Starting qr.refine on Fri Jun 21 16:33:19 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//6ZM8.mtz Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/6ZM8.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/6ZM8.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/6ZM8.pdb" miller_array { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//6ZM8.mtz" } default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//6ZM8.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)=0.1780 0.1791 0.1632 n_refl.: 200663 re-set all scales: r(all,work,free)=0.1780 0.1791 0.1632 n_refl.: 200663 remove outliers: r(all,work,free)=0.1780 0.1791 0.1632 n_refl.: 200650 bulk-solvent and scaling: r(all,work,free)=0.1268 0.1263 0.1379 n_refl.: 200650 remove outliers: r(all,work,free)=0.1266 0.1260 0.1375 n_refl.: 200598 Resolution Compl Nwork Nfree R_work kiso kani kmask 38.636-10.170 99.01 94 6 0.1728 275.403 270.239 0.973 1.005 0.390 10.167-7.973 99.01 98 2 0.1765 239.764 228.353 1.013 1.006 0.407 7.970-6.248 99.54 206 11 0.1943 201.961 193.404 0.985 1.004 0.400 6.247-4.898 99.54 395 37 0.1727 241.690 235.254 1.001 1.005 0.381 4.897-3.840 99.66 838 50 0.1350 304.091 299.063 1.017 1.005 0.317 3.839-3.010 99.68 1748 112 0.1343 275.979 270.431 1.039 1.004 0.176 3.009-2.359 99.79 3642 184 0.1353 184.050 181.300 1.043 1.004 0.110 2.359-1.850 99.95 7566 372 0.1191 137.601 136.085 1.108 1.003 0.000 1.849-1.450 99.93 15594 806 0.1049 77.600 76.786 1.139 1.001 0.000 1.450-1.137 99.88 32223 1744 0.0905 48.633 48.287 1.177 0.998 0.000 1.136-0.891 99.91 66883 3493 0.1154 23.842 23.847 1.217 0.993 0.000 0.891-0.780 96.83 61314 3180 0.2740 9.141 8.271 1.020 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1994 b_overall=0.2942 ------------------------------------------------------------------------------- Starting r-factors: ******************* r_work=0.1260 r_free=0.1375 ------------------------------------------------------------------------------- Setting refinement target ************************* ml max_atoms = 50000 debug_rss = False debug = False scattering_table = wk1995 it1992 *n_gaussian electron neutron use_reduce = False cluster { charge_cutoff = 8 clustering = False charge_embedding = False two_buffers = False maxnum_residues_in_cluster = 15 bcc_threshold = 9 select_within_radius = 7 clustering_method = gnc *bcc altloc_method = average *subtract save_clusters = True bond_with_altloc = True re_calculate_rmsd_tolerance = 0.5 } restraints = cctbx *qm expansion = True quantum { engine_name = mopac *aimnet2 torchani terachem turbomole pyscf orca \ gaussian xtb server basis = Auto charge = None method = Auto memory = None nproc = 1 server_url = "http://127.0.0.1:8000" qm_addon = gcp dftd3 gcp-d3 qm_addon_method = None } refine { dry_run = False sf_algorithm = *direct fft refinement_target_name = *ml ls_wunit_k1 mode = opt *refine gtest number_of_macro_cycles = 1 number_of_weight_search_cycles = 10 number_of_refine_cycles = 5 number_of_micro_cycles = 50 data_weight = None skip_weight_search = False adjust_restraints_weight_scale_value = 2 max_iterations_weight = 100 max_iterations_refine = 50 use_ase_lbfgs = False line_search = True stpmax = 0.2 gradient_only = True refine_sites = True refine_adp = False restraints_weight_scale = 1 shake_sites = False use_convergence_test = True max_bond_rmsd = 0.03 max_angle_rmsd = 3 stop_one_found_first_good_weight = True max_r_work_r_free_gap = 5 r_tolerance = 0.001 rmsd_tolerance = 0.01 opt_log = False pre_opt = False pre_opt_stpmax = 0.1 pre_opt_iter = 10 pre_opt_switch = 2 pre_opt_gconv = 3000 minimizer = *lbfgs lbfgsb shift_evaluation = max *mean } parallel { method = *multiprocessing slurm pbs sge lsf threading nproc = 1 qsub_command = None } output_file_name_prefix = None output_folder_name = "pdb" rst_file = None dump_gradients = None output { filename = None file_name = None prefix = None suffix = None serial = 0 serial_format = "%03d" target_output_format = None *pdb mmcif overwrite = False } ------------------------------------------------------------------------------- Extracting model **************** Symmetric amino acids flipped Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 139": "OD1" <-> "OD2" 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: 4197 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 3129 Classifications: {'peptide': 208} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 198} Chain: "A" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 1068 Classifications: {'water': 356} Link IDs: {None: 355} Time building chain proxies: 0.57, per 1000 atoms: 0.14 Number of scatterers: 4197 At special positions: 0 Unit cell: (34.087, 77.272, 35.728, 90, 104.195, 90) Space group: P 1 21 1 (No. 4) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 664 8.00 N 285 7.00 C 1039 6.00 H 2205 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 144 " distance=2.02 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: 1.50 Adding C-beta torsion restraints... Number of C-beta restraints generated: 368 Time building geometry restraints manager: 1.61 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: 2204 1.04 - 1.23: 87 1.23 - 1.43: 737 1.43 - 1.63: 864 1.63 - 1.83: 5 Bond restraints: 3897 Sorted by residual: bond pdb=" N TRP A 131 " pdb=" H TRP A 131 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" NE2 GLN A 143 " pdb="HE22 GLN A 143 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N ARG A 56 " pdb=" H ARG A 56 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N ASN A 153 " pdb=" H ASN A 153 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N TYR A 106 " pdb=" H TYR A 106 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 ... (remaining 3892 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.68: 488 106.68 - 113.64: 3211 113.64 - 120.60: 1328 120.60 - 127.56: 948 127.56 - 134.51: 34 Bond angle restraints: 6009 Sorted by residual: angle pdb=" CA PHE A 5 " pdb=" CB PHE A 5 " pdb=" CG PHE A 5 " ideal model delta sigma weight residual 113.80 117.21 -3.41 1.00e+00 1.00e+00 1.16e+01 angle pdb=" C THR A 128 " pdb=" N SER A 129 " pdb=" CA SER A 129 " ideal model delta sigma weight residual 121.70 127.83 -6.13 1.80e+00 3.09e-01 1.16e+01 angle pdb=" CA PHE A 151 " pdb=" CB PHE A 151 " pdb=" CG PHE A 151 " ideal model delta sigma weight residual 113.80 110.54 3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" CA GLN A 72 " pdb=" CB GLN A 72 " pdb=" CG GLN A 72 " ideal model delta sigma weight residual 114.10 108.35 5.75 2.00e+00 2.50e-01 8.26e+00 angle pdb=" N SER A 84 " pdb=" CA SER A 84 " pdb=" CB SER A 84 " ideal model delta sigma weight residual 110.50 115.14 -4.64 1.70e+00 3.46e-01 7.44e+00 ... (remaining 6004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 1423 16.69 - 33.37: 82 33.37 - 50.05: 21 50.05 - 66.74: 17 66.74 - 83.42: 2 Dihedral angle restraints: 1545 sinusoidal: 774 harmonic: 771 Sorted by residual: dihedral pdb=" CA PHE A 54 " pdb=" C PHE A 54 " pdb=" N ILE A 55 " pdb=" CA ILE A 55 " ideal model delta harmonic sigma weight residual 180.00 155.37 24.63 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA ASN A 192 " pdb=" C ASN A 192 " pdb=" N TRP A 193 " pdb=" CA TRP A 193 " ideal model delta harmonic sigma weight residual 180.00 162.40 17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO A 12 " pdb=" C PRO A 12 " pdb=" N THR A 13 " pdb=" CA THR A 13 " ideal model delta harmonic sigma weight residual 180.00 -162.76 -17.24 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 1542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 146 0.072 - 0.144: 53 0.144 - 0.215: 20 0.215 - 0.287: 4 0.287 - 0.358: 2 Chirality restraints: 225 Sorted by residual: chirality pdb=" CB VAL A 121 " pdb=" CA VAL A 121 " pdb=" CG1 VAL A 121 " pdb=" CG2 VAL A 121 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA SER A 84 " pdb=" N SER A 84 " pdb=" C SER A 84 " pdb=" CB SER A 84 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA VAL A 133 " pdb=" N VAL A 133 " pdb=" C VAL A 133 " pdb=" CB VAL A 133 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 222 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 185 " -0.123 2.00e-02 2.50e+03 4.93e-02 