Starting qr.refine on Fri Jun 21 15:30:11 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found miller_array, /net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//2PND.mtz Found model, /net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/2PND.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//2PND.mtz" } default_miller_array = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/finalised//2PND.mtz" model { file = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/2PND.pdb" } default_model = "/net/cci-gpu-00/raid1/scratch1/pavel/highres/phenix/2PND.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)=0.1694 0.1675 0.2074 n_refl.: 51757 re-set all scales: r(all,work,free)=0.1694 0.1675 0.2074 n_refl.: 51757 remove outliers: r(all,work,free)=0.1694 0.1675 0.2074 n_refl.: 51754 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1193 0.1449 n_refl.: 51754 remove outliers: r(all,work,free)=0.1205 0.1192 0.1449 n_refl.: 51750 Resolution Compl Nwork Nfree R_work kiso kani kmask 31.404-8.345 81.30 92 8 0.3373 183.219 170.218 1.055 0.950 0.470 8.232-6.663 94.34 95 5 0.2519 191.421 185.061 0.985 0.950 0.424 6.647-5.377 96.24 173 6 0.2087 221.880 215.528 1.052 0.950 0.406 5.365-4.336 90.25 312 12 0.1445 282.315 275.038 1.087 0.949 0.360 4.332-3.500 96.43 585 36 0.1259 307.090 303.604 1.071 0.948 0.170 3.499-2.826 99.83 1156 52 0.1263 245.130 241.167 1.065 0.946 0.160 2.825-2.282 100.00 2146 114 0.1387 169.843 167.029 1.082 0.943 0.000 2.281-1.842 100.00 4019 190 0.1168 135.814 134.207 1.113 0.939 0.000 1.842-1.488 100.00 7536 401 0.1095 75.526 74.398 1.116 0.930 0.000 1.488-1.201 100.00 14170 731 0.0978 48.678 47.958 1.147 0.919 0.000 1.201-0.970 71.02 18885 1026 0.1186 33.773 33.497 1.098 0.964 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.2038 ------------------------------------------------------------------------------- Starting r-factors: ******************* r_work=0.1192 r_free=0.1449 ------------------------------------------------------------------------------- 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 None 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: 2659 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 1948 Classifications: {'peptide': 119} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "A" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 711 Classifications: {'water': 237} Link IDs: {None: 236} Time building chain proxies: 0.40, per 1000 atoms: 0.15 Number of scatterers: 2659 At special positions: 0 Unit cell: (31.334, 50.684, 62.809, 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 3 16.00 O 414 8.00 N 182 7.00 C 606 6.00 H 1454 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: 1.08 Adding C-beta torsion restraints... Number of C-beta restraints generated: 220 Time building geometry restraints manager: 1.16 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: 1452 1.04 - 1.23: 51 1.23 - 1.43: 363 1.43 - 1.63: 572 1.63 - 1.82: 4 Bond restraints: 2442 Sorted by residual: bond pdb=" N VAL A 10 " pdb=" H VAL A 10 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N GLU A 8 " pdb=" H GLU A 8 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE2 GLN A 85 " pdb="HE21 GLN A 85 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N VAL A 96 " pdb=" H VAL A 96 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ILE A 23 " pdb=" H ILE A 23 " ideal model delta sigma weight residual 1.020 0.859 0.161 2.00e-02 2.50e+03 6.46e+01 ... (remaining 2437 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.15: 300 106.15 - 113.06: 2284 113.06 - 119.97: 522 119.97 - 126.88: 672 126.88 - 133.79: 18 Bond angle restraints: 3796 Sorted by residual: angle pdb=" CA ASN A 82 " pdb=" CB ASN A 82 " pdb=" CG ASN A 82 " ideal model delta sigma weight residual 112.60 116.08 -3.48 1.00e+00 1.00e+00 1.21e+01 angle pdb=" CA ASP A 109 " pdb=" CB ASP A 109 " pdb=" CG ASP A 109 " ideal model delta sigma weight residual 112.60 115.71 -3.11 1.00e+00 1.00e+00 9.67e+00 angle pdb=" CG GLN A 80 " pdb=" CD GLN A 80 " pdb=" NE2 GLN A 80 " ideal model delta sigma weight residual 116.40 120.71 -4.31 1.50e+00 4.44e-01 8.25e+00 angle pdb=" C LEU A 67 " pdb=" CA LEU A 67 " pdb=" CB LEU A 67 " ideal model delta sigma weight residual 110.10 104.92 5.18 1.90e+00 2.77e-01 7.43e+00 angle pdb=" C ARG A 66 " pdb=" CA ARG A 66 " pdb=" CB ARG A 66 " ideal model delta sigma weight residual 110.10 105.07 5.03 1.90e+00 2.77e-01 7.00e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 835 17.44 - 34.88: 51 34.88 - 52.31: 16 52.31 - 69.75: 