Starting qr.refine on Thu Jun 20 17:02:56 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4R5R.mtz Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4R5R.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/4R5R.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4R5R.pdb" miller_array { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4R5R.mtz" } default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4R5R.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)=0.2149 0.2148 0.2184 n_refl.: 67502 re-set all scales: r(all,work,free)=0.2149 0.2148 0.2184 n_refl.: 67502 remove outliers: r(all,work,free)=0.2097 0.2092 0.2184 n_refl.: 67499 bulk-solvent and scaling: r(all,work,free)=0.1449 0.1441 0.1597 n_refl.: 67499 remove outliers: r(all,work,free)=0.1448 0.1440 0.1597 n_refl.: 67498 Resolution Compl Nwork Nfree R_work kiso kani kmask 19.997-8.097 82.91 94 3 0.2338 150.709 142.601 1.001 1.000 0.370 8.032-6.584 99.01 94 6 0.1996 162.529 156.774 1.036 1.001 0.375 6.581-5.402 99.44 164 12 0.2114 163.038 157.989 1.027 1.001 0.376 5.392-4.419 97.13 292 13 0.1716 202.552 199.019 1.043 1.003 0.359 4.418-3.621 97.21 520 38 0.1546 216.961 212.996 1.097 1.005 0.300 3.620-2.967 99.34 1005 52 0.1514 172.121 170.486 1.086 1.006 0.130 2.967-2.431 100.00 1801 115 0.1671 106.603 104.730 1.058 1.010 0.000 2.430-1.992 100.00 3268 160 0.1439 73.449 72.056 1.087 1.018 0.000 1.992-1.632 100.00 5917 343 0.1346 35.505 35.169 1.083 1.028 0.000 1.632-1.337 99.89 10815 573 0.1092 15.354 15.276 1.071 1.047 0.000 1.337-1.096 99.72 19512 1023 0.1068 5.471 5.454 1.071 1.085 0.000 1.096-0.960 97.49 20601 1077 0.1191 1.572 1.574 1.017 1.139 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0916 b_overall=-0.0459 ------------------------------------------------------------------------------- Starting r-factors: ******************* r_work=0.1440 r_free=0.1597 ------------------------------------------------------------------------------- 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 10": "OE1" <-> "OE2" Residue "B GLU 34": "OE1" <-> "OE2" 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: 2768 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 988 Classifications: {'peptide': 68} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 61} Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 988 Classifications: {'peptide': 68} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 61} Chain: "A" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 417 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "B" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 375 Classifications: {'water': 125} Link IDs: {None: 124} Time building chain proxies: 0.43, per 1000 atoms: 0.16 Number of scatterers: 2768 At special positions: 0 Unit cell: (18.083, 79.986, 39.497, 90, 91.3, 90) Space group: P 1 21 1 (No. 4) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 26 16.00 O1- 14 9.00 O 450 8.00 N 196 7.00 C 598 6.00 H 1484 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 19 " distance=2.04 Simple disulfide: pdb=" SG CYS A 6 " - pdb=" SG CYS A 14 " distance=2.05 Simple disulfide: pdb=" SG CYS A 13 " - pdb=" SG CYS A 36 " distance=2.02 Simple disulfide: pdb=" SG CYS A 27 " - pdb=" SG CYS A 33 " distance=2.05 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 45 " - pdb=" SG CYS A 64 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 19 " distance=2.04 Simple disulfide: pdb=" SG CYS B 6 " - pdb=" SG CYS B 14 " distance=2.05 Simple disulfide: pdb=" SG CYS B 13 " - pdb=" SG CYS B 36 " distance=2.03 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 33 " distance=2.05 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 57 " distance=2.04 Simple disulfide: pdb=" SG CYS B 45 " - pdb=" SG CYS B 64 " distance=2.01 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: 