Starting qr.refine on Thu Jun 20 16:47:49 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//2PND.mtz Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/2PND.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/2PND.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/2PND.pdb" miller_array { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//2PND.mtz" } default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//2PND.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)=0.1694 0.1675 0.2074 n_refl.: 51757 re-set all scales: r(all,work,free)=0.1694 0.1675 0.2074 n_refl.: 51757 remove outliers: r(all,work,free)=0.1694 0.1675 0.2074 n_refl.: 51754 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1193 0.1449 n_refl.: 51754 remove outliers: r(all,work,free)=0.1205 0.1192 0.1449 n_refl.: 51750 Resolution Compl Nwork Nfree R_work kiso kani kmask 31.404-8.345 81.30 92 8 0.3373 183.219 170.218 1.055 0.950 0.470 8.232-6.663 94.34 95 5 0.2519 191.421 185.061 0.985 0.950 0.424 6.647-5.377 96.24 173 6 0.2087 221.880 215.528 1.052 0.950 0.406 5.365-4.336 90.25 312 12 0.1445 282.315 275.038 1.087 0.949 0.360 4.332-3.500 96.43 585 36 0.1259 307.090 303.604 1.071 0.948 0.170 3.499-2.826 99.83 1156 52 0.1263 245.130 241.167 1.065 0.946 0.160 2.825-2.282 100.00 2146 114 0.1387 169.843 167.029 1.082 0.943 0.000 2.281-1.842 100.00 4019 190 0.1168 135.814 134.207 1.113 0.939 0.000 1.842-1.488 100.00 7536 401 0.1095 75.526 74.398 1.116 0.930 0.000 1.488-1.201 100.00 14170 731 0.0978 48.678 47.958 1.147 0.919 0.000 1.201-0.970 71.02 18885 1026 0.1186 33.773 33.497 1.098 0.964 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.2038 ------------------------------------------------------------------------------- Starting r-factors: ******************* r_work=0.1192 r_free=0.1449 ------------------------------------------------------------------------------- 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: 2659 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1948 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "A" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 711 Classifications: {'water': 237} Link IDs: {None: 236} Time building chain proxies: 0.46, per 1000 atoms: 0.17 Number of scatterers: 2659 At special positions: 0 Unit cell: (31.334, 50.684, 62.809, 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 3 16.00 O 414 8.00 N 182 7.00 C 606 6.00 H 1454 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: 220 Time building geometry restraints manager: 1.32 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: 1452 1.04 - 1.23: 51 1.23 - 1.43: 363 1.43 - 1.63: 572 1.63 - 1.82: 4 Bond restraints: 2442 Sorted by residual: bond pdb=" N VAL A 10 " pdb=" H VAL A 10 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLU A 8 " pdb=" H GLU A 8 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE2 GLN A 85 " pdb="HE21 GLN A 85 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N VAL A 96 " pdb=" H VAL A 96 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ILE A 23 " pdb=" H ILE A 23 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 ... (remaining 2437 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.15: 300 106.15 - 113.06: 2284 113.06 - 119.97: 522 119.97 - 126.88: 672 126.88 - 133.79: 18 Bond angle restraints: 3796 Sorted by residual: angle pdb=" CA ASN A 82 " pdb=" CB ASN A 82 " pdb=" CG ASN A 82 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 angle pdb=" CA ASP A 109 " pdb=" CB ASP A 109 " pdb=" CG ASP A 109 " ideal model delta sigma weight residual 112.60 115.71 -3.11 1.00e+00 1.00e+00 9.67e+00 angle pdb=" CG GLN A 80 " pdb=" CD GLN A 80 " pdb=" NE2 GLN A 80 " ideal model delta sigma weight residual 116.40 120.71 -4.31 1.50e+00 4.44e-01 8.25e+00 angle pdb=" C LEU A 67 " pdb=" CA LEU A 67 " pdb=" CB LEU A 67 " ideal model delta sigma weight residual 110.10 104.92 5.18 1.90e+00 2.77e-01 7.43e+00 angle pdb=" C ARG A 66 " pdb=" CA ARG A 66 " pdb=" CB ARG A 66 " ideal model delta sigma weight residual 110.10 105.07 5.03 1.90e+00 2.77e-01 7.00e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 835 17.44 - 34.88: 51 34.88 - 52.31: 16 52.31 - 69.75: 5 69.75 - 87.19: 2 Dihedral angle restraints: 909 sinusoidal: 513 harmonic: 396 Sorted by residual: dihedral pdb=" CA LYS A 36 " pdb=" C LYS A 36 " pdb=" N TRP A 37 " pdb=" CA TRP A 37 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TRP A 98 " pdb=" C TRP A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CB GLU A 95 " pdb=" CG GLU A 95 " pdb=" CD GLU A 95 " pdb=" OE1 GLU A 95 " ideal model delta sinusoidal sigma weight residual 0.00 -87.19 87.19 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 59 0.059 - 0.117: 51 0.117 - 0.175: 26 0.175 - 0.234: 10 0.234 - 0.292: 3 Chirality restraints: 149 Sorted by residual: chirality pdb=" CA LYS A 15 " pdb=" N LYS A 15 " pdb=" C LYS A 15 " pdb=" CB LYS A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL A 10 " pdb=" N VAL A 10 " pdb=" C VAL A 10 " pdb=" CB VAL A 10 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLN A 59 " pdb=" N GLN A 59 " pdb=" C GLN A 59 " pdb=" CB GLN A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 146 not shown) Planarity restraints: 284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 37 " -0.031 2.00e-02 2.50e+03 2.15e-02 1.84e+01 pdb=" CG TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 37 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 37 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP A 37 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 37 " 0.025 2.00e-02 2.50e+03 pdb=" CE3 TRP A 37 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 37 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 37 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 37 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TRP A 37 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP A 37 " 0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP A 37 " 0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 37 " 0.014 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 37 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP A 37 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 92 " -0.052 2.00e-02 2.50e+03 2.27e-02 1.54e+01 pdb=" CG TYR A 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 92 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 92 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 92 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 92 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 92 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TYR A 92 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 TYR A 92 " 0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR A 92 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR A 92 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 24 " -0.038 2.00e-02 2.50e+03 1.91e-02 1.09e+01 pdb=" CG TYR A 24 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 24 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 24 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 24 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 24 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 24 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 24 " -0.035 2.00e-02 2.50e+03 pdb=" HD1 TYR A 24 " 0.029 2.00e-02 2.50e+03 pdb=" HD2 TYR A 24 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR A 24 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 