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_4806716.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4806716.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4806716.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.44, per 1000 atoms: 0.36 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: 2.775 distance_ideal: 2.720 ideal - model: -0.055 slack: 0.000 delta_slack: -0.055 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: 2.772 distance_ideal: 2.710 ideal - model: -0.062 slack: 0.000 delta_slack: -0.062 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: 0.76 Conformation dependent library (CDL) restraints added in 113.6 milliseconds Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.04: 932 1.04 - 1.25: 2333 1.25 - 1.46: 1351 1.46 - 1.68: 1256 1.68 - 1.89: 62 Bond restraints: 5934 Sorted by residual: bond pdb=" ND1 HIS A 116 " pdb=" CE1 HIS A 116 " ideal model delta sigma weight residual 1.321 1.069 0.252 1.00e-02 1.00e+04 6.35e+02 bond pdb=" CA ALA A 148 " pdb=" C ALA A 148 " ideal model delta sigma weight residual 1.523 1.780 -0.257 1.35e-02 5.49e+03 3.63e+02 bond pdb=" C VAL A 144 " pdb=" O VAL A 144 " ideal model delta sigma weight residual 1.235 1.423 -0.188 9.90e-03 1.02e+04 3.62e+02 bond pdb=" N GLY A 157 " pdb=" H GLY A 157 " ideal model delta sigma weight residual 0.860 1.232 -0.372 2.00e-02 2.50e+03 3.46e+02 bond pdb=" C GLU B 17 " pdb=" O GLU B 17 " ideal model delta sigma weight residual 1.236 1.462 -0.226 1.22e-02 6.72e+03 3.43e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 5474 4.03 - 8.05: 3627 8.05 - 12.08: 1376 12.08 - 16.11: 301 16.11 - 20.14: 32 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA THR B 91 " pdb=" C THR B 91 " pdb=" O THR B 91 " ideal model delta sigma weight residual 120.82 138.48 -17.66 1.05e+00 9.07e-01 2.83e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 106.69 12.51 9.00e-01 1.23e+00 1.93e+02 angle pdb=" CA LEU A 9 " pdb=" C LEU A 9 " pdb=" N ALA A 10 " ideal model delta sigma weight residual 116.29 134.29 -18.00 1.30e+00 5.92e-01 1.92e+02 angle pdb=" CA SER A 85 " pdb=" C SER A 85 " pdb=" O SER A 85 " ideal model delta sigma weight residual 120.32 135.50 -15.18 1.10e+00 8.26e-01 1.90e+02 angle pdb=" NE ARG A 175 " pdb=" CZ ARG A 175 " pdb=" NH2 ARG A 175 " ideal model delta sigma weight residual 119.20 107.02 12.18 9.00e-01 1.23e+00 1.83e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 1856 17.41 - 34.83: 127 34.83 - 52.24: 49 52.24 - 69.66: 13 69.66 - 87.07: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA ALA B 107 " pdb=" C ALA B 107 " pdb=" N ALA B 108 " pdb=" CA ALA B 108 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA ALA B 57 " pdb=" C ALA B 57 " pdb=" N PRO B 58 " pdb=" CA PRO B 58 " ideal model delta harmonic sigma weight residual 180.00 155.77 24.23 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.248: 226 0.248 - 0.494: 152 0.494 - 0.740: 88 0.740 - 0.987: 21 0.987 - 1.233: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA GLN A 184 " pdb=" N GLN A 184 " pdb=" C GLN A 184 " pdb=" CB GLN A 184 " both_signs ideal model delta sigma weight residual False 2.51 3.74 -1.23 2.00e-01 2.50e+01 3.80e+01 chirality pdb=" CA ALA B 55 " pdb=" N ALA B 55 " pdb=" C ALA B 55 " pdb=" CB ALA B 55 " both_signs ideal model delta sigma weight residual False 2.48 3.56 -1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CA ALA A 35 " pdb=" N ALA A 35 " pdb=" C ALA A 35 " pdb=" CB ALA A 35 " both_signs ideal model delta sigma weight residual False 2.48 3.56 -1.07 2.00e-01 2.50e+01 2.87e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.065 2.00e-02 2.50e+03 6.97e-02 1.94e+02 pdb=" CG TRP A 146 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.088 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.111 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.052 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.041 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.177 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.046 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.009 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.189 2.00e-02 2.50e+03 7.44e-02 1.66e+02 pdb=" CG PHE B 164 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.099 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.043 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.055 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.105 2.00e-02 2.50e+03 6.44e-02 1.24e+02 pdb=" CG PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.134 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.009 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 23 1.60 - 2.35: 2250 2.35 - 3.10: 22171 3.10 - 3.85: 33115 3.85 - 4.60: 52750 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110309 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.851 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.912 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.966 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.071 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.144 2.620 ... (remaining 110304 