Starting qr.refine on Thu Jun 20 16:23:33 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//3NJW.mtz Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/3NJW.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/3NJW.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/3NJW.pdb" miller_array { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//3NJW.mtz" } default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//3NJW.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)=0.1203 0.1191 0.1309 n_refl.: 10638 re-set all scales: r(all,work,free)=0.1203 0.1191 0.1309 n_refl.: 10638 remove outliers: r(all,work,free)=0.1203 0.1191 0.1309 n_refl.: 10635 bulk-solvent and scaling: r(all,work,free)=0.0975 0.0960 0.1114 n_refl.: 10635 remove outliers: r(all,work,free)=0.0974 0.0959 0.1114 n_refl.: 10633 Resolution Compl Nwork Nfree R_work kiso kani kmask 8.943-4.242 99.02 90 11 0.1232 109.791 107.466 0.988 0.929 0.159 4.237-3.403 100.00 90 10 0.0649 116.782 116.274 1.010 0.931 0.133 3.400-2.732 100.00 159 17 0.0915 82.726 82.078 1.024 0.931 0.000 2.728-2.190 100.00 313 35 0.0881 68.541 68.292 1.052 0.932 0.000 2.188-1.756 100.00 585 64 0.0833 51.893 51.608 1.109 0.933 0.000 1.756-1.409 100.00 1103 123 0.0800 33.847 33.888 1.155 0.934 0.000 1.408-1.130 100.00 2106 235 0.0749 24.213 24.257 1.180 0.936 0.000 1.130-0.907 99.89 4002 445 0.1226 13.525 13.545 1.184 0.939 0.000 0.906-0.865 89.06 1121 124 0.2093 6.828 6.392 0.973 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0648 b_overall=-0.0042 ------------------------------------------------------------------------------- Starting r-factors: ******************* r_work=0.0959 r_free=0.1114 ------------------------------------------------------------------------------- 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 None 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: 343 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 268 Classifications: {'peptide': 19} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'CIS': 1, 'PTRANS': 4, 'TRANS': 13} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 75 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 0.12, per 1000 atoms: 0.35 Number of scatterers: 343 At special positions: 0 Unit cell: (19.465, 21.432, 29.523, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 O 49 8.00 N 23 7.00 C 95 6.00 H 174 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 19 " distance=2.04 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: 0.13 Adding C-beta torsion restraints... Number of C-beta restraints generated: 32 Time building geometry restraints manager: 0.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 174 1.03 - 1.23: 9 1.23 - 1.42: 61 1.42 - 1.62: 81 1.62 - 1.81: 2 Bond restraints: 327 Sorted by residual: bond pdb=" N THR A 15 " pdb=" H THR A 15 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N TRP A 4 " pdb=" H TRP A 4 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N CYS A 6 " pdb=" H CYS A 6 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU A 2 " pdb=" H LEU A 2 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" NE1 TRP A 17 " pdb=" HE1 TRP A 17 " ideal model delta sigma weight residual 1.020 0.860 0.160 2.00e-02 2.50e+03 6.44e+01 ... (remaining 322 not shown) Histogram of bond angle deviations from ideal: 101.60 - 108.16: 99 108.16 - 114.72: 249 114.72 - 121.28: 96 121.28 - 127.84: 74 127.84 - 134.40: 9 Bond angle restraints: 527 Sorted by residual: angle pdb=" C PRO A 7 " pdb=" N SER A 8 " pdb=" CA SER A 8 " ideal model delta sigma weight residual 121.70 127.55 -5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" C TRP A 13 " pdb=" CA TRP A 13 " pdb=" CB TRP A 13 " ideal model delta sigma weight residual 110.10 116.16 -6.06 1.90e+00 2.77e-01 1.02e+01 angle pdb=" C ASP A 9 " pdb=" CA ASP A 9 " pdb=" CB ASP A 9 " ideal model delta sigma weight residual 