Starting qr.refine on Thu Jun 20 17:37:43 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//1TT8.mtz Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/1TT8.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/1TT8.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/1TT8.pdb" miller_array { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//1TT8.mtz" } default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//1TT8.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)=0.1350 0.1344 0.1527 n_refl.: 63699 re-set all scales: r(all,work,free)=0.1350 0.1344 0.1527 n_refl.: 63699 remove outliers: r(all,work,free)=0.1343 0.1337 0.1527 n_refl.: 63691 bulk-solvent and scaling: r(all,work,free)=0.1254 0.1248 0.1414 n_refl.: 63691 remove outliers: r(all,work,free)=0.1251 0.1245 0.1412 n_refl.: 63671 Resolution Compl Nwork Nfree R_work kiso kani kmask 9.517-7.089 77.69 91 3 0.1875 145.137 142.186 1.049 0.950 0.288 7.071-6.186 97.09 94 6 0.1859 127.069 124.773 1.075 0.948 0.281 6.180-5.403 98.12 153 4 0.1805 126.335 123.906 1.069 0.949 0.260 5.400-4.722 98.70 220 8 0.1320 175.950 176.959 1.120 0.950 0.255 4.720-4.127 99.14 337 10 0.1123 206.529 206.026 1.074 0.950 0.252 4.123-3.607 98.83 491 15 0.1108 184.845 184.289 1.066 0.950 0.243 3.606-3.152 98.34 745 27 0.1288 157.496 155.984 1.045 0.949 0.190 3.152-2.756 98.30 1120 38 0.1328 114.013 112.386 1.005 0.950 0.024 2.755-2.408 98.05 1641 67 0.1384 89.993 88.837 0.998 0.949 0.000 2.408-2.105 97.52 2466 85 0.1202 82.174 80.850 1.047 0.949 0.000 2.105-1.840 96.44 3682 111 0.1099 66.052 65.269 1.098 0.949 0.000 1.840-1.608 95.64 5402 213 0.1086 42.846 42.378 1.103 0.949 0.000 1.608-1.405 93.98 8008 294 0.1061 30.595 30.291 1.119 0.949 0.000 1.405-1.228 91.46 11706 393 0.1192 23.010 22.622 1.134 0.949 0.000 1.228-1.074 87.95 16774 584 0.1324 17.372 16.999 1.117 0.949 0.000 1.074-0.997 60.43 8566 317 0.1991 11.207 10.747 1.019 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0366 b_overall=-0.0142 ------------------------------------------------------------------------------- Starting r-factors: ******************* r_work=0.1245 r_free=0.1412 ------------------------------------------------------------------------------- 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 52": "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: 3804 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 2676 Classifications: {'peptide': 164} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 13, 'TRANS': 150} Chain: "A" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 1128 Unusual residues: {'PHB': 1} Classifications: {'undetermined': 1, 'water': 371} Link IDs: {None: 371} Time building chain proxies: 0.51, per 1000 atoms: 0.13 Number of scatterers: 3804 At special positions: 0 Unit cell: (31.315, 33.849, 39.776, 67.57, 87.83, 65.66) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 O 614 8.00 N 226 7.00 C 854 6.00 H 2108 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Custom bonds: Warning: Ignoring bond with distance_ideal = None: atom_selection_1 = None atom_selection_2 = None Total number of added/changed bonds: 0 Custom angles: Warning: Ignoring angle with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None Total number of new custom angles: 0 Total number of changed angles: 0 Custom dihedrals: Warning: Ignoring dihedral with angle_ideal = None: atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None atom_selection_4 = None Total number of custom dihedrals: 0 Custom planarities: Warning: Ignoring planarity with with sigma <= 0: Total number of custom planarities: 0 Custom parallelities: Warning: Ignoring parallelity with empty atom selection. Total number of custom parallelities: 0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Adding C-beta torsion restraints... Number of C-beta restraints generated: 306 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.02: 2108 1.02 - 1.21: 1 1.21 - 1.39: 514 1.39 - 1.58: 836 1.58 - 1.76: 4 Bond