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_4806716_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= 0.2029 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.295742 | | target function (ml) not normalized (work): 804648.394463 | | target function (ml) not normalized (free): 16513.689061 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2138 0.1927 6.6825 6.3214| | 2: 2.94 - 2.33 1.00 7339 128 0.1613 0.1699 5.5432 5.6016| | 3: 2.33 - 2.04 0.96 6939 150 0.1619 0.1622 5.126 5.1632| | 4: 2.04 - 1.85 1.00 7170 155 0.1745 0.1419 4.9554 4.9266| | 5: 1.85 - 1.72 0.99 7113 159 0.1926 0.1674 4.7959 4.8004| | 6: 1.72 - 1.62 0.99 7102 142 0.1990 0.1935 4.6657 4.7087| | 7: 1.62 - 1.54 0.99 7104 148 0.2049 0.1538 4.5559 4.4518| | 8: 1.54 - 1.47 0.96 6798 152 0.2017 0.2192 4.4646 4.5132| | 9: 1.47 - 1.41 0.98 6938 155 0.2081 0.2192 4.3883 4.4975| | 10: 1.41 - 1.36 0.99 7022 150 0.2118 0.2184 4.302 4.4057| | 11: 1.36 - 1.32 0.99 6997 151 0.2094 0.2050 4.2313 4.2045| | 12: 1.32 - 1.28 0.98 6976 149 0.2087 0.2098 4.1718 4.2693| | 13: 1.28 - 1.25 0.98 6907 166 0.1987 0.2094 4.1074 4.1789| | 14: 1.25 - 1.22 0.98 7015 113 0.2069 0.2265 4.0712 4.1901| | 15: 1.22 - 1.19 0.98 6957 137 0.2098 0.1964 4.0356 3.9884| | 16: 1.19 - 1.17 0.93 6604 132 0.2112 0.2220 4.0005 4.0926| | 17: 1.17 - 1.14 0.98 6941 135 0.2146 0.1861 3.9515 3.9562| | 18: 1.14 - 1.12 0.98 6875 142 0.2212 0.2565 3.929 3.9688| | 19: 1.12 - 1.10 0.97 6949 106 0.2263 0.1962 3.8706 3.8502| | 20: 1.10 - 1.08 0.97 6884 147 0.2317 0.2220 3.821 3.8299| | 21: 1.08 - 1.07 0.97 6852 152 0.2402 0.2783 3.785 3.8306| | 22: 1.07 - 1.05 0.97 6838 135 0.2546 0.2433 3.7428 3.7244| | 23: 1.05 - 1.03 0.97 6829 159 0.2725 0.2454 3.7279 3.7784| | 24: 1.03 - 1.02 0.96 6785 133 0.2871 0.2662 3.6967 3.7503| | 25: 1.02 - 1.01 0.93 6552 130 0.3073 0.3190 3.6766 3.8005| | 26: 1.01 - 0.99 0.96 6767 158 0.3219 0.3289 3.6303 3.6344| | 27: 0.99 - 0.98 0.94 6648 131 0.3401 0.3319 3.6431 3.6222| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.70 0.91 0.98 36544.55| | 2: 2.94 - 2.33 7339 128 0.85 21.42 1.09 1.03 15432.24| | 3: 2.33 - 2.04 6939 150 0.93 12.33 1.11 1.06 4059.45| | 4: 2.04 - 1.85 7170 155 0.93 12.90 1.11 1.06 2570.67| | 5: 1.85 - 1.72 7113 159 0.92 14.84 1.11 1.07 1886.55| | 6: 1.72 - 1.62 7102 142 0.91 15.90 1.11 1.07 1474.53| | 7: 1.62 - 1.54 7104 148 0.90 16.50 1.12 1.07 1177.92| | 8: 1.54 - 1.47 6798 152 0.89 17.75 1.10 1.06 1091.25| | 9: 1.47 - 1.41 6938 155 0.88 18.90 1.10 1.07 976.29| | 10: 1.41 - 1.36 7022 150 0.87 20.17 1.10 1.06 865.87| | 11: 1.36 - 1.32 6997 151 0.88 19.28 1.08 1.07 710.99| | 12: 1.32 - 1.28 6976 149 0.88 19.46 1.08 1.04 631.29| | 13: 1.28 - 1.25 6907 166 0.87 19.72 1.07 1.04 594.74| | 14: 1.25 - 1.22 7015 113 0.87 20.74 1.07 1.03 569.06| | 15: 1.22 - 1.19 6957 137 0.87 20.39 1.08 1.04 519.54| | 16: 1.19 - 1.17 6604 132 0.87 20.28 1.07 1.03 481.44| | 17: 1.17 - 1.14 6941 135 0.87 20.66 1.08 1.02 425.87| | 18: 1.14 - 1.12 6875 142 0.87 20.93 1.08 0.99 387.61| | 19: 1.12 - 1.10 6949 106 0.86 21.23 1.07 0.99 351.14| | 20: 1.10 - 1.08 6884 147 0.86 22.06 1.06 0.98 330.89| | 21: 1.08 - 1.07 6852 152 0.85 22.94 1.06 0.99 320.27| | 22: 1.07 - 1.05 6838 135 0.83 24.48 1.06 0.99 307.43| | 23: 1.05 - 1.03 6829 159 0.81 26.60 1.05 0.98 309.23| | 24: 1.03 - 1.02 6785 133 0.78 29.07 1.05 0.97 318.91| | 25: 1.02 - 1.01 6552 130 0.76 31.49 1.04 0.92 321.64| | 26: 1.01 - 0.99 6767 158 0.73 33.55 1.03 0.90 310.33| | 27: 0.99 - 0.98 6648 131 0.74 33.44 1.04 0.86 282.19| |alpha: min = 0.86 max = 1.07 mean = 1.01| |beta: min = 282.19 max = 36544.55 mean = 2842.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.97 mean = 21.31| |phase err.(test): min = 0.00 max = 89.47 mean = 21.35| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.257 2950 Z= 5.390 Angle : 5.210 18.002 4018 Z= 3.702 Chirality : 0.396 1.233 492 Planarity : 0.032 0.127 512 Dihedral : 12.772 87.069 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.92 % Favored : 94.56 % Rotamer: Outliers : 0.32 % Allowed : 5.16 % Favored : 94.52 % Cbeta Deviations : 31.74 % 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: -2.52 (0.38), residues: 386 helix: -2.44 (0.34), residues: 146 sheet: -1.56 (0.50), residues: 86 loop : -0.58 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.080 0.014 ARG B 83 TYR 0.087 0.030 TYR B 67 PHE 0.132 0.039 PHE B 164 TRP 0.104 0.036 TRP A 146 HIS 0.064 0.024 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2029 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.295742 | | target function (ml) not normalized (work): 804648.394463 | | target function (ml) not normalized (free): 16513.689061 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2027 0.2029 0.1952 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2027 0.2029 0.1952 n_refl.: 191155 remove outliers: r(all,work,free)=0.2027 0.2029 0.1952 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2024 0.2027 0.1952 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1798 0.1796 0.1885 n_refl.: 191145 remove outliers: r(all,work,free)=0.1796 0.1795 0.1885 n_refl.: 191141 ======================== 