Starting qr.refine on Fri Jun 21 15:57:50 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4O8H.mtz Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4O8H.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- mode=refine restraints=qm engine=aimnet2 clustering=false minimizer=lbfgs number_of_weight_search_cycles=10 number_of_refine_cycles=5 expansion=true use_reduce=False select_within_radius=7 max_iterations_weight=100 max_bond_rmsd=0.03 max_angle_rmsd=3.0 gradient_only=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4O8H.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4O8H.pdb" miller_array { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4O8H.mtz" } default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4O8H.mtz" } use_reduce = False cluster { clustering = false select_within_radius = 7 } expansion = true quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server } refine { number_of_weight_search_cycles = 10 max_iterations_weight = 100 gradient_only = True max_angle_rmsd = 3.0 } Starting job =============================================================================== Validate inputs: ------------------------------------------------------------------------------- Refinement start **************** ------------------------------------------------------------------------------- Extracting fmodel ***************** start: r(all,work,free)=0.1310 0.1315 0.1270 n_refl.: 123342 re-set all scales: r(all,work,free)=0.1310 0.1315 0.1270 n_refl.: 123342 remove outliers: r(all,work,free)=0.1301 0.1307 0.1270 n_refl.: 123340 bulk-solvent and scaling: r(all,work,free)=0.1047 0.1041 0.1167 n_refl.: 123340 remove outliers: r(all,work,free)=0.1047 0.1041 0.1167 n_refl.: 123340 Resolution Compl Nwork Nfree R_work kiso kani kmask 29.596-10.246 100.00 93 6 0.1940 501.763 472.028 1.163 0.899 0.400 10.177-7.930 100.00 91 9 0.1746 479.446 466.441 1.161 0.900 0.400 7.929-6.185 100.00 198 10 0.1815 368.221 364.283 1.189 0.900 0.410 6.173-4.813 100.00 395 17 0.1446 435.838 425.627 1.166 0.900 0.440 4.812-3.754 100.00 805 46 0.1124 582.622 577.475 1.202 0.900 0.440 3.748-2.922 100.00 1685 76 0.1231 509.393 502.445 1.202 0.900 0.260 2.922-2.277 100.00 3410 183 0.1302 334.469 328.589 1.159 0.900 0.000 2.276-1.774 99.99 7110 384 0.1091 251.691 247.484 1.208 0.900 0.000 1.774-1.382 100.00 14808 836 0.0981 141.287 138.870 1.189 0.900 0.000 1.382-1.077 99.96 31030 1619 0.0794 95.308 93.755 1.184 0.899 0.000 1.077-0.850 95.46 57526 3003 0.1064 46.673 45.766 1.191 0.898 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0669 b_overall=-0.0081 ------------------------------------------------------------------------------- Starting r-factors: ******************* r_work=0.1041 r_free=0.1167 ------------------------------------------------------------------------------- Setting refinement target ************************* ml max_atoms = 50000 debug_rss = False debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = False cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 7 clustering_method = gnc *bcc altloc_method = average *subtract save_clusters = True bond_with_altloc = True re_calculate_rmsd_tolerance = 0.5 } restraints = cctbx *qm expansion = True quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server basis = Auto charge = None method = Auto memory = None nproc = 1 server_url = "http://127.0.0.1:8000" qm_addon = gcp dftd3 gcp-d3 qm_addon_method = None } refine { dry_run = False sf_algorithm = *direct fft refinement_target_name = *ml ls_wunit_k1 mode = opt *refine gtest number_of_macro_cycles = 1 number_of_weight_search_cycles = 10 number_of_refine_cycles = 5 number_of_micro_cycles = 50 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 100 max_iterations_refine = 50 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = True refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.03 max_angle_rmsd = 3 stop_one_found_first_good_weight = True max_r_work_r_free_gap = 5 r_tolerance = 0.001 rmsd_tolerance = 0.01 opt_log = False pre_opt = False pre_opt_stpmax = 0.1 pre_opt_iter = 10 pre_opt_switch = 2 pre_opt_gconv = 3000 minimizer = *lbfgs lbfgsb shift_evaluation = max *mean } parallel { method = *multiprocessing slurm pbs sge lsf threading nproc = 1 qsub_command = None } output_file_name_prefix = None output_folder_name = "pdb" rst_file = None dump_gradients = None output { filename = None file_name = None prefix = None suffix = None serial = 0 serial_format = "%03d" target_output_format = None *pdb mmcif overwrite = False } ------------------------------------------------------------------------------- Extracting model **************** Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-gpu-00/raid1/scratch1/pavel/phenix/modules/chem_data/mon_lib" Total number of atoms: 3428 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2473 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 955 Unusual residues: {'1PE': 1, 'PEG': 1} Classifications: {'undetermined': 2, 'water': 300} Link IDs: {None: 301} Time building chain proxies: 0.50, per 1000 atoms: 0.15 Number of scatterers: 3428 At special positions: 0 Unit cell: (57.02, 57.02, 87.159, 90, 90, 90) Space group: P 41 21 2 (No. 92) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 7 16.00 O 541 8.00 N 216 7.00 C 799 6.00 H 1865 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.24 Adding C-beta torsion restraints... Number of C-beta restraints generated: 284 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 1861 1.04 - 1.24: 133 1.24 - 1.44: 430 1.44 - 1.64: 719 1.64 - 1.83: 10 Bond restraints: 3153 Sorted by residual: bond pdb=" NH2 ARG A 55 " pdb="HH21 ARG A 55 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N VAL A 138 " pdb=" H VAL A 138 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" NE2 HIS A 126 " pdb=" HE2 HIS A 126 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N TYR A 48 " pdb=" H TYR A 48 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH1 ARG A 55 " pdb="HH11 ARG A 55 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 93.38 - 101.57: 3 101.57 - 109.76: 2091 109.76 - 117.95: 1680 117.95 - 126.14: 1111 126.14 - 134.34: 26 Bond angle restraints: 4911 Sorted by residual: angle pdb=" CA ASP A 11 " pdb=" CB ASP A 11 " pdb=" CG ASP A 11 " ideal model delta sigma weight residual 112.60 117.76 -5.16 1.00e+00 1.00e+00 2.66e+01 angle pdb=" C ASP A 11 " pdb=" CA ASP A 11 " pdb=" CB ASP A 11 " ideal model delta sigma weight residual 110.10 102.28 7.82 1.90e+00 2.77e-01 1.69e+01 angle pdb=" CG MET A 136 " pdb=" SD MET A 136 " pdb=" CE MET A 136 " ideal model delta sigma weight residual 100.90 93.38 7.52 2.20e+00 2.07e-01 1.17e+01 angle pdb=" CB GLU A 23 " pdb=" CG GLU A 23 " pdb=" CD GLU A 23 " ideal model delta sigma weight residual 112.60 117.98 -5.38 1.70e+00 3.46e-01 1.00e+01 angle pdb=" N ARG A 151 " pdb=" CA ARG A 151 " pdb=" CB ARG A 151 " ideal model delta sigma weight residual 110.50 105.68 4.82 1.70e+00 3.46e-01 8.02e+00 ... (remaining 4906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.66: 1150 25.66 - 51.33: 32 51.33 - 76.99: 15 76.99 - 102.65: 0 102.65 - 128.32: 1 Dihedral angle restraints: 1198 sinusoidal: 659 harmonic: 539 Sorted by residual: dihedral pdb=" CA THR A 52 " pdb=" C THR A 52 " pdb=" N PHE A 53 " pdb=" CA PHE A 53 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" OH4 1PE A 202 " pdb=" C14 1PE A 202 " pdb=" C24 1PE A 202 " pdb=" OH5 1PE A 202 " ideal model delta sinusoidal sigma weight residual -65.42 62.90 -128.32 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" C ASP A 11 " pdb=" N ASP A 11 " pdb=" CA ASP A 11 " pdb=" CB ASP A 11 " ideal model delta harmonic sigma weight residual -122.60 -113.35 -9.25 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 1195 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 83 0.058 - 0.115: 58 0.115 - 0.172: 32 0.172 - 0.229: 9 0.229 - 0.286: 4 Chirality restraints: 186 Sorted by residual: chirality pdb=" CA GLU A 134 " pdb=" N GLU A 134 " pdb=" C GLU A 134 " pdb=" CB GLU A 134 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ILE A 117 " pdb=" N ILE A 117 " pdb=" C ILE A 117 " pdb=" CB ILE A 117 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA ASP A 11 " pdb=" N ASP A 11 " pdb=" C ASP A 11 " pdb=" CB ASP A 11 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 183 not shown) Planarity restraints: 