Starting qr.refine on Fri Jun 21 15:21:49 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4JP6.mtz Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4JP6.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//4JP6.mtz" } default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//4JP6.mtz" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4JP6.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/4JP6.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)=0.2334 0.2350 0.2150 n_refl.: 61516 re-set all scales: r(all,work,free)=0.2334 0.2350 0.2150 n_refl.: 61516 remove outliers: r(all,work,free)=0.2334 0.2351 0.2151 n_refl.: 61506 bulk-solvent and scaling: r(all,work,free)=0.1571 0.1558 0.1825 n_refl.: 61506 remove outliers: r(all,work,free)=0.1571 0.1558 0.1825 n_refl.: 61505 Resolution Compl Nwork Nfree R_work kiso kani kmask 36.755-9.175 99.01 95 5 0.2967 236.113 216.544 0.785 1.009 0.400 9.162-7.294 100.00 96 5 0.2311 251.270 243.461 0.991 1.010 0.430 7.286-5.810 100.00 171 9 0.2409 218.869 211.543 0.940 1.010 0.430 5.802-4.623 100.00 314 17 0.1813 275.703 266.099 0.962 1.010 0.425 4.620-3.682 100.00 633 33 0.1541 325.229 313.708 0.992 1.007 0.420 3.680-2.930 100.00 1220 65 0.1830 263.204 253.695 1.035 1.005 0.082 2.930-2.333 99.96 2355 124 0.1803 181.754 174.074 0.984 1.000 0.000 2.333-1.857 99.98 4602 242 0.1660 139.625 132.461 1.063 0.992 0.000 1.857-1.478 99.98 9002 473 0.1465 78.879 75.202 1.071 0.979 0.000 1.478-1.177 99.97 17663 930 0.1379 49.725 47.565 1.117 0.958 0.000 1.177-1.000 99.95 22279 1172 0.1375 33.240 32.178 1.167 0.932 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0009 b_overall=-0.3839 ------------------------------------------------------------------------------- Starting r-factors: ******************* r_work=0.1558 r_free=0.1825 ------------------------------------------------------------------------------- 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 ASP 33": "OD1" <-> "OD2" Residue "A GLU 75": "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: 2330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1865 Classifications: {'peptide': 122} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PCA%NH3:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 465 Classifications: {'water': 155} Link IDs: {None: 154} Time building chain proxies: 0.38, per 1000 atoms: 0.16 Number of scatterers: 2330 At special positions: 0 Unit cell: (27.688, 54.971, 73.509, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 333 8.00 N 176 7.00 C 602 6.00 H 1213 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 61 " distance=2.06 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 84 " distance=2.08 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 120 " distance=2.06 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Adding C-beta torsion restraints... Number of C-beta restraints generated: 220 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 1213 1.03 - 1.23: 20 1.23 - 1.43: 432 1.43 - 1.62: 531 1.62 - 1.82: 6 Bond restraints: 2202 Sorted by residual: bond pdb=" NH1 ARG A 66 " pdb="HH11 ARG A 66 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" NH1 ARG A 73 " pdb="HH12 ARG A 73 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ARG A 7 " pdb=" H ARG A 7 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH2 ARG A 79 " pdb="HH21 ARG A 79 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N PHE A 49 " pdb=" H PHE A 49 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 ... (remaining 2197 not shown) Histogram of bond angle deviations from ideal: 101.78 - 108.42: 702 108.42 - 115.05: 1676 115.05 - 121.69: 724 121.69 - 128.33: 417 128.33 - 134.96: 13 Bond angle restraints: 3532 Sorted by residual: angle pdb=" C ASN A 114 " pdb=" CA ASN A 114 " pdb=" CB