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 0.4241 400.535 294.834 0.432 0.914 0.303 13.296-10.522 100.00 100 1 0.2516 534.497 520.581 0.781 0.915 0.255 10.503-8.327 99.45 178 3 0.2494 565.118 554.992 0.964 0.916 0.230 8.318-6.595 100.00 360 8 0.2443 414.736 402.966 0.966 0.916 0.170 6.588-5.215 100.00 711 7 0.2281 381.101 364.470 0.942 0.916 0.130 5.214-4.128 98.38 1367 28 0.1486 557.435 549.529 1.064 0.917 0.070 4.126-3.266 94.74 2603 46 0.1365 508.132 497.939 1.131 0.919 0.030 3.266-2.585 99.86 5447 97 0.1444 342.774 337.310 1.103 0.919 0.030 2.585-2.046 97.45 10613 204 0.1379 258.603 254.362 1.106 0.922 0.000 2.046-1.619 99.39 21536 464 0.1620 153.054 150.011 1.120 0.925 0.000 1.619-1.281 98.00 42464 925 0.1914 82.395 80.585 1.101 0.930 0.000 1.281-0.980 96.53 101826 2056 0.2309 44.203 41.993 1.072 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0545 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1795 r_free=0.1885 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1796 r_free=0.1889 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.099341 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 581.056896 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 0.1272 0.1505 0.0233 0.039 1.2 11.0 0.0 0.3 0 11.050 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.05 2.33 1.118 13.091 581.057 0.019 12.98 15.72 2.74 1.272 13.365 581.057 0.018 Individual atomic B min max mean iso aniso Overall: 5.23 73.02 15.08 1.42 435 3274 Protein: 5.23 40.30 11.05 1.42 0 2902 Water: 6.39 73.02 29.57 N/A 435 370 Other: 16.02 30.37 23.19 N/A 0 2 Chain A: 5.38 59.75 13.09 N/A 0 1626 Chain B: 5.23 73.02 12.82 N/A 0 1648 Chain S: 11.24 65.11 31.01 N/A 435 0 Histogram: Values Number of atoms 5.23 - 12.01 2164 12.01 - 18.79 638 18.79 - 25.57 319 25.57 - 32.35 253 32.35 - 39.13 162 39.13 - 45.91 106 45.91 - 52.69 43 52.69 - 59.47 19 59.47 - 66.24 4 66.24 - 73.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1573 r_work=0.1297 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1568 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1559 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1559 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015700 | | target function (ls_wunit_k1) not normalized (work): 2940.572747 | | target function (ls_wunit_k1) not normalized (free): 118.556336 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1559 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1475 0.1473 0.1637 n_refl.: 191141 remove outliers: r(all,work,free)=0.1475 0.1473 0.1637 n_refl.: 191141 overall B=0.14 to atoms: r(all,work,free)=0.1496 0.1494 0.1646 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1544 n_refl.: 191141 remove outliers: r(all,work,free)=0.1279 0.1273 0.1543 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 0.3567 402.814 377.117 0.460 1.002 0.270 13.296-10.522 100.00 100 1 0.2116 534.497 527.374 0.713 1.003 0.235 10.503-8.327 99.45 178 3 0.1764 565.118 564.880 0.854 1.003 0.230 8.318-6.595 100.00 360 8 0.1698 414.736 411.987 0.874 1.003 0.155 6.588-5.215 100.00 711 7 0.1531 381.101 373.568 0.852 1.003 0.150 5.214-4.128 98.38 1367 28 0.0900 557.435 554.782 0.938 1.004 0.049 4.126-3.266 94.74 2603 46 0.0834 508.132 503.983 1.002 1.004 0.019 3.266-2.585 99.86 5447 97 0.0925 342.774 340.221 0.985 1.004 0.005 2.585-2.046 97.45 10613 204 0.0954 258.603 256.343 0.996 1.005 0.000 2.046-1.619 99.39 21536 464 0.1092 153.054 151.402 1.013 1.005 0.000 1.619-1.281 98.00 42464 925 0.1274 82.395 81.446 1.006 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1868 44.202 42.168 0.983 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0320 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1543 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1543 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1543 | n_water=805 | time (s): 3.040 (total time: 3.040) Filter (dist) r_work=0.1279 r_free=0.1550 | n_water=792 | time (s): 96.170 (total time: 99.210) Filter (q & B) r_work=0.1279 r_free=0.1550 | n_water=788 | time (s): 5.270 (total time: 104.480) Compute maps r_work=0.1279 r_free=0.1550 | n_water=788 | time (s): 2.070 (total time: 106.550) Filter (map) r_work=0.1306 r_free=0.1529 | n_water=648 | time (s): 5.400 (total time: 111.950) Find peaks r_work=0.1306 r_free=0.1529 | n_water=648 | time (s): 0.700 (total time: 112.650) Add new water r_work=0.1328 r_free=0.1554 | n_water=962 | time (s): 3.880 (total time: 116.530) Refine new water occ: r_work=0.1282 r_free=0.1504 adp: r_work=0.1270 r_free=0.1507 occ: r_work=0.1272 r_free=0.1502 adp: r_work=0.1266 r_free=0.1504 occ: r_work=0.1268 r_free=0.1502 adp: r_work=0.1265 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1265 r_free=0.1504 r_work=0.1265 r_free=0.1504 | n_water=962 | time (s): 74.120 (total time: 190.650) Filter (q & B) r_work=0.1269 r_free=0.1508 | n_water=886 | time (s): 4.830 (total time: 195.480) Filter (dist only) r_work=0.1269 r_free=0.1507 | n_water=885 | time (s): 115.270 (total time: 310.