379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 112 " 0.052 2.00e-02 2.50e+03 2.29e-02 1.58e+01 pdb=" CG PHE A 112 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 112 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 112 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE A 112 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 112 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 112 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE A 112 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 PHE A 112 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 PHE A 112 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 112 " -0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 112 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 113 " -0.044 2.00e-02 2.50e+03 2.26e-02 1.53e+01 pdb=" CG PHE A 113 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 PHE A 113 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 113 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 113 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 113 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 113 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 113 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 113 " 0.043 2.00e-02 2.50e+03 pdb=" HE1 PHE A 113 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 113 " -0.030 2.00e-02 2.50e+03 pdb=" HZ PHE A 113 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 121 " 0.000 2.00e-02 2.50e+03 1.93e-02 1.50e+01 pdb=" CG TRP A 121 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP A 121 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 121 " 0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP A 121 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 121 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 121 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 121 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 121 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 121 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP A 121 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TRP A 121 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP A 121 " -0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 121 " 0.012 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 121 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP A 121 " -0.024 2.00e-02 2.50e+03 ... (remaining 376 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 613 2.18 - 2.79: 7476 2.79 - 3.39: 12276 3.39 - 4.00: 18392 4.00 - 4.60: 26817 Nonbonded interactions: 65574 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 148 " pdb=" O HOH A 599 " model vdw sym.op. 1.578 1.800 x+1/2,-y+3/2,-z-1/4 nonbonded pdb=" O HOH A 599 " pdb=" HZ1 LYS A 148 " model vdw sym.op. 1.578 1.800 x-1/2,-y+3/2,-z-1/4 nonbonded pdb="HH22 ARG A 151 " pdb=" O HOH A 493 " model vdw 1.634 1.800 nonbonded pdb=" HZ1 LYS A 49 " pdb=" O HOH A 599 " model vdw 1.659 1.800 nonbonded pdb=" O PRO A 16 " pdb=" H1 HOH A 474 " model vdw 1.705 1.800 ... (remaining 65569 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 7 15.96 2 O 541 7.97 2 N 216 6.97 2 C 799 5.97 2 H 1865 1.00 3 sf(0) = scattering factor at diffraction angle 0. Setting QM defaults Setting QM method to HF Setting QM basis to 6-31g Start: Rw: 0.1041 Rf: 0.1167 Rf-Rw: 0.0126 bond: 0.009 angle: 1.48 clash: 0.0 rota: 0.00 rama: f: 96.91 o: 0.00 Z: 0.04 cb: 0.00 shift start/prev: 0.017 0.017 Optimal weight search: Data weight (initial): 11441.488753651998 r_work: 0.10407 shift mean: 0.000 shift max: 0.000 1 r_work: 0.11977 shift mean: 0.013 shift max: 0.200 2 r_work: 0.11977 shift mean: 0.000 shift max: 0.000 3 r_work: 0.11484 shift mean: 0.002 shift max: 0.037 4 r_work: 0.11036 shift mean: 0.002 shift max: 0.046 5 r_work: 0.10782 shift mean: 0.001 shift max: 0.027 6 r_work: 0.10631 shift mean: 0.001 shift max: 0.019 7 r_work: 0.10537 shift mean: 0.000 shift max: 0.014 8 r_work: 0.10473 shift mean: 0.000 shift max: 0.011 9 r_work: 0.10433 shift mean: 0.000 shift max: 0.009 10 r_work: 0.10405 shift mean: 0.000 shift max: 0.007 11 r_work: 0.10386 shift mean: 0.000 shift max: 0.006 12 r_work: 0.10373 shift mean: 0.000 shift