Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4779266.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4779266.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4779266.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.49, per 1000 atoms: 0.37 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.690 distance_ideal: 2.720 ideal - model: 0.030 slack: 0.000 delta_slack: 0.030 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.715 distance_ideal: 2.710 ideal - model: -0.005 slack: 0.000 delta_slack: -0.005 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.11 Conformation dependent library (CDL) restraints added in 122.0 milliseconds Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 0.99: 449 0.99 - 1.22: 2623 1.22 - 1.45: 1429 1.45 - 1.68: 1370 1.68 - 1.90: 63 Bond restraints: 5934 Sorted by residual: bond pdb=" C VAL B 173 " pdb=" N GLY B 174 " ideal model delta sigma weight residual 1.325 1.514 -0.189 9.40e-03 1.13e+04 4.05e+02 bond pdb=" N ARG B 49 " pdb=" H ARG B 49 " ideal model delta sigma weight residual 0.860 1.243 -0.383 2.00e-02 2.50e+03 3.66e+02 bond pdb=" NH1 ARG A 149 " pdb="HH12 ARG A 149 " ideal model delta sigma weight residual 0.860 1.243 -0.383 2.00e-02 2.50e+03 3.66e+02 bond pdb=" NH1 ARG B 100 " pdb="HH12 ARG B 100 " ideal model delta sigma weight residual 0.860 1.241 -0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" CD1 LEU B 172 " pdb="HD11 LEU B 172 " ideal model delta sigma weight residual 0.970 1.337 -0.367 2.00e-02 2.50e+03 3.37e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 5488 4.03 - 8.05: 3539 8.05 - 12.08: 1421 12.08 - 16.10: 321 16.10 - 20.12: 41 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.45 138.39 -15.94 7.20e-01 1.93e+00 4.90e+02 angle pdb=" NE ARG A 83 " pdb=" CZ ARG A 83 " pdb=" NH2 ARG A 83 " ideal model delta sigma weight residual 119.20 137.81 -18.61 9.00e-01 1.23e+00 4.27e+02 angle pdb=" O PHE B 119 " pdb=" C PHE B 119 " pdb=" N PRO B 120 " ideal model delta sigma weight residual 121.34 135.90 -14.56 8.90e-01 1.26e+00 2.67e+02 angle pdb=" CA LEU A 59 " pdb=" C LEU A 59 " pdb=" O LEU A 59 " ideal model delta sigma weight residual 120.63 103.78 16.85 1.08e+00 8.57e-01 2.43e+02 angle pdb=" O VAL A 89 " pdb=" C VAL A 89 " pdb=" N GLU A 90 " ideal model delta sigma weight residual 121.91 106.68 15.23 9.80e-01 1.04e+00 2.42e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 1853 17.89 - 35.78: 136 35.78 - 53.68: 46 53.68 - 71.57: 12 71.57 - 89.46: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA VAL A 32 " pdb=" C VAL A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta harmonic sigma weight residual 180.00 151.91 28.09 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 152.78 27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N ILE A 70 " pdb=" CA ILE A 70 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 238 0.252 - 0.505: 166 0.505 - 0.757: 72 0.757 - 1.009: 12 1.009 - 1.261: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.33 -1.26 2.00e-01 2.50e+01 3.98e+01 chirality pdb=" CA ALA B 44 " pdb=" N ALA B 44 " pdb=" C ALA B 44 " pdb=" CB ALA B 44 " both_signs ideal model delta sigma weight residual False 2.48 3.65 -1.16 2.00e-01 2.50e+01 3.38e+01 chirality pdb=" CA LEU B 53 " pdb=" N LEU B 53 " pdb=" C LEU B 53 " pdb=" CB LEU B 53 " both_signs ideal model delta sigma weight residual False 2.51 3.63 -1.12 2.00e-01 2.50e+01 3.13e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.102 2.00e-02 2.50e+03 7.52e-02 1.70e+02 pdb=" CG PHE A 119 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.085 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.122 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " 0.055 2.00e-02 2.50e+03 6.50e-02 1.69e+02 pdb=" CG TRP B 146 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.086 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.124 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.051 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.051 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.062 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.064 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.050 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.031 2.00e-02 2.50e+03 6.31e-02 1.59e+02 pdb=" CG TRP A 146 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.067 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.039 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.082 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.057 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.138 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.081 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.062 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.59: 21 1.59 - 2.34: 2187 2.34 - 3.10: 22080 3.10 - 3.85: 33112 3.85 - 4.60: 52851 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110251 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.840 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.890 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.052 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.062 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.180 2.620 ... (remaining 110246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 12 15.96 2 Mg 2 11.97 3 O 1357 7.97 2 N 488 6.98 3 C 1850 5.99 3 H 2984 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6693 n_use_u_iso = 3419 n_use_u_aniso = 3274 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 6693 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6693 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3419 aniso = 3274) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (1426 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_4779266_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2035 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.296281 | | target function (ml) not normalized (work): 804749.367751 | | target function (ml) not normalized (free): 16487.683068 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2130 0.1936 6.6853 6.3113| | 2: 2.94 - 2.33 1.00 7339 128 0.1630 0.1609 5.5298 5.5859| | 3: 2.33 - 2.04 0.96 6939 150 0.1640 0.1373 5.1406 5.0198| | 4: 2.04 - 1.85 1.00 7170 155 0.1741 0.1518 4.9546 4.9841| | 5: 1.85 - 1.72 0.99 7113 159 0.1915 0.1784 4.7908 4.8538| | 6: 1.72 - 1.62 0.99 7102 142 0.1979 0.1906 4.6572 4.6637| | 7: 1.62 - 1.54 0.99 7104 148 0.2022 0.1604 4.5574 4.5011| | 8: 1.54 - 1.47 0.96 6798 152 0.2068 0.2199 4.4789 4.4984| | 9: 1.47 - 1.41 0.98 6938 155 0.2089 0.2142 4.3898 4.4539| | 10: 1.41 - 1.36 0.99 7022 150 0.2134 0.2061 4.3027 4.3571| | 11: 1.36 - 1.32 0.99 6997 151 0.2076 0.2000 4.2094 4.2113| | 12: 1.32 - 1.28 0.98 6976 149 0.2059 0.1932 4.1609 4.1853| | 13: 1.28 - 1.25 0.98 6907 166 0.2046 0.2251 4.126 4.2095| | 14: 1.25 - 1.22 0.98 7015 113 0.2095 0.2232 4.0776 4.2433| | 15: 1.22 - 1.19 0.98 6957 137 0.2098 0.2068 4.047 4.0839| | 16: 1.19 - 1.17 0.93 6604 132 0.2165 0.2274 4.0174 4.0937| | 17: 1.17 - 1.14 0.98 6941 135 0.2187 0.1866 3.9525 3.9691| | 18: 1.14 - 1.12 0.98 6875 142 0.2224 0.2413 3.9177 3.9453| | 19: 1.12 - 1.10 0.97 6949 106 0.2289 0.2345 3.8731 3.9331| | 20: 1.10 - 1.08 0.97 6884 147 0.2323 0.2381 3.8212 3.8811| | 21: 1.08 - 1.07 0.97 6852 152 0.2429 0.2532 3.793 3.7498| | 22: 1.07 - 1.05 