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.253651 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 601.630637 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 0.1254 0.1530 0.0276 0.042 1.1 21.4 0.0 0.3 0 11.627 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.30 2.76 2.057 15.202 601.631 0.015 12.33 15.15 2.82 2.457 15.259 601.631 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 72.06 16.34 1.21 517 3272 Protein: 5.42 40.53 10.99 1.21 0 2902 Water: 6.62 72.06 33.87 N/A 517 368 Other: 16.38 32.33 24.35 N/A 0 2 Chain A: 5.52 55.65 13.01 N/A 0 1624 Chain B: 5.42 68.16 12.85 N/A 0 1648 Chain S: 10.74 72.06 37.94 N/A 517 0 Histogram: Values Number of atoms 5.42 - 12.09 2146 12.09 - 18.75 666 18.75 - 25.42 253 25.42 - 32.08 224 32.08 - 38.74 178 38.74 - 45.41 163 45.41 - 52.07 93 52.07 - 58.74 38 58.74 - 65.40 25 65.40 - 72.06 3 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1515 r_work=0.1233 r_free=0.1516 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1516 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 = 0.1227 r_free = 0.1516 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1516 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013545 | | target function (ls_wunit_k1) not normalized (work): 2537.022437 | | target function (ls_wunit_k1) not normalized (free): 102.765653 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1516 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1442 0.1439 0.1604 n_refl.: 191139 remove outliers: r(all,work,free)=0.1442 0.1439 0.1604 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1438 0.1435 0.1602 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1522 n_refl.: 191139 remove outliers: r(all,work,free)=0.1239 0.1234 0.1522 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 0.3261 402.814 375.306 0.483 0.961 0.261 13.296-10.522 100.00 100 1 0.1892 534.497 526.287 0.765 0.962 0.224 10.503-8.327 99.45 178 3 0.1449 565.118 566.794 0.925 0.962 0.191 8.318-6.595 100.00 360 8 0.1551 414.736 413.778 0.940 0.962 0.153 6.588-5.215 100.00 711 7 0.1353 381.101 376.515 0.914 0.962 0.133 5.214-4.128 98.38 1367 28 0.0837 557.435 555.895 0.997 0.962 0.090 4.126-3.266 94.74 2603 46 0.0766 508.132 505.699 1.061 0.962 0.015 3.266-2.585 99.86 5447 97 0.0861 342.774 341.247 1.048 0.961 0.010 2.585-2.046 97.45 10613 204 0.0899 258.603 256.765 1.060 0.960 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.617 1.082 0.959 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.352 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.217 1.060 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0607 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1522 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1522 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1522 | n_water=885 | time (s): 3.710 (total time: 3.710) Filter (dist) r_work=0.1235 r_free=0.1522 | n_water=880 | time (s): 111.050 (total time: 114.760) Filter (q & B) r_work=0.1235 r_free=0.1522 | n_water=876 | time (s): 5.660 (total time: 120.420) Compute maps r_work=0.1235 r_free=0.1522 | n_water=876 | time (s): 2.380 (total time: 122.800) Filter (map) r_work=0.1272 r_free=0.1519 | n_water=694 | time (s): 6.080 (total time: 128.880) Find peaks r_work=0.1272 r_free=0.1519 | n_water=694 | time (s): 0.670 (total time: 129.550) Add new water r_work=0.1295 r_free=0.1551 | n_water=1013 | time (s): 4.890 (total time: 134.440) Refine new water occ: r_work=0.1251 r_free=0.1514 adp: r_work=0.1251 r_free=0.1515 occ: r_work=0.1247 r_free=0.1512 adp: r_work=0.1247 r_free=0.1513 occ: r_work=0.1245 r_free=0.1510 adp: r_work=0.1244 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1512 r_work=0.1244 r_free=0.1512 | n_water=1013 | time (s): 293.270 (total time: 427.710) Filter (q & B) r_work=0.1249 r_free=0.1519 | n_water=880 | time (s): 6.810 (total time: 434.520) Filter (dist only) r_work=0.1249 r_free=0.1518 | n_water=879 | time (s): 118.280 (total time: 552.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.720613 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.870658 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 0.1238 0.1432 0.0194 0.035 1.1 8.0 0.0 0.0 0 0.860 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.32 1.94 1.935 14.609 16.871 3.938 12.32 13.96 1.64 2.209 14.521 16.871 3.896 Individual atomic B min max mean iso aniso Overall: 5.55 67.80 15.32 1.07 512 3271 Protein: 5.55 36.96 10.76 1.07 0 2902 Water: 6.68 67.80 30.36 N/A 512 367 Other: 14.12 28.14 21.13 N/A 0 2 Chain A: 5.57 54.77 12.79 N/A 0 1624 Chain B: 5.55 67.80 12.57 N/A 0 1647 Chain S: 13.37 62.11 32.19 N/A 512 0 Histogram: Values Number of atoms 5.55 - 11.77 2135 11.77 - 18.00 680 18.00 - 24.22 301 24.22 - 30.45 229 30.45 - 36.67 174 36.67 - 42.90 148 42.90 - 49.12 75 49.12 - 55.35 31 55.35 - 61.57 6 61.57 - 67.80 4 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1397 r_work=0.1233 r_free=0.1398 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1398 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1384 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890201 | | target function (ml) not normalized (work): 728626.928533 | | target function (ml) not normalized (free): 15219.491055 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1226 0.1384 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1443 0.1442 0.1489 n_refl.: 191139 remove outliers: r(all,work,free)=0.1443 0.1442 0.1489 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1436 0.1485 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1380 n_refl.: 191139 remove outliers: r(all,work,free)=0.1225 0.1221 0.1380 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3716 398.895 357.722 0.413 0.946 0.237 13.296-10.522 98.02 98 1 0.2334 528.900 509.764 0.717 0.947 0.209 10.503-8.327 98.35 176 3 0.1951 555.265 557.206 0.886 0.947 0.176 8.318-6.595 100.00 360 8 0.2105 414.736 410.140 0.897 0.947 0.133 6.588-5.215 100.00 711 7 0.1824 381.101 370.978 0.888 0.947 0.113 5.214-4.128 98.38 1367 28 0.1166 557.435 552.167 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1088 508.132 501.471 1.033 0.948 0.009 3.266-2.585 99.86 5447 97 0.1080 342.774 338.984 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0962 258.603 255.836 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.412 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1049 82.395 81.494 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.324 1.038 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1056 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1381 | n_water=879 | time (s): 2.870 (total time: 2.870) Filter (dist) r_work=0.1222 r_free=0.1383 | n_water=877 | time (s): 109.700 (total time: 112.570) Filter (q & B) r_work=0.1223 r_free=0.1380 | n_water=864 | time (s): 5.300 (total time: 117.870) Compute maps r_work=0.1223 r_free=0.1380 | n_water=864 | time (s): 1.750 (total time: 119.620) Filter (map) r_work=0.1247 r_free=0.1386 | n_water=720 | time (s): 4.090 (total time: 123.710) Find peaks r_work=0.1247 r_free=0.1386 | n_water=720 | time (s): 0.560 (total time: 124.270) Add new water r_work=0.1262 r_free=0.1399 | n_water=967 | time (s): 4.130 (total time: 128.400) Refine new water occ: r_work=0.1213 r_free=0.1364 adp: r_work=0.1205 r_free=0.1359 occ: r_work=0.1203 r_free=0.1361 adp: r_work=0.1203 r_free=0.1361 occ: r_work=0.1203 r_free=0.1361 adp: r_work=0.1203 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1361 r_work=0.1203 r_free=0.1361 | n_water=967 | time (s): 153.580 (total time: 281.980) Filter (q & B) r_work=0.1207 r_free=0.1365 | n_water=846 | time (s): 4.710 (total time: 286.690) Filter (dist only) r_work=0.1208 r_free=0.1364 | n_water=844 | time (s): 104.750 (total time: 391.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.599851 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.752876 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 0.1364 0.0158 0.036 1.1 5.6 0.0 0.3 0 0.800 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.64 1.58 1.838 14.139 15.753 3.873 11.99 13.60 1.60 1.952 14.096 15.753 3.866 Individual atomic B min max mean iso aniso Overall: 5.52 67.36 14.84 1.00 477 3271 Protein: 5.52 33.69 10.67 1.00 0 2902 Water: 5.84 67.36 29.16 N/A 477 367 Other: 13.98 27.28 20.63 N/A 0 2 Chain A: 5.55 53.71 12.65 N/A 0 1624 Chain B: 5.52 67.36 12.46 N/A 0 1647 Chain S: 5.84 61.99 30.49 N/A 477 0 Histogram: Values Number of atoms 5.52 - 11.70 2117 11.70 - 17.89 726 17.89 - 24.07 334 24.07 - 30.25 197 30.25 - 36.44 143 36.44 - 42.62 128 42.62 - 48.81 66 48.81 - 54.99 26 54.99 - 61.18 8 61.18 - 67.36 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1360 r_work=0.1200 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1361 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1357 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863737 | | target function (ml) not normalized (work): 723647.030711 | | target function (ml) not normalized (free): 15133.451607 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1415 0.1413 0.1483 n_refl.: 191133 remove outliers: r(all,work,free)=0.1415 0.1413 0.1483 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1408 0.1406 0.1478 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1355 n_refl.: 191133 remove outliers: r(all,work,free)=0.1198 0.1195 0.1355 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3599 360.999 314.530 0.412 0.950 0.239 13.296-10.522 96.04 96 1 0.2279 480.567 455.466 0.705 0.952 0.201 10.503-8.327 98.35 176 3 0.2071 502.936 495.834 0.862 0.952 0.183 8.318-6.595 100.00 360 8 0.2205 375.651 370.263 0.885 0.952 0.125 6.588-5.215 100.00 711 7 0.1914 345.186 335.429 0.880 0.952 0.100 5.214-4.128 98.38 1367 28 0.1202 504.902 499.710 0.969 0.952 0.090 4.126-3.266 94.74 2603 46 0.1117 460.246 454.253 1.030 0.952 0.005 3.266-2.585 99.86 5447 97 0.1083 310.471 307.301 1.017 0.951 0.000 2.585-2.046 97.45 10613 204 0.0932 234.232 231.889 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0916 138.630 137.375 1.053 0.949 0.000 1.619-1.281 98.00 42464 925 0.0989 74.631 73.929 1.051 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.036 38.382 1.039 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1173 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1196 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1358 | n_water=844 | time (s): 3.120 (total time: 3.120) Filter (dist) r_work=0.1196 r_free=0.1357 | n_water=843 | time (s): 102.140 (total time: 105.260) Filter (q & B) r_work=0.1196 r_free=0.1357 | n_water=834 | time (s): 4.580 (total time: 109.840) Compute maps r_work=0.1196 r_free=0.1357 | n_water=834 | time (s): 2.030 (total time: 111.870) Filter (map) r_work=0.1221 r_free=0.1367 | n_water=720 | time (s): 5.020 (total time: 116.890) Find peaks r_work=0.1221 r_free=0.1367 | n_water=720 | time (s): 0.560 (total time: 117.450) Add new water r_work=0.1235 r_free=0.1387 | n_water=966 | time (s): 4.220 (total time: 121.670) Refine new water occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1193 r_free=0.1352 occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1190 r_free=0.1351 occ: r_work=0.1188 r_free=0.1350 adp: r_work=0.1188 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1350 r_work=0.1188 r_free=0.1350 | n_water=966 | time (s): 252.460 (total time: 374.130) Filter (q & B) r_work=0.1192 r_free=0.1350 | n_water=885 | time (s): 5.410 (total time: 379.540) Filter (dist only) r_work=0.1192 r_free=0.1350 | n_water=883 | time (s): 115.540 (total time: 495.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565033 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.443440 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1353 0.0158 0.036 1.1 6.6 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.53 1.58 1.795 14.127 15.443 3.764 12.01 13.55 1.55 1.930 14.075 15.443 3.761 Individual atomic B min max mean iso aniso Overall: 5.51 66.71 14.89 0.94 516 3271 Protein: 5.51 31.02 10.56 0.94 0 2902 Water: 5.94 66.71 29.11 N/A 516 367 Other: 13.88 25.00 19.44 N/A 0 2 Chain A: 5.60 51.98 12.50 N/A 0 1624 Chain B: 5.51 66.71 12.33 N/A 0 1647 Chain S: 5.94 61.84 30.58 N/A 516 0 Histogram: Values Number of atoms 5.51 - 11.63 2114 11.63 - 17.75 750 17.75 - 23.87 304 23.87 - 29.99 222 29.99 - 36.11 165 36.11 - 42.23 128 42.23 - 48.35 70 48.35 - 54.47 24 54.47 - 60.59 7 60.59 - 66.71 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1355 r_work=0.1201 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1356 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1356 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760034 | | target function (ml) not normalized (work): 704213.055249 | | target function (ml) not normalized (free): 14743.078971 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1495 n_refl.: 191130 remove outliers: r(all,work,free)=0.1401 0.1399 0.1495 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1394 0.1392 0.1490 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1354 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1354 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3632 356.856 334.162 0.425 0.952 0.231 13.296-10.522 96.04 96 1 0.2335 480.567 464.071 0.711 0.953 0.193 10.503-8.327 98.35 176 3 0.2109 502.936 496.577 0.862 0.953 0.173 8.318-6.595 100.00 360 8 0.2149 375.651 370.783 0.883 0.953 0.110 6.588-5.215 100.00 711 7 0.1934 345.186 335.319 0.881 0.953 0.095 5.214-4.128 98.38 1367 28 0.1205 504.902 499.783 0.968 0.954 0.049 4.126-3.266 94.74 2603 46 0.1138 460.246 453.649 1.030 0.954 0.005 3.266-2.585 99.86 5447 97 0.1104 310.471 307.092 1.015 0.953 0.000 2.585-2.046 97.45 10613 204 0.0947 234.232 231.740 1.028 0.953 0.000 2.046-1.619 99.39 21536 464 0.0917 138.630 137.301 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0977 74.631 73.915 1.048 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.036 38.376 1.036 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1305 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1354 | n_water=883 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1197 r_free=0.1354 | n_water=883 | time (s): 106.100 (total time: 108.610) Filter (q & B) r_work=0.1198 r_free=0.1354 | n_water=873 | time (s): 4.040 (total time: 112.650) Compute maps r_work=0.1198 r_free=0.1354 | n_water=873 | time (s): 1.800 (total time: 114.450) Filter (map) r_work=0.1219 r_free=0.1355 | n_water=756 | time (s): 4.190 (total time: 118.640) Find peaks r_work=0.1219 r_free=0.1355 | n_water=756 | time (s): 0.580 (total time: 119.220) Add new water r_work=0.1229 r_free=0.1373 | n_water=968 | time (s): 3.960 (total time: 123.180) Refine new water occ: r_work=0.1196 r_free=0.1346 adp: r_work=0.1196 r_free=0.1347 occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1344 occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1343 r_work=0.1192 r_free=0.1343 | n_water=968 | time (s): 213.630 (total time: 336.810) Filter (q & B) r_work=0.1195 r_free=0.1344 | n_water=894 | time (s): 5.480 (total time: 342.290) Filter (dist only) r_work=0.1196 r_free=0.1343 | n_water=893 | time (s): 116.610 (total time: 458.