Starting qr.refine on Fri Jun 21 15:06:26 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 { 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" 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" } 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: 0.11, per 1000 atoms: 0.32 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: 0.12 Adding C-beta torsion restraints... Number of C-beta restraints generated: 32 Time building geometry restraints manager: 0.13 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 Start: Rw: 0.0959 Rf: 0.1114 Rf-Rw: 0.0155 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: 0.000 0.000 Optimal weight search: Data weight (initial): 1146.843256542622 r_work: 0.09587 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13341 shift mean: 0.024 shift max: 0.200 2 r_work: 0.13341 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12272 shift mean: 0.004 shift max: 0.036 4 r_work: 0.11205 shift mean: 0.003 shift max: 0.044 5 r_work: 0.10575 shift mean: 0.002 shift max: 0.028 6 r_work: 0.10223 shift mean: 0.001 shift max: 0.019 7 r_work: 0.09989 shift mean: 0.001 shift max: 0.015 8 r_work: 0.09835 shift mean: 0.001 shift max: 0.011 9 r_work: 0.09738 shift mean: 0.000 shift max: 0.009 10 r_work: 0.09667 shift mean: 0.000 shift max: 0.007 11 r_work: 0.09618 shift mean: 0.000 shift max: 0.006 12 r_work: 0.09581 shift mean: 0.000 shift max: 0.005 13 r_work: 0.09555 shift mean: 0.000 shift max: 0.004 14 r_work: 0.09535 shift mean: 0.000 shift max: 0.003 15 r_work: 0.09521 shift mean: 0.000 shift max: 0.003 16 r_work: 0.09511 shift mean: 0.001 shift max: 0.003 17 r_work: 0.09500 shift mean: 0.001 shift max: 0.002 18 r_work: 0.09493 shift mean: 0.001 shift max: 0.002 19 r_work: 0.09488 shift mean: 0.001 shift max: 0.004 20 r_work: 0.09487 shift mean: 0.002 shift max: 0.005 21 r_work: 0.09490 shift mean: 0.003 shift max: 0.009 22 r_work: 0.09497 shift mean: 0.003 shift max: 0.011 23 r_work: 0.09504 shift mean: 0.004 shift max: 0.014 24 r_work: 0.09511 shift mean: 0.003 shift max: 0.013 25 r_work: 0.09515 shift mean: 0.004 shift max: 0.017 26 r_work: 0.09514 shift mean: 0.003 shift max: 0.014 27 r_work: 0.09515 shift mean: 0.004 shift max: 0.017 28 r_work: 0.09511 shift mean: 0.003 shift max: 0.014 29 r_work: 0.09511 shift mean: 0.003 shift max: 0.012 30 r_work: 0.09512 shift mean: 0.003 shift max: 0.012 31 r_work: 0.09514 shift mean: 0.002 shift max: 0.009 32 r_work: 0.09516 shift mean: 0.002 shift max: 0.008 33 r_work: 0.09519 shift mean: 0.002 shift max: 0.009 34 r_work: 0.09520 shift mean: 0.002 shift max: 0.006 35 r_work: 0.09523 shift mean: 0.002 shift max: 0.008 36 r_work: 0.09524 shift mean: 0.001 shift max: 0.005 37 r_work: 0.09526 shift mean: 0.002 shift max: 0.006 38 r_work: 0.09527 shift mean: 0.003 shift max: 0.009 39 r_work: 0.09525 shift mean: 0.002 shift max: 0.007 40 r_work: 0.09524 shift mean: 0.002 shift max: 0.005 41 r_work: 0.09527 shift mean: 0.002 shift max: 0.007 42 r_work: 0.09526 shift mean: 0.001 shift max: 0.005 43 r_work: 0.09529 shift mean: 0.001 shift max: 0.005 44 r_work: 0.09528 shift mean: 0.002 shift max: 0.007 45 r_work: 