1.14 Adding C-beta torsion restraints... Number of C-beta restraints generated: 248 Time building geometry restraints manager: 1.23 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: 1484 1.04 - 1.24: 122 1.24 - 1.44: 292 1.44 - 1.64: 594 1.64 - 1.84: 28 Bond restraints: 2520 Sorted by residual: bond pdb=" NH2 ARG A 49 " pdb="HH21 ARG A 49 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.48e+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 6.48e+01 bond pdb=" N GLU A 34 " pdb=" H GLU A 34 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N GLU A 3 " pdb=" H GLU A 3 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 bond pdb=" N GLU B 34 " pdb=" H GLU B 34 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.47e+01 ... (remaining 2515 not shown) Histogram of bond angle deviations from ideal: 98.28 - 104.89: 318 104.89 - 111.51: 2144 111.51 - 118.13: 555 118.13 - 124.75: 801 124.75 - 131.37: 58 Bond angle restraints: 3876 Sorted by residual: angle pdb=" CG GLU B 29 " pdb=" CD GLU B 29 " pdb=" OE2 GLU B 29 " ideal model delta sigma weight residual 118.40 108.23 10.17 2.30e+00 1.89e-01 1.95e+01 angle pdb=" CG GLU B 29 " pdb=" CD GLU B 29 " pdb=" OE1 GLU B 29 " ideal model delta sigma weight residual 118.40 126.25 -7.85 2.30e+00 1.89e-01 1.16e+01 angle pdb=" C GLU B 29 " pdb=" CA GLU B 29 " pdb=" CB GLU B 29 " ideal model delta sigma weight residual 110.10 103.80 6.30 1.90e+00 2.77e-01 1.10e+01 angle pdb=" C LYS B 41 " pdb=" N ARG B 42 " pdb=" CA ARG B 42 " ideal model delta sigma weight residual 121.70 127.54 -5.84 1.80e+00 3.09e-01 1.05e+01 angle pdb=" C LYS A 41 " pdb=" N ARG A 42 " pdb=" CA ARG A 42 " ideal model delta sigma weight residual 121.70 126.66 -4.96 1.80e+00 3.09e-01 7.59e+00 ... (remaining 3871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.40: 880 15.40 - 30.80: 68 30.80 - 46.20: 20 46.20 - 61.60: 9 61.60 - 77.00: 1 Dihedral angle restraints: 978 sinusoidal: 570 harmonic: 408 Sorted by residual: dihedral pdb=" C ARG A 42 " pdb=" N ARG A 42 " pdb=" CA ARG A 42 " pdb=" CB ARG A 42 " ideal model delta harmonic sigma weight residual -122.60 -132.96 10.36 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CA ARG A 42 " pdb=" CB ARG A 42 " ideal model delta harmonic sigma weight residual 122.80 132.97 -10.17 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" C ARG B 42 " pdb=" N ARG B 42 " pdb=" CA ARG B 42 " pdb=" CB ARG B 42 " ideal model delta harmonic sigma weight residual -122.60 -131.37 8.77 0 2.50e+00 1.60e-01 1.23e+01 ... (remaining 975 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.087: 96 0.087 - 0.174: 33 0.174 - 0.260: 5 0.260 - 0.347: 2 0.347 - 0.433: 2 Chirality restraints: 138 Sorted by residual: chirality pdb=" CA ARG A 42 " pdb=" N ARG A 42 " pdb=" C ARG A 42 " pdb=" CB ARG A 42 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ARG B 42 " pdb=" N ARG B 42 " pdb=" C ARG B 42 " pdb=" CB ARG B 42 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA CYS A 19 " pdb=" N CYS A 19 " pdb=" C CYS A 19 " pdb=" CB CYS A 19 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 135 not shown) Planarity restraints: 316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 29 " -0.032 2.00e-02 2.50e+03 6.37e-02 4.06e+01 pdb=" CD GLU B 29 " 0.110 2.00e-02 2.50e+03 pdb=" OE1 GLU B 29 " -0.042 2.00e-02 2.50e+03 pdb=" OE2 GLU B 29 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " 0.048 2.00e-02 2.50e+03 2.21e-02 1.47e+01 pdb=" CG TYR A 67 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 TYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR A 67 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR A 67 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 38 " 0.037 2.00e-02 2.50e+03 1.74e-02 9.08e+00 pdb=" CG PHE A 38 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE A 38 