Starting qr.refine on Fri Jun 21 15:43:58 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 { 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" 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" } 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: 0.41, per 1000 atoms: 0.15 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: 1.03 Adding C-beta torsion restraints... Number of C-beta restraints generated: 248 Time building geometry restraints manager: 1.10 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 Start: Rw: 0.1440 Rf: 0.1597 Rf-Rw: 0.0157 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: 0.003 0.003 Optimal weight search: Data weight (initial): 11034.265334401005 r_work: 0.14396 shift mean: 0.000 shift max: 0.000 1 r_work: 0.14928 shift mean: 0.016 shift max: 0.181 2 r_work: 0.15073 shift mean: 0.002 shift max: 0.019 3 r_work: 0.14831 shift mean: 0.002 shift max: 0.036 4 r_work: 0.14628 shift mean: 0.002 shift max: 0.041 5 r_work: 0.14506 shift mean: 0.001 shift max: 0.027 6 r_work: 0.14433 shift mean: 0.001 shift max: 0.020 7 r_work: 0.14385 shift mean: 0.000 shift max: 0.014 8 r_work: 0.14352 shift mean: 0.000 shift max: 0.012 9 r_work: 0.14332 shift mean: 0.000 shift max: 0.009 10 r_work: 0.14317 shift mean: 0.000 shift max: 0.008 11 r_work: 0.14307 shift mean: 0.000 shift max: 0.006 12 r_work: 0.14301 shift mean: 0.000 shift max: 0.005 13 r_work: 0.14295 shift mean: 0.000 shift max: 0.005 14 r_work: 0.14291 shift mean: 0.000 shift max: 0.003 15 r_work: 0.14289 shift mean: 0.000 shift max: 0.005 16 r_work: 0.14287 shift mean: 0.000 shift max: 0.004 17 r_work: 0.14284 shift mean: 0.000 shift max: 0.005 18 r_work: 0.14282 shift mean: 0.001 shift max: 0.006 19 r_work: 0.14279 shift mean: 0.001 shift max: 0.008 20 r_work: 0.14276 shift mean: 0.001 shift max: 0.009 21 r_work: 0.14273 shift mean: 0.001 shift max: 0.009 22 r_work: 0.14273 shift mean: 0.002 shift max: 0.011 23 r_work: 0.14271 shift mean: 0.002 shift max: 0.011 24 r_work: 0.14272 shift mean: 0.002 shift max: 0.014 25 r_work: 0.14272 shift mean: 0.003 shift max: 0.016 26 r_work: 0.14273 shift mean: 0.003 shift max: 0.018 27 r_work: 0.14276 shift mean: 0.003 shift max: 0.018 28 r_work: 0.14278 shift mean: 0.003 shift max: 0.018 29 r_work: 0.14279 shift mean: 0.003 shift max: 0.017 30 r_work: 0.14281 shift mean: 0.003 shift max: 0.014 31 r_work: 0.14283 shift mean: 0.003 shift max: 0.012 32 r_work: 0.14285 shift mean: 0.002 shift max: 0.010 33 r_work: 0.14286 shift mean: 0.002 shift max: 0.009 34 r_work: 0.14287 shift mean: 0.002 shift max: 0.009 35 r_work: 0.14289 shift mean: 0.002 shift max: 0.009 36 r_work: 0.14289 shift mean: 0.001 shift max: 0.008 37 r_work: 0.14289 shift mean: 0.001 shift max: 0.008 38 r_work: 0.14288 shift mean: 0.001 shift max: 0.008 39 r_work: 0.14288 shift mean: 0.001 shift max: 0.008 40 r_work: 0.14287 shift mean: 0.001 shift max: 0.006 41 r_work: 0.14286 shift mean: 0.001 shift max: 0.008 42 r_work: 0.14283 shift mean: 0.001 shift max: 0.006 43 r_work: 0.14282 shift mean: 0.002 shift max: 0.007 44 r_work: 0.14278 shift mean: 0.002 shift max: 0.009 45 r_work: 0.14275 shift mean: 0.002 shift max: 0.010 46 r_work: 0.14272 shift mean: 0.002 shift max: 0.010 47 r_work: 0.14270 shift mean: 0.002 shift max: 0.011 48 r_work: 0.14269 shift mean: 0.002 shift max: 0.011 49 r_work: 0.14267 shift mean: 0.001 shift max: 0.010 50 r_work: 0.14265 shift mean: 0.001 shift max: 0.009 51 r_work: 0.14264 shift mean: 0.001 shift max: 0.008 52 r_work: 0.14263 shift mean: 0.001 shift max: 0.008 53 r_work: 0.14262 shift mean: 0.001 shift max: 0.006 54 r_work: 0.14261 shift mean: 0.001 shift max: 0.006 55 r_work: 0.14260 shift mean: 0.001 shift max: 0.005 56 