restraints: 3463 Sorted by residual: bond pdb=" NE2 GLN A 57 " pdb="HE22 GLN A 57 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.49e+01 bond pdb=" NE ARG A 72 " pdb=" HE ARG A 72 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLY A 132 " pdb=" H GLY A 132 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH1 ARG A 37 " pdb="HH11 ARG A 37 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH1 ARG A 141 " pdb="HH12 ARG A 141 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 ... (remaining 3458 not shown) Histogram of bond angle deviations from ideal: 96.33 - 103.84: 131 103.84 - 111.35: 3290 111.35 - 118.85: 793 118.85 - 126.36: 1079 126.36 - 133.87: 30 Bond angle restraints: 5323 Sorted by residual: angle pdb=" C GLU A 52 " pdb=" CA GLU A 52 " pdb=" CB GLU A 52 " ideal model delta sigma weight residual 110.10 119.41 -9.31 1.90e+00 2.77e-01 2.40e+01 angle pdb=" CG GLU A 52 " pdb=" CD GLU A 52 " pdb=" OE1 GLU A 52 " ideal model delta sigma weight residual 118.40 128.97 -10.57 2.30e+00 1.89e-01 2.11e+01 angle pdb=" CG GLU A 52 " pdb=" CD GLU A 52 " pdb=" OE2 GLU A 52 " ideal model delta sigma weight residual 118.40 108.41 9.99 2.30e+00 1.89e-01 1.89e+01 angle pdb=" CB GLU A 52 " pdb=" CA GLU A 52 " pdb=" HA GLU A 52 " ideal model delta sigma weight residual 109.00 96.33 12.67 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CA GLU A 52 " pdb=" CB GLU A 52 " pdb=" CG GLU A 52 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 ... (remaining 5318 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 1163 17.46 - 34.93: 62 34.93 - 52.39: 24 52.39 - 69.85: 6 69.85 - 87.32: 5 Dihedral angle restraints: 1260 sinusoidal: 719 harmonic: 541 Sorted by residual: dihedral pdb=" C GLU A 52 " pdb=" N GLU A 52 " pdb=" CA GLU A 52 " pdb=" CB GLU A 52 " ideal model delta harmonic sigma weight residual -122.60 -138.49 15.89 0 2.50e+00 1.60e-01 4.04e+01 dihedral pdb=" N GLU A 52 " pdb=" C GLU A 52 " pdb=" CA GLU A 52 " pdb=" CB GLU A 52 " ideal model delta harmonic sigma weight residual 122.80 137.13 -14.33 0 2.50e+00 1.60e-01 3.28e+01 dihedral pdb=" CA ILE A 78 " pdb=" C ILE A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 156.11 23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 1257 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.117: 165 0.117 - 0.232: 40 0.232 - 0.348: 2 0.348 - 0.464: 0 0.464 - 0.579: 1 Chirality restraints: 208 Sorted by residual: chirality pdb=" CA GLU A 52 " pdb=" N GLU A 52 " pdb=" C GLU A 52 " pdb=" CB GLU A 52 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.39e+00 chirality pdb=" CA LYS A 15 " pdb=" N LYS A 15 " pdb=" C LYS A 15 " pdb=" CB LYS A 15 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA SER A 1 " pdb=" N SER A 1 " pdb=" C SER A 1 " pdb=" CB SER A 1 " both_signs ideal model delta sigma weight residual False 2.57 2.32 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 205 not shown) Planarity restraints: 384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 PHB A 400 " -0.006 2.00e-02 2.50e+03 3.61e-02 3.92e+01 pdb=" C1' PHB A 400 " -0.056 2.00e-02 2.50e+03 pdb=" C2 PHB A 400 " 0.015 2.00e-02 2.50e+03 pdb=" C3 PHB A 400 " -0.005 2.00e-02 2.50e+03 pdb=" C4 PHB A 400 " 0.040 2.00e-02 2.50e+03 pdb=" C5 PHB A 400 " -0.007 2.00e-02 2.50e+03 pdb=" C6 PHB A 400 " 0.018 2.00e-02 2.50e+03 pdb=" O4 PHB A 400 " 0.013 2.00e-02 2.50e+03 pdb=" H2 PHB A 400 " 0.043 2.00e-02 2.50e+03 pdb=" H3 PHB A 400 " -0.048 2.00e-02 2.50e+03 pdb=" H5 PHB A 400 " -0.057 2.00e-02 2.50e+03 pdb=" H6 PHB A 400 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 87 " 0.055 2.00e-02 2.50e+03 2.84e-02 3.23e+01 pdb=" CG TRP A 87 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 87 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP A 87 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 87 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 87 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 87 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 