ASN A 114 " ideal model delta sigma weight residual 110.10 116.55 -6.45 1.90e+00 2.77e-01 1.15e+01 angle pdb=" C LEU A 91 " pdb=" CA LEU A 91 " pdb=" CB LEU A 91 " ideal model delta sigma weight residual 110.10 105.41 4.69 1.90e+00 2.77e-01 6.08e+00 angle pdb=" CA TRP A 40 " pdb=" CB TRP A 40 " pdb=" CG TRP A 40 " ideal model delta sigma weight residual 113.60 118.21 -4.61 1.90e+00 2.77e-01 5.88e+00 angle pdb=" CB ASN A 114 " pdb=" CA ASN A 114 " pdb=" HA ASN A 114 " ideal model delta sigma weight residual 109.00 101.78 7.22 3.00e+00 1.11e-01 5.79e+00 angle pdb=" N PCA A 1 " pdb=" CA PCA A 1 " pdb=" CB PCA A 1 " ideal model delta sigma weight residual 110.50 106.44 4.06 1.70e+00 3.46e-01 5.69e+00 ... (remaining 3527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.97: 790 11.97 - 23.93: 80 23.93 - 35.89: 13 35.89 - 47.85: 14 47.85 - 59.82: 10 Dihedral angle restraints: 907 sinusoidal: 472 harmonic: 435 Sorted by residual: dihedral pdb=" CA THR A 47 " pdb=" C THR A 47 " pdb=" N ALA A 48 " pdb=" CA ALA A 48 " ideal model delta harmonic sigma weight residual 180.00 156.03 23.97 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA VAL A 113 " pdb=" C VAL A 113 " pdb=" N ASN A 114 " pdb=" CA ASN A 114 " ideal model delta harmonic sigma weight residual 180.00 160.98 19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LEU A 65 " pdb=" C LEU A 65 " pdb=" N ARG A 66 " pdb=" CA ARG A 66 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 904 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 81 0.065 - 0.129: 37 0.129 - 0.193: 11 0.193 - 0.257: 7 0.257 - 0.321: 1 Chirality restraints: 137 Sorted by residual: chirality pdb=" CA ASP A 35 " pdb=" N ASP A 35 " pdb=" C ASP A 35 " pdb=" CB ASP A 35 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA GLN A 116 " pdb=" N GLN A 116 " pdb=" C GLN A 116 " pdb=" CB GLN A 116 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ASP A 102 " pdb=" N ASP A 102 " pdb=" C ASP A 102 " pdb=" CB ASP A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 134 not shown) Planarity restraints: 292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 12 " -0.025 2.00e-02 2.50e+03 2.80e-02 2.35e+01 pdb=" CG PHE A 12 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 PHE A 12 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 12 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 12 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 12 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 12 " -0.021 2.00e-02 2.50e+03 pdb=" HD1 PHE A 12 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 12 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 12 " 0.042 2.00e-02 2.50e+03 pdb=" HE2 PHE A 12 " 0.040 2.00e-02 2.50e+03 pdb=" HZ PHE A 12 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 49 " -0.023 2.00e-02 2.50e+03 2.74e-02 2.26e+01 pdb=" CG PHE A 49 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 49 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 49 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 49 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 49 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 49 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 49 " 0.065 2.00e-02 2.50e+03 pdb=" HD2 PHE A 49 " 0.008 2.00e-02 2.50e+03 pdb=" HE1 PHE A 49 " -0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE A 49 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 49 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 96 " 0.030 2.00e-02 2.50e+03 2.60e-02 2.02e+01 pdb=" CG PHE A 96 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE A 96 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 96 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE A 96 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 96 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 