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_6790396.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/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6790396.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6790396.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } 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 2 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: 1.60, per 1000 atoms: 0.24 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: 2.780 distance_ideal: 2.720 ideal - model: -0.060 slack: 0.000 delta_slack: -0.060 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: 2.758 distance_ideal: 2.710 ideal - model: -0.048 slack: 0.000 delta_slack: -0.048 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: 0.74 Conformation dependent library (CDL) restraints added in 115.3 milliseconds Time building geometry restraints manager: 1.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.00: 550 1.00 - 1.22: 2528 1.22 - 1.44: 1398 1.44 - 1.67: 1389 1.67 - 1.89: 69 Bond restraints: 5934 Sorted by residual: bond pdb=" N ARG A 149 " pdb=" H ARG A 149 " ideal model delta sigma weight residual 0.860 1.252 -0.392 2.00e-02 2.50e+03 3.84e+02 bond pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 1.244 1.051 0.194 1.00e-02 1.00e+04 3.74e+02 bond pdb=" C ILE A 191 " pdb=" O ILE A 191 " ideal model delta sigma weight residual 1.237 1.024 0.213 1.13e-02 7.83e+03 3.55e+02 bond pdb=" NZ LYS A 167 " pdb=" HZ2 LYS A 167 " ideal model delta sigma weight residual 0.890 1.260 -0.370 2.00e-02 2.50e+03 3.43e+02 bond pdb=" CA ARG A 100 " pdb=" C ARG A 100 " ideal model delta sigma weight residual 1.526 1.280 0.246 1.36e-02 5.41e+03 3.27e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 5771 4.24 - 8.48: 3518 8.48 - 12.73: 1268 12.73 - 16.97: 234 16.97 - 21.21: 19 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ILE A 76 " pdb=" C ILE A 76 " pdb=" N LYS A 77 " ideal model delta sigma weight residual 121.91 138.56 -16.65 9.80e-01 1.04e+00 2.89e+02 angle pdb=" NE ARG B 175 " pdb=" CZ ARG B 175 " pdb=" NH1 ARG B 175 " ideal model delta sigma weight residual 121.50 136.45 -14.95 1.00e+00 1.00e+00 2.24e+02 angle pdb=" O LYS A 177 " pdb=" C LYS A 177 " pdb=" N ALA A 178 " ideal model delta sigma weight residual 122.07 107.38 14.69 1.03e+00 9.43e-01 2.03e+02 angle pdb=" NE ARG A 143 " pdb=" CZ ARG A 143 " pdb=" NH1 ARG A 143 " ideal model delta sigma weight residual 121.50 135.55 -14.05 1.00e+00 1.00e+00 1.97e+02 angle pdb=" O TYR A 67 " pdb=" C TYR A 67 " pdb=" N ASP A 68 " ideal model delta sigma weight residual 122.96 107.54 15.42 1.13e+00 7.83e-01 1.86e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.90: 1841 16.90 - 33.79: 140 33.79 - 50.68: 51 50.68 - 67.58: 13 67.58 - 84.47: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA VAL B 173 " pdb=" C VAL B 173 " pdb=" N GLY B 174 " pdb=" CA GLY B 174 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -155.82 -24.18 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA ILE B 105 " pdb=" C ILE B 105 " pdb=" N CYS B 106 " pdb=" CA CYS B 106 " ideal model delta harmonic sigma weight residual 180.00 156.77 23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 185 0.214 - 0.427: 173 0.427 - 0.641: 87 0.641 - 0.854: 39 0.854 - 1.068: 8 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE A 162 " pdb=" N ILE A 162 " pdb=" C ILE A 162 " pdb=" CB ILE A 162 " both_signs ideal model delta sigma weight residual False 2.43 1.37 1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA ALA A 55 " pdb=" N ALA A 55 " pdb=" C ALA A 55 " pdb=" CB ALA A 55 " both_signs ideal model delta sigma weight residual False 2.48 1.48 1.00 2.00e-01 2.50e+01 2.52e+01 chirality pdb=" CB VAL A 71 " pdb=" CA VAL A 71 " pdb=" CG1 VAL A 71 " pdb=" CG2 VAL A 71 " both_signs ideal model delta sigma weight residual False -2.63 -3.61 0.98 2.00e-01 2.50e+01 2.39e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.091 2.00e-02 2.50e+03 8.14e-02 1.99e+02 pdb=" CG PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.140 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.080 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.160 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.041 2.00e-02 2.50e+03 5.71e-02 1.31e+02 pdb=" CG TRP B 146 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.110 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.061 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.107 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.090 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.017 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.019 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.017 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.025 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.070 2.00e-02 2.50e+03 6.47e-02 1.26e+02 pdb=" CG PHE A 127 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " 0.088 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " -0.076 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " 0.111 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE A 127 " -0.016 2.00e-02 2.50e+03 pdb=" HD2 PHE A 127 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 127 " -0.088 2.00e-02 2.50e+03 pdb=" HE2 PHE A 127 " 0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 127 " -0.072 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 26 1.60 - 2.35: 2330 2.35 - 3.10: 22130 3.10 - 3.85: 32951 3.85 - 4.60: 52714 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110151 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.855 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.020 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.031 2.620 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.096 2.100 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.154 2.620 ... (remaining 110146 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_6790396_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= 0.2028 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.299438 | | target function (ml) not normalized (work): 805340.700681 | | target function (ml) not normalized (free): 16560.603338 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2132 0.1970 6.6963 6.3158| | 2: 2.94 - 2.33 1.00 7339 128 0.1620 0.1635 5.5341 5.6023| | 3: 2.33 - 2.04 0.96 6939 150 0.1621 0.1628 5.1347 5.1306| | 4: 2.04 - 1.85 1.00 7170 155 0.1733 0.1505 4.9495 4.9526| | 5: 1.85 - 1.72 0.99 7113 159 0.1896 0.1750 4.7806 4.8583| | 6: 1.72 - 1.62 0.99 7102 142 0.1989 0.1872 4.6677 4.6798| | 7: 1.62 - 1.54 0.99 7104 148 0.2000 0.1654 4.5549 4.4838| | 8: 1.54 - 1.47 0.96 6798 152 0.2073 0.2157 4.4809 4.5541| | 9: 1.47 - 1.41 0.98 6938 155 0.2080 0.2171 4.3942 4.4771| | 10: 1.41 - 1.36 0.99 7022 150 0.2130 0.2255 4.3232 4.4| | 11: 1.36 - 1.32 0.99 6997 151 0.2106 0.2053 4.2377 4.2497| | 12: 1.32 - 1.28 0.98 6976 149 0.2077 0.1911 4.1819 4.1448| | 13: 1.28 - 1.25 0.98 6907 166 0.2030 0.2281 4.1207 4.2017| | 14: 1.25 - 1.22 0.98 7015 113 0.2062 0.2187 4.0772 4.2464| | 15: 1.22 - 1.19 0.98 6957 137 0.2098 0.2167 4.0385 4.1169| | 16: 1.19 - 1.17 0.93 6604 132 0.2109 0.1909 4.0024 4.0038| | 17: 1.17 - 1.14 0.98 6941 135 0.2150 0.2146 3.9601 4.0447| | 18: 1.14 - 1.12 0.98 6875 142 0.2219 0.2399 3.9146 3.9772| | 19: 1.12 - 1.10 0.97 6949 106 0.2245 0.2527 3.8721 4.002| | 20: 1.10 - 1.08 0.97 6884 147 0.2337 0.2425 3.8343 3.894| | 