110.10 115.73 -5.63 1.90e+00 2.77e-01 8.77e+00 angle pdb=" CA ILE A 10 " pdb=" C ILE A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 116.90 120.78 -3.88 1.50e+00 4.44e-01 6.69e+00 angle pdb=" CA THR A 15 " pdb=" CB THR A 15 " pdb=" OG1 THR A 15 " ideal model delta sigma weight residual 109.60 105.87 3.73 1.50e+00 4.44e-01 6.18e+00 ... (remaining 522 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 9.48: 113 9.48 - 18.95: 18 18.95 - 28.41: 2 28.41 - 37.88: 2 37.88 - 47.35: 5 Dihedral angle restraints: 140 sinusoidal: 72 harmonic: 68 Sorted by residual: dihedral pdb=" C ASP A 9 " pdb=" N ASP A 9 " pdb=" CA ASP A 9 " pdb=" CB ASP A 9 " ideal model delta harmonic sigma weight residual -122.60 -130.37 7.77 0 2.50e+00 1.60e-01 9.66e+00 dihedral pdb=" C ILE A 10 " pdb=" N ILE A 10 " pdb=" CA ILE A 10 " pdb=" CB ILE A 10 " ideal model delta harmonic sigma weight residual -122.00 -129.69 7.69 0 2.50e+00 1.60e-01 9.45e+00 dihedral pdb=" CA SER A 8 " pdb=" C SER A 8 " pdb=" N ASP A 9 " pdb=" CA ASP A 9 " ideal model delta harmonic sigma weight residual 180.00 165.44 14.56 0 5.00e+00 4.00e-02 8.48e+00 ... (remaining 137 not shown) Histogram of chiral volume deviations from ideal: 0.006 - 0.060: 10 0.060 - 0.114: 6 0.114 - 0.167: 2 0.167 - 0.221: 0 0.221 - 0.275: 1 Chirality restraints: 19 Sorted by residual: chirality pdb=" CA ASP A 9 " pdb=" N ASP A 9 " pdb=" C ASP A 9 " pdb=" CB ASP A 9 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE A 10 " pdb=" N ILE A 10 " pdb=" C ILE A 10 " pdb=" CB ILE A 10 " both_signs ideal model delta sigma weight residual False 2.43 2.29 0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA PRO A 11 " pdb=" N PRO A 11 " pdb=" C PRO A 11 " pdb=" CB PRO A 11 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 16 not shown) Planarity restraints: 41 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 4 " -0.007 2.00e-02 2.50e+03 2.28e-02 2.09e+01 pdb=" CG TRP A 4 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 4 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 4 " -0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP A 4 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 4 " -0.023 2.00e-02 2.50e+03 pdb=" CE3 TRP A 4 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 4 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 4 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 4 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP A 4 " 0.055 2.00e-02 2.50e+03 pdb=" HE1 TRP A 4 " -0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP A 4 " 0.026 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 4 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 4 " 0.009 2.00e-02 2.50e+03 pdb=" HH2 TRP A 4 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 13 " -0.027 2.00e-02 2.50e+03 1.99e-02 1.58e+01 pdb=" CG TRP A 13 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 13 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP A 13 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 13 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 13 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 13 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 13 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 13 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 13 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TRP A 13 " 0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 13 " 0.032 2.00e-02 2.50e+03 pdb=" HE3 TRP A 13 " 0.014 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 13 " 0.004 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 13 " 0.033 2.00e-02 2.50e+03 pdb=" HH2 TRP A 13 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 17 " 0.019 2.00e-02 2.50e+03 1.72e-02 1.19e+01 pdb=" CG TRP A 17 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP A 17 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 17 " -0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP A 17 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 17 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 17 " -0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 17 " -0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 17 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 17 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 TRP A 17 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 TRP A 17 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 17 " -0.015 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 17 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 17 " 0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP A 17 " 0.027 2.00e-02 2.50e+03 ... (remaining 38 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 46 2.01 - 2.66: 582 2.66 - 3.30: 1373 3.30 - 3.95: 2167 3.95 - 4.60: 3370 Nonbonded interactions: 7538 Sorted by model distance: nonbonded pdb=" N GLY A 1 " pdb=" CG ASP A 9 " model vdw 1.359 3.250 nonbonded pdb=" O HOH A1013 " pdb=" O HOH A1112 " model vdw 1.525 2.200 nonbonded pdb=" H1 HOH A1012 " pdb=" O HOH A1112 " model vdw 1.567 1.800 nonbonded pdb=" H2 HOH A1012 " pdb=" O HOH A1112 " model vdw 1.591 1.800 nonbonded pdb=" O HOH A1013 " pdb=" H2 HOH A1112 " model vdw 1.632 1.800 ... (remaining 7533 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 2 15.96 2 O 49 7.97 2 N 23 6.97 2 C 95 5.97 2 H 174 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 Optimize H with d.o.f. start: r_work=0.0959 r_free=0.1114 final: r_work=0.0968 r_free=0.1086 Start: Rw: 0.0968 Rf: 0.1086 Rf-Rw: 0.0118 bond: 0.008 angle: 1.72 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.38 cb: 0.00 shift start/prev: 0.069 0.069 Optimal weight search: Data weight (initial): 153.10768706120527 r_work: 0.09684 shift mean: 0.000 shift max: 0.000 1 r_work: 0.11836 shift mean: 0.017 shift max: 0.200 2 r_work: 0.11836 shift mean: 0.000 shift max: 0.000 3 r_work: 0.11287 shift mean: 0.001 shift max: 0.023 4 r_work: 0.10798 shift mean: 0.001 shift max: 0.024 5 r_work: 0.10483 shift mean: 0.001 shift max: 0.018 6 r_work: 0.10281 shift mean: 0.001 shift max: 0.014 7 r_work: 0.10146 shift mean: 0.000 shift max: 0.011 8 r_work: 0.10058 shift mean: 0.000 shift max: 0.009 9 r_work: 0.09998 shift mean: 0.000 shift max: 0.007 10 r_work: 0.09958 shift mean: 0.000 shift max: 0.006 11 r_work: 0.09929 shift mean: 0.001 shift max: 0.005 12 r_work: 0.09910 shift mean: 0.001 shift max: 0.004 13 r_work: 0.09899 shift mean: 0.001 shift max: 0.004 14 r_work: 0.09893 shift mean: 0.001 shift max: 0.004 15 r_work: 0.09892 shift mean: 0.001 shift max: 0.007 16 r_work: 0.09897 shift mean: 0.001 shift max: 0.009 17 r_work: 0.09910 shift mean: 0.002 shift max: 0.013 18 r_work: 0.09930 shift mean: 0.002 shift max: 0.019 19 r_work: 0.09962 shift mean: 0.003 shift max: 0.027 20 r_work: 0.10011 shift mean: 0.004 shift max: 0.039 21 r_work: 0.10040 shift mean: 0.002 shift max: 0.027 22 r_work: 0.10063 shift mean: 0.002 shift max: 0.027 23 r_work: 0.10088 shift mean: 0.003 shift max: 0.028 24 r_work: 0.10114 shift mean: 0.003 shift max: 0.031 25 r_work: 0.10128 shift mean: 0.002 shift max: 0.018 26 r_work: 0.10149 shift mean: 0.002 shift max: 0.023 27 r_work: 0.10181 shift mean: 0.003 shift max: 0.029 28 r_work: 0.10203 shift mean: 0.002 shift max: 0.020 29 r_work: 0.10224 shift mean: 0.001 shift max: 0.015 30 r_work: 0.10240 shift mean: 0.001 shift max: 0.012 31 r_work: 0.10249 shift mean: 0.001 shift max: 0.010 32 r_work: 0.10258 shift mean: 0.001 shift max: 0.011 33 r_work: 0.10266 shift mean: 0.001 shift max: 0.012 34 r_work: 0.10270 shift mean: 0.001 shift max: 0.012 35 r_work: 0.10274 shift mean: 0.002 shift max: 0.016 36 r_work: 0.10273 shift mean: 0.002 shift max: 0.014 37 r_work: 0.10272 shift mean: 0.002 shift max: 0.017 38 r_work: 0.10268 shift mean: 