96 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE A 96 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE A 96 " -0.030 2.00e-02 2.50e+03 pdb=" HE1 PHE A 96 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 96 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 96 " -0.037 2.00e-02 2.50e+03 ... (remaining 289 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.83: 21 1.83 - 2.52: 2153 2.52 - 3.22: 8056 3.22 - 3.91: 12483 3.91 - 4.60: 18691 Nonbonded interactions: 41404 Sorted by model distance: nonbonded pdb="HH12 ARG A 73 " pdb=" O HOH A 250 " model vdw sym.op. 1.141 1.800 -x+3/2,-y,z+1/2 nonbonded pdb="HH21 ARG A 73 " pdb=" H2 HOH A 334 " model vdw 1.407 2.000 nonbonded pdb="HH22 ARG A 73 " pdb=" H1 HOH A 334 " model vdw 1.449 2.000 nonbonded pdb="HE21 GLN A 116 " pdb=" O HOH A 251 " model vdw 1.553 1.800 nonbonded pdb="HE22 GLN A 116 " pdb=" O HOH A 316 " model vdw 1.557 1.800 ... (remaining 41399 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 6 15.96 2 O 333 7.97 2 N 176 6.97 2 C 602 5.97 2 H 1213 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: 0.1558 Rf: 0.1825 Rf-Rw: 0.0267 bond: 0.009 angle: 1.35 clash: 3.8 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -1.03 cb: 0.00 shift start/prev: 0.004 0.004 Optimal weight search: Data weight (initial): 10877.054692456619 r_work: 0.15581 shift mean: 0.000 shift max: 0.000 1 r_work: 0.16008 shift mean: 0.018 shift max: 0.114 2 r_work: 0.17233 shift mean: 0.014 shift max: 0.086 3 r_work: 0.16730 shift mean: 0.003 shift max: 0.051 4 r_work: 0.16280 shift mean: 0.004 shift max: 0.043 5 r_work: 0.16006 shift mean: 0.002 shift max: 0.024 6 r_work: 0.15832 shift mean: 0.002 shift max: 0.021 7 r_work: 0.15719 shift mean: 0.001 shift max: 0.013 8 r_work: 0.15646 shift mean: 0.001 shift max: 0.011 9 r_work: 0.15593 shift mean: 0.001 shift max: 0.008 10 r_work: 0.15556 shift mean: 0.001 shift max: 0.008 11 r_work: 0.15527 shift mean: 0.001 shift max: 0.006 12 r_work: 0.15507 shift mean: 0.001 shift max: 0.006 13 r_work: 0.15492 shift mean: 0.001 shift max: 0.005 14 r_work: 0.15479 shift mean: 0.001 shift max: 0.004 15 r_work: 0.15469 shift mean: 0.001 shift max: 0.007 16 r_work: 0.15462 shift mean: 0.002 shift max: 0.007 17 r_work: 0.15458 shift mean: 0.002 shift max: 0.005 18 r_work: 0.15457 shift mean: 0.002 shift max: 0.007 19 r_work: 0.15457 shift mean: 0.003 shift max: 0.008 20 r_work: 0.15458 shift mean: 0.004 shift max: 0.012 21 r_work: 0.15460 shift mean: 0.003 shift max: 0.012 22 r_work: 0.15460 shift mean: 0.004 shift max: 0.015 23 r_work: 0.15458 shift mean: 0.004 shift max: 0.014 24 r_work: 0.15460 shift mean: 0.004 shift max: 0.015 25 r_work: 0.15456 shift mean: 0.003 shift max: 0.012 26 r_work: 0.15454 shift mean: 0.003 shift max: 0.011 27 r_work: 0.15452 shift mean: 0.003 shift max: 0.012 28 r_work: 0.15449 shift mean: 0.002 shift max: 0.009 29 r_work: 0.15449 shift mean: 0.002 shift max: 0.008 30 r_work: 0.15448 shift mean: 0.002 shift max: 0.009 31 r_work: 0.15447 shift mean: 0.002 shift max: 0.008 32 r_work: 0.15444 shift mean: 0.002 shift max: 0.010 33 r_work: 0.15442 shift mean: 0.002 shift max: 0.010 34 r_work: 0.15438 shift mean: 0.003 shift max: 0.012 35 r_work: 0.15433 shift mean: 0.002 shift max: 0.011 36 r_work: 0.15429 shift mean: 0.003 shift max: 0.014 37 r_work: 0.15426 shift mean: 0.002 shift max: 0.009 38 r_work: 0.15422 shift mean: 0.002 shift max: 0.011 39 r_work: 0.15416 shift mean: 0.002 shift max: 0.010 40 r_work: 0.15412 shift mean: 0.002 shift max: 0.009 41 r_work: 0.15408 shift mean: 0.002 shift max: 0.009 42 r_work: 0.15405 shift mean: 0.002 shift max: 0.008 43 r_work: 0.15403 shift mean: 0.001 shift max: 0.007 44 r_work: 0.15400 shift mean: 0.002 shift max: 0.009 45 