24 " 0.023 2.00e-02 2.50e+03 ... (remaining 281 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 242 2.03 - 2.68: 4683 2.68 - 3.32: 10274 3.32 - 3.96: 15672 3.96 - 4.60: 23290 Nonbonded interactions: 54161 Sorted by model distance: nonbonded pdb="HE22 GLN A 80 " pdb=" O HOH A 178 " model vdw 1.393 1.800 nonbonded pdb=" OE1 GLN A 80 " pdb=" O HOH A 171 " model vdw 1.444 2.200 nonbonded pdb=" H2 GLY A 0 " pdb=" O HOH A 297 " model vdw 1.534 1.800 nonbonded pdb=" O HOH A 306 " pdb=" H2 HOH A 341 " model vdw sym.op. 1.633 1.800 -x+1,y+1/2,-z+1/2 nonbonded pdb=" O HOH A 151 " pdb=" H2 HOH A 178 " model vdw sym.op. 1.647 1.800 -x+1,y+1/2,-z+1/2 ... (remaining 54156 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 3 15.96 2 O 414 7.97 2 N 182 6.97 2 C 606 5.97 2 H 1454 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=0.1192 r_free=0.1449 final: r_work=0.1207 r_free=0.1457 Start: Rw: 0.1207 Rf: 0.1457 Rf-Rw: 0.0250 bond: 0.011 angle: 1.48 clash: 4.1 rota: 0.92 rama: f: 93.16 o: 0.00 Z: 1.02 cb: 0.00 shift start/prev: 0.083 0.083 Optimal weight search: Data weight (initial): 1618.000125798867 r_work: 0.12067 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12823 shift mean: 0.012 shift max: 0.200 2 r_work: 0.12823 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12576 shift mean: 0.001 shift max: 0.039 4 r_work: 0.12368 shift mean: 0.001 shift max: 0.039 5 r_work: 0.12246 shift mean: 0.001 shift max: 0.028 6 r_work: 0.12167 shift mean: 0.000 shift max: 0.020 7 r_work: 0.12115 shift mean: 0.000 shift max: 0.015 8 r_work: 0.12082 shift mean: 0.000 shift max: 0.012 9 r_work: 0.12056 shift mean: 0.000 shift max: 0.010 10 r_work: 0.12039 shift mean: 0.000 shift max: 0.008 11 r_work: 0.12027 shift mean: 0.000 shift max: 0.006 12 r_work: 0.12018 shift mean: 0.000 shift max: 0.006 13 r_work: 0.12012 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12007 shift mean: 0.000 shift max: 0.005 15 r_work: 0.12004 shift mean: 0.001 shift max: 0.008 16 r_work: 0.12003 shift mean: 0.001 shift max: 0.008 17 r_work: 0.12005 shift mean: 0.001 shift max: 0.012 18 r_work: 0.12006 shift mean: 0.001 shift max: 0.018 19 r_work: 0.12011 shift mean: 0.002 shift max: 0.025 20 r_work: 0.12016 shift mean: 0.002 shift max: 0.029 21 r_work: 0.12019 shift mean: 0.002 shift max: 0.029 22 r_work: 0.12022 shift mean: 0.002 shift max: 0.031 23 r_work: 0.12028 shift mean: 0.003 shift max: 0.044 24 r_work: 0.12029 shift mean: 0.002 shift max: 0.024 25 r_work: 0.12029 shift mean: 0.002 shift max: 0.026 26 r_work: 0.12028 shift mean: 0.002 shift max: 0.038 27 r_work: 0.12029 shift mean: 0.002 shift max: 0.031 28 r_work: 0.12030 shift mean: 0.002 shift max: 0.031 29 r_work: 0.12031 shift mean: 0.002 shift max: 0.029 30 r_work: 0.12034 shift mean: 0.002 shift max: 0.028 31 r_work: 0.12037 shift mean: 0.003 shift max: 0.040 32 r_work: 0.12039 shift mean: 0.001 shift max: 0.020 33 r_work: 0.12040 shift mean: 0.002 shift max: 0.029 34 r_work: 0.12039 shift mean: 0.002 shift max: 0.030 35 r_work: 0.12039 shift mean: 0.002 shift max: 0.031 36 r_work: 0.12039 shift mean: 0.002 shift max: 0.028 37 r_work: 0.12037 shift mean: 0.002 shift max: 0.021 38 r_work: 0.12037 shift mean: 0.002 shift max: 0.024 39 r_work: 0.12039 shift mean: 0.003 shift max: 0.038 40 r_work: 0.12038 shift mean: 0.002 shift max: 0.027 41 r_work: 0.12038 shift mean: 0.002 shift max: 0.032 42 r_work: 0.12037 shift mean: 0.002 shift max: 0.032 43 r_work: 0.12037 shift mean: 0.002 shift max: 0.026 44 r_work: 0.12037 shift mean: 0.002 shift max: 0.032 45 r_work: 0.12036 shift mean: 0.002 shift max: 0.027 46 r_work: 0.12037 shift mean: 0.002 shift max: 0.025 47 r_work: 0.12037 shift mean: 0.002 shift max: 0.026 48 r_work: 