r_work: 0.14259 shift mean: 0.001 shift max: 0.004 57 r_work: 0.14259 shift mean: 0.001 shift max: 0.004 58 r_work: 0.14259 shift mean: 0.001 shift max: 0.004 59 r_work: 0.14258 shift mean: 0.001 shift max: 0.003 60 r_work: 0.14257 shift mean: 0.001 shift max: 0.003 61 r_work: 0.14256 shift mean: 0.001 shift max: 0.004 62 r_work: 0.14255 shift mean: 0.001 shift max: 0.004 63 r_work: 0.14253 shift mean: 0.001 shift max: 0.004 64 r_work: 0.14251 shift mean: 0.001 shift max: 0.005 65 r_work: 0.14250 shift mean: 0.001 shift max: 0.005 66 r_work: 0.14248 shift mean: 0.001 shift max: 0.005 67 r_work: 0.14246 shift mean: 0.001 shift max: 0.005 68 r_work: 0.14245 shift mean: 0.001 shift max: 0.006 69 r_work: 0.14243 shift mean: 0.001 shift max: 0.005 70 r_work: 0.14241 shift mean: 0.001 shift max: 0.005 71 r_work: 0.14239 shift mean: 0.001 shift max: 0.005 72 r_work: 0.14237 shift mean: 0.000 shift max: 0.004 73 r_work: 0.14235 shift mean: 0.000 shift max: 0.004 74 r_work: 0.14233 shift mean: 0.000 shift max: 0.003 75 r_work: 0.14231 shift mean: 0.000 shift max: 0.003 76 r_work: 0.14230 shift mean: 0.000 shift max: 0.002 77 r_work: 0.14229 shift mean: 0.000 shift max: 0.002 78 r_work: 0.14228 shift mean: 0.000 shift max: 0.002 79 r_work: 0.14227 shift mean: 0.000 shift max: 0.002 80 r_work: 0.14225 shift mean: 0.000 shift max: 0.002 81 r_work: 0.14225 shift mean: 0.000 shift max: 0.001 82 r_work: 0.14224 shift mean: 0.000 shift max: 0.001 83 r_work: 0.14223 shift mean: 0.000 shift max: 0.002 84 r_work: 0.14222 shift mean: 0.000 shift max: 0.001 85 r_work: 0.14221 shift mean: 0.000 shift max: 0.001 86 r_work: 0.14220 shift mean: 0.000 shift max: 0.001 87 r_work: 0.14219 shift mean: 0.000 shift max: 0.002 88 r_work: 0.14219 shift mean: 0.000 shift max: 0.001 89 r_work: 0.14218 shift mean: 0.000 shift max: 0.002 90 r_work: 0.14218 shift mean: 0.000 shift max: 0.002 91 r_work: 0.14218 shift mean: 0.000 shift max: 0.002 92 r_work: 0.14218 shift mean: 0.000 shift max: 0.002 93 r_work: 0.14218 shift mean: 0.000 shift max: 0.001 94 r_work: 0.14217 shift mean: 0.000 shift max: 0.002 95 r_work: 0.14217 shift mean: 0.000 shift max: 0.001 96 r_work: 0.14217 shift mean: 0.000 shift max: 0.001 97 r_work: 0.14217 shift mean: 0.000 shift max: 0.001 98 r_work: 0.14217 shift mean: 0.000 shift max: 0.001 99 r_work: 0.14217 shift mean: 0.000 shift max: 0.001 100 r_work: 0.14216 shift mean: 0.000 shift max: 0.001 101 r_work: 0.14216 shift mean: 0.000 shift max: 0.001 102 0: Rw: 0.1422 Rf: 0.1600 Rf-Rw: 0.0179 bond: 0.026 angle: 2.27 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.33 cb: 3.23 shift start/prev: 0.070 0.067 rws(prev): 1.000 rws: 1.000 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1422 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.1415 0.1596 At refinement start Rw: 0.1415 Rf: 0.1596 Rf-Rw: 0.0180 bond: 0.026 angle: 2.27 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.33 cb: 3.23 shift start/prev: 0.070 0.000 Refinement: r_work: 0.14155 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15462 shift mean: 0.009 shift max: 0.200 2 r_work: 0.15462 shift mean: 0.000 shift max: 0.000 3 r_work: 0.15038 shift mean: 0.002 shift max: 0.040 4 r_work: 0.14688 shift mean: 0.002 shift max: 0.045 5 r_work: 0.14484 shift mean: 0.001 shift max: 0.028 6 r_work: 0.14361 shift mean: 0.001 shift max: 0.018 7 r_work: 0.14285 shift mean: 0.001 shift max: 0.015 8 r_work: 0.14238 shift mean: 0.000 shift max: 0.011 9 r_work: 0.14208 shift mean: 0.000 shift max: 0.009 10 r_work: 0.14187 shift mean: 0.000 shift max: 0.008 11 r_work: 0.14175 shift mean: 0.000 shift max: 0.005 12 r_work: 0.14167 shift mean: 0.000 shift max: 0.004 13 r_work: 0.14161 shift mean: 0.000 shift