0.97 6838 135 0.2540 0.2484 3.7471 3.7577| | 23: 1.05 - 1.03 0.97 6829 159 0.2694 0.2496 3.7278 3.7831| | 24: 1.03 - 1.02 0.96 6785 133 0.2865 0.2904 3.6993 3.7804| | 25: 1.02 - 1.01 0.93 6552 130 0.3064 0.2818 3.6738 3.6785| | 26: 1.01 - 0.99 0.96 6767 158 0.3189 0.3278 3.6249 3.6041| | 27: 0.99 - 0.98 0.94 6648 131 0.3391 0.3066 3.6327 3.5683| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.43 0.91 0.97 35245.52| | 2: 2.94 - 2.33 7339 128 0.86 20.76 1.08 1.03 14561.46| | 3: 2.33 - 2.04 6939 150 0.94 11.28 1.11 1.07 3607.52| | 4: 2.04 - 1.85 7170 155 0.93 12.36 1.11 1.07 2442.77| | 5: 1.85 - 1.72 7113 159 0.92 14.72 1.12 1.08 1887.83| | 6: 1.72 - 1.62 7102 142 0.91 16.01 1.11 1.07 1490.87| | 7: 1.62 - 1.54 7104 148 0.90 16.87 1.11 1.07 1227.31| | 8: 1.54 - 1.47 6798 152 0.89 17.52 1.11 1.06 1066.31| | 9: 1.47 - 1.41 6938 155 0.89 18.50 1.10 1.06 928.24| | 10: 1.41 - 1.36 7022 150 0.87 19.81 1.09 1.05 827.67| | 11: 1.36 - 1.32 6997 151 0.88 19.42 1.09 1.03 692.54| | 12: 1.32 - 1.28 6976 149 0.88 19.67 1.08 1.02 626.80| | 13: 1.28 - 1.25 6907 166 0.88 19.68 1.07 1.02 588.50| | 14: 1.25 - 1.22 7015 113 0.86 21.25 1.08 1.02 592.20| | 15: 1.22 - 1.19 6957 137 0.86 21.68 1.08 1.03 573.41| | 16: 1.19 - 1.17 6604 132 0.86 21.29 1.08 1.02 520.74| | 17: 1.17 - 1.14 6941 135 0.86 21.60 1.09 1.02 455.46| | 18: 1.14 - 1.12 6875 142 0.86 21.13 1.08 1.02 404.52| | 19: 1.12 - 1.10 6949 106 0.86 21.67 1.08 1.02 373.38| | 20: 1.10 - 1.08 6884 147 0.85 22.16 1.06 1.01 342.55| | 21: 1.08 - 1.07 6852 152 0.85 22.88 1.06 1.01 320.82| | 22: 1.07 - 1.05 6838 135 0.83 24.59 1.05 1.00 312.55| | 23: 1.05 - 1.03 6829 159 0.81 26.44 1.05 0.98 313.82| | 24: 1.03 - 1.02 6785 133 0.79 28.49 1.04 0.97 310.95| | 25: 1.02 - 1.01 6552 130 0.78 29.51 1.02 0.94 291.30| | 26: 1.01 - 0.99 6767 158 0.77 30.69 1.02 0.93 272.35| | 27: 0.99 - 0.98 6648 131 0.77 30.81 1.03 0.93 258.36| |alpha: min = 0.93 max = 1.08 mean = 1.02| |beta: min = 258.36 max = 35245.52 mean = 2737.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.08| |phase err.(test): min = 0.00 max = 89.93 mean = 21.02| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.231 2950 Z= 5.477 Angle : 5.253 18.606 4018 Z= 3.762 Chirality : 0.375 1.261 492 Planarity : 0.034 0.147 512 Dihedral : 13.013 89.460 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.92 % Favored : 94.82 % Rotamer: Outliers : 0.65 % Allowed : 3.87 % Favored : 95.48 % Cbeta Deviations : 30.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.37), residues: 386 helix: -2.67 (0.30), residues: 144 sheet: -1.57 (0.47), residues: 86 loop : -0.24 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.103 0.020 ARG B 97 TYR 0.111 0.042 TYR A 194 PHE 0.107 0.040 PHE B 164 TRP 0.111 0.040 TRP B 146 HIS 0.100 0.038 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2035 r_free= 0.1933 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.296281 | | target function (ml) not normalized (work): 804749.367751 | | target function (ml) not normalized (free): 16487.683068 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2032 0.2035 0.1933 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2032 0.2035 0.1933 n_refl.: 191155 remove outliers: r(all,work,free)=0.2032 0.2035 0.1933 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2032 0.2035 0.1934 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1801 0.1799 0.1872 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1797 0.1872 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4068 402.814 292.455 0.436 0.911 0.303 13.296-10.522 99.01 99 1 0.2518 528.187 519.831 0.790 0.912 0.256 10.503-8.327 99.45 178 3 0.2524 565.118 556.136 0.972 0.912 0.233 8.318-6.595 100.00 360 8 0.2483 414.736 404.236 0.969 0.912 0.165 6.588-5.215 100.00 711 7 0.2280 381.101 366.197 0.956 0.912 0.150 5.214-4.128 98.38 1367 28 0.1493 557.435 549.165 1.073 0.912 0.090 4.126-3.266 94.74 2603 46 0.1324 508.132 499.669 1.145 0.913 0.030 3.266-2.585 99.86 5447 97 0.1447 342.774 337.760 1.120 0.912 0.014 2.585-2.046 97.45 10613 204 0.1402 258.603 254.356 1.125 0.911 0.000 2.046-1.619 99.39 21536 464 0.1605 153.054 149.821 1.145 0.910 0.000 1.619-1.281 98.00 42464 925 0.1918 82.395 80.253 1.130 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2322 44.203 41.677 1.113 0.903 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0054 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1872 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1797 r_free=0.1872 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.291898 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.446070 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1271 0.1507 0.0236 0.039 1.2 10.5 0.0 0.3 0 11.146 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.07 2.36 1.118 13.114 575.446 0.018 12.98 15.74 2.76 1.268 13.377 575.446 0.017 Individual atomic B min max mean iso aniso Overall: 5.19 73.05 15.08 1.41 435 3274 Protein: 5.19 40.40 11.03 1.41 0 2902 Water: 6.35 73.05 29.67 N/A 435 370 Other: 16.12 30.01 23.06 N/A 0 2 Chain A: 5.35 60.20 13.08 N/A 0 1626 Chain B: 5.19 73.05 12.81 N/A 0 1648 Chain S: 11.47 64.23 31.13 N/A 435 0 Histogram: Values Number of atoms 5.19 - 11.97 2168 11.97 - 18.76 633 18.76 - 25.54 313 25.54 - 32.33 261 32.33 - 39.12 158 39.12 - 45.90 106 45.90 - 52.69 45 52.69 - 59.47 19 59.47 - 66.26 5 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1575 r_work=0.1298 r_free=0.1570 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1570 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015583 | | target function (ls_wunit_k1) not normalized (work): 2918.715557 | | target function (ls_wunit_k1) not normalized (free): 117.614089 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1556 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1634 n_refl.: 191139 remove outliers: r(all,work,free)=0.1470 0.1467 0.1634 n_refl.: 191139 overall B=0.16 to atoms: r(all,work,free)=0.1493 0.1490 0.1645 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1275 0.1549 n_refl.: 191139 remove outliers: r(all,work,free)=0.1281 0.1275 0.1548 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3614 402.814 378.734 0.472 0.997 0.281 13.296-10.522 99.01 99 1 0.2088 528.187 522.439 0.718 0.999 0.255 10.503-8.327 99.45 178 3 0.1757 565.118 561.637 0.856 0.999 0.203 8.318-6.595 100.00 360 8 0.1700 414.736 412.482 0.877 0.998 0.155 6.588-5.215 100.00 711 7 0.1524 381.101 373.706 0.857 0.999 0.150 5.214-4.128 98.38 1367 28 0.0900 557.435 554.922 0.942 0.999 0.059 4.126-3.266 94.74 2603 46 0.0827 508.132 504.289 1.008 1.000 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.315 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.323 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1092 153.054 151.370 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.403 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.170 0.989 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0366 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1548 | n_water=805 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1279 r_free=0.1551 | n_water=795 | time (s): 97.320 (total time: 99.840) Filter (q & B) r_work=0.1280 r_free=0.1550 | n_water=790 | time (s): 4.330 (total time: 104.170) Compute maps r_work=0.1280 r_free=0.1550 | n_water=790 | time (s): 2.020 (total time: 106.190) Filter (map) r_work=0.1307 r_free=0.1536 | n_water=650 | time (s): 4.840 (total time: 111.030) Find peaks r_work=0.1307 r_free=0.1536 | n_water=650 | time (s): 0.640 (total time: 111.670) Add new water r_work=0.1329 r_free=0.1565 | n_water=942 | time (s): 5.030 (total time: 116.700) Refine new water occ: r_work=0.1288 r_free=0.1524 adp: r_work=0.1276 r_free=0.1518 occ: r_work=0.1278 r_free=0.1516 adp: r_work=0.1272 r_free=0.1513 occ: r_work=0.1273 r_free=0.1512 adp: r_work=0.1273 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1273 r_free=0.1512 r_work=0.1273 r_free=0.1512 | n_water=942 | time (s): 94.220 (total time: 210.920) Filter (q & B) r_work=0.1276 r_free=0.1513 | n_water=880 | time (s): 4.380 (total time: 215.300) Filter (dist only) r_work=0.1276 r_free=0.1513 | n_water=879 | time (s): 109.900 (total time: 325.