Starting phenix.refine on Mon May 20 17:17:06 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=True secondary_structure.enabled=False main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/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 { 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 TYR 53": "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: 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: 2.00, per 1000 atoms: 0.40 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: 2.57 Conformation dependent library (CDL) restraints added in 373.1 milliseconds 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 572 Time building geometry restraints manager: 2.47 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 { ramachandran_plot_restraints { enabled = True } 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 ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 15.741296 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 0.2396 0.2685 0.0289 0.003 0.6 8.5 2.0 6.8 0 0.125 0.2378 0.2679 0.0301 0.003 0.6 8.7 2.0 6.8 0 0.250 0.2342 0.2660 0.0318 0.004 0.7 9.9 2.0 6.8 0 0.500 0.2292 0.2644 0.0352 0.004 0.7 9.7 2.0 6.4 0 1.000 0.2226 0.2646 0.0420 0.006 0.8 12.5 2.3 6.4 0 2.000 0.2171 0.2654 0.0484 0.007 0.9 13.3 2.3 6.4 0 3.000 0.2148 0.2662 0.0514 0.009 1.0 14.7 2.7 6.8 0 4.000 0.2129 0.2666 0.0537 0.010 1.1 15.7 2.7 6.8 0 5.000 0.2116 0.2672 0.0556 0.012 1.2 16.3 2.3 6.8 0 6.000 0.2102 0.2670 0.0568 0.014 1.3 16.5 2.3 7.1 0 7.000 0.2086 0.2679 0.0593 0.015 1.4 18.8 2.3 7.1 0 8.000 0.2070 0.2681 0.0610 0.017 1.5 19.4 2.3 7.1 0 9.000 0.2063 0.2680 0.0617 0.018 1.5 20.0 2.3 7.5 0 10.000 0.2088 0.2682 0.0593 0.015 1.4 18.6 2.3 7.1 0 7.871 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2396 0.2685 0.0289 0.003 0.6 8.5 2.0 6.8 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.96 26.85 2.89 5.550 67.315 0.217 0.065 23.95 26.12 2.17 6.160 68.230 0.007 0.065 23.66 26.09 2.42 6.172 68.226 0.027 0.063 22.90 25.98 3.08 6.706 68.294 0.109 0.060 22.40 25.89 3.49 7.645 68.422 0.217 0.057 22.08 25.85 3.77 8.592 68.610 0.326 0.056 21.81 25.90 4.09 9.815 68.945 0.435 0.055 21.68 25.94 4.26 10.477 69.074 0.543 0.054 21.58 25.97 4.39 11.012 69.177 0.652 0.054 21.50 25.98 4.47 11.469 69.272 0.761 0.053 21.44 26.01 4.57 11.904 69.364 0.869 0.053 21.40 26.03 4.63 12.202 69.420 0.978 0.053 21.32 26.05 4.73 12.888 69.609 1.087 0.052 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.326 Accepted refinement result: 22.08 25.85 3.77 8.592 68.610 0.326 0.056 Individual atomic B min max mean iso aniso Overall: 21.81 119.72 70.24 7.71 2452 0 Protein: 21.81 119.72 70.24 7.71 2452 0 Chain A: 37.90 119.72 77.00 N/A 1226 0 Chain B: 21.81 118.40 63.48 N/A 1226 0 Histogram: Values Number of atoms 21.81 - 31.60 4 31.60 - 41.39 108 41.39 - 51.18 381 51.18 - 60.97 446 60.97 - 70.77 396 70.77 - 80.56 298 80.56 - 90.35 233 90.35 - 100.14 411 100.14 - 109.93 152 109.93 - 119.72 23 =========================== Idealize ADP of riding H ========================== r_work=0.2208 r_free=0.2585 r_work=0.2181 