max: 0.005 13 r_work: 0.10364 shift mean: 0.000 shift max: 0.004 14 r_work: 0.10357 shift mean: 0.000 shift max: 0.003 15 r_work: 0.10352 shift mean: 0.000 shift max: 0.003 16 r_work: 0.10348 shift mean: 0.000 shift max: 0.003 17 r_work: 0.10346 shift mean: 0.000 shift max: 0.003 18 r_work: 0.10343 shift mean: 0.000 shift max: 0.003 19 r_work: 0.10341 shift mean: 0.000 shift max: 0.004 20 r_work: 0.10340 shift mean: 0.001 shift max: 0.005 21 r_work: 0.10341 shift mean: 0.001 shift max: 0.006 22 r_work: 0.10344 shift mean: 0.001 shift max: 0.006 23 r_work: 0.10350 shift mean: 0.002 shift max: 0.006 24 r_work: 0.10356 shift mean: 0.002 shift max: 0.007 25 r_work: 0.10366 shift mean: 0.003 shift max: 0.010 26 r_work: 0.10375 shift mean: 0.003 shift max: 0.011 27 r_work: 0.10384 shift mean: 0.003 shift max: 0.011 28 r_work: 0.10392 shift mean: 0.004 shift max: 0.015 29 r_work: 0.10396 shift mean: 0.003 shift max: 0.010 30 r_work: 0.10404 shift mean: 0.004 shift max: 0.016 31 r_work: 0.10404 shift mean: 0.002 shift max: 0.008 32 r_work: 0.10403 shift mean: 0.002 shift max: 0.008 33 r_work: 0.10403 shift mean: 0.002 shift max: 0.008 34 r_work: 0.10403 shift mean: 0.002 shift max: 0.006 35 r_work: 0.10403 shift mean: 0.002 shift max: 0.006 36 r_work: 0.10404 shift mean: 0.001 shift max: 0.005 37 r_work: 0.10403 shift mean: 0.001 shift max: 0.006 38 r_work: 0.10404 shift mean: 0.001 shift max: 0.006 39 r_work: 0.10403 shift mean: 0.002 shift max: 0.006 40 r_work: 0.10403 shift mean: 0.002 shift max: 0.006 41 r_work: 0.10402 shift mean: 0.002 shift max: 0.007 42 r_work: 0.10401 shift mean: 0.002 shift max: 0.007 43 r_work: 0.10400 shift mean: 0.002 shift max: 0.008 44 r_work: 0.10398 shift mean: 0.002 shift max: 0.007 45 r_work: 0.10396 shift mean: 0.002 shift max: 0.009 46 r_work: 0.10395 shift mean: 0.002 shift max: 0.007 47 r_work: 0.10394 shift mean: 0.002 shift max: 0.008 48 r_work: 0.10392 shift mean: 0.001 shift max: 0.007 49 r_work: 0.10391 shift mean: 0.001 shift max: 0.006 50 r_work: 0.10391 shift mean: 0.001 shift max: 0.007 51 r_work: 0.10390 shift mean: 0.001 shift max: 0.006 52 r_work: 0.10389 shift mean: 0.001 shift max: 0.005 53 r_work: 0.10389 shift mean: 0.001 shift max: 0.006 54 r_work: 0.10389 shift mean: 0.001 shift max: 0.005 55 r_work: 0.10388 shift mean: 0.001 shift max: 0.007 56 r_work: 0.10388 shift mean: 0.001 shift max: 0.005 57 r_work: 0.10387 shift mean: 0.001 shift max: 0.006 58 r_work: 0.10386 shift mean: 0.001 shift max: 0.007 59 r_work: 0.10385 shift mean: 0.001 shift max: 0.007 60 r_work: 0.10384 shift mean: 0.001 shift max: 0.008 61 r_work: 0.10383 shift mean: 0.001 shift max: 0.007 62 r_work: 0.10381 shift mean: 0.001 shift max: 0.007 63 r_work: 0.10380 shift mean: 0.001 shift max: 0.007 64 r_work: 0.10379 shift mean: 0.001 shift max: 0.006 65 r_work: 0.10377 shift mean: 0.001 shift max: 0.005 66 r_work: 0.10376 shift mean: 0.001 shift max: 0.004 67 r_work: 0.10375 shift mean: 0.001 shift max: 0.004 68 r_work: 0.10373 shift mean: 0.001 shift max: 0.004 69 r_work: 0.10372 shift mean: 0.001 shift max: 0.003 70 r_work: 0.10371 shift mean: 0.001 shift max: 0.004 71 r_work: 0.10369 shift mean: 0.001 shift max: 0.004 72 r_work: 0.10367 shift mean: 0.001 shift max: 0.005 73 r_work: 0.10366 shift mean: 0.001 shift max: 0.005 74 r_work: 0.10364 shift mean: 0.001 shift max: 0.005 75 r_work: 0.10362 shift mean: 0.001 shift max: 0.006 76 r_work: 0.10361 shift mean: 0.001 shift max: 0.005 77 r_work: 0.10358 shift mean: 0.001 shift max: 0.005 78 r_work: 0.10357 shift mean: 0.001 shift max: 0.004 79 r_work: 0.10356 shift mean: 0.001 shift max: 0.005 80 r_work: 0.10354 shift mean: 0.001 shift max: 0.003 81 r_work: 0.10353 shift mean: 0.001 shift max: 0.004 82 r_work: 0.10352 shift mean: 0.000 shift max: 0.003 83 r_work: 0.10351 shift mean: 0.001 shift max: 0.003 84 r_work: 0.10349 shift mean: 0.001 shift max: 0.003 85 r_work: 0.10348 shift mean: 0.000 shift max: 0.003 86 r_work: 0.10347 shift mean: 0.001 shift max: 0.004 87 r_work: 0.10345 shift mean: 0.000 shift max: 0.002 88 r_work: 0.10344 shift mean: 0.001 shift max: 0.004 89 r_work: 0.10342 shift mean: 0.000 shift max: 0.003 90 r_work: 