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_8840372.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8840372.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8840372.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" } 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 =============================================================================== 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: 1.63, 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: 2.631 distance_ideal: 2.720 ideal - model: 0.089 slack: 0.000 delta_slack: 0.089 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: 2.710 distance_ideal: 2.710 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 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: 0.90 Conformation dependent library (CDL) restraints added in 118.6 milliseconds Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.76 - 0.99: 478 0.99 - 1.22: 2594 1.22 - 1.45: 1419 1.45 - 1.67: 1380 1.67 - 1.90: 63 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL A 150 " pdb=" CB VAL A 150 " ideal model delta sigma weight residual 1.541 1.785 -0.245 1.05e-02 9.07e+03 5.42e+02 bond pdb=" CD2 HIS B 116 " pdb=" HD2 HIS B 116 " ideal model delta sigma weight residual 0.930 1.333 -0.403 2.00e-02 2.50e+03 4.05e+02 bond pdb=" N LYS A 133 " pdb=" CA LYS A 133 " ideal model delta sigma weight residual 1.457 1.225 0.232 1.16e-02 7.43e+03 4.00e+02 bond pdb=" CB ILE A 45 " pdb=" HB ILE A 45 " ideal model delta sigma weight residual 0.970 1.348 -0.378 2.00e-02 2.50e+03 3.57e+02 bond pdb=" N LEU B 72 " pdb=" CA LEU B 72 " ideal model delta sigma weight residual 1.456 1.244 0.212 1.13e-02 7.83e+03 3.52e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 5556 4.07 - 8.14: 3615 8.14 - 12.21: 1329 12.21 - 16.28: 286 16.28 - 20.35: 24 Bond angle restraints: 10810 Sorted by residual: angle pdb=" ND1 HIS A 116 " pdb=" CG HIS A 116 " pdb=" CD2 HIS A 116 " ideal model delta sigma weight residual 106.10 122.94 -16.84 1.00e+00 1.00e+00 2.83e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 128.74 -14.94 1.00e+00 1.00e+00 2.23e+02 angle pdb=" NE ARG B 143 " pdb=" CZ ARG B 143 " pdb=" NH2 ARG B 143 " ideal model delta sigma weight residual 119.20 132.25 -13.05 9.00e-01 1.23e+00 2.10e+02 angle pdb=" NE ARG A 149 " pdb=" CZ ARG A 149 " pdb=" NH2 ARG A 149 " ideal model delta sigma weight residual 119.20 131.66 -12.46 9.00e-01 1.23e+00 1.92e+02 angle pdb=" O ALA B 108 " pdb=" C ALA B 108 " pdb=" N PRO B 109 " ideal model delta sigma weight residual 121.32 105.68 15.64 1.15e+00 7.56e-01 1.85e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 1822 16.35 - 32.70: 157 32.70 - 49.05: 44 49.05 - 65.40: 21 65.40 - 81.74: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: 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 180.00 150.32 29.68 0 5.00e+00 4.00e-02 3.52e+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 -153.03 -26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual 180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.229: 241 0.229 - 0.458: 141 0.458 - 0.687: 78 0.687 - 0.916: 29 0.916 - 1.145: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ALA A 108 " pdb=" N ALA A 108 " pdb=" C ALA A 108 " pdb=" CB ALA A 108 " both_signs ideal model delta sigma weight residual False 2.48 1.34 1.14 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" CA PRO B 115 " pdb=" N PRO B 115 " pdb=" C PRO B 115 " pdb=" CB PRO B 115 " both_signs ideal model delta sigma weight residual False 2.72 1.62 1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.66 -0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " 0.012 2.00e-02 2.50e+03 8.02e-02 2.57e+02 pdb=" CG TRP B 146 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.150 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.141 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.056 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.103 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.123 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.014 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.030 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.123 2.00e-02 2.50e+03 8.56e-02 2.20e+02 pdb=" CG PHE B 164 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.100 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.032 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.095 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.072 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 82 " 0.096 2.00e-02 2.50e+03 8.18e-02 2.01e+02 pdb=" CG PHE B 82 " -0.106 2.00e-02 2.50e+03 pdb=" CD1 PHE B 82 " -0.112 2.00e-02 2.50e+03 pdb=" CD2 PHE B 82 " -0.077 2.00e-02 2.50e+03 pdb=" CE1 PHE B 82 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 PHE B 82 " -0.073 2.00e-02 2.50e+03 pdb=" CZ PHE B 82 " 0.108 2.00e-02 2.50e+03 pdb=" HD1 PHE B 82 " 0.067 2.00e-02 2.50e+03 pdb=" HD2 PHE B 82 " 0.059 2.00e-02 2.50e+03 pdb=" HE1 PHE B 82 " -0.084 2.00e-02 2.50e+03 pdb=" HE2 PHE B 82 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE B 82 " 0.039 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 30 1.64 - 2.38: 2697 2.38 - 3.12: 22419 3.12 - 3.86: 32980 3.86 - 4.60: 52249 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110375 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.900 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.974 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.032 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.110 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.163 2.620 ... (remaining 110370 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_8840372_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= 0.2032 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.298683 | | target function (ml) not normalized (work): 805199.269362 | | target function (ml) not normalized (free): 16526.900393 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2144 0.2002 6.6768 6.3225| | 2: 2.94 - 2.33 1.00 7339 128 0.1611 0.1520 5.543 5.5827| | 3: 2.33 - 2.04 0.96 6939 150 0.1629 0.1600 5.1383 5.1561| | 4: 2.04 - 1.85 1.00 7170 155 0.1741 0.1603 4.9552 5.0279| | 5: 1.85 - 1.72 0.99 7113 159 0.1909 0.1716 4.7903 4.8281| | 6: 1.72 - 1.62 0.99 7102 142 0.1978 0.1950 4.6704 4.7397| | 7: 1.62 - 1.54 0.99 7104 148 0.2022 0.1871 4.56 4.6069| | 8: 1.54 - 1.47 0.96 6798 152 0.2034 0.2251 4.4744 4.5524| | 9: 1.47 - 1.41 0.98 6938 155 0.2097 0.2153 4.3924 4.4643| | 10: 1.41 - 1.36 0.99 7022 150 0.2112 0.2089 4.3007 4.3452| | 11: 1.36 - 1.32 0.99 6997 151 0.2148 0.1768 4.2402 4.1087| | 12: 1.32 - 1.28 0.98 6976 149 0.2093 0.1938 4.1766 4.2348| | 13: 1.28 - 1.25 0.98 6907 166 0.1986 0.1986 4.1002 4.1085| | 14: 1.25 - 1.22 0.98 7015 113 0.2073 0.2463 4.0737 4.3783| | 15: 1.22 - 1.19 0.98 6957 137 0.2101 0.1818 4.0471 3.9758| | 16: 1.19 - 1.17 0.93 6604 132 0.2097 0.2192 4.001 4.0451| | 17: 1.17 - 1.14 0.98 6941 135 0.2179 0.1866 3.9654 3.9498| | 18: 1.14 - 1.12 0.98 6875 142 0.2244 0.2098 3.9327 3.8594| | 19: 1.12 - 1.10 0.97 6949 106 0.2263 0.2436 3.8687 3.9853| | 20: 1.10 - 1.08 0.97 6884 147 0.2333 0.2299 3.8219 3.8695| | 21: 1.08 - 1.07 0.97 6852 152 0.2428 0.2815 3.7905 3.8605| | 22: 1.07 - 1.05 0.97 6838 135 0.2532 0.2481 3.7472 3.7577| | 23: 1.05 - 1.03 0.97 6829 159 0.2730 0.2651 3.7298 3.8206| | 24: 1.03 - 1.02 0.96 6785 133 0.2888 0.2723 3.7013 3.7394| | 25: 1.02 - 1.01 0.93 