r_work: 0.15397 shift mean: 0.001 shift max: 0.007 46 r_work: 0.15396 shift mean: 0.001 shift max: 0.006 47 r_work: 0.15394 shift mean: 0.001 shift max: 0.007 48 r_work: 0.15392 shift mean: 0.001 shift max: 0.005 49 r_work: 0.15390 shift mean: 0.001 shift max: 0.006 50 r_work: 0.15388 shift mean: 0.001 shift max: 0.005 51 r_work: 0.15387 shift mean: 0.001 shift max: 0.006 52 r_work: 0.15386 shift mean: 0.001 shift max: 0.005 53 r_work: 0.15383 shift mean: 0.001 shift max: 0.008 54 r_work: 0.15382 shift mean: 0.001 shift max: 0.004 55 r_work: 0.15379 shift mean: 0.001 shift max: 0.007 56 r_work: 0.15378 shift mean: 0.001 shift max: 0.005 57 r_work: 0.15376 shift mean: 0.001 shift max: 0.006 58 r_work: 0.15375 shift mean: 0.001 shift max: 0.004 59 r_work: 0.15373 shift mean: 0.001 shift max: 0.005 60 r_work: 0.15371 shift mean: 0.001 shift max: 0.005 61 r_work: 0.15369 shift mean: 0.001 shift max: 0.006 62 r_work: 0.15368 shift mean: 0.001 shift max: 0.004 63 r_work: 0.15365 shift mean: 0.001 shift max: 0.005 64 r_work: 0.15364 shift mean: 0.001 shift max: 0.004 65 r_work: 0.15362 shift mean: 0.001 shift max: 0.006 66 r_work: 0.15361 shift mean: 0.001 shift max: 0.004 67 r_work: 0.15358 shift mean: 0.001 shift max: 0.006 68 r_work: 0.15357 shift mean: 0.001 shift max: 0.005 69 r_work: 0.15354 shift mean: 0.001 shift max: 0.006 70 r_work: 0.15351 shift mean: 0.001 shift max: 0.006 71 r_work: 0.15350 shift mean: 0.001 shift max: 0.006 72 r_work: 0.15347 shift mean: 0.001 shift max: 0.007 73 r_work: 0.15345 shift mean: 0.001 shift max: 0.007 74 r_work: 0.15342 shift mean: 0.001 shift max: 0.006 75 r_work: 0.15339 shift mean: 0.001 shift max: 0.007 76 r_work: 0.15337 shift mean: 0.001 shift max: 0.006 77 r_work: 0.15334 shift mean: 0.001 shift max: 0.007 78 r_work: 0.15332 shift mean: 0.001 shift max: 0.005 79 r_work: 0.15329 shift mean: 0.001 shift max: 0.006 80 r_work: 0.15327 shift mean: 0.001 shift max: 0.005 81 r_work: 0.15325 shift mean: 0.001 shift max: 0.007 82 r_work: 0.15323 shift mean: 0.001 shift max: 0.006 83 r_work: 0.15321 shift mean: 0.001 shift max: 0.006 84 r_work: 0.15318 shift mean: 0.001 shift max: 0.007 85 r_work: 0.15317 shift mean: 0.001 shift max: 0.006 86 r_work: 0.15314 shift mean: 0.001 shift max: 0.007 87 r_work: 0.15313 shift mean: 0.001 shift max: 0.007 88 r_work: 0.15312 shift mean: 0.001 shift max: 0.005 89 r_work: 0.15310 shift mean: 0.001 shift max: 0.007 90 r_work: 0.15308 shift mean: 0.001 shift max: 0.005 91 r_work: 0.15308 shift mean: 0.001 shift max: 0.006 92 r_work: 0.15307 shift mean: 0.001 shift max: 0.005 93 r_work: 0.15306 shift mean: 0.001 shift max: 0.005 94 r_work: 0.15305 shift mean: 0.001 shift max: 0.006 95 r_work: 0.15304 shift mean: 0.001 shift max: 0.004 96 r_work: 0.15303 shift mean: 0.001 shift max: 0.005 97 r_work: 0.15303 shift mean: 0.001 shift max: 0.005 98 r_work: 0.15302 shift mean: 0.001 shift max: 0.004 99 r_work: 0.15300 shift mean: 0.001 shift max: 0.004 100 r_work: 0.15299 shift mean: 0.001 shift max: 0.004 101 r_work: 0.15298 shift mean: 0.001 shift max: 0.004 102 0: Rw: 0.1530 Rf: 0.1836 Rf-Rw: 0.0306 bond: 0.027 angle: 2.22 clash: 4.3 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.91 cb: 0.91 shift start/prev: 0.088 0.084 rws(prev): 1.000 rws: 1.000 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1530 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.1527 0.1831 At refinement start Rw: 0.1527 Rf: 0.1831 Rf-Rw: 0.0304 bond: 0.027 angle: 2.22 clash: 4.3 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.91 cb: 0.91 shift start/prev: 0.088 0.000 Refinement: r_work: 0.15270 shift mean: 0.000 shift max: 0.000 1 r_work: 0.15851 shift mean: 0.012 shift max: 0.200 2 r_work: 0.15851 shift mean: 0.000 shift max: 0.000 3 r_work: 0.15657 shift