87 " 0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 87 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 87 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 TRP A 87 " -0.045 2.00e-02 2.50e+03 pdb=" HE1 TRP A 87 " -0.005 2.00e-02 2.50e+03 pdb=" HE3 TRP A 87 " -0.025 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 87 " 0.061 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 87 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP A 87 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 27 " 0.015 2.00e-02 2.50e+03 2.51e-02 2.52e+01 pdb=" CG TRP A 27 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP A 27 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 27 " -0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 27 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 27 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A 27 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 27 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 27 " -0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP A 27 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 TRP A 27 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP A 27 " 0.021 2.00e-02 2.50e+03 pdb=" HE3 TRP A 27 " 0.048 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 27 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 27 " -0.051 2.00e-02 2.50e+03 pdb=" HH2 TRP A 27 " 0.047 2.00e-02 2.50e+03 ... (remaining 381 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 425 2.06 - 2.70: 7175 2.70 - 3.33: 14557 3.33 - 3.97: 21977 3.97 - 4.60: 32501 Nonbonded interactions: 76635 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 108 " pdb=" O HOH A 704 " model vdw 1.428 1.800 nonbonded pdb=" H1 HOH A 527 " pdb=" O HOH A 674 " model vdw 1.577 1.800 nonbonded pdb=" HG SER A 147 " pdb=" O HOH A 480 " model vdw 1.618 1.800 nonbonded pdb="HH21 ARG A 133 " pdb=" O HOH A 763 " model vdw 1.621 1.800 nonbonded pdb=" O ARG A 9 " pdb=" H2 HOH A 569 " model vdw 1.622 1.800 ... (remaining 76630 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 2 15.96 2 O 614 7.97 2 N 226 6.97 2 C 854 5.97 2 H 2108 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=0.1245 r_free=0.1412 final: r_work=0.1264 r_free=0.1431 Start: Rw: 0.1264 Rf: 0.1431 Rf-Rw: 0.0167 bond: 0.015 angle: 1.73 clash: 5.2 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.89 cb: 0.65 shift start/prev: 0.081 0.082 Optimal weight search: Data weight (initial): 2614.9289547697913 r_work: 0.12638 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12732 shift mean: 0.012 shift max: 0.116 2 r_work: 0.12668 shift mean: 0.001 shift max: 0.027 3 r_work: 0.12624 shift mean: 0.001 shift max: 0.013 4 r_work: 0.12591 shift mean: 0.001 shift max: 0.013 5 r_work: 0.12571 shift mean: 0.001 shift max: 0.009 6 r_work: 0.12556 shift mean: 0.001 shift max: 0.009 7 r_work: 0.12546 shift mean: 0.001 shift max: 0.012 8 r_work: 0.12540 shift mean: 0.001 shift max: 0.009 9 r_work: 0.12537 shift mean: 0.001 shift max: 0.011 10 r_work: 0.12537 shift mean: 0.001 shift max: 0.013 11 r_work: 0.12538 shift mean: 0.002 shift max: 0.017 12 r_work: 0.12539 shift mean: 0.002 shift max: 0.018 13 r_work: 0.12541 shift mean: 0.002 shift max: 0.021 14 r_work: 0.12544 shift mean: 0.003 shift max: 0.029 15 r_work: 0.12542 shift mean: 0.003 shift max: 0.028 16 r_work: 0.12542 shift mean: 0.003 shift max: 0.032 17 r_work: 0.12542 shift mean: 0.003 shift max: 0.030 18 r_work: 0.12542 shift mean: 0.002 shift max: 0.026 19 r_work: 0.12544 shift mean: 0.003 shift max: 0.030 20 r_work: 0.12545 shift mean: 0.002 shift max: 0.021 21 r_work: 0.12548 shift mean: 0.002 shift max: 0.021 22 r_work: 0.12551 shift mean: 0.003 shift max: 0.024 23 r_work: 0.12554 shift mean: 0.002 shift max: 0.017 24 r_work: 0.12558 shift mean: 0.003 shift max: 0.017 25 r_work: 0.12560 shift mean: 0.002 shift max: 0.013 26 r_work: 0.12564 shift mean: 0.002 shift max: 0.014 27 r_work: 0.12566 shift mean: 0.002 shift max: 0.014 