6552 130 0.3067 0.2905 3.6701 3.6999| | 26: 1.01 - 0.99 0.96 6767 158 0.3189 0.3193 3.629 3.6138| | 27: 0.99 - 0.98 0.94 6648 131 0.3422 0.2978 3.6555 3.5737| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.85 20.76 0.91 0.97 36613.94| | 2: 2.94 - 2.33 7339 128 0.85 21.40 1.08 1.03 15429.52| | 3: 2.33 - 2.04 6939 150 0.93 12.47 1.11 1.07 4129.03| | 4: 2.04 - 1.85 7170 155 0.92 13.50 1.11 1.08 2819.15| | 5: 1.85 - 1.72 7113 159 0.91 16.04 1.12 1.08 2170.21| | 6: 1.72 - 1.62 7102 142 0.89 17.26 1.11 1.07 1741.09| | 7: 1.62 - 1.54 7104 148 0.88 18.60 1.11 1.06 1439.50| | 8: 1.54 - 1.47 6798 152 0.88 18.88 1.10 1.06 1213.61| | 9: 1.47 - 1.41 6938 155 0.88 19.17 1.10 1.06 997.35| | 10: 1.41 - 1.36 7022 150 0.87 19.59 1.09 1.06 818.20| | 11: 1.36 - 1.32 6997 151 0.88 18.87 1.08 1.04 662.26| | 12: 1.32 - 1.28 6976 149 0.88 18.78 1.08 1.04 586.26| | 13: 1.28 - 1.25 6907 166 0.88 18.74 1.07 1.04 550.78| | 14: 1.25 - 1.22 7015 113 0.87 20.00 1.08 1.05 544.61| | 15: 1.22 - 1.19 6957 137 0.87 20.41 1.08 1.04 524.64| | 16: 1.19 - 1.17 6604 132 0.88 19.95 1.07 1.04 473.76| | 17: 1.17 - 1.14 6941 135 0.87 19.94 1.08 1.03 410.33| | 18: 1.14 - 1.12 6875 142 0.88 19.86 1.08 1.00 355.20| | 19: 1.12 - 1.10 6949 106 0.87 21.09 1.07 1.00 351.60| | 20: 1.10 - 1.08 6884 147 0.85 22.54 1.06 0.98 342.18| | 21: 1.08 - 1.07 6852 152 0.83 24.39 1.06 0.99 352.05| | 22: 1.07 - 1.05 6838 135 0.82 25.90 1.05 0.97 337.53| | 23: 1.05 - 1.03 6829 159 0.80 27.83 1.05 0.97 334.11| | 24: 1.03 - 1.02 6785 133 0.78 29.17 1.05 0.97 319.93| | 25: 1.02 - 1.01 6552 130 0.78 29.95 1.03 0.94 297.09| | 26: 1.01 - 0.99 6767 158 0.77 30.61 1.03 0.93 270.53| | 27: 0.99 - 0.98 6648 131 0.78 29.28 1.03 0.93 235.05| |alpha: min = 0.93 max = 1.08 mean = 1.02| |beta: min = 235.05 max = 36613.94 mean = 2883.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 21.22| |phase err.(test): min = 0.00 max = 89.31 mean = 21.33| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.245 2950 Z= 5.403 Angle : 5.119 16.896 4018 Z= 3.631 Chirality : 0.363 1.145 492 Planarity : 0.035 0.201 512 Dihedral : 13.003 81.745 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.78 % Allowed : 4.40 % Favored : 94.82 % Rotamer: Outliers : 1.61 % Allowed : 5.16 % Favored : 93.23 % Cbeta Deviations : 28.09 % 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: -2.45 (0.39), residues: 386 helix: -3.19 (0.27), residues: 144 sheet: -1.33 (0.48), residues: 82 loop : 0.16 (0.51), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.080 0.016 ARG B 100 TYR 0.112 0.037 TYR B 67 PHE 0.133 0.039 PHE B 82 TRP 0.153 0.041 TRP B 146 HIS 0.094 0.030 HIS B 96 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= 0.2032 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.298683 | | target function (ml) not normalized (work): 805199.269362 | | target function (ml) not normalized (free): 16526.900393 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2030 0.2032 0.1957 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2030 0.2032 0.1957 n_refl.: 191155 remove outliers: r(all,work,free)=0.2030 0.2033 0.1957 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2031 0.2033 0.1958 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1801 0.1799 0.1893 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1797 0.1892 n_refl.: 191140 ======================== 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 0.4214 400.535 296.997 0.434 0.912 0.295 13.296-10.522 100.00 100 1 0.2605 534.497 518.298 0.779 0.913 0.242 10.503-8.327 99.45 178 3 0.2551 565.118 555.311 0.971 0.913 0.219 8.318-6.595 100.00 360 8 0.2509 414.736 403.238 0.971 0.913 0.165 6.588-5.215 100.00 711 7 0.2257 381.101 365.640 0.958 0.913 0.150 5.214-4.128 98.38 1367 28 0.1494 557.435 549.374 1.073 0.913 0.090 4.126-3.266 94.74 2603 46 0.1338 508.132 499.739 1.148 0.913 0.060 3.266-2.585 99.86 5447 97 0.1446 342.774 337.739 1.119 0.912 0.000 2.585-2.046 97.45 10613 204 0.1396 258.603 254.155 1.126 0.912 0.000 2.046-1.619 99.39 21536 464 0.1603 153.054 149.872 1.143 0.910 0.000 1.619-1.281 98.00 42464 925 0.1922 82.395 80.207 1.131 0.908 0.000 1.281-0.980 96.53 101826 2055 0.2318 44.202 41.656 1.112 0.903 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0090 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1892 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 r_work=0.1801 r_free=0.1897 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.166694 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.337779 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 0.1276 0.1505 0.0229 0.040 1.2 11.2 0.0 0.3 0 11.083 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.76 15.05 2.29 1.117 13.116 573.338 0.019 13.00 15.73 2.73 1.249 13.350 573.338 0.018 Individual atomic B min max mean iso aniso Overall: 5.20 73.05 15.03 1.40 435 3274 Protein: 5.20 40.32 11.01 1.40 0 2902 Water: 6.33 73.05 29.49 N/A 435 370 Other: 16.02 30.93 23.47 N/A 0 2 Chain A: 5.36 59.48 13.06 N/A 0 1626 Chain B: 5.20 73.05 12.78 N/A 0 1648 Chain S: 11.91 64.65 30.90 N/A 435 0 Histogram: Values Number of atoms 5.20 - 11.99 2165 11.99 - 18.77 642 18.77 - 25.56 310 25.56 - 32.34 265 32.34 - 39.13 157 39.13 - 45.91 106 45.91 - 52.69 41 52.69 - 59.48 17 59.48 - 66.26 5 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1301 r_free=0.1573 r_work=0.1300 r_free=0.1569 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1300 r_free = 0.1569 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 = 0.1285 r_free = 0.1557 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1285 r_free= 0.1557 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015738 | | target function (ls_wunit_k1) not normalized (work): 2947.632025 | | target function (ls_wunit_k1) not normalized (free): 114.696126 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1285 0.1557 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1476 0.1473 0.1635 n_refl.: 191140 remove outliers: r(all,work,free)=0.1476 0.1473 0.1635 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1499 0.1497 0.1646 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1278 0.1548 n_refl.: 191140 remove outliers: r(all,work,free)=0.1283 0.1278 0.1548 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3608 402.814 376.552 0.480 0.962 0.270 13.296-10.522 100.00 100 1 0.2141 534.497 529.327 0.742 0.964 0.224 10.503-8.327 99.45 178 3 0.1780 565.118 563.540 0.891 0.964 0.210 8.318-6.595 100.00 360 8 0.1702 414.736 412.313 0.910 0.964 0.155 6.588-5.215 100.00 711 7 0.1532 381.101 373.634 0.888 0.964 0.150 5.214-4.128 98.38 1367 28 0.0902 557.435 554.801 0.976 0.964 0.065 4.126-3.266 94.74 2603 46 0.0831 508.132 503.920 1.045 0.965 0.050 3.266-2.585 99.86 5447 97 0.0924 342.774 340.262 1.025 0.964 0.000 2.585-2.046 97.45 10613 204 0.0956 258.603 256.327 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1095 153.054 151.348 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.421 1.048 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.194 1.026 0.964 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0354 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1278 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1548 | n_water=805 | time (s): 2.700 (total time: 2.700) Filter (dist) r_work=0.1282 r_free=0.1553 | n_water=794 | time (s): 97.660 (total time: 100.360) Filter (q & B) r_work=0.1282 r_free=0.1551 | n_water=791 | time (s): 4.800 (total time: 105.160) Compute maps r_work=0.1282 r_free=0.1551 | n_water=791 | time (s): 2.450 (total time: 107.610) Filter (map) r_work=0.1311 r_free=0.1531 | n_water=644 | time (s): 5.340 (total time: 112.950) Find peaks r_work=0.1311 r_free=0.1531 | n_water=644 | time (s): 0.630 (total time: 113.580) Add new water r_work=0.1335 r_free=0.1571 | n_water=947 | time (s): 3.910 (total time: 117.490) Refine new water occ: r_work=0.1288 r_free=0.1512 adp: r_work=0.1276 r_free=0.1511 occ: r_work=0.1278 r_free=0.1505 adp: r_work=0.1272 r_free=0.1507 occ: r_work=0.1273 r_free=0.1503 adp: r_work=0.1270 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1270 r_free=0.1504 r_work=0.1270 r_free=0.1504 | n_water=947 | time (s): 82.690 (total time: 200.180) Filter (q & B) r_work=0.1274 r_free=0.1506 | n_water=882 | time (s): 5.580 (total time: 205.760) Filter (dist only) r_work=0.1274 r_free=0.1505 | n_water=880 | time (s): 110.120 (total time: 315.