7.29e+01 pdb=" CG TYR A 185 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR A 185 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 185 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR A 185 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR A 185 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 185 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR A 185 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TYR A 185 " 0.048 2.00e-02 2.50e+03 pdb=" HD2 TYR A 185 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 TYR A 185 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 TYR A 185 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 140 " 0.066 2.00e-02 2.50e+03 3.47e-02 4.82e+01 pdb=" CG TRP A 140 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 140 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 140 " -0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP A 140 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 140 " -0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP A 140 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 140 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 140 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 140 " 0.026 2.00e-02 2.50e+03 pdb=" HD1 TRP A 140 " 0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 140 " -0.017 2.00e-02 2.50e+03 pdb=" HE3 TRP A 140 " -0.069 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 140 " -0.025 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 140 " 0.026 2.00e-02 2.50e+03 pdb=" HH2 TRP A 140 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 158 " -0.040 2.00e-02 2.50e+03 3.45e-02 4.76e+01 pdb=" CG TRP A 158 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP A 158 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 158 " 0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP A 158 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP A 158 " 0.041 2.00e-02 2.50e+03 pdb=" CE3 TRP A 158 " 0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 158 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 158 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP A 158 " -0.020 2.00e-02 2.50e+03 pdb=" HD1 TRP A 158 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 TRP A 158 " 0.015 2.00e-02 2.50e+03 pdb=" HE3 TRP A 158 " 0.062 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 158 " 0.017 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 158 " -0.047 2.00e-02 2.50e+03 pdb=" HH2 TRP A 158 " -0.046 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 958 2.20 - 2.80: 8820 2.80 - 3.40: 14771 3.40 - 4.00: 21940 4.00 - 4.60: 31676 Nonbonded interactions: 78165 Sorted by model distance: nonbonded pdb=" O HOH A 394 " pdb=" O HOH A 409 " model vdw 1.599 2.200 nonbonded pdb=" H2 HOH A 569 " pdb=" O HOH A 603 " model vdw 1.607 1.800 nonbonded pdb=" H1 HOH A 415 " pdb=" O HOH A 447 " model vdw 1.621 1.800 nonbonded pdb=" H1 HOH A 569 " pdb=" O HOH A 589 " model vdw 1.642 1.800 nonbonded pdb=" H2 HOH A 415 " pdb=" O HOH A 447 " model vdw 1.643 1.800 ... (remaining 78160 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 4 15.96 2 O 664 7.97 2 N 285 6.97 2 C 1039 5.97 2 H 2205 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: 0.1260 Rf: 0.1375 Rf-Rw: 0.0115 bond: 0.008 angle: 1.35 clash: 1.9 rota: 0.00 rama: f: 99.03 o: 0.00 Z: -0.05 cb: 0.00 shift start/prev: 0.002 0.002 Optimal weight search: Data weight (initial): 19326.483486007968 r_work: 0.12599 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13181 shift mean: 0.012 shift max: 0.200 2 r_work: 0.13181 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12993 shift mean: 0.001 shift max: 0.037 4 r_work: 0.12824 shift mean: 0.001 shift max: 0.043 5 r_work: 0.12732 shift mean: 0.001 shift max: 0.029 6 r_work: 0.12675 shift mean: 0.000 shift max: 0.020 7 r_work: 0.12638 shift mean: 0.000 shift max: 0.015 8 r_work: 0.12612 shift mean: 0.000 shift max: 0.013 9 r_work: 0.12591 shift mean: 0.000 shift max: 0.010 10 r_work: 0.12577 shift mean: 0.000 shift max: 0.008 11 r_work: 0.12566 shift mean: 0.000 shift max: 