r_free=0.2569 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2181 r_free= 0.2569 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ls_wunit_k1) (work): 0.054746 | | target function (ls_wunit_k1) not normalized (work): 463.858791 | | target function (ls_wunit_k1) not normalized (free): 75.608826 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2223 0.2181 0.2569 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3661 0.3634 0.3882 n_refl.: 9446 remove outliers: r(all,work,free)=0.3661 0.3634 0.3882 n_refl.: 9446 overall B=0.00 to atoms: r(all,work,free)=0.3661 0.3634 0.3882 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2222 0.2180 0.2572 n_refl.: 9446 remove outliers: r(all,work,free)=0.2222 0.2180 0.2572 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 0.3115 1505.599 1380.027 1.269 1.024 0.390 14.006-11.401 95.00 85 10 0.2272 1688.160 1699.881 1.177 1.023 0.330 11.401-9.290 97.27 153 25 0.1556 2010.761 1966.613 1.140 1.022 0.320 9.217-7.555 99.08 294 28 0.1712 1375.180 1367.710 1.132 1.018 0.313 7.516-6.153 99.14 515 63 0.2310 896.681 862.460 0.999 1.013 0.310 6.131-5.015 99.81 954 115 0.2194 841.645 808.136 0.921 1.005 0.280 5.003-4.077 99.75 1757 207 0.1755 925.574 903.276 1.049 0.992 0.230 4.074-3.318 98.51 3188 384 0.2389 553.087 528.112 1.081 0.972 0.069 3.316-3.104 91.27 1438 130 0.3269 312.537 280.257 0.951 0.956 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.9289 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.183551 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.050927 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 0.2173 0.2531 0.0359 0.002 0.5 5.6 1.3 6.4 0 0.125 0.2102 0.2516 0.0414 0.003 0.6 5.6 1.3 7.5 0 0.250 0.2035 0.2513 0.0477 0.004 0.7 7.9 1.7 7.9 0 0.500 0.1983 0.2525 0.0541 0.007 0.9 11.1 2.0 8.3 0 1.000 0.1943 0.2526 0.0582 0.011 1.1 15.5 2.0 7.9 0 2.000 0.1926 0.2523 0.0597 0.015 1.4 15.9 2.0 7.5 0 3.000 0.1905 0.2531 0.0626 0.020 1.7 18.8 2.0 8.3 0 4.000 0.1894 0.2540 0.0646 0.023 1.9 19.8 1.7 8.3 0 5.000 0.1884 0.2547 0.0662 0.027 2.0 19.4 1.7 8.3 0 6.000 0.1852 0.2584 0.0732 0.027 2.1 16.9 2.3 15.8 0 7.000 0.1845 0.2591 0.0746 0.029 2.2 19.0 2.7 18.0 0 8.000 0.1842 0.2607 0.0765 0.032 2.4 20.0 2.7 19.2 0 9.000 0.1831 0.2602 0.0770 0.035 2.5 21.4 3.0 19.2 0 10.000 0.1930 0.2522 0.0592 0.014 1.3 15.9 2.0 7.9 0 2.592 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2173 0.2531 0.0359 0.002 0.5 5.6 1.3 6.4 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.73 25.31 3.59 11.765 77.793 0.051 6.648 25.49 26.52 1.03 11.585 83.113 0.002 6.697 24.37 25.73 1.36 11.342 82.218 0.006 6.680 22.72 24.93 2.21 11.802 79.519 0.025 6.644 21.77 24.90 3.14 12.260 78.885 0.051 6.625 21.42 24.97 3.54 12.785 78.916 0.076 6.619 21.26 25.04 3.78 13.351 79.144 0.102 6.615 21.07 25.04 3.98 13.414 79.005 0.127 6.613 21.00 25.09 4.09 13.688 79.100 0.153 6.612 20.95 25.14 4.19 13.972 79.223 0.178 6.611 20.93 25.17 4.23 14.035 79.210 0.204 6.611 20.91 25.20 4.29 14.248 79.304 0.229 6.611 20.89 25.23 4.34 14.441 79.390 0.255 6.610 