21: 1.08 - 1.07 0.97 6852 152 0.2407 0.2682 3.7846 3.8144| | 22: 1.07 - 1.05 0.97 6838 135 0.2545 0.2775 3.7569 3.8508| | 23: 1.05 - 1.03 0.97 6829 159 0.2741 0.2567 3.7362 3.7779| | 24: 1.03 - 1.02 0.96 6785 133 0.2859 0.2435 3.6946 3.6804| | 25: 1.02 - 1.01 0.93 6552 130 0.3059 0.3042 3.6752 3.7679| | 26: 1.01 - 0.99 0.96 6767 158 0.3207 0.3250 3.6285 3.6175| | 27: 0.99 - 0.98 0.94 6648 131 0.3410 0.3235 3.6405 3.5849| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.24 0.91 0.98 34846.54| | 2: 2.94 - 2.33 7339 128 0.86 20.92 1.09 1.03 14831.11| | 3: 2.33 - 2.04 6939 150 0.93 12.38 1.11 1.07 4079.95| | 4: 2.04 - 1.85 7170 155 0.93 13.14 1.11 1.07 2671.64| | 5: 1.85 - 1.72 7113 159 0.91 15.18 1.11 1.08 1972.83| | 6: 1.72 - 1.62 7102 142 0.91 15.84 1.11 1.09 1504.86| | 7: 1.62 - 1.54 7104 148 0.90 16.37 1.11 1.09 1197.63| | 8: 1.54 - 1.47 6798 152 0.89 17.62 1.11 1.08 1087.70| | 9: 1.47 - 1.41 6938 155 0.88 19.04 1.10 1.07 990.86| | 10: 1.41 - 1.36 7022 150 0.87 20.32 1.09 1.06 882.23| | 11: 1.36 - 1.32 6997 151 0.87 19.80 1.08 1.05 727.37| | 12: 1.32 - 1.28 6976 149 0.88 19.10 1.07 1.06 618.71| | 13: 1.28 - 1.25 6907 166 0.88 19.41 1.07 1.05 581.16| | 14: 1.25 - 1.22 7015 113 0.87 20.26 1.07 1.06 568.50| | 15: 1.22 - 1.19 6957 137 0.86 21.21 1.08 1.04 555.91| | 16: 1.19 - 1.17 6604 132 0.87 21.02 1.08 1.03 508.89| | 17: 1.17 - 1.14 6941 135 0.86 21.84 1.08 1.01 470.75| | 18: 1.14 - 1.12 6875 142 0.86 21.92 1.08 1.00 424.30| | 19: 1.12 - 1.10 6949 106 0.85 22.88 1.07 1.01 412.59| | 20: 1.10 - 1.08 6884 147 0.84 23.77 1.06 1.00 384.94| | 21: 1.08 - 1.07 6852 152 0.83 24.79 1.06 0.99 364.53| | 22: 1.07 - 1.05 6838 135 0.82 25.73 1.04 0.99 339.31| | 23: 1.05 - 1.03 6829 159 0.81 26.73 1.05 0.98 316.82| | 24: 1.03 - 1.02 6785 133 0.80 28.09 1.05 1.00 311.09| | 25: 1.02 - 1.01 6552 130 0.78 29.49 1.03 0.96 295.10| | 26: 1.01 - 0.99 6767 158 0.76 31.65 1.03 0.93 285.60| | 27: 0.99 - 0.98 6648 131 0.75 32.07 1.04 0.88 265.66| |alpha: min = 0.88 max = 1.09 mean = 1.02| |beta: min = 265.66 max = 34846.54 mean = 2772.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.43| |phase err.(test): min = 0.00 max = 89.68 mean = 21.46| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.250 2950 Z= 5.594 Angle : 5.168 16.647 4018 Z= 3.675 Chirality : 0.381 1.068 492 Planarity : 0.034 0.123 512 Dihedral : 12.629 84.468 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 0.97 % Allowed : 4.52 % Favored : 94.52 % Cbeta Deviations : 31.46 % 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: -2.13 (0.39), residues: 386 helix: -2.32 (0.33), residues: 146 sheet: -1.02 (0.53), residues: 86 loop : -0.36 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.022 ARG B 100 TYR 0.102 0.034 TYR A 67 PHE 0.104 0.034 PHE B 95 TRP 0.102 0.046 TRP B 146 HIS 0.066 0.028 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= 0.2028 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.299438 | | target function (ml) not normalized (work): 805340.700681 | | target function (ml) not normalized (free): 16560.603338 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2026 0.2028 0.1978 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2026 0.2028 0.1978 n_refl.: 191155 remove outliers: r(all,work,free)=0.2026 0.2028 0.1978 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2023 0.2025 0.1977 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1800 0.1798 0.1926 n_refl.: 191145 remove outliers: r(all,work,free)=0.1798 0.1796 0.1924 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 96.04 94 3 0.4216 400.535 295.384 0.430 0.914 0.299 13.296-10.522 99.01 99 1 0.2508 528.187 518.907 0.778 0.915 0.248 10.503-8.327 98.90 177 3 0.2515 564.205 556.704 0.962 0.915 0.223 8.318-6.595 100.00 360 8 0.2461 414.736 400.711 0.960 0.915 0.165 6.588-5.215 100.00 711 7 0.2282 381.101 364.681 0.950 0.916 0.124 5.214-4.128 98.38 1367 28 0.1496 557.435 548.996 1.061 0.917 0.090 4.126-3.266 94.74 2603 46 0.1350 508.132 498.516 1.133 0.918 0.030 3.266-2.585 99.86 5447 97 0.1432 342.774 337.758 1.105 0.919 0.000 2.585-2.046 97.45 10613 204 0.1396 258.603 254.292 1.108 0.921 0.000 2.046-1.619 99.39 21536 464 0.1601 153.054 150.053 1.122 0.924 0.000 1.619-1.281 98.00 42464 925 0.1928 82.395 80.492 1.100 0.930 0.000 1.281-0.980 96.53 101826 2055 0.2313 44.202 42.023 1.074 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0570 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1796 r_free=0.1924 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 123 ASN Total number of N/Q/H flips: 2 r_work=0.1801 r_free=0.1924 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.982718 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 562.139047 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 0.1273 0.1502 0.0229 0.038 1.2 11.4 0.0 0.3 0 11.491 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.02 2.29 1.118 13.090 562.139 0.018 12.97 15.64 2.68 1.236 13.360 562.139 0.017 Individual atomic B min max mean iso aniso Overall: 5.22 73.02 15.07 1.40 435 3274 Protein: 5.22 40.38 11.04 1.40 0 2902 Water: 6.36 73.02 29.57 N/A 435 370 Other: 15.91 29.89 22.90 N/A 0 2 Chain A: 5.43 60.24 13.09 N/A 0 1626 Chain B: 5.22 73.02 12.82 N/A 0 1648 Chain S: 11.22 62.74 30.98 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.00 2161 12.00 - 18.78 643 18.78 - 25.56 314 25.56 - 32.34 263 32.34 - 39.12 155 39.12 - 45.90 107 45.90 - 52.68 43 52.68 - 59.46 17 59.46 - 66.24 5 66.24 - 73.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1565 r_work=0.1296 r_free=0.1560 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1560 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 = 0.1281 r_free = 0.1549 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015555 | | target function (ls_wunit_k1) not normalized (work): 2913.316959 | | target function (ls_wunit_k1) not normalized (free): 115.641656 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1549 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1474 0.1472 0.1624 n_refl.: 191138 remove outliers: r(all,work,free)=0.1474 0.1472 0.1624 n_refl.: 191138 overall B=0.14 to atoms: r(all,work,free)=0.1495 0.1493 0.1633 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1277 0.1272 0.1537 n_refl.: 191138 remove outliers: r(all,work,free)=0.1277 0.1272 0.1537 n_refl.: 191137 ======================== 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 0.3605 402.814 374.589 0.479 0.962 0.275 13.296-10.522 99.01 99 1 0.2076 528.187 524.075 0.740 0.963 0.234 10.503-8.327 98.90 177 3 0.1724 564.205 564.559 0.889 0.963 0.220 8.318-6.595 100.00 360 8 0.1707 414.736 413.094 0.909 0.963 0.150 6.588-5.215 100.00 711 7 0.1532 381.101 373.780 0.888 0.963 0.140 5.214-4.128 98.38 1367 28 0.0902 557.435 554.705 0.975 0.964 0.055 4.126-3.266 94.74 2603 46 0.0831 508.132 504.160 1.044 0.965 0.018 3.266-2.585 99.86 5447 97 0.0924 342.774 340.205 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.387 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1087 153.054 151.407 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1273 82.395 81.438 1.047 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.169 1.023 0.968 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0319 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1272 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1537 | n_water=805 | time (s): 3.440 (total time: 3.440) Filter (dist) r_work=0.1276 