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.849920 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 578.404258 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1261 0.1527 0.0267 0.041 1.1 18.4 0.0 0.0 0 11.425 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.61 15.27 2.67 2.053 15.014 578.404 0.015 12.35 15.13 2.78 2.437 15.216 578.404 0.014 Individual atomic B min max mean iso aniso Overall: 5.32 70.28 16.27 1.21 511 3272 Protein: 5.32 40.97 10.99 1.21 0 2902 Water: 6.58 70.28 33.68 N/A 511 368 Other: 16.24 31.83 24.03 N/A 0 2 Chain A: 5.52 55.80 13.05 N/A 0 1624 Chain B: 5.32 68.21 12.87 N/A 0 1648 Chain S: 12.79 70.28 37.48 N/A 511 0 Histogram: Values Number of atoms 5.32 - 11.81 2095 11.81 - 18.31 701 18.31 - 24.81 252 24.81 - 31.30 212 31.30 - 37.80 176 37.80 - 44.29 170 44.29 - 50.79 103 50.79 - 57.29 45 57.29 - 63.78 21 63.78 - 70.28 8 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1513 r_work=0.1236 r_free=0.1514 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1514 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1511 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1511 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013597 | | target function (ls_wunit_k1) not normalized (work): 2546.716417 | | target function (ls_wunit_k1) not normalized (free): 103.898491 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1511 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1437 0.1617 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1437 0.1617 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1437 0.1434 0.1615 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1236 0.1520 n_refl.: 191138 remove outliers: r(all,work,free)=0.1242 0.1236 0.1520 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3261 402.814 376.735 0.495 0.962 0.275 13.296-10.522 99.01 99 1 0.1912 528.187 521.004 0.765 0.963 0.250 10.503-8.327 99.45 178 3 0.1457 565.118 566.751 0.919 0.963 0.173 8.318-6.595 100.00 360 8 0.1549 414.736 414.919 0.937 0.963 0.167 6.588-5.215 100.00 711 7 0.1353 381.101 376.577 0.911 0.963 0.137 5.214-4.128 98.38 1367 28 0.0834 557.435 556.138 0.995 0.963 0.090 4.126-3.266 94.74 2603 46 0.0772 508.132 505.577 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0863 342.774 341.360 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0904 258.603 256.769 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1050 153.054 151.601 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.336 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.211 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0555 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1519 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1519 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1519 | n_water=879 | time (s): 3.490 (total time: 3.490) Filter (dist) r_work=0.1238 r_free=0.1522 | n_water=873 | time (s): 124.760 (total time: 128.250) Filter (q & B) r_work=0.1238 r_free=0.1522 | n_water=871 | time (s): 4.310 (total time: 132.560) Compute maps r_work=0.1238 r_free=0.1522 | n_water=871 | time (s): 2.520 (total time: 135.080) Filter (map) r_work=0.1277 r_free=0.1518 | n_water=685 | time (s): 4.780 (total time: 139.860) Find peaks r_work=0.1277 r_free=0.1518 | n_water=685 | time (s): 0.770 (total time: 140.630) Add new water r_work=0.1300 r_free=0.1555 | n_water=991 | time (s): 5.140 (total time: 145.770) Refine new water occ: r_work=0.1256 r_free=0.1514 adp: r_work=0.1256 r_free=0.1514 occ: r_work=0.1252 r_free=0.1511 adp: r_work=0.1252 r_free=0.1511 occ: r_work=0.1249 r_free=0.1510 adp: r_work=0.1249 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1249 r_free=0.1509 r_work=0.1249 r_free=0.1509 | n_water=991 | time (s): 290.910 (total time: 436.680) Filter (q & B) r_work=0.1252 r_free=0.1516 | n_water=866 | time (s): 5.680 (total time: 442.360) Filter (dist only) r_work=0.1253 r_free=0.1516 | n_water=865 | time (s): 115.320 (total time: 557.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.718097 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.359250 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1240 0.1440 0.0199 0.034 1.1 8.0 0.0 0.0 0 0.859 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.40 1.99 1.938 14.589 16.359 3.938 12.32 14.02 1.70 2.178 14.510 16.359 3.897 Individual atomic B min max mean iso aniso Overall: 5.53 67.92 15.29 1.08 498 3271 Protein: 5.53 37.58 10.79 1.08 0 2902 Water: 6.70 67.92 30.37 N/A 498 367 Other: 14.19 28.46 21.32 N/A 0 2 Chain A: 5.56 55.17 12.85 N/A 0 1624 Chain B: 5.53 67.92 12.63 N/A 0 1647 Chain S: 12.20 63.15 32.05 N/A 498 0 Histogram: Values Number of atoms 5.53 - 11.77 2126 11.77 - 18.00 687 18.00 - 24.24 295 24.24 - 30.48 226 30.48 - 36.72 181 36.72 - 42.96 141 42.96 - 49.20 78 49.20 - 55.44 24 55.44 - 61.68 9 61.68 - 67.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1402 r_work=0.1233 r_free=0.1403 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1403 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1395 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891770 | | target function (ml) not normalized (work): 728916.777035 | | target function (ml) not normalized (free): 15222.593427 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1395 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1446 0.1445 0.1497 n_refl.: 191138 remove outliers: r(all,work,free)=0.1446 0.1445 0.1497 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1439 0.1493 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1391 n_refl.: 191138 remove outliers: r(all,work,free)=0.1227 0.1224 0.1391 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3798 398.008 362.730 0.429 0.946 0.256 13.296-10.522 98.02 98 1 0.2349 528.900 504.483 0.711 0.948 0.230 10.503-8.327 98.90 177 3 0.1978 557.261 556.874 0.882 0.948 0.195 8.318-6.595 100.00 360 8 0.2098 414.736 409.662 0.897 0.947 0.138 6.588-5.215 100.00 711 7 0.1831 381.101 370.798 0.883 0.947 0.113 5.214-4.128 98.38 1367 28 0.1170 557.435 552.049 0.973 0.947 0.080 4.126-3.266 94.74 2603 46 0.1093 508.132 501.257 1.032 0.948 0.009 3.266-2.585 99.86 5447 97 0.1077 342.774 339.253 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0966 258.603 255.798 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.431 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.494 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.321 