0.10341 shift mean: 0.000 shift max: 0.003 91 r_work: 0.10339 shift mean: 0.001 shift max: 0.003 92 r_work: 0.10338 shift mean: 0.000 shift max: 0.003 93 r_work: 0.10336 shift mean: 0.001 shift max: 0.004 94 r_work: 0.10335 shift mean: 0.000 shift max: 0.003 95 r_work: 0.10334 shift mean: 0.000 shift max: 0.003 96 r_work: 0.10333 shift mean: 0.000 shift max: 0.004 97 r_work: 0.10332 shift mean: 0.000 shift max: 0.003 98 r_work: 0.10331 shift mean: 0.000 shift max: 0.003 99 r_work: 0.10330 shift mean: 0.001 shift max: 0.004 100 r_work: 0.10328 shift mean: 0.000 shift max: 0.003 101 r_work: 0.10328 shift mean: 0.000 shift max: 0.003 102 0: Rw: 0.1033 Rf: 0.1168 Rf-Rw: 0.0135 bond: 0.018 angle: 1.89 clash: 0.4 rota: 0.00 rama: f: 96.91 o: 0.00 Z: -0.04 cb: 0.70 shift start/prev: 0.086 0.069 rws(prev): 1.000 rws: 1.000 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1033 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.1030 0.1167 At refinement start Rw: 0.1030 Rf: 0.1167 Rf-Rw: 0.0136 bond: 0.018 angle: 1.89 clash: 0.4 rota: 0.00 rama: f: 96.91 o: 0.00 Z: -0.04 cb: 0.70 shift start/prev: 0.086 0.000 Refinement: r_work: 0.10303 shift mean: 0.000 shift max: 0.000 1 r_work: 0.11479 shift mean: 0.006 shift max: 0.200 2 r_work: 0.11479 shift mean: 0.000 shift max: 0.000 3 r_work: 0.11088 shift mean: 0.001 shift max: 0.039 4 r_work: 0.10760 shift mean: 0.001 shift max: 0.044 5 r_work: 0.10574 shift mean: 0.001 shift max: 0.027 6 r_work: 0.10468 shift mean: 0.001 shift max: 0.020 7 r_work: 0.10400 shift mean: 0.000 shift max: 0.014 8 r_work: 0.10362 shift mean: 0.000 shift max: 0.011 9 r_work: 0.10335 shift mean: 0.000 shift max: 0.009 10 r_work: 0.10320 shift mean: 0.000 shift max: 0.007 11 r_work: 0.10311 shift mean: 0.000 shift max: 0.006 12 r_work: 0.10305 shift mean: 0.000 shift max: 0.004 13 r_work: 0.10301 shift mean: 0.000 shift max: 0.004 14 r_work: 0.10299 shift mean: 0.000 shift max: 0.003 15 r_work: 0.10298 shift mean: 0.000 shift max: 0.002 16 r_work: 0.10297 shift mean: 0.000 shift max: 0.002 17 r_work: 0.10297 shift mean: 0.000 shift max: 0.001 18 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 19 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 20 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 22 r_work: 0.10296 shift mean: 0.000 shift max: 0.000 23 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 24 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 25 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 26 r_work: 0.10296 shift mean: 0.000 shift max: 0.000 27 r_work: 0.10296 shift mean: 0.000 shift max: 0.000 28 r_work: 0.10296 shift mean: 0.000 shift max: 0.000 29 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 30 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 31 r_work: 0.10296 shift mean: 0.000 shift max: 0.001 32 r_work: 0.10295 shift mean: 0.000 shift max: 0.001 33 r_work: 0.10295 shift mean: 0.000 shift max: 0.001 34 r_work: 0.10294 shift mean: 0.000 shift max: 0.002 35 r_work: 0.10293 shift mean: 0.000 shift max: 0.002 36 r_work: 0.10292 shift mean: 0.000 shift max: 0.003 37 r_work: 0.10292 shift mean: 0.000 shift max: 0.002 38 r_work: 0.10291 shift mean: 0.000 shift max: 0.002 39 r_work: 0.10290 shift mean: 0.000 shift max: 0.002 40 r_work: 0.10289 shift mean: 0.000 shift max: 0.002 41 r_work: 0.10288 shift mean: 0.000 shift max: 0.002 42 r_work: 0.10288 shift mean: 0.000 shift max: 0.002 43 r_work: 0.10287 shift mean: 0.000 shift max: 0.002 44 r_work: 0.10287 shift mean: 0.000 shift max: 0.002 45 r_work: 0.10287 shift mean: 0.000 shift max: 0.002 46 r_work: 0.10286 shift mean: 0.000 shift max: 0.001 47 r_work: 0.10286 shift mean: 0.000 shift max: 0.002 48 r_work: 0.10285 shift mean: 0.000 shift max: 0.002 49 r_work: 0.10285 shift mean: 0.000 shift max: 0.002 50 r_work: 0.10284 shift mean: 0.000 shift max: 0.003 51 r_work: 0.10284 shift mean: 0.000 shift max: 0.003 52 0: Rw: 0.1028 Rf: 0.1165 Rf-Rw: 0.0137 bond: 0.018 angle: 1.88 clash: 0.4 rota: 0.00 rama: f: 96.91 o: 0.00 Z: -0.02 cb: 0.00 shift start/prev: 0.087 0.007 n_fev: 52 r_work: 0.10284 shift mean: 0.000 shift max: 0.000 1 r_work: 0.11696 shift mean: 0.012 shift max: 0.181 2 r_work: 