28 r_work: 0.12568 shift mean: 0.002 shift max: 0.011 29 r_work: 0.12571 shift mean: 0.002 shift max: 0.014 30 r_work: 0.12575 shift mean: 0.003 shift max: 0.017 31 r_work: 0.12578 shift mean: 0.002 shift max: 0.014 32 r_work: 0.12581 shift mean: 0.003 shift max: 0.016 33 r_work: 0.12584 shift mean: 0.002 shift max: 0.013 34 r_work: 0.12586 shift mean: 0.003 shift max: 0.014 35 r_work: 0.12588 shift mean: 0.002 shift max: 0.013 36 r_work: 0.12589 shift mean: 0.002 shift max: 0.009 37 r_work: 0.12590 shift mean: 0.002 shift max: 0.012 38 r_work: 0.12589 shift mean: 0.002 shift max: 0.015 39 r_work: 0.12589 shift mean: 0.002 shift max: 0.009 40 r_work: 0.12590 shift mean: 0.002 shift max: 0.015 41 r_work: 0.12590 shift mean: 0.001 shift max: 0.008 42 r_work: 0.12588 shift mean: 0.002 shift max: 0.010 43 r_work: 0.12586 shift mean: 0.002 shift max: 0.012 44 r_work: 0.12584 shift mean: 0.002 shift max: 0.009 45 r_work: 0.12583 shift mean: 0.002 shift max: 0.011 46 r_work: 0.12582 shift mean: 0.002 shift max: 0.011 47 r_work: 0.12581 shift mean: 0.002 shift max: 0.012 48 r_work: 0.12581 shift mean: 0.002 shift max: 0.020 49 r_work: 0.12581 shift mean: 0.001 shift max: 0.007 50 r_work: 0.12580 shift mean: 0.001 shift max: 0.009 51 r_work: 0.12578 shift mean: 0.002 shift max: 0.013 52 r_work: 0.12577 shift mean: 0.002 shift max: 0.011 53 r_work: 0.12576 shift mean: 0.002 shift max: 0.011 54 r_work: 0.12575 shift mean: 0.002 shift max: 0.012 55 r_work: 0.12574 shift mean: 0.002 shift max: 0.013 56 r_work: 0.12575 shift mean: 0.002 shift max: 0.015 57 r_work: 0.12575 shift mean: 0.001 shift max: 0.009 58 r_work: 0.12575 shift mean: 0.002 shift max: 0.014 59 r_work: 0.12575 shift mean: 0.001 shift max: 0.009 60 r_work: 0.12575 shift mean: 0.001 shift max: 0.009 61 r_work: 0.12575 shift mean: 0.002 shift max: 0.013 62 r_work: 0.12575 shift mean: 0.001 shift max: 0.008 63 r_work: 0.12575 shift mean: 0.002 shift max: 0.011 64 r_work: 0.12575 shift mean: 0.001 shift max: 0.012 65 r_work: 0.12576 shift mean: 0.001 shift max: 0.007 66 r_work: 0.12577 shift mean: 0.002 shift max: 0.016 67 r_work: 0.12578 shift mean: 0.001 shift max: 0.007 68 r_work: 0.12579 shift mean: 0.001 shift max: 0.009 69 r_work: 0.12579 shift mean: 0.001 shift max: 0.009 70 r_work: 0.12580 shift mean: 0.001 shift max: 0.008 71 r_work: 0.12581 shift mean: 0.001 shift max: 0.009 72 r_work: 0.12584 shift mean: 0.001 shift max: 0.011 73 r_work: 0.12585 shift mean: 0.001 shift max: 0.006 74 r_work: 0.12587 shift mean: 0.002 shift max: 0.012 75 r_work: 0.12588 shift mean: 0.001 shift max: 0.008 76 r_work: 0.12590 shift mean: 0.001 shift max: 0.011 77 r_work: 0.12592 shift mean: 0.001 shift max: 0.011 78 r_work: 0.12594 shift mean: 0.001 shift max: 0.012 79 r_work: 0.12595 shift mean: 0.001 shift max: 0.008 80 r_work: 0.12596 shift mean: 0.001 shift max: 0.010 81 r_work: 0.12598 shift mean: 0.001 shift max: 0.012 82 r_work: 0.12600 shift mean: 0.001 shift max: 0.012 83 r_work: 0.12601 shift mean: 0.001 shift max: 0.013 84 r_work: 0.12603 shift mean: 0.001 shift max: 0.015 85 r_work: 0.12604 shift mean: 0.001 shift max: 0.010 86 r_work: 0.12606 shift mean: 0.002 shift max: 0.016 87 r_work: 0.12607 shift mean: 0.001 shift max: 0.010 88 r_work: 0.12608 shift mean: 0.001 shift max: 0.013 89 r_work: 0.12609 shift mean: 0.001 shift max: 0.014 90 r_work: 0.12608 shift mean: 0.001 shift max: 0.013 91 r_work: 0.12608 shift mean: 0.001 shift max: 0.013 92 r_work: 0.12608 shift mean: 0.001 shift max: 0.013 93 r_work: 0.12608 shift mean: 0.001 shift max: 0.012 94 r_work: 0.12608 shift mean: 0.002 shift max: 0.016 95 r_work: 0.12608 shift mean: 0.001 shift max: 0.008 96 r_work: 0.12608 shift mean: 0.001 shift max: 0.010 97 r_work: 0.12607 shift mean: 0.001 shift max: 0.011 98 r_work: 0.12607 shift mean: 0.001 shift max: 0.010 99 r_work: 0.12607 shift mean: 0.001 shift max: 0.010 100 r_work: 0.12607 shift mean: 0.001 shift max: 0.010 101 0: Rw: 0.1261 Rf: 0.1435 Rf-Rw: 