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 38 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 38 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 38 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 38 " 0.011 2.00e-02 2.50e+03 pdb=" HD1 PHE A 38 " -0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 38 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 38 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 38 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 38 " 0.033 2.00e-02 2.50e+03 ... (remaining 313 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 615 2.18 - 2.79: 5817 2.79 - 3.39: 9730 3.39 - 4.00: 14541 4.00 - 4.60: 21299 Nonbonded interactions: 52002 Sorted by model distance: nonbonded pdb=" O HOH B 156 " pdb=" H2 HOH B 218 " model vdw 1.581 1.800 nonbonded pdb=" H1 HOH A 151 " pdb=" O HOH B 118 " model vdw sym.op. 1.592 1.800 -x+1,y-1/2,-z+1 nonbonded pdb=" HZ3 LYS B 40 " pdb=" O HOH A 177 " model vdw 1.620 1.800 nonbonded pdb=" HB3 GLN B 35 " pdb="HE21 GLN B 35 " model vdw 1.626 2.170 nonbonded pdb=" OE1 GLN B 35 " pdb=" H2 HOH B 118 " model vdw 1.683 1.800 ... (remaining 51997 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: 6 Type Number sf(0) Gaussians S 26 15.96 2 O1- 14 8.97 3 O 450 7.97 2 N 196 6.97 2 C 598 5.97 2 H 1484 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=0.1440 r_free=0.1597 final: r_work=0.1476 r_free=0.1650 Start: Rw: 0.1476 Rf: 0.1650 Rf-Rw: 0.0174 bond: 0.009 angle: 1.51 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.21 cb: 0.81 shift start/prev: 0.083 0.087 Optimal weight search: Data weight (initial): 1533.3520072190026 r_work: 0.14756 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15256 shift mean: 0.013 shift max: 0.168 2 r_work: 0.15491 shift mean: 0.003 shift max: 0.032 3 r_work: 0.15234 shift mean: 0.002 shift max: 0.038 4 r_work: 0.15019 shift mean: 0.002 shift max: 0.044 5 r_work: 0.14894 shift mean: 0.001 shift max: 0.027 6 r_work: 0.14821 shift mean: 0.001 shift max: 0.018 7 r_work: 0.14774 shift mean: 0.001 shift max: 0.015 8 r_work: 0.14743 shift mean: 0.000 shift max: 0.012 9 r_work: 0.14724 shift mean: 0.000 shift max: 0.009 10 r_work: 0.14713 shift mean: 0.000 shift max: 0.007 11 r_work: 0.14706 shift mean: 0.000 shift max: 0.006 12 r_work: 0.14701 shift mean: 0.000 shift max: 0.005 13 r_work: 0.14698 shift mean: 0.000 shift max: 0.005 14 r_work: 0.14697 shift mean: 0.000 shift max: 0.005 15 r_work: 0.14696 shift mean: 0.000 shift max: 0.004 16 r_work: 0.14696 shift mean: 0.000 shift max: 0.005 17 r_work: 0.14696 shift mean: 0.000 shift max: 0.005 18 r_work: 0.14697 shift mean: 0.000 shift max: 0.008 19 r_work: 0.14698 shift mean: 0.000 shift max: 0.006 20 r_work: 0.14699 shift mean: 0.000 shift max: 0.008 21 r_work: 0.14700 shift mean: 0.001 shift max: 0.007 22 r_work: 0.14701 shift mean: 0.001 shift max: 0.011 23 r_work: 0.14702 shift mean: 0.001 shift max: 0.012 24 r_work: 0.14704 shift mean: 0.001 shift max: 0.011 25 r_work: 0.14705 shift mean: 0.001 shift max: 0.010 26 r_work: 0.14708 shift mean: 0.002 shift max: 0.016 27 r_work: 0.14716 shift mean: 0.003 shift max: 0.033 28 r_work: 0.14718 shift mean: 0.001 shift max: 0.016 29 r_work: 0.14719 shift mean: 0.001 shift max: 0.012 30 r_work: 0.14726 shift mean: 0.002 shift max: 0.025 31 r_work: 0.14727 shift mean: 0.001 shift max: 0.010 32 r_work: 0.14727 shift mean: 0.001 shift max: 0.008 33 r_work: 0.14727 shift mean: 0.001 shift max: 0.009 34 r_work: 0.14727 shift mean: 0.001 shift max: 0.007 35 r_work: 0.14727 shift mean: 0.001 shift max: 0.007 36 r_work: 0.14728 shift mean: 0.001 shift max: 0.006 37 r_work: 0.14730 shift mean: 0.001 shift max: 0.007 38 r_work: 0.14731 shift mean: 0.001 shift max: 0.005 39 r_work: 0.14732 shift mean: 0.001 shift max: 0.006 40 r_work: 0.14734 