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.051 Accepted refinement result: 21.77 24.90 3.14 12.260 78.885 0.051 6.625 Individual atomic B min max mean iso aniso Overall: 28.26 127.08 72.45 8.83 2452 0 Protein: 28.26 127.08 72.45 8.83 2452 0 Chain A: 33.14 125.37 79.81 N/A 1226 0 Chain B: 28.26 127.08 65.09 N/A 1226 0 Histogram: Values Number of atoms 28.26 - 38.14 29 38.14 - 48.03 228 48.03 - 57.91 435 57.91 - 67.79 446 67.79 - 77.67 370 77.67 - 87.55 358 87.55 - 97.44 257 97.44 - 107.32 192 107.32 - 117.20 101 117.20 - 127.08 36 =========================== Idealize ADP of riding H ========================== r_work=0.2177 r_free=0.2490 r_work=0.2184 r_free=0.2496 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2184 r_free= 0.2496 coordinate error (max.-lik. estimate): 0.42 A | | | | normalized target function (ml) (work): 6.625380 | | target function (ml) not normalized (work): 56136.841559 | | target function (ml) not normalized (free): 6593.289018 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2218 0.2184 0.2496 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3741 0.3715 0.3962 n_refl.: 9446 remove outliers: r(all,work,free)=0.3741 0.3715 0.3962 n_refl.: 9446 overall B=0.00 to atoms: r(all,work,free)=0.3741 0.3715 0.3962 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2220 0.2184 0.2516 n_refl.: 9446 remove outliers: r(all,work,free)=0.2220 0.2184 0.2516 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 0.3031 1505.599 1396.125 1.140 1.016 0.365 14.006-11.401 95.00 85 10 0.2217 1688.160 1694.710 1.144 1.015 0.331 11.401-9.290 97.27 153 25 0.1534 2010.761 1963.840 1.099 1.014 0.320 9.217-7.555 99.08 294 28 0.1749 1375.180 1361.178 1.123 1.012 0.320 7.516-6.153 99.14 515 63 0.2474 896.681 854.213 0.996 1.009 0.300 6.131-5.015 99.81 954 115 0.2361 841.645 797.320 0.903 1.003 0.270 5.003-4.077 99.75 1757 207 0.1809 925.574 897.391 1.030 0.994 0.230 4.074-3.318 98.51 3188 384 0.2300 553.087 526.008 1.064 0.980 0.070 3.316-3.104 91.27 1438 130 0.3040 312.537 280.954 0.945 0.969 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=1.2636 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 600 Ramachandran restraints generated. 300 Oldfield, 0 Emsley, 300 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2184 r_free=0.2516 After: r_work=0.2184 r_free=0.2516 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.062648 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.048926 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 0.2184 0.2516 0.0332 0.002 0.5 6.1 1.3 6.4 0 0.125 0.2182 0.2516 0.0334 0.002 0.5 6.1 1.3 6.4 0 0.250 0.2166 0.2506 0.0341 0.004 0.5 6.1 1.3 6.4 0 0.500 0.2047 0.2485 0.0438 0.011 1.1 8.9 1.0 7.9 0 1.000 0.1974 0.2500 0.0525 0.012 1.3 12.7 1.7 7.9 0 2.000 0.1938 0.2531 0.0593 0.016 1.6 15.3 1.7 7.9 0 3.000 0.1921 0.2548 0.0627 0.018 1.7 20.4 1.7 8.3 0 4.000 0.1896 0.2558 0.0662 0.022 2.1 22.4 2.0 9.0 0 5.000 0.1891 0.2558 0.0667 0.023 2.2 21.2 2.0 9.0 0 6.000 0.1872 0.2561 0.0689 0.026 2.4 20.6 2.0 9.4 0 7.000 0.1857 0.2572 0.0715 0.029 2.7 23.4 2.0 10.2 0 8.000 