r_free=0.1541 | n_water=794 | time (s): 97.640 (total time: 101.080) Filter (q & B) r_work=0.1277 r_free=0.1541 | n_water=791 | time (s): 5.270 (total time: 106.350) Compute maps r_work=0.1277 r_free=0.1541 | n_water=791 | time (s): 2.140 (total time: 108.490) Filter (map) r_work=0.1302 r_free=0.1525 | n_water=657 | time (s): 5.350 (total time: 113.840) Find peaks r_work=0.1302 r_free=0.1525 | n_water=657 | time (s): 0.670 (total time: 114.510) Add new water r_work=0.1324 r_free=0.1554 | n_water=965 | time (s): 4.210 (total time: 118.720) Refine new water occ: r_work=0.1281 r_free=0.1502 adp: r_work=0.1269 r_free=0.1501 occ: r_work=0.1272 r_free=0.1498 adp: r_work=0.1265 r_free=0.1500 occ: r_work=0.1266 r_free=0.1497 adp: r_work=0.1264 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1264 r_free=0.1498 r_work=0.1264 r_free=0.1498 | n_water=965 | time (s): 85.140 (total time: 203.860) Filter (q & B) r_work=0.1269 r_free=0.1503 | n_water=888 | time (s): 5.060 (total time: 208.920) Filter (dist only) r_work=0.1269 r_free=0.1501 | n_water=886 | time (s): 112.000 (total time: 320.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.008149 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 594.092000 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 0.1252 0.1517 0.0266 0.041 1.1 19.0 0.0 0.3 0 12.004 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.17 2.66 2.047 15.225 594.092 0.014 12.34 15.13 2.79 2.407 15.263 594.092 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 68.82 16.36 1.20 518 3272 Protein: 5.40 39.90 11.01 1.20 0 2902 Water: 6.72 68.82 33.89 N/A 518 368 Other: 16.42 32.22 24.32 N/A 0 2 Chain A: 5.64 56.95 13.01 N/A 0 1624 Chain B: 5.40 68.82 12.84 N/A 0 1648 Chain S: 13.17 67.02 38.08 N/A 518 0 Histogram: Values Number of atoms 5.40 - 11.74 2065 11.74 - 18.08 711 18.08 - 24.43 264 24.43 - 30.77 212 30.77 - 37.11 172 37.11 - 43.45 169 43.45 - 49.79 98 49.79 - 56.14 54 56.14 - 62.48 30 62.48 - 68.82 15 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1513 r_work=0.1235 r_free=0.1514 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 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 = 0.1514 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1514 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013470 | | target function (ls_wunit_k1) not normalized (work): 2522.794412 | | target function (ls_wunit_k1) not normalized (free): 98.491573 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1514 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1441 0.1439 0.1603 n_refl.: 191137 remove outliers: r(all,work,free)=0.1441 0.1439 0.1603 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1438 0.1435 0.1601 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1519 n_refl.: 191137 remove outliers: r(all,work,free)=0.1241 0.1236 0.1519 n_refl.: 191137 ======================== 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 0.3388 402.814 377.299 0.493 0.963 0.273 13.296-10.522 99.01 99 1 0.1873 528.187 519.730 0.760 0.964 0.233 10.503-8.327 98.90 177 3 0.1400 564.205 566.728 0.919 0.964 0.179 8.318-6.595 100.00 360 8 0.1555 414.736 414.684 0.935 0.963 0.150 6.588-5.215 100.00 711 7 0.1352 381.101 377.118 0.912 0.963 0.140 5.214-4.128 98.38 1367 28 0.0829 557.435 556.134 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0756 508.132 505.423 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0859 342.774 341.327 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0903 258.603 256.803 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.628 1.081 0.960 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.347 1.074 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.210 1.060 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0607 ============================ 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=886 | time (s): 3.070 (total time: 3.070) Filter (dist) r_work=0.1238 r_free=0.1519 | n_water=879 | time (s): 114.950 (total time: 118.020) Filter (q & B) r_work=0.1238 r_free=0.1519 | n_water=877 | time (s): 4.710 (total time: 122.730) Compute maps r_work=0.1238 r_free=0.1519 | n_water=877 | time (s): 2.600 (total time: 125.330) Filter (map) r_work=0.1275 r_free=0.1528 | n_water=691 | time (s): 4.630 (total time: 129.960) Find peaks r_work=0.1275 r_free=0.1528 | n_water=691 | time (s): 0.920 (total time: 130.880) Add new water r_work=0.1297 r_free=0.1555 | n_water=1022 | time (s): 5.420 (total time: 136.300) Refine new water occ: r_work=0.1252 r_free=0.1517 adp: r_work=0.1252 r_free=0.1518 occ: r_work=0.1248 r_free=0.1515 adp: r_work=0.1248 r_free=0.1516 occ: r_work=0.1245 r_free=0.1513 adp: r_work=0.1245 r_free=0.1515 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1515 r_work=0.1245 r_free=0.1515 | n_water=1022 | time (s): 283.350 (total time: 419.650) Filter (q & B) r_work=0.1250 r_free=0.1516 | n_water=874 | time (s): 4.720 (total time: 424.370) Filter (dist only) r_work=0.1251 r_free=0.1516 | n_water=873 | time (s): 107.940 (total time: 532.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.725916 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.927065 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 0.1242 0.1442 0.0200 0.035 1.1 7.8 0.0 0.0 0 0.863 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.42 14.42 2.00 1.935 14.604 15.927 3.941 12.37 13.98 1.61 2.301 14.487 15.927 3.897 Individual atomic B min max mean iso aniso Overall: 5.54 68.19 15.24 1.04 506 3271 Protein: 5.54 35.59 10.71 1.04 0 2902 Water: 6.71 68.19 30.26 N/A 506 367 Other: 13.76 27.95 20.85 N/A 0 2 Chain A: 5.61 55.51 12.72 N/A 0 1624 Chain B: 5.54 68.19 12.51 N/A 0 1647 Chain S: 13.77 63.95 32.22 N/A 506 0 Histogram: Values Number of atoms 5.54 - 11.81 2141 11.81 - 18.07 702 18.07 - 24.34 277 24.34 - 30.60 240 30.60 - 36.87 173 36.87 - 43.13 140 43.13 - 49.40 71 49.40 - 55.66 22 55.66 - 61.93 8 61.93 - 68.19 3 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1398 r_work=0.1237 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1399 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1389 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1389 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891608 | | target function (ml) not normalized (work): 728882.569222 | | target function (ml) not normalized (free): 15220.509888 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1388 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1449 0.1449 0.1482 n_refl.: 191137 remove outliers: r(all,work,free)=0.1449 0.1449 0.1482 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1442 0.1442 0.1477 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1381 n_refl.: 191137 remove outliers: r(all,work,free)=0.1229 0.1226 0.1381 n_refl.: 191134 ======================== 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 0.3782 398.008 362.599 0.431 0.946 0.257 13.296-10.522 99.01 99 1 0.2407 528.187 510.189 0.717 0.947 0.229 10.503-8.327 97.80 175 3 0.1915 554.286 558.904 0.884 0.947 0.178 8.318-6.595 100.00 360 8 0.2089 414.736 410.525 0.901 0.946 0.137 6.588-5.215 100.00 711 7 0.1832 381.101 370.636 0.889 0.947 0.135 5.214-4.128 98.38 1367 28 0.1180 557.435 551.965 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1102 508.132 501.378 1.035 0.947 0.009 3.266-2.585 99.86 5447 97 0.1093 342.774 338.998 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0969 258.603 