max: 0.004 14 r_work: 0.14158 shift mean: 0.000 shift max: 0.003 15 r_work: 0.14155 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14154 shift mean: 0.000 shift max: 0.002 17 r_work: 0.14153 shift mean: 0.000 shift max: 0.002 18 r_work: 0.14153 shift mean: 0.000 shift max: 0.001 19 r_work: 0.14152 shift mean: 0.000 shift max: 0.001 20 r_work: 0.14152 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 22 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 23 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 24 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 25 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 26 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 27 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 28 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 29 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 30 r_work: 0.14152 shift mean: 0.000 shift max: 0.000 31 r_work: 0.14151 shift mean: 0.000 shift max: 0.000 32 r_work: 0.14151 shift mean: 0.000 shift max: 0.000 33 r_work: 0.14151 shift mean: 0.000 shift max: 0.000 34 r_work: 0.14151 shift mean: 0.000 shift max: 0.001 35 r_work: 0.14150 shift mean: 0.000 shift max: 0.000 36 r_work: 0.14150 shift mean: 0.000 shift max: 0.001 37 r_work: 0.14150 shift mean: 0.000 shift max: 0.001 38 r_work: 0.14150 shift mean: 0.000 shift max: 0.001 39 r_work: 0.14150 shift mean: 0.000 shift max: 0.001 40 r_work: 0.14150 shift mean: 0.000 shift max: 0.001 41 r_work: 0.14150 shift mean: 0.000 shift max: 0.001 42 r_work: 0.14150 shift mean: 0.000 shift max: 0.001 43 r_work: 0.14149 shift mean: 0.000 shift max: 0.001 44 r_work: 0.14149 shift mean: 0.000 shift max: 0.001 45 r_work: 0.14148 shift mean: 0.000 shift max: 0.001 46 r_work: 0.14148 shift mean: 0.000 shift max: 0.001 47 r_work: 0.14147 shift mean: 0.000 shift max: 0.002 48 r_work: 0.14147 shift mean: 0.000 shift max: 0.002 49 r_work: 0.14146 shift mean: 0.000 shift max: 0.002 50 r_work: 0.14145 shift mean: 0.001 shift max: 0.003 51 r_work: 0.14145 shift mean: 0.001 shift max: 0.003 52 0: Rw: 0.1414 Rf: 0.1597 Rf-Rw: 0.0183 bond: 0.026 angle: 2.26 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.33 cb: 3.23 shift start/prev: 0.071 0.005 n_fev: 52 r_work: 0.14145 shift mean: 0.000 shift max: 0.000 1 r_work: 0.14628 shift mean: 0.005 shift max: 0.200 2 r_work: 0.14628 shift mean: 0.000 shift max: 0.000 3 r_work: 0.14457 shift mean: 0.001 shift max: 0.038 4 r_work: 0.14333 shift mean: 0.001 shift max: 0.038 5 r_work: 0.14257 shift mean: 0.001 shift max: 0.028 6 r_work: 0.14212 shift mean: 0.000 shift max: 0.020 7 r_work: 0.14183 shift mean: 0.000 shift max: 0.016 8 r_work: 0.14167 shift mean: 0.000 shift max: 0.012 9 r_work: 0.14156 shift mean: 0.000 shift max: 0.010 10 r_work: 0.14150 shift mean: 0.000 shift max: 0.008 11 r_work: 0.14145 shift mean: 0.000 shift max: 0.006 12 r_work: 0.14143 shift mean: 0.000 shift max: 0.005 13 r_work: 0.14143 shift mean: 0.000 shift max: 0.004 14 r_work: 0.14142 shift mean: 0.000 shift max: 0.003 15 r_work: 0.14142 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14142 shift mean: 0.000 shift max: 0.003 17 r_work: 0.14142 shift mean: 0.000 shift max: 0.001 18 r_work: 0.14141 shift mean: 0.000 shift max: 0.002 19 r_work: 0.14141 shift mean: 0.000 shift max: 0.001 20 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 21 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 22 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 23 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 24 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 25 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 26 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 27 