0.11971 shift mean: 0.001 shift max: 0.019 3 r_work: 0.11432 shift mean: 0.003 shift max: 0.040 4 r_work: 0.10988 shift mean: 0.002 shift max: 0.050 5 r_work: 0.10725 shift mean: 0.002 shift max: 0.025 6 r_work: 0.10565 shift mean: 0.001 shift max: 0.020 7 r_work: 0.10457 shift mean: 0.001 shift max: 0.015 8 r_work: 0.10390 shift mean: 0.001 shift max: 0.011 9 r_work: 0.10351 shift mean: 0.001 shift max: 0.009 10 r_work: 0.10326 shift mean: 0.000 shift max: 0.006 11 r_work: 0.10310 shift mean: 0.000 shift max: 0.006 12 r_work: 0.10300 shift mean: 0.000 shift max: 0.004 13 r_work: 0.10294 shift mean: 0.000 shift max: 0.004 14 r_work: 0.10290 shift mean: 0.000 shift max: 0.002 15 r_work: 0.10287 shift mean: 0.000 shift max: 0.002 16 r_work: 0.10285 shift mean: 0.000 shift max: 0.001 17 r_work: 0.10284 shift mean: 0.000 shift max: 0.002 18 r_work: 0.10283 shift mean: 0.000 shift max: 0.001 19 r_work: 0.10283 shift mean: 0.000 shift max: 0.001 20 r_work: 0.10282 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10282 shift mean: 0.000 shift max: 0.001 22 r_work: 0.10282 shift mean: 0.000 shift max: 0.000 23 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 24 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 25 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 26 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 27 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 28 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 29 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 30 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 31 r_work: 0.10281 shift mean: 0.000 shift max: 0.000 32 r_work: 0.10281 shift mean: 0.000 shift max: 0.001 33 r_work: 0.10281 shift mean: 0.000 shift max: 0.001 34 r_work: 0.10280 shift mean: 0.000 shift max: 0.001 35 r_work: 0.10280 shift mean: 0.000 shift max: 0.001 36 r_work: 0.10280 shift mean: 0.000 shift max: 0.001 37 r_work: 0.10280 shift mean: 0.000 shift max: 0.002 38 r_work: 0.10279 shift mean: 0.000 shift max: 0.002 39 r_work: 0.10279 shift mean: 0.000 shift max: 0.002 40 r_work: 0.10279 shift mean: 0.000 shift max: 0.003 41 r_work: 0.10278 shift mean: 0.000 shift max: 0.003 42 r_work: 0.10278 shift mean: 0.000 shift max: 0.003 43 r_work: 0.10278 shift mean: 0.000 shift max: 0.003 44 r_work: 0.10277 shift mean: 0.000 shift max: 0.002 45 r_work: 0.10277 shift mean: 0.000 shift max: 0.003 46 r_work: 0.10277 shift mean: 0.000 shift max: 0.002 47 r_work: 0.10276 shift mean: 0.000 shift max: 0.002 48 r_work: 0.10276 shift mean: 0.000 shift max: 0.003 49 r_work: 0.10276 shift mean: 0.000 shift max: 0.002 50 r_work: 0.10276 shift mean: 0.000 shift max: 0.003 51 r_work: 0.10276 shift mean: 0.000 shift max: 0.003 52 1: Rw: 0.1028 Rf: 0.1166 Rf-Rw: 0.0138 bond: 0.018 angle: 1.92 clash: 0.4 rota: 0.00 rama: f: 96.91 o: 0.00 Z: -0.03 cb: 0.70 shift start/prev: 0.089 0.006 n_fev: 52 r_work: 0.10276 shift mean: 0.000 shift max: 0.000 1 r_work: 0.11785 shift mean: 0.012 shift max: 0.200 2 r_work: 0.11785 shift mean: 0.000 shift max: 0.000 3 r_work: 0.11291 shift mean: 0.002 shift max: 0.039 4 r_work: 0.10899 shift mean: 0.002 shift max: 0.043 5 r_work: 0.10662 shift mean: 0.001 shift max: 0.028 6 r_work: 0.10518 shift mean: 0.001 shift max: 0.020 7 r_work: 0.10428 shift mean: 0.001 shift max: 0.015 8 r_work: 0.10371 shift mean: 0.001 shift max: 0.011 9 r_work: 0.10334 shift mean: 0.001 shift max: 0.009 10 r_work: 0.10312 shift mean: 0.000 shift max: 0.007 11 r_work: 0.10297 shift mean: 0.000 shift max: 0.006 12 r_work: 0.10288 shift mean: 0.000 shift max: 0.004 13 r_work: 0.10282 shift mean: 0.000 shift max: 0.004 14 r_work: 0.10279 shift mean: 0.000 shift max: 0.003 15 r_work: 0.10276 shift mean: 0.000 shift max: 0.002 16 r_work: 0.10275 shift mean: 0.000 shift max: 0.002 17 r_work: 0.10274 shift mean: 0.000 shift max: 0.001 18 r_work: 0.10273 shift mean: 0.000 shift max: 0.001 19 r_work: 0.10273 shift mean: 0.000 shift max: 0.001 20 r_work: 0.10273 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10273 shift mean: 0.000 shift max: 0.001 22 r_work: 0.10272 shift mean: 0.000 shift max: 0.001 23 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 24 