255.719 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0970 153.054 151.404 1.058 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.484 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1690 44.202 42.310 1.040 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1162 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1381 | n_water=873 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1226 r_free=0.1381 | n_water=873 | time (s): 103.540 (total time: 106.630) Filter (q & B) r_work=0.1227 r_free=0.1380 | n_water=862 | time (s): 5.430 (total time: 112.060) Compute maps r_work=0.1227 r_free=0.1380 | n_water=862 | time (s): 1.910 (total time: 113.970) Filter (map) r_work=0.1248 r_free=0.1376 | n_water=726 | time (s): 4.730 (total time: 118.700) Find peaks r_work=0.1248 r_free=0.1376 | n_water=726 | time (s): 0.880 (total time: 119.580) Add new water r_work=0.1263 r_free=0.1389 | n_water=969 | time (s): 4.210 (total time: 123.790) Refine new water occ: r_work=0.1214 r_free=0.1355 adp: r_work=0.1207 r_free=0.1351 occ: r_work=0.1205 r_free=0.1352 adp: r_work=0.1205 r_free=0.1350 occ: r_work=0.1203 r_free=0.1352 adp: r_work=0.1203 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1350 r_work=0.1203 r_free=0.1350 | n_water=969 | time (s): 335.840 (total time: 459.630) Filter (q & B) r_work=0.1208 r_free=0.1365 | n_water=870 | time (s): 5.330 (total time: 464.960) Filter (dist only) r_work=0.1208 r_free=0.1365 | n_water=869 | time (s): 108.440 (total time: 573.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570012 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.843923 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 0.1206 0.1368 0.0161 0.036 1.1 5.4 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.68 1.61 1.817 14.175 15.844 3.874 12.00 13.67 1.68 1.932 14.134 15.844 3.864 Individual atomic B min max mean iso aniso Overall: 5.52 67.51 14.95 0.99 502 3271 Protein: 5.52 32.65 10.64 0.99 0 2902 Water: 5.94 67.51 29.34 N/A 502 367 Other: 13.93 26.06 20.00 N/A 0 2 Chain A: 5.59 53.88 12.59 N/A 0 1624 Chain B: 5.52 67.51 12.41 N/A 0 1647 Chain S: 5.94 63.69 30.96 N/A 502 0 Histogram: Values Number of atoms 5.52 - 11.72 2116 11.72 - 17.91 743 17.91 - 24.11 288 24.11 - 30.31 242 30.31 - 36.51 164 36.51 - 42.71 127 42.71 - 48.91 64 48.91 - 55.11 19 55.11 - 61.31 8 61.31 - 67.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1368 r_work=0.1200 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1368 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1367 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861927 | | target function (ml) not normalized (work): 723311.866117 | | target function (ml) not normalized (free): 15134.621221 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1367 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1426 0.1426 0.1468 n_refl.: 191134 remove outliers: r(all,work,free)=0.1426 0.1426 0.1468 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1418 0.1417 0.1463 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1363 n_refl.: 191134 remove outliers: r(all,work,free)=0.1198 0.1195 0.1363 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 93.07 91 3 0.3763 361.230 319.454 0.399 0.946 0.225 13.296-10.522 96.04 96 1 0.2287 480.471 446.049 0.701 0.948 0.200 10.503-8.327 97.80 175 3 0.2038 501.949 497.341 0.866 0.948 0.158 8.318-6.595 100.00 360 8 0.2156 375.576 370.248 0.896 0.947 0.115 6.588-5.215 100.00 711 7 0.1900 345.116 335.158 0.885 0.948 0.110 5.214-4.128 98.38 1367 28 0.1202 504.800 499.750 0.974 0.948 0.080 4.126-3.266 94.74 2603 46 0.1122 460.153 453.861 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1098 310.408 307.183 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0937 234.185 231.789 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0911 138.602 137.345 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0983 74.615 73.921 1.053 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.028 38.374 1.039 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1312 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1363 | n_water=869 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1195 r_free=0.1363 | n_water=869 | time (s): 107.080 (total time: 109.790) Filter (q & B) r_work=0.1196 r_free=0.1363 | n_water=863 | time (s): 4.640 (total time: 114.430) Compute maps r_work=0.1196 r_free=0.1363 | n_water=863 | time (s): 2.570 (total time: 117.000) Filter (map) r_work=0.1217 r_free=0.1359 | n_water=747 | time (s): 4.140 (total time: 121.140) Find peaks r_work=0.1217 r_free=0.1359 | n_water=747 | time (s): 0.770 (total time: 121.910) Add new water r_work=0.1228 r_free=0.1375 | n_water=965 | time (s): 4.590 (total time: 126.500) Refine new water occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1190 r_free=0.1347 adp: r_work=0.1190 r_free=0.1347 occ: r_work=0.1188 r_free=0.1348 adp: r_work=0.1188 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1347 r_work=0.1188 r_free=0.1347 | n_water=965 | time (s): 230.820 (total time: 357.320) Filter (q & B) r_work=0.1193 r_free=0.1351 | n_water=887 | time (s): 4.510 (total time: 361.830) Filter (dist only) r_work=0.1193 r_free=0.1351 | n_water=886 | time (s): 110.630 (total time: 472.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.603898 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.939964 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 0.1358 0.0162 0.037 1.1 6.1 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.58 1.62 1.779 14.117 14.940 3.762 11.98 13.59 1.61 1.814 14.101 14.940 3.760 Individual atomic B min max mean iso aniso Overall: 5.56 67.27 14.97 0.95 519 3271 Protein: 5.56 31.58 10.59 0.95 0 2902 Water: 5.93 67.27 29.33 N/A 519 367 Other: 13.83 25.43 19.63 N/A 0 2 Chain A: 5.63 53.27 12.51 N/A 0 1624 Chain B: 5.56 67.27 12.34 N/A 0 1647 Chain S: 5.93 63.60 31.05 N/A 519 0 Histogram: Values Number of atoms 5.56 - 11.73 2139 11.73 - 17.90 731 17.90 - 24.07 296 24.07 - 30.24 229 30.24 - 36.41 170 36.41 - 42.58 127 42.58 - 48.76 68 48.76 - 54.93 20 54.93 - 61.10 8 61.10 - 67.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1360 r_work=0.1198 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1360 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1362 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759200 | | target function (ml) not normalized (work): 704056.859011 | | target function (ml) not normalized (free): 14741.345097 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1477 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1402 0.1477 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1395 0.1394 0.1471 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1361 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1361 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 93.07 91 3 0.3763 361.230 324.808 0.394 0.951 0.211 13.296-10.522 96.04 96 1 0.2305 480.471 460.851 0.716 0.953 0.189 10.503-8.327 97.80 175 3 0.2058 501.949 495.926 0.860 0.953 0.148 8.318-6.595 100.00 360 8 0.2143 375.576 370.591 0.889 0.953 0.105 6.588-5.215 100.00 711 7 0.1888 345.116 335.186 0.879 0.953 0.084 5.214-4.128 98.38 1367 28 0.1215 504.800 499.231 0.969 0.953 0.070 4.126-3.266 94.74 2603 46 0.1138 460.153 453.369 1.030 0.953 0.005 3.266-2.585 99.86 5447 97 0.1104 310.408 307.095 1.017 0.953 0.000 2.585-2.046 97.45 10613 204 0.0944 234.185 231.747 