5 69.75 - 87.19: 2 Dihedral angle restraints: 909 sinusoidal: 513 harmonic: 396 Sorted by residual: dihedral pdb=" CA LYS A 36 " pdb=" C LYS A 36 " pdb=" N TRP A 37 " pdb=" CA TRP A 37 " ideal model delta harmonic sigma weight residual 180.00 161.43 18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA TRP A 98 " pdb=" C TRP A 98 " pdb=" N GLN A 99 " pdb=" CA GLN A 99 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CB GLU A 95 " pdb=" CG GLU A 95 " pdb=" CD GLU A 95 " pdb=" OE1 GLU A 95 " ideal model delta sinusoidal sigma weight residual 0.00 -87.19 87.19 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 59 0.059 - 0.117: 51 0.117 - 0.175: 26 0.175 - 0.234: 10 0.234 - 0.292: 3 Chirality restraints: 149 Sorted by residual: 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 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA VAL A 10 " pdb=" N VAL A 10 " pdb=" C VAL A 10 " pdb=" CB VAL A 10 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA GLN A 59 " pdb=" N GLN A 59 " pdb=" C GLN A 59 " pdb=" CB GLN A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 146 not shown) Planarity restraints: 284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 37 " -0.031 2.00e-02 2.50e+03 2.15e-02 1.84e+01 pdb=" CG TRP A 37 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 37 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 37 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP A 37 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 37 " 0.025 2.00e-02 2.50e+03 pdb=" CE3 TRP A 37 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 37 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 37 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 37 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TRP A 37 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP A 37 " 0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP A 37 " 0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 37 " 0.014 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 37 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP A 37 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 92 " -0.052 2.00e-02 2.50e+03 2.27e-02 1.54e+01 pdb=" CG TYR A 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 92 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 92 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 92 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 92 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR A 92 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 TYR A 92 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 TYR A 92 " 0.036 2.00e-02 2.50e+03 pdb=" HE1 TYR A 92 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR A 92 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 24 " -0.038 2.00e-02 2.50e+03 1.91e-02 1.09e+01 pdb=" CG TYR A 24 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 24 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 24 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 24 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 24 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 24 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 24 " -0.035 2.00e-02 2.50e+03 pdb=" HD1 TYR A 24 " 0.029 2.00e-02 2.50e+03 pdb=" HD2 TYR A 24 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR A 24 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 24 " 0.023 2.00e-02 2.50e+03 ... (remaining 281 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 242 2.03 - 2.68: 4683 2.68 - 3.32: 10274 3.32 - 3.96: 15672 3.96 - 4.60: 23290 Nonbonded interactions: 54161 Sorted by model distance: nonbonded pdb="HE22 GLN A 80 " pdb=" O HOH A 178 " model vdw 1.393 1.800 nonbonded pdb=" OE1 GLN A 80 " pdb=" O HOH A 171 " model vdw 1.444 2.200 nonbonded pdb=" H2 GLY A 0 " pdb=" O HOH A 297 " model vdw 1.534 1.800 nonbonded pdb=" O HOH A 306 " pdb=" H2 HOH A 341 " model vdw sym.op. 1.633 1.800 -x+1,y+1/2,-z+1/2 nonbonded pdb=" O HOH A 151 " pdb=" H2 HOH A 178 " model vdw sym.op. 1.647 1.800 -x+1,y+1/2,-z+1/2 ... (remaining 54156 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 3 15.96 2 O 414 7.97 2 N 182 6.97 2 C 606 5.97 2 H 1454 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: 0.1192 Rf: 0.1449 Rf-Rw: 0.0257 bond: 0.011 angle: 1.48 clash: 4.1 rota: 0.92 rama: f: 93.16 o: 0.00 Z: 1.02 cb: 0.00 shift start/prev: 0.000 0.000 Optimal weight search: Data weight (initial): 11698.129070333567 r_work: 0.11922 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12592 shift mean: 0.014 shift max: 0.200 2 r_work: 