0.002 shift max: 0.015 39 r_work: 0.10264 shift mean: 0.003 shift max: 0.021 40 r_work: 0.10262 shift mean: 0.002 shift max: 0.013 41 r_work: 0.10259 shift mean: 0.002 shift max: 0.018 42 r_work: 0.10253 shift mean: 0.002 shift max: 0.013 43 r_work: 0.10247 shift mean: 0.002 shift max: 0.014 44 r_work: 0.10245 shift mean: 0.001 shift max: 0.011 45 r_work: 0.10242 shift mean: 0.002 shift max: 0.012 46 r_work: 0.10239 shift mean: 0.002 shift max: 0.011 47 r_work: 0.10240 shift mean: 0.002 shift max: 0.013 48 r_work: 0.10239 shift mean: 0.001 shift max: 0.010 49 r_work: 0.10242 shift mean: 0.002 shift max: 0.012 50 r_work: 0.10242 shift mean: 0.002 shift max: 0.013 51 r_work: 0.10244 shift mean: 0.002 shift max: 0.011 52 r_work: 0.10247 shift mean: 0.002 shift max: 0.016 53 r_work: 0.10248 shift mean: 0.001 shift max: 0.010 54 r_work: 0.10248 shift mean: 0.002 shift max: 0.013 55 r_work: 0.10247 shift mean: 0.002 shift max: 0.013 56 r_work: 0.10247 shift mean: 0.001 shift max: 0.012 57 r_work: 0.10244 shift mean: 0.002 shift max: 0.016 58 r_work: 0.10243 shift mean: 0.001 shift max: 0.010 59 r_work: 0.10240 shift mean: 0.001 shift max: 0.012 60 r_work: 0.10236 shift mean: 0.001 shift max: 0.011 61 r_work: 0.10231 shift mean: 0.001 shift max: 0.010 62 r_work: 0.10223 shift mean: 0.001 shift max: 0.013 63 r_work: 0.10219 shift mean: 0.001 shift max: 0.010 64 r_work: 0.10213 shift mean: 0.001 shift max: 0.011 65 r_work: 0.10208 shift mean: 0.001 shift max: 0.011 66 r_work: 0.10203 shift mean: 0.001 shift max: 0.011 67 r_work: 0.10199 shift mean: 0.001 shift max: 0.009 68 r_work: 0.10196 shift mean: 0.001 shift max: 0.010 69 r_work: 0.10194 shift mean: 0.001 shift max: 0.009 70 r_work: 0.10192 shift mean: 0.002 shift max: 0.014 71 r_work: 0.10190 shift mean: 0.001 shift max: 0.008 72 r_work: 0.10188 shift mean: 0.001 shift max: 0.010 73 r_work: 0.10187 shift mean: 0.002 shift max: 0.012 74 r_work: 0.10187 shift mean: 0.001 shift max: 0.009 75 r_work: 0.10186 shift mean: 0.002 shift max: 0.014 76 r_work: 0.10186 shift mean: 0.001 shift max: 0.007 77 r_work: 0.10186 shift mean: 0.001 shift max: 0.010 78 r_work: 0.10190 shift mean: 0.001 shift max: 0.012 79 r_work: 0.10191 shift mean: 0.001 shift max: 0.008 80 r_work: 0.10194 shift mean: 0.001 shift max: 0.009 81 r_work: 0.10196 shift mean: 0.001 shift max: 0.009 82 r_work: 0.10198 shift mean: 0.001 shift max: 0.007 83 r_work: 0.10200 shift mean: 0.001 shift max: 0.011 84 r_work: 0.10201 shift mean: 0.001 shift max: 0.008 85 r_work: 0.10200 shift mean: 0.001 shift max: 0.009 86 r_work: 0.10200 shift mean: 0.001 shift max: 0.012 87 r_work: 0.10197 shift mean: 0.001 shift max: 0.011 88 r_work: 0.10195 shift mean: 0.001 shift max: 0.009 89 r_work: 0.10191 shift mean: 0.001 shift max: 0.010 90 r_work: 0.10189 shift mean: 0.001 shift max: 0.007 91 r_work: 0.10188 shift mean: 0.001 shift max: 0.009 92 r_work: 0.10184 shift mean: 0.002 shift max: 0.015 93 r_work: 0.10181 shift mean: 0.001 shift max: 0.009 94 r_work: 0.10177 shift mean: 0.001 shift max: 0.011 95 r_work: 0.10173 shift mean: 0.001 shift max: 0.008 96 r_work: 0.10170 shift mean: 0.001 shift max: 0.010 97 r_work: 0.10168 shift mean: 0.001 shift max: 0.008 98 r_work: 0.10164 shift mean: 0.001 shift max: 0.007 99 r_work: 0.10160 shift mean: 0.001 shift max: 0.009 100 r_work: 0.10157 shift mean: 0.001 shift max: 0.006 101 r_work: 0.10153 shift mean: 0.001 shift max: 0.006 102 0: Rw: 0.1015 Rf: 0.1170 Rf-Rw: 0.0155 bond: 0.011 angle: 1.88 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.44 cb: 0.00 shift start/prev: 0.116 0.084 rws(prev): 1.000 rws: 1.000 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1170 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.1014 0.1169 At refinement start Rw: 0.1014 Rf: 0.1169 Rf-Rw: 0.0155 bond: 0.011 angle: 1.88 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.44 