shift mean: 0.001 shift max: 0.007 41 r_work: 0.14736 shift mean: 0.001 shift max: 0.006 42 r_work: 0.14739 shift mean: 0.001 shift max: 0.008 43 r_work: 0.14740 shift mean: 0.001 shift max: 0.008 44 r_work: 0.14743 shift mean: 0.001 shift max: 0.010 45 r_work: 0.14745 shift mean: 0.001 shift max: 0.009 46 r_work: 0.14748 shift mean: 0.001 shift max: 0.009 47 r_work: 0.14749 shift mean: 0.001 shift max: 0.009 48 r_work: 0.14751 shift mean: 0.001 shift max: 0.009 49 r_work: 0.14754 shift mean: 0.001 shift max: 0.010 50 r_work: 0.14756 shift mean: 0.001 shift max: 0.007 51 r_work: 0.14758 shift mean: 0.001 shift max: 0.007 52 r_work: 0.14763 shift mean: 0.001 shift max: 0.009 53 r_work: 0.14766 shift mean: 0.001 shift max: 0.008 54 r_work: 0.14769 shift mean: 0.001 shift max: 0.008 55 r_work: 0.14771 shift mean: 0.001 shift max: 0.005 56 r_work: 0.14774 shift mean: 0.001 shift max: 0.007 57 r_work: 0.14777 shift mean: 0.001 shift max: 0.006 58 r_work: 0.14780 shift mean: 0.001 shift max: 0.007 59 r_work: 0.14782 shift mean: 0.001 shift max: 0.005 60 r_work: 0.14783 shift mean: 0.001 shift max: 0.005 61 r_work: 0.14785 shift mean: 0.001 shift max: 0.005 62 r_work: 0.14786 shift mean: 0.001 shift max: 0.006 63 r_work: 0.14788 shift mean: 0.001 shift max: 0.006 64 r_work: 0.14789 shift mean: 0.001 shift max: 0.006 65 r_work: 0.14790 shift mean: 0.001 shift max: 0.006 66 r_work: 0.14790 shift mean: 0.001 shift max: 0.006 67 r_work: 0.14791 shift mean: 0.001 shift max: 0.006 68 r_work: 0.14792 shift mean: 0.001 shift max: 0.005 69 r_work: 0.14793 shift mean: 0.001 shift max: 0.006 70 r_work: 0.14793 shift mean: 0.001 shift max: 0.004 71 r_work: 0.14794 shift mean: 0.001 shift max: 0.005 72 r_work: 0.14794 shift mean: 0.001 shift max: 0.005 73 r_work: 0.14794 shift mean: 0.001 shift max: 0.005 74 r_work: 0.14794 shift mean: 0.001 shift max: 0.005 75 r_work: 0.14794 shift mean: 0.001 shift max: 0.005 76 r_work: 0.14794 shift mean: 0.001 shift max: 0.005 77 r_work: 0.14793 shift mean: 0.001 shift max: 0.005 78 r_work: 0.14793 shift mean: 0.001 shift max: 0.005 79 r_work: 0.14793 shift mean: 0.001 shift max: 0.005 80 r_work: 0.14792 shift mean: 0.001 shift max: 0.005 81 r_work: 0.14792 shift mean: 0.001 shift max: 0.004 82 r_work: 0.14791 shift mean: 0.001 shift max: 0.004 83 r_work: 0.14792 shift mean: 0.001 shift max: 0.005 84 r_work: 0.14792 shift mean: 0.001 shift max: 0.004 85 r_work: 0.14792 shift mean: 0.001 shift max: 0.004 86 r_work: 0.14792 shift mean: 0.001 shift max: 0.004 87 r_work: 0.14793 shift mean: 0.001 shift max: 0.004 88 r_work: 0.14793 shift mean: 0.001 shift max: 0.005 89 r_work: 0.14793 shift mean: 0.001 shift max: 0.004 90 r_work: 0.14794 shift mean: 0.001 shift max: 0.005 91 r_work: 0.14794 shift mean: 0.000 shift max: 0.004 92 r_work: 0.14795 shift mean: 0.001 shift max: 0.005 93 r_work: 0.14796 shift mean: 0.000 shift max: 0.003 94 r_work: 0.14797 shift mean: 0.001 shift max: 0.005 95 r_work: 0.14797 shift mean: 0.000 shift max: 0.004 96 r_work: 0.14799 shift mean: 0.001 shift max: 0.005 97 r_work: 0.14799 shift mean: 0.000 shift max: 0.004 98 r_work: 0.14799 shift mean: 0.001 shift max: 0.005 99 r_work: 0.14800 shift mean: 0.000 shift max: 0.004 100 r_work: 0.14801 shift mean: 0.001 shift max: 0.005 101 r_work: 0.14801 shift mean: 0.000 shift max: 0.004 102 0: Rw: 0.1480 Rf: 0.1671 Rf-Rw: 0.0191 bond: 0.015 angle: 1.92 clash: 2.5 rota: 0.86 rama: f: 99.24 o: 0.00 Z: -0.28 cb: 2.42 shift start/prev: 0.103 0.055 rws(prev): 1.000 rws: 1.000 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1671 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.1480 0.1674 At refinement start Rw: 0.1480 Rf: 0.1674 Rf-Rw: 0.0194 bond: 0.015 angle: 1.92 clash: 2.5 rota: 0.86 rama: f: 99.24 o: 0.00 Z: -0.28 cb: 2.42 shift start/prev: 0.103 0.000 