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1003 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1391 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1391 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1391 | n_water=865 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1224 r_free=0.1391 | n_water=865 | time (s): 101.210 (total time: 103.680) Filter (q & B) r_work=0.1225 r_free=0.1391 | n_water=849 | time (s): 5.590 (total time: 109.270) Compute maps r_work=0.1225 r_free=0.1391 | n_water=849 | time (s): 2.020 (total time: 111.290) Filter (map) r_work=0.1243 r_free=0.1396 | n_water=722 | time (s): 5.420 (total time: 116.710) Find peaks r_work=0.1243 r_free=0.1396 | n_water=722 | time (s): 0.870 (total time: 117.580) Add new water r_work=0.1258 r_free=0.1413 | n_water=962 | time (s): 5.460 (total time: 123.040) Refine new water occ: r_work=0.1212 r_free=0.1379 adp: r_work=0.1204 r_free=0.1375 occ: r_work=0.1202 r_free=0.1375 adp: r_work=0.1202 r_free=0.1374 occ: r_work=0.1202 r_free=0.1375 adp: r_work=0.1201 r_free=0.1375 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1375 r_work=0.1201 r_free=0.1375 | n_water=962 | time (s): 275.800 (total time: 398.840) Filter (q & B) r_work=0.1207 r_free=0.1381 | n_water=856 | time (s): 4.550 (total time: 403.390) Filter (dist only) r_work=0.1207 r_free=0.1382 | n_water=854 | time (s): 106.430 (total time: 509.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.562155 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.864305 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1385 0.0177 0.036 1.1 6.3 0.0 0.0 0 0.781 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.85 1.77 1.848 14.232 15.864 3.876 12.04 13.79 1.75 2.005 14.173 15.864 3.867 Individual atomic B min max mean iso aniso Overall: 5.49 67.47 14.94 1.00 487 3271 Protein: 5.49 33.93 10.67 1.00 0 2902 Water: 5.82 67.47 29.42 N/A 487 367 Other: 13.88 27.18 20.53 N/A 0 2 Chain A: 5.57 53.97 12.68 N/A 0 1624 Chain B: 5.49 67.47 12.49 N/A 0 1647 Chain S: 5.82 63.20 30.75 N/A 487 0 Histogram: Values Number of atoms 5.49 - 11.69 2120 11.69 - 17.89 726 17.89 - 24.08 291 24.08 - 30.28 232 30.28 - 36.48 158 36.48 - 42.68 132 42.68 - 48.87 64 48.87 - 55.07 24 55.07 - 61.27 9 61.27 - 67.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1379 r_work=0.1204 r_free=0.1380 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1380 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1378 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864781 | | target function (ml) not normalized (work): 723850.259337 | | target function (ml) not normalized (free): 15139.877280 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1378 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1431 0.1430 0.1477 n_refl.: 191135 remove outliers: r(all,work,free)=0.1431 0.1430 0.1477 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1423 0.1423 0.1472 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1199 0.1375 n_refl.: 191135 remove outliers: r(all,work,free)=0.1202 0.1199 0.1375 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3721 360.293 327.467 0.414 0.948 0.248 13.296-10.522 97.03 97 1 0.2469 481.055 454.555 0.695 0.950 0.188 10.503-8.327 98.35 176 3 0.2109 502.649 496.258 0.865 0.950 0.163 8.318-6.595 100.00 360 8 0.2236 375.436 370.717 0.888 0.949 0.125 6.588-5.215 100.00 711 7 0.1902 344.988 335.403 0.881 0.950 0.120 5.214-4.128 98.38 1367 28 0.1208 504.613 498.870 0.971 0.950 0.080 4.126-3.266 94.74 2603 46 0.1134 459.982 453.232 1.032 0.950 0.005 3.266-2.585 99.86 5447 97 0.1085 310.293 307.093 1.019 0.949 0.000 2.585-2.046 97.45 10613 204 0.0942 234.098 231.581 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0918 138.551 137.236 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0986 74.588 73.874 1.055 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1658 40.013 38.350 1.045 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1177 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1375 | n_water=854 | time (s): 3.310 (total time: 3.310) Filter (dist) r_work=0.1199 r_free=0.1374 | n_water=853 | time (s): 106.340 (total time: 109.650) Filter (q & B) r_work=0.1199 r_free=0.1373 | n_water=844 | time (s): 4.530 (total time: 114.180) Compute maps r_work=0.1199 r_free=0.1373 | n_water=844 | time (s): 2.070 (total time: 116.250) Filter (map) r_work=0.1223 r_free=0.1372 | n_water=721 | time (s): 5.490 (total time: 121.740) Find peaks r_work=0.1223 r_free=0.1372 | n_water=721 | time (s): 0.730 (total time: 122.470) Add new water r_work=0.1237 r_free=0.1388 | n_water=962 | time (s): 4.400 (total time: 126.870) Refine new water occ: r_work=0.1199 r_free=0.1347 adp: r_work=0.1199 r_free=0.1348 occ: r_work=0.1196 r_free=0.1345 adp: r_work=0.1196 r_free=0.1345 occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1193 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1343 r_work=0.1193 r_free=0.1343 | n_water=962 | time (s): 261.310 (total time: 388.180) Filter (q & B) r_work=0.1197 r_free=0.1351 | n_water=882 | time (s): 5.000 (total time: 393.180) Filter (dist only) r_work=0.1197 r_free=0.1350 | n_water=881 | time (s): 112.870 (total time: 506.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.583093 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.623386 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1355 0.0156 0.035 1.1 7.2 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.55 1.56 1.795 14.147 15.623 3.763 12.02 13.56 1.54 1.982 14.089 15.623 3.760 Individual atomic B min max mean iso aniso Overall: 5.55 66.40 14.91 0.93 514 3271 Protein: 5.55 30.51 10.54 0.93 0 2902 Water: 5.93 66.40 29.32 N/A 514 367 Other: 13.89 23.84 18.86 N/A 0 2 Chain A: 5.64 50.86 12.49 N/A 0 1624 Chain B: 5.55 66.40 12.33 N/A 0 1647 Chain S: 5.93 63.43 30.83 N/A 514 0 Histogram: Values Number of atoms 5.55 - 11.64 2114 11.64 - 17.72 762 17.72 - 23.81 284 23.81 - 29.89 206 29.89 - 35.98 182 35.98 - 42.06 131 42.06 - 48.15 72 48.15 - 54.23 24 54.23 - 60.32 8 60.32 - 66.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1356 r_work=0.1202 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1356 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1353 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758353 | | target function (ml) not normalized (work): 703909.497768 | | target function (ml) not normalized (free): 14728.891217 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1353 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1424 0.1424 0.1475 n_refl.: 191133 remove outliers: r(all,work,free)=0.1424 0.1424 0.1475 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1416 0.1415 0.1470 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1352 n_refl.: 191133 remove outliers: r(all,work,free)=0.1201 0.1198 0.1352 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3763 357.003 318.106 0.387 0.946 0.214 13.296-10.522 96.04 96 1 0.2390 480.292 456.187 0.695 0.948 0.153 10.503-8.327 98.35 176 3 0.2168 502.649 495.108 0.863 0.948 0.130 8.318-6.595 100.00 360 8 0.2169 375.436 371.758 0.886 0.948 0.105 6.588-5.215 100.00 711 7 0.1902 344.988 335.777 0.885 0.948 0.100 5.214-4.128 98.38 1367 28 0.1206 504.613 498.780 0.973 0.948 0.060 4.126-3.266 94.74 2603 46 0.1152 459.982 453.005 1.035 0.949 0.005 