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 28 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 29 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 30 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 31 r_work: 0.14141 shift mean: 0.000 shift max: 0.000 32 r_work: 0.14140 shift mean: 0.000 shift max: 0.000 33 r_work: 0.14140 shift mean: 0.000 shift max: 0.000 34 r_work: 0.14140 shift mean: 0.000 shift max: 0.000 35 r_work: 0.14140 shift mean: 0.000 shift max: 0.000 36 r_work: 0.14140 shift mean: 0.000 shift max: 0.000 37 r_work: 0.14139 shift mean: 0.000 shift max: 0.001 38 r_work: 0.14140 shift mean: 0.000 shift max: 0.001 39 r_work: 0.14140 shift mean: 0.000 shift max: 0.001 40 r_work: 0.14140 shift mean: 0.000 shift max: 0.001 41 r_work: 0.14139 shift mean: 0.000 shift max: 0.001 42 r_work: 0.14139 shift mean: 0.000 shift max: 0.001 43 r_work: 0.14139 shift mean: 0.000 shift max: 0.001 44 r_work: 0.14139 shift mean: 0.000 shift max: 0.001 45 r_work: 0.14139 shift mean: 0.000 shift max: 0.001 46 r_work: 0.14139 shift mean: 0.000 shift max: 0.001 47 r_work: 0.14138 shift mean: 0.000 shift max: 0.001 48 r_work: 0.14138 shift mean: 0.000 shift max: 0.001 49 r_work: 0.14137 shift mean: 0.000 shift max: 0.001 50 r_work: 0.14138 shift mean: 0.000 shift max: 0.002 51 r_work: 0.14137 shift mean: 0.000 shift max: 0.002 52 1: Rw: 0.1414 Rf: 0.1598 Rf-Rw: 0.0185 bond: 0.026 angle: 2.26 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.36 cb: 3.23 shift start/prev: 0.073 0.004 n_fev: 52 r_work: 0.14137 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15368 shift mean: 0.006 shift max: 0.200 2 r_work: 0.15368 shift mean: 0.000 shift max: 0.000 3 r_work: 0.14974 shift mean: 0.001 shift max: 0.039 4 r_work: 0.14647 shift mean: 0.001 shift max: 0.043 5 r_work: 0.14456 shift mean: 0.001 shift max: 0.028 6 r_work: 0.14344 shift mean: 0.001 shift max: 0.019 7 r_work: 0.14269 shift mean: 0.000 shift max: 0.015 8 r_work: 0.14223 shift mean: 0.000 shift max: 0.011 9 r_work: 0.14193 shift mean: 0.000 shift max: 0.009 10 r_work: 0.14172 shift mean: 0.000 shift max: 0.007 11 r_work: 0.14160 shift mean: 0.000 shift max: 0.006 12 r_work: 0.14151 shift mean: 0.000 shift max: 0.005 13 r_work: 0.14146 shift mean: 0.000 shift max: 0.003 14 r_work: 0.14142 shift mean: 0.000 shift max: 0.003 15 r_work: 0.14140 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14139 shift mean: 0.000 shift max: 0.002 17 r_work: 0.14138 shift mean: 0.000 shift max: 0.001 18 r_work: 0.14137 shift mean: 0.000 shift max: 0.002 19 r_work: 0.14137 shift mean: 0.000 shift max: 0.001 20 r_work: 0.14136 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14136 shift mean: 0.000 shift max: 0.001 22 r_work: 0.14136 shift mean: 0.000 shift max: 0.001 23 r_work: 0.14136 shift mean: 0.000 shift max: 0.000 24 r_work: 0.14136 shift mean: 0.000 shift max: 0.000 25 r_work: 0.14136 shift mean: 0.000 shift max: 0.000 26 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 27 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 28 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 29 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 30 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 31 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 32 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 33 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 34 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 35 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 36 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 37 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 38 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 39 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 40 