0.12037 shift mean: 0.001 shift max: 0.019 49 r_work: 0.12037 shift mean: 0.002 shift max: 0.020 50 r_work: 0.12036 shift mean: 0.002 shift max: 0.025 51 r_work: 0.12035 shift mean: 0.002 shift max: 0.019 52 r_work: 0.12033 shift mean: 0.001 shift max: 0.018 53 r_work: 0.12031 shift mean: 0.002 shift max: 0.020 54 r_work: 0.12031 shift mean: 0.001 shift max: 0.014 55 r_work: 0.12029 shift mean: 0.002 shift max: 0.016 56 r_work: 0.12028 shift mean: 0.001 shift max: 0.012 57 r_work: 0.12028 shift mean: 0.002 shift max: 0.015 58 r_work: 0.12027 shift mean: 0.001 shift max: 0.008 59 r_work: 0.12026 shift mean: 0.001 shift max: 0.009 60 r_work: 0.12025 shift mean: 0.001 shift max: 0.012 61 r_work: 0.12024 shift mean: 0.001 shift max: 0.011 62 r_work: 0.12023 shift mean: 0.001 shift max: 0.010 63 r_work: 0.12022 shift mean: 0.001 shift max: 0.010 64 r_work: 0.12023 shift mean: 0.001 shift max: 0.012 65 r_work: 0.12022 shift mean: 0.001 shift max: 0.011 66 r_work: 0.12023 shift mean: 0.001 shift max: 0.013 67 r_work: 0.12024 shift mean: 0.001 shift max: 0.013 68 r_work: 0.12024 shift mean: 0.001 shift max: 0.012 69 r_work: 0.12026 shift mean: 0.002 shift max: 0.016 70 r_work: 0.12026 shift mean: 0.001 shift max: 0.011 71 r_work: 0.12027 shift mean: 0.001 shift max: 0.011 72 r_work: 0.12028 shift mean: 0.001 shift max: 0.013 73 r_work: 0.12029 shift mean: 0.001 shift max: 0.008 74 r_work: 0.12030 shift mean: 0.001 shift max: 0.010 75 r_work: 0.12030 shift mean: 0.001 shift max: 0.013 76 r_work: 0.12030 shift mean: 0.001 shift max: 0.009 77 r_work: 0.12031 shift mean: 0.001 shift max: 0.010 78 r_work: 0.12032 shift mean: 0.001 shift max: 0.010 79 r_work: 0.12031 shift mean: 0.001 shift max: 0.010 80 r_work: 0.12033 shift mean: 0.001 shift max: 0.011 81 r_work: 0.12034 shift mean: 0.001 shift max: 0.010 82 r_work: 0.12035 shift mean: 0.001 shift max: 0.010 83 r_work: 0.12036 shift mean: 0.001 shift max: 0.010 84 r_work: 0.12037 shift mean: 0.001 shift max: 0.011 85 r_work: 0.12037 shift mean: 0.001 shift max: 0.010 86 r_work: 0.12038 shift mean: 0.001 shift max: 0.011 87 r_work: 0.12040 shift mean: 0.001 shift max: 0.010 88 r_work: 0.12041 shift mean: 0.001 shift max: 0.010 89 r_work: 0.12043 shift mean: 0.001 shift max: 0.012 90 r_work: 0.12044 shift mean: 0.001 shift max: 0.009 91 r_work: 0.12045 shift mean: 0.001 shift max: 0.012 92 r_work: 0.12047 shift mean: 0.001 shift max: 0.009 93 r_work: 0.12047 shift mean: 0.001 shift max: 0.010 94 r_work: 0.12048 shift mean: 0.001 shift max: 0.012 95 r_work: 0.12050 shift mean: 0.001 shift max: 0.009 96 r_work: 0.12051 shift mean: 0.001 shift max: 0.011 97 r_work: 0.12051 shift mean: 0.001 shift max: 0.009 98 r_work: 0.12053 shift mean: 0.001 shift max: 0.011 99 r_work: 0.12053 shift mean: 0.001 shift max: 0.007 100 r_work: 0.12053 shift mean: 0.001 shift max: 0.010 101 r_work: 0.12053 shift mean: 0.001 shift max: 0.010 102 0: Rw: 0.1205 Rf: 0.1465 Rf-Rw: 0.0260 bond: 0.018 angle: 1.92 clash: 6.2 rota: 0.00 rama: f: 94.02 o: 0.00 Z: 0.93 cb: 0.00 shift start/prev: 0.125 0.087 rws(prev): 1.000 rws: 1.000 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1465 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.1205 0.1465 At refinement start Rw: 0.1205 Rf: 0.1465 Rf-Rw: 0.0260 bond: 0.018 angle: 1.92 clash: 6.2 rota: 0.00 rama: f: 94.02 o: 0.00 Z: 0.93 cb: 0.00 shift start/prev: 0.125 0.000 Refinement: r_work: 0.12049 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12631 shift mean: 0.004 shift max: 0.200 2 r_work: 0.12631 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12440 shift mean: 0.001 shift max: 0.038 4 r_work: 0.12278 shift mean: 0.001 shift max: 0.039 5 r_work: 0.12191 shift mean: 0.000 shift