0.007 12 r_work: 0.12556 shift mean: 0.000 shift max: 0.006 13 r_work: 0.12549 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12542 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12537 shift mean: 0.001 shift max: 0.004 16 r_work: 0.12532 shift mean: 0.001 shift max: 0.004 17 r_work: 0.12530 shift mean: 0.001 shift max: 0.005 18 r_work: 0.12529 shift mean: 0.001 shift max: 0.007 19 r_work: 0.12529 shift mean: 0.002 shift max: 0.008 20 r_work: 0.12532 shift mean: 0.002 shift max: 0.011 21 r_work: 0.12536 shift mean: 0.003 shift max: 0.017 22 r_work: 0.12541 shift mean: 0.003 shift max: 0.019 23 r_work: 0.12546 shift mean: 0.004 shift max: 0.022 24 r_work: 0.12550 shift mean: 0.004 shift max: 0.025 25 r_work: 0.12553 shift mean: 0.003 shift max: 0.019 26 r_work: 0.12557 shift mean: 0.004 shift max: 0.021 27 r_work: 0.12558 shift mean: 0.002 shift max: 0.014 28 r_work: 0.12558 shift mean: 0.002 shift max: 0.012 29 r_work: 0.12559 shift mean: 0.002 shift max: 0.012 30 r_work: 0.12560 shift mean: 0.002 shift max: 0.009 31 r_work: 0.12561 shift mean: 0.002 shift max: 0.008 32 r_work: 0.12561 shift mean: 0.001 shift max: 0.006 33 r_work: 0.12562 shift mean: 0.002 shift max: 0.006 34 r_work: 0.12562 shift mean: 0.002 shift max: 0.010 35 r_work: 0.12562 shift mean: 0.001 shift max: 0.004 36 r_work: 0.12561 shift mean: 0.002 shift max: 0.006 37 r_work: 0.12561 shift mean: 0.002 shift max: 0.005 38 r_work: 0.12558 shift mean: 0.002 shift max: 0.006 39 r_work: 0.12555 shift mean: 0.002 shift max: 0.009 40 r_work: 0.12551 shift mean: 0.002 shift max: 0.009 41 r_work: 0.12548 shift mean: 0.002 shift max: 0.010 42 r_work: 0.12544 shift mean: 0.002 shift max: 0.012 43 r_work: 0.12542 shift mean: 0.002 shift max: 0.009 44 r_work: 0.12539 shift mean: 0.002 shift max: 0.010 45 r_work: 0.12536 shift mean: 0.001 shift max: 0.010 46 r_work: 0.12535 shift mean: 0.001 shift max: 0.009 47 r_work: 0.12533 shift mean: 0.001 shift max: 0.009 48 r_work: 0.12531 shift mean: 0.001 shift max: 0.007 49 r_work: 0.12530 shift mean: 0.001 shift max: 0.009 50 r_work: 0.12528 shift mean: 0.001 shift max: 0.008 51 r_work: 0.12528 shift mean: 0.001 shift max: 0.006 52 r_work: 0.12527 shift mean: 0.001 shift max: 0.009 53 r_work: 0.12527 shift mean: 0.001 shift max: 0.006 54 r_work: 0.12527 shift mean: 0.001 shift max: 0.009 55 r_work: 0.12527 shift mean: 0.001 shift max: 0.006 56 r_work: 0.12526 shift mean: 0.001 shift max: 0.007 57 r_work: 0.12525 shift mean: 0.001 shift max: 0.008 58 r_work: 0.12525 shift mean: 0.001 shift max: 0.006 59 r_work: 0.12524 shift mean: 0.001 shift max: 0.006 60 r_work: 0.12524 shift mean: 0.001 shift max: 0.006 61 r_work: 0.12523 shift mean: 0.001 shift max: 0.005 62 r_work: 0.12522 shift mean: 0.001 shift max: 0.005 63 r_work: 0.12521 shift mean: 0.001 shift max: 0.005 64 r_work: 0.12519 shift mean: 0.001 shift max: 0.005 65 r_work: 0.12518 shift mean: 0.001 shift max: 0.004 66 r_work: 0.12516 shift mean: 0.001 shift max: 0.006 67 r_work: 0.12514 shift mean: 0.001 shift max: 0.006 68 r_work: 0.12512 shift mean: 0.001 shift max: 0.008 69 r_work: 0.12510 shift mean: 0.001 shift max: 0.006 70 r_work: 0.12507 shift mean: 0.001 shift max: 0.009 71 r_work: 0.12505 shift mean: 0.001 shift max: 0.006 72 r_work: 0.12503 shift mean: 0.001 shift max: 0.007 73 r_work: 0.12501 shift mean: 0.000 shift max: 0.005 74 r_work: 0.12500 shift mean: 0.001 shift max: 0.006 75 r_work: 0.12498 shift mean: 0.001 shift max: 0.005 76 r_work: 0.12497 shift mean: 0.000 shift max: 0.005 77 r_work: 0.12496 shift mean: 0.000 shift max: 0.005 78 r_work: 0.12494 shift mean: 0.001 shift max: 0.006 79 r_work: 0.12494 shift mean: 0.000 shift max: 0.003 80 r_work: 0.12493 shift mean: 0.000 shift max: 0.005 81 r_work: 0.12492 shift mean: 0.000 shift max: 0.004 82 r_work: 0.12491 shift mean: 0.000 shift max: 0.005 83 r_work: 0.12490 shift mean: 0.000 shift max: 0.005 84 r_work: 0.12489 shift mean: 0.000 shift max: 0.005 85 r_work: 0.12488 shift mean: 0.001 shift max: 0.005 86 r_work: 0.12487 shift mean: 0.000 shift max: 0.005 87 r_work: 0.12486 shift mean: 