0.12592 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12368 shift mean: 0.001 shift max: 0.037 4 r_work: 0.12168 shift mean: 0.001 shift max: 0.040 5 r_work: 0.12054 shift mean: 0.001 shift max: 0.028 6 r_work: 0.11982 shift mean: 0.000 shift max: 0.021 7 r_work: 0.11932 shift mean: 0.000 shift max: 0.017 8 r_work: 0.11897 shift mean: 0.000 shift max: 0.013 9 r_work: 0.11872 shift mean: 0.000 shift max: 0.010 10 r_work: 0.11851 shift mean: 0.000 shift max: 0.009 11 r_work: 0.11836 shift mean: 0.000 shift max: 0.007 12 r_work: 0.11822 shift mean: 0.000 shift max: 0.006 13 r_work: 0.11812 shift mean: 0.001 shift max: 0.005 14 r_work: 0.11804 shift mean: 0.001 shift max: 0.006 15 r_work: 0.11795 shift mean: 0.001 shift max: 0.006 16 r_work: 0.11788 shift mean: 0.001 shift max: 0.007 17 r_work: 0.11783 shift mean: 0.002 shift max: 0.008 18 r_work: 0.11780 shift mean: 0.002 shift max: 0.008 19 r_work: 0.11779 shift mean: 0.003 shift max: 0.011 20 r_work: 0.11779 shift mean: 0.003 shift max: 0.012 21 r_work: 0.11777 shift mean: 0.004 shift max: 0.019 22 r_work: 0.11775 shift mean: 0.003 shift max: 0.011 23 r_work: 0.11777 shift mean: 0.005 shift max: 0.017 24 r_work: 0.11771 shift mean: 0.003 shift max: 0.011 25 r_work: 0.11764 shift mean: 0.003 shift max: 0.011 26 r_work: 0.11758 shift mean: 0.004 shift max: 0.012 27 r_work: 0.11755 shift mean: 0.002 shift max: 0.008 28 r_work: 0.11754 shift mean: 0.002 shift max: 0.008 29 r_work: 0.11750 shift mean: 0.003 shift max: 0.013 30 r_work: 0.11751 shift mean: 0.002 shift max: 0.006 31 r_work: 0.11747 shift mean: 0.002 shift max: 0.009 32 r_work: 0.11743 shift mean: 0.002 shift max: 0.008 33 r_work: 0.11739 shift mean: 0.002 shift max: 0.010 34 r_work: 0.11731 shift mean: 0.003 shift max: 0.011 35 r_work: 0.11726 shift mean: 0.003 shift max: 0.011 36 r_work: 0.11719 shift mean: 0.003 shift max: 0.015 37 r_work: 0.11714 shift mean: 0.002 shift max: 0.009 38 r_work: 0.11706 shift mean: 0.003 shift max: 0.014 39 r_work: 0.11702 shift mean: 0.002 shift max: 0.007 40 r_work: 0.11698 shift mean: 0.002 shift max: 0.009 41 r_work: 0.11695 shift mean: 0.002 shift max: 0.009 42 r_work: 0.11691 shift mean: 0.001 shift max: 0.007 43 r_work: 0.11688 shift mean: 0.002 shift max: 0.010 44 r_work: 0.11684 shift mean: 0.002 shift max: 0.009 45 r_work: 0.11681 shift mean: 0.001 shift max: 0.008 46 r_work: 0.11679 shift mean: 0.002 shift max: 0.011 47 r_work: 0.11678 shift mean: 0.001 shift max: 0.007 48 r_work: 0.11675 shift mean: 0.002 shift max: 0.009 49 r_work: 0.11672 shift mean: 0.002 shift max: 0.010 50 r_work: 0.11669 shift mean: 0.001 shift max: 0.007 51 r_work: 0.11666 shift mean: 0.001 shift max: 0.008 52 r_work: 0.11662 shift mean: 0.001 shift max: 0.007 53 r_work: 0.11660 shift mean: 0.001 shift max: 0.005 54 r_work: 0.11658 shift mean: 0.001 shift max: 0.007 55 r_work: 0.11654 shift mean: 0.001 shift max: 0.007 56 r_work: 0.11650 shift mean: 0.001 shift max: 0.006 57 r_work: 0.11647 shift mean: 0.001 shift max: 0.006 58 r_work: 0.11643 shift mean: 0.001 shift max: 0.006 59 r_work: 0.11640 shift mean: 0.001 shift max: 0.005 60 r_work: 0.11637 shift mean: 0.001 shift max: 0.006 61 r_work: 0.11634 shift mean: 0.001 shift max: 0.004 62 r_work: 0.11630 shift mean: 0.001 shift max: 0.006 63 r_work: 0.11627 shift mean: 0.001 shift max: 0.005 64 r_work: 0.11624 shift mean: 0.001 shift max: 0.004 65 r_work: 0.11622 shift mean: 0.001 shift max: 0.004 66 r_work: 0.11619 shift mean: 0.001 shift max: 0.004 67 r_work: 0.11616 shift mean: 0.001 shift max: 0.004 68 r_work: 0.11613 shift mean: 0.001 shift max: 0.004 69 r_work: 0.11612 shift mean: 0.001 shift max: 0.003 70 r_work: 0.11610 shift mean: 0.001 shift max: 0.004 71 r_work: 0.11607 shift mean: 0.001 shift max: 0.004 72 r_work: 0.11605 shift mean: 0.001 shift max: 0.003 73 r_work: 0.11602 shift mean: 0.001 shift max: 0.005 74 r_work: 0.11599 shift mean: 0.001 shift max: 0.005 75 r_work: 0.11597 shift mean: 0.001 shift max: 0.004 76 r_work: 0.11595 shift mean: 0.001 shift max: 0.004 77 r_work: 0.11592 shift mean: 0.001 shift max: 0.005 78 r_work: 0.11591 shift mean: 0.001 shift max: 0.004 79 r_work: 0.11589 shift mean: 0.001 shift max: 0.004 80 r_work: 0.11587 shift mean: 0.001 shift max: 0.004 81 r_work: 0.11586 shift mean: 0.001 shift max: 0.005 82 r_work: 0.11584 shift mean: 0.001 shift max: 0.004 83 r_work: 0.11583 shift mean: 0.001 shift max: 0.004 84 r_work: 0.11581 shift mean: 0.001 shift max: 0.005 85 r_work: 0.11579 shift mean: 0.001 shift max: 0.004 86 r_work: 0.11577 shift