0.09530 shift mean: 0.001 shift max: 0.004 46 r_work: 0.09531 shift mean: 0.001 shift max: 0.006 47 r_work: 0.09534 shift mean: 0.001 shift max: 0.007 48 r_work: 0.09536 shift mean: 0.002 shift max: 0.008 49 r_work: 0.09540 shift mean: 0.001 shift max: 0.007 50 r_work: 0.09546 shift mean: 0.002 shift max: 0.010 51 r_work: 0.09548 shift mean: 0.001 shift max: 0.006 52 r_work: 0.09550 shift mean: 0.002 shift max: 0.011 53 r_work: 0.09552 shift mean: 0.001 shift max: 0.005 54 r_work: 0.09553 shift mean: 0.001 shift max: 0.008 55 r_work: 0.09554 shift mean: 0.001 shift max: 0.005 56 r_work: 0.09554 shift mean: 0.001 shift max: 0.006 57 r_work: 0.09552 shift mean: 0.001 shift max: 0.006 58 r_work: 0.09550 shift mean: 0.001 shift max: 0.006 59 r_work: 0.09549 shift mean: 0.001 shift max: 0.004 60 r_work: 0.09543 shift mean: 0.001 shift max: 0.006 61 r_work: 0.09541 shift mean: 0.001 shift max: 0.004 62 r_work: 0.09536 shift mean: 0.001 shift max: 0.005 63 r_work: 0.09531 shift mean: 0.001 shift max: 0.005 64 r_work: 0.09526 shift mean: 0.001 shift max: 0.005 65 r_work: 0.09520 shift mean: 0.001 shift max: 0.006 66 r_work: 0.09515 shift mean: 0.001 shift max: 0.005 67 r_work: 0.09511 shift mean: 0.001 shift max: 0.004 68 r_work: 0.09506 shift mean: 0.001 shift max: 0.005 69 r_work: 0.09501 shift mean: 0.001 shift max: 0.004 70 r_work: 0.09497 shift mean: 0.001 shift max: 0.004 71 r_work: 0.09492 shift mean: 0.001 shift max: 0.006 72 r_work: 0.09488 shift mean: 0.001 shift max: 0.003 73 r_work: 0.09484 shift mean: 0.001 shift max: 0.006 74 r_work: 0.09480 shift mean: 0.001 shift max: 0.003 75 r_work: 0.09476 shift mean: 0.001 shift max: 0.005 76 r_work: 0.09470 shift mean: 0.001 shift max: 0.006 77 r_work: 0.09465 shift mean: 0.001 shift max: 0.006 78 r_work: 0.09459 shift mean: 0.001 shift max: 0.006 79 r_work: 0.09455 shift mean: 0.001 shift max: 0.007 80 r_work: 0.09452 shift mean: 0.001 shift max: 0.005 81 r_work: 0.09450 shift mean: 0.001 shift max: 0.005 82 r_work: 0.09449 shift mean: 0.001 shift max: 0.004 83 r_work: 0.09446 shift mean: 0.001 shift max: 0.005 84 r_work: 0.09445 shift mean: 0.001 shift max: 0.005 85 r_work: 0.09443 shift mean: 0.001 shift max: 0.004 86 r_work: 0.09444 shift mean: 0.001 shift max: 0.005 87 r_work: 0.09445 shift mean: 0.001 shift max: 0.005 88 r_work: 0.09445 shift mean: 0.001 shift max: 0.005 89 r_work: 0.09447 shift mean: 0.001 shift max: 0.007 90 r_work: 0.09448 shift mean: 0.001 shift max: 0.004 91 r_work: 0.09448 shift mean: 0.001 shift max: 0.005 92 r_work: 0.09448 shift mean: 0.001 shift max: 0.005 93 r_work: 0.09449 shift mean: 0.001 shift max: 0.005 94 r_work: 0.09450 shift mean: 0.001 shift max: 0.006 95 r_work: 0.09449 shift mean: 0.001 shift max: 0.004 96 r_work: 0.09449 shift mean: 0.001 shift max: 0.005 97 r_work: 0.09449 shift mean: 0.001 shift max: 0.006 98 r_work: 0.09448 shift mean: 0.001 shift max: 0.004 99 r_work: 0.09448 shift mean: 0.001 shift max: 0.005 100 r_work: 0.09446 shift mean: 0.001 shift max: 0.005 101 r_work: 0.09446 shift mean: 0.001 shift max: 0.004 102 0: Rw: 0.0945 Rf: 0.1099 Rf-Rw: 0.0154 bond: 0.015 angle: 1.92 