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.116141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 592.395615 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 0.1257 0.1528 0.0270 0.041 1.1 19.5 0.0 0.0 0 12.058 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.28 2.70 2.044 15.174 592.396 0.015 12.34 15.14 2.79 2.415 15.251 592.396 0.014 Individual atomic B min max mean iso aniso Overall: 5.31 72.90 16.36 1.22 512 3272 Protein: 5.31 40.66 10.98 1.22 0 2902 Water: 6.53 72.90 34.05 N/A 512 368 Other: 16.11 33.76 24.94 N/A 0 2 Chain A: 5.54 55.36 13.03 N/A 0 1624 Chain B: 5.31 68.20 12.84 N/A 0 1648 Chain S: 13.55 72.90 38.22 N/A 512 0 Histogram: Values Number of atoms 5.31 - 12.07 2149 12.07 - 18.83 672 18.83 - 25.59 263 25.59 - 32.35 206 32.35 - 39.10 176 39.10 - 45.86 162 45.86 - 52.62 86 52.62 - 59.38 47 59.38 - 66.14 15 66.14 - 72.90 8 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1514 r_work=0.1235 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1515 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 = 0.1510 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013602 | | target function (ls_wunit_k1) not normalized (work): 2547.634864 | | target function (ls_wunit_k1) not normalized (free): 100.448691 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1510 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1440 0.1437 0.1611 n_refl.: 191139 remove outliers: r(all,work,free)=0.1440 0.1437 0.1611 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1437 0.1433 0.1609 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1517 n_refl.: 191139 remove outliers: r(all,work,free)=0.1241 0.1236 0.1517 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3205 402.814 379.469 0.485 0.962 0.265 13.296-10.522 100.00 100 1 0.1940 534.497 525.377 0.762 0.963 0.213 10.503-8.327 99.45 178 3 0.1480 565.118 566.213 0.921 0.963 0.174 8.318-6.595 100.00 360 8 0.1535 414.736 414.148 0.937 0.963 0.155 6.588-5.215 100.00 711 7 0.1349 381.101 376.521 0.913 0.963 0.150 5.214-4.128 98.38 1367 28 0.0837 557.435 556.157 0.995 0.963 0.100 4.126-3.266 94.74 2603 46 0.0767 508.132 505.467 1.060 0.963 0.022 3.266-2.585 99.86 5447 97 0.0865 342.774 341.155 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0906 258.603 256.736 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.609 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.362 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.218 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0572 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1517 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1517 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1517 | n_water=880 | time (s): 3.120 (total time: 3.120) Filter (dist) r_work=0.1238 r_free=0.1519 | n_water=873 | time (s): 108.130 (total time: 111.250) Filter (q & B) r_work=0.1239 r_free=0.1521 | n_water=872 | time (s): 5.650 (total time: 116.900) Compute maps r_work=0.1239 r_free=0.1521 | n_water=872 | time (s): 1.730 (total time: 118.630) Filter (map) r_work=0.1276 r_free=0.1528 | n_water=682 | time (s): 5.020 (total time: 123.650) Find peaks r_work=0.1276 r_free=0.1528 | n_water=682 | time (s): 0.700 (total time: 124.350) Add new water r_work=0.1302 r_free=0.1568 | n_water=996 | time (s): 5.390 (total time: 129.740) Refine new water occ: r_work=0.1256 r_free=0.1522 adp: r_work=0.1256 r_free=0.1523 occ: r_work=0.1252 r_free=0.1520 adp: r_work=0.1252 r_free=0.1520 occ: r_work=0.1249 r_free=0.1517 adp: r_work=0.1248 r_free=0.1517 ADP+occupancy (water only), MIN, final r_work=0.1248 r_free=0.1517 r_work=0.1248 r_free=0.1517 | n_water=996 | time (s): 366.510 (total time: 496.250) Filter (q & B) r_work=0.1252 r_free=0.1523 | n_water=867 | time (s): 4.950 (total time: 501.200) Filter (dist only) r_work=0.1253 r_free=0.1523 | n_water=866 | time (s): 110.630 (total time: 611.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.666261 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.617585 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 0.1241 0.1443 0.0202 0.034 1.1 7.5 0.0 0.0 0 0.833 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.43 2.02 1.936 14.569 16.618 3.939 12.36 14.04 1.68 2.260 14.464 16.618 3.898 Individual atomic B min max mean iso aniso Overall: 5.54 67.74 15.22 1.05 501 3269 Protein: 5.54 36.28 10.73 1.05 0 2902 Water: 6.67 67.74 30.25 N/A 501 365 Other: 13.99 29.77 21.88 N/A 0 2 Chain A: 5.59 54.68 12.77 N/A 0 1624 Chain B: 5.54 67.74 12.50 N/A 0 1645 Chain S: 14.06 64.58 32.09 N/A 501 0 Histogram: Values Number of atoms 5.54 - 11.76 2130 11.76 - 17.98 690 17.98 - 24.20 302 24.20 - 30.42 222 30.42 - 36.64 176 36.64 - 42.86 145 42.86 - 49.08 70 49.08 - 55.30 24 55.30 - 61.52 6 61.52 - 67.74 5 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1404 r_work=0.1237 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1405 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1392 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.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892469 | | target function (ml) not normalized (work): 729051.644289 | | target function (ml) not normalized (free): 15229.647401 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1230 0.1391 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1444 0.1444 0.1480 n_refl.: 191139 remove outliers: r(all,work,free)=0.1444 0.1444 0.1480 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1438 0.1437 0.1476 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1384 n_refl.: 191139 remove outliers: r(all,work,free)=0.1229 0.1226 0.1384 n_refl.: 191136 ======================== 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 0.3705 398.008 364.142 0.420 0.947 0.238 13.296-10.522 99.01 99 1 0.2444 528.187 509.987 0.705 0.948 0.195 10.503-8.327 98.90 177 3 0.2085 557.261 556.051 0.879 0.948 0.173 8.318-6.595 100.00 360 8 0.2127 414.736 409.621 0.900 0.948 0.138 6.588-5.215 100.00 711 7 0.1894 381.101 370.745 0.885 0.948 0.120 5.214-4.128 98.38 1367 28 0.1172 557.435 552.266 0.971 0.948 0.080 4.126-3.266 94.74 2603 46 0.1092 508.132 501.410 1.032 0.948 0.005 3.266-2.585 99.86 5447 97 0.1084 342.774 339.116 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0969 258.603 255.686 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0974 153.054 151.393 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.493 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.313 