mean: 0.002 shift max: 0.038 4 r_work: 0.15511 shift mean: 0.002 shift max: 0.037 5 r_work: 0.15420 shift mean: 0.001 shift max: 0.027 6 r_work: 0.15365 shift mean: 0.001 shift max: 0.021 7 r_work: 0.15328 shift mean: 0.001 shift max: 0.017 8 r_work: 0.15305 shift mean: 0.001 shift max: 0.014 9 r_work: 0.15291 shift mean: 0.001 shift max: 0.009 10 r_work: 0.15282 shift mean: 0.000 shift max: 0.007 11 r_work: 0.15277 shift mean: 0.000 shift max: 0.006 12 r_work: 0.15273 shift mean: 0.000 shift max: 0.005 13 r_work: 0.15270 shift mean: 0.000 shift max: 0.004 14 r_work: 0.15269 shift mean: 0.000 shift max: 0.003 15 r_work: 0.15268 shift mean: 0.000 shift max: 0.002 16 r_work: 0.15267 shift mean: 0.000 shift max: 0.002 17 r_work: 0.15266 shift mean: 0.000 shift max: 0.002 18 r_work: 0.15266 shift mean: 0.000 shift max: 0.001 19 r_work: 0.15266 shift mean: 0.000 shift max: 0.001 20 r_work: 0.15265 shift mean: 0.000 shift max: 0.001 21 r_work: 0.15265 shift mean: 0.000 shift max: 0.001 22 r_work: 0.15265 shift mean: 0.000 shift max: 0.001 23 r_work: 0.15265 shift mean: 0.000 shift max: 0.001 24 r_work: 0.15265 shift mean: 0.000 shift max: 0.001 25 r_work: 0.15264 shift mean: 0.000 shift max: 0.000 26 r_work: 0.15264 shift mean: 0.000 shift max: 0.001 27 r_work: 0.15264 shift mean: 0.000 shift max: 0.001 28 r_work: 0.15264 shift mean: 0.000 shift max: 0.001 29 r_work: 0.15264 shift mean: 0.000 shift max: 0.001 30 r_work: 0.15264 shift mean: 0.000 shift max: 0.001 31 r_work: 0.15263 shift mean: 0.000 shift max: 0.002 32 r_work: 0.15263 shift mean: 0.000 shift max: 0.002 33 r_work: 0.15262 shift mean: 0.000 shift max: 0.002 34 r_work: 0.15262 shift mean: 0.000 shift max: 0.003 35 r_work: 0.15262 shift mean: 0.001 shift max: 0.004 36 r_work: 0.15262 shift mean: 0.000 shift max: 0.003 37 r_work: 0.15261 shift mean: 0.001 shift max: 0.005 38 r_work: 0.15260 shift mean: 0.001 shift max: 0.005 39 r_work: 0.15260 shift mean: 0.001 shift max: 0.005 40 r_work: 0.15259 shift mean: 0.001 shift max: 0.006 41 r_work: 0.15258 shift mean: 0.001 shift max: 0.005 42 r_work: 0.15257 shift mean: 0.001 shift max: 0.006 43 r_work: 0.15256 shift mean: 0.001 shift max: 0.006 44 r_work: 0.15256 shift mean: 0.000 shift max: 0.004 45 r_work: 0.15255 shift mean: 0.001 shift max: 0.005 46 r_work: 0.15254 shift mean: 0.000 shift max: 0.004 47 r_work: 0.15253 shift mean: 0.000 shift max: 0.004 48 r_work: 0.15252 shift mean: 0.001 shift max: 0.005 49 r_work: 0.15252 shift mean: 0.000 shift max: 0.004 50 r_work: 0.15250 shift mean: 0.001 shift max: 0.006 51 r_work: 0.15249 shift mean: 0.000 shift max: 0.005 52 0: Rw: 0.1525 Rf: 0.1832 Rf-Rw: 0.0307 bond: 0.027 angle: 2.20 clash: 4.3 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.90 cb: 0.91 shift start/prev: 0.093 0.012 n_fev: 52 r_work: 0.15249 shift mean: 0.000 shift max: 0.000 1 r_work: 0.16286 shift mean: 0.010 shift max: 0.200 2 r_work: 0.16286 shift mean: 0.000 shift max: 0.000 3 r_work: 0.15951 shift mean: 0.002 shift max: 0.039 4 r_work: 0.15654 shift mean: 0.002 shift max: 0.046 5 r_work: 0.15495 shift mean: 0.001 shift max: 0.028 6 r_work: 0.15403 shift mean: 0.001 shift max: 0.019 7 r_work: 0.15348 shift mean: 0.001 shift max: 0.014 8 r_work: 0.15313 shift mean: 0.001 shift max: 0.011 9 r_work: 0.15290 shift mean: 0.000 shift max: 0.008 10 r_work: 0.15276 shift mean: 0.000 shift max: 0.007 11 r_work: 0.15267 shift mean: 0.000 shift max: 0.006 12 r_work: 0.15261 shift mean: 0.000 shift max: 0.004 13 r_work: 0.15257 shift mean: 0.000 shift max: 0.004 14 r_work: 0.15255 shift mean: 0.000 shift max: 0.003 15 r_work: 0.15253 shift mean: 0.000 shift max: 0.002 16 r_work: 0.15251 shift mean: 0.000 shift max: 0.002 17 r_work: 0.15250 shift mean: 0.000 shift max: 0.002 18 r_work: 0.15250 