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.46 cb: 0.00 shift start/prev: 0.074 0.074 rws(prev): 1.000 rws: 1.000 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.0945 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.0945 0.1092 At refinement start Rw: 0.0945 Rf: 0.1092 Rf-Rw: 0.0147 bond: 0.015 angle: 1.92 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.46 cb: 0.00 shift start/prev: 0.074 0.000 Refinement: r_work: 0.09453 shift mean: 0.000 shift max: 0.000 1 r_work: 0.14170 shift mean: 0.026 shift max: 0.200 2 r_work: 0.12086 shift mean: 0.008 shift max: 0.060 3 r_work: 0.11245 shift mean: 0.003 shift max: 0.027 4 r_work: 0.10573 shift mean: 0.003 shift max: 0.027 5 r_work: 0.10139 shift mean: 0.002 shift max: 0.020 6 r_work: 0.09888 shift mean: 0.002 shift max: 0.014 7 r_work: 0.09718 shift mean: 0.001 shift max: 0.011 8 r_work: 0.09613 shift mean: 0.001 shift max: 0.008 9 r_work: 0.09543 shift mean: 0.001 shift max: 0.007 10 r_work: 0.09502 shift mean: 0.001 shift max: 0.005 11 r_work: 0.09477 shift mean: 0.001 shift max: 0.004 12 r_work: 0.09461 shift mean: 0.000 shift max: 0.003 13 r_work: 0.09449 shift mean: 0.000 shift max: 0.003 14 r_work: 0.09443 shift mean: 0.000 shift max: 0.002 15 r_work: 0.09440 shift mean: 0.000 shift max: 0.002 16 r_work: 0.09438 shift mean: 0.000 shift max: 0.001 17 r_work: 0.09437 shift mean: 0.000 shift max: 0.001 18 r_work: 0.09436 shift mean: 0.000 shift max: 0.001 19 r_work: 0.09435 shift mean: 0.000 shift max: 0.001 20 r_work: 0.09435 shift mean: 0.000 shift max: 0.001 21 r_work: 0.09435 shift mean: 0.000 shift max: 0.001 22 r_work: 0.09435 shift mean: 0.000 shift max: 0.000 23 r_work: 0.09435 shift mean: 0.000 shift max: 0.000 24 r_work: 0.09436 shift mean: 0.000 shift max: 0.000 25 r_work: 0.09436 shift mean: 0.000 shift max: 0.000 26 r_work: 0.09435 shift mean: 0.000 shift max: 0.000 27 r_work: 0.09435 shift mean: 0.000 shift max: 0.000 28 r_work: 0.09435 shift mean: 0.000 shift max: 0.001 29 r_work: 0.09436 shift mean: 0.000 shift max: 0.001 30 r_work: 0.09437 shift mean: 0.000 shift max: 0.001 31 r_work: 0.09437 shift mean: 0.000 shift max: 0.001 32 r_work: 0.09438 shift mean: 0.000 shift max: 0.002 33 r_work: 0.09438 shift mean: 0.000 shift max: 0.003 34 r_work: 0.09438 shift mean: 0.000 shift max: 0.003 35 r_work: 0.09437 shift mean: 0.000 shift max: 0.003 36 r_work: 0.09437 shift mean: 0.001 shift max: 0.004 37 r_work: 0.09436 shift mean: 0.000 shift max: 0.003 38 r_work: 0.09435 shift mean: 0.001 shift max: 0.005 39 r_work: 0.09434 shift mean: 0.001 shift max: 0.004 40 r_work: 0.09431 shift mean: 0.001 shift max: 0.005 41 r_work: 0.09428 shift mean: 0.000 shift max: 0.003 42 r_work: 0.09426 shift mean: 0.000 shift max: 0.004 43 r_work: 0.09424 shift mean: 0.001 shift max: 0.004 44 r_work: 0.09421 shift mean: 0.000 shift max: 0.003 45 r_work: 0.09418 shift mean: 0.001 shift max: 0.004 46 r_work: 0.09416 shift mean: 0.001 shift max: 0.004 47 r_work: 0.09414 shift mean: 0.001 shift max: 0.004 48 r_work: 0.09413 shift mean: 0.000 shift max: 0.004 49 r_work: 0.09411 shift mean: 0.001 shift max: 0.005 50 r_work: 0.09409 shift mean: 0.001 