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 25 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 26 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 27 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 28 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 29 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 30 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 31 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 32 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 33 r_work: 0.10272 shift mean: 0.000 shift max: 0.000 34 r_work: 0.10272 shift mean: 0.000 shift max: 0.001 35 r_work: 0.10271 shift mean: 0.000 shift max: 0.001 36 r_work: 0.10271 shift mean: 0.000 shift max: 0.001 37 r_work: 0.10271 shift mean: 0.000 shift max: 0.001 38 r_work: 0.10271 shift mean: 0.000 shift max: 0.001 39 r_work: 0.10271 shift mean: 0.000 shift max: 0.001 40 r_work: 0.10271 shift mean: 0.000 shift max: 0.002 41 r_work: 0.10270 shift mean: 0.000 shift max: 0.002 42 r_work: 0.10270 shift mean: 0.000 shift max: 0.002 43 r_work: 0.10270 shift mean: 0.000 shift max: 0.002 44 r_work: 0.10270 shift mean: 0.000 shift max: 0.002 45 r_work: 0.10269 shift mean: 0.000 shift max: 0.002 46 r_work: 0.10269 shift mean: 0.000 shift max: 0.002 47 r_work: 0.10269 shift mean: 0.000 shift max: 0.002 48 r_work: 0.10269 shift mean: 0.000 shift max: 0.002 49 r_work: 0.10269 shift mean: 0.000 shift max: 0.001 50 r_work: 0.10269 shift mean: 0.000 shift max: 0.001 51 r_work: 0.10269 shift mean: 0.000 shift max: 0.001 52 2: Rw: 0.1027 Rf: 0.1164 Rf-Rw: 0.0137 bond: 0.018 angle: 1.90 clash: 0.4 rota: 0.00 rama: f: 96.91 o: 0.00 Z: -0.02 cb: 0.00 shift start/prev: 0.090 0.004 n_fev: 52 r_work: 0.10269 shift mean: 0.000 shift max: 0.000 1 r_work: 0.11343 shift mean: 0.010 shift max: 0.200 2 r_work: 0.11343 shift mean: 0.000 shift max: 0.000 3 r_work: 0.10992 shift mean: 0.002 shift max: 0.040 4 r_work: 0.10686 shift mean: 0.002 shift max: 0.046 5 r_work: 0.10522 shift mean: 0.001 shift max: 0.029 6 r_work: 0.10430 shift mean: 0.001 shift max: 0.019 7 r_work: 0.10372 shift mean: 0.001 shift max: 0.015 8 r_work: 0.10336 shift mean: 0.001 shift max: 0.011 9 r_work: 0.10312 shift mean: 0.000 shift max: 0.009 10 r_work: 0.10297 shift mean: 0.000 shift max: 0.006 11 r_work: 0.10287 shift mean: 0.000 shift max: 0.005 12 r_work: 0.10280 shift mean: 0.000 shift max: 0.004 13 r_work: 0.10276 shift mean: 0.000 shift max: 0.003 14 r_work: 0.10273 shift mean: 0.000 shift max: 0.003 15 r_work: 0.10271 shift mean: 0.000 shift max: 0.002 16 r_work: 0.10270 shift mean: 0.000 shift max: 0.002 17 r_work: 0.10269 shift mean: 0.000 shift max: 0.001 18 r_work: 0.10268 shift mean: 0.000 shift max: 0.001 19 r_work: 0.10268 shift mean: 0.000 shift max: 0.001 20 r_work: 0.10267 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10267 shift mean: 0.000 shift max: 0.001 22 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 23 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 24 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 25 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 26 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 27 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 28 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 29 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 30 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 31 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 32 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 33 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 34 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 35 r_work: 0.10267 shift mean: 0.000 shift max: 0.000 36 r_work: 0.10267 shift mean: 0.000 shift max: 0.001 37 r_work: 0.10267 shift mean: 0.000 shift max: 0.001 38 r_work: 0.10267 shift mean: 0.000 shift max: 0.001 39 r_work: 0.10267 shift mean: 0.000 shift max: 0.001 40 r_work: 0.10267 shift mean: 0.000 shift max: 0.001 41 r_work: 0.10267 shift mean: 0.000 shift max: 0.002 42 r_work: 0.10267 shift mean: 0.000 shift max: 0.002 43 r_work: 0.10267 shift mean: 0.000 shift max: 0.002 44 r_work: 0.10266 shift mean: 0.000 shift max: 0.002 45 r_work: 0.10266 