max: 0.027 6 r_work: 0.12136 shift mean: 0.000 shift max: 0.020 7 r_work: 0.12105 shift mean: 0.000 shift max: 0.015 8 r_work: 0.12084 shift mean: 0.000 shift max: 0.012 9 r_work: 0.12071 shift mean: 0.000 shift max: 0.009 10 r_work: 0.12063 shift mean: 0.000 shift max: 0.008 11 r_work: 0.12058 shift mean: 0.000 shift max: 0.006 12 r_work: 0.12054 shift mean: 0.000 shift max: 0.005 13 r_work: 0.12052 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12051 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12050 shift mean: 0.000 shift max: 0.003 16 r_work: 0.12049 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12048 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12048 shift mean: 0.000 shift max: 0.002 19 r_work: 0.12048 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12047 shift mean: 0.000 shift max: 0.002 21 r_work: 0.12047 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12047 shift mean: 0.000 shift max: 0.002 23 r_work: 0.12047 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12047 shift mean: 0.000 shift max: 0.002 25 r_work: 0.12046 shift mean: 0.000 shift max: 0.004 26 r_work: 0.12046 shift mean: 0.001 shift max: 0.006 27 r_work: 0.12046 shift mean: 0.001 shift max: 0.006 28 r_work: 0.12046 shift mean: 0.001 shift max: 0.007 29 r_work: 0.12046 shift mean: 0.001 shift max: 0.007 30 r_work: 0.12046 shift mean: 0.001 shift max: 0.006 31 r_work: 0.12046 shift mean: 0.000 shift max: 0.005 32 r_work: 0.12047 shift mean: 0.001 shift max: 0.007 33 r_work: 0.12047 shift mean: 0.000 shift max: 0.004 34 r_work: 0.12048 shift mean: 0.001 shift max: 0.006 35 r_work: 0.12048 shift mean: 0.001 shift max: 0.007 36 r_work: 0.12049 shift mean: 0.001 shift max: 0.008 37 r_work: 0.12050 shift mean: 0.001 shift max: 0.013 38 r_work: 0.12050 shift mean: 0.001 shift max: 0.010 39 r_work: 0.12051 shift mean: 0.001 shift max: 0.011 40 r_work: 0.12052 shift mean: 0.001 shift max: 0.012 41 r_work: 0.12054 shift mean: 0.001 shift max: 0.015 42 r_work: 0.12053 shift mean: 0.001 shift max: 0.012 43 r_work: 0.12054 shift mean: 0.001 shift max: 0.013 44 r_work: 0.12054 shift mean: 0.001 shift max: 0.012 45 r_work: 0.12054 shift mean: 0.001 shift max: 0.012 46 r_work: 0.12055 shift mean: 0.001 shift max: 0.017 47 r_work: 0.12055 shift mean: 0.001 shift max: 0.014 48 r_work: 0.12056 shift mean: 0.001 shift max: 0.012 49 r_work: 0.12056 shift mean: 0.001 shift max: 0.017 50 r_work: 0.12056 shift mean: 0.001 shift max: 0.015 51 r_work: 0.12056 shift mean: 0.001 shift max: 0.011 52 0: Rw: 0.1206 Rf: 0.1463 Rf-Rw: 0.0257 bond: 0.017 angle: 1.94 clash: 5.6 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.96 cb: 0.00 shift start/prev: 0.131 0.022 n_fev: 52 r_work: 0.12056 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13086 shift mean: 0.010 shift max: 0.200 2 r_work: 0.12871 shift mean: 0.001 shift max: 0.024 3 r_work: 0.12599 shift mean: 0.002 shift max: 0.034 4 r_work: 0.12393 shift mean: 0.001 shift max: 0.034 5 r_work: 0.12269 shift mean: 0.001 shift max: 0.024 6 r_work: 0.12190 shift mean: 0.001 shift max: 0.017 7 r_work: 0.12143 shift mean: 0.001 shift max: 0.014 8 r_work: 0.12110 shift mean: 0.000 shift max: 0.011 9 r_work: 0.12090 shift mean: 0.000 shift max: 0.009 10 r_work: 0.12076 shift mean: 0.000 shift max: 0.007 11 r_work: 0.12069 shift mean: 0.000 shift max: 0.006 12 r_work: 0.12063 shift mean: 0.000 shift max: 0.005 13 r_work: 0.12060 shift mean: 0.000 shift max: 0.003 14 r_work: 0.12057 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12056 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12055 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12054 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12054 shift mean: 