shift max: 0.005 51 r_work: 0.09410 shift mean: 0.001 shift max: 0.006 52 0: Rw: 0.0941 Rf: 0.1090 Rf-Rw: 0.0150 bond: 0.015 angle: 1.93 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.45 cb: 0.00 shift start/prev: 0.081 0.011 n_fev: 52 r_work: 0.09410 shift mean: 0.000 shift max: 0.000 1 r_work: 0.14695 shift mean: 0.033 shift max: 0.200 2 r_work: 0.10963 shift mean: 0.017 shift max: 0.105 3 r_work: 0.10470 shift mean: 0.003 shift max: 0.018 4 r_work: 0.10103 shift mean: 0.002 shift max: 0.016 5 r_work: 0.09866 shift mean: 0.002 shift max: 0.012 6 r_work: 0.09713 shift mean: 0.001 shift max: 0.010 7 r_work: 0.09615 shift mean: 0.001 shift max: 0.008 8 r_work: 0.09550 shift mean: 0.001 shift max: 0.006 9 r_work: 0.09508 shift mean: 0.001 shift max: 0.004 10 r_work: 0.09477 shift mean: 0.001 shift max: 0.004 11 r_work: 0.09460 shift mean: 0.000 shift max: 0.003 12 r_work: 0.09444 shift mean: 0.000 shift max: 0.003 13 r_work: 0.09436 shift mean: 0.000 shift max: 0.002 14 r_work: 0.09430 shift mean: 0.000 shift max: 0.001 15 r_work: 0.09425 shift mean: 0.000 shift max: 0.001 16 r_work: 0.09422 shift mean: 0.000 shift max: 0.001 17 r_work: 0.09420 shift mean: 0.000 shift max: 0.001 18 r_work: 0.09419 shift mean: 0.000 shift max: 0.000 19 r_work: 0.09417 shift mean: 0.000 shift max: 0.001 20 r_work: 0.09417 shift mean: 0.000 shift max: 0.000 21 r_work: 0.09416 shift mean: 0.000 shift max: 0.000 22 r_work: 0.09415 shift mean: 0.000 shift max: 0.000 23 r_work: 0.09415 shift mean: 0.000 shift max: 0.000 24 r_work: 0.09414 shift mean: 0.000 shift max: 0.000 25 r_work: 0.09413 shift mean: 0.000 shift max: 0.000 26 r_work: 0.09412 shift mean: 0.000 shift max: 0.000 27 r_work: 0.09411 shift mean: 0.000 shift max: 0.000 28 r_work: 0.09410 shift mean: 0.000 shift max: 0.001 29 r_work: 0.09411 shift mean: 0.000 shift max: 0.001 30 r_work: 0.09410 shift mean: 0.000 shift max: 0.001 31 r_work: 0.09410 shift mean: 0.000 shift max: 0.001 32 r_work: 0.09410 shift mean: 0.000 shift max: 0.002 33 r_work: 0.09409 shift mean: 0.000 shift max: 0.003 34 r_work: 0.09408 shift mean: 0.000 shift max: 0.003 35 r_work: 0.09408 shift mean: 0.000 shift max: 0.002 36 r_work: 0.09407 shift mean: 0.000 shift max: 0.004 37 r_work: 0.09407 shift mean: 0.000 shift max: 0.003 38 r_work: 0.09407 shift mean: 0.001 shift max: 0.005 39 r_work: 0.09408 shift mean: 0.000 shift max: 0.003 40 r_work: 0.09407 shift mean: 0.000 shift max: 0.004 41 r_work: 0.09408 shift mean: 0.000 shift max: 0.003 42 r_work: 0.09408 shift mean: 0.000 shift max: 0.003 43 r_work: 0.09408 shift mean: 0.000 shift max: 0.003 44 r_work: 0.09408 shift mean: 0.000 shift max: 0.003 45 r_work: 0.09408 shift mean: 0.000 shift max: 0.003 46 r_work: 0.09407 shift mean: 0.000 shift max: 0.002 47 r_work: 0.09407 shift mean: 0.001 shift max: 0.005 48 r_work: 0.09407 shift mean: 0.000 shift max: 0.004 49 r_work: 0.09406 shift mean: 0.001 shift max: 0.006 50 r_work: 0.09404 shift mean: 0.001 shift max: 0.007 51 r_work: 0.09404 shift mean: 0.001 shift max: 0.007 52 1: Rw: 0.0940 Rf: 0.1089 Rf-Rw: 0.0149 bond: 0.015 angle: 1.92 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.47 