1.041 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1062 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1384 | n_water=866 | time (s): 2.840 (total time: 2.840) Filter (dist) r_work=0.1226 r_free=0.1384 | n_water=866 | time (s): 117.840 (total time: 120.680) Filter (q & B) r_work=0.1227 r_free=0.1382 | n_water=852 | time (s): 4.570 (total time: 125.250) Compute maps r_work=0.1227 r_free=0.1382 | n_water=852 | time (s): 2.380 (total time: 127.630) Filter (map) r_work=0.1248 r_free=0.1381 | n_water=715 | time (s): 4.130 (total time: 131.760) Find peaks r_work=0.1248 r_free=0.1381 | n_water=715 | time (s): 0.680 (total time: 132.440) Add new water r_work=0.1262 r_free=0.1407 | n_water=955 | time (s): 5.090 (total time: 137.530) Refine new water occ: r_work=0.1216 r_free=0.1357 adp: r_work=0.1208 r_free=0.1354 occ: r_work=0.1206 r_free=0.1354 adp: r_work=0.1206 r_free=0.1354 occ: r_work=0.1204 r_free=0.1353 adp: r_work=0.1204 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1353 r_work=0.1204 r_free=0.1353 | n_water=955 | time (s): 359.120 (total time: 496.650) Filter (q & B) r_work=0.1208 r_free=0.1360 | n_water=852 | time (s): 4.970 (total time: 501.620) Filter (dist only) r_work=0.1209 r_free=0.1359 | n_water=851 | time (s): 109.400 (total time: 611.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.627301 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.417092 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 0.1205 0.1359 0.0154 0.035 1.1 6.8 0.0 0.3 0 0.814 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.59 1.54 1.822 14.175 15.417 3.875 12.01 13.56 1.55 1.917 14.136 15.417 3.867 Individual atomic B min max mean iso aniso Overall: 5.52 67.31 14.94 0.99 486 3269 Protein: 5.52 33.26 10.65 0.99 0 2902 Water: 5.94 67.31 29.57 N/A 486 365 Other: 13.95 28.19 21.07 N/A 0 2 Chain A: 5.52 54.49 12.64 N/A 0 1624 Chain B: 5.52 67.31 12.40 N/A 0 1645 Chain S: 5.94 64.18 31.23 N/A 486 0 Histogram: Values Number of atoms 5.52 - 11.70 2113 11.70 - 17.88 729 17.88 - 24.06 285 24.06 - 30.24 235 30.24 - 36.41 169 36.41 - 42.59 128 42.59 - 48.77 65 48.77 - 54.95 19 54.95 - 61.13 8 61.13 - 67.31 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1356 r_work=0.1201 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1356 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1355 target_work(ml) = 3.865 | | 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.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865146 | | target function (ml) not normalized (work): 723922.588656 | | target function (ml) not normalized (free): 15141.715776 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1354 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1425 0.1425 0.1457 n_refl.: 191136 remove outliers: r(all,work,free)=0.1425 0.1425 0.1457 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1417 0.1452 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191136 remove outliers: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3825 360.616 323.944 0.416 0.947 0.246 13.296-10.522 99.01 99 1 0.2518 478.565 457.499 0.697 0.949 0.190 10.503-8.327 98.35 176 3 0.2184 503.099 496.943 0.867 0.949 0.151 8.318-6.595 100.00 360 8 0.2151 375.773 370.706 0.891 0.948 0.121 6.588-5.215 100.00 711 7 0.1904 345.297 335.866 0.885 0.948 0.103 5.214-4.128 98.38 1367 28 0.1188 505.065 500.054 0.973 0.949 0.080 4.126-3.266 94.74 2603 46 0.1110 460.394 453.991 1.033 0.949 0.005 3.266-2.585 99.86 5447 97 0.1077 310.571 307.435 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0945 234.308 231.752 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0920 138.675 137.328 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0990 74.655 73.928 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.049 38.382 1.039 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1203 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1355 | n_water=851 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1199 r_free=0.1356 | n_water=850 | time (s): 105.800 (total time: 108.130) Filter (q & B) r_work=0.1199 r_free=0.1355 | n_water=844 | time (s): 4.160 (total time: 112.290) Compute maps r_work=0.1199 r_free=0.1355 | n_water=844 | time (s): 1.690 (total time: 113.980) Filter (map) r_work=0.1223 r_free=0.1367 | n_water=721 | time (s): 4.690 (total time: 118.670) Find peaks r_work=0.1223 r_free=0.1367 | n_water=721 | time (s): 0.600 (total time: 119.270) Add new water r_work=0.1236 r_free=0.1396 | n_water=944 | time (s): 5.160 (total time: 124.430) Refine new water occ: r_work=0.1199 r_free=0.1353 adp: r_work=0.1199 r_free=0.1353 occ: r_work=0.1197 r_free=0.1352 adp: r_work=0.1197 r_free=0.1351 occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1350 r_work=0.1195 r_free=0.1350 | n_water=944 | time (s): 242.380 (total time: 366.810) Filter (q & B) r_work=0.1198 r_free=0.1358 | n_water=869 | time (s): 5.170 (total time: 371.980) Filter (dist only) r_work=0.1198 r_free=0.1358 | n_water=868 | time (s): 111.920 (total time: 483.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.577860 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.801845 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 0.1202 0.1361 0.0159 0.036 1.1 7.7 0.0 0.3 0 0.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.61 1.59 1.785 14.091 14.802 3.767 12.07 13.65 1.58 1.904 14.042 14.802 3.765 Individual atomic B min max mean iso aniso Overall: 5.54 66.68 14.86 0.93 505 3267 Protein: 5.54 30.79 10.54 0.93 0 2902 Water: 6.04 66.68 29.27 N/A 505 363 Other: 13.84 26.07 19.95 N/A 0 2 Chain A: 5.57 54.19 12.48 N/A 0 1623 Chain B: 5.54 66.68 12.25 N/A 0 1644 Chain S: 6.04 64.10 30.98 N/A 505 0 Histogram: Values Number of atoms 5.54 - 11.65 2121 11.65 - 17.76 747 17.76 - 23.88 292 23.88 - 29.99 203 29.99 - 36.11 186 36.11 - 42.22 123 42.22 - 48.34 66 48.34 - 54.45 23 54.45 - 60.56 6 60.56 - 66.68 5 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1365 r_work=0.1207 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1365 target_work(ml) = 3.765 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1364 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1205 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.763879 | | target function (ml) not normalized (work): 704951.928476 | | target function (ml) not normalized (free): 14755.389258 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1205 0.1364 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1429 0.1428 0.1477 n_refl.: 191135 remove outliers: r(all,work,free)=0.1429 0.1428 0.1477 n_refl.: 191135 overall B=-0.04 to atoms: r(all,work,free)=0.1421 0.1420 0.1472 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1204 0.1362 n_refl.: 191135 remove outliers: r(all,work,free)=0.1206 0.1203 0.1362 n_refl.: 191132 ======================== 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 0.3822 361.420 317.680 0.401 0.949 0.230 13.296-10.522 97.03 97 1 0.2472 481.486 451.739 0.694 0.950 0.194 10.503-8.327 98.35 176 3 0.2171 503.099 497.163 0.860 0.950 0.160 8.318-6.595 100.00 360 8 0.2191 375.773 370.675 0.887 0.950 0.114 6.588-5.215 100.00 711 7 0.1925 345.297 335.455 0.884 0.950 0.097 5.214-4.128 98.38 1367 28 0.1214 505.065 499.974 0.972 0.950 0.080 4.126-3.266 94.74 2603 46 0.1141 460.394 453.578 1.033 0.950 0.005 3.266-2.585 99.86 5447 97 0.1109 310.571 307.419 1.020 0.949 0.000 