cb: 0.00 shift start/prev: 0.116 0.000 Refinement: r_work: 0.10143 shift mean: 0.000 shift max: 0.000 1 r_work: 0.14137 shift mean: 0.019 shift max: 0.200 2 r_work: 0.10602 shift mean: 0.014 shift max: 0.145 3 r_work: 0.10467 shift mean: 0.001 shift max: 0.010 4 r_work: 0.10372 shift mean: 0.001 shift max: 0.009 5 r_work: 0.10307 shift mean: 0.001 shift max: 0.007 6 r_work: 0.10267 shift mean: 0.000 shift max: 0.005 7 r_work: 0.10236 shift mean: 0.000 shift max: 0.005 8 r_work: 0.10219 shift mean: 0.000 shift max: 0.003 9 r_work: 0.10206 shift mean: 0.000 shift max: 0.003 10 r_work: 0.10199 shift mean: 0.000 shift max: 0.002 11 r_work: 0.10192 shift mean: 0.000 shift max: 0.002 12 r_work: 0.10189 shift mean: 0.000 shift max: 0.001 13 r_work: 0.10185 shift mean: 0.000 shift max: 0.001 14 r_work: 0.10183 shift mean: 0.000 shift max: 0.001 15 r_work: 0.10181 shift mean: 0.000 shift max: 0.001 16 r_work: 0.10179 shift mean: 0.000 shift max: 0.001 17 r_work: 0.10176 shift mean: 0.000 shift max: 0.001 18 r_work: 0.10174 shift mean: 0.000 shift max: 0.000 19 r_work: 0.10173 shift mean: 0.000 shift max: 0.001 20 r_work: 0.10172 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10170 shift mean: 0.000 shift max: 0.002 22 r_work: 0.10169 shift mean: 0.000 shift max: 0.002 23 r_work: 0.10167 shift mean: 0.000 shift max: 0.003 24 r_work: 0.10166 shift mean: 0.000 shift max: 0.003 25 r_work: 0.10166 shift mean: 0.000 shift max: 0.004 26 r_work: 0.10165 shift mean: 0.001 shift max: 0.006 27 r_work: 0.10166 shift mean: 0.001 shift max: 0.005 28 r_work: 0.10169 shift mean: 0.001 shift max: 0.006 29 r_work: 0.10174 shift mean: 0.001 shift max: 0.007 30 r_work: 0.10179 shift mean: 0.001 shift max: 0.005 31 r_work: 0.10185 shift mean: 0.001 shift max: 0.006 32 r_work: 0.10190 shift mean: 0.001 shift max: 0.005 33 r_work: 0.10194 shift mean: 0.001 shift max: 0.004 34 r_work: 0.10199 shift mean: 0.000 shift max: 0.004 35 r_work: 0.10203 shift mean: 0.000 shift max: 0.004 36 r_work: 0.10208 shift mean: 0.001 shift max: 0.004 37 r_work: 0.10212 shift mean: 0.001 shift max: 0.005 38 r_work: 0.10217 shift mean: 0.001 shift max: 0.005 39 r_work: 0.10222 shift mean: 0.001 shift max: 0.007 40 r_work: 0.10229 shift mean: 0.001 shift max: 0.010 41 r_work: 0.10236 shift mean: 0.001 shift max: 0.010 42 r_work: 0.10240 shift mean: 0.001 shift max: 0.013 43 r_work: 0.10245 shift mean: 0.002 shift max: 0.016 44 r_work: 0.10247 shift mean: 0.002 shift max: 0.016 45 r_work: 0.10247 shift mean: 0.002 shift max: 0.018 46 r_work: 0.10246 shift mean: 0.002 shift max: 0.015 47 r_work: 0.10246 shift mean: 0.002 shift max: 0.016 48 r_work: 0.10241 shift mean: 0.001 shift max: 0.014 49 r_work: 0.10240 shift mean: 0.001 shift max: 0.011 50 r_work: 0.10236 shift mean: 0.001 shift max: 0.013 51 r_work: 0.10234 shift mean: 0.001 shift max: 0.012 52 0: Rw: 0.1023 Rf: 0.1179 Rf-Rw: 0.0156 bond: 0.011 angle: 1.88 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.45 cb: 0.00 shift start/prev: 0.125 0.025 n_fev: 52 r_work: 0.10234 shift mean: 0.000 shift max: 0.000 1 r_work: 0.14964 shift mean: 0.015 shift max: 0.200 2 r_work: 0.10398 shift mean: 0.013 shift max: 0.170 3 r_work: 0.10349 shift mean: 0.000 shift max: 0.005 4 r_work: 0.10315 shift mean: 0.000 shift max: 0.004 5 r_work: 0.10289 shift mean: 0.000 shift max: 0.004 6 r_work: 0.10274 shift mean: 0.000 shift max: 0.003 7 r_work: 0.10263 shift mean: 0.000 shift max: 0.002 8 r_work: 0.10255 shift mean: 0.000 shift max: 0.002 9 r_work: 0.10250 shift mean: 0.000 shift max: 0.002 10 r_work: 0.10247 shift mean: 0.000 shift max: 0.001 11 r_work: 0.10244 shift mean: 0.000 shift max: 0.001 12 r_work: 0.10242 shift mean: 0.000 shift max: 0.001 13 r_work: 0.10242 shift mean: 0.000 shift max: 0.001 14 r_work: 0.10241 shift mean: 0.000 shift max: 0.001 15 r_work: 0.10239 shift mean: 0.000 shift max: 