0.1869 0.2560 0.0691 0.028 2.4 21.6 2.0 9.8 0 9.000 0.1860 0.2566 0.0706 0.029 2.6 21.8 2.0 10.5 0 10.000 0.1936 0.2529 0.0593 0.016 1.6 15.5 1.7 7.9 0 3.031 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2166 0.2506 0.0341 0.004 0.5 6.1 1.3 6.4 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.66 25.06 3.41 12.370 79.973 0.049 6.625 25.48 26.64 1.16 11.127 85.519 0.001 6.693 24.32 25.89 1.57 10.885 84.465 0.006 6.679 22.63 24.91 2.28 11.762 81.252 0.024 6.648 21.44 24.99 3.55 11.912 80.971 0.049 6.624 20.86 25.13 4.26 12.803 80.767 0.073 6.610 20.70 25.28 4.58 13.453 80.739 0.098 6.608 20.59 25.38 4.80 13.986 80.902 0.122 6.606 20.51 25.47 4.96 14.426 81.061 0.147 6.605 20.46 25.54 5.08 14.836 81.228 0.171 6.604 20.45 25.57 5.11 14.947 81.217 0.196 6.604 20.53 25.55 5.02 14.698 80.999 0.220 6.606 20.51 25.59 5.08 14.881 81.078 0.245 6.606 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: 22.63 24.91 2.28 11.762 81.252 0.024 6.648 Individual atomic B min max mean iso aniso Overall: 34.64 133.10 75.03 5.73 2452 0 Protein: 34.64 133.10 75.03 5.73 2452 0 Chain A: 42.78 133.10 83.24 N/A 1226 0 Chain B: 34.64 122.08 66.83 N/A 1226 0 Histogram: Values Number of atoms 34.64 - 44.48 54 44.48 - 54.33 290 54.33 - 64.18 490 64.18 - 74.02 519 74.02 - 83.87 361 83.87 - 93.71 248 93.71 - 103.56 215 103.56 - 113.41 183 113.41 - 123.25 81 123.25 - 133.10 11 =========================== Idealize ADP of riding H ========================== r_work=0.2263 r_free=0.2491 r_work=0.2278 r_free=0.2494 ----------X-ray data---------- |--(resolution: 3.10 - 25.19 A, n_refl.=9446 (all), 10.30 % free)-------------| | | | r_work= 0.2278 r_free= 0.2494 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 6.652692 | | target function (ml) not normalized (work): 56368.256684 | | target function (ml) not normalized (free): 6592.681090 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2186 0.2479 7.1768 7.4046| | 2: 5.91 - 4.71 1.00 1245 142 0.2133 0.2304 6.9425 7.0364| | 3: 4.70 - 4.12 1.00 1230 149 0.1903 0.2070 6.8313 6.9127| | 4: 4.11 - 3.74 0.99 1195 141 0.2411 0.2583 6.6593 6.7248| | 5: 3.74 - 3.47 0.99 1236 140 0.2361 0.2638 6.4834 6.5942| | 6: 3.47 - 3.27 0.98 1167 145 0.2696 0.2984 6.2737 6.3306| | 7: 3.27 - 3.10 0.90 1124 101 0.3369 0.3737 6.1139 6.2029| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.79 26.33 0.98 0.98 313590.54| | 2: 5.91 - 4.71 1245 142 0.76 30.68 1.01 0.99 279892.16| | 3: 4.70 - 4.12 1230 149 0.83 23.93 1.01 1.01 179977.54| | 4: 4.11 - 3.74 1195 141 0.78 29.07 1.06 1.00 136387.69| | 5: 3.74 - 3.47 1236 140 0.79 28.04 1.02 0.99 92578.42| | 6: 3.47 - 3.27 1167 145 0.76 30.94 0.96 0.93 61098.37| | 7: 3.27 - 3.10 1124 101 0.65 40.49 1.02 0.91 51393.20| |alpha: min = 0.91 max = 1.01 mean = 0.97| |beta: min = 51393.20 max = 313590.54 mean = 162452.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 90.00 mean = 29.77| |phase err.