2.585-2.046 97.45 10613 204 0.0959 234.308 231.771 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0922 138.675 137.370 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0980 74.655 73.950 1.054 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.049 38.380 1.043 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1259 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1362 | n_water=868 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1203 r_free=0.1362 | n_water=868 | time (s): 102.950 (total time: 105.530) Filter (q & B) r_work=0.1204 r_free=0.1362 | n_water=860 | time (s): 4.810 (total time: 110.340) Compute maps r_work=0.1204 r_free=0.1362 | n_water=860 | time (s): 2.440 (total time: 112.780) Filter (map) r_work=0.1226 r_free=0.1359 | n_water=736 | time (s): 4.710 (total time: 117.490) Find peaks r_work=0.1226 r_free=0.1359 | n_water=736 | time (s): 0.560 (total time: 118.050) Add new water r_work=0.1238 r_free=0.1385 | n_water=934 | time (s): 4.870 (total time: 122.920) Refine new water occ: r_work=0.1203 r_free=0.1345 adp: r_work=0.1203 r_free=0.1346 occ: r_work=0.1201 r_free=0.1342 adp: r_work=0.1201 r_free=0.1343 occ: r_work=0.1199 r_free=0.1340 adp: r_work=0.1199 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1340 r_work=0.1199 r_free=0.1340 | n_water=934 | time (s): 226.770 (total time: 349.690) Filter (q & B) r_work=0.1203 r_free=0.1349 | n_water=873 | time (s): 5.660 (total time: 355.350) Filter (dist only) r_work=0.1203 r_free=0.1349 | n_water=872 | time (s): 117.720 (total time: 473.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.601748 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.964935 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 0.1361 0.0155 0.037 1.1 6.5 0.0 0.3 0 0.801 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.61 1.55 1.741 13.936 14.965 3.765 12.06 13.61 1.55 1.836 13.896 14.965 3.761 Individual atomic B min max mean iso aniso Overall: 5.55 65.43 14.73 0.90 509 3267 Protein: 5.55 29.15 10.46 0.90 0 2902 Water: 5.84 65.43 28.91 N/A 509 363 Other: 13.82 22.92 18.37 N/A 0 2 Chain A: 5.60 53.62 12.35 N/A 0 1623 Chain B: 5.55 65.43 12.15 N/A 0 1644 Chain S: 5.84 64.06 30.62 N/A 509 0 Histogram: Values Number of atoms 5.55 - 11.53 2094 11.53 - 17.52 788 17.52 - 23.51 278 23.51 - 29.50 200 29.50 - 35.49 185 35.49 - 41.47 124 41.47 - 47.46 73 47.46 - 53.45 23 53.45 - 59.44 7 59.44 - 65.43 4 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1361 r_work=0.1206 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1362 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1357 target_work(ml) = 3.760 | | 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759986 | | target function (ml) not normalized (work): 704211.491182 | | target function (ml) not normalized (free): 14744.749304 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1358 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1408 0.1407 0.1464 n_refl.: 191132 remove outliers: r(all,work,free)=0.1408 0.1407 0.1464 n_refl.: 191132 overall B=-0.22 to atoms: r(all,work,free)=0.1371 0.1370 0.1442 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1356 n_refl.: 191132 remove outliers: r(all,work,free)=0.1205 0.1202 0.1356 n_refl.: 191131 ======================== 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 0.3848 361.116 308.152 0.384 0.952 0.195 13.296-10.522 97.03 97 1 0.2430 481.486 461.220 0.708 0.953 0.160 10.503-8.327 98.35 176 3 0.2265 503.099 496.264 0.877 0.954 0.140 8.318-6.595 100.00 360 8 0.2210 375.773 370.913 0.906 0.953 0.103 6.588-5.215 100.00 711 7 0.1940 345.297 335.636 0.902 0.953 0.087 5.214-4.128 98.38 1367 28 0.1229 505.065 499.878 0.994 0.954 0.080 4.126-3.266 94.74 2603 46 0.1153 460.394 453.421 1.056 0.954 0.005 3.266-2.585 99.86 5447 97 0.1122 310.571 307.346 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0958 234.308 231.781 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0912 138.675 137.393 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0972 74.655 73.962 1.055 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.049 38.384 1.028 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0480 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1355 | n_water=872 | time (s): 2.910 (total time: 2.910) Filter (dist) r_work=0.1203 r_free=0.1356 | n_water=871 | time (s): 111.020 (total time: 113.930) Filter (q & B) r_work=0.1203 r_free=0.1354 | n_water=863 | time (s): 5.740 (total time: 119.670) Compute maps r_work=0.1203 r_free=0.1354 | n_water=863 | time (s): 2.230 (total time: 121.900) Filter (map) r_work=0.1227 r_free=0.1355 | n_water=742 | time (s): 5.480 (total time: 127.380) Find peaks r_work=0.1227 r_free=0.1355 | n_water=742 | time (s): 0.870 (total time: 128.250) Add new water r_work=0.1238 r_free=0.1368 | n_water=953 | time (s): 5.200 (total time: 133.450) Refine new water occ: r_work=0.1201 r_free=0.1344 adp: r_work=0.1201 r_free=0.1344 occ: r_work=0.1199 r_free=0.1345 adp: r_work=0.1198 r_free=0.1344 occ: r_work=0.1197 r_free=0.1345 adp: r_work=0.1197 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1344 r_work=0.1197 r_free=0.1344 | n_water=953 | time (s): 146.740 (total time: 280.190) Filter (q & B) r_work=0.1200 r_free=0.1348 | n_water=890 | time (s): 5.090 (total time: 285.280) Filter (dist only) r_work=0.1200 r_free=0.1347 | n_water=889 | time (s): 112.390 (total time: 397.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.583684 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.683400 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 0.1347 0.0144 0.037 1.1 5.3 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.47 1.44 1.712 13.683 14.683 3.760 12.04 13.50 1.46 1.751 13.663 14.683 3.758 Individual atomic B min max mean iso aniso Overall: 5.39 63.95 14.54 0.88 526 3267 Protein: 5.39 28.47 10.23 0.88 0 2902 Water: 5.70 63.95 28.59 N/A 526 363 Other: 13.66 21.91 17.79 N/A 0 2 Chain A: 5.42 52.88 12.09 N/A 0 1623 Chain B: 5.39 63.95 11.89 N/A 0 1644 Chain S: 5.70 63.80 30.37 N/A 526 0 Histogram: Values Number of atoms 5.39 - 11.24 2065 11.24 - 17.10 812 17.10 - 22.95 275 22.95 - 28.81 209 28.81 - 34.67 185 34.67 - 40.52 131 40.52 - 46.38 78 46.38 - 52.24 25 52.24 - 58.09 9 58.09 - 63.95 4 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1350 r_work=0.1204 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1350 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1350 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757429 | | target function (ml) not normalized (work): 703728.966790 | | target function (ml) not normalized (free): 14732.942553 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1350 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1366 0.1365 0.1441 n_refl.: 191131 remove outliers: r(all,work,free)=0.1366 0.1365 0.1441 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1374 0.1373 0.1445 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1340 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1340 n_refl.: 191131 ======================== 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 0.3781 361.116 327.943 0.400 0.996 0.205 13.296-10.522 97.03 97 1 0.2448 481.486 459.939 0.681 0.997 0.152 10.503-8.327 98.35 176 3 0.2249 503.099 495.730 0.845 0.998 0.127 8.318-6.595 100.00 360 8 0.2211 375.773 370.829 0.873 0.998 0.103 6.588-5.215 100.00 711 7 0.1932 345.297 335.552 0.871 