0.002 16 r_work: 0.10238 shift mean: 0.000 shift max: 0.000 17 r_work: 0.10236 shift mean: 0.000 shift max: 0.001 18 r_work: 0.10236 shift mean: 0.000 shift max: 0.001 19 r_work: 0.10236 shift mean: 0.000 shift max: 0.000 20 r_work: 0.10232 shift mean: 0.000 shift max: 0.003 21 r_work: 0.10231 shift mean: 0.000 shift max: 0.002 22 r_work: 0.10228 shift mean: 0.000 shift max: 0.003 23 r_work: 0.10225 shift mean: 0.001 shift max: 0.005 24 r_work: 0.10219 shift mean: 0.001 shift max: 0.008 25 r_work: 0.10215 shift mean: 0.001 shift max: 0.005 26 r_work: 0.10212 shift mean: 0.001 shift max: 0.005 27 r_work: 0.10211 shift mean: 0.000 shift max: 0.004 28 r_work: 0.10209 shift mean: 0.000 shift max: 0.004 29 r_work: 0.10208 shift mean: 0.000 shift max: 0.003 30 r_work: 0.10208 shift mean: 0.000 shift max: 0.003 31 r_work: 0.10208 shift mean: 0.000 shift max: 0.003 32 r_work: 0.10208 shift mean: 0.000 shift max: 0.004 33 r_work: 0.10209 shift mean: 0.000 shift max: 0.003 34 r_work: 0.10210 shift mean: 0.000 shift max: 0.004 35 r_work: 0.10210 shift mean: 0.001 shift max: 0.005 36 r_work: 0.10210 shift mean: 0.001 shift max: 0.004 37 r_work: 0.10209 shift mean: 0.001 shift max: 0.005 38 r_work: 0.10209 shift mean: 0.001 shift max: 0.005 39 r_work: 0.10208 shift mean: 0.001 shift max: 0.005 40 r_work: 0.10207 shift mean: 0.001 shift max: 0.007 41 r_work: 0.10205 shift mean: 0.001 shift max: 0.005 42 r_work: 0.10203 shift mean: 0.001 shift max: 0.005 43 r_work: 0.10203 shift mean: 0.001 shift max: 0.005 44 r_work: 0.10201 shift mean: 0.001 shift max: 0.005 45 r_work: 0.10199 shift mean: 0.001 shift max: 0.006 46 r_work: 0.10198 shift mean: 0.000 shift max: 0.005 47 r_work: 0.10198 shift mean: 0.001 shift max: 0.006 48 r_work: 0.10198 shift mean: 0.001 shift max: 0.007 49 r_work: 0.10199 shift mean: 0.001 shift max: 0.007 50 r_work: 0.10199 shift mean: 0.001 shift max: 0.007 51 r_work: 0.10201 shift mean: 0.001 shift max: 0.008 52 r_work: 0.10204 shift mean: 0.001 shift max: 0.007 53 1: Rw: 0.1020 Rf: 0.1171 Rf-Rw: 0.0151 bond: 0.011 angle: 1.88 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.46 cb: 0.00 shift start/prev: 0.128 0.017 n_fev: 53 r_work: 0.10204 shift mean: 0.000 shift max: 0.000 1 r_work: 0.14685 shift mean: 0.018 shift max: 0.200 2 r_work: 0.10277 shift mean: 0.016 shift max: 0.181 3 r_work: 0.10255 shift mean: 0.000 shift max: 0.003 4 r_work: 0.10242 shift mean: 0.000 shift max: 0.003 5 r_work: 0.10232 shift mean: 0.000 shift max: 0.002 6 r_work: 0.10225 shift mean: 0.000 shift max: 0.002 7 r_work: 0.10221 shift mean: 0.000 shift max: 0.001 8 r_work: 0.10218 shift mean: 0.000 shift max: 0.001 9 r_work: 0.10215 shift mean: 0.000 shift max: 0.001 10 r_work: 0.10214 shift mean: 0.000 shift max: 0.001 11 r_work: 0.10213 shift mean: 0.000 shift max: 0.001 12 r_work: 0.10213 shift mean: 0.000 shift max: 0.001 13 r_work: 0.10211 shift mean: 0.000 shift max: 0.001 14 r_work: 0.10211 shift mean: 0.000 shift max: 0.000 15 r_work: 0.10210 shift mean: 0.000 shift max: 0.001 16 r_work: 0.10210 shift mean: 0.000 shift max: 0.000 17 r_work: 0.10210 shift mean: 0.000 shift max: 0.000 18 r_work: 0.10210 shift mean: 0.000 shift max: 0.001 19 r_work: 0.10209 shift mean: 0.000 shift max: 0.001 20 r_work: 0.10209 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10208 shift mean: 0.000 shift max: 0.002 22 r_work: 0.10207 shift mean: 0.000 shift max: 0.003 23 r_work: 0.10209 shift mean: 0.000 shift max: 0.002 24 r_work: 0.10208 shift mean: 0.001 shift max: 0.003 25 r_work: 0.10208 shift mean: 0.000 shift max: 0.002 26 r_work: 0.10211 shift mean: 0.000 shift max: 0.003 27 r_work: 0.10213 shift mean: 0.000 shift max: 0.002 28 r_work: 0.10214 shift mean: 0.000 shift max: 0.002 29 r_work: 0.10217 shift mean: 0.000 shift max: 0.003 30 r_work: 0.10219 shift mean: 0.000 shift max: 0.003 31 r_work: 0.10222 shift mean: 