shift mean: 0.000 shift max: 0.003 46 r_work: 0.10266 shift mean: 0.000 shift max: 0.002 47 r_work: 0.10265 shift mean: 0.000 shift max: 0.002 48 r_work: 0.10265 shift mean: 0.000 shift max: 0.002 49 r_work: 0.10265 shift mean: 0.000 shift max: 0.002 50 r_work: 0.10264 shift mean: 0.000 shift max: 0.002 51 r_work: 0.10264 shift mean: 0.000 shift max: 0.002 52 3: Rw: 0.1026 Rf: 0.1165 Rf-Rw: 0.0138 bond: 0.018 angle: 1.92 clash: 0.4 rota: 0.00 rama: f: 96.91 o: 0.00 Z: -0.03 cb: 0.70 shift start/prev: 0.091 0.004 n_fev: 52 r_work: 0.10264 shift mean: 0.000 shift max: 0.000 1 r_work: 0.11812 shift mean: 0.009 shift max: 0.200 2 r_work: 0.11574 shift mean: 0.001 shift max: 0.018 3 r_work: 0.11144 shift mean: 0.002 shift max: 0.036 4 r_work: 0.10794 shift mean: 0.001 shift max: 0.038 5 r_work: 0.10591 shift mean: 0.001 shift max: 0.025 6 r_work: 0.10468 shift mean: 0.001 shift max: 0.019 7 r_work: 0.10392 shift mean: 0.001 shift max: 0.013 8 r_work: 0.10345 shift mean: 0.000 shift max: 0.010 9 r_work: 0.10315 shift mean: 0.000 shift max: 0.008 10 r_work: 0.10295 shift mean: 0.000 shift max: 0.006 11 r_work: 0.10283 shift mean: 0.000 shift max: 0.005 12 r_work: 0.10275 shift mean: 0.000 shift max: 0.004 13 r_work: 0.10271 shift mean: 0.000 shift max: 0.003 14 r_work: 0.10268 shift mean: 0.000 shift max: 0.003 15 r_work: 0.10266 shift mean: 0.000 shift max: 0.002 16 r_work: 0.10265 shift mean: 0.000 shift max: 0.002 17 r_work: 0.10264 shift mean: 0.000 shift max: 0.001 18 r_work: 0.10264 shift mean: 0.000 shift max: 0.001 19 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 20 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 22 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 23 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 24 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 25 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 26 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 27 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 28 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 29 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 30 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 31 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 32 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 33 r_work: 0.10263 shift mean: 0.000 shift max: 0.000 34 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 35 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 36 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 37 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 38 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 39 r_work: 0.10263 shift mean: 0.000 shift max: 0.001 40 r_work: 0.10263 shift mean: 0.000 shift max: 0.002 41 r_work: 0.10263 shift mean: 0.000 shift max: 0.002 42 r_work: 0.10263 shift mean: 0.000 shift max: 0.002 43 r_work: 0.10262 shift mean: 0.000 shift max: 0.002 44 r_work: 0.10262 shift mean: 0.000 shift max: 0.002 45 r_work: 0.10262 shift mean: 0.000 shift max: 0.002 46 r_work: 0.10262 shift mean: 0.000 shift max: 0.002 47 r_work: 0.10262 shift mean: 0.000 shift max: 0.002 48 r_work: 0.10262 shift mean: 0.000 shift max: 0.002 49 r_work: 0.10261 shift mean: 0.000 shift max: 0.002 50 r_work: 0.10261 shift mean: 0.000 shift max: 0.001 51 r_work: 0.10261 shift mean: 0.000 shift max: 0.001 52 4: Rw: 0.1026 Rf: 0.1164 Rf-Rw: 0.0138 bond: 0.018 angle: 1.91 clash: 0.4 rota: 0.00 rama: f: 96.91 o: 0.00 Z: -0.02 cb: 0.00 shift start/prev: 0.092 0.003 n_fev: 52 At refinement end: Rw: 0.1026 Rf: 0.1164 Rf-Rw: 0.0138 bond: 0.018 angle: 1.91 clash: 0.4 rota: 0.00 rama: f: 96.91 o: 0.00 Z: -0.02 cb: 0.00 shift start/prev: 0.092 0.003 Best Rwork, Rfree (after refinement): 0.1026 0.1164 See 4O8H_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 914.22 seconds wall clock time: 15 minutes 25.80 seconds (925.80 seconds total) /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/ase/__init__.py:21: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. if LooseVersion(np.__version__) < '1.9': /net/cci-gpu-00/raid1/scratch1/pavel/phenix/conda_base/lib/python3.8/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead. other = LooseVersion(other)