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0909 138.602 137.303 1.052 0.952 0.000 1.619-1.281 98.00 42464 925 0.0974 74.615 73.906 1.050 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.028 38.360 1.038 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1396 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1361 | n_water=886 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1195 r_free=0.1361 | n_water=886 | time (s): 108.930 (total time: 111.870) Filter (q & B) r_work=0.1195 r_free=0.1360 | n_water=875 | time (s): 4.510 (total time: 116.380) Compute maps r_work=0.1195 r_free=0.1360 | n_water=875 | time (s): 2.030 (total time: 118.410) Filter (map) r_work=0.1217 r_free=0.1359 | n_water=763 | time (s): 5.380 (total time: 123.790) Find peaks r_work=0.1217 r_free=0.1359 | n_water=763 | time (s): 0.560 (total time: 124.350) Add new water r_work=0.1228 r_free=0.1372 | n_water=986 | time (s): 3.980 (total time: 128.330) Refine new water occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1187 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1342 r_work=0.1187 r_free=0.1342 | n_water=986 | time (s): 231.230 (total time: 359.560) Filter (q & B) r_work=0.1193 r_free=0.1349 | n_water=905 | time (s): 6.240 (total time: 365.800) Filter (dist only) r_work=0.1193 r_free=0.1349 | n_water=904 | time (s): 123.110 (total time: 488.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.600724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.163851 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 0.1352 0.0156 0.037 1.1 7.8 0.0 0.3 0 0.800 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.52 1.56 1.757 14.074 14.164 3.760 12.01 13.57 1.56 1.898 14.028 14.164 3.759 Individual atomic B min max mean iso aniso Overall: 5.60 66.00 14.91 0.89 537 3271 Protein: 5.60 28.96 10.47 0.89 0 2902 Water: 6.00 66.00 29.13 N/A 537 367 Other: 13.87 22.70 18.29 N/A 0 2 Chain A: 5.62 51.91 12.36 N/A 0 1624 Chain B: 5.60 66.00 12.21 N/A 0 1647 Chain S: 6.00 63.32 30.89 N/A 537 0 Histogram: Values Number of atoms 5.60 - 11.64 2122 11.64 - 17.68 771 17.68 - 23.72 274 23.72 - 29.76 226 29.76 - 35.80 168 35.80 - 41.84 135 41.84 - 47.88 78 47.88 - 53.92 24 53.92 - 59.96 7 59.96 - 66.00 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1358 r_work=0.1201 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1358 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1357 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758272 | | target function (ml) not normalized (work): 703883.096375 | | target function (ml) not normalized (free): 14732.598006 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1467 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1402 0.1467 n_refl.: 191130 overall B=-0.25 to atoms: r(all,work,free)=0.1364 0.1363 0.1446 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1356 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1198 0.1356 n_refl.: 191128 ======================== 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 0.3836 356.703 323.250 0.393 0.949 0.201 13.296-10.522 95.05 95 1 0.2256 479.573 453.727 0.726 0.951 0.165 10.503-8.327 97.80 175 3 0.2108 501.949 496.749 0.885 0.951 0.147 8.318-6.595 100.00 360 8 0.2155 375.576 370.606 0.911 0.951 0.095 6.588-5.215 100.00 711 7 0.1889 345.116 335.287 0.906 0.951 0.090 5.214-4.128 98.38 1367 28 0.1227 504.800 499.338 0.994 0.952 0.035 4.126-3.266 94.74 2603 46 0.1147 460.153 453.063 1.057 0.952 0.005 3.266-2.585 99.86 5447 97 0.1112 310.408 307.131 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0951 234.185 231.770 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0911 138.602 137.330 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0973 74.615 73.915 1.048 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.028 38.358 1.015 0.957 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0555 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1357 | n_water=904 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1199 r_free=0.1357 | n_water=904 | time (s): 112.300 (total time: 114.910) Filter (q & B) r_work=0.1200 r_free=0.1356 | n_water=896 | time (s): 4.530 (total time: 119.440) Compute maps r_work=0.1200 r_free=0.1356 | n_water=896 | time (s): 2.040 (total time: 121.480) Filter (map) r_work=0.1222 r_free=0.1355 | n_water=777 | time (s): 4.610 (total time: 126.090) Find peaks r_work=0.1222 r_free=0.1355 | n_water=777 | time (s): 0.570 (total time: 126.660) Add new water r_work=0.1231 r_free=0.1365 | n_water=984 | time (s): 4.430 (total time: 131.090) Refine new water occ: r_work=0.1199 r_free=0.1338 adp: r_work=0.1199 r_free=0.1338 occ: r_work=0.1197 r_free=0.1338 adp: r_work=0.1197 r_free=0.1338 occ: r_work=0.1196 r_free=0.1338 adp: r_work=0.1195 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1338 r_work=0.1195 r_free=0.1338 | n_water=984 | time (s): 180.630 (total time: 311.720) Filter (q & B) r_work=0.1199 r_free=0.1347 | n_water=905 | time (s): 5.190 (total time: 316.910) Filter (dist only) r_work=0.1200 r_free=0.1347 | n_water=903 | time (s): 114.910 (total time: 431.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.528406 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.654126 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 5.4 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.53 1.50 1.711 13.702 13.654 3.760 12.04 13.55 1.51 1.753 13.687 13.654 3.758 Individual atomic B min max mean iso aniso Overall: 5.37 64.60 14.60 0.87 536 3271 Protein: 5.37 28.16 10.21 0.87 0 2902 Water: 5.84 64.60 28.69 N/A 536 367 Other: 13.72 22.05 17.88 N/A 0 2 Chain A: 5.44 51.22 12.05 N/A 0 1624 Chain B: 5.37 64.60 11.92 N/A 0 1647 Chain S: 5.84 62.93 30.54 N/A 536 0 Histogram: Values Number of atoms 5.37 - 11.29 2094 11.29 - 17.21 793 17.21 - 23.14 273 23.14 - 29.06 223 29.06 - 34.98 176 34.98 - 40.91 126 40.91 - 46.83 82 46.83 - 52.76 30 52.76 - 58.68 6 58.68 - 64.60 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) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1354 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757902 | | target function (ml) not normalized (work): 703806.104855 | | target function (ml) not normalized (free): 14729.264745 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1354 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1372 0.1370 0.1446 n_refl.: 191128 remove outliers: r(all,work,free)=0.1372 0.1370 0.1446 n_refl.: 191128 overall B=0.06 to atoms: r(all,work,free)=0.1379 0.1378 0.1450 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1345 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1345 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 92.08 90 3 0.3843 356.703 318.128 0.377 0.976 0.195 13.296-10.522 95.05 95 1 0.2247 479.573 462.544 0.720 0.978 0.149 10.503-8.327 97.80 175 3 0.2134 501.949 495.227 0.865 0.978 0.127 8.315-6.595 100.00 359 8 0.2139 374.630 370.589 0.890 0.978 0.091 6.588-5.215 100.00 711 7 0.1909 345.116 335.050 0.886 0.979 0.073 5.214-4.128 98.38 1367 28 0.1240 504.800 498.539 0.976 0.980 0.029 4.126-3.266 94.74 2603 46 0.1152 460.153 452.415 1.039 0.981 0.000 3.266-2.585 99.86 5447 97 0.1119 310.408 306.874 1.022 0.981 0.000 2.585-2.046 97.45 10613 204 0.0958 234.185 231.603 1.030 0.983 0.000 2.046-1.619 99.39 21536 464 0.0911 138.602 137.224 1.045 0.986 0.000 1.619-1.281 98.00 42464 925 0.0953 74.615 73.947 1.033 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1633 