0.000 shift max: 0.002 32 r_work: 0.10225 shift mean: 0.000 shift max: 0.003 33 r_work: 0.10228 shift mean: 0.000 shift max: 0.003 34 r_work: 0.10230 shift mean: 0.000 shift max: 0.003 35 r_work: 0.10233 shift mean: 0.001 shift max: 0.004 36 r_work: 0.10233 shift mean: 0.001 shift max: 0.004 37 r_work: 0.10235 shift mean: 0.001 shift max: 0.004 38 r_work: 0.10236 shift mean: 0.001 shift max: 0.004 39 r_work: 0.10236 shift mean: 0.001 shift max: 0.004 40 r_work: 0.10237 shift mean: 0.001 shift max: 0.005 41 r_work: 0.10237 shift mean: 0.000 shift max: 0.003 42 r_work: 0.10236 shift mean: 0.001 shift max: 0.004 43 r_work: 0.10236 shift mean: 0.000 shift max: 0.003 44 r_work: 0.10234 shift mean: 0.000 shift max: 0.004 45 r_work: 0.10233 shift mean: 0.000 shift max: 0.004 46 r_work: 0.10232 shift mean: 0.000 shift max: 0.004 47 r_work: 0.10231 shift mean: 0.001 shift max: 0.005 48 r_work: 0.10230 shift mean: 0.001 shift max: 0.006 49 r_work: 0.10230 shift mean: 0.000 shift max: 0.005 50 r_work: 0.10229 shift mean: 0.001 shift max: 0.008 51 r_work: 0.10228 shift mean: 0.001 shift max: 0.007 52 r_work: 0.10228 shift mean: 0.001 shift max: 0.009 53 2: Rw: 0.1023 Rf: 0.1173 Rf-Rw: 0.0150 bond: 0.011 angle: 1.88 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.46 cb: 0.00 shift start/prev: 0.133 0.014 n_fev: 53 r_work: 0.10228 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13401 shift mean: 0.015 shift max: 0.200 2 r_work: 0.10309 shift mean: 0.013 shift max: 0.174 3 r_work: 0.10284 shift mean: 0.000 shift max: 0.005 4 r_work: 0.10269 shift mean: 0.000 shift max: 0.004 5 r_work: 0.10255 shift mean: 0.000 shift max: 0.004 6 r_work: 0.10246 shift mean: 0.000 shift max: 0.003 7 r_work: 0.10242 shift mean: 0.000 shift max: 0.002 8 r_work: 0.10238 shift mean: 0.000 shift max: 0.002 9 r_work: 0.10235 shift mean: 0.000 shift max: 0.001 10 r_work: 0.10234 shift mean: 0.000 shift max: 0.001 11 r_work: 0.10233 shift mean: 0.000 shift max: 0.001 12 r_work: 0.10232 shift mean: 0.000 shift max: 0.001 13 r_work: 0.10232 shift mean: 0.000 shift max: 0.000 14 r_work: 0.10231 shift mean: 0.000 shift max: 0.001 15 r_work: 0.10231 shift mean: 0.000 shift max: 0.000 16 r_work: 0.10231 shift mean: 0.000 shift max: 0.000 17 r_work: 0.10231 shift mean: 0.000 shift max: 0.000 18 r_work: 0.10231 shift mean: 0.000 shift max: 0.000 19 r_work: 0.10231 shift mean: 0.000 shift max: 0.000 20 r_work: 0.10230 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10230 shift mean: 0.000 shift max: 0.001 22 r_work: 0.10229 shift mean: 0.000 shift max: 0.002 23 r_work: 0.10228 shift mean: 0.000 shift max: 0.002 24 r_work: 0.10227 shift mean: 0.000 shift max: 0.002 25 r_work: 0.10227 shift mean: 0.000 shift max: 0.002 26 r_work: 0.10227 shift mean: 0.000 shift max: 0.003 27 r_work: 0.10226 shift mean: 0.000 shift max: 0.002 28 r_work: 0.10227 shift mean: 0.000 shift max: 0.003 29 r_work: 0.10227 shift mean: 0.000 shift max: 0.002 30 r_work: 0.10229 shift mean: 0.000 shift max: 0.002 31 r_work: 0.10229 shift mean: 0.000 shift max: 0.003 32 r_work: 0.10230 shift mean: 0.000 shift max: 0.003 33 r_work: 0.10230 shift mean: 0.000 shift max: 0.004 34 r_work: 0.10230 shift mean: 0.000 shift max: 0.004 35 r_work: 0.10230 shift mean: 0.000 shift max: 0.003 36 r_work: 0.10230 shift mean: 0.001 shift max: 0.005 37 r_work: 0.10228 shift mean: 0.001 shift max: 0.005 38 r_work: 0.10229 shift mean: 0.001 shift max: 0.006 39 r_work: 0.10228 shift mean: 0.001 shift max: 0.005 40 r_work: 0.10227 shift mean: 0.001 shift max: 0.006 41 r_work: 0.10226 shift mean: 0.000 shift max: 0.004 42 r_work: 0.10226 shift mean: 0.001 shift max: 0.005 43 r_work: 0.10226 shift mean: 0.000 shift max: 0.004 44 r_work: 0.10226 shift mean: 0.000 shift max: 0.003 45 r_work: 0.10225 shift mean: 0.000 shift max: 0.004 46 r_work: 0.10225 shift mean: 0.000 shift max: 0.003 47 