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.543277 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.373755 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 0.1198 0.1349 0.0150 0.037 1.1 5.8 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.49 1.50 1.748 14.009 14.374 3.761 12.01 13.53 1.52 1.855 13.971 14.374 3.759 Individual atomic B min max mean iso aniso Overall: 5.59 65.63 14.84 0.89 526 3271 Protein: 5.59 29.02 10.47 0.89 0 2902 Water: 5.89 65.63 29.03 N/A 526 367 Other: 13.86 22.45 18.15 N/A 0 2 Chain A: 5.62 50.59 12.37 N/A 0 1624 Chain B: 5.59 65.63 12.21 N/A 0 1647 Chain S: 5.89 62.11 30.68 N/A 526 0 Histogram: Values Number of atoms 5.59 - 11.59 2103 11.59 - 17.59 779 17.59 - 23.60 292 23.60 - 29.60 216 29.60 - 35.61 163 35.61 - 41.61 127 41.61 - 47.62 79 47.62 - 53.62 28 53.62 - 59.63 6 59.63 - 65.63 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1354 r_work=0.1201 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1354 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1353 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758439 | | target function (ml) not normalized (work): 703910.534139 | | target function (ml) not normalized (free): 14735.822305 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1353 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1491 n_refl.: 191129 remove outliers: r(all,work,free)=0.1400 0.1398 0.1491 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1392 0.1390 0.1485 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1202 0.1199 0.1351 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3624 356.856 330.636 0.407 0.952 0.211 13.296-10.522 96.04 96 1 0.2297 480.567 464.346 0.703 0.953 0.171 10.503-8.327 98.35 176 3 0.2176 502.936 495.662 0.860 0.954 0.150 8.318-6.595 100.00 360 8 0.2138 375.651 370.540 0.884 0.953 0.111 6.588-5.215 100.00 711 7 0.1929 345.186 335.439 0.880 0.953 0.090 5.214-4.128 98.38 1367 28 0.1222 504.902 499.741 0.970 0.954 0.070 4.126-3.266 94.74 2603 46 0.1147 460.246 453.616 1.031 0.954 0.005 3.266-2.585 99.86 5447 97 0.1113 310.471 307.135 1.016 0.954 0.000 2.585-2.046 97.45 10613 204 0.0953 234.232 231.715 1.028 0.954 0.000 2.046-1.619 99.39 21536 464 0.0916 138.630 137.323 1.050 0.953 0.000 1.619-1.281 98.00 42464 925 0.0971 74.631 73.930 1.048 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.036 38.376 1.035 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1424 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1351 | n_water=893 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1199 r_free=0.1351 | n_water=893 | time (s): 109.270 (total time: 112.420) Filter (q & B) r_work=0.1199 r_free=0.1351 | n_water=887 | time (s): 3.990 (total time: 116.410) Compute maps r_work=0.1199 r_free=0.1351 | n_water=887 | time (s): 1.550 (total time: 117.960) Filter (map) r_work=0.1219 r_free=0.1355 | n_water=775 | time (s): 5.320 (total time: 123.280) Find peaks r_work=0.1219 r_free=0.1355 | n_water=775 | time (s): 0.660 (total time: 123.940) Add new water r_work=0.1229 r_free=0.1370 | n_water=984 | time (s): 4.070 (total time: 128.010) Refine new water occ: r_work=0.1197 r_free=0.1353 adp: r_work=0.1197 r_free=0.1353 occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1351 occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1193 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1350 r_work=0.1193 r_free=0.1350 | n_water=984 | time (s): 301.130 (total time: 429.140) Filter (q & B) r_work=0.1196 r_free=0.1354 | n_water=911 | time (s): 5.380 (total time: 434.520) Filter (dist only) r_work=0.1197 r_free=0.1353 | n_water=910 | time (s): 112.490 (total time: 547.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.552204 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.336031 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 0.1200 0.1359 0.0159 0.038 1.1 6.1 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.59 1.59 1.711 13.916 14.336 3.760 12.01 13.62 1.62 1.746 13.903 14.336 3.757 Individual atomic B min max mean iso aniso Overall: 5.58 64.57 14.82 0.88 543 3271 Protein: 5.58 28.49 10.42 0.88 0 2902 Water: 5.95 64.57 28.84 N/A 543 367 Other: 13.87 22.00 17.93 N/A 0 2 Chain A: 5.65 50.12 12.28 N/A 0 1624 Chain B: 5.58 64.57 12.14 N/A 0 1647 Chain S: 5.95 62.30 30.55 N/A 543 0 Histogram: Values Number of atoms 5.58 - 11.47 2081 11.47 - 17.37 802 17.37 - 23.27 283 23.27 - 29.17 222 29.17 - 35.07 175 35.07 - 40.97 126 40.97 - 46.87 84 46.87 - 52.77 30 52.77 - 58.67 7 58.67 - 64.57 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1362 r_work=0.1201 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1364 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756996 | | target function (ml) not normalized (work): 703640.289227 | | target function (ml) not normalized (free): 14737.517648 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1495 n_refl.: 191129 remove outliers: r(all,work,free)=0.1400 0.1398 0.1495 n_refl.: 191129 overall B=-0.01 to atoms: r(all,work,free)=0.1398 0.1396 0.1493 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1188 0.1350 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3638 356.856 327.671 0.419 0.916 0.193 13.296-10.522 95.05 95 1 0.2290 479.669 456.333 0.737 0.917 0.148 10.503-8.327 98.35 176 3 0.2174 502.936 494.508 0.912 0.917 0.127 8.315-6.595 100.00 359 8 0.2108 374.705 370.196 0.937 0.917 0.105 6.588-5.215 100.00 711 7 0.1941 345.186 334.957 0.933 0.918 0.087 