0.000 shift max: 0.002 19 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12052 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12052 shift mean: 0.000 shift max: 0.001 23 r_work: 0.12052 shift mean: 0.000 shift max: 0.002 24 r_work: 0.12052 shift mean: 0.000 shift max: 0.002 25 r_work: 0.12052 shift mean: 0.000 shift max: 0.002 26 r_work: 0.12052 shift mean: 0.000 shift max: 0.005 27 r_work: 0.12052 shift mean: 0.000 shift max: 0.005 28 r_work: 0.12052 shift mean: 0.000 shift max: 0.007 29 r_work: 0.12053 shift mean: 0.001 shift max: 0.010 30 r_work: 0.12052 shift mean: 0.001 shift max: 0.011 31 r_work: 0.12052 shift mean: 0.001 shift max: 0.012 32 r_work: 0.12051 shift mean: 0.001 shift max: 0.013 33 r_work: 0.12051 shift mean: 0.001 shift max: 0.009 34 r_work: 0.12051 shift mean: 0.001 shift max: 0.011 35 r_work: 0.12051 shift mean: 0.001 shift max: 0.007 36 r_work: 0.12051 shift mean: 0.001 shift max: 0.007 37 r_work: 0.12051 shift mean: 0.000 shift max: 0.006 38 r_work: 0.12050 shift mean: 0.000 shift max: 0.006 39 r_work: 0.12051 shift mean: 0.000 shift max: 0.004 40 r_work: 0.12051 shift mean: 0.000 shift max: 0.005 41 r_work: 0.12050 shift mean: 0.000 shift max: 0.005 42 r_work: 0.12050 shift mean: 0.000 shift max: 0.003 43 r_work: 0.12050 shift mean: 0.001 shift max: 0.005 44 r_work: 0.12051 shift mean: 0.001 shift max: 0.006 45 r_work: 0.12051 shift mean: 0.001 shift max: 0.006 46 r_work: 0.12052 shift mean: 0.001 shift max: 0.009 47 r_work: 0.12052 shift mean: 0.001 shift max: 0.011 48 r_work: 0.12052 shift mean: 0.001 shift max: 0.009 49 r_work: 0.12053 shift mean: 0.002 shift max: 0.015 50 r_work: 0.12054 shift mean: 0.001 shift max: 0.013 51 r_work: 0.12054 shift mean: 0.001 shift max: 0.011 52 1: Rw: 0.1205 Rf: 0.1466 Rf-Rw: 0.0260 bond: 0.018 angle: 1.96 clash: 6.7 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.94 cb: 0.00 shift start/prev: 0.136 0.017 n_fev: 52 r_work: 0.12054 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12715 shift mean: 0.007 shift max: 0.200 2 r_work: 0.12715 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12490 shift mean: 0.001 shift max: 0.039 4 r_work: 0.12310 shift mean: 0.001 shift max: 0.039 5 r_work: 0.12209 shift mean: 0.001 shift max: 0.027 6 r_work: 0.12151 shift mean: 0.001 shift max: 0.020 7 r_work: 0.12114 shift mean: 0.000 shift max: 0.016 8 r_work: 0.12091 shift mean: 0.000 shift max: 0.012 9 r_work: 0.12077 shift mean: 0.000 shift max: 0.009 10 r_work: 0.12069 shift mean: 0.000 shift max: 0.007 11 r_work: 0.12063 shift mean: 0.000 shift max: 0.006 12 r_work: 0.12059 shift mean: 0.000 shift max: 0.005 13 r_work: 0.12056 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12056 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12054 shift mean: 0.000 shift max: 0.003 16 r_work: 0.12054 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12054 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 19 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 23 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12053 shift mean: 0.000 shift max: 0.001 25 r_work: 0.12053 shift mean: 0.000 shift max: 0.002 26 r_work: 0.12053 shift mean: 0.000 shift max: 0.004 27 r_work: 0.12053 shift mean: 0.000 shift max: 0.004 28 r_work: 0.12054 shift mean: 0.000 shift max: 0.007 29 r_work: 0.12053 shift mean: 0.000 shift max: 0.008 30 r_work: 0.12053 shift mean: 0.001 shift max: 0.011 31 r_work: 0.12053 shift mean: 0.001 shift max: 0.011 32 r_work: 0.12053 shift mean: 0.001 shift max: 0.010 33 r_work: 0.12052 shift mean: 0.001 shift max: 0.015 34 r_work: 0.12052 shift mean: 0.001 shift max: 0.009 35 r_work: 0.12051 shift mean: 0.001 shift max: 0.009 36 r_work: 0.12052 shift mean: 0.001 