mean: 0.001 shift max: 0.005 87 r_work: 0.11576 shift mean: 0.001 shift max: 0.005 88 r_work: 0.11574 shift mean: 0.001 shift max: 0.004 89 r_work: 0.11572 shift mean: 0.001 shift max: 0.004 90 r_work: 0.11571 shift mean: 0.001 shift max: 0.004 91 r_work: 0.11570 shift mean: 0.001 shift max: 0.004 92 r_work: 0.11569 shift mean: 0.001 shift max: 0.004 93 r_work: 0.11567 shift mean: 0.001 shift max: 0.003 94 r_work: 0.11567 shift mean: 0.001 shift max: 0.005 95 r_work: 0.11566 shift mean: 0.001 shift max: 0.004 96 r_work: 0.11565 shift mean: 0.001 shift max: 0.004 97 r_work: 0.11563 shift mean: 0.001 shift max: 0.005 98 r_work: 0.11561 shift mean: 0.001 shift max: 0.004 99 r_work: 0.11560 shift mean: 0.001 shift max: 0.004 100 r_work: 0.11559 shift mean: 0.001 shift max: 0.005 101 r_work: 0.11557 shift mean: 0.001 shift max: 0.004 102 0: Rw: 0.1156 Rf: 0.1445 Rf-Rw: 0.0289 bond: 0.032 angle: 2.33 clash: 8.7 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.91 cb: 0.91 shift start/prev: 0.084 0.084 rws(prev): 1.000 rws: 1.000 n_fev: 102 0: Rw: 0.1156 Rf: 0.1445 Rf-Rw: 0.0289 bond: 0.032 angle: 2.33 clash: 8.7 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.91 cb: 0.91 shift start/prev: 0.084 0.084 rws(prev): 1.000 rws: 1.500 n_fev: 102 (NEXT) r_work: 0.11922 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12626 shift mean: 0.017 shift max: 0.195 2 r_work: 0.12670 shift mean: 0.000 shift max: 0.005 3 r_work: 0.12444 shift mean: 0.001 shift max: 0.039 4 r_work: 0.12242 shift mean: 0.001 shift max: 0.040 5 r_work: 0.12120 shift mean: 0.000 shift max: 0.029 6 r_work: 0.12040 shift mean: 0.000 shift max: 0.022 7 r_work: 0.11985 shift mean: 0.000 shift max: 0.017 8 r_work: 0.11942 shift mean: 0.000 shift max: 0.014 9 r_work: 0.11908 shift mean: 0.001 shift max: 0.011 10 r_work: 0.11882 shift mean: 0.001 shift max: 0.009 11 r_work: 0.11859 shift mean: 0.001 shift max: 0.007 12 r_work: 0.11840 shift mean: 0.001 shift max: 0.006 13 r_work: 0.11825 shift mean: 0.001 shift max: 0.007 14 r_work: 0.11810 shift mean: 0.002 shift max: 0.008 15 r_work: 0.11800 shift mean: 0.002 shift max: 0.011 16 r_work: 0.11796 shift mean: 0.002 shift max: 0.008 17 r_work: 0.11796 shift mean: 0.003 shift max: 0.009 18 r_work: 0.11797 shift mean: 0.004 shift max: 0.013 19 r_work: 0.11801 shift mean: 0.003 shift max: 0.013 20 r_work: 0.11804 shift mean: 0.004 shift max: 0.017 21 r_work: 0.11804 shift mean: 0.003 shift max: 0.013 22 r_work: 0.11804 shift mean: 0.005 shift max: 0.024 23 r_work: 0.11798 shift mean: 0.003 shift max: 0.012 24 r_work: 0.11791 shift mean: 0.003 shift max: 0.013 25 r_work: 0.11783 shift mean: 0.003 shift max: 0.014 26 r_work: 0.11779 shift mean: 0.002 shift max: 0.010 27 r_work: 0.11775 shift mean: 0.002 shift max: 0.010 28 r_work: 0.11773 shift mean: 0.002 shift max: 0.010 29 r_work: 0.11771 shift mean: 0.002 shift max: 0.008 30 r_work: 0.11770 shift mean: 0.002 shift max: 0.009 31 r_work: 0.11766 shift mean: 0.002 shift max: 0.011 32 r_work: 0.11764 shift mean: 0.002 shift max: 0.009 33 r_work: 0.11760 shift mean: 0.003 shift max: 0.014 34 r_work: 0.11754 shift mean: 0.003 shift max: 0.014 35 r_work: 0.11750 shift mean: 0.002 shift max: 0.013 36 r_work: 0.11745 shift mean: 0.003 shift max: 0.015 37 r_work: 0.11741 shift mean: 0.002 shift max: 0.012 38 r_work: 0.11737 shift mean: 0.002 shift max: 0.013 39 r_work: 0.11732 shift mean: 0.003 shift max: 0.015 40 r_work: 0.11730 shift mean: 0.001 shift max: 0.009 41 r_work: 0.11727 shift mean: 0.002 shift max: 0.015 42 r_work: 0.11724 shift mean: 0.002 shift max: 0.011 43 r_work: 0.11722 shift mean: 0.001 shift max: 0.008 44 r_work: 0.11720 shift mean: 0.002 shift max: 0.013 45 r_work: 0.11718 shift mean: 0.001 shift max: 0.008 46 r_work: 0.11716 shift mean: 0.001 shift max: 0.008 47 r_work: 0.11713 shift mean: 0.001 shift max: 0.010 48 r_work: 0.11710 shift mean: 0.001 shift max: 0.009 49 r_work: 0.11709 shift mean: 0.001 shift max: 0.005 50 r_work: 0.11706 shift mean: 0.001 shift max: 0.008 51 r_work: 0.11703 shift mean: 0.001 shift max: 0.007 52 r_work: 0.11699 shift mean: 0.001 shift max: 0.008 53 r_work: 0.11696 shift mean: 0.001 shift max: 0.007 54 r_work: 0.11694 shift mean: 0.001 shift max: 0.006 55 r_work: 0.11690 shift mean: 0.001 shift max: 0.007 56 r_work: 0.11685 shift mean: 0.001 shift max: 0.008 57 r_work: 0.11683 shift mean: 0.001 shift max: 0.005 58 r_work: 0.11679 shift mean: 0.001 shift max: 0.008 59 r_work: 0.11676 shift mean: 0.001 shift max: 0.006 60 r_work: 0.11673 shift mean: 0.001 shift