0.0175 bond: 0.023 angle: 2.42 clash: 4.5 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.83 cb: 1.31 shift start/prev: 0.133 0.100 rws(prev): 1.000 rws: 1.000 n_fev: 101 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1435 Best restraints scale: 1.0 Best Rwork, Rfree (at refinement start): 0.1260 0.1432 At refinement start Rw: 0.1260 Rf: 0.1432 Rf-Rw: 0.0173 bond: 0.023 angle: 2.42 clash: 4.5 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.83 cb: 1.31 shift start/prev: 0.133 0.000 Refinement: r_work: 0.12597 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12812 shift mean: 0.002 shift max: 0.200 2 r_work: 0.12812 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12737 shift mean: 0.000 shift max: 0.038 4 r_work: 0.12677 shift mean: 0.000 shift max: 0.038 5 r_work: 0.12644 shift mean: 0.000 shift max: 0.026 6 r_work: 0.12626 shift mean: 0.000 shift max: 0.019 7 r_work: 0.12615 shift mean: 0.000 shift max: 0.015 8 r_work: 0.12608 shift mean: 0.000 shift max: 0.011 9 r_work: 0.12603 shift mean: 0.000 shift max: 0.009 10 r_work: 0.12601 shift mean: 0.000 shift max: 0.008 11 r_work: 0.12599 shift mean: 0.000 shift max: 0.006 12 r_work: 0.12598 shift mean: 0.000 shift max: 0.004 13 r_work: 0.12597 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12597 shift mean: 0.000 shift max: 0.004 15 r_work: 0.12597 shift mean: 0.000 shift max: 0.003 16 r_work: 0.12597 shift mean: 0.000 shift max: 0.003 17 r_work: 0.12597 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12597 shift mean: 0.000 shift max: 0.002 19 r_work: 0.12597 shift mean: 0.000 shift max: 0.002 20 r_work: 0.12597 shift mean: 0.000 shift max: 0.004 21 r_work: 0.12597 shift mean: 0.000 shift max: 0.002 22 r_work: 0.12597 shift mean: 0.000 shift max: 0.002 23 r_work: 0.12598 shift mean: 0.001 shift max: 0.005 24 r_work: 0.12598 shift mean: 0.001 shift max: 0.006 25 r_work: 0.12598 shift mean: 0.001 shift max: 0.007 26 r_work: 0.12598 shift mean: 0.001 shift max: 0.006 27 r_work: 0.12598 shift mean: 0.001 shift max: 0.005 28 r_work: 0.12599 shift mean: 0.001 shift max: 0.006 29 r_work: 0.12599 shift mean: 0.001 shift max: 0.008 30 r_work: 0.12599 shift mean: 0.000 shift max: 0.004 31 r_work: 0.12600 shift mean: 0.001 shift max: 0.009 32 r_work: 0.12601 shift mean: 0.001 shift max: 0.008 33 r_work: 0.12601 shift mean: 0.001 shift max: 0.007 34 r_work: 0.12602 shift mean: 0.001 shift max: 0.011 35 r_work: 0.12603 shift mean: 0.001 shift max: 0.013 36 r_work: 0.12604 shift mean: 0.002 shift max: 0.016 37 r_work: 0.12604 shift mean: 0.001 shift max: 0.010 38 r_work: 0.12605 shift mean: 0.002 shift max: 0.017 39 r_work: 0.12606 shift mean: 0.001 shift max: 0.011 40 r_work: 0.12607 shift mean: 0.001 shift max: 0.012 41 r_work: 0.12607 shift mean: 0.001 shift max: 0.014 42 r_work: 0.12609 shift mean: 0.001 shift max: 0.011 43 r_work: 0.12610 shift mean: 0.001 shift max: 0.014 44 r_work: 0.12610 shift mean: 0.001 shift max: 0.012 45 r_work: 0.12611 shift mean: 0.001 shift max: 0.009 46 r_work: 0.12613 shift mean: 0.001 shift max: 0.013 47 r_work: 0.12614 shift mean: 0.001 shift max: 0.010 48 r_work: 0.12615 shift mean: 0.001 shift max: 0.011 49 r_work: 0.12616 shift mean: 0.001 shift max: 0.013 50 r_work: 0.12617 shift mean: 0.001 shift max: 0.011 51 r_work: 0.12617 shift mean: 0.001 shift max: 0.009 52 0: Rw: 0.1262 Rf: 0.1432 Rf-Rw: 0.0170 bond: 0.022 angle: 2.43 clash: 4.5 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.90 cb: 1.31 shift start/prev: 0.141 0.024 n_fev: 52 r_work: 0.12617 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12919 shift mean: 0.012 shift max: 0.175 2 r_work: 0.12930 shift mean: 0.000 shift max: 0.003 3 r_work: 0.12820 shift mean: 0.002 shift max: 0.031 4 r_work: 0.12746 shift mean: 0.002 shift max: 0.024 5 r_work: 0.12695 shift mean: 0.001 shift max: 0.020 6 r_work: 0.12662 shift mean: 0.001 shift max: 0.025 7 r_work: 0.12643 shift mean: 0.001 shift max: 0.014 8 r_work: 0.12632 shift mean: 0.001 