 Chirality : 0.099 0.322 380 Planarity : 0.006 0.038 430 Dihedral : 16.447 75.649 948 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 24.21 Ramachandran Plot: Outliers : 2.67 % Allowed : 8.33 % Favored : 89.00 % Rotamer: Outliers : 7.14 % Allowed : 9.77 % Favored : 83.08 % 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: -4.35 (0.35), residues: 300 helix: -2.77 (0.30), residues: 134 sheet: -1.20 (0.62), residues: 48 loop : -3.64 (0.41), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 18 TYR 0.044 0.013 TYR B 14 PHE 0.031 0.006 PHE B 70 TRP 0.014 0.003 TRP B 68 HIS 0.001 0.001 HIS B 64 Individual atomic B min max mean iso aniso Overall: 3.07 82.07 54.06 7.85 2452 0 Protein: 3.07 82.07 54.06 7.85 2452 0 Chain A: 19.98 82.07 60.93 N/A 1226 0 Chain B: 3.07 82.07 47.19 N/A 1226 0 Histogram: Values Number of atoms 3.07 - 10.97 7 10.97 - 18.87 37 18.87 - 26.77 157 26.77 - 34.67 269 34.67 - 42.57 432 42.57 - 50.47 311 50.47 - 58.37 225 58.37 - 66.27 175 66.27 - 74.17 168 74.17 - 82.07 671 |-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 - 25.19 A, n_refl.=9450 (all), 10.31 % free)-------------| | | | r_work= 0.3217 r_free= 0.3511 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 3.705103 | | target function (ml) not normalized (work): 31404.451511 | | target function (ml) not normalized (free): 3715.470795 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3247 0.3217 0.3511 n_refl.: 9450 re-set all scales: r(all,work,free)=0.3247 0.3217 0.3511 n_refl.: 9450 remove outliers: r(all,work,free)=0.3236 0.3204 0.3511 n_refl.: 9446 overall B=13.55 to atoms: r(all,work,free)=0.3613 0.3590 0.3804 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2315 0.2277 0.2633 n_refl.: 9446 remove outliers: r(all,work,free)=0.2315 0.2277 0.2633 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3157 2409.358 2177.841 1.252 1.038 0.395 14.006-11.401 95.00 85 10 0.2454 2701.504 2688.352 1.107 1.036 0.323 11.401-9.290 97.27 153 25 0.1596 3217.750 3143.081 1.127 1.033 0.319 9.217-7.555 99.08 294 28 0.1790 2200.652 2184.414 1.105 1.028 0.314 7.516-6.153 99.14 515 63 0.2361 1434.928 1379.068 0.969 1.020 0.306 6.131-5.015 99.81 954 115 0.2370 1346.854 1284.162 0.869 1.007 0.241 5.003-4.077 99.75 1757 207 0.1907 1481.164 1430.652 1.031 0.989 0.219 4.074-3.318 98.51 3188 384 0.2391 885.086 840.039 1.055 0.960 0.089 3.316-3.104 91.27 1438 130 0.3486 500.142 441.212 0.903 0.937 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0493 b_overall=4.7319 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 16.000366 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.217311 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 0.2428 0.2680 0.0252 0.002 0.5 5.0 2.7 6.8 0 0.125 0.2396 0.2665 0.0269 0.002 0.5 5.0 2.7 6.8 0 0.250 0.2325 0.2649 0.0324 0.003 0.5 5.9 2.7 6.8 0 0.500 0.2244 0.2638 0.0394 0.003 0.6 9.1 3.3 6.8 0 1.000 0.2177 0.2655 0.0477 0.005 0.7 11.1 3.3 6.8 0 2.000 0.2155 0.2670 0.0515 0.007 0.8 13.9 3.0 7.1 0 3.000 0.2136 0.2677 0.0541 0.009 1.0 14.5 3.0 7.1 0 4.000 0.2123 0.2694 0.0571 0.010 1.1 16.1 3.0 7.1 0 5.000 0.2107 0.2696 0.0589 0.012 1.2 17.2 3.3 7.1 0 6.000 0.2094 0.2687 0.0593 0.013 1.3 17.6 3.3 7.1 0 7.000 0.2079 0.2690 0.0611 0.015 1.4 18.2 3.3 7.5 0 8.000 0.2071 0.2682 0.0611 0.016 1.4 19.4 2.7 7.5 0 9.000 0.2058 0.2682 0.0624 0.018 1.5 19.8 2.7 7.5 0 10.000 0.2079 0.2690 0.0611 0.015 1.4 18.2 3.3 7.5 0 8.000 