max: 0.007 61 r_work: 0.11670 shift mean: 0.001 shift max: 0.007 62 r_work: 0.11666 shift mean: 0.001 shift max: 0.007 63 r_work: 0.11662 shift mean: 0.001 shift max: 0.007 64 r_work: 0.11660 shift mean: 0.001 shift max: 0.006 65 r_work: 0.11657 shift mean: 0.001 shift max: 0.007 66 r_work: 0.11653 shift mean: 0.001 shift max: 0.007 67 r_work: 0.11652 shift mean: 0.001 shift max: 0.005 68 r_work: 0.11649 shift mean: 0.001 shift max: 0.008 69 r_work: 0.11647 shift mean: 0.001 shift max: 0.005 70 r_work: 0.11645 shift mean: 0.001 shift max: 0.006 71 r_work: 0.11643 shift mean: 0.001 shift max: 0.007 72 r_work: 0.11641 shift mean: 0.001 shift max: 0.006 73 r_work: 0.11640 shift mean: 0.001 shift max: 0.006 74 r_work: 0.11638 shift mean: 0.001 shift max: 0.008 75 r_work: 0.11637 shift mean: 0.001 shift max: 0.005 76 r_work: 0.11636 shift mean: 0.001 shift max: 0.005 77 r_work: 0.11635 shift mean: 0.001 shift max: 0.006 78 r_work: 0.11633 shift mean: 0.001 shift max: 0.005 79 r_work: 0.11632 shift mean: 0.001 shift max: 0.006 80 r_work: 0.11630 shift mean: 0.001 shift max: 0.005 81 r_work: 0.11629 shift mean: 0.001 shift max: 0.006 82 r_work: 0.11627 shift mean: 0.001 shift max: 0.006 83 r_work: 0.11625 shift mean: 0.001 shift max: 0.005 84 r_work: 0.11624 shift mean: 0.001 shift max: 0.006 85 r_work: 0.11622 shift mean: 0.001 shift max: 0.005 86 r_work: 0.11621 shift mean: 0.001 shift max: 0.006 87 r_work: 0.11619 shift mean: 0.001 shift max: 0.006 88 r_work: 0.11618 shift mean: 0.001 shift max: 0.005 89 r_work: 0.11616 shift mean: 0.001 shift max: 0.008 90 r_work: 0.11615 shift mean: 0.001 shift max: 0.005 91 r_work: 0.11614 shift mean: 0.001 shift max: 0.006 92 r_work: 0.11612 shift mean: 0.001 shift max: 0.007 93 r_work: 0.11612 shift mean: 0.001 shift max: 0.005 94 r_work: 0.11610 shift mean: 0.001 shift max: 0.006 95 r_work: 0.11610 shift mean: 0.001 shift max: 0.006 96 r_work: 0.11610 shift mean: 0.001 shift max: 0.004 97 r_work: 0.11609 shift mean: 0.001 shift max: 0.006 98 r_work: 0.11608 shift mean: 0.001 shift max: 0.005 99 r_work: 0.11608 shift mean: 0.001 shift max: 0.006 100 r_work: 0.11608 shift mean: 0.001 shift max: 0.005 101 r_work: 0.11606 shift mean: 0.001 shift max: 0.005 102 1: Rw: 0.1161 Rf: 0.1447 Rf-Rw: 0.0286 bond: 0.029 angle: 2.23 clash: 6.7 rota: 0.00 rama: f: 94.02 o: 0.00 Z: 0.94 cb: 0.00 shift start/prev: 0.085 0.010 rws(prev): 1.500 rws: 1.500 n_fev: 102 Optimal weight found. Stopping weight search. Best Rfree from above: 0.1161 Best restraints scale: 1.5 Best Rwork, Rfree (at refinement start): 0.1159 0.1440 At refinement start Rw: 0.1159 Rf: 0.1440 Rf-Rw: 0.0281 bond: 0.029 angle: 2.23 clash: 6.7 rota: 0.00 rama: f: 94.02 o: 0.00 Z: 0.94 cb: 0.00 shift start/prev: 0.085 0.000 Refinement: r_work: 0.11587 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12406 shift mean: 0.010 shift max: 0.200 2 r_work: 0.12406 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12125 shift mean: 0.002 shift max: 0.039 4 r_work: 0.11902 shift mean: 0.002 shift max: 0.040 5 r_work: 0.11775 shift mean: 0.001 shift max: 0.027 6 r_work: 0.11699 shift mean: 0.001 shift max: 0.020 7 r_work: 0.11651 shift mean: 0.001 shift max: 0.016 8 r_work: 0.11624 shift mean: 0.000 shift max: 0.012 9 r_work: 0.11606 shift mean: 0.000 shift max: 0.009 10 r_work: 0.11593 shift mean: 0.000 shift max: 0.008 11 r_work: 0.11587 shift mean: 0.000 shift max: 0.006 12 r_work: 0.11582 shift mean: 0.000 shift max: 0.005 13 r_work: 0.11580 shift mean: 0.000 shift max: 0.003 14 r_work: 0.11578 shift mean: 0.000 shift max: 0.004 15 r_work: 0.11577 shift mean: 0.000 shift max: 0.002 16 r_work: 0.11577 shift mean: 0.000 shift max: 0.002 17 r_work: 0.11577 shift mean: 0.000 shift max: 0.002 18 r_work: 0.11577 shift mean: 0.000 shift max: 0.001 19 r_work: 0.11577 shift mean: 0.000 shift max: 0.001 20 r_work: 0.11577 shift mean: 0.000 shift max: 0.001 21 r_work: 0.11578 shift mean: 0.000 shift max: 0.001 22 r_work: 0.11577 shift mean: 0.000 shift max: 0.001 23 r_work: 0.11578 shift mean: 0.000 shift max: 0.000 24 r_work: 0.11578 shift mean: 0.000 shift max: 0.001 25 r_work: 0.11578 shift mean: 0.000 shift max: 0.000 26 r_work: 0.11579 shift mean: 0.000 shift max: 0.001 27 r_work: 0.11579 shift mean: 0.000 shift max: 0.001 28 r_work: 0.11580 shift mean: 0.000 shift max: 0.001 29 r_work: 0.11581 shift mean: 0.000 shift max: 0.001 30 r_work: 0.11581 shift mean: 0.000 shift max: 0.002 31 r_work: 0.11582 shift mean: 0.000 shift max: 0.002 32 r_work: 0.11582 shift mean: 0.000 shift max: 