shift max: 0.012 9 r_work: 0.12625 shift mean: 0.000 shift max: 0.010 10 r_work: 0.12621 shift mean: 0.000 shift max: 0.007 11 r_work: 0.12618 shift mean: 0.000 shift max: 0.005 12 r_work: 0.12616 shift mean: 0.000 shift max: 0.004 13 r_work: 0.12615 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12615 shift mean: 0.000 shift max: 0.004 15 r_work: 0.12615 shift mean: 0.000 shift max: 0.003 16 r_work: 0.12615 shift mean: 0.000 shift max: 0.003 17 r_work: 0.12615 shift mean: 0.000 shift max: 0.003 18 r_work: 0.12615 shift mean: 0.000 shift max: 0.003 19 r_work: 0.12615 shift mean: 0.000 shift max: 0.002 20 r_work: 0.12615 shift mean: 0.000 shift max: 0.003 21 r_work: 0.12615 shift mean: 0.000 shift max: 0.002 22 r_work: 0.12615 shift mean: 0.000 shift max: 0.003 23 r_work: 0.12616 shift mean: 0.000 shift max: 0.004 24 r_work: 0.12616 shift mean: 0.000 shift max: 0.006 25 r_work: 0.12617 shift mean: 0.000 shift max: 0.009 26 r_work: 0.12617 shift mean: 0.001 shift max: 0.011 27 r_work: 0.12617 shift mean: 0.001 shift max: 0.012 28 r_work: 0.12618 shift mean: 0.001 shift max: 0.012 29 r_work: 0.12618 shift mean: 0.001 shift max: 0.013 30 r_work: 0.12618 shift mean: 0.001 shift max: 0.014 31 r_work: 0.12619 shift mean: 0.001 shift max: 0.015 32 r_work: 0.12619 shift mean: 0.001 shift max: 0.012 33 r_work: 0.12620 shift mean: 0.001 shift max: 0.018 34 r_work: 0.12620 shift mean: 0.001 shift max: 0.014 35 r_work: 0.12621 shift mean: 0.001 shift max: 0.016 36 r_work: 0.12621 shift mean: 0.001 shift max: 0.014 37 r_work: 0.12621 shift mean: 0.001 shift max: 0.011 38 r_work: 0.12622 shift mean: 0.001 shift max: 0.011 39 r_work: 0.12622 shift mean: 0.001 shift max: 0.010 40 r_work: 0.12623 shift mean: 0.001 shift max: 0.010 41 r_work: 0.12623 shift mean: 0.001 shift max: 0.010 42 r_work: 0.12624 shift mean: 0.001 shift max: 0.007 43 r_work: 0.12625 shift mean: 0.001 shift max: 0.012 44 r_work: 0.12625 shift mean: 0.001 shift max: 0.009 45 r_work: 0.12627 shift mean: 0.001 shift max: 0.014 46 r_work: 0.12628 shift mean: 0.001 shift max: 0.012 47 r_work: 0.12628 shift mean: 0.001 shift max: 0.013 48 r_work: 0.12629 shift mean: 0.001 shift max: 0.013 49 r_work: 0.12630 shift mean: 0.001 shift max: 0.014 50 r_work: 0.12631 shift mean: 0.001 shift max: 0.010 51 r_work: 0.12633 shift mean: 0.001 shift max: 0.013 52 1: Rw: 0.1263 Rf: 0.1433 Rf-Rw: 0.0170 bond: 0.022 angle: 2.44 clash: 4.5 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.84 cb: 1.31 shift start/prev: 0.149 0.023 n_fev: 52 r_work: 0.12633 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12863 shift mean: 0.003 shift max: 0.200 2 r_work: 0.12863 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12783 shift mean: 0.001 shift max: 0.038 4 r_work: 0.12720 shift mean: 0.001 shift max: 0.037 5 r_work: 0.12683 shift mean: 0.000 shift max: 0.027 6 r_work: 0.12664 shift mean: 0.000 shift max: 0.019 7 r_work: 0.12651 shift mean: 0.000 shift max: 0.016 8 r_work: 0.12643 shift mean: 0.000 shift max: 0.012 9 r_work: 0.12639 shift mean: 0.000 shift max: 0.009 10 r_work: 0.12636 shift mean: 0.000 shift max: 0.008 11 r_work: 0.12634 shift mean: 0.000 shift max: 0.006 12 r_work: 0.12633 shift mean: 0.000 shift max: 0.005 13 r_work: 0.12633 shift mean: 0.000 shift max: 0.004 14 r_work: 0.12632 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12632 shift mean: 0.000 shift max: 0.003 16 r_work: 0.12632 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12632 shift mean: 0.000 shift max: 0.003 18 r_work: 0.12631 shift mean: 0.000 shift max: 0.001 19 r_work: 0.12631 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12632 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12632 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12632 shift mean: 0.000 shift max: 0.001 23 r_work: 0.12632 shift mean: 0.000 shift max: 0.002 24 r_work: 0.12632 shift mean: 0.000 shift max: 0.003 25 r_work: 0.12632 shift mean: 0.000 shift max: 0.006 26 r_work: 0.12632 shift