40.028 38.330 0.998 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0613 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1345 | n_water=903 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1192 r_free=0.1345 | n_water=903 | time (s): 108.140 (total time: 110.550) Filter (q & B) r_work=0.1192 r_free=0.1343 | n_water=896 | time (s): 4.300 (total time: 114.850) Compute maps r_work=0.1192 r_free=0.1343 | n_water=896 | time (s): 1.790 (total time: 116.640) Filter (map) r_work=0.1217 r_free=0.1352 | n_water=778 | time (s): 4.400 (total time: 121.040) Find peaks r_work=0.1217 r_free=0.1352 | n_water=778 | time (s): 0.800 (total time: 121.840) Add new water r_work=0.1224 r_free=0.1358 | n_water=988 | time (s): 4.000 (total time: 125.840) Refine new water occ: r_work=0.1190 r_free=0.1328 adp: r_work=0.1190 r_free=0.1329 occ: r_work=0.1188 r_free=0.1327 adp: r_work=0.1188 r_free=0.1328 occ: r_work=0.1186 r_free=0.1327 adp: r_work=0.1186 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1328 r_work=0.1186 r_free=0.1328 | n_water=988 | time (s): 296.760 (total time: 422.600) Filter (q & B) r_work=0.1190 r_free=0.1331 | n_water=918 | time (s): 4.230 (total time: 426.830) Filter (dist only) r_work=0.1190 r_free=0.1332 | n_water=916 | time (s): 119.800 (total time: 546.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.514401 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.008086 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 0.1193 0.1334 0.0141 0.038 1.1 7.7 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.34 1.41 1.666 13.735 14.008 3.756 11.92 13.36 1.43 1.678 13.730 14.008 3.754 Individual atomic B min max mean iso aniso Overall: 5.48 63.64 14.68 0.87 549 3271 Protein: 5.48 28.02 10.29 0.87 0 2902 Water: 5.89 63.64 28.58 N/A 549 367 Other: 13.79 22.10 17.94 N/A 0 2 Chain A: 5.61 50.94 12.10 N/A 0 1624 Chain B: 5.48 63.64 11.96 N/A 0 1647 Chain S: 5.89 62.83 30.47 N/A 549 0 Histogram: Values Number of atoms 5.48 - 11.30 2067 11.30 - 17.11 826 17.11 - 22.93 273 22.93 - 28.74 213 28.74 - 34.56 182 34.56 - 40.38 126 40.38 - 46.19 87 46.19 - 52.01 36 52.01 - 57.83 5 57.83 - 63.64 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1336 r_work=0.1193 r_free=0.1336 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1336 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1335 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1335 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753038 | | target function (ml) not normalized (work): 702891.415905 | | target function (ml) not normalized (free): 14718.836818 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1335 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1384 0.1383 0.1445 n_refl.: 191127 remove outliers: r(all,work,free)=0.1384 0.1383 0.1445 n_refl.: 191127 overall B=0.01 to atoms: r(all,work,free)=0.1386 0.1385 0.1446 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1190 0.1326 n_refl.: 191127 remove outliers: r(all,work,free)=0.1192 0.1189 0.1326 n_refl.: 191125 ======================== 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 90.10 88 3 0.3654 356.144 309.920 0.301 0.987 0.050 13.296-10.522 95.05 95 1 0.2273 479.573 461.116 0.693 0.988 0.096 10.503-8.327 97.80 175 3 0.2182 501.949 495.403 0.850 0.989 0.099 8.315-6.595 100.00 359 8 0.2131 374.630 370.062 0.876 0.989 0.086 6.588-5.215 100.00 711 7 0.1902 345.116 335.024 0.876 0.989 0.077 5.214-4.128 98.38 1367 28 0.1236 504.800 498.808 0.966 0.990 0.029 4.126-3.266 94.74 2603 46 0.1156 460.153 452.689 1.028 0.992 0.000 3.266-2.585 99.86 5447 97 0.1122 310.408 306.895 1.012 0.993 0.000 2.585-2.046 97.45 10613 204 0.0959 234.185 231.634 1.019 0.995 0.000 2.046-1.619 99.39 21536 464 0.0907 138.602 137.284 1.035 0.999 0.000 1.619-1.281 98.00 42464 925 0.0946 74.615 73.984 1.025 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.028 38.334 0.992 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0178 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1326 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1190 r_free=0.1330 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1330 | n_water=916 | time (s): 2.900 (total time: 2.900) Filter (dist) r_work=0.1190 r_free=0.1330 | n_water=916 | time (s): 114.680 (total time: 117.580) Filter (q & B) r_work=0.1191 r_free=0.1331 | n_water=901 | time (s): 4.430 (total time: 122.010) Compute maps r_work=0.1191 r_free=0.1331 | n_water=901 | time (s): 1.840 (total time: 123.850) Filter (map) r_work=0.1217 r_free=0.1344 | n_water=778 | time (s): 5.130 (total time: 128.980) Find peaks r_work=0.1217 r_free=0.1344 | n_water=778 | time (s): 0.670 (total time: 129.650) Add new water r_work=0.1222 r_free=0.1351 | n_water=978 | time (s): 4.070 (total time: 133.720) Refine new water occ: r_work=0.1190 r_free=0.1324 adp: r_work=0.1190 r_free=0.1324 occ: r_work=0.1188 r_free=0.1325 adp: r_work=0.1188 r_free=0.1325 occ: r_work=0.1187 r_free=0.1326 adp: r_work=0.1187 r_free=0.1326 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1326 r_work=0.1187 r_free=0.1326 | n_water=978 | time (s): 217.710 (total time: 351.430) Filter (q & B) r_work=0.1190 r_free=0.1334 | n_water=909 | time (s): 4.960 (total time: 356.390) Filter (dist only) r_work=0.1191 r_free=0.1333 | n_water=906 | time (s): 119.490 (total time: 475.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.538242 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.063394 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 0.1194 0.1343 0.0149 0.039 1.1 6.6 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.43 1.49 1.672 13.679 14.063 3.756 11.93 13.44 1.51 1.668 13.680 14.063 3.753 Individual atomic B min max mean iso aniso Overall: 5.50 63.39 14.57 0.86 539 3271 Protein: 5.50 27.98 10.32 0.86 0 2902 Water: 5.93 63.39 28.16 N/A 539 367 Other: 13.81 22.17 17.99 N/A 0 2 Chain A: 5.61 50.86 12.10 N/A 0 1624 Chain B: 5.50 63.39 11.98 N/A 0 1647 Chain S: 5.93 62.80 29.90 N/A 539 0 Histogram: Values Number of atoms 5.50 - 11.29 2056 11.29 - 17.08 832 17.08 - 22.86 285 22.86 - 28.65 222 28.65 - 34.44 184 34.44 - 40.23 105 40.23 - 46.02 79 46.02 - 51.81 38 51.81 - 57.60 4 57.60 - 63.39 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1344 r_work=0.1194 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1344 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1345 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191125 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753173 | | target function (ml) not normalized (work): 702909.245455 | | target function (ml) not normalized (free): 14725.972800 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1345 n_refl.: 191125 re-set all scales: r(all,work,free)=0.1383 0.1381 0.1469 n_refl.: 191125 remove outliers: r(all,work,free)=0.1383 0.1381 0.1469 n_refl.: 191125 overall B=-0.00 to atoms: r(all,work,free)=0.1382 0.1381 0.1468 n_refl.: 191125 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1342 n_refl.: 191125 remove outliers: r(all,work,free)=0.1195 0.1192 0.1342 n_refl.: 191125 ======================== 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 90.10 88 3 0.3682 356.144 327.455 0.336 0.918 0.040 13.296-10.522 95.05 95 1 0.2323 479.573 460.274 0.736 0.919 0.080 10.503-8.327 97.80 175 3 0.2241 501.949 494.236 0.908 0.919 0.099 8.315-6.595 100.00 359 8 0.2146 374.630 369.814 0.941 0.919 0.083 6.588-5.215 