0.003 33 r_work: 0.11581 shift mean: 0.000 shift max: 0.003 34 r_work: 0.11581 shift mean: 0.001 shift max: 0.003 35 r_work: 0.11580 shift mean: 0.001 shift max: 0.003 36 r_work: 0.11578 shift mean: 0.001 shift max: 0.004 37 r_work: 0.11578 shift mean: 0.000 shift max: 0.003 38 r_work: 0.11577 shift mean: 0.001 shift max: 0.004 39 r_work: 0.11576 shift mean: 0.000 shift max: 0.002 40 r_work: 0.11574 shift mean: 0.001 shift max: 0.004 41 r_work: 0.11573 shift mean: 0.000 shift max: 0.003 42 r_work: 0.11572 shift mean: 0.001 shift max: 0.003 43 r_work: 0.11570 shift mean: 0.001 shift max: 0.004 44 r_work: 0.11570 shift mean: 0.001 shift max: 0.004 45 r_work: 0.11569 shift mean: 0.001 shift max: 0.004 46 r_work: 0.11568 shift mean: 0.001 shift max: 0.005 47 r_work: 0.11567 shift mean: 0.001 shift max: 0.004 48 r_work: 0.11566 shift mean: 0.001 shift max: 0.006 49 r_work: 0.11565 shift mean: 0.001 shift max: 0.007 50 r_work: 0.11565 shift mean: 0.001 shift max: 0.008 51 r_work: 0.11564 shift mean: 0.001 shift max: 0.009 52 0: Rw: 0.1156 Rf: 0.1441 Rf-Rw: 0.0285 bond: 0.030 angle: 2.24 clash: 6.7 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.91 cb: 0.00 shift start/prev: 0.093 0.014 n_fev: 52 r_work: 0.11564 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12487 shift mean: 0.008 shift max: 0.200 2 r_work: 0.12487 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12181 shift mean: 0.002 shift max: 0.039 4 r_work: 0.11936 shift mean: 0.001 shift max: 0.040 5 r_work: 0.11794 shift mean: 0.001 shift max: 0.028 6 r_work: 0.11707 shift mean: 0.001 shift max: 0.021 7 r_work: 0.11655 shift mean: 0.001 shift max: 0.015 8 r_work: 0.11622 shift mean: 0.000 shift max: 0.012 9 r_work: 0.11601 shift mean: 0.000 shift max: 0.009 10 r_work: 0.11588 shift mean: 0.000 shift max: 0.008 11 r_work: 0.11580 shift mean: 0.000 shift max: 0.005 12 r_work: 0.11574 shift mean: 0.000 shift max: 0.005 13 r_work: 0.11571 shift mean: 0.000 shift max: 0.004 14 r_work: 0.11569 shift mean: 0.000 shift max: 0.003 15 r_work: 0.11567 shift mean: 0.000 shift max: 0.002 16 r_work: 0.11567 shift mean: 0.000 shift max: 0.002 17 r_work: 0.11566 shift mean: 0.000 shift max: 0.001 18 r_work: 0.11566 shift mean: 0.000 shift max: 0.001 19 r_work: 0.11565 shift mean: 0.000 shift max: 0.001 20 r_work: 0.11565 shift mean: 0.000 shift max: 0.001 21 r_work: 0.11565 shift mean: 0.000 shift max: 0.001 22 r_work: 0.11564 shift mean: 0.000 shift max: 0.001 23 r_work: 0.11564 shift mean: 0.000 shift max: 0.001 24 r_work: 0.11564 shift mean: 0.000 shift max: 0.000 25 r_work: 0.11564 shift mean: 0.000 shift max: 0.001 26 r_work: 0.11564 shift mean: 0.000 shift max: 0.000 27 r_work: 0.11563 shift mean: 0.000 shift max: 0.001 28 r_work: 0.11564 shift mean: 0.000 shift max: 0.001 29 r_work: 0.11564 shift mean: 0.000 shift max: 0.001 30 r_work: 0.11563 shift mean: 0.000 shift max: 0.001 31 r_work: 0.11563 shift mean: 0.000 shift max: 0.001 32 r_work: 0.11563 shift mean: 0.000 shift max: 0.002 33 r_work: 0.11562 shift mean: 0.000 shift max: 0.002 34 r_work: 0.11562 shift mean: 0.000 shift max: 0.002 35 r_work: 0.11560 shift mean: 0.000 shift max: 0.003 36 r_work: 0.11561 shift mean: 0.000 shift max: 0.003 37 r_work: 0.11560 shift mean: 0.001 shift max: 0.004 38 r_work: 0.11559 shift mean: 0.000 shift max: 0.003 39 r_work: 0.11559 shift mean: 0.000 shift max: 0.003 40 r_work: 0.11559 shift mean: 0.000 shift max: 0.004 41 r_work: 0.11559 shift mean: 0.000 shift max: 0.002 42 r_work: 0.11559 shift mean: 0.000 shift max: 0.002 43 r_work: 0.11559 shift mean: 0.000 shift max: 0.002 44 r_work: 0.11559 shift mean: 0.000 shift max: 0.003 45 r_work: 0.11559 shift mean: 0.000 shift max: 0.002 46 r_work: 0.11559 shift mean: 0.000 shift max: 0.002 47 r_work: 0.11559 shift mean: 0.000 shift max: 0.002 48 r_work: 0.11560 shift mean: 0.000 shift max: 0.003 49 r_work: 0.11560 shift mean: 0.000 shift max: 0.003 50 r_work: 0.11560 shift mean: 0.000 shift max: 0.003 51 r_work: 0.11560 shift mean: 0.000 shift max: 0.004 52 1: Rw: 0.1156 Rf: 0.1440 Rf-Rw: 0.0284 bond: 0.029 angle: 2.24 clash: 6.7 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.94 cb: 0.00 shift start/prev: 0.095 0.008 n_fev: 52 r_work: 0.11560 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12322 shift mean: 0.008 shift max: 0.200 2 r_work: 0.12322 shift mean: 0.000 shift max: 0.000 3 r_work: 0.12061 shift mean: 0.002 shift max: 0.039 4 r_work: 0.11857 shift mean: 0.001 shift max: 0.040 5 r_work: 0.11741 shift mean: 0.001 shift max: 0.027 6 r_work: 0.11672 