0.001 shift max: 0.006 88 r_work: 0.12486 shift mean: 0.000 shift max: 0.004 89 r_work: 0.12485 shift mean: 0.001 shift max: 0.005 90 r_work: 0.12484 shift mean: 0.000 shift max: 0.003 91 r_work: 0.12483 shift mean: 0.001 shift max: 0.004 92 r_work: 0.12483 shift mean: 0.001 shift max: 0.004 93 r_work: 0.12482 shift mean: 0.001 shift max: 0.004 94 r_work: 0.12481 shift mean: 0.001 shift max: 0.005 95 r_work: 0.12481 shift mean: 0.000 shift max: 0.004 96 r_work: 0.12480 shift mean: 0.001 shift max: 0.005 97 r_work: 0.12479 shift mean: 0.001 shift max: 0.005 98 r_work: 0.12478 shift mean: 0.000 shift max: 0.004 99 r_work: 0.12478 shift mean: 0.001 shift max: 0.006 100 r_work: 0.12477 shift mean: 0.001 shift max: 0.005 101 r_work: 0.12477 shift mean: 0.001 shift max: 0.005 102 0: Rw: 0.1248 Rf: 0.1392 Rf-Rw: 0.0145 bond: 0.019 angle: 1.87 clash: 1.6 rota: 0.00 rama: f: 98.54 o: 0.00 Z: -0.15 cb: 0.54 shift start/prev: 0.075 0.073 rws(prev): 1.000 rws: 1.000 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1248 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.1247 0.1387 At refinement start Rw: 0.1247 Rf: 0.1387 Rf-Rw: 0.0140 bond: 0.019 angle: 1.87 clash: 1.6 rota: 0.00 rama: f: 98.54 o: 0.00 Z: -0.15 cb: 0.54 shift start/prev: 0.075 0.000 Refinement: r_work: 0.12468 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13102 shift mean: 0.007 shift max: 0.200 2 r_work: 0.13102 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12889 shift mean: 0.001 shift max: 0.039 4 r_work: 0.12706 shift mean: 0.001 shift max: 0.044 5 r_work: 0.12610 shift mean: 0.001 shift max: 0.028 6 r_work: 0.12556 shift mean: 0.001 shift max: 0.019 7 r_work: 0.12522 shift mean: 0.000 shift max: 0.015 8 r_work: 0.12502 shift mean: 0.000 shift max: 0.011 9 r_work: 0.12489 shift mean: 0.000 shift max: 0.009 10 r_work: 0.12480 shift mean: 0.000 shift max: 0.007 11 r_work: 0.12474 shift mean: 0.000 shift max: 0.005 12 r_work: 0.12471 shift mean: 0.000 shift max: 0.005 13 r_work: 0.12468 shift mean: 0.000 shift max: 0.003 14 r_work: 0.12467 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12466 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12465 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12465 shift mean: 0.000 shift max: 0.001 18 r_work: 0.12464 shift mean: 0.000 shift max: 0.002 19 r_work: 0.12464 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12464 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12464 shift mean: 0.000 shift max: 0.000 22 r_work: 0.12464 shift mean: 0.000 shift max: 0.001 23 r_work: 0.12464 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12464 shift mean: 0.000 shift max: 0.000 25 r_work: 0.12464 shift mean: 0.000 shift max: 0.000 26 r_work: 0.12464 shift mean: 0.000 shift max: 0.000 27 r_work: 0.12464 shift mean: 0.000 shift max: 0.001 28 r_work: 0.12464 shift mean: 0.000 shift max: 0.001 29 r_work: 0.12463 shift mean: 0.000 shift max: 0.001 30 r_work: 0.12463 shift mean: 0.000 shift max: 0.001 31 r_work: 0.12463 shift mean: 0.000 shift max: 0.002 32 r_work: 0.12463 shift mean: 0.000 shift max: 0.001 33 r_work: 0.12462 shift mean: 0.000 shift max: 0.003 34 r_work: 0.12462 shift mean: 0.000 shift max: 0.003 35 r_work: 0.12461 shift mean: 0.000 shift max: 0.003 36 r_work: 0.12461 shift mean: 0.000 shift max: 0.004 37 r_work: 0.12460 shift mean: 0.000 shift max: 0.004 38 r_work: 0.12459 shift mean: 0.000 shift max: 0.003 39 r_work: 0.12459 shift mean: 0.000 shift max: 0.004 40 r_work: 0.12459 shift mean: 0.000 shift max: 0.003 41 r_work: 0.12459 shift mean: 0.000 shift max: 0.003 42 r_work: 0.12459 shift mean: 0.000 shift max: 0.003 43 r_work: 0.12459 shift mean: 0.000 shift max: 0.003 44 r_work: 0.12458 shift mean: 0.000 shift max: 0.004 45 r_work: 0.12458 shift mean: 0.000 shift max: 0.003 46 r_work: 0.12458 shift mean: 0.000 shift max: 0.004 47 r_work: 0.12458 shift mean: 0.000 shift max: 0.004 48 r_work: 0.12457 shift mean: 0.001 shift max: 0.005 49 r_work: 0.12457 shift mean: 0.000 shift max: 0.005 50 r_work: 0.12457 shift mean: 0.001 shift max: 0.007 51 r_work: 0.12456 shift mean: 