3.266-2.585 99.86 5447 97 0.1100 310.293 307.023 1.022 0.948 0.000 2.585-2.046 97.45 10613 204 0.0952 234.098 231.604 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0914 138.551 137.279 1.056 0.948 0.000 1.619-1.281 98.00 42464 925 0.0974 74.588 73.893 1.053 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.013 38.347 1.038 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1331 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1352 | n_water=881 | time (s): 2.800 (total time: 2.800) Filter (dist) r_work=0.1198 r_free=0.1352 | n_water=881 | time (s): 109.670 (total time: 112.470) Filter (q & B) r_work=0.1199 r_free=0.1352 | n_water=872 | time (s): 4.060 (total time: 116.530) Compute maps r_work=0.1199 r_free=0.1352 | n_water=872 | time (s): 2.010 (total time: 118.540) Filter (map) r_work=0.1220 r_free=0.1365 | n_water=752 | time (s): 5.220 (total time: 123.760) Find peaks r_work=0.1220 r_free=0.1365 | n_water=752 | time (s): 0.740 (total time: 124.500) Add new water r_work=0.1230 r_free=0.1378 | n_water=965 | time (s): 4.410 (total time: 128.910) Refine new water occ: r_work=0.1196 r_free=0.1352 adp: r_work=0.1196 r_free=0.1353 occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1194 r_free=0.1351 occ: r_work=0.1192 r_free=0.1348 adp: r_work=0.1192 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1349 r_work=0.1192 r_free=0.1349 | n_water=965 | time (s): 334.750 (total time: 463.660) Filter (q & B) r_work=0.1196 r_free=0.1352 | n_water=891 | time (s): 4.720 (total time: 468.380) Filter (dist only) r_work=0.1196 r_free=0.1351 | n_water=889 | time (s): 112.440 (total time: 580.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.574315 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.822048 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1357 0.0158 0.037 1.1 6.6 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.57 1.58 1.739 13.972 14.822 3.759 12.03 13.59 1.56 1.812 13.944 14.822 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 65.19 14.81 0.90 522 3271 Protein: 5.57 28.97 10.46 0.90 0 2902 Water: 6.04 65.19 29.02 N/A 522 367 Other: 13.83 22.21 18.02 N/A 0 2 Chain A: 5.61 50.34 12.38 N/A 0 1624 Chain B: 5.57 65.19 12.22 N/A 0 1647 Chain S: 6.04 63.54 30.56 N/A 522 0 Histogram: Values Number of atoms 5.57 - 11.54 2095 11.54 - 17.50 785 17.50 - 23.46 285 23.46 - 29.42 204 29.42 - 35.38 182 35.38 - 41.34 128 41.34 - 47.30 70 47.30 - 53.26 34 53.26 - 59.23 6 59.23 - 65.19 4 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1359 r_work=0.1203 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757441 | | target function (ml) not normalized (work): 703727.311934 | | target function (ml) not normalized (free): 14733.896077 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1358 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1406 0.1405 0.1481 n_refl.: 191130 remove outliers: r(all,work,free)=0.1406 0.1405 0.1481 n_refl.: 191130 overall B=-0.22 to atoms: r(all,work,free)=0.1369 0.1368 0.1459 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3833 357.003 320.680 0.383 0.952 0.197 13.296-10.522 96.04 96 1 0.2371 480.292 461.585 0.714 0.953 0.148 10.503-8.327 98.35 176 3 0.2177 502.649 494.966 0.878 0.954 0.127 8.318-6.595 100.00 360 8 0.2153 375.436 371.822 0.905 0.953 0.103 6.588-5.215 100.00 711 7 0.1909 344.988 335.638 0.901 0.953 0.083 5.214-4.128 98.38 1367 28 0.1215 504.613 498.830 0.994 0.954 0.060 4.126-3.266 94.74 2603 46 0.1161 459.982 452.860 1.056 0.954 0.009 3.266-2.585 99.86 5447 97 0.1115 310.293 306.947 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0955 234.098 231.577 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0913 138.551 137.245 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0968 74.588 73.891 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.013 38.343 1.026 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0493 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1358 | n_water=889 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1199 r_free=0.1359 | n_water=888 | time (s): 109.390 (total time: 111.690) Filter (q & B) r_work=0.1200 r_free=0.1357 | n_water=879 | time (s): 4.250 (total time: 115.940) Compute maps r_work=0.1200 r_free=0.1357 | n_water=879 | time (s): 2.120 (total time: 118.060) Filter (map) r_work=0.1221 r_free=0.1360 | n_water=764 | time (s): 5.600 (total time: 123.660) Find peaks r_work=0.1221 r_free=0.1360 | n_water=764 | time (s): 0.770 (total time: 124.430) Add new water r_work=0.1230 r_free=0.1369 | n_water=957 | time (s): 4.090 (total time: 128.520) Refine new water occ: r_work=0.1198 r_free=0.1344 adp: r_work=0.1198 r_free=0.1344 occ: r_work=0.1197 r_free=0.1343 adp: r_work=0.1197 r_free=0.1344 occ: r_work=0.1195 r_free=0.1343 adp: r_work=0.1195 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1344 r_work=0.1195 r_free=0.1344 | n_water=957 | time (s): 263.730 (total time: 392.250) Filter (q & B) r_work=0.1199 r_free=0.1348 | n_water=887 | time (s): 4.920 (total time: 397.170) Filter (dist only) r_work=0.1199 r_free=0.1347 | n_water=886 | time (s): 109.970 (total time: 507.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567173 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.645976 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1353 0.0150 0.037 1.1 5.6 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.53 1.50 1.710 13.681 14.646 3.759 12.04 13.55 1.51 1.736 13.664 14.646 3.757 Individual atomic B min max mean iso aniso Overall: 5.41 64.03 14.55 0.88 520 3270 Protein: 5.41 28.29 10.24 0.88 0 2902 Water: 5.78 64.03 28.66 N/A 520 366 Other: 13.65 22.12 17.88 N/A 0 2 Chain A: 5.47 49.81 12.11 N/A 0 1624 Chain B: 5.41 64.03 11.95 N/A 0 1646 Chain S: 5.78 63.41 30.38 N/A 520 0 Histogram: Values Number of atoms 5.41 - 11.27 2076 11.27 - 17.13 807 17.13 - 23.00 272 23.00 - 28.86 204 28.86 - 34.72 181 34.72 - 40.58 126 40.58 - 46.45 79 46.45 - 52.31 33 52.31 - 58.17 8 58.17 - 64.03 4 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1355 r_work=0.1204 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1356 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1353 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756071 | | target function (ml) not normalized (work): 703470.830249 | | target function (ml) not normalized (free): 14728.519725 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1203 0.1353 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1379 0.1378 0.1453 n_refl.: 191130 remove outliers: r(all,work,free)=0.1379 0.1378 0.1453 n_refl.: 191130 overall B=0.05 to atoms: r(all,work,free)=0.1386 0.1385 0.1457 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1341 n_refl.: 191130 remove outliers: r(all,work,free)=0.1196 0.1193 0.1341 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3782 348.434 318.154 0.374 0.976 0.193 13.296-10.522 96.04 96 1 0.2344 480.292 462.019 0.699 0.977 0.139 10.503-8.327 98.35 176 3 0.2215 502.649 494.264 0.862 0.978 0.116 8.318-6.595 100.00 360 8 0.2194 375.436 370.605 0.889 0.977 0.101 6.588-5.215 100.00 711 7 0.1930 344.988 335.033 0.886 0.978 0.087 5.214-4.128 98.38 1367 28 0.1236 504.613 498.211 0.979 0.979 0.049 4.126-3.266 94.74 2603 46 0.1170 459.982 452.222 1.040 0.980 0.009 3.266-2.585 99.86 5447 97 0.1121 310.293 306.582 