shift mean: 0.001 shift max: 0.020 7 r_work: 0.11629 shift mean: 0.001 shift max: 0.016 8 r_work: 0.11603 shift mean: 0.000 shift max: 0.012 9 r_work: 0.11585 shift mean: 0.000 shift max: 0.010 10 r_work: 0.11574 shift mean: 0.000 shift max: 0.007 11 r_work: 0.11568 shift mean: 0.000 shift max: 0.006 12 r_work: 0.11563 shift mean: 0.000 shift max: 0.005 13 r_work: 0.11560 shift mean: 0.000 shift max: 0.004 14 r_work: 0.11558 shift mean: 0.000 shift max: 0.003 15 r_work: 0.11557 shift mean: 0.000 shift max: 0.002 16 r_work: 0.11557 shift mean: 0.000 shift max: 0.002 17 r_work: 0.11556 shift mean: 0.000 shift max: 0.003 18 r_work: 0.11556 shift mean: 0.000 shift max: 0.001 19 r_work: 0.11556 shift mean: 0.000 shift max: 0.001 20 r_work: 0.11556 shift mean: 0.000 shift max: 0.001 21 r_work: 0.11555 shift mean: 0.000 shift max: 0.000 22 r_work: 0.11556 shift mean: 0.000 shift max: 0.001 23 r_work: 0.11556 shift mean: 0.000 shift max: 0.001 24 r_work: 0.11556 shift mean: 0.000 shift max: 0.001 25 r_work: 0.11556 shift mean: 0.000 shift max: 0.000 26 r_work: 0.11556 shift mean: 0.000 shift max: 0.000 27 r_work: 0.11556 shift mean: 0.000 shift max: 0.001 28 r_work: 0.11556 shift mean: 0.000 shift max: 0.001 29 r_work: 0.11557 shift mean: 0.000 shift max: 0.001 30 r_work: 0.11557 shift mean: 0.000 shift max: 0.001 31 r_work: 0.11557 shift mean: 0.000 shift max: 0.001 32 r_work: 0.11557 shift mean: 0.000 shift max: 0.002 33 r_work: 0.11557 shift mean: 0.000 shift max: 0.001 34 r_work: 0.11557 shift mean: 0.000 shift max: 0.003 35 r_work: 0.11557 shift mean: 0.000 shift max: 0.003 36 r_work: 0.11556 shift mean: 0.000 shift max: 0.003 37 r_work: 0.11556 shift mean: 0.000 shift max: 0.004 38 r_work: 0.11555 shift mean: 0.000 shift max: 0.003 39 r_work: 0.11554 shift mean: 0.000 shift max: 0.004 40 r_work: 0.11554 shift mean: 0.000 shift max: 0.003 41 r_work: 0.11554 shift mean: 0.000 shift max: 0.003 42 r_work: 0.11554 shift mean: 0.000 shift max: 0.002 43 r_work: 0.11553 shift mean: 0.000 shift max: 0.003 44 r_work: 0.11553 shift mean: 0.000 shift max: 0.003 45 r_work: 0.11552 shift mean: 0.000 shift max: 0.003 46 r_work: 0.11552 shift mean: 0.000 shift max: 0.003 47 r_work: 0.11552 shift mean: 0.000 shift max: 0.003 48 r_work: 0.11552 shift mean: 0.000 shift max: 0.003 49 r_work: 0.11552 shift mean: 0.000 shift max: 0.004 50 r_work: 0.11552 shift mean: 0.000 shift max: 0.003 51 r_work: 0.11552 shift mean: 0.000 shift max: 0.004 52 2: Rw: 0.1155 Rf: 0.1441 Rf-Rw: 0.0286 bond: 0.030 angle: 2.25 clash: 7.2 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.90 cb: 0.91 shift start/prev: 0.098 0.007 n_fev: 52 r_work: 0.11552 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12807 shift mean: 0.014 shift max: 0.190 2 r_work: 0.12922 shift mean: 0.001 shift max: 0.010 3 r_work: 0.12473 shift mean: 0.003 shift max: 0.040 4 r_work: 0.12125 shift mean: 0.002 shift max: 0.045 5 r_work: 0.11911 shift mean: 0.002 shift max: 0.026 6 r_work: 0.11777 shift mean: 0.001 shift max: 0.022 7 r_work: 0.11689 shift mean: 0.001 shift max: 0.017 8 r_work: 0.11633 shift mean: 0.001 shift max: 0.014 9 r_work: 0.11601 shift mean: 0.001 shift max: 0.010 10 r_work: 0.11582 shift mean: 0.001 shift max: 0.007 11 r_work: 0.11570 shift mean: 0.000 shift max: 0.006 12 r_work: 0.11564 shift mean: 0.000 shift max: 0.004 13 r_work: 0.11558 shift mean: 0.000 shift max: 0.004 14 r_work: 0.11556 shift mean: 0.000 shift max: 0.003 15 r_work: 0.11554 shift mean: 0.000 shift max: 0.002 16 r_work: 0.11552 shift mean: 0.000 shift max: 0.003 17 r_work: 0.11552 shift mean: 0.000 shift max: 0.001 18 r_work: 0.11551 shift mean: 0.000 shift max: 0.001 19 r_work: 0.11551 shift mean: 0.000 shift max: 0.001 20 r_work: 0.11551 shift mean: 0.000 shift max: 0.001 21 r_work: 0.11550 shift mean: 0.000 shift max: 0.001 22 r_work: 0.11550 shift mean: 0.000 shift max: 0.001 23 r_work: 0.11550 shift mean: 0.000 shift max: 0.000 24 r_work: 0.11550 shift mean: 0.000 shift max: 0.000 25 r_work: 0.11550 shift mean: 0.000 shift max: 0.000 26 r_work: 0.11550 shift mean: 0.000 shift max: 0.000 27 r_work: 0.11550 shift mean: 0.000 shift max: 0.000 28 r_work: 0.11550 shift mean: 0.000 shift max: 0.000 29 r_work: 0.11550 shift mean: 0.000 shift max: 0.001 30 r_work: 0.11550 shift mean: 0.000 shift max: 0.001 31 r_work: 0.11550 shift mean: 0.000 shift max: 0.001 32 r_work: 0.11550 shift mean: 0.000 shift max: 0.001 33 r_work: 0.11549 shift mean: 0.000 shift max: 0.001 34 r_work: 0.11549 shift mean: 0.000 shift max: 0.001 35 r_work: 0.11549 