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2396 0.2665 0.0269 0.002 0.5 5.0 2.7 6.8 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.96 26.65 2.69 5.550 67.315 0.217 0.064 23.90 25.90 2.00 6.149 68.229 0.007 0.063 23.61 25.83 2.21 6.152 68.227 0.027 0.062 22.88 25.63 2.74 6.657 68.298 0.109 0.058 22.41 25.48 3.07 7.509 68.418 0.217 0.056 22.13 25.45 3.32 8.319 68.578 0.326 0.055 21.85 25.42 3.57 9.486 68.929 0.435 0.054 21.73 25.45 3.73 10.065 69.042 0.543 0.053 21.64 25.47 3.84 10.555 69.140 0.652 0.053 21.57 25.51 3.94 10.968 69.225 0.761 0.052 21.48 25.52 4.04 11.618 69.402 0.869 0.052 21.41 25.52 4.11 12.130 69.533 0.978 0.052 21.37 25.54 4.17 12.478 69.613 1.087 0.051 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.435 Accepted refinement result: 21.85 25.42 3.57 9.486 68.929 0.435 0.054 Individual atomic B min max mean iso aniso Overall: 24.98 123.92 70.88 8.62 2452 0 Protein: 24.98 123.92 70.88 8.62 2452 0 Chain A: 37.53 123.55 77.71 N/A 1226 0 Chain B: 24.98 123.92 64.06 N/A 1226 0 Histogram: Values Number of atoms 24.98 - 34.87 16 34.87 - 44.77 195 44.77 - 54.66 421 54.66 - 64.56 443 64.56 - 74.45 359 74.45 - 84.34 263 84.34 - 94.24 398 94.24 - 104.13 233 104.13 - 114.03 107 114.03 - 123.92 17 =========================== Idealize ADP of riding H ========================== r_work=0.2185 r_free=0.2542 r_work=0.2158 r_free=0.2533 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2158 r_free= 0.2533 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ls_wunit_k1) (work): 0.052438 | | target function (ls_wunit_k1) not normalized (work): 444.303584 | | target function (ls_wunit_k1) not normalized (free): 74.739515 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2198 0.2158 0.2533 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3656 0.3628 0.3891 n_refl.: 9446 remove outliers: r(all,work,free)=0.3656 0.3628 0.3891 n_refl.: 9446 overall B=2.36 to atoms: r(all,work,free)=0.3741 0.3713 0.3968 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2194 0.2152 0.2539 n_refl.: 9446 remove outliers: r(all,work,free)=0.2194 0.2152 0.2539 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.2921 1496.264 1402.130 1.107 1.039 0.364 14.006-11.401 95.00 85 10 0.2235 1677.693 1692.007 1.110 1.037 0.330 11.401-9.290 97.27 153 25 0.1496 1998.293 1960.042 1.075 1.034 0.318 9.217-7.555 99.08 294 28 0.1623 1366.653 1364.789 1.079 1.028 0.317 7.516-6.153 99.14 515 63 0.2274 891.122 859.947 0.951 1.020 0.296 6.131-5.015 99.81 954 115 0.2175 836.426 802.637 0.881 1.006 0.265 5.003-4.077 99.75 1757 207 0.1708 919.835 901.112 1.029 0.986 0.223 4.074-3.318 98.51 3188 384 0.2390 549.658 525.418 1.090 0.956 0.076 3.316-3.104 91.27 1438 130 0.3319 310.599 278.993 0.973 0.930 0.066 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.5378 ============================ 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 = 5.537027 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049474 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 0.2097 0.2487 0.0390 0.002 0.5 5.2 2.7 6.4 0 0.125 0.2047 0.2483 0.0436 0.003 0.5 5.9 2.7 6.4 0 0.250 0.2000 0.2516 0.0516 0.004 0.6 7.5 2.7 6.8 0 0.500 0.1964 0.2536 0.0572 0.007 0.8 9.9 2.7 7.5 0 1.000 0.1937 0.2556 0.0619 0.011 1.1 14.5 3.3 7.9 0 2.000 0.1912 0.2561 0.0649 0.016 1.4 15.9 3.3 8.3 0 3.000 0.1903 0.2547 0.0644 0.018 1.5 14.1 3.0 8.3 0 4.000 0.1869 0.2613 0.0744 0.021 1.7 17.4 5.7 12.4 0 5.000 0.1861 0.2610 