shift mean: 0.000 shift max: 0.001 19 r_work: 0.15249 shift mean: 0.000 shift max: 0.001 20 r_work: 0.15249 shift mean: 0.000 shift max: 0.001 21 r_work: 0.15248 shift mean: 0.000 shift max: 0.001 22 r_work: 0.15249 shift mean: 0.000 shift max: 0.001 23 r_work: 0.15249 shift mean: 0.000 shift max: 0.000 24 r_work: 0.15249 shift mean: 0.000 shift max: 0.001 25 r_work: 0.15248 shift mean: 0.000 shift max: 0.001 26 r_work: 0.15248 shift mean: 0.000 shift max: 0.000 27 r_work: 0.15248 shift mean: 0.000 shift max: 0.000 28 r_work: 0.15248 shift mean: 0.000 shift max: 0.000 29 r_work: 0.15247 shift mean: 0.000 shift max: 0.001 30 r_work: 0.15247 shift mean: 0.000 shift max: 0.001 31 r_work: 0.15247 shift mean: 0.000 shift max: 0.001 32 r_work: 0.15247 shift mean: 0.000 shift max: 0.001 33 r_work: 0.15247 shift mean: 0.000 shift max: 0.002 34 r_work: 0.15247 shift mean: 0.000 shift max: 0.002 35 r_work: 0.15247 shift mean: 0.000 shift max: 0.003 36 r_work: 0.15247 shift mean: 0.000 shift max: 0.002 37 r_work: 0.15248 shift mean: 0.000 shift max: 0.003 38 r_work: 0.15247 shift mean: 0.000 shift max: 0.002 39 r_work: 0.15247 shift mean: 0.000 shift max: 0.004 40 r_work: 0.15246 shift mean: 0.000 shift max: 0.003 41 r_work: 0.15246 shift mean: 0.000 shift max: 0.003 42 r_work: 0.15245 shift mean: 0.000 shift max: 0.004 43 r_work: 0.15245 shift mean: 0.000 shift max: 0.003 44 r_work: 0.15245 shift mean: 0.000 shift max: 0.004 45 r_work: 0.15244 shift mean: 0.000 shift max: 0.003 46 r_work: 0.15244 shift mean: 0.000 shift max: 0.004 47 r_work: 0.15244 shift mean: 0.000 shift max: 0.002 48 r_work: 0.15243 shift mean: 0.000 shift max: 0.004 49 r_work: 0.15243 shift mean: 0.000 shift max: 0.003 50 r_work: 0.15243 shift mean: 0.000 shift max: 0.004 51 r_work: 0.15242 shift mean: 0.000 shift max: 0.003 52 1: Rw: 0.1524 Rf: 0.1832 Rf-Rw: 0.0308 bond: 0.027 angle: 2.21 clash: 4.3 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.91 cb: 0.91 shift start/prev: 0.095 0.006 n_fev: 52 r_work: 0.15242 shift mean: 0.000 shift max: 0.000 1 r_work: 0.16453 shift mean: 0.014 shift max: 0.200 2 r_work: 0.15576 shift mean: 0.007 shift max: 0.101 3 r_work: 0.15464 shift mean: 0.001 shift max: 0.019 4 r_work: 0.15382 shift mean: 0.001 shift max: 0.018 5 r_work: 0.15333 shift mean: 0.001 shift max: 0.013 6 r_work: 0.15302 shift mean: 0.001 shift max: 0.010 7 r_work: 0.15282 shift mean: 0.001 shift max: 0.008 8 r_work: 0.15269 shift mean: 0.000 shift max: 0.006 9 r_work: 0.15259 shift mean: 0.000 shift max: 0.005 10 r_work: 0.15254 shift mean: 0.000 shift max: 0.004 11 r_work: 0.15249 shift mean: 0.000 shift max: 0.003 12 r_work: 0.15247 shift mean: 0.000 shift max: 0.002 13 r_work: 0.15245 shift mean: 0.000 shift max: 0.002 14 r_work: 0.15244 shift mean: 0.000 shift max: 0.002 15 r_work: 0.15243 shift mean: 0.000 shift max: 0.002 16 r_work: 0.15242 shift mean: 0.000 shift max: 0.001 17 r_work: 0.15242 shift mean: 0.000 shift max: 0.001 18 r_work: 0.15242 shift mean: 0.000 shift max: 0.001 19 r_work: 0.15242 shift mean: 0.000 shift max: 0.001 20 r_work: 0.15241 shift mean: 0.000 shift max: 0.000 21 r_work: 0.15241 shift mean: 0.000 shift max: 0.001 22 r_work: 0.15241 shift mean: 0.000 shift max: 0.000 23 r_work: 0.15241 shift mean: 0.000 shift max: 0.000 24 r_work: 0.15241 shift mean: 0.000 shift max: 0.000 25 r_work: 0.15241 shift mean: 0.000 shift max: 0.000 26 r_work: 0.15241 shift mean: 0.000 shift max: 0.000 27 r_work: 0.15241 shift mean: 0.000 shift max: 0.000 28 r_work: 0.15241 shift mean: 0.000 shift max: 0.001 29 r_work: 0.15241 shift mean: 0.000 shift max: 0.001 30 r_work: 0.15240 shift mean: 0.000 shift max: 0.001 31 r_work: 0.15240 shift mean: 0.000 shift max: 0.001 32 r_work: 0.15240 shift mean: 0.000 shift max: 0.001 33 r_work: 