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0959 234.098 231.450 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0909 138.551 137.151 1.047 0.984 0.000 1.619-1.281 98.00 42464 925 0.0949 74.588 73.921 1.036 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.013 38.314 1.002 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0599 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1341 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1341 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1341 | n_water=886 | time (s): 3.360 (total time: 3.360) Filter (dist) r_work=0.1193 r_free=0.1342 | n_water=885 | time (s): 111.140 (total time: 114.500) Filter (q & B) r_work=0.1193 r_free=0.1341 | n_water=877 | time (s): 5.370 (total time: 119.870) Compute maps r_work=0.1193 r_free=0.1341 | n_water=877 | time (s): 1.760 (total time: 121.630) Filter (map) r_work=0.1214 r_free=0.1353 | n_water=765 | time (s): 4.980 (total time: 126.610) Find peaks r_work=0.1214 r_free=0.1353 | n_water=765 | time (s): 0.680 (total time: 127.290) Add new water r_work=0.1223 r_free=0.1365 | n_water=970 | time (s): 4.480 (total time: 131.770) Refine new water occ: r_work=0.1189 r_free=0.1332 adp: r_work=0.1189 r_free=0.1332 occ: r_work=0.1187 r_free=0.1331 adp: r_work=0.1187 r_free=0.1332 occ: r_work=0.1186 r_free=0.1331 adp: r_work=0.1186 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1332 r_work=0.1186 r_free=0.1332 | n_water=970 | time (s): 281.490 (total time: 413.260) Filter (q & B) r_work=0.1190 r_free=0.1339 | n_water=891 | time (s): 4.610 (total time: 417.870) Filter (dist only) r_work=0.1191 r_free=0.1338 | n_water=890 | time (s): 114.770 (total time: 532.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.503061 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.259631 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1343 0.0148 0.038 1.1 6.0 0.0 0.3 0 0.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.43 1.48 1.674 13.703 14.260 3.755 11.95 13.45 1.49 1.675 13.699 14.260 3.754 Individual atomic B min max mean iso aniso Overall: 5.45 63.74 14.61 0.87 524 3270 Protein: 5.45 28.23 10.31 0.87 0 2902 Water: 5.93 63.74 28.64 N/A 524 366 Other: 13.71 22.11 17.91 N/A 0 2 Chain A: 5.57 49.78 12.15 N/A 0 1624 Chain B: 5.45 63.74 12.00 N/A 0 1646 Chain S: 5.93 63.51 30.45 N/A 524 0 Histogram: Values Number of atoms 5.45 - 11.28 2061 11.28 - 17.11 822 17.11 - 22.93 272 22.93 - 28.76 203 28.76 - 34.59 185 34.59 - 40.42 126 40.42 - 46.25 79 46.25 - 52.08 33 52.08 - 57.91 9 57.91 - 63.74 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1345 r_work=0.1196 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1345 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1346 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753538 | | target function (ml) not normalized (work): 702992.653338 | | target function (ml) not normalized (free): 14721.395601 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1346 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1393 0.1392 0.1463 n_refl.: 191129 remove outliers: r(all,work,free)=0.1393 0.1392 0.1463 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1396 0.1395 0.1464 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1346 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1193 0.1346 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3831 348.434 309.119 0.387 0.911 0.187 13.296-10.522 95.05 95 1 0.2275 479.395 455.421 0.747 0.912 0.134 10.503-8.327 98.35 176 3 0.2213 502.649 494.746 0.920 0.913 0.108 8.315-6.595 100.00 359 8 0.2175 374.491 370.635 0.948 0.913 0.093 6.588-5.215 100.00 711 7 0.1943 344.988 334.958 0.947 0.913 0.080 5.214-4.128 98.38 1367 28 0.1235 504.613 498.265 1.047 0.914 0.049 4.126-3.266 94.74 2603 46 0.1174 459.982 452.392 1.113 0.915 0.009 3.266-2.585 99.86 5447 97 0.1127 310.293 306.779 1.096 0.916 0.000 2.585-2.046 97.45 10613 204 0.0963 234.098 231.474 1.104 0.918 0.000 2.046-1.619 99.39 21536 464 0.0910 138.551 137.190 1.122 0.921 0.000 1.619-1.281 98.00 42464 925 0.0945 74.588 73.941 1.112 0.925 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.013 38.303 1.079 0.933 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0207 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1346 | n_water=890 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1193 r_free=0.1345 | n_water=889 | time (s): 122.520 (total time: 125.020) Filter (q & B) r_work=0.1193 r_free=0.1345 | n_water=879 | time (s): 4.310 (total time: 129.330) Compute maps r_work=0.1193 r_free=0.1345 | n_water=879 | time (s): 1.750 (total time: 131.080) Filter (map) r_work=0.1217 r_free=0.1350 | n_water=762 | time (s): 5.480 (total time: 136.560) Find peaks r_work=0.1217 r_free=0.1350 | n_water=762 | time (s): 0.540 (total time: 137.100) Add new water r_work=0.1225 r_free=0.1363 | n_water=970 | time (s): 4.290 (total time: 141.390) Refine new water occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1190 r_free=0.1335 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1335 occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1186 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1335 r_work=0.1186 r_free=0.1335 | n_water=970 | time (s): 208.090 (total time: 349.480) Filter (q & B) r_work=0.1190 r_free=0.1344 | n_water=899 | time (s): 4.910 (total time: 354.390) Filter (dist only) r_work=0.1191 r_free=0.1343 | n_water=897 | time (s): 115.360 (total time: 469.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.528133 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.205370 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1347 0.0153 0.038 1.1 7.0 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.47 1.53 1.677 13.713 14.205 3.754 11.95 13.49 1.54 1.689 13.709 14.205 3.753 Individual atomic B min max mean iso aniso Overall: 5.54 63.67 14.60 0.86 532 3269 Protein: 5.54 27.98 10.33 0.86 0 2902 Water: 5.96 63.67 28.41 N/A 532 365 Other: 13.78 22.06 17.92 N/A 0 2 Chain A: 5.60 49.47 12.14 N/A 0 1624 Chain B: 5.54 62.72 11.98 N/A 0 1645 Chain S: 5.96 63.67 30.20 N/A 532 0 Histogram: Values Number of atoms 5.54 - 11.36 2075 11.36 - 17.17 819 17.17 - 22.98 273 22.98 - 28.80 204 28.80 - 34.61 195 34.61 - 40.42 116 40.42 - 46.23 74 46.23 - 52.05 32 52.05 - 57.86 9 57.86 - 63.67 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1350 r_work=0.1195 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1352 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752966 | | target function (ml) not normalized (work): 702877.964907 | | target function (ml) not normalized (free): 14723.856337 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1352 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1476 n_refl.: 191127 remove outliers: r(all,work,free)=0.1401 0.1400 0.1476 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1401 0.1399 0.1476 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1351 n_refl.: 191127 remove outliers: r(all,work,free)=0.1196 0.1193 0.1351 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3856 348.434 308.412 0.346 0.994 0.175 13.296-10.522 95.05 95 1 0.2273 479.395 463.627 0.694 0.996 0.126 10.503-8.327 98.35 176 3 0.2223 502.649 495.258 0.840 0.997 0.105 8.315-6.595 100.00 359 8 0.2171 374.491 370.286 0.864 0.996 0.093 6.588-5.215 