Refinement: r_work: 0.14798 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15816 shift mean: 0.011 shift max: 0.200 2 r_work: 0.15816 shift mean: 0.000 shift max: 0.000 3 r_work: 0.15492 shift mean: 0.002 shift max: 0.039 4 r_work: 0.15209 shift mean: 0.002 shift max: 0.048 5 r_work: 0.15051 shift mean: 0.001 shift max: 0.029 6 r_work: 0.14959 shift mean: 0.001 shift max: 0.019 7 r_work: 0.14905 shift mean: 0.001 shift max: 0.013 8 r_work: 0.14869 shift mean: 0.001 shift max: 0.012 9 r_work: 0.14847 shift mean: 0.000 shift max: 0.008 10 r_work: 0.14833 shift mean: 0.000 shift max: 0.007 11 r_work: 0.14823 shift mean: 0.000 shift max: 0.005 12 r_work: 0.14816 shift mean: 0.000 shift max: 0.004 13 r_work: 0.14812 shift mean: 0.000 shift max: 0.004 14 r_work: 0.14808 shift mean: 0.000 shift max: 0.004 15 r_work: 0.14806 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14805 shift mean: 0.000 shift max: 0.002 17 r_work: 0.14804 shift mean: 0.000 shift max: 0.001 18 r_work: 0.14803 shift mean: 0.000 shift max: 0.003 19 r_work: 0.14802 shift mean: 0.000 shift max: 0.001 20 r_work: 0.14802 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14802 shift mean: 0.000 shift max: 0.001 22 r_work: 0.14802 shift mean: 0.000 shift max: 0.000 23 r_work: 0.14801 shift mean: 0.000 shift max: 0.001 24 r_work: 0.14801 shift mean: 0.000 shift max: 0.000 25 r_work: 0.14801 shift mean: 0.000 shift max: 0.001 26 r_work: 0.14801 shift mean: 0.000 shift max: 0.000 27 r_work: 0.14801 shift mean: 0.000 shift max: 0.001 28 r_work: 0.14801 shift mean: 0.000 shift max: 0.001 29 r_work: 0.14801 shift mean: 0.000 shift max: 0.001 30 r_work: 0.14802 shift mean: 0.000 shift max: 0.001 31 r_work: 0.14802 shift mean: 0.000 shift max: 0.001 32 r_work: 0.14803 shift mean: 0.000 shift max: 0.001 33 r_work: 0.14803 shift mean: 0.000 shift max: 0.001 34 r_work: 0.14803 shift mean: 0.000 shift max: 0.001 35 r_work: 0.14804 shift mean: 0.000 shift max: 0.002 36 r_work: 0.14805 shift mean: 0.000 shift max: 0.003 37 r_work: 0.14805 shift mean: 0.000 shift max: 0.003 38 r_work: 0.14806 shift mean: 0.000 shift max: 0.004 39 r_work: 0.14808 shift mean: 0.001 shift max: 0.005 40 r_work: 0.14809 shift mean: 0.001 shift max: 0.006 41 r_work: 0.14811 shift mean: 0.001 shift max: 0.007 42 r_work: 0.14814 shift mean: 0.001 shift max: 0.009 43 r_work: 0.14817 shift mean: 0.001 shift max: 0.008 44 r_work: 0.14819 shift mean: 0.001 shift max: 0.009 45 r_work: 0.14822 shift mean: 0.001 shift max: 0.010 46 r_work: 0.14824 shift mean: 0.001 shift max: 0.010 47 r_work: 0.14826 shift mean: 0.001 shift max: 0.009 48 r_work: 0.14829 shift mean: 0.001 shift max: 0.009 49 r_work: 0.14833 shift mean: 0.001 shift max: 0.010 50 r_work: 0.14836 shift mean: 0.001 shift max: 0.008 51 r_work: 0.14840 shift mean: 0.001 shift max: 0.009 52 0: Rw: 0.1484 Rf: 0.1675 Rf-Rw: 0.0191 bond: 0.015 angle: 1.95 clash: 2.0 rota: 0.86 rama: f: 99.24 o: 0.00 Z: -0.30 cb: 2.42 shift start/prev: 0.108 0.016 n_fev: 52 r_work: 0.14840 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15865 shift mean: 0.011 shift max: 0.200 2 r_work: 0.15865 shift mean: 0.000 shift max: 0.000 3 r_work: 0.15527 shift mean: 0.002 shift max: 0.038 4 r_work: 0.15260 shift mean: 0.002 shift max: 0.043 5 r_work: 0.15096 shift mean: 0.001 shift max: 0.030 6 r_work: 0.15002 shift mean: 0.001 shift max: 0.020 7 r_work: 0.14941 shift mean: 0.001 shift max: 0.015 8 r_work: 0.14904 shift mean: 0.001 shift max: 0.011 9 r_work: 0.14882 shift mean: 0.000 shift max: 0.008 10 r_work: 0.14866 shift mean: 0.000 shift max: 0.007 11 r_work: 0.14856 shift mean: 0.000 shift max: 0.005 12 r_work: 0.14850 shift mean: 0.000 shift max: 0.005 13 r_work: 0.14847 shift mean: 0.000 shift max: 0.003 14 r_work: 0.14843 shift mean: 0.000 shift max: 0.003 15 r_work: 0.14842 