shift max: 0.012 37 r_work: 0.12052 shift mean: 0.000 shift max: 0.006 38 r_work: 0.12052 shift mean: 0.000 shift max: 0.007 39 r_work: 0.12052 shift mean: 0.000 shift max: 0.005 40 r_work: 0.12052 shift mean: 0.000 shift max: 0.005 41 r_work: 0.12053 shift mean: 0.000 shift max: 0.005 42 r_work: 0.12053 shift mean: 0.000 shift max: 0.004 43 r_work: 0.12054 shift mean: 0.000 shift max: 0.004 44 r_work: 0.12054 shift mean: 0.000 shift max: 0.004 45 r_work: 0.12054 shift mean: 0.000 shift max: 0.005 46 r_work: 0.12054 shift mean: 0.000 shift max: 0.006 47 r_work: 0.12055 shift mean: 0.001 shift max: 0.007 48 r_work: 0.12056 shift mean: 0.001 shift max: 0.008 49 r_work: 0.12057 shift mean: 0.001 shift max: 0.014 50 r_work: 0.12059 shift mean: 0.001 shift max: 0.016 51 r_work: 0.12060 shift mean: 0.001 shift max: 0.017 52 2: Rw: 0.1206 Rf: 0.1469 Rf-Rw: 0.0263 bond: 0.017 angle: 1.94 clash: 7.2 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.95 cb: 0.00 shift start/prev: 0.141 0.014 n_fev: 52 r_work: 0.12060 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12817 shift mean: 0.011 shift max: 0.200 2 r_work: 0.12741 shift mean: 0.001 shift max: 0.011 3 r_work: 0.12508 shift mean: 0.002 shift max: 0.037 4 r_work: 0.12337 shift mean: 0.002 shift max: 0.035 5 r_work: 0.12232 shift mean: 0.001 shift max: 0.026 6 r_work: 0.12169 shift mean: 0.001 shift max: 0.019 7 r_work: 0.12129 shift mean: 0.001 shift max: 0.016 8 r_work: 0.12102 shift mean: 0.001 shift max: 0.012 9 r_work: 0.12086 shift mean: 0.000 shift max: 0.009 10 r_work: 0.12075 shift mean: 0.000 shift max: 0.008 11 r_work: 0.12068 shift mean: 0.000 shift max: 0.006 12 r_work: 0.12065 shift mean: 0.000 shift max: 0.004 13 r_work: 0.12062 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12060 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12059 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12058 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12058 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12057 shift mean: 0.000 shift max: 0.001 19 r_work: 0.12057 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12057 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12057 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12057 shift mean: 0.000 shift max: 0.001 23 r_work: 0.12057 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12057 shift mean: 0.000 shift max: 0.001 25 r_work: 0.12057 shift mean: 0.000 shift max: 0.002 26 r_work: 0.12057 shift mean: 0.000 shift max: 0.003 27 r_work: 0.12057 shift mean: 0.000 shift max: 0.004 28 r_work: 0.12058 shift mean: 0.000 shift max: 0.005 29 r_work: 0.12058 shift mean: 0.000 shift max: 0.007 30 r_work: 0.12059 shift mean: 0.000 shift max: 0.008 31 r_work: 0.12059 shift mean: 0.000 shift max: 0.009 32 r_work: 0.12059 shift mean: 0.001 shift max: 0.011 33 r_work: 0.12059 shift mean: 0.001 shift max: 0.012 34 r_work: 0.12059 shift mean: 0.001 shift max: 0.013 35 r_work: 0.12060 shift mean: 0.001 shift max: 0.011 36 r_work: 0.12060 shift mean: 0.001 shift max: 0.010 37 r_work: 0.12061 shift mean: 0.001 shift max: 0.010 38 r_work: 0.12061 shift mean: 0.001 shift max: 0.009 39 r_work: 0.12062 shift mean: 0.000 shift max: 0.005 40 r_work: 0.12062 shift mean: 0.000 shift max: 0.005 41 r_work: 0.12062 shift mean: 0.000 shift max: 0.004 42 r_work: 0.12062 shift mean: 0.000 shift max: 0.005 43 r_work: 0.12063 shift mean: 0.000 shift max: 0.004 44 r_work: 0.12063 shift mean: 0.000 shift max: 0.006 45 r_work: 0.12063 shift mean: 0.000 shift max: 0.004 46 r_work: 0.12064 shift mean: 0.001 shift max: 0.008 47 r_work: 0.12064 shift mean: 0.001 shift max: 0.008 48 r_work: 0.12065 shift mean: 0.001 shift max: 0.009 49 r_work: 0.12066 shift mean: 