mean: 0.001 shift max: 0.008 27 r_work: 0.12632 shift mean: 0.001 shift max: 0.010 28 r_work: 0.12632 shift mean: 0.000 shift max: 0.008 29 r_work: 0.12631 shift mean: 0.001 shift max: 0.009 30 r_work: 0.12631 shift mean: 0.000 shift max: 0.008 31 r_work: 0.12631 shift mean: 0.000 shift max: 0.008 32 r_work: 0.12631 shift mean: 0.001 shift max: 0.009 33 r_work: 0.12631 shift mean: 0.000 shift max: 0.007 34 r_work: 0.12631 shift mean: 0.001 shift max: 0.010 35 r_work: 0.12631 shift mean: 0.001 shift max: 0.010 36 r_work: 0.12631 shift mean: 0.001 shift max: 0.011 37 r_work: 0.12631 shift mean: 0.001 shift max: 0.013 38 r_work: 0.12632 shift mean: 0.001 shift max: 0.014 39 r_work: 0.12632 shift mean: 0.001 shift max: 0.016 40 r_work: 0.12632 shift mean: 0.001 shift max: 0.016 41 r_work: 0.12633 shift mean: 0.001 shift max: 0.017 42 r_work: 0.12634 shift mean: 0.001 shift max: 0.016 43 r_work: 0.12633 shift mean: 0.001 shift max: 0.014 44 r_work: 0.12634 shift mean: 0.001 shift max: 0.010 45 r_work: 0.12634 shift mean: 0.001 shift max: 0.014 46 r_work: 0.12634 shift mean: 0.001 shift max: 0.011 47 r_work: 0.12634 shift mean: 0.001 shift max: 0.013 48 r_work: 0.12634 shift mean: 0.001 shift max: 0.012 49 r_work: 0.12634 shift mean: 0.001 shift max: 0.014 50 r_work: 0.12634 shift mean: 0.001 shift max: 0.014 51 r_work: 0.12634 shift mean: 0.001 shift max: 0.016 52 2: Rw: 0.1263 Rf: 0.1434 Rf-Rw: 0.0171 bond: 0.022 angle: 2.42 clash: 4.5 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.84 cb: 1.31 shift start/prev: 0.153 0.016 n_fev: 52 r_work: 0.12634 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12889 shift mean: 0.011 shift max: 0.156 2 r_work: 0.12752 shift mean: 0.004 shift max: 0.050 3 r_work: 0.12711 shift mean: 0.001 shift max: 0.017 4 r_work: 0.12685 shift mean: 0.001 shift max: 0.016 5 r_work: 0.12665 shift mean: 0.001 shift max: 0.019 6 r_work: 0.12654 shift mean: 0.001 shift max: 0.010 7 r_work: 0.12647 shift mean: 0.000 shift max: 0.007 8 r_work: 0.12642 shift mean: 0.000 shift max: 0.006 9 r_work: 0.12639 shift mean: 0.000 shift max: 0.004 10 r_work: 0.12637 shift mean: 0.000 shift max: 0.005 11 r_work: 0.12636 shift mean: 0.000 shift max: 0.004 12 r_work: 0.12635 shift mean: 0.000 shift max: 0.005 13 r_work: 0.12634 shift mean: 0.000 shift max: 0.003 14 r_work: 0.12634 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12633 shift mean: 0.000 shift max: 0.002 16 r_work: 0.12633 shift mean: 0.000 shift max: 0.002 17 r_work: 0.12633 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12633 shift mean: 0.000 shift max: 0.002 19 r_work: 0.12633 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12633 shift mean: 0.000 shift max: 0.002 21 r_work: 0.12633 shift mean: 0.000 shift max: 0.002 22 r_work: 0.12633 shift mean: 0.000 shift max: 0.002 23 r_work: 0.12633 shift mean: 0.000 shift max: 0.003 24 r_work: 0.12633 shift mean: 0.000 shift max: 0.005 25 r_work: 0.12633 shift mean: 0.001 shift max: 0.007 26 r_work: 0.12633 shift mean: 0.001 shift max: 0.009 27 r_work: 0.12633 shift mean: 0.001 shift max: 0.010 28 r_work: 0.12634 shift mean: 0.001 shift max: 0.010 29 r_work: 0.12634 shift mean: 0.001 shift max: 0.012 30 r_work: 0.12635 shift mean: 0.001 shift max: 0.011 31 r_work: 0.12636 shift mean: 0.001 shift max: 0.011 32 r_work: 0.12636 shift mean: 0.001 shift max: 0.009 33 r_work: 0.12637 shift mean: 0.001 shift max: 0.008 34 r_work: 0.12637 shift mean: 0.001 shift max: 0.007 35 r_work: 0.12638 shift mean: 0.001 shift max: 0.007 36 r_work: 0.12638 shift mean: 0.001 shift max: 0.007 37 r_work: 0.12639 shift mean: 0.001 shift max: 0.008 38 r_work: 0.12640 shift mean: 0.001 shift max: 0.008 39 r_work: 0.12640 shift mean: 0.001 shift max: 0.009 40 r_work: 0.12641 shift mean: 0.001 shift max: 0.010 41 r_work: 0.12641 shift mean: 0.001 shift max: 0.010 42 r_work: 0.12642 shift mean: 0.001 shift max: 0.013 43 r_work: 0.12643 shift mean: 0.001 shift max: 0.012 44 r_work: 0.12643 shift mean: 