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14841 shift mean: 0.000 shift max: 0.002 17 r_work: 0.14840 shift mean: 0.000 shift max: 0.002 18 r_work: 0.14840 shift mean: 0.000 shift max: 0.002 19 r_work: 0.14839 shift mean: 0.000 shift max: 0.002 20 r_work: 0.14839 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14839 shift mean: 0.000 shift max: 0.001 22 r_work: 0.14839 shift mean: 0.000 shift max: 0.001 23 r_work: 0.14838 shift mean: 0.000 shift max: 0.002 24 r_work: 0.14838 shift mean: 0.000 shift max: 0.002 25 r_work: 0.14838 shift mean: 0.000 shift max: 0.002 26 r_work: 0.14837 shift mean: 0.000 shift max: 0.002 27 r_work: 0.14837 shift mean: 0.000 shift max: 0.002 28 r_work: 0.14837 shift mean: 0.000 shift max: 0.003 29 r_work: 0.14836 shift mean: 0.000 shift max: 0.002 30 r_work: 0.14836 shift mean: 0.000 shift max: 0.003 31 r_work: 0.14836 shift mean: 0.000 shift max: 0.003 32 r_work: 0.14835 shift mean: 0.000 shift max: 0.003 33 r_work: 0.14835 shift mean: 0.000 shift max: 0.003 34 r_work: 0.14834 shift mean: 0.000 shift max: 0.003 35 r_work: 0.14834 shift mean: 0.000 shift max: 0.004 36 r_work: 0.14834 shift mean: 0.000 shift max: 0.004 37 r_work: 0.14833 shift mean: 0.000 shift max: 0.004 38 r_work: 0.14833 shift mean: 0.000 shift max: 0.004 39 r_work: 0.14833 shift mean: 0.000 shift max: 0.004 40 r_work: 0.14833 shift mean: 0.001 shift max: 0.004 41 r_work: 0.14834 shift mean: 0.001 shift max: 0.004 42 r_work: 0.14834 shift mean: 0.000 shift max: 0.003 43 r_work: 0.14834 shift mean: 0.001 shift max: 0.004 44 r_work: 0.14834 shift mean: 0.000 shift max: 0.003 45 r_work: 0.14834 shift mean: 0.000 shift max: 0.003 46 r_work: 0.14834 shift mean: 0.000 shift max: 0.003 47 r_work: 0.14834 shift mean: 0.000 shift max: 0.003 48 r_work: 0.14835 shift mean: 0.000 shift max: 0.003 49 r_work: 0.14834 shift mean: 0.000 shift max: 0.003 50 r_work: 0.14835 shift mean: 0.000 shift max: 0.004 51 r_work: 0.14836 shift mean: 0.000 shift max: 0.004 52 1: Rw: 0.1484 Rf: 0.1682 Rf-Rw: 0.0199 bond: 0.015 angle: 1.94 clash: 2.0 rota: 0.86 rama: f: 99.24 o: 0.00 Z: -0.27 cb: 2.42 shift start/prev: 0.112 0.009 n_fev: 52 r_work: 0.14836 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15833 shift mean: 0.007 shift max: 0.200 2 r_work: 0.15833 shift mean: 0.000 shift max: 0.000 3 r_work: 0.15501 shift mean: 0.001 shift max: 0.039 4 r_work: 0.15234 shift mean: 0.001 shift max: 0.044 5 r_work: 0.15073 shift mean: 0.001 shift max: 0.029 6 r_work: 0.14981 shift mean: 0.001 shift max: 0.019 7 r_work: 0.14927 shift mean: 0.000 shift max: 0.015 8 r_work: 0.14891 shift mean: 0.000 shift max: 0.011 9 r_work: 0.14871 shift mean: 0.000 shift max: 0.009 10 r_work: 0.14857 shift mean: 0.000 shift max: 0.008 11 r_work: 0.14848 shift mean: 0.000 shift max: 0.006 12 r_work: 0.14843 shift mean: 0.000 shift max: 0.005 13 r_work: 0.14840 shift mean: 0.000 shift max: 0.004 14 r_work: 0.14838 shift mean: 0.000 shift max: 0.003 15 r_work: 0.14837 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14836 shift mean: 0.000 shift max: 0.002 17 r_work: 0.14836 shift mean: 0.000 shift max: 0.002 18 r_work: 0.14836 shift mean: 0.000 shift max: 0.002 19 r_work: 0.14836 shift mean: 0.000 shift max: 0.001 20 r_work: 0.14836 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14836 shift mean: 0.000 shift max: 0.001 22 r_work: 0.14837 shift mean: 0.000 shift max: 0.001 23 r_work: 0.14837 shift mean: 0.000 shift max: 0.000 24 r_work: 0.14837 shift mean: 0.000 shift max: 0.001 25 r_work: 0.14837 shift mean: 0.000 shift max: 0.001 26 r_work: 0.14837 shift mean: 0.000 shift max: 0.002 27 r_work: 0.14837 shift mean: 0.000 shift max: 0.001 28 r_work: 0.14838 shift mean: 0.000 shift max: 0.001 29 r_work: 0.14838 shift mean: 0.000 shift max: 0.002 30 r_work: 0.14839 shift mean: 0.000 