cb: 0.00 shift start/prev: 0.085 0.010 n_fev: 52 r_work: 0.09404 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15566 shift mean: 0.033 shift max: 0.200 2 r_work: 0.10294 shift mean: 0.022 shift max: 0.134 3 r_work: 0.09984 shift mean: 0.002 shift max: 0.013 4 r_work: 0.09778 shift mean: 0.002 shift max: 0.011 5 r_work: 0.09639 shift mean: 0.001 shift max: 0.008 6 r_work: 0.09546 shift mean: 0.001 shift max: 0.007 7 r_work: 0.09494 shift mean: 0.001 shift max: 0.005 8 r_work: 0.09458 shift mean: 0.001 shift max: 0.005 9 r_work: 0.09434 shift mean: 0.001 shift max: 0.003 10 r_work: 0.09420 shift mean: 0.000 shift max: 0.003 11 r_work: 0.09410 shift mean: 0.000 shift max: 0.003 12 r_work: 0.09403 shift mean: 0.000 shift max: 0.002 13 r_work: 0.09399 shift mean: 0.000 shift max: 0.002 14 r_work: 0.09396 shift mean: 0.000 shift max: 0.001 15 r_work: 0.09395 shift mean: 0.000 shift max: 0.001 16 r_work: 0.09395 shift mean: 0.000 shift max: 0.001 17 r_work: 0.09394 shift mean: 0.000 shift max: 0.001 18 r_work: 0.09394 shift mean: 0.000 shift max: 0.001 19 r_work: 0.09394 shift mean: 0.000 shift max: 0.000 20 r_work: 0.09393 shift mean: 0.000 shift max: 0.000 21 r_work: 0.09394 shift mean: 0.000 shift max: 0.000 22 r_work: 0.09393 shift mean: 0.000 shift max: 0.000 23 r_work: 0.09393 shift mean: 0.000 shift max: 0.000 24 r_work: 0.09393 shift mean: 0.000 shift max: 0.000 25 r_work: 0.09393 shift mean: 0.000 shift max: 0.000 26 r_work: 0.09393 shift mean: 0.000 shift max: 0.001 27 r_work: 0.09392 shift mean: 0.000 shift max: 0.001 28 r_work: 0.09392 shift mean: 0.000 shift max: 0.001 29 r_work: 0.09392 shift mean: 0.000 shift max: 0.002 30 r_work: 0.09391 shift mean: 0.000 shift max: 0.002 31 r_work: 0.09391 shift mean: 0.000 shift max: 0.003 32 r_work: 0.09390 shift mean: 0.000 shift max: 0.003 33 r_work: 0.09389 shift mean: 0.000 shift max: 0.003 34 r_work: 0.09388 shift mean: 0.000 shift max: 0.003 35 r_work: 0.09388 shift mean: 0.000 shift max: 0.003 36 r_work: 0.09386 shift mean: 0.000 shift max: 0.002 37 r_work: 0.09384 shift mean: 0.000 shift max: 0.002 38 r_work: 0.09385 shift mean: 0.000 shift max: 0.003 39 r_work: 0.09384 shift mean: 0.000 shift max: 0.002 40 r_work: 0.09384 shift mean: 0.000 shift max: 0.002 41 r_work: 0.09383 shift mean: 0.000 shift max: 0.002 42 r_work: 0.09383 shift mean: 0.000 shift max: 0.002 43 r_work: 0.09383 shift mean: 0.000 shift max: 0.003 44 r_work: 0.09383 shift mean: 0.000 shift max: 0.002 45 r_work: 0.09382 shift mean: 0.000 shift max: 0.003 46 r_work: 0.09381 shift mean: 0.000 shift max: 0.004 47 r_work: 0.09380 shift mean: 0.000 shift max: 0.004 48 r_work: 0.09380 shift mean: 0.001 shift max: 0.006 49 r_work: 0.09379 shift mean: 0.000 shift max: 0.005 50 r_work: 0.09379 shift mean: 0.001 shift max: 0.008 51 r_work: 0.09378 shift mean: 0.001 shift max: 0.007 52 2: Rw: 0.0938 Rf: 0.1087 Rf-Rw: 0.0149 bond: 0.015 angle: 1.93 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.44 cb: 0.00 shift start/prev: 0.089 0.008 n_fev: 52 r_work: 0.09378 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13380 shift mean: 0.017 shift max: 0.200 