0.998 0.087 5.214-4.128 98.38 1367 28 0.1233 505.065 499.339 0.958 0.999 0.070 4.126-3.266 94.74 2603 46 0.1154 460.394 453.181 1.019 1.000 0.005 3.266-2.585 99.86 5447 97 0.1122 310.571 307.000 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0962 234.308 231.600 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0906 138.675 137.290 1.026 1.004 0.000 1.619-1.281 98.00 42464 925 0.0951 74.655 73.996 1.016 1.007 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.049 38.362 0.983 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0638 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1340 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1340 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1340 | n_water=889 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1193 r_free=0.1340 | n_water=888 | time (s): 123.330 (total time: 126.060) Filter (q & B) r_work=0.1194 r_free=0.1340 | n_water=884 | time (s): 4.310 (total time: 130.370) Compute maps r_work=0.1194 r_free=0.1340 | n_water=884 | time (s): 1.950 (total time: 132.320) Filter (map) r_work=0.1216 r_free=0.1344 | n_water=767 | time (s): 4.000 (total time: 136.320) Find peaks r_work=0.1216 r_free=0.1344 | n_water=767 | time (s): 0.680 (total time: 137.000) Add new water r_work=0.1226 r_free=0.1355 | n_water=962 | time (s): 5.360 (total time: 142.360) Refine new water occ: r_work=0.1193 r_free=0.1329 adp: r_work=0.1193 r_free=0.1329 occ: r_work=0.1191 r_free=0.1329 adp: r_work=0.1191 r_free=0.1330 occ: r_work=0.1189 r_free=0.1330 adp: r_work=0.1189 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1331 r_work=0.1189 r_free=0.1331 | n_water=962 | time (s): 267.130 (total time: 409.490) Filter (q & B) r_work=0.1192 r_free=0.1335 | n_water=899 | time (s): 4.110 (total time: 413.600) Filter (dist only) r_work=0.1192 r_free=0.1334 | n_water=898 | time (s): 114.980 (total time: 528.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.572684 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.990401 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 0.1341 0.0147 0.038 1.1 4.9 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.41 1.47 1.674 13.716 13.990 3.756 11.95 13.43 1.48 1.683 13.704 13.990 3.755 Individual atomic B min max mean iso aniso Overall: 5.46 63.84 14.62 0.87 535 3267 Protein: 5.46 28.22 10.30 0.87 0 2902 Water: 5.87 63.84 28.58 N/A 535 363 Other: 13.72 22.05 17.88 N/A 0 2 Chain A: 5.55 52.70 12.12 N/A 0 1623 Chain B: 5.46 63.48 11.93 N/A 0 1644 Chain S: 5.87 63.84 30.46 N/A 535 0 Histogram: Values Number of atoms 5.46 - 11.30 2066 11.30 - 17.13 818 17.13 - 22.97 271 22.97 - 28.81 217 28.81 - 34.65 183 34.65 - 40.49 127 40.49 - 46.32 78 46.32 - 52.16 28 52.16 - 58.00 10 58.00 - 63.84 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1343 r_work=0.1196 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1343 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754490 | | target function (ml) not normalized (work): 703178.411486 | | target function (ml) not normalized (free): 14724.024178 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1344 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1380 0.1379 0.1455 n_refl.: 191131 remove outliers: r(all,work,free)=0.1380 0.1379 0.1455 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1382 0.1381 0.1457 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1343 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1343 n_refl.: 191131 ======================== 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 0.3717 361.116 328.740 0.434 0.914 0.203 13.296-10.522 97.03 97 1 0.2401 481.486 460.602 0.736 0.916 0.146 10.503-8.327 98.35 176 3 0.2247 503.099 495.434 0.918 0.916 0.120 8.318-6.595 100.00 360 8 0.2209 375.773 370.897 0.948 0.916 0.093 6.588-5.215 100.00 711 7 0.1951 345.297 335.475 0.946 0.916 0.077 5.214-4.128 98.38 1367 28 0.1249 505.065 499.299 1.042 0.917 0.060 4.126-3.266 94.74 2603 46 0.1158 460.394 453.072 1.110 0.918 0.000 3.266-2.585 99.86 5447 97 0.1127 310.571 306.903 1.091 0.919 0.000 2.585-2.046 97.45 10613 204 0.0962 234.308 231.592 1.101 0.920 0.000 2.046-1.619 99.39 21536 464 0.0907 138.675 137.304 1.119 0.923 0.000 1.619-1.281 98.00 42464 925 0.0946 74.655 74.005 1.110 0.927 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.049 38.350 1.077 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0221 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1343 | n_water=898 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1193 r_free=0.1343 | n_water=898 | time (s): 103.320 (total time: 105.850) Filter (q & B) r_work=0.1193 r_free=0.1342 | n_water=891 | time (s): 4.320 (total time: 110.170) Compute maps r_work=0.1193 r_free=0.1342 | n_water=891 | time (s): 1.800 (total time: 111.970) Filter (map) r_work=0.1217 r_free=0.1348 | n_water=773 | time (s): 4.300 (total time: 116.270) Find peaks r_work=0.1217 r_free=0.1348 | n_water=773 | time (s): 0.680 (total time: 116.950) Add new water r_work=0.1225 r_free=0.1361 | n_water=969 | time (s): 4.060 (total time: 121.010) Refine new water occ: r_work=0.1192 r_free=0.1337 adp: r_work=0.1192 r_free=0.1337 occ: r_work=0.1190 r_free=0.1337 adp: r_work=0.1190 r_free=0.1337 occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1189 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1337 r_work=0.1189 r_free=0.1337 | n_water=969 | time (s): 209.250 (total time: 330.260) Filter (q & B) r_work=0.1192 r_free=0.1342 | n_water=903 | time (s): 4.140 (total time: 334.400) Filter (dist only) r_work=0.1192 r_free=0.1341 | n_water=902 | time (s): 115.050 (total time: 449.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.643297 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.305141 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1348 0.0153 0.038 1.1 6.5 0.0 0.3 0 0.822 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.48 1.53 1.675 13.712 13.305 3.755 11.98 13.51 1.53 1.691 13.701 13.305 3.756 Individual atomic B min max mean iso aniso Overall: 5.54 63.79 14.59 0.85 539 3267 Protein: 5.54 27.79 10.31 0.85 0 2902 Water: 5.93 63.79 28.34 N/A 539 363 Other: 13.79 22.03 17.91 N/A 0 2 Chain A: 5.61 52.30 12.11 N/A 0 1623 Chain B: 5.54 62.65 11.93 N/A 0 1644 Chain S: 5.93 63.79 30.18 N/A 539 0 Histogram: Values Number of atoms 5.54 - 11.37 2078 11.37 - 17.19 820 17.19 - 23.02 273 23.02 - 28.84 207 28.84 - 34.67 194 34.67 - 40.49 120 40.49 - 46.32 75 46.32 - 52.14 28 52.14 - 57.97 8 57.97 - 63.79 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1351 r_work=0.1198 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1351 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1352 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755402 | | target function (ml) not normalized (work): 703349.298031 | | target function (ml) not normalized (free): 14735.310817 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1352 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1475 n_refl.: 191131 remove outliers: r(all,work,free)=0.1395 0.1393 0.1475 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1394 0.1393 0.1474 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1350 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1350 n_refl.: 191131 ======================== 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 0.3748 361.116 327.502 0.428 0.915 0.199 13.296-10.522 97.03 97 1 0.2433 481.486 461.029 