0.001 shift max: 0.007 52 0: Rw: 0.1246 Rf: 0.1386 Rf-Rw: 0.0141 bond: 0.019 angle: 1.88 clash: 2.2 rota: 0.00 rama: f: 98.54 o: 0.00 Z: -0.13 cb: 0.54 shift start/prev: 0.078 0.009 n_fev: 52 r_work: 0.12456 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13384 shift mean: 0.011 shift max: 0.200 2 r_work: 0.13384 shift mean: 0.000 shift max: 0.000 3 r_work: 0.13072 shift mean: 0.002 shift max: 0.040 4 r_work: 0.12820 shift mean: 0.002 shift max: 0.048 5 r_work: 0.12681 shift mean: 0.001 shift max: 0.027 6 r_work: 0.12597 shift mean: 0.001 shift max: 0.020 7 r_work: 0.12545 shift mean: 0.001 shift max: 0.013 8 r_work: 0.12511 shift mean: 0.001 shift max: 0.012 9 r_work: 0.12490 shift mean: 0.001 shift max: 0.008 10 r_work: 0.12476 shift mean: 0.000 shift max: 0.008 11 r_work: 0.12468 shift mean: 0.000 shift max: 0.005 12 r_work: 0.12463 shift mean: 0.000 shift max: 0.005 13 r_work: 0.12460 shift mean: 0.000 shift max: 0.003 14 r_work: 0.12457 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12456 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12455 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12455 shift mean: 0.000 shift max: 0.001 18 r_work: 0.12455 shift mean: 0.000 shift max: 0.001 19 r_work: 0.12454 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12454 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12454 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12454 shift mean: 0.000 shift max: 0.000 23 r_work: 0.12454 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12454 shift mean: 0.000 shift max: 0.000 25 r_work: 0.12454 shift mean: 0.000 shift max: 0.000 26 r_work: 0.12454 shift mean: 0.000 shift max: 0.000 27 r_work: 0.12454 shift mean: 0.000 shift max: 0.000 28 r_work: 0.12454 shift mean: 0.000 shift max: 0.000 29 r_work: 0.12454 shift mean: 0.000 shift max: 0.000 30 r_work: 0.12454 shift mean: 0.000 shift max: 0.001 31 r_work: 0.12454 shift mean: 0.000 shift max: 0.001 32 r_work: 0.12454 shift mean: 0.000 shift max: 0.001 33 r_work: 0.12453 shift mean: 0.000 shift max: 0.002 34 r_work: 0.12453 shift mean: 0.000 shift max: 0.002 35 r_work: 0.12453 shift mean: 0.000 shift max: 0.002 36 r_work: 0.12453 shift mean: 0.000 shift max: 0.003 37 r_work: 0.12452 shift mean: 0.000 shift max: 0.003 38 r_work: 0.12452 shift mean: 0.000 shift max: 0.003 39 r_work: 0.12452 shift mean: 0.000 shift max: 0.003 40 r_work: 0.12452 shift mean: 0.000 shift max: 0.003 41 r_work: 0.12452 shift mean: 0.000 shift max: 0.003 42 r_work: 0.12452 shift mean: 0.000 shift max: 0.003 43 r_work: 0.12451 shift mean: 0.000 shift max: 0.002 44 r_work: 0.12451 shift mean: 0.000 shift max: 0.003 45 r_work: 0.12451 shift mean: 0.000 shift max: 0.002 46 r_work: 0.12451 shift mean: 0.000 shift max: 0.003 47 r_work: 0.12451 shift mean: 0.000 shift max: 0.003 48 r_work: 0.12451 shift mean: 0.000 shift max: 0.003 49 r_work: 0.12451 shift mean: 0.000 shift max: 0.003 50 r_work: 0.12451 shift mean: 0.000 shift max: 0.004 51 r_work: 0.12451 shift mean: 0.001 shift max: 0.006 52 1: Rw: 0.1245 Rf: 0.1388 Rf-Rw: 0.0143 bond: 0.019 angle: 1.90 clash: 1.9 rota: 0.00 rama: f: 98.54 o: 0.00 Z: -0.15 cb: 0.54 shift start/prev: 0.080 0.007 n_fev: 52 r_work: 0.12451 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13204 shift mean: 0.007 shift max: 0.200 2 r_work: 0.13204 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12951 shift mean: 0.001 shift max: 0.039 4 r_work: 0.12739 shift mean: 0.001 shift max: 0.044 5 r_work: 0.12624 shift mean: 0.001 shift max: 0.028 6 r_work: 0.12558 shift mean: 0.001 shift max: 0.020 7 r_work: 0.12518 shift mean: 0.000 shift max: 0.015 8 r_work: 0.12493 shift mean: 0.000 shift max: 0.011 9 r_work: 0.12477 shift mean: 0.000 shift max: 0.009 10 r_work: 0.12467 shift mean: 0.000 shift max: 0.007 11 r_work: 0.12460 shift mean: 0.000 shift max: 0.005 12 r_work: 0.12456 shift mean: 0.000 shift max: 0.004 13 r_work: 0.12454 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12452 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12451 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12450 