shift max: 0.003 31 r_work: 0.14839 shift mean: 0.000 shift max: 0.002 32 r_work: 0.14839 shift mean: 0.000 shift max: 0.003 33 r_work: 0.14840 shift mean: 0.000 shift max: 0.003 34 r_work: 0.14840 shift mean: 0.000 shift max: 0.003 35 r_work: 0.14841 shift mean: 0.000 shift max: 0.003 36 r_work: 0.14841 shift mean: 0.000 shift max: 0.004 37 r_work: 0.14842 shift mean: 0.000 shift max: 0.003 38 r_work: 0.14843 shift mean: 0.000 shift max: 0.003 39 r_work: 0.14844 shift mean: 0.000 shift max: 0.004 40 r_work: 0.14844 shift mean: 0.000 shift max: 0.003 41 r_work: 0.14845 shift mean: 0.000 shift max: 0.003 42 r_work: 0.14846 shift mean: 0.000 shift max: 0.004 43 r_work: 0.14847 shift mean: 0.000 shift max: 0.003 44 r_work: 0.14847 shift mean: 0.000 shift max: 0.003 45 r_work: 0.14848 shift mean: 0.000 shift max: 0.003 46 r_work: 0.14849 shift mean: 0.000 shift max: 0.003 47 r_work: 0.14850 shift mean: 0.000 shift max: 0.003 48 r_work: 0.14850 shift mean: 0.000 shift max: 0.003 49 r_work: 0.14851 shift mean: 0.000 shift max: 0.003 50 r_work: 0.14852 shift mean: 0.000 shift max: 0.004 51 r_work: 0.14853 shift mean: 0.000 shift max: 0.004 52 2: Rw: 0.1485 Rf: 0.1677 Rf-Rw: 0.0192 bond: 0.015 angle: 1.95 clash: 2.0 rota: 0.86 rama: f: 99.24 o: 0.00 Z: -0.29 cb: 2.42 shift start/prev: 0.114 0.007 n_fev: 52 r_work: 0.14853 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15779 shift mean: 0.009 shift max: 0.200 2 r_work: 0.15581 shift mean: 0.001 shift max: 0.025 3 r_work: 0.15344 shift mean: 0.001 shift max: 0.032 4 r_work: 0.15157 shift mean: 0.001 shift max: 0.031 5 r_work: 0.15044 shift mean: 0.001 shift max: 0.024 6 r_work: 0.14975 shift mean: 0.001 shift max: 0.020 7 r_work: 0.14930 shift mean: 0.001 shift max: 0.017 8 r_work: 0.14903 shift mean: 0.000 shift max: 0.013 9 r_work: 0.14888 shift mean: 0.000 shift max: 0.008 10 r_work: 0.14877 shift mean: 0.000 shift max: 0.006 11 r_work: 0.14870 shift mean: 0.000 shift max: 0.004 12 r_work: 0.14865 shift mean: 0.000 shift max: 0.003 13 r_work: 0.14861 shift mean: 0.000 shift max: 0.004 14 r_work: 0.14859 shift mean: 0.000 shift max: 0.002 15 r_work: 0.14857 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14855 shift mean: 0.000 shift max: 0.002 17 r_work: 0.14855 shift mean: 0.000 shift max: 0.001 18 r_work: 0.14854 shift mean: 0.000 shift max: 0.002 19 r_work: 0.14853 shift mean: 0.000 shift max: 0.001 20 r_work: 0.14852 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14852 shift mean: 0.000 shift max: 0.001 22 r_work: 0.14852 shift mean: 0.000 shift max: 0.001 23 r_work: 0.14852 shift mean: 0.000 shift max: 0.001 24 r_work: 0.14852 shift mean: 0.000 shift max: 0.001 25 r_work: 0.14852 shift mean: 0.000 shift max: 0.001 26 r_work: 0.14852 shift mean: 0.000 shift max: 0.001 27 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 28 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 29 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 30 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 31 r_work: 0.14851 shift mean: 0.000 shift max: 0.002 32 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 33 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 34 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 35 r_work: 0.14851 shift mean: 0.000 shift max: 0.002 36 r_work: 0.14850 shift mean: 0.000 shift max: 0.002 37 r_work: 0.14851 shift mean: 0.000 shift max: 0.002 38 r_work: 0.14850 shift mean: 0.000 shift max: 0.002 39 r_work: 0.14850 shift mean: 0.000 shift max: 0.002 40 r_work: 0.14850 shift mean: 0.000 shift max: 0.002 41 r_work: 0.14850 shift mean: 0.000 shift max: 0.002 42 r_work: 0.14850 shift mean: 0.000 shift max: 0.003 43 r_work: 0.14850 shift mean: 0.000 shift max: 0.003 44 r_work: 0.14850 shift mean: 0.000 shift max: 0.003 45 r_work: 0.14850 shift mean: 0.000 shift