shift mean: 0.000 shift max: 0.002 36 r_work: 0.11549 shift mean: 0.000 shift max: 0.002 37 r_work: 0.11548 shift mean: 0.000 shift max: 0.002 38 r_work: 0.11548 shift mean: 0.000 shift max: 0.002 39 r_work: 0.11548 shift mean: 0.000 shift max: 0.002 40 r_work: 0.11548 shift mean: 0.000 shift max: 0.003 41 r_work: 0.11548 shift mean: 0.000 shift max: 0.002 42 r_work: 0.11547 shift mean: 0.000 shift max: 0.003 43 r_work: 0.11548 shift mean: 0.000 shift max: 0.002 44 r_work: 0.11548 shift mean: 0.000 shift max: 0.003 45 r_work: 0.11547 shift mean: 0.000 shift max: 0.003 46 r_work: 0.11548 shift mean: 0.000 shift max: 0.002 47 r_work: 0.11548 shift mean: 0.000 shift max: 0.002 48 r_work: 0.11548 shift mean: 0.000 shift max: 0.003 49 r_work: 0.11547 shift mean: 0.000 shift max: 0.002 50 r_work: 0.11547 shift mean: 0.000 shift max: 0.003 51 r_work: 0.11547 shift mean: 0.000 shift max: 0.003 52 3: Rw: 0.1155 Rf: 0.1440 Rf-Rw: 0.0286 bond: 0.029 angle: 2.26 clash: 7.2 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.93 cb: 0.00 shift start/prev: 0.101 0.007 n_fev: 52 r_work: 0.11547 shift mean: 0.000 shift max: 0.000 1 r_work: 0.12728 shift mean: 0.014 shift max: 0.153 2 r_work: 0.12711 shift mean: 0.000 shift max: 0.001 3 r_work: 0.12321 shift mean: 0.003 shift max: 0.030 4 r_work: 0.12036 shift mean: 0.002 shift max: 0.029 5 r_work: 0.11855 shift mean: 0.002 shift max: 0.020 6 r_work: 0.11741 shift mean: 0.001 shift max: 0.016 7 r_work: 0.11670 shift mean: 0.001 shift max: 0.011 8 r_work: 0.11623 shift mean: 0.001 shift max: 0.010 9 r_work: 0.11591 shift mean: 0.001 shift max: 0.010 10 r_work: 0.11573 shift mean: 0.001 shift max: 0.006 11 r_work: 0.11562 shift mean: 0.000 shift max: 0.005 12 r_work: 0.11556 shift mean: 0.000 shift max: 0.004 13 r_work: 0.11551 shift mean: 0.000 shift max: 0.003 14 r_work: 0.11549 shift mean: 0.000 shift max: 0.003 15 r_work: 0.11547 shift mean: 0.000 shift max: 0.004 16 r_work: 0.11546 shift mean: 0.000 shift max: 0.001 17 r_work: 0.11545 shift mean: 0.000 shift max: 0.002 18 r_work: 0.11545 shift mean: 0.000 shift max: 0.001 19 r_work: 0.11545 shift mean: 0.000 shift max: 0.001 20 r_work: 0.11545 shift mean: 0.000 shift max: 0.000 21 r_work: 0.11545 shift mean: 0.000 shift max: 0.001 22 r_work: 0.11545 shift mean: 0.000 shift max: 0.000 23 r_work: 0.11544 shift mean: 0.000 shift max: 0.000 24 r_work: 0.11545 shift mean: 0.000 shift max: 0.000 25 r_work: 0.11545 shift mean: 0.000 shift max: 0.000 26 r_work: 0.11545 shift mean: 0.000 shift max: 0.000 27 r_work: 0.11545 shift mean: 0.000 shift max: 0.000 28 r_work: 0.11545 shift mean: 0.000 shift max: 0.000 29 r_work: 0.11545 shift mean: 0.000 shift max: 0.000 30 r_work: 0.11545 shift mean: 0.000 shift max: 0.001 31 r_work: 0.11545 shift mean: 0.000 shift max: 0.001 32 r_work: 0.11546 shift mean: 0.000 shift max: 0.001 33 r_work: 0.11546 shift mean: 0.000 shift max: 0.001 34 r_work: 0.11546 shift mean: 0.000 shift max: 0.001 35 r_work: 0.11546 shift mean: 0.000 shift max: 0.002 36 r_work: 0.11545 shift mean: 0.000 shift max: 0.002 37 r_work: 0.11545 shift mean: 0.000 shift max: 0.002 38 r_work: 0.11546 shift mean: 0.000 shift max: 0.002 39 r_work: 0.11545 shift mean: 0.000 shift max: 0.003 40 r_work: 0.11545 shift mean: 0.000 shift max: 0.003 41 r_work: 0.11545 shift mean: 0.000 shift max: 0.003 42 r_work: 0.11545 shift mean: 0.000 shift max: 0.003 43 r_work: 0.11545 shift mean: 0.000 shift max: 0.003 44 r_work: 0.11545 shift mean: 0.000 shift max: 0.002 45 r_work: 0.11545 shift mean: 0.000 shift max: 0.003 46 r_work: 0.11545 shift mean: 0.000 shift max: 0.002 47 r_work: 0.11545 shift mean: 0.000 shift max: 0.002 48 r_work: 0.11544 shift mean: 0.000 shift max: 0.002 49 r_work: 0.11544 shift mean: 0.000 shift max: 0.002 50 r_work: 0.11544 shift mean: 0.000 shift max: 0.002 51 r_work: 0.11543 shift mean: 0.000 shift max: 0.003 52 4: Rw: 0.1154 Rf: 0.1442 Rf-Rw: 0.0287 bond: 0.030 angle: 2.26 clash: 6.7 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.90 cb: 0.91 shift start/prev: 0.103 0.006 n_fev: 52 At refinement end: Rw: 0.1154 Rf: 0.1442 Rf-Rw: 0.0287 bond: 0.030 angle: 2.26 clash: 6.7 rota: 0.92 rama: f: 94.02 o: 0.00 Z: 0.90 cb: 0.91 shift start/prev: 0.103 0.006 Best Rwork, Rfree (after refinement): 0.1154 0.1442 See 2PND_refined.pdb in pdb folder. =============================================================================== Job complete usr+sys time: 811.78 seconds wall clock time: 13 minutes 44.78 seconds (824.78 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)