0.0750 0.023 1.9 18.4 5.7 12.4 0 6.000 0.1868 0.2569 0.0701 0.031 2.2 18.4 3.0 8.6 0 7.000 0.1842 0.2644 0.0802 0.029 2.2 20.4 7.0 15.0 0 8.000 0.1835 0.2640 0.0805 0.031 2.4 20.2 7.7 15.4 0 9.000 0.1830 0.2637 0.0807 0.034 2.5 20.4 8.0 14.7 0 10.000 0.1919 0.2554 0.0635 0.014 1.3 15.3 3.7 7.9 0 2.769 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2097 0.2487 0.0390 0.002 0.5 5.2 2.7 6.4 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.97 24.87 3.90 12.172 80.899 0.049 6.627 24.79 25.96 1.18 11.630 86.034 0.001 6.676 23.66 25.23 1.58 11.435 84.881 0.006 6.659 22.21 24.70 2.49 12.048 82.507 0.025 6.628 21.33 24.67 3.35 12.447 81.853 0.049 6.610 21.01 24.71 3.70 12.984 81.912 0.074 6.602 20.71 24.78 4.07 13.384 82.016 0.099 6.597 20.60 24.86 4.26 13.653 82.025 0.124 6.597 20.54 24.92 4.38 13.901 82.085 0.148 6.596 20.48 24.99 4.50 14.204 82.211 0.173 6.596 20.46 25.03 4.58 14.290 82.207 0.198 6.596 20.42 25.07 4.65 14.518 82.304 0.223 6.596 20.41 25.11 4.70 14.657 82.357 0.247 6.596 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.049 Accepted refinement result: 21.33 24.67 3.35 12.447 81.853 0.049 6.610 Individual atomic B min max mean iso aniso Overall: 32.23 129.00 75.18 8.60 2452 0 Protein: 32.23 129.00 75.18 8.60 2452 0 Chain A: 35.51 128.78 82.55 N/A 1226 0 Chain B: 32.23 129.00 67.80 N/A 1226 0 Histogram: Values Number of atoms 32.23 - 41.91 40 41.91 - 51.59 239 51.59 - 61.26 425 61.26 - 70.94 459 70.94 - 80.62 371 80.62 - 90.29 330 90.29 - 99.97 257 99.97 - 109.64 197 109.64 - 119.32 90 119.32 - 129.00 44 =========================== Idealize ADP of riding H ========================== r_work=0.2133 r_free=0.2467 r_work=0.2146 r_free=0.2476 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2146 r_free= 0.2476 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ml) (work): 6.611026 | | target function (ml) not normalized (work): 56015.227207 | | target function (ml) not normalized (free): 6583.670889 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2181 0.2146 0.2476 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3827 0.3804 0.4016 n_refl.: 9446 remove outliers: r(all,work,free)=0.3827 0.3804 0.4016 n_refl.: 9446 overall B=-1.22 to atoms: r(all,work,free)=0.3780 0.3757 0.3974 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2180 0.2144 0.2478 n_refl.: 9446 remove outliers: r(all,work,free)=0.2180 0.2144 0.2478 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3053 1496.264 1388.306 1.059 1.018 0.353 14.006-11.401 95.00 85 10 0.2140 1677.693 1687.673 1.076 1.017 0.321 11.401-9.290 97.27 153 25 0.1475 1998.293 1955.548 1.068 1.016 0.321 9.217-7.555 99.08 294 28 0.1702 1366.653 1356.380 1.085 1.013 0.315 7.516-6.153 99.14 515 63 0.2393 891.122 852.131 0.968 1.009 0.302 6.131-5.015 99.81 954 115 0.2341 836.426 794.085 0.892 1.002 0.283 5.003-4.077 99.75 1757 207 0.1773 919.835 894.018 1.013 0.992 0.234 4.074-3.318 98.51 3188 384 0.2251 549.658 523.441 1.057 0.975 0.076 3.316-3.104 91.27 1438 130 0.3038 310.599 279.986 0.942 0.962 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.2674 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2144 r_free=0.2478 After: r_work=0.2144 r_free=0.2478 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.876492 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.047109 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 0.2143 0.2478 0.0335 0.002 0.5 5.4 2.7 6.4 0 0.125 