max: 0.003 46 r_work: 0.14851 shift mean: 0.000 shift max: 0.002 47 r_work: 0.14850 shift mean: 0.000 shift max: 0.003 48 r_work: 0.14851 shift mean: 0.000 shift max: 0.003 49 r_work: 0.14851 shift mean: 0.000 shift max: 0.003 50 r_work: 0.14851 shift mean: 0.000 shift max: 0.003 51 r_work: 0.14851 shift mean: 0.000 shift max: 0.003 52 3: Rw: 0.1485 Rf: 0.1683 Rf-Rw: 0.0198 bond: 0.015 angle: 1.95 clash: 2.0 rota: 0.86 rama: f: 99.24 o: 0.00 Z: -0.29 cb: 2.42 shift start/prev: 0.116 0.006 n_fev: 52 r_work: 0.14851 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15780 shift mean: 0.009 shift max: 0.200 2 r_work: 0.15330 shift mean: 0.003 shift max: 0.060 3 r_work: 0.15168 shift mean: 0.001 shift max: 0.026 4 r_work: 0.15055 shift mean: 0.001 shift max: 0.020 5 r_work: 0.14978 shift mean: 0.001 shift max: 0.018 6 r_work: 0.14932 shift mean: 0.001 shift max: 0.015 7 r_work: 0.14902 shift mean: 0.000 shift max: 0.012 8 r_work: 0.14883 shift mean: 0.000 shift max: 0.009 9 r_work: 0.14872 shift mean: 0.000 shift max: 0.006 10 r_work: 0.14864 shift mean: 0.000 shift max: 0.005 11 r_work: 0.14860 shift mean: 0.000 shift max: 0.004 12 r_work: 0.14855 shift mean: 0.000 shift max: 0.004 13 r_work: 0.14854 shift mean: 0.000 shift max: 0.002 14 r_work: 0.14853 shift mean: 0.000 shift max: 0.002 15 r_work: 0.14852 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 17 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 18 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 19 r_work: 0.14850 shift mean: 0.000 shift max: 0.001 20 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 22 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 23 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 24 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 25 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 26 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 27 r_work: 0.14851 shift mean: 0.000 shift max: 0.002 28 r_work: 0.14851 shift mean: 0.000 shift max: 0.001 29 r_work: 0.14852 shift mean: 0.000 shift max: 0.002 30 r_work: 0.14852 shift mean: 0.000 shift max: 0.002 31 r_work: 0.14852 shift mean: 0.000 shift max: 0.002 32 r_work: 0.14852 shift mean: 0.000 shift max: 0.002 33 r_work: 0.14853 shift mean: 0.000 shift max: 0.002 34 r_work: 0.14853 shift mean: 0.000 shift max: 0.002 35 r_work: 0.14853 shift mean: 0.000 shift max: 0.003 36 r_work: 0.14853 shift mean: 0.000 shift max: 0.004 37 r_work: 0.14854 shift mean: 0.000 shift max: 0.003 38 r_work: 0.14854 shift mean: 0.000 shift max: 0.004 39 r_work: 0.14855 shift mean: 0.000 shift max: 0.004 40 r_work: 0.14855 shift mean: 0.000 shift max: 0.003 41 r_work: 0.14855 shift mean: 0.000 shift max: 0.004 42 r_work: 0.14855 shift mean: 0.000 shift max: 0.005 43 r_work: 0.14855 shift mean: 0.000 shift max: 0.004 44 r_work: 0.14855 shift mean: 0.000 shift max: 0.004 45 r_work: 0.14856 shift mean: 0.000 shift max: 0.004 46 r_work: 0.14856 shift mean: 0.000 shift max: 0.003 47 r_work: 0.14857 shift mean: 0.000 shift max: 0.003 48 r_work: 0.14858 shift mean: 0.000 shift max: 0.003 49 r_work: 0.14859 shift mean: 0.000 shift max: 0.004 50 r_work: 0.14860 shift mean: 0.000 shift max: 0.004 51 r_work: 0.14861 shift mean: 0.001 shift max: 0.006 52 4: Rw: 0.1486 Rf: 0.1679 Rf-Rw: 0.0193 bond: 0.015 angle: 1.95 clash: 2.0 rota: 0.86 rama: f: 99.24 o: 0.00 Z: -0.30 cb: 2.42 shift start/prev: 0.119 0.007 n_fev: 52 At refinement end: Rw: 0.1486 Rf: 0.1679 Rf-Rw: 0.0193 bond: 0.015 angle: 1.95 clash: 2.0 rota: 0.86 rama: f: 99.24 o: 0.00 Z: -0.30 cb: 2.42 shift start/prev: 0.119 0.007 Best Rwork, Rfree (after refinement): 0.1486 0.1679 See 4R5R_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 929.70 seconds wall clock time: 15 minutes 42.59 seconds (942.59 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)