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 41 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 42 r_work: 0.14135 shift mean: 0.000 shift max: 0.000 43 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 44 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 45 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 46 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 47 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 48 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 49 r_work: 0.14134 shift mean: 0.000 shift max: 0.001 50 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 51 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 52 2: Rw: 0.1413 Rf: 0.1598 Rf-Rw: 0.0185 bond: 0.026 angle: 2.26 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.37 cb: 3.23 shift start/prev: 0.073 0.002 n_fev: 52 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15760 shift mean: 0.007 shift max: 0.200 2 r_work: 0.15760 shift mean: 0.000 shift max: 0.000 3 r_work: 0.15246 shift mean: 0.001 shift max: 0.040 4 r_work: 0.14797 shift mean: 0.001 shift max: 0.043 5 r_work: 0.14538 shift mean: 0.001 shift max: 0.030 6 r_work: 0.14388 shift mean: 0.001 shift max: 0.020 7 r_work: 0.14294 shift mean: 0.000 shift max: 0.015 8 r_work: 0.14235 shift mean: 0.000 shift max: 0.011 9 r_work: 0.14199 shift mean: 0.000 shift max: 0.010 10 r_work: 0.14174 shift mean: 0.000 shift max: 0.007 11 r_work: 0.14159 shift mean: 0.000 shift max: 0.006 12 r_work: 0.14149 shift mean: 0.000 shift max: 0.005 13 r_work: 0.14144 shift mean: 0.000 shift max: 0.004 14 r_work: 0.14140 shift mean: 0.000 shift max: 0.003 15 r_work: 0.14138 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14137 shift mean: 0.000 shift max: 0.002 17 r_work: 0.14136 shift mean: 0.000 shift max: 0.002 18 r_work: 0.14135 shift mean: 0.000 shift max: 0.001 19 r_work: 0.14134 shift mean: 0.000 shift max: 0.002 20 r_work: 0.14134 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14134 shift mean: 0.000 shift max: 0.001 22 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 23 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 24 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 25 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 26 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 27 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 28 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 29 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 30 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 31 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 32 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 33 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 34 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 35 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 36 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 37 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 38 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 39 r_work: 0.14134 shift mean: 0.000 shift max: 0.000 40 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 41 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 42 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 43 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 44 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 45 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 46 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 47 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 48 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 49 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 50 r_work: 0.14133 shift mean: 0.000 shift max: 0.001 51 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 