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12450 shift mean: 0.000 shift max: 0.001 18 r_work: 0.12450 shift mean: 0.000 shift max: 0.002 19 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 23 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12449 shift mean: 0.000 shift max: 0.000 25 r_work: 0.12449 shift mean: 0.000 shift max: 0.000 26 r_work: 0.12449 shift mean: 0.000 shift max: 0.000 27 r_work: 0.12449 shift mean: 0.000 shift max: 0.000 28 r_work: 0.12449 shift mean: 0.000 shift max: 0.000 29 r_work: 0.12449 shift mean: 0.000 shift max: 0.000 30 r_work: 0.12449 shift mean: 0.000 shift max: 0.000 31 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 32 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 33 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 34 r_work: 0.12449 shift mean: 0.000 shift max: 0.001 35 r_work: 0.12448 shift mean: 0.000 shift max: 0.001 36 r_work: 0.12448 shift mean: 0.000 shift max: 0.003 37 r_work: 0.12448 shift mean: 0.000 shift max: 0.002 38 r_work: 0.12448 shift mean: 0.000 shift max: 0.003 39 r_work: 0.12448 shift mean: 0.000 shift max: 0.003 40 r_work: 0.12448 shift mean: 0.000 shift max: 0.002 41 r_work: 0.12447 shift mean: 0.000 shift max: 0.003 42 r_work: 0.12447 shift mean: 0.000 shift max: 0.002 43 r_work: 0.12447 shift mean: 0.000 shift max: 0.002 44 r_work: 0.12447 shift mean: 0.000 shift max: 0.002 45 r_work: 0.12447 shift mean: 0.000 shift max: 0.002 46 r_work: 0.12446 shift mean: 0.000 shift max: 0.002 47 r_work: 0.12446 shift mean: 0.000 shift max: 0.002 48 r_work: 0.12446 shift mean: 0.000 shift max: 0.002 49 r_work: 0.12446 shift mean: 0.000 shift max: 0.002 50 r_work: 0.12446 shift mean: 0.000 shift max: 0.003 51 r_work: 0.12446 shift mean: 0.000 shift max: 0.003 52 2: Rw: 0.1245 Rf: 0.1387 Rf-Rw: 0.0143 bond: 0.019 angle: 1.90 clash: 2.2 rota: 0.00 rama: f: 98.54 o: 0.00 Z: -0.13 cb: 0.54 shift start/prev: 0.082 0.005 n_fev: 52 r_work: 0.12446 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13287 shift mean: 0.011 shift max: 0.200 2 r_work: 0.13287 shift mean: 0.000 shift max: 0.000 3 r_work: 0.13005 shift mean: 0.002 shift max: 0.040 4 r_work: 0.12783 shift mean: 0.002 shift max: 0.047 5 r_work: 0.12654 shift mean: 0.001 shift max: 0.027 6 r_work: 0.12577 shift mean: 0.001 shift max: 0.021 7 r_work: 0.12530 shift mean: 0.001 shift max: 0.013 8 r_work: 0.12499 shift mean: 0.001 shift max: 0.012 9 r_work: 0.12480 shift mean: 0.001 shift max: 0.008 10 r_work: 0.12467 shift mean: 0.000 shift max: 0.008 11 r_work: 0.12459 shift mean: 0.000 shift max: 0.005 12 r_work: 0.12455 shift mean: 0.000 shift max: 0.004 13 r_work: 0.12452 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12449 shift mean: 0.000 shift max: 0.002 15 r_work: 0.12448 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12447 shift mean: 0.000 shift max: 0.001 17 r_work: 0.12447 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12446 shift mean: 0.000 shift max: 0.001 19 r_work: 0.12446 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12446 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12446 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 23 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 24 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 25 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 26 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 27 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 28 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 29 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 30 r_work: 0.12445 shift mean: 0.000 shift max: 0.000 31 r_work: 0.12445 shift mean: 0.000 shift max: 0.001 32 r_work: 0.12445 shift mean: 0.000 shift max: 0.001 33 r_work: 0.12445 shift mean: 0.000 shift max: 0.001 34 r_work: 0.12445 shift mean: 0.000 shift max: 0.001 35 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 36 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 37 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 38 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 39 r_work: 0.12444 shift mean: 