0.001 shift max: 0.016 50 r_work: 0.12067 shift mean: 0.001 shift max: 0.014 51 r_work: 0.12068 shift mean: 0.001 shift max: 0.017 52 3: Rw: 0.1207 Rf: 0.1472 Rf-Rw: 0.0265 bond: 0.018 angle: 1.96 clash: 7.2 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.95 cb: 0.00 shift start/prev: 0.145 0.013 n_fev: 52 r_work: 0.12068 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12885 shift mean: 0.010 shift max: 0.200 2 r_work: 0.12630 shift mean: 0.002 shift max: 0.035 3 r_work: 0.12437 shift mean: 0.001 shift max: 0.032 4 r_work: 0.12291 shift mean: 0.001 shift max: 0.031 5 r_work: 0.12207 shift mean: 0.001 shift max: 0.022 6 r_work: 0.12154 shift mean: 0.001 shift max: 0.017 7 r_work: 0.12120 shift mean: 0.001 shift max: 0.013 8 r_work: 0.12100 shift mean: 0.000 shift max: 0.010 9 r_work: 0.12087 shift mean: 0.000 shift max: 0.008 10 r_work: 0.12078 shift mean: 0.000 shift max: 0.007 11 r_work: 0.12073 shift mean: 0.000 shift max: 0.005 12 r_work: 0.12069 shift mean: 0.000 shift max: 0.004 13 r_work: 0.12068 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12067 shift mean: 0.000 shift max: 0.002 15 r_work: 0.12066 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12066 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12065 shift mean: 0.000 shift max: 0.001 18 r_work: 0.12065 shift mean: 0.000 shift max: 0.001 19 r_work: 0.12065 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12065 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12065 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12065 shift mean: 0.000 shift max: 0.001 23 r_work: 0.12065 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12065 shift mean: 0.000 shift max: 0.002 25 r_work: 0.12065 shift mean: 0.000 shift max: 0.002 26 r_work: 0.12065 shift mean: 0.000 shift max: 0.003 27 r_work: 0.12065 shift mean: 0.000 shift max: 0.004 28 r_work: 0.12065 shift mean: 0.000 shift max: 0.004 29 r_work: 0.12065 shift mean: 0.000 shift max: 0.003 30 r_work: 0.12065 shift mean: 0.000 shift max: 0.006 31 r_work: 0.12065 shift mean: 0.000 shift max: 0.005 32 r_work: 0.12065 shift mean: 0.000 shift max: 0.008 33 r_work: 0.12064 shift mean: 0.000 shift max: 0.009 34 r_work: 0.12064 shift mean: 0.001 shift max: 0.011 35 r_work: 0.12063 shift mean: 0.001 shift max: 0.011 36 r_work: 0.12063 shift mean: 0.001 shift max: 0.011 37 r_work: 0.12062 shift mean: 0.000 shift max: 0.009 38 r_work: 0.12062 shift mean: 0.000 shift max: 0.009 39 r_work: 0.12061 shift mean: 0.000 shift max: 0.008 40 r_work: 0.12062 shift mean: 0.000 shift max: 0.005 41 r_work: 0.12062 shift mean: 0.000 shift max: 0.007 42 r_work: 0.12062 shift mean: 0.000 shift max: 0.003 43 r_work: 0.12062 shift mean: 0.000 shift max: 0.004 44 r_work: 0.12062 shift mean: 0.000 shift max: 0.003 45 r_work: 0.12062 shift mean: 0.000 shift max: 0.004 46 r_work: 0.12062 shift mean: 0.000 shift max: 0.004 47 r_work: 0.12062 shift mean: 0.000 shift max: 0.004 48 r_work: 0.12063 shift mean: 0.000 shift max: 0.005 49 r_work: 0.12063 shift mean: 0.000 shift max: 0.005 50 r_work: 0.12062 shift mean: 0.000 shift max: 0.007 51 r_work: 0.12063 shift mean: 0.000 shift max: 0.008 52 4: Rw: 0.1206 Rf: 0.1473 Rf-Rw: 0.0267 bond: 0.018 angle: 1.95 clash: 7.2 rota: 0.92 rama: f: 93.16 o: 0.00 Z: 0.96 cb: 0.00 shift start/prev: 0.148 0.009 n_fev: 52 At refinement end: Rw: 0.1206 Rf: 0.1473 Rf-Rw: 0.0267 bond: 0.018 angle: 1.95 clash: 7.2 rota: 0.92 rama: f: 93.16 o: 0.00 Z: 0.96 cb: 0.00 shift start/prev: 0.148 0.009 Best Rwork, Rfree (after refinement): 0.1206 0.1473 See 2PND_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 885.23 seconds wall clock time: 15 minutes 3.22 seconds (903.22 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)