100.00 711 7 0.1953 345.116 334.554 0.939 0.920 0.073 5.214-4.128 98.38 1367 28 0.1258 504.800 498.669 1.038 0.921 0.024 4.126-3.266 94.74 2603 46 0.1170 460.153 452.538 1.107 0.922 0.000 3.266-2.585 99.86 5447 97 0.1127 310.408 306.799 1.089 0.923 0.000 2.585-2.046 97.45 10613 204 0.0964 234.185 231.543 1.096 0.925 0.000 2.046-1.619 99.39 21536 464 0.0908 138.602 137.249 1.115 0.929 0.000 1.619-1.281 98.00 42464 925 0.0942 74.615 73.973 1.104 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.028 38.313 1.071 0.946 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=0.1192 r_free=0.1342 After: r_work=0.1193 r_free=0.1342 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1342 | n_water=906 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1193 r_free=0.1343 | n_water=905 | time (s): 119.530 (total time: 122.070) Filter (q & B) r_work=0.1193 r_free=0.1343 | n_water=895 | time (s): 4.750 (total time: 126.820) Compute maps r_work=0.1193 r_free=0.1343 | n_water=895 | time (s): 2.360 (total time: 129.180) Filter (map) r_work=0.1215 r_free=0.1347 | n_water=790 | time (s): 5.910 (total time: 135.090) Find peaks r_work=0.1215 r_free=0.1347 | n_water=790 | time (s): 0.910 (total time: 136.000) Add new water r_work=0.1220 r_free=0.1352 | n_water=980 | time (s): 4.560 (total time: 140.560) Refine new water occ: r_work=0.1189 r_free=0.1326 adp: r_work=0.1190 r_free=0.1326 occ: r_work=0.1188 r_free=0.1325 adp: r_work=0.1188 r_free=0.1325 occ: r_work=0.1187 r_free=0.1324 adp: r_work=0.1187 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1325 r_work=0.1187 r_free=0.1325 | n_water=980 | time (s): 297.120 (total time: 437.680) Filter (q & B) r_work=0.1190 r_free=0.1331 | n_water=911 | time (s): 5.230 (total time: 442.910) Filter (dist only) r_work=0.1191 r_free=0.1330 | n_water=908 | time (s): 118.530 (total time: 561.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.542088 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.408212 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 0.1194 0.1335 0.0141 0.039 1.2 9.4 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.35 1.41 1.673 13.715 14.408 3.755 11.93 13.34 1.41 1.666 13.717 14.408 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 62.75 14.62 0.86 541 3271 Protein: 5.56 28.04 10.34 0.86 0 2902 Water: 6.01 62.75 28.28 N/A 541 367 Other: 13.86 22.18 18.02 N/A 0 2 Chain A: 5.65 50.62 12.10 N/A 0 1624 Chain B: 5.56 62.51 11.98 N/A 0 1647 Chain S: 6.01 62.75 30.21 N/A 541 0 Histogram: Values Number of atoms 5.56 - 11.28 2047 11.28 - 17.00 839 17.00 - 22.72 276 22.72 - 28.44 223 28.44 - 34.15 181 34.15 - 39.87 116 39.87 - 45.59 79 45.59 - 51.31 36 51.31 - 57.03 9 57.03 - 62.75 6 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1334 r_work=0.1194 r_free=0.1334 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1334 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1333 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191125 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1333 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753846 | | target function (ml) not normalized (work): 703035.321173 | | target function (ml) not normalized (free): 14724.847851 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7393 127 0.1355 0.1357 5.6819 5.7334| | 2: 2.94 - 2.33 1.00 7339 128 0.1074 0.1327 5.0689 5.1665| | 3: 2.33 - 2.04 0.96 6939 150 0.0903 0.1151 4.6531 4.737| | 4: 2.04 - 1.85 1.00 7170 155 0.0903 0.1079 4.3914 4.5702| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0984 4.1492 4.2363| | 6: 1.72 - 1.62 0.99 7102 142 0.0892 0.1075 3.9429 4.0643| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0965 3.8003 3.9337| | 8: 1.54 - 1.47 0.96 6798 152 0.0894 0.1303 3.7015 3.9049| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1116 3.624 3.7568| | 10: 1.41 - 1.36 0.99 7022 150 0.0977 0.1192 3.5574 3.6835| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1131 3.4873 3.5905| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1134 3.4618 3.5874| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1254 3.4407 3.5696| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1586 3.4343 3.6898| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1249 3.4497 3.494| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1533 3.4653 3.6515| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1223 3.4331 3.4425| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1702 3.4379 3.5319| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1771 3.4191 3.6062| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1570 3.4093 3.4297| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2142 3.4177 3.5044| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1960 3.4132 3.4143| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2022 3.4335 3.4881| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2267 3.4366 3.5137| | 25: 1.02 - 1.01 0.93 6552 130 0.2615 0.2513 3.4499 3.525| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2875 3.4156 3.4236| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2796 3.4696 3.394| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7393 127 0.93 11.11 1.00 0.96 10406.95| | 2: 2.94 - 2.33 7339 128 0.93 12.32 0.99 0.96 4857.80| | 3: 2.33 - 2.04 6939 150 0.96 7.58 1.01 0.96 1691.25| | 4: 2.04 - 1.85 7170 155 0.96 7.60 1.00 0.96 996.54| | 5: 1.85 - 1.72 7113 159 0.96 8.01 1.00 0.96 627.62| | 6: 1.72 - 1.62 7102 142 0.96 7.91 1.00 0.96 438.18| | 7: 1.62 - 1.54 7104 148 0.96 8.12 1.01 0.97 335.91| | 8: 1.54 - 1.47 6798 152 0.96 8.29 1.01 0.97 279.82| | 9: 1.47 - 1.41 6938 155 0.96 8.51 1.00 0.98 232.46| | 10: 1.41 - 1.36 7022 150 0.96 8.98 1.00 0.97 204.10| | 11: 1.36 - 1.32 6997 151 0.96 9.01 0.99 0.96 176.87| | 12: 1.32 - 1.28 6975 149 0.96 9.07 0.98 0.95 163.03| | 13: 1.28 - 1.25 6907 166 0.96 9.65 1.01 0.96 160.84| | 14: 1.25 - 1.22 7015 112 0.95 10.82 1.01 0.96 165.15| | 15: 1.22 - 1.19 6956 137 0.94 11.32 1.01 0.98 167.87| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.01 0.96 160.46| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.96 154.03| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.95 147.66| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.95 151.20| | 20: 1.10 - 1.08 6884 147 0.92 15.19 1.00 0.94 149.86| | 21: 1.08 - 1.07 6852 152 0.91 16.60 1.00 0.93 153.05| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.93 154.85| | 23: 1.05 - 1.03 6827 159 0.87 20.54 0.99 0.92 165.34| | 24: 1.03 - 1.02 6784 133 0.85 23.22 0.99 0.93 179.91| | 25: 1.02 - 1.01 6552 130 0.83 25.20 0.98 0.90 182.66| | 26: 1.01 - 0.99 6767 158 0.81 26.59 0.98 0.88 176.37| | 27: 0.99 - 0.98 6647 131 0.82 26.14 0.99 0.87 159.79| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.66 max = 10406.95 mean = 882.77| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.26| |phase err.