0.15240 shift mean: 0.000 shift max: 0.002 34 r_work: 0.15239 shift mean: 0.000 shift max: 0.002 35 r_work: 0.15239 shift mean: 0.000 shift max: 0.003 36 r_work: 0.15239 shift mean: 0.000 shift max: 0.003 37 r_work: 0.15238 shift mean: 0.000 shift max: 0.004 38 r_work: 0.15238 shift mean: 0.000 shift max: 0.004 39 r_work: 0.15237 shift mean: 0.000 shift max: 0.006 40 r_work: 0.15237 shift mean: 0.000 shift max: 0.004 41 r_work: 0.15236 shift mean: 0.000 shift max: 0.005 42 r_work: 0.15236 shift mean: 0.000 shift max: 0.005 43 r_work: 0.15235 shift mean: 0.000 shift max: 0.006 44 r_work: 0.15235 shift mean: 0.000 shift max: 0.004 45 r_work: 0.15234 shift mean: 0.000 shift max: 0.006 46 r_work: 0.15233 shift mean: 0.000 shift max: 0.005 47 r_work: 0.15233 shift mean: 0.000 shift max: 0.004 48 r_work: 0.15232 shift mean: 0.000 shift max: 0.006 49 r_work: 0.15232 shift mean: 0.000 shift max: 0.005 50 r_work: 0.15231 shift mean: 0.000 shift max: 0.006 51 r_work: 0.15230 shift mean: 0.000 shift max: 0.007 52 2: Rw: 0.1523 Rf: 0.1832 Rf-Rw: 0.0309 bond: 0.027 angle: 2.22 clash: 4.3 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.91 cb: 0.91 shift start/prev: 0.097 0.007 n_fev: 52 r_work: 0.15230 shift mean: 0.000 shift max: 0.000 1 r_work: 0.16209 shift mean: 0.012 shift max: 0.200 2 r_work: 0.15863 shift mean: 0.003 shift max: 0.042 3 r_work: 0.15643 shift mean: 0.002 shift max: 0.031 4 r_work: 0.15480 shift mean: 0.002 shift max: 0.031 5 r_work: 0.15383 shift mean: 0.001 shift max: 0.022 6 r_work: 0.15324 shift mean: 0.001 shift max: 0.016 7 r_work: 0.15288 shift mean: 0.001 shift max: 0.013 8 r_work: 0.15266 shift mean: 0.001 shift max: 0.010 9 r_work: 0.15252 shift mean: 0.000 shift max: 0.007 10 r_work: 0.15243 shift mean: 0.000 shift max: 0.006 11 r_work: 0.15238 shift mean: 0.000 shift max: 0.004 12 r_work: 0.15235 shift mean: 0.000 shift max: 0.004 13 r_work: 0.15233 shift mean: 0.000 shift max: 0.003 14 r_work: 0.15231 shift mean: 0.000 shift max: 0.002 15 r_work: 0.15230 shift mean: 0.000 shift max: 0.002 16 r_work: 0.15229 shift mean: 0.000 shift max: 0.002 17 r_work: 0.15229 shift mean: 0.000 shift max: 0.001 18 r_work: 0.15228 shift mean: 0.000 shift max: 0.001 19 r_work: 0.15229 shift mean: 0.000 shift max: 0.001 20 r_work: 0.15229 shift mean: 0.000 shift max: 0.000 21 r_work: 0.15229 shift mean: 0.000 shift max: 0.001 22 r_work: 0.15229 shift mean: 0.000 shift max: 0.000 23 r_work: 0.15229 shift mean: 0.000 shift max: 0.000 24 r_work: 0.15229 shift mean: 0.000 shift max: 0.000 25 r_work: 0.15229 shift mean: 0.000 shift max: 0.000 26 r_work: 0.15228 shift mean: 0.000 shift max: 0.000 27 r_work: 0.15228 shift mean: 0.000 shift max: 0.000 28 r_work: 0.15228 shift mean: 0.000 shift max: 0.000 29 r_work: 0.15228 shift mean: 0.000 shift max: 0.000 30 r_work: 0.15228 shift mean: 0.000 shift max: 0.001 31 r_work: 0.15228 shift mean: 0.000 shift max: 0.001 32 r_work: 0.15228 shift mean: 0.000 shift max: 0.001 33 r_work: 0.15228 shift mean: 0.000 shift max: 0.001 34 r_work: 0.15228 shift mean: 0.000 shift max: 0.001 35 r_work: 0.15228 shift mean: 0.000 shift max: 0.001 36 r_work: 0.15228 shift mean: 0.000 shift max: 0.002 37 r_work: 0.15228 shift mean: 0.000 shift max: 0.002 38 r_work: 0.15228 shift mean: 0.000 shift max: 0.002 39 r_work: 0.15227 shift mean: 0.000 shift max: 0.003 40 r_work: 0.15228 shift mean: 0.000 shift max: 0.003 41 r_work: 0.15227 shift mean: 0.000 shift max: 0.004 42 r_work: 0.15226 shift mean: 0.000 shift max: 0.003 43 r_work: 0.15226 shift mean: 0.000 shift max: 0.003 44 r_work: 0.15226 shift mean: 0.000 shift max: 0.003 45 r_work: 0.15226 shift mean: 0.000 shift max: 0.003 46 r_work: 0.15226 shift mean: 0.000 shift max: 0.003 47 r_work: 0.15225 shift mean: 0.000 shift max: 0.003 48 