0.2141 0.2477 0.0337 0.002 0.5 5.4 2.7 6.4 0 0.250 0.2130 0.2477 0.0346 0.004 0.5 5.9 3.0 6.4 0 0.500 0.2053 0.2480 0.0427 0.011 0.8 8.9 2.7 6.4 0 1.000 0.1950 0.2524 0.0574 0.013 1.4 18.2 3.3 7.9 0 2.000 0.1940 0.2499 0.0559 0.014 1.4 15.5 3.3 7.5 0 3.000 0.1920 0.2517 0.0597 0.018 1.6 16.1 3.3 8.3 0 4.000 0.1880 0.2549 0.0669 0.023 2.2 23.4 3.7 9.0 0 5.000 0.1876 0.2532 0.0656 0.024 2.2 23.0 3.7 9.0 0 6.000 0.1867 0.2543 0.0676 0.027 2.5 23.8 4.0 9.8 0 7.000 0.1866 0.2529 0.0663 0.026 2.4 22.6 4.0 9.8 0 8.000 0.1851 0.2533 0.0682 0.030 2.6 21.2 4.0 9.8 0 9.000 0.1841 0.2561 0.0720 0.031 2.9 24.6 4.3 12.0 0 10.000 0.1942 0.2499 0.0557 0.014 1.3 14.3 3.0 7.5 0 2.938 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2143 0.2478 0.0335 0.002 0.5 5.4 2.7 6.4 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.43 24.78 3.35 12.623 81.819 0.047 6.613 25.25 26.20 0.95 11.152 87.409 0.001 6.681 24.22 25.72 1.50 10.833 86.990 0.006 6.665 22.19 24.52 2.33 12.093 82.774 0.024 6.634 21.12 24.60 3.48 12.522 82.257 0.047 6.609 20.58 24.71 4.13 13.316 82.620 0.071 6.597 20.51 24.79 4.28 13.811 82.443 0.094 6.594 20.44 24.86 4.42 14.163 82.504 0.118 6.593 20.39 24.93 4.55 14.483 82.633 0.141 6.593 20.41 24.93 4.52 14.481 82.539 0.165 6.593 20.38 24.96 4.57 14.643 82.604 0.188 6.592 20.34 25.00 4.66 14.899 82.745 0.212 6.592 20.32 25.03 4.71 15.057 82.820 0.236 6.591 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.024 Accepted refinement result: 22.19 24.52 2.33 12.093 82.774 0.024 6.634 Individual atomic B min max mean iso aniso Overall: 38.06 127.85 75.89 5.53 2452 0 Protein: 38.06 127.85 75.89 5.53 2452 0 Chain A: 38.06 127.85 83.79 N/A 1226 0 Chain B: 38.87 122.78 67.99 N/A 1226 0 Histogram: Values Number of atoms 38.06 - 47.04 62 47.04 - 56.02 302 56.02 - 65.00 451 65.00 - 73.98 503 73.98 - 82.95 357 82.95 - 91.93 226 91.93 - 100.91 215 100.91 - 109.89 200 109.89 - 118.87 107 118.87 - 127.85 29 =========================== Idealize ADP of riding H ========================== r_work=0.2219 r_free=0.2452 r_work=0.2231 r_free=0.2456 ----------X-ray data---------- |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2231 r_free= 0.2456 coordinate error (max.-lik. estimate): 0.38 A | | | | normalized target function (ml) (work): 6.637190 | | target function (ml) not normalized (work): 56236.909473 | | target function (ml) not normalized (free): 6581.082903 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 25.19 - 5.92 0.99 1276 155 0.2126 0.2463 7.1573 7.3943| | 2: 5.91 - 4.71 1.00 1245 142 0.2095 0.2269 6.9304 7.0444| | 3: 4.70 - 4.12 1.00 1230 149 0.1839 0.2057 6.8043 6.904| | 4: 4.11 - 3.74 0.99 1195 141 0.2354 0.2498 6.6438 6.6971| | 5: 3.74 - 3.47 0.99 1236 140 0.2309 0.2480 6.4611 6.5532| | 6: 3.47 - 3.27 0.98 1167 145 0.2714 0.3130 6.2678 6.3475| | 7: 3.27 - 3.10 0.90 1124 101 0.3360 0.3550 6.1093 6.1765| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 25.19 - 5.92 1276 155 0.80 26.03 0.98 1.01 306446.24| | 2: 5.91 - 4.71 1245 142 0.76 30.31 1.00 1.02 272912.74| | 3: 4.70 - 4.12 1230 149 0.83 23.48 1.02 1.05 173486.96| | 4: 4.11 - 3.74 1195 141 0.78 28.44 1.06 1.04 130939.12| | 5: 3.74 - 3.47 1236 140 0.80 27.46 1.01 1.02 88177.12| | 6: 3.47 - 3.27 1167 145 0.76 30.72 0.96 0.96 59391.30| | 7: 3.27 - 3.10 1124 101 0.65 40.19 1.02 0.94 50516.75| |alpha: min = 0.94 max = 1.05 mean = 1.01| |beta: min = 50516.75 max = 306446.24 mean = 157646.69| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.78 mean = 29.36| |phase err.