0.000 shift max: 0.003 40 r_work: 0.12444 shift mean: 0.000 shift max: 0.003 41 r_work: 0.12444 shift mean: 0.000 shift max: 0.003 42 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 43 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 44 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 45 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 46 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 47 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 48 r_work: 0.12444 shift mean: 0.000 shift max: 0.003 49 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 50 r_work: 0.12444 shift mean: 0.000 shift max: 0.003 51 r_work: 0.12444 shift mean: 0.000 shift max: 0.004 52 3: Rw: 0.1244 Rf: 0.1388 Rf-Rw: 0.0144 bond: 0.019 angle: 1.92 clash: 2.2 rota: 0.00 rama: f: 98.54 o: 0.00 Z: -0.15 cb: 0.54 shift start/prev: 0.084 0.005 n_fev: 52 r_work: 0.12444 shift mean: 0.000 shift max: 0.000 1 r_work: 0.13321 shift mean: 0.010 shift max: 0.200 2 r_work: 0.13256 shift mean: 0.000 shift max: 0.008 3 r_work: 0.12983 shift mean: 0.002 shift max: 0.038 4 r_work: 0.12762 shift mean: 0.002 shift max: 0.044 5 r_work: 0.12637 shift mean: 0.001 shift max: 0.026 6 r_work: 0.12563 shift mean: 0.001 shift max: 0.019 7 r_work: 0.12518 shift mean: 0.001 shift max: 0.014 8 r_work: 0.12490 shift mean: 0.001 shift max: 0.011 9 r_work: 0.12472 shift mean: 0.000 shift max: 0.008 10 r_work: 0.12460 shift mean: 0.000 shift max: 0.007 11 r_work: 0.12454 shift mean: 0.000 shift max: 0.005 12 r_work: 0.12449 shift mean: 0.000 shift max: 0.004 13 r_work: 0.12446 shift mean: 0.000 shift max: 0.003 14 r_work: 0.12445 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12444 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12443 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12442 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 19 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12442 shift mean: 0.000 shift max: 0.000 23 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12442 shift mean: 0.000 shift max: 0.000 25 r_work: 0.12442 shift mean: 0.000 shift max: 0.000 26 r_work: 0.12442 shift mean: 0.000 shift max: 0.000 27 r_work: 0.12442 shift mean: 0.000 shift max: 0.000 28 r_work: 0.12442 shift mean: 0.000 shift max: 0.000 29 r_work: 0.12442 shift mean: 0.000 shift max: 0.000 30 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 31 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 32 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 33 r_work: 0.12442 shift mean: 0.000 shift max: 0.001 34 r_work: 0.12442 shift mean: 0.000 shift max: 0.002 35 r_work: 0.12442 shift mean: 0.000 shift max: 0.002 36 r_work: 0.12442 shift mean: 0.000 shift max: 0.002 37 r_work: 0.12442 shift mean: 0.000 shift max: 0.002 38 r_work: 0.12442 shift mean: 0.000 shift max: 0.003 39 r_work: 0.12442 shift mean: 0.000 shift max: 0.002 40 r_work: 0.12442 shift mean: 0.000 shift max: 0.002 41 r_work: 0.12442 shift mean: 0.000 shift max: 0.002 42 r_work: 0.12441 shift mean: 0.000 shift max: 0.002 43 r_work: 0.12441 shift mean: 0.000 shift max: 0.002 44 r_work: 0.12441 shift mean: 0.000 shift max: 0.001 45 r_work: 0.12441 shift mean: 0.000 shift max: 0.001 46 r_work: 0.12441 shift mean: 0.000 shift max: 0.001 47 r_work: 0.12441 shift mean: 0.000 shift max: 0.001 48 r_work: 0.12441 shift mean: 0.000 shift max: 0.001 49 r_work: 0.12441 shift mean: 0.000 shift max: 0.001 50 r_work: 0.12441 shift mean: 0.000 shift max: 0.001 51 r_work: 0.12440 shift mean: 0.000 shift max: 0.002 52 4: Rw: 0.1244 Rf: 0.1388 Rf-Rw: 0.0144 bond: 0.019 angle: 1.91 clash: 1.9 rota: 0.00 rama: f: 98.54 o: 0.00 Z: -0.13 cb: 0.54 shift start/prev: 0.085 0.004 n_fev: 52 At refinement end: Rw: 0.1244 Rf: 0.1388 Rf-Rw: 0.0144 bond: 0.019 angle: 1.91 clash: 1.9 rota: 0.00 rama: f: 98.54 o: 0.00 Z: -0.13 cb: 0.54 shift start/prev: 0.085 0.004 Best Rwork, Rfree (after refinement): 0.1244 0.1388 See 6ZM8_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 1052.13 seconds wall clock time: 17 minutes 45.50 seconds (1065.50 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)