100.00 711 7 0.1948 344.988 335.163 0.866 0.997 0.083 5.214-4.128 98.38 1367 28 0.1243 504.613 498.255 0.959 0.998 0.049 4.126-3.266 94.74 2603 46 0.1182 459.982 452.199 1.020 0.999 0.009 3.266-2.585 99.86 5447 97 0.1130 310.293 306.712 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0964 234.098 231.423 1.012 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.551 137.179 1.028 1.006 0.000 1.619-1.281 98.00 42464 925 0.0942 74.588 73.939 1.020 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.013 38.296 0.991 1.022 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1193 r_free=0.1351 After: r_work=0.1194 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1194 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1351 | n_water=897 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1194 r_free=0.1353 | n_water=896 | time (s): 117.780 (total time: 120.240) Filter (q & B) r_work=0.1196 r_free=0.1354 | n_water=879 | time (s): 5.290 (total time: 125.530) Compute maps r_work=0.1196 r_free=0.1354 | n_water=879 | time (s): 1.700 (total time: 127.230) Filter (map) r_work=0.1218 r_free=0.1356 | n_water=764 | time (s): 5.260 (total time: 132.490) Find peaks r_work=0.1218 r_free=0.1356 | n_water=764 | time (s): 0.860 (total time: 133.350) Add new water r_work=0.1225 r_free=0.1370 | n_water=964 | time (s): 4.570 (total time: 137.920) Refine new water occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1341 occ: r_work=0.1189 r_free=0.1341 adp: r_work=0.1189 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1342 r_work=0.1189 r_free=0.1342 | n_water=964 | time (s): 205.570 (total time: 343.490) Filter (q & B) r_work=0.1193 r_free=0.1350 | n_water=896 | time (s): 4.170 (total time: 347.660) Filter (dist only) r_work=0.1194 r_free=0.1349 | n_water=893 | time (s): 114.380 (total time: 462.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550093 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.710282 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1354 0.0157 0.038 1.2 7.7 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.54 1.57 1.675 13.690 13.710 3.755 11.97 13.56 1.59 1.667 13.692 13.710 3.754 Individual atomic B min max mean iso aniso Overall: 5.55 63.68 14.57 0.85 528 3269 Protein: 5.55 27.93 10.35 0.85 0 2902 Water: 5.95 63.68 28.27 N/A 528 365 Other: 13.82 22.06 17.94 N/A 0 2 Chain A: 5.66 49.42 12.14 N/A 0 1624 Chain B: 5.55 62.48 11.98 N/A 0 1645 Chain S: 5.95 63.68 30.09 N/A 528 0 Histogram: Values Number of atoms 5.55 - 11.36 2067 11.36 - 17.17 830 17.17 - 22.99 272 22.99 - 28.80 207 28.80 - 34.61 191 34.61 - 40.43 114 40.43 - 46.24 71 46.24 - 52.05 32 52.05 - 57.87 9 57.87 - 63.68 4 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1357 r_work=0.1198 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1357 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1358 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754429 | | target function (ml) not normalized (work): 703151.924468 | | target function (ml) not normalized (free): 14723.952694 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1370 0.1466 5.6919 5.7519| | 2: 2.94 - 2.33 1.00 7339 128 0.1079 0.1391 5.08 5.1951| | 3: 2.33 - 2.04 0.96 6939 150 0.0914 0.1169 4.6614 4.7492| | 4: 2.04 - 1.85 1.00 7170 155 0.0903 0.1051 4.392 4.563| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.0988 4.15 4.2293| | 6: 1.72 - 1.62 0.99 7102 142 0.0897 0.1101 3.9463 4.0832| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0978 3.7989 3.9414| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1293 3.6997 3.8862| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1118 3.62 3.7485| | 10: 1.41 - 1.36 0.99 7022 150 0.0974 0.1190 3.5559 3.6767| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1129 3.4856 3.59| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1137 3.4622 3.5909| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1251 3.4392 3.5676| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1592 3.4335 3.6805| | 15: 1.22 - 1.19 0.98 6956 137 0.1170 0.1236 3.4478 3.4848| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1548 3.4637 3.6544| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1217 3.4317 3.432| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1705 3.4369 3.5313| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1745 3.4188 3.5926| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1582 3.4098 3.4325| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2143 3.4186 3.505| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1939 3.4129 3.4123| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2030 3.4332 3.4896| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2260 3.4355 3.51| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2500 3.4493 3.5208| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2855 3.4155 3.4224| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2798 3.4685 3.3964| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7395 127 0.93 11.53 1.00 0.96 11002.54| | 2: 2.94 - 2.33 7339 128 0.93 12.69 0.99 0.95 5063.62| | 3: 2.33 - 2.04 6939 150 0.96 7.60 1.01 0.95 1693.04| | 4: 2.04 - 1.85 7170 155 0.96 7.59 1.00 0.95 992.41| | 5: 1.85 - 1.72 7113 159 0.96 7.99 1.00 0.96 624.84| | 6: 1.72 - 1.62 7102 142 0.96 7.99 1.00 0.96 441.06| | 7: 1.62 - 1.54 7104 148 0.96 8.12 1.01 0.97 336.99| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 0.97 277.52| | 9: 1.47 - 1.41 6938 155 0.96 8.40 1.00 0.98 229.27| | 10: 1.41 - 1.36 7022 150 0.96 8.87 1.00 0.97 202.01| | 11: 1.36 - 1.32 6997 151 0.96 8.97 0.99 0.96 175.75| | 12: 1.32 - 1.28 6975 149 0.96 9.09 0.98 0.95 162.42| | 13: 1.28 - 1.25 6907 166 0.96 9.61 1.01 0.96 159.41| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.96 163.58| | 15: 1.22 - 1.19 6956 137 0.95 11.19 1.01 0.98 165.70| | 16: 1.19 - 1.17 6604 132 0.95 11.36 1.01 0.96 158.68| | 17: 1.17 - 1.14 6940 135 0.94 12.15 1.01 0.96 152.01| | 18: 1.14 - 1.12 6875 142 0.94 12.68 1.01 0.95 146.45| | 19: 1.12 - 1.10 6948 106 0.93 14.10 1.00 0.95 150.33| | 20: 1.10 - 1.08 6884 147 0.92 15.21 1.00 0.94 149.93| | 21: 1.08 - 1.07 6852 152 0.91 16.65 1.00 0.93 153.27| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.93 155.10| | 23: 1.05 - 1.03 6827 159 0.87 20.53 0.99 0.92 165.08| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.99 0.93 179.08| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.98 0.90 181.89| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.89 176.40| | 27: 0.99 - 0.98 6647 131 0.82 26.33 0.99 0.87 161.26| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.45 max = 11002.54 mean = 913.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.27| |phase err.