0.001 shift max: 0.015 45 r_work: 0.12644 shift mean: 0.001 shift max: 0.016 46 r_work: 0.12645 shift mean: 0.001 shift max: 0.017 47 r_work: 0.12646 shift mean: 0.001 shift max: 0.018 48 r_work: 0.12647 shift mean: 0.001 shift max: 0.019 49 r_work: 0.12648 shift mean: 0.001 shift max: 0.015 50 r_work: 0.12649 shift mean: 0.001 shift max: 0.019 51 r_work: 0.12649 shift mean: 0.001 shift max: 0.016 52 3: Rw: 0.1265 Rf: 0.1432 Rf-Rw: 0.0167 bond: 0.022 angle: 2.43 clash: 4.5 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.88 cb: 1.31 shift start/prev: 0.160 0.021 n_fev: 52 r_work: 0.12649 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12972 shift mean: 0.007 shift max: 0.200 2 r_work: 0.12865 shift mean: 0.001 shift max: 0.038 3 r_work: 0.12791 shift mean: 0.001 shift max: 0.031 4 r_work: 0.12738 shift mean: 0.001 shift max: 0.028 5 r_work: 0.12705 shift mean: 0.001 shift max: 0.022 6 r_work: 0.12685 shift mean: 0.000 shift max: 0.016 7 r_work: 0.12672 shift mean: 0.000 shift max: 0.013 8 r_work: 0.12664 shift mean: 0.000 shift max: 0.010 9 r_work: 0.12659 shift mean: 0.000 shift max: 0.008 10 r_work: 0.12655 shift mean: 0.000 shift max: 0.007 11 r_work: 0.12653 shift mean: 0.000 shift max: 0.005 12 r_work: 0.12651 shift mean: 0.000 shift max: 0.004 13 r_work: 0.12650 shift mean: 0.000 shift max: 0.003 14 r_work: 0.12650 shift mean: 0.000 shift max: 0.003 15 r_work: 0.12649 shift mean: 0.000 shift max: 0.003 16 r_work: 0.12649 shift mean: 0.000 shift max: 0.001 17 r_work: 0.12648 shift mean: 0.000 shift max: 0.002 18 r_work: 0.12648 shift mean: 0.000 shift max: 0.001 19 r_work: 0.12648 shift mean: 0.000 shift max: 0.001 20 r_work: 0.12648 shift mean: 0.000 shift max: 0.001 21 r_work: 0.12648 shift mean: 0.000 shift max: 0.001 22 r_work: 0.12648 shift mean: 0.000 shift max: 0.001 23 r_work: 0.12648 shift mean: 0.000 shift max: 0.001 24 r_work: 0.12648 shift mean: 0.000 shift max: 0.001 25 r_work: 0.12648 shift mean: 0.000 shift max: 0.002 26 r_work: 0.12647 shift mean: 0.000 shift max: 0.002 27 r_work: 0.12647 shift mean: 0.000 shift max: 0.003 28 r_work: 0.12646 shift mean: 0.000 shift max: 0.005 29 r_work: 0.12646 shift mean: 0.000 shift max: 0.005 30 r_work: 0.12645 shift mean: 0.001 shift max: 0.007 31 r_work: 0.12645 shift mean: 0.001 shift max: 0.007 32 r_work: 0.12645 shift mean: 0.001 shift max: 0.011 33 r_work: 0.12644 shift mean: 0.001 shift max: 0.008 34 r_work: 0.12643 shift mean: 0.001 shift max: 0.009 35 r_work: 0.12643 shift mean: 0.001 shift max: 0.007 36 r_work: 0.12643 shift mean: 0.001 shift max: 0.006 37 r_work: 0.12643 shift mean: 0.000 shift max: 0.006 38 r_work: 0.12643 shift mean: 0.000 shift max: 0.004 39 r_work: 0.12642 shift mean: 0.000 shift max: 0.005 40 r_work: 0.12642 shift mean: 0.000 shift max: 0.004 41 r_work: 0.12642 shift mean: 0.000 shift max: 0.005 42 r_work: 0.12642 shift mean: 0.000 shift max: 0.005 43 r_work: 0.12642 shift mean: 0.000 shift max: 0.005 44 r_work: 0.12643 shift mean: 0.000 shift max: 0.006 45 r_work: 0.12643 shift mean: 0.000 shift max: 0.007 46 r_work: 0.12643 shift mean: 0.001 shift max: 0.008 47 r_work: 0.12644 shift mean: 0.001 shift max: 0.009 48 r_work: 0.12644 shift mean: 0.001 shift max: 0.009 49 r_work: 0.12644 shift mean: 0.001 shift max: 0.011 50 r_work: 0.12644 shift mean: 0.001 shift max: 0.010 51 r_work: 0.12644 shift mean: 0.001 shift max: 0.011 52 4: Rw: 0.1264 Rf: 0.1432 Rf-Rw: 0.0168 bond: 0.022 angle: 2.42 clash: 4.5 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.89 cb: 1.31 shift start/prev: 0.162 0.013 n_fev: 52 At refinement end: Rw: 0.1264 Rf: 0.1432 Rf-Rw: 0.0168 bond: 0.022 angle: 2.42 clash: 4.5 rota: 0.69 rama: f: 98.77 o: 0.00 Z: -0.89 cb: 1.31 shift start/prev: 0.162 0.013 Best Rwork, Rfree (after refinement): 0.1264 0.1432 See 1TT8_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 1307.38 seconds wall clock time: 17 minutes 28.41 seconds (1048.41 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)