2 r_work: 0.11502 shift mean: 0.005 shift max: 0.064 3 r_work: 0.10820 shift mean: 0.002 shift max: 0.027 4 r_work: 0.10295 shift mean: 0.002 shift max: 0.024 5 r_work: 0.09957 shift mean: 0.001 shift max: 0.018 6 r_work: 0.09747 shift mean: 0.001 shift max: 0.014 7 r_work: 0.09611 shift mean: 0.001 shift max: 0.011 8 r_work: 0.09530 shift mean: 0.001 shift max: 0.008 9 r_work: 0.09472 shift mean: 0.001 shift max: 0.007 10 r_work: 0.09439 shift mean: 0.000 shift max: 0.005 11 r_work: 0.09417 shift mean: 0.000 shift max: 0.004 12 r_work: 0.09404 shift mean: 0.000 shift max: 0.003 13 r_work: 0.09394 shift mean: 0.000 shift max: 0.003 14 r_work: 0.09387 shift mean: 0.000 shift max: 0.002 15 r_work: 0.09383 shift mean: 0.000 shift max: 0.002 16 r_work: 0.09382 shift mean: 0.000 shift max: 0.001 17 r_work: 0.09381 shift mean: 0.000 shift max: 0.001 18 r_work: 0.09379 shift mean: 0.000 shift max: 0.001 19 r_work: 0.09379 shift mean: 0.000 shift max: 0.000 20 r_work: 0.09378 shift mean: 0.000 shift max: 0.001 21 r_work: 0.09378 shift mean: 0.000 shift max: 0.001 22 r_work: 0.09378 shift mean: 0.000 shift max: 0.001 23 r_work: 0.09378 shift mean: 0.000 shift max: 0.000 24 r_work: 0.09378 shift mean: 0.000 shift max: 0.000 25 r_work: 0.09377 shift mean: 0.000 shift max: 0.000 26 r_work: 0.09378 shift mean: 0.000 shift max: 0.000 27 r_work: 0.09377 shift mean: 0.000 shift max: 0.000 28 r_work: 0.09377 shift mean: 0.000 shift max: 0.000 29 r_work: 0.09377 shift mean: 0.000 shift max: 0.000 30 r_work: 0.09377 shift mean: 0.000 shift max: 0.000 31 r_work: 0.09377 shift mean: 0.000 shift max: 0.000 32 r_work: 0.09376 shift mean: 0.000 shift max: 0.000 33 r_work: 0.09376 shift mean: 0.000 shift max: 0.001 34 r_work: 0.09377 shift mean: 0.000 shift max: 0.001 35 r_work: 0.09377 shift mean: 0.000 shift max: 0.001 36 r_work: 0.09377 shift mean: 0.000 shift max: 0.001 37 r_work: 0.09377 shift mean: 0.000 shift max: 0.002 38 r_work: 0.09376 shift mean: 0.000 shift max: 0.002 39 r_work: 0.09375 shift mean: 0.000 shift max: 0.002 40 r_work: 0.09375 shift mean: 0.000 shift max: 0.002 41 r_work: 0.09375 shift mean: 0.000 shift max: 0.002 42 r_work: 0.09375 shift mean: 0.000 shift max: 0.003 43 r_work: 0.09376 shift mean: 0.000 shift max: 0.003 44 r_work: 0.09375 shift mean: 0.000 shift max: 0.002 45 r_work: 0.09375 shift mean: 0.000 shift max: 0.002 46 r_work: 0.09375 shift mean: 0.000 shift max: 0.002 47 r_work: 0.09375 shift mean: 0.000 shift max: 0.003 48 r_work: 0.09375 shift mean: 0.000 shift max: 0.002 49 r_work: 0.09374 shift mean: 0.000 shift max: 0.002 50 r_work: 0.09374 shift mean: 0.000 shift max: 0.002 51 r_work: 0.09374 shift mean: 0.000 shift max: 0.002 52 r_work: 0.09373 shift mean: 0.000 shift max: 0.002 53 3: Rw: 0.0937 Rf: 0.1086 Rf-Rw: 0.0148 bond: 0.015 angle: 1.93 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.47 cb: 0.00 shift start/prev: 0.091 0.004 n_fev: 53 r_work: 0.09373 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13629 shift mean: 0.018 shift max: 0.200 2 r_work: 0.09489 shift mean: 0.015 shift max: 0.169 3 r_work: 0.09445 shift mean: 0.001 shift max: 0.006 4 r_work: 0.09415 