0.730 0.917 0.139 10.503-8.327 98.35 176 3 0.2268 503.099 494.262 0.912 0.917 0.108 8.318-6.595 100.00 360 8 0.2222 375.773 371.121 0.944 0.917 0.090 6.588-5.215 100.00 711 7 0.1976 345.297 335.172 0.944 0.918 0.077 5.214-4.128 98.38 1367 28 0.1261 505.065 499.235 1.039 0.918 0.039 4.126-3.266 94.74 2603 46 0.1169 460.394 452.881 1.109 0.919 0.005 3.266-2.585 99.86 5447 97 0.1137 310.571 306.845 1.090 0.920 0.000 2.585-2.046 97.45 10613 204 0.0966 234.308 231.590 1.100 0.922 0.000 2.046-1.619 99.39 21536 464 0.0907 138.675 137.310 1.118 0.926 0.000 1.619-1.281 98.00 42464 925 0.0945 74.655 74.010 1.109 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.049 38.341 1.078 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0110 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1196 r_free=0.1350 After: r_work=0.1197 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1197 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1351 | n_water=902 | time (s): 3.400 (total time: 3.400) Filter (dist) r_work=0.1197 r_free=0.1351 | n_water=902 | time (s): 118.600 (total time: 122.000) Filter (q & B) r_work=0.1198 r_free=0.1352 | n_water=885 | time (s): 4.140 (total time: 126.140) Compute maps r_work=0.1198 r_free=0.1352 | n_water=885 | time (s): 1.810 (total time: 127.950) Filter (map) r_work=0.1223 r_free=0.1358 | n_water=766 | time (s): 5.530 (total time: 133.480) Find peaks r_work=0.1223 r_free=0.1358 | n_water=766 | time (s): 0.590 (total time: 134.070) Add new water r_work=0.1231 r_free=0.1367 | n_water=975 | time (s): 4.150 (total time: 138.220) Refine new water occ: r_work=0.1195 r_free=0.1340 adp: r_work=0.1195 r_free=0.1341 occ: r_work=0.1193 r_free=0.1341 adp: r_work=0.1193 r_free=0.1341 occ: r_work=0.1192 r_free=0.1341 adp: r_work=0.1191 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1342 r_work=0.1191 r_free=0.1342 | n_water=975 | time (s): 301.160 (total time: 439.380) Filter (q & B) r_work=0.1195 r_free=0.1349 | n_water=905 | time (s): 5.260 (total time: 444.640) Filter (dist only) r_work=0.1195 r_free=0.1349 | n_water=902 | time (s): 118.220 (total time: 562.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533689 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.256143 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 0.1197 0.1351 0.0154 0.038 1.1 8.9 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.51 1.54 1.668 13.697 14.256 3.757 11.94 13.50 1.55 1.653 13.703 14.256 3.753 Individual atomic B min max mean iso aniso Overall: 5.57 63.82 14.60 0.87 539 3267 Protein: 5.57 28.12 10.35 0.87 0 2902 Water: 5.93 63.82 28.28 N/A 539 363 Other: 13.83 22.15 17.99 N/A 0 2 Chain A: 5.66 51.94 12.11 N/A 0 1623 Chain B: 5.57 61.67 11.94 N/A 0 1644 Chain S: 5.93 63.82 30.20 N/A 539 0 Histogram: Values Number of atoms 5.57 - 11.40 2071 11.40 - 17.22 828 17.22 - 23.05 274 23.05 - 28.87 213 28.87 - 34.70 185 34.70 - 40.52 116 40.52 - 46.35 82 46.35 - 52.17 28 52.17 - 58.00 6 58.00 - 63.82 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1350 r_work=0.1195 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752870 | | target function (ml) not normalized (work): 702874.935311 | | target function (ml) not normalized (free): 14719.760578 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1370 0.1483 5.6987 5.7779| | 2: 2.94 - 2.33 1.00 7339 128 0.1082 0.1347 5.0871 5.1789| | 3: 2.33 - 2.04 0.96 6939 150 0.0900 0.1156 4.6513 4.7312| | 4: 2.04 - 1.85 1.00 7170 155 0.0896 0.1044 4.3845 4.5573| | 5: 1.85 - 1.72 0.99 7113 159 0.0924 0.0976 4.141 4.2286| | 6: 1.72 - 1.62 0.99 7102 142 0.0891 0.1069 3.9389 4.0648| | 7: 1.62 - 1.54 0.99 7104 148 0.0886 0.0965 3.7934 3.9329| | 8: 1.54 - 1.47 0.96 6798 152 0.0886 0.1280 3.6935 3.8941| | 9: 1.47 - 1.41 0.98 6938 155 0.0921 0.1090 3.6149 3.7339| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1172 3.5517 3.673| | 11: 1.36 - 1.32 0.99 6997 151 0.0990 0.1128 3.4827 3.5883| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1134 3.4583 3.5876| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1235 3.4365 3.5659| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1569 3.4323 3.6752| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1246 3.449 3.496| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1559 3.4655 3.6633| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1221 3.4336 3.4427| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1693 3.4376 3.5309| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1744 3.4188 3.5957| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1568 3.41 3.4301| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2143 3.4183 3.5066| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1969 3.4135 3.417| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2028 3.4334 3.486| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2254 3.4361 3.5101| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2511 3.4494 3.5261| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2881 3.4159 3.4263| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2803 3.4696 3.3942| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7399 127 0.93 11.78 1.00 0.96 11524.41| | 2: 2.94 - 2.33 7339 128 0.92 12.91 0.99 0.96 5207.03| | 3: 2.33 - 2.04 6939 150 0.96 7.52 1.01 0.95 1660.15| | 4: 2.04 - 1.85 7170 155 0.96 7.45 1.00 0.95 973.71| | 5: 1.85 - 1.72 7113 159 0.96 7.85 1.00 0.96 615.33| | 6: 1.72 - 1.62 7102 142 0.96 7.85 1.00 0.96 432.78| | 7: 1.62 - 1.54 7104 148 0.96 8.04 1.01 0.97 332.08| | 8: 1.54 - 1.47 6798 152 0.96 8.16 1.01 0.97 274.85| | 9: 1.47 - 1.41 6938 155 0.96 8.34 1.00 0.98 226.64| | 10: 1.41 - 1.36 7022 150 0.96 8.81 1.00 0.97 199.53| | 11: 1.36 - 1.32 6997 151 0.96 8.89 0.99 0.96 173.73| | 12: 1.32 - 1.28 6975 149 0.96 8.99 0.98 0.95 161.14| | 13: 1.28 - 1.25 6907 166 0.96 9.53 1.01 0.96 158.56| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.97 163.59| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.01 0.98 167.32| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.01 0.96 161.11| | 17: 1.17 - 1.14 6940 135 0.94 12.26 1.01 0.96 154.40| | 18: 1.14 - 1.12 6875 142 0.94 12.71 1.01 0.95 147.26| | 19: 1.12 - 1.10 6948 106 0.93 14.09 1.00 0.95 150.44| | 20: 1.10 - 1.08 6884 147 0.92 15.17 1.00 0.94 149.74| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.93 153.47| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.93 155.27| | 23: 1.05 - 1.03 6827 159 0.87 20.53 0.99 0.92 165.27| | 24: 1.03 - 1.02 6784 133 0.85 23.20 0.99 0.93 179.72| | 25: 1.02 - 1.01 6552 130 0.83 25.19 0.98 0.90 182.81| | 26: 1.01 - 0.99 6767 158 0.81 26.63 0.98 0.89 176.92| | 27: 0.99 - 0.98 6647 131 0.82 26.20 0.99 0.87 160.41| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.26 max = 11524.41 mean = 937.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.94 mean = 13.26| |phase err.