(test): min = 0.00 max = 88.51 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1333 n_refl.: 191125 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1462 n_refl.: 191125 remove outliers: r(all,work,free)=0.1391 0.1390 0.1462 n_refl.: 191125 overall B=-0.05 to atoms: r(all,work,free)=0.1384 0.1383 0.1458 n_refl.: 191125 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1334 n_refl.: 191125 remove outliers: r(all,work,free)=0.1195 0.1192 0.1334 n_refl.: 191125 ======================== 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 90.10 88 3 0.3679 356.144 326.970 0.326 0.919 0.040 13.296-10.522 95.05 95 1 0.2314 479.573 462.012 0.719 0.920 0.090 10.503-8.327 97.80 175 3 0.2215 501.949 494.946 0.885 0.920 0.089 8.315-6.595 100.00 359 8 0.2142 374.630 370.012 0.914 0.920 0.079 6.588-5.215 100.00 711 7 0.1938 345.116 334.752 0.914 0.921 0.070 5.214-4.128 98.38 1367 28 0.1240 504.800 498.532 1.011 0.922 0.020 4.126-3.266 94.74 2603 46 0.1165 460.153 452.483 1.080 0.923 0.000 3.266-2.585 99.86 5447 97 0.1124 310.408 306.950 1.061 0.925 0.000 2.585-2.046 97.45 10613 204 0.0964 234.185 231.588 1.067 0.927 0.000 2.046-1.619 99.39 21536 464 0.0910 138.602 137.239 1.084 0.931 0.000 1.619-1.281 98.00 42464 925 0.0947 74.615 73.965 1.072 0.938 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.028 38.305 1.037 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0111 ================= 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 : 0.2028 0.1978 0.083 5.168 5.2 78.0 14.6 805 0.000 1_bss: 0.1796 0.1924 0.083 5.168 5.2 78.0 14.6 805 0.000 1_settarget: 0.1796 0.1924 0.083 5.168 5.2 78.0 14.6 805 0.000 1_nqh: 0.1801 0.1924 0.083 5.168 5.2 78.0 14.6 805 0.003 1_weight: 0.1801 0.1924 0.083 5.168 5.2 78.0 14.6 805 0.003 1_xyzrec: 0.1273 0.1502 0.038 1.162 5.2 78.0 14.6 805 0.158 1_adp: 0.1297 0.1565 0.038 1.162 5.2 73.0 15.1 805 0.158 1_regHadp: 0.1296 0.1560 0.038 1.162 5.2 73.0 15.1 805 0.158 1_occ: 0.1281 0.1549 0.038 1.162 5.2 73.0 15.1 805 0.158 2_bss: 0.1272 0.1537 0.038 1.162 5.4 73.2 15.2 805 0.158 2_settarget: 0.1272 0.1537 0.038 1.162 5.4 73.2 15.2 805 0.158 2_updatecdl: 0.1272 0.1537 0.038 1.173 5.4 73.2 15.2 805 0.158 2_nqh: 0.1272 0.1537 0.038 1.173 5.4 73.2 15.2 805 0.158 2_sol: 0.1269 0.1501 0.038 1.173 5.4 73.2 16.3 886 n/a 2_weight: 0.1269 0.1501 0.038 1.173 5.4 73.2 16.3 886 n/a 2_xyzrec: 0.1252 0.1517 0.041 1.140 5.4 73.2 16.3 886 n/a 2_adp: 0.1235 0.1513 0.041 1.140 5.4 68.8 16.4 886 n/a 2_regHadp: 0.1235 0.1514 0.041 1.140 5.4 68.8 16.4 886 n/a 2_occ: 0.1229 0.1514 0.041 1.140 5.4 68.8 16.4 886 n/a 3_bss: 0.1236 0.1519 0.041 1.140 5.4 68.8 16.3 886 n/a 3_settarget: 0.1236 0.1519 0.041 1.140 5.4 68.8 16.3 886 n/a 3_updatecdl: 0.1236 0.1519 0.041 1.148 5.4 68.8 16.3 886 n/a 3_nqh: 0.1236 0.1519 0.041 1.148 5.4 68.8 16.3 886 n/a 3_sol: 0.1251 0.1516 0.041 1.148 5.4 68.8 15.4 873 n/a 3_weight: 0.1251 0.1516 0.041 1.148 5.4 68.8 15.4 873 n/a 3_xyzrec: 0.1242 0.1442 0.035 1.102 5.4 68.8 15.4 873 n/a 3_adp: 0.1237 0.1398 0.035 1.102 5.5 68.2 15.2 873 n/a 3_regHadp: 0.1237 0.1399 0.035 1.102 5.5 68.2 15.2 873 n/a 3_occ: 0.1231 0.1389 0.035 1.102 5.5 68.2 15.2 873 n/a 4_bss: 0.1226 0.1381 0.035 1.102 5.5 68.2 15.2 873 n/a 4_settarget: 0.1226 0.1381 0.035 1.102 5.5 68.2 15.2 873 n/a 4_updatecdl: 0.1226 0.1381 0.035 1.103 5.5 68.2 15.2 873 n/a 4_nqh: 0.1226 0.1381 0.035 1.103 5.5 68.2 15.2 873 n/a 4_sol: 0.1208 0.1365 0.035 1.103 5.5 68.2 15.0 869 n/a 4_weight: 0.1208 0.1365 0.035 1.103 5.5 68.2 15.0 869 n/a 4_xyzrec: 0.1206 0.1368 0.036 1.119 5.5 68.2 15.0 869 n/a 4_adp: 0.1200 0.1368 0.036 1.119 5.5 67.5 15.0 869 n/a 4_regHadp: 0.1200 0.1368 0.036 1.119 5.5 67.5 15.0 869 n/a 4_occ: 0.1197 0.1367 0.036 1.119 5.5 67.5 15.0 869 n/a 5_bss: 0.1195 0.1363 0.036 1.119 5.5 67.5 14.9 869 n/a 5_settarget: 0.1195 0.1363 0.036 1.119 5.5 67.5 14.9 869 n/a 5_updatecdl: 0.1195 0.1363 0.036 1.119 5.5 67.5 14.9 869 n/a 5_nqh: 0.1195 0.1363 0.036 1.119 5.5 67.5 14.9 869 n/a 5_sol: 0.1193 0.1351 0.036 1.119 5.5 67.5 15.0 886 n/a 5_weight: 0.1193 0.1351 0.036 1.119 5.5 67.5 15.0 886 n/a 5_xyzrec: 0.1196 0.1358 0.037 1.130 5.5 67.5 15.0 886 n/a 5_adp: 0.1198 0.1360 0.037 1.130 5.6 67.3 15.0 886 n/a 5_regHadp: 0.1198 0.1360 0.037 1.130 5.6 67.3 15.0 886 n/a 5_occ: 0.1196 0.1362 0.037 1.130 5.6 67.3 15.0 886 n/a 6_bss: 0.1195 0.1361 0.037 1.130 5.5 67.2 14.9 886 n/a 6_settarget: 0.1195 0.1361 0.037 1.130 5.5 67.2 14.9 886 n/a 6_updatecdl: 0.1195 0.1361 0.037 1.131 5.5 67.2 14.9 886 n/a 6_nqh: 0.1195 0.1361 0.037 1.131 5.5 67.2 14.9 886 n/a 6_sol: 0.1193 0.1349 0.037 1.131 5.5 67.2 15.0 904 n/a 6_weight: 0.1193 0.1349 0.037 1.131 5.5 67.2 15.0 904 n/a 6_xyzrec: 0.1196 0.1352 0.037 1.138 5.5 67.2 15.0 904 n/a 6_adp: 0.1201 0.1358 0.037 1.138 5.6 66.0 14.9 904 n/a 6_regHadp: 0.1201 0.1358 0.037 1.138 5.6 66.0 14.9 904 n/a 6_occ: 0.1199 0.1357 0.037 1.138 5.6 66.0 14.9 904 n/a 7_bss: 0.1199 0.1357 0.037 1.138 5.3 65.8 14.7 904 n/a 7_settarget: 0.1199 0.1357 0.037 1.138 5.3 65.8 14.7 904 n/a 7_updatecdl: 0.1199 0.1357 0.037 1.137 5.3 65.8 14.7 904 n/a 7_nqh: 0.1199 0.1357 0.037 1.137 5.3 65.8 14.7 904 n/a 7_sol: 0.1200 0.1347 0.037 1.137 5.3 65.8 14.6 903 n/a 7_weight: 0.1200 0.1347 0.037 1.137 5.3 65.8 14.6 903 n/a 7_xyzrec: 0.1203 0.1353 0.037 1.123 5.3 65.8 14.6 903 n/a 7_adp: 0.1204 0.1355 0.037 1.123 5.4 64.6 14.6 903 n/a 7_regHadp: 0.1204 0.1356 0.037 1.123 5.4 64.6 14.6 903 n/a 7_occ: 0.1202 0.1354 0.037 1.123 5.4 64.6 14.6 903 n/a 8_bss: 0.1192 0.1345 0.037 1.123 5.4 64.7 14.7 903 n/a 8_settarget: 0.1192 0.1345 0.037 1.123 5.4 64.7 14.7 903 n/a 8_updatecdl: 0.1192 0.1345 0.037 1.123 5.4 64.7 14.7 903 n/a 8_nqh: 0.1192 0.1345 0.037 1.123 5.4 64.7 14.7 903 n/a 8_sol: 0.1190 0.1332 0.037 1.123 5.4 64.7 14.7 916 n/a 8_weight: 0.1190 0.1332 0.037 1.123 5.4 64.7 14.7 916 n/a 8_xyzrec: 0.1193 0.1334 0.038 1.112 5.4 64.7 14.7 916 n/a 8_adp: 0.1193 0.1336 0.038 1.112 5.5 63.6 14.7 916 n/a 8_regHadp: 0.1193 0.1336 0.038 1.112 5.5 63.6 14.7 916 n/a 8_occ: 0.1191 0.1335 0.038 1.112 5.5 63.6 14.7 916 n/a 9_bss: 0.1189 0.1326 0.038 1.112 5.5 63.7 14.7 916 n/a 9_settarget: 0.1189 0.1326 0.038 1.112 5.5 63.7 14.7 916 n/a 9_updatecdl: 0.1189 0.1326 0.038 1.112 5.5 63.7 14.7 916 n/a 9_nqh: 0.1190 0.1330 0.038 1.112 5.5 63.7 14.7 916 n/a 9_sol: 0.1191 0.1333 0.038 1.112 5.5 63.7 14.6 906 n/a 9_weight: 0.1191 0.1333 0.038 1.112 5.5 63.7 14.6 906 n/a 9_xyzrec: 0.1194 0.1343 0.039 1.111 5.5 63.7 14.6 906 n/a 9_adp: 0.1194 0.1344 0.039 1.111 5.5 63.4 14.6 906 n/a 9_regHadp: 0.1194 0.1344 0.039 1.111 5.5 63.4 14.6 906 n/a 9_occ: 0.1193 0.1345 0.039 1.111 5.5 63.4 14.6 906 n/a 10_bss: 0.1192 0.1342 0.039 1.111 5.5 63.4 14.6 906 n/a 10_settarget: 0.1192 0.1342 0.039 1.111 5.5 63.4 14.6 906 n/a 10_updatecdl: 0.1192 0.1342 0.039 1.112 5.5 63.4 14.6 906 n/a 10_setrh: 0.1193 0.1342 0.039 1.112 5.5 63.4 14.6 906 n/a 10_nqh: 0.1193 0.1342 0.039 1.112 5.5 63.4 14.6 906 n/a 10_sol: 0.1191 0.1330 0.039 1.112 5.5 63.4 14.6 908 n/a 10_weight: 0.1191 0.1330 0.039 1.112 5.5 63.4 14.6 908 n/a 10_xyzrec: 0.1194 0.1335 0.039 1.158 5.5 63.4 14.6 908 n/a 10_adp: 0.1193 0.1334 0.039 1.158 5.6 62.7 14.6 908 n/a 10_regHadp: 0.1194 0.1334 0.039 1.158 5.6 62.7 14.6 908 n/a 10_occ: 0.1192 0.1333 0.039 1.158 5.6 62.7 14.6 908 n/a end: 0.1192 0.1334 0.039 1.158 5.5 62.7 14.6 908 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6790396_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6790396_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.1800 Refinement macro-cycles (run) : 12338.4000 Write final files (write_after_run_outputs) : 143.2000 Total : 12487.7800 Total CPU time: 3.48 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:45:23 PST -0800 (1736736323.08 s) Start R-work = 0.1796, R-free = 0.1924 Final R-work = 0.1192, R-free = 0.1334 =============================================================================== Job complete usr+sys time: 12759.99 seconds wall clock time: 213 minutes 42.90 seconds (12822.90 seconds total)