(test): min = 0.00 max = 88.71 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1358 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1413 0.1411 0.1491 n_refl.: 191127 remove outliers: r(all,work,free)=0.1413 0.1411 0.1491 n_refl.: 191127 overall B=-0.06 to atoms: r(all,work,free)=0.1403 0.1402 0.1485 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1357 n_refl.: 191127 remove outliers: r(all,work,free)=0.1199 0.1196 0.1357 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3817 348.434 309.169 0.338 0.994 0.173 13.296-10.522 95.05 95 1 0.2287 479.395 463.285 0.677 0.995 0.125 10.503-8.327 98.35 176 3 0.2211 502.649 495.055 0.820 0.996 0.098 8.315-6.595 100.00 359 8 0.2167 374.491 370.125 0.842 0.996 0.090 6.588-5.215 100.00 711 7 0.1957 344.988 335.035 0.846 0.997 0.085 5.214-4.128 98.38 1367 28 0.1248 504.613 498.304 0.936 0.998 0.044 4.126-3.266 94.74 2603 46 0.1184 459.982 452.193 0.997 0.999 0.005 3.266-2.585 99.86 5447 97 0.1132 310.293 306.742 0.980 1.000 0.000 2.585-2.046 97.45 10613 204 0.0971 234.098 231.426 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0913 138.551 137.173 1.001 1.007 0.000 1.619-1.281 98.00 42464 925 0.0945 74.588 73.938 0.992 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.013 38.290 0.960 1.026 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0129 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2035 0.1933 0.081 5.253 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1872 0.081 5.253 5.2 78.0 14.6 805 0.000 1_settarget: 0.1797 0.1872 0.081 5.253 5.2 78.0 14.6 805 0.000 1_nqh: 0.1797 0.1872 0.081 5.253 5.2 78.0 14.6 805 0.000 1_weight: 0.1797 0.1872 0.081 5.253 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1507 0.039 1.151 5.2 78.0 14.6 805 0.157 1_adp: 0.1299 0.1575 0.039 1.151 5.2 73.0 15.1 805 0.157 1_regHadp: 0.1298 0.1570 0.039 1.151 5.2 73.0 15.1 805 0.157 1_occ: 0.1283 0.1556 0.039 1.151 5.2 73.0 15.1 805 0.157 2_bss: 0.1275 0.1548 0.039 1.151 5.3 73.2 15.2 805 0.157 2_settarget: 0.1275 0.1548 0.039 1.151 5.3 73.2 15.2 805 0.157 2_updatecdl: 0.1275 0.1548 0.039 1.163 5.3 73.2 15.2 805 0.157 2_nqh: 0.1275 0.1548 0.039 1.163 5.3 73.2 15.2 805 0.157 2_sol: 0.1276 0.1513 0.039 1.163 5.3 73.2 15.9 879 n/a 2_weight: 0.1276 0.1513 0.039 1.163 5.3 73.2 15.9 879 n/a 2_xyzrec: 0.1261 0.1527 0.041 1.123 5.3 73.2 15.9 879 n/a 2_adp: 0.1235 0.1513 0.041 1.123 5.3 70.3 16.3 879 n/a 2_regHadp: 0.1236 0.1514 0.041 1.123 5.3 70.3 16.3 879 n/a 2_occ: 0.1229 0.1511 0.041 1.123 5.3 70.3 16.3 879 n/a 3_bss: 0.1236 0.1519 0.041 1.123 5.3 70.3 16.3 879 n/a 3_settarget: 0.1236 0.1519 0.041 1.123 5.3 70.3 16.3 879 n/a 3_updatecdl: 0.1236 0.1519 0.041 1.132 5.3 70.3 16.3 879 n/a 3_nqh: 0.1236 0.1519 0.041 1.132 5.3 70.3 16.3 879 n/a 3_sol: 0.1253 0.1516 0.041 1.132 5.3 68.2 15.4 865 n/a 3_weight: 0.1253 0.1516 0.041 1.132 5.3 68.2 15.4 865 n/a 3_xyzrec: 0.1240 0.1440 0.034 1.104 5.3 68.2 15.4 865 n/a 3_adp: 0.1232 0.1402 0.034 1.104 5.5 67.9 15.3 865 n/a 3_regHadp: 0.1233 0.1403 0.034 1.104 5.5 67.9 15.3 865 n/a 3_occ: 0.1228 0.1395 0.034 1.104 5.5 67.9 15.3 865 n/a 4_bss: 0.1224 0.1391 0.034 1.104 5.5 67.9 15.3 865 n/a 4_settarget: 0.1224 0.1391 0.034 1.104 5.5 67.9 15.3 865 n/a 4_updatecdl: 0.1224 0.1391 0.034 1.105 5.5 67.9 15.3 865 n/a 4_nqh: 0.1224 0.1391 0.034 1.105 5.5 67.9 15.3 865 n/a 4_sol: 0.1207 0.1382 0.034 1.105 5.5 67.9 15.0 854 n/a 4_weight: 0.1207 0.1382 0.034 1.105 5.5 67.9 15.0 854 n/a 4_xyzrec: 0.1207 0.1385 0.036 1.119 5.5 67.9 15.0 854 n/a 4_adp: 0.1204 0.1379 0.036 1.119 5.5 67.5 14.9 854 n/a 4_regHadp: 0.1204 0.1380 0.036 1.119 5.5 67.5 14.9 854 n/a 4_occ: 0.1201 0.1378 0.036 1.119 5.5 67.5 14.9 854 n/a 5_bss: 0.1199 0.1375 0.036 1.119 5.5 67.4 14.9 854 n/a 5_settarget: 0.1199 0.1375 0.036 1.119 5.5 67.4 14.9 854 n/a 5_updatecdl: 0.1199 0.1375 0.036 1.120 5.5 67.4 14.9 854 n/a 5_nqh: 0.1199 0.1375 0.036 1.120 5.5 67.4 14.9 854 n/a 5_sol: 0.1197 0.1350 0.036 1.120 5.5 67.4 15.0 881 n/a 5_weight: 0.1197 0.1350 0.036 1.120 5.5 67.4 15.0 881 n/a 5_xyzrec: 0.1199 0.1355 0.035 1.132 5.5 67.4 15.0 881 n/a 5_adp: 0.1202 0.1356 0.035 1.132 5.6 66.4 14.9 881 n/a 5_regHadp: 0.1202 0.1356 0.035 1.132 5.6 66.4 14.9 881 n/a 5_occ: 0.1199 0.1353 0.035 1.132 5.6 66.4 14.9 881 n/a 6_bss: 0.1198 0.1352 0.035 1.132 5.5 66.4 14.9 881 n/a 6_settarget: 0.1198 0.1352 0.035 1.132 5.5 66.4 14.9 881 n/a 6_updatecdl: 0.1198 0.1352 0.035 1.132 5.5 66.4 14.9 881 n/a 6_nqh: 0.1198 0.1352 0.035 1.132 5.5 66.4 14.9 881 n/a 6_sol: 0.1196 0.1351 0.035 1.132 5.5 66.4 14.9 889 n/a 6_weight: 0.1196 0.1351 0.035 1.132 5.5 66.4 14.9 889 n/a 6_xyzrec: 0.1199 0.1357 0.037 1.132 5.5 66.4 14.9 889 n/a 6_adp: 0.1203 0.1359 0.037 1.132 5.6 65.2 14.8 889 n/a 6_regHadp: 0.1203 0.1360 0.037 1.132 5.6 65.2 14.8 889 n/a 6_occ: 0.1200 0.1358 0.037 1.132 5.6 65.2 14.8 889 n/a 7_bss: 0.1199 0.1358 0.037 1.132 5.3 65.0 14.6 889 n/a 7_settarget: 0.1199 0.1358 0.037 1.132 5.3 65.0 14.6 889 n/a 7_updatecdl: 0.1199 0.1358 0.037 1.132 5.3 65.0 14.6 889 n/a 7_nqh: 0.1199 0.1358 0.037 1.132 5.3 65.0 14.6 889 n/a 7_sol: 0.1199 0.1347 0.037 1.132 5.3 65.0 14.6 886 n/a 7_weight: 0.1199 0.1347 0.037 1.132 5.3 65.0 14.6 886 n/a 7_xyzrec: 0.1203 0.1353 0.037 1.124 5.3 65.0 14.6 886 n/a 7_adp: 0.1204 0.1355 0.037 1.124 5.4 64.0 14.5 886 n/a 7_regHadp: 0.1204 0.1356 0.037 1.124 5.4 64.0 14.5 886 n/a 7_occ: 0.1203 0.1353 0.037 1.124 5.4 64.0 14.5 886 n/a 8_bss: 0.1193 0.1341 0.037 1.124 5.5 64.1 14.6 886 n/a 8_settarget: 0.1193 0.1341 0.037 1.124 5.5 64.1 14.6 886 n/a 8_updatecdl: 0.1193 0.1341 0.037 1.124 5.5 64.1 14.6 886 n/a 8_nqh: 0.1193 0.1341 0.037 1.124 5.5 64.1 14.6 886 n/a 8_sol: 0.1191 0.1338 0.037 1.124 5.5 64.1 14.6 890 n/a 8_weight: 0.1191 0.1338 0.037 1.124 5.5 64.1 14.6 890 n/a 8_xyzrec: 0.1195 0.1343 0.038 1.112 5.5 64.1 14.6 890 n/a 8_adp: 0.1195 0.1345 0.038 1.112 5.4 63.7 14.6 890 n/a 8_regHadp: 0.1196 0.1345 0.038 1.112 5.4 63.7 14.6 890 n/a 8_occ: 0.1194 0.1346 0.038 1.112 5.4 63.7 14.6 890 n/a 9_bss: 0.1193 0.1346 0.038 1.112 5.5 63.7 14.6 890 n/a 9_settarget: 0.1193 0.1346 0.038 1.112 5.5 63.7 14.6 890 n/a 9_updatecdl: 0.1193 0.1346 0.038 1.112 5.5 63.7 14.6 890 n/a 9_nqh: 0.1193 0.1346 0.038 1.112 5.5 63.7 14.6 890 n/a 9_sol: 0.1191 0.1343 0.038 1.112 5.5 63.7 14.6 897 n/a 9_weight: 0.1191 0.1343 0.038 1.112 5.5 63.7 14.6 897 n/a 9_xyzrec: 0.1195 0.1347 0.038 1.115 5.5 63.7 14.6 897 n/a 9_adp: 0.1195 0.1350 0.038 1.115 5.5 63.7 14.6 897 n/a 9_regHadp: 0.1195 0.1350 0.038 1.115 5.5 63.7 14.6 897 n/a 9_occ: 0.1194 0.1352 0.038 1.115 5.5 63.7 14.6 897 n/a 10_bss: 0.1193 0.1351 0.038 1.115 5.5 63.7 14.6 897 n/a 10_settarget: 0.1193 0.1351 0.038 1.115 5.5 63.7 14.6 897 n/a 10_updatecdl: 0.1193 0.1351 0.038 1.115 5.5 63.7 14.6 897 n/a 10_setrh: 0.1194 0.1351 0.038 1.115 5.5 63.7 14.6 897 n/a 10_nqh: 0.1194 0.1351 0.038 1.115 5.5 63.7 14.6 897 n/a 10_sol: 0.1194 0.1349 0.038 1.115 5.5 63.7 14.6 893 n/a 10_weight: 0.1194 0.1349 0.038 1.115 5.5 63.7 14.6 893 n/a 10_xyzrec: 0.1196 0.1354 0.038 1.163 5.5 63.7 14.6 893 n/a 10_adp: 0.1197 0.1357 0.038 1.163 5.5 63.7 14.6 893 n/a 10_regHadp: 0.1198 0.1357 0.038 1.163 5.5 63.7 14.6 893 n/a 10_occ: 0.1197 0.1358 0.038 1.163 5.5 63.7 14.6 893 n/a end: 0.1196 0.1357 0.038 1.163 5.5 63.6 14.5 893 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4779266_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4779266_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.3700 Refinement macro-cycles (run) : 12301.1200 Write final files (write_after_run_outputs) : 154.9400 Total : 12463.4300 Total CPU time: 3.47 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:59 PST -0800 (1736736299.96 s) Start R-work = 0.1797, R-free = 0.1872 Final R-work = 0.1196, R-free = 0.1357 =============================================================================== Job complete usr+sys time: 12751.28 seconds wall clock time: 213 minutes 31.27 seconds (12811.27 seconds total)