r_work: 0.10226 shift mean: 0.000 shift max: 0.003 48 r_work: 0.10225 shift mean: 0.000 shift max: 0.003 49 r_work: 0.10226 shift mean: 0.000 shift max: 0.003 50 r_work: 0.10226 shift mean: 0.000 shift max: 0.003 51 r_work: 0.10225 shift mean: 0.001 shift max: 0.005 52 3: Rw: 0.1023 Rf: 0.1169 Rf-Rw: 0.0146 bond: 0.011 angle: 1.88 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.46 cb: 0.00 shift start/prev: 0.135 0.011 n_fev: 52 r_work: 0.10225 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13573 shift mean: 0.017 shift max: 0.145 2 r_work: 0.10239 shift mean: 0.016 shift max: 0.137 3 r_work: 0.10234 shift mean: 0.000 shift max: 0.001 4 r_work: 0.10232 shift mean: 0.000 shift max: 0.001 5 r_work: 0.10230 shift mean: 0.000 shift max: 0.001 6 r_work: 0.10228 shift mean: 0.000 shift max: 0.001 7 r_work: 0.10228 shift mean: 0.000 shift max: 0.001 8 r_work: 0.10227 shift mean: 0.000 shift max: 0.000 9 r_work: 0.10227 shift mean: 0.000 shift max: 0.001 10 r_work: 0.10226 shift mean: 0.000 shift max: 0.000 11 r_work: 0.10226 shift mean: 0.000 shift max: 0.000 12 r_work: 0.10226 shift mean: 0.000 shift max: 0.000 13 r_work: 0.10226 shift mean: 0.000 shift max: 0.000 14 r_work: 0.10226 shift mean: 0.000 shift max: 0.001 15 r_work: 0.10226 shift mean: 0.000 shift max: 0.000 16 r_work: 0.10226 shift mean: 0.000 shift max: 0.000 17 r_work: 0.10226 shift mean: 0.000 shift max: 0.000 18 r_work: 0.10226 shift mean: 0.000 shift max: 0.001 19 r_work: 0.10226 shift mean: 0.000 shift max: 0.001 20 r_work: 0.10226 shift mean: 0.000 shift max: 0.001 21 r_work: 0.10227 shift mean: 0.000 shift max: 0.002 22 r_work: 0.10227 shift mean: 0.000 shift max: 0.002 23 r_work: 0.10228 shift mean: 0.000 shift max: 0.003 24 r_work: 0.10229 shift mean: 0.000 shift max: 0.003 25 r_work: 0.10230 shift mean: 0.000 shift max: 0.002 26 r_work: 0.10231 shift mean: 0.000 shift max: 0.003 27 r_work: 0.10232 shift mean: 0.000 shift max: 0.002 28 r_work: 0.10232 shift mean: 0.000 shift max: 0.002 29 r_work: 0.10232 shift mean: 0.000 shift max: 0.002 30 r_work: 0.10233 shift mean: 0.000 shift max: 0.003 31 r_work: 0.10234 shift mean: 0.000 shift max: 0.002 32 r_work: 0.10235 shift mean: 0.000 shift max: 0.003 33 r_work: 0.10235 shift mean: 0.000 shift max: 0.003 34 r_work: 0.10237 shift mean: 0.001 shift max: 0.005 35 r_work: 0.10238 shift mean: 0.000 shift max: 0.004 36 r_work: 0.10239 shift mean: 0.001 shift max: 0.006 37 r_work: 0.10241 shift mean: 0.000 shift max: 0.004 38 r_work: 0.10242 shift mean: 0.000 shift max: 0.005 39 r_work: 0.10243 shift mean: 0.000 shift max: 0.004 40 r_work: 0.10244 shift mean: 0.000 shift max: 0.005 41 r_work: 0.10244 shift mean: 0.000 shift max: 0.004 42 r_work: 0.10246 shift mean: 0.000 shift max: 0.004 43 r_work: 0.10246 shift mean: 0.000 shift max: 0.005 44 r_work: 0.10246 shift mean: 0.000 shift max: 0.005 45 r_work: 0.10246 shift mean: 0.000 shift max: 0.004 46 r_work: 0.10247 shift mean: 0.001 shift max: 0.007 47 r_work: 0.10247 shift mean: 0.000 shift max: 0.005 48 r_work: 0.10247 shift mean: 0.001 shift max: 0.009 49 r_work: 0.10248 shift mean: 0.001 shift max: 0.016 50 r_work: 0.10247 shift mean: 0.001 shift max: 0.016 51 r_work: 0.10248 shift mean: 0.001 shift max: 0.014 52 r_work: 0.10247 shift mean: 0.002 shift max: 0.026 53 4: Rw: 0.1025 Rf: 0.1172 Rf-Rw: 0.0147 bond: 0.011 angle: 1.88 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.46 cb: 0.00 shift start/prev: 0.140 0.014 n_fev: 53 At refinement end: Rw: 0.1025 Rf: 0.1172 Rf-Rw: 0.0147 bond: 0.011 angle: 1.88 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.46 cb: 0.00 shift start/prev: 0.140 0.014 Best Rwork, Rfree (after refinement): 0.1025 0.1172 See 3NJW_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 170.95 seconds wall clock time: 2 minutes 59.63 seconds (179.63 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)