(test): min = 0.00 max = 89.55 mean = 28.54| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2301 0.2278 0.2494 n_refl.: 9446 re-set all scales: r(all,work,free)=0.3889 0.3868 0.4062 n_refl.: 9446 remove outliers: r(all,work,free)=0.3889 0.3868 0.4062 n_refl.: 9446 overall B=-1.63 to atoms: r(all,work,free)=0.3828 0.3807 0.4006 n_refl.: 9446 bulk-solvent and scaling: r(all,work,free)=0.2296 0.2272 0.2496 n_refl.: 9446 remove outliers: r(all,work,free)=0.2296 0.2272 0.2496 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 0.3017 1505.599 1393.628 1.100 1.023 0.366 14.006-11.401 95.00 85 10 0.2214 1688.160 1692.191 1.109 1.023 0.332 11.401-9.290 97.27 153 25 0.1530 2010.761 1967.636 1.067 1.021 0.321 9.217-7.555 99.08 294 28 0.1779 1375.180 1360.178 1.096 1.018 0.322 7.516-6.153 99.14 515 63 0.2498 896.681 854.960 0.974 1.013 0.303 6.131-5.015 99.81 954 115 0.2367 841.645 799.196 0.889 1.005 0.274 5.003-4.077 99.75 1757 207 0.1911 925.574 896.439 1.018 0.992 0.225 4.074-3.318 98.51 3188 384 0.2455 553.087 524.690 1.058 0.972 0.059 3.316-3.104 91.27 1438 130 0.3208 312.537 280.552 0.966 0.957 0.052 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.3410 ================= 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_updatephipsi: 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 0.2685 0.003 0.643 16.6 95.6 67.6 0 0.147 1_adp: 0.2208 0.2585 0.003 0.643 21.8 119.7 70.2 0 0.147 1_regHadp: 0.2181 0.2569 0.003 0.643 21.8 119.7 70.2 0 0.147 2_bss: 0.2180 0.2572 0.003 0.643 21.8 119.7 70.2 0 0.147 2_settarget: 0.2180 0.2572 0.003 0.643 21.8 119.7 70.2 0 0.147 2_updatephipsi: 0.2180 0.2572 0.003 0.643 21.8 119.7 70.2 0 0.147 2_updatecdl: 0.2180 0.2572 0.003 0.689 21.8 119.7 70.2 0 0.147 2_weight: 0.2180 0.2572 0.003 0.689 21.8 119.7 70.2 0 0.147 2_xyzrec: 0.2173 0.2531 0.002 0.499 21.8 119.7 70.2 0 0.232 2_adp: 0.2177 0.2490 0.002 0.499 28.3 127.1 72.4 0 0.232 2_regHadp: 0.2184 0.2496 0.002 0.499 28.3 127.1 72.4 0 0.232 3_bss: 0.2184 0.2516 0.002 0.499 28.3 127.1 72.4 0 0.232 3_settarget: 0.2184 0.2516 0.002 0.499 28.3 127.1 72.4 0 0.232 3_updatephipsi: 0.2184 0.2516 0.002 0.499 28.3 127.1 72.4 0 0.232 3_updatecdl: 0.2184 0.2516 0.002 0.534 28.3 127.1 72.4 0 0.232 3_setrh: 0.2184 0.2516 0.002 0.534 28.3 127.1 72.4 0 0.232 3_weight: 0.2184 0.2516 0.002 0.534 28.3 127.1 72.4 0 0.232 3_xyzrec: 0.2166 0.2506 0.004 0.539 28.3 127.1 72.4 0 0.232 3_adp: 0.2263 0.2491 0.004 0.539 34.6 133.1 75.0 0 0.232 3_regHadp: 0.2278 0.2494 0.004 0.539 34.6 133.1 75.0 0 0.232 end: 0.2272 0.2496 0.004 0.539 33.0 131.5 73.4 0 0.232 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1x24_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V2/1x24_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.9900 Refinement macro-cycles (run) : 239.4800 Write final files (write_after_run_outputs) : 22.9600 Total : 270.4300 Total CPU time: 5.11 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:17 PDT -0700 (1716251657.71 s) Start R-work = 0.2277, R-free = 0.2633 Final R-work = 0.2272, R-free = 0.2496 =============================================================================== Job complete usr+sys time: 331.84 seconds wall clock time: 17 minutes 41.82 seconds (1061.82 seconds total)