(test): min = 0.00 max = 86.30 mean = 28.08| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2256 0.2231 0.2456 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3921 0.3903 0.4070 n_refl.: 9446 remove outliers: r(all,work,free)=0.3921 0.3903 0.4070 n_refl.: 9446 overall B=-3.08 to atoms: r(all,work,free)=0.3805 0.3786 0.3963 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2252 0.2227 0.2457 n_refl.: 9446 remove outliers: r(all,work,free)=0.2252 0.2227 0.2457 n_refl.: 9446 ======================== 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 25.192-14.006 95.24 89 11 0.3046 1496.264 1390.575 1.090 1.020 0.353 14.006-11.401 95.00 85 10 0.2142 1677.693 1686.794 1.109 1.019 0.322 11.401-9.290 97.27 153 25 0.1462 1998.293 1960.475 1.102 1.018 0.322 9.217-7.555 99.08 294 28 0.1731 1366.653 1355.615 1.120 1.015 0.320 7.516-6.153 99.14 515 63 0.2428 891.122 853.637 1.003 1.011 0.315 6.131-5.015 99.81 954 115 0.2322 836.426 796.446 0.916 1.003 0.287 5.003-4.077 99.75 1757 207 0.1847 919.835 894.415 1.039 0.992 0.239 4.074-3.318 98.51 3188 384 0.2422 549.658 522.054 1.075 0.974 0.068 3.316-3.104 91.27 1438 130 0.3214 310.599 279.076 0.975 0.959 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.7669 ================= 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 : 0.3217 0.3511 0.009 1.390 3.1 82.1 54.1 0 0.000 1_bss: 0.2277 0.2633 0.009 1.390 16.6 95.6 67.6 0 0.000 1_settarget: 0.2277 0.2633 0.009 1.390 16.6 95.6 67.6 0 0.000 1_weight: 0.2277 0.2633 0.009 1.390 16.6 95.6 67.6 0 0.000 1_xyzrec: 0.2396 0.2665 0.002 0.488 16.6 95.6 67.6 0 0.194 1_adp: 0.2185 0.2542 0.002 0.488 25.0 123.9 70.9 0 0.194 1_regHadp: 0.2158 0.2533 0.002 0.488 25.0 123.9 70.9 0 0.194 2_bss: 0.2152 0.2539 0.002 0.488 27.3 126.3 73.2 0 0.194 2_settarget: 0.2152 0.2539 0.002 0.488 27.3 126.3 73.2 0 0.194 2_updatecdl: 0.2152 0.2539 0.002 0.576 27.3 126.3 73.2 0 0.194 2_weight: 0.2152 0.2539 0.002 0.576 27.3 126.3 73.2 0 0.194 2_xyzrec: 0.2097 0.2487 0.002 0.474 27.3 126.3 73.2 0 0.211 2_adp: 0.2133 0.2467 0.002 0.474 32.2 129.0 75.2 0 0.211 2_regHadp: 0.2146 0.2476 0.002 0.474 32.2 129.0 75.2 0 0.211 3_bss: 0.2144 0.2478 0.002 0.474 31.0 127.8 74.0 0 0.211 3_settarget: 0.2144 0.2478 0.002 0.474 31.0 127.8 74.0 0 0.211 3_updatecdl: 0.2144 0.2478 0.002 0.515 31.0 127.8 74.0 0 0.211 3_setrh: 0.2144 0.2478 0.002 0.515 31.0 127.8 74.0 0 0.211 3_weight: 0.2144 0.2478 0.002 0.515 31.0 127.8 74.0 0 0.211 3_xyzrec: 0.2143 0.2478 0.002 0.484 31.0 127.8 74.0 0 0.211 3_adp: 0.2219 0.2452 0.002 0.484 38.1 127.8 75.9 0 0.211 3_regHadp: 0.2231 0.2456 0.002 0.484 38.1 127.8 75.9 0 0.211 end: 0.2227 0.2457 0.002 0.484 35.0 124.8 72.8 0 0.211 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1x24_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V1/1x24_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.0400 Refinement macro-cycles (run) : 219.7900 Write final files (write_after_run_outputs) : 23.7900 Total : 248.6200 Total CPU time: 4.50 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:32:51 PDT -0700 (1716251571.25 s) Start R-work = 0.2277, R-free = 0.2633 Final R-work = 0.2227, R-free = 0.2457 =============================================================================== Job complete usr+sys time: 296.33 seconds wall clock time: 17 minutes 3.13 seconds (1023.13 seconds total)