shift mean: 0.000 shift max: 0.005 5 r_work: 0.09399 shift mean: 0.000 shift max: 0.004 6 r_work: 0.09385 shift mean: 0.000 shift max: 0.004 7 r_work: 0.09379 shift mean: 0.000 shift max: 0.002 8 r_work: 0.09376 shift mean: 0.000 shift max: 0.002 9 r_work: 0.09373 shift mean: 0.000 shift max: 0.002 10 r_work: 0.09372 shift mean: 0.000 shift max: 0.001 11 r_work: 0.09372 shift mean: 0.000 shift max: 0.001 12 r_work: 0.09372 shift mean: 0.000 shift max: 0.001 13 r_work: 0.09372 shift mean: 0.000 shift max: 0.001 14 r_work: 0.09372 shift mean: 0.000 shift max: 0.001 15 r_work: 0.09371 shift mean: 0.000 shift max: 0.000 16 r_work: 0.09371 shift mean: 0.000 shift max: 0.001 17 r_work: 0.09370 shift mean: 0.000 shift max: 0.000 18 r_work: 0.09371 shift mean: 0.000 shift max: 0.000 19 r_work: 0.09370 shift mean: 0.000 shift max: 0.000 20 r_work: 0.09370 shift mean: 0.000 shift max: 0.000 21 r_work: 0.09370 shift mean: 0.000 shift max: 0.000 22 r_work: 0.09370 shift mean: 0.000 shift max: 0.000 23 r_work: 0.09370 shift mean: 0.000 shift max: 0.000 24 r_work: 0.09370 shift mean: 0.000 shift max: 0.000 25 r_work: 0.09370 shift mean: 0.000 shift max: 0.000 26 r_work: 0.09371 shift mean: 0.000 shift max: 0.001 27 r_work: 0.09371 shift mean: 0.000 shift max: 0.001 28 r_work: 0.09372 shift mean: 0.000 shift max: 0.001 29 r_work: 0.09372 shift mean: 0.000 shift max: 0.001 30 r_work: 0.09372 shift mean: 0.000 shift max: 0.001 31 r_work: 0.09371 shift mean: 0.000 shift max: 0.001 32 r_work: 0.09370 shift mean: 0.000 shift max: 0.002 33 r_work: 0.09369 shift mean: 0.000 shift max: 0.002 34 r_work: 0.09369 shift mean: 0.000 shift max: 0.002 35 r_work: 0.09368 shift mean: 0.000 shift max: 0.003 36 r_work: 0.09367 shift mean: 0.000 shift max: 0.002 37 r_work: 0.09367 shift mean: 0.000 shift max: 0.003 38 r_work: 0.09366 shift mean: 0.000 shift max: 0.002 39 r_work: 0.09366 shift mean: 0.000 shift max: 0.003 40 r_work: 0.09366 shift mean: 0.000 shift max: 0.002 41 r_work: 0.09366 shift mean: 0.000 shift max: 0.003 42 r_work: 0.09365 shift mean: 0.000 shift max: 0.001 43 r_work: 0.09364 shift mean: 0.000 shift max: 0.001 44 r_work: 0.09363 shift mean: 0.000 shift max: 0.001 45 r_work: 0.09363 shift mean: 0.000 shift max: 0.002 46 r_work: 0.09362 shift mean: 0.000 shift max: 0.002 47 r_work: 0.09361 shift mean: 0.000 shift max: 0.001 48 r_work: 0.09361 shift mean: 0.000 shift max: 0.002 49 r_work: 0.09360 shift mean: 0.000 shift max: 0.002 50 r_work: 0.09359 shift mean: 0.000 shift max: 0.002 51 r_work: 0.09359 shift mean: 0.000 shift max: 0.002 52 4: Rw: 0.0936 Rf: 0.1086 Rf-Rw: 0.0150 bond: 0.015 angle: 1.93 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.45 cb: 0.00 shift start/prev: 0.093 0.005 n_fev: 52 At refinement end: Rw: 0.0936 Rf: 0.1086 Rf-Rw: 0.0150 bond: 0.015 angle: 1.93 clash: 0.0 rota: 0.00 rama: f: 88.24 o: 0.00 Z: -3.45 cb: 0.00 shift start/prev: 0.093 0.005 Best Rwork, Rfree (after refinement): 0.0936 0.1086 See 3NJW_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 144.49 seconds wall clock time: 2 minutes 32.49 seconds (152.49 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)