52 3: Rw: 0.1413 Rf: 0.1599 Rf-Rw: 0.0185 bond: 0.026 angle: 2.26 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.37 cb: 3.23 shift start/prev: 0.074 0.001 n_fev: 52 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15200 shift mean: 0.005 shift max: 0.200 2 r_work: 0.15200 shift mean: 0.000 shift max: 0.000 3 r_work: 0.14853 shift mean: 0.001 shift max: 0.040 4 r_work: 0.14570 shift mean: 0.001 shift max: 0.044 5 r_work: 0.14405 shift mean: 0.001 shift max: 0.028 6 r_work: 0.14304 shift mean: 0.000 shift max: 0.020 7 r_work: 0.14241 shift mean: 0.000 shift max: 0.014 8 r_work: 0.14201 shift mean: 0.000 shift max: 0.012 9 r_work: 0.14176 shift mean: 0.000 shift max: 0.009 10 r_work: 0.14160 shift mean: 0.000 shift max: 0.007 11 r_work: 0.14150 shift mean: 0.000 shift max: 0.006 12 r_work: 0.14144 shift mean: 0.000 shift max: 0.004 13 r_work: 0.14139 shift mean: 0.000 shift max: 0.004 14 r_work: 0.14137 shift mean: 0.000 shift max: 0.003 15 r_work: 0.14135 shift mean: 0.000 shift max: 0.002 16 r_work: 0.14134 shift mean: 0.000 shift max: 0.002 17 r_work: 0.14134 shift mean: 0.000 shift max: 0.002 18 r_work: 0.14133 shift mean: 0.000 shift max: 0.001 19 r_work: 0.14133 shift mean: 0.000 shift max: 0.001 20 r_work: 0.14133 shift mean: 0.000 shift max: 0.001 21 r_work: 0.14133 shift mean: 0.000 shift max: 0.001 22 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 23 r_work: 0.14133 shift mean: 0.000 shift max: 0.001 24 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 25 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 26 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 27 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 28 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 29 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 30 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 31 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 32 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 33 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 34 r_work: 0.14133 shift mean: 0.000 shift max: 0.000 35 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 36 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 37 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 38 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 39 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 40 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 41 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 42 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 43 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 44 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 45 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 46 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 47 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 48 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 49 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 50 r_work: 0.14132 shift mean: 0.000 shift max: 0.000 51 r_work: 0.14131 shift mean: 0.000 shift max: 0.001 52 r_work: 0.14131 shift mean: 0.000 shift max: 0.001 53 r_work: 0.14131 shift mean: 0.000 shift max: 0.000 54 4: Rw: 0.1413 Rf: 0.1599 Rf-Rw: 0.0186 bond: 0.026 angle: 2.26 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.37 cb: 3.23 shift start/prev: 0.074 0.001 n_fev: 54 At refinement end: Rw: 0.1413 Rf: 0.1599 Rf-Rw: 0.0186 bond: 0.026 angle: 2.26 clash: 3.5 rota: 0.00 rama: f: 99.24 o: 0.00 Z: -0.37 cb: 3.23 shift start/prev: 0.074 0.001 Best Rwork, Rfree (after refinement): 0.1413 0.1599 See 4R5R_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 818.27 seconds wall clock time: 13 minutes 48.65 seconds (828.65 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)