(test): min = 0.00 max = 89.41 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1350 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1485 n_refl.: 191131 remove outliers: r(all,work,free)=0.1400 0.1398 0.1485 n_refl.: 191131 overall B=-0.06 to atoms: r(all,work,free)=0.1390 0.1389 0.1479 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1349 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1349 n_refl.: 191131 ======================== 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 0.3764 361.116 327.810 0.384 0.976 0.189 13.296-10.522 97.03 97 1 0.2464 481.486 461.674 0.664 0.978 0.131 10.503-8.327 98.35 176 3 0.2259 503.099 493.561 0.834 0.979 0.101 8.318-6.595 100.00 360 8 0.2199 375.773 371.085 0.863 0.978 0.085 6.588-5.215 100.00 711 7 0.1970 345.297 335.132 0.862 0.979 0.073 5.214-4.128 98.38 1367 28 0.1249 505.065 499.305 0.950 0.980 0.034 4.126-3.266 94.74 2603 46 0.1168 460.394 452.844 1.015 0.981 0.005 3.266-2.585 99.86 5447 97 0.1129 310.571 307.031 0.997 0.983 0.000 2.585-2.046 97.45 10613 204 0.0965 234.308 231.594 1.004 0.985 0.000 2.046-1.619 99.39 21536 464 0.0904 138.675 137.307 1.020 0.989 0.000 1.619-1.281 98.00 42464 925 0.0942 74.655 74.010 1.009 0.996 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.049 38.336 0.978 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0127 ================= 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 : 0.2032 0.1957 0.080 5.119 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1892 0.080 5.119 5.2 78.0 14.6 805 0.000 1_settarget: 0.1797 0.1892 0.080 5.119 5.2 78.0 14.6 805 0.000 1_nqh: 0.1801 0.1897 0.080 5.119 5.2 78.0 14.6 805 0.002 1_weight: 0.1801 0.1897 0.080 5.119 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1276 0.1505 0.040 1.167 5.2 78.0 14.6 805 0.157 1_adp: 0.1301 0.1573 0.040 1.167 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1300 0.1569 0.040 1.167 5.2 73.0 15.0 805 0.157 1_occ: 0.1285 0.1557 0.040 1.167 5.2 73.0 15.0 805 0.157 2_bss: 0.1278 0.1548 0.040 1.167 5.4 73.2 15.2 805 0.157 2_settarget: 0.1278 0.1548 0.040 1.167 5.4 73.2 15.2 805 0.157 2_updatecdl: 0.1278 0.1548 0.040 1.177 5.4 73.2 15.2 805 0.157 2_nqh: 0.1278 0.1548 0.040 1.177 5.4 73.2 15.2 805 0.157 2_sol: 0.1274 0.1505 0.040 1.177 5.4 73.2 16.2 880 n/a 2_weight: 0.1274 0.1505 0.040 1.177 5.4 73.2 16.2 880 n/a 2_xyzrec: 0.1257 0.1528 0.041 1.144 5.4 73.2 16.2 880 n/a 2_adp: 0.1234 0.1514 0.041 1.144 5.3 72.9 16.4 880 n/a 2_regHadp: 0.1235 0.1515 0.041 1.144 5.3 72.9 16.4 880 n/a 2_occ: 0.1229 0.1510 0.041 1.144 5.3 72.9 16.4 880 n/a 3_bss: 0.1236 0.1517 0.041 1.144 5.3 72.9 16.3 880 n/a 3_settarget: 0.1236 0.1517 0.041 1.144 5.3 72.9 16.3 880 n/a 3_updatecdl: 0.1236 0.1517 0.041 1.150 5.3 72.9 16.3 880 n/a 3_nqh: 0.1236 0.1517 0.041 1.150 5.3 72.9 16.3 880 n/a 3_sol: 0.1253 0.1523 0.041 1.150 5.3 68.2 15.4 866 n/a 3_weight: 0.1253 0.1523 0.041 1.150 5.3 68.2 15.4 866 n/a 3_xyzrec: 0.1241 0.1443 0.034 1.098 5.3 68.2 15.4 866 n/a 3_adp: 0.1236 0.1404 0.034 1.098 5.5 67.7 15.2 866 n/a 3_regHadp: 0.1237 0.1405 0.034 1.098 5.5 67.7 15.2 866 n/a 3_occ: 0.1230 0.1392 0.034 1.098 5.5 67.7 15.2 866 n/a 4_bss: 0.1226 0.1384 0.034 1.098 5.5 67.7 15.2 866 n/a 4_settarget: 0.1226 0.1384 0.034 1.098 5.5 67.7 15.2 866 n/a 4_updatecdl: 0.1226 0.1384 0.035 1.100 5.5 67.7 15.2 866 n/a 4_nqh: 0.1226 0.1384 0.035 1.100 5.5 67.7 15.2 866 n/a 4_sol: 0.1209 0.1359 0.035 1.100 5.5 67.7 15.0 851 n/a 4_weight: 0.1209 0.1359 0.035 1.100 5.5 67.7 15.0 851 n/a 4_xyzrec: 0.1205 0.1359 0.035 1.128 5.5 67.7 15.0 851 n/a 4_adp: 0.1201 0.1356 0.035 1.128 5.5 67.3 14.9 851 n/a 4_regHadp: 0.1201 0.1356 0.035 1.128 5.5 67.3 14.9 851 n/a 4_occ: 0.1199 0.1355 0.035 1.128 5.5 67.3 14.9 851 n/a 5_bss: 0.1198 0.1355 0.035 1.128 5.5 67.3 14.9 851 n/a 5_settarget: 0.1198 0.1355 0.035 1.128 5.5 67.3 14.9 851 n/a 5_updatecdl: 0.1198 0.1355 0.035 1.129 5.5 67.3 14.9 851 n/a 5_nqh: 0.1198 0.1355 0.035 1.129 5.5 67.3 14.9 851 n/a 5_sol: 0.1198 0.1358 0.035 1.129 5.5 67.3 14.9 868 n/a 5_weight: 0.1198 0.1358 0.035 1.129 5.5 67.3 14.9 868 n/a 5_xyzrec: 0.1202 0.1361 0.036 1.133 5.5 67.3 14.9 868 n/a 5_adp: 0.1207 0.1365 0.036 1.133 5.5 66.7 14.9 868 n/a 5_regHadp: 0.1207 0.1365 0.036 1.133 5.5 66.7 14.9 868 n/a 5_occ: 0.1205 0.1364 0.036 1.133 5.5 66.7 14.9 868 n/a 6_bss: 0.1203 0.1362 0.036 1.133 5.5 66.6 14.8 868 n/a 6_settarget: 0.1203 0.1362 0.036 1.133 5.5 66.6 14.8 868 n/a 6_updatecdl: 0.1203 0.1362 0.036 1.133 5.5 66.6 14.8 868 n/a 6_nqh: 0.1203 0.1362 0.036 1.133 5.5 66.6 14.8 868 n/a 6_sol: 0.1203 0.1349 0.036 1.133 5.5 66.6 14.8 872 n/a 6_weight: 0.1203 0.1349 0.036 1.133 5.5 66.6 14.8 872 n/a 6_xyzrec: 0.1206 0.1361 0.037 1.138 5.5 66.6 14.8 872 n/a 6_adp: 0.1206 0.1361 0.037 1.138 5.5 65.4 14.7 872 n/a 6_regHadp: 0.1206 0.1362 0.037 1.138 5.5 65.4 14.7 872 n/a 6_occ: 0.1203 0.1357 0.037 1.138 5.5 65.4 14.7 872 n/a 7_bss: 0.1203 0.1355 0.037 1.138 5.3 65.2 14.5 872 n/a 7_settarget: 0.1203 0.1355 0.037 1.138 5.3 65.2 14.5 872 n/a 7_updatecdl: 0.1203 0.1355 0.037 1.137 5.3 65.2 14.5 872 n/a 7_nqh: 0.1203 0.1355 0.037 1.137 5.3 65.2 14.5 872 n/a 7_sol: 0.1200 0.1347 0.037 1.137 5.3 65.2 14.6 889 n/a 7_weight: 0.1200 0.1347 0.037 1.137 5.3 65.2 14.6 889 n/a 7_xyzrec: 0.1203 0.1347 0.037 1.137 5.3 65.2 14.6 889 n/a 7_adp: 0.1204 0.1350 0.037 1.137 5.4 63.9 14.5 889 n/a 7_regHadp: 0.1204 0.1350 0.037 1.137 5.4 63.9 14.5 889 n/a 7_occ: 0.1202 0.1350 0.037 1.137 5.4 63.9 14.5 889 n/a 8_bss: 0.1193 0.1340 0.037 1.137 5.4 64.0 14.6 889 n/a 8_settarget: 0.1193 0.1340 0.037 1.137 5.4 64.0 14.6 889 n/a 8_updatecdl: 0.1193 0.1340 0.037 1.137 5.4 64.0 14.6 889 n/a 8_nqh: 0.1193 0.1340 0.037 1.137 5.4 64.0 14.6 889 n/a 8_sol: 0.1192 0.1334 0.037 1.137 5.4 64.0 14.6 898 n/a 8_weight: 0.1192 0.1334 0.037 1.137 5.4 64.0 14.6 898 n/a 8_xyzrec: 0.1194 0.1341 0.038 1.121 5.4 64.0 14.6 898 n/a 8_adp: 0.1196 0.1343 0.038 1.121 5.5 63.8 14.6 898 n/a 8_regHadp: 0.1196 0.1343 0.038 1.121 5.5 63.8 14.6 898 n/a 8_occ: 0.1194 0.1344 0.038 1.121 5.5 63.8 14.6 898 n/a 9_bss: 0.1193 0.1343 0.038 1.121 5.5 63.9 14.6 898 n/a 9_settarget: 0.1193 0.1343 0.038 1.121 5.5 63.9 14.6 898 n/a 9_updatecdl: 0.1193 0.1343 0.038 1.121 5.5 63.9 14.6 898 n/a 9_nqh: 0.1193 0.1343 0.038 1.121 5.5 63.9 14.6 898 n/a 9_sol: 0.1192 0.1341 0.038 1.121 5.5 63.9 14.6 902 n/a 9_weight: 0.1192 0.1341 0.038 1.121 5.5 63.9 14.6 902 n/a 9_xyzrec: 0.1195 0.1348 0.038 1.133 5.5 63.9 14.6 902 n/a 9_adp: 0.1198 0.1351 0.038 1.133 5.5 63.8 14.6 902 n/a 9_regHadp: 0.1198 0.1351 0.038 1.133 5.5 63.8 14.6 902 n/a 9_occ: 0.1197 0.1352 0.038 1.133 5.5 63.8 14.6 902 n/a 10_bss: 0.1196 0.1350 0.038 1.133 5.5 63.8 14.6 902 n/a 10_settarget: 0.1196 0.1350 0.038 1.133 5.5 63.8 14.6 902 n/a 10_updatecdl: 0.1196 0.1350 0.038 1.133 5.5 63.8 14.6 902 n/a 10_setrh: 0.1197 0.1351 0.038 1.133 5.5 63.8 14.6 902 n/a 10_nqh: 0.1197 0.1351 0.038 1.133 5.5 63.8 14.6 902 n/a 10_sol: 0.1195 0.1349 0.038 1.133 5.5 63.8 14.6 902 n/a 10_weight: 0.1195 0.1349 0.038 1.133 5.5 63.8 14.6 902 n/a 10_xyzrec: 0.1197 0.1351 0.038 1.145 5.5 63.8 14.6 902 n/a 10_adp: 0.1194 0.1350 0.038 1.145 5.6 63.8 14.6 902 n/a 10_regHadp: 0.1195 0.1350 0.038 1.145 5.6 63.8 14.6 902 n/a 10_occ: 0.1193 0.1350 0.038 1.145 5.6 63.8 14.6 902 n/a end: 0.1193 0.1349 0.038 1.145 5.5 63.8 14.5 902 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8840372_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8840372_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.4400 Refinement macro-cycles (run) : 12300.2400 Write final files (write_after_run_outputs) : 135.5900 Total : 12443.2700 Total CPU time: 3.47 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:35 PST -0800 (1736736275.39 s) Start R-work = 0.1797, R-free = 0.1892 Final R-work = 0.1193, R-free = 0.1349 =============================================================================== Job complete usr+sys time: 12683.60 seconds wall clock time: 212 minutes 25.03 seconds (12745.03 seconds total)