r_work: 0.15224 shift mean: 0.000 shift max: 0.003 49 r_work: 0.15224 shift mean: 0.000 shift max: 0.002 50 r_work: 0.15224 shift mean: 0.000 shift max: 0.003 51 r_work: 0.15223 shift mean: 0.000 shift max: 0.002 52 3: Rw: 0.1522 Rf: 0.1832 Rf-Rw: 0.0310 bond: 0.027 angle: 2.22 clash: 4.3 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.90 cb: 0.91 shift start/prev: 0.099 0.004 n_fev: 52 r_work: 0.15223 shift mean: 0.000 shift max: 0.000 1 r_work: 0.16207 shift mean: 0.016 shift max: 0.164 2 r_work: 0.15399 shift mean: 0.010 shift max: 0.099 3 r_work: 0.15340 shift mean: 0.001 shift max: 0.013 4 r_work: 0.15299 shift mean: 0.001 shift max: 0.012 5 r_work: 0.15275 shift mean: 0.001 shift max: 0.007 6 r_work: 0.15257 shift mean: 0.001 shift max: 0.008 7 r_work: 0.15246 shift mean: 0.000 shift max: 0.005 8 r_work: 0.15239 shift mean: 0.000 shift max: 0.005 9 r_work: 0.15235 shift mean: 0.000 shift max: 0.003 10 r_work: 0.15232 shift mean: 0.000 shift max: 0.003 11 r_work: 0.15229 shift mean: 0.000 shift max: 0.002 12 r_work: 0.15228 shift mean: 0.000 shift max: 0.002 13 r_work: 0.15227 shift mean: 0.000 shift max: 0.001 14 r_work: 0.15226 shift mean: 0.000 shift max: 0.001 15 r_work: 0.15225 shift mean: 0.000 shift max: 0.001 16 r_work: 0.15225 shift mean: 0.000 shift max: 0.001 17 r_work: 0.15225 shift mean: 0.000 shift max: 0.001 18 r_work: 0.15224 shift mean: 0.000 shift max: 0.000 19 r_work: 0.15225 shift mean: 0.000 shift max: 0.001 20 r_work: 0.15224 shift mean: 0.000 shift max: 0.000 21 r_work: 0.15224 shift mean: 0.000 shift max: 0.000 22 r_work: 0.15224 shift mean: 0.000 shift max: 0.000 23 r_work: 0.15224 shift mean: 0.000 shift max: 0.000 24 r_work: 0.15224 shift mean: 0.000 shift max: 0.000 25 r_work: 0.15224 shift mean: 0.000 shift max: 0.000 26 r_work: 0.15224 shift mean: 0.000 shift max: 0.000 27 r_work: 0.15223 shift mean: 0.000 shift max: 0.000 28 r_work: 0.15223 shift mean: 0.000 shift max: 0.001 29 r_work: 0.15223 shift mean: 0.000 shift max: 0.001 30 r_work: 0.15222 shift mean: 0.000 shift max: 0.001 31 r_work: 0.15222 shift mean: 0.000 shift max: 0.001 32 r_work: 0.15222 shift mean: 0.000 shift max: 0.001 33 r_work: 0.15222 shift mean: 0.000 shift max: 0.002 34 r_work: 0.15221 shift mean: 0.000 shift max: 0.002 35 r_work: 0.15221 shift mean: 0.000 shift max: 0.003 36 r_work: 0.15221 shift mean: 0.000 shift max: 0.003 37 r_work: 0.15221 shift mean: 0.000 shift max: 0.004 38 r_work: 0.15220 shift mean: 0.000 shift max: 0.005 39 r_work: 0.15219 shift mean: 0.000 shift max: 0.006 40 r_work: 0.15219 shift mean: 0.000 shift max: 0.005 41 r_work: 0.15218 shift mean: 0.000 shift max: 0.007 42 r_work: 0.15217 shift mean: 0.000 shift max: 0.006 43 r_work: 0.15217 shift mean: 0.000 shift max: 0.007 44 r_work: 0.15216 shift mean: 0.000 shift max: 0.007 45 r_work: 0.15215 shift mean: 0.000 shift max: 0.006 46 r_work: 0.15215 shift mean: 0.000 shift max: 0.007 47 r_work: 0.15214 shift mean: 0.000 shift max: 0.006 48 r_work: 0.15214 shift mean: 0.000 shift max: 0.006 49 r_work: 0.15214 shift mean: 0.000 shift max: 0.008 50 r_work: 0.15213 shift mean: 0.000 shift max: 0.007 51 r_work: 0.15213 shift mean: 0.000 shift max: 0.007 52 4: Rw: 0.1521 Rf: 0.1832 Rf-Rw: 0.0311 bond: 0.027 angle: 2.23 clash: 4.3 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.91 cb: 0.91 shift start/prev: 0.102 0.007 n_fev: 52 At refinement end: Rw: 0.1521 Rf: 0.1832 Rf-Rw: 0.0311 bond: 0.027 angle: 2.23 clash: 4.3 rota: 0.00 rama: f: 98.32 o: 0.00 Z: -0.91 cb: 0.91 shift start/prev: 0.102 0.007 Best Rwork, Rfree (after refinement): 0.1521 0.1832 See 4JP6_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 489.17 seconds wall clock time: 8 minutes 19.72 seconds (499.72 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)