5.214-4.128 98.38 1367 28 0.1236 504.902 498.776 1.029 0.919 0.039 4.126-3.266 94.74 2603 46 0.1150 460.246 452.957 1.095 0.920 0.005 3.266-2.585 99.86 5447 97 0.1116 310.471 306.911 1.078 0.921 0.000 2.585-2.046 97.45 10613 204 0.0960 234.232 231.590 1.088 0.923 0.000 2.046-1.619 99.39 21536 464 0.0908 138.630 137.254 1.107 0.926 0.000 1.619-1.281 98.00 42464 925 0.0946 74.631 73.988 1.100 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.036 38.345 1.071 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0313 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1350 | n_water=910 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1188 r_free=0.1350 | n_water=910 | time (s): 107.630 (total time: 110.570) Filter (q & B) r_work=0.1189 r_free=0.1349 | n_water=899 | time (s): 4.290 (total time: 114.860) Compute maps r_work=0.1189 r_free=0.1349 | n_water=899 | time (s): 2.470 (total time: 117.330) Filter (map) r_work=0.1209 r_free=0.1356 | n_water=789 | time (s): 3.940 (total time: 121.270) Find peaks r_work=0.1209 r_free=0.1356 | n_water=789 | time (s): 0.720 (total time: 121.990) Add new water r_work=0.1216 r_free=0.1366 | n_water=992 | time (s): 3.850 (total time: 125.840) Refine new water occ: r_work=0.1186 r_free=0.1345 adp: r_work=0.1186 r_free=0.1346 occ: r_work=0.1184 r_free=0.1343 adp: r_work=0.1184 r_free=0.1345 occ: r_work=0.1183 r_free=0.1341 adp: r_work=0.1183 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1343 r_work=0.1183 r_free=0.1343 | n_water=992 | time (s): 201.140 (total time: 326.980) Filter (q & B) r_work=0.1187 r_free=0.1350 | n_water=914 | time (s): 4.970 (total time: 331.950) Filter (dist only) r_work=0.1187 r_free=0.1349 | n_water=913 | time (s): 115.670 (total time: 447.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.515793 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.471837 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 0.1190 0.1357 0.0167 0.038 1.1 5.8 0.0 0.3 0 0.758 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.57 1.67 1.696 13.867 13.472 3.756 11.92 13.60 1.68 1.696 13.865 13.472 3.755 Individual atomic B min max mean iso aniso Overall: 5.58 64.30 14.78 0.86 546 3271 Protein: 5.58 28.27 10.42 0.86 0 2902 Water: 6.06 64.30 28.62 N/A 546 367 Other: 13.85 21.99 17.92 N/A 0 2 Chain A: 5.67 50.00 12.26 N/A 0 1624 Chain B: 5.58 64.30 12.12 N/A 0 1647 Chain S: 6.06 62.35 30.30 N/A 546 0 Histogram: Values Number of atoms 5.58 - 11.46 2078 11.46 - 17.33 806 17.33 - 23.20 289 23.20 - 29.07 224 29.07 - 34.94 170 34.94 - 40.81 123 40.81 - 46.69 86 46.69 - 52.56 29 52.56 - 58.43 8 58.43 - 64.30 4 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1360 r_work=0.1192 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1360 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1362 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754667 | | target function (ml) not normalized (work): 703196.501052 | | target function (ml) not normalized (free): 14729.254054 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1362 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1405 0.1403 0.1511 n_refl.: 191127 remove outliers: r(all,work,free)=0.1405 0.1403 0.1511 n_refl.: 191127 overall B=-0.02 to atoms: r(all,work,free)=0.1402 0.1400 0.1508 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1362 n_refl.: 191127 remove outliers: r(all,work,free)=0.1194 0.1190 0.1362 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3617 356.856 327.629 0.386 0.994 0.197 13.296-10.522 95.05 95 1 0.2283 479.669 466.288 0.690 0.996 0.144 10.503-8.327 98.35 176 3 0.2219 502.936 494.320 0.838 0.996 0.120 8.315-6.595 100.00 359 8 0.2122 374.705 369.384 0.860 0.996 0.096 6.588-5.215 100.00 711 7 0.1969 345.186 334.834 0.858 0.997 0.080 5.214-4.128 98.38 1367 28 0.1239 504.902 498.871 0.948 0.998 0.039 4.126-3.266 94.74 2603 46 0.1159 460.246 453.030 1.010 0.999 0.005 3.266-2.585 99.86 5447 97 0.1121 310.471 306.851 0.993 1.000 0.000 2.585-2.046 97.45 10613 204 0.0961 234.232 231.522 1.003 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.630 137.256 1.020 1.007 0.000 1.619-1.281 98.00 42464 925 0.0945 74.631 73.982 1.014 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.036 38.329 0.989 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0530 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1362 | n_water=913 | time (s): 2.950 (total time: 2.950) Filter (dist) r_work=0.1190 r_free=0.1362 | n_water=913 | time (s): 110.180 (total time: 113.130) Filter (q & B) r_work=0.1191 r_free=0.1362 | n_water=904 | time (s): 4.520 (total time: 117.650) Compute maps r_work=0.1191 r_free=0.1362 | n_water=904 | time (s): 1.960 (total time: 119.610) Filter (map) r_work=0.1211 r_free=0.1359 | n_water=795 | time (s): 4.130 (total time: 123.740) Find peaks r_work=0.1211 r_free=0.1359 | n_water=795 | time (s): 0.580 (total time: 124.320) Add new water r_work=0.1218 r_free=0.1371 | n_water=995 | time (s): 4.610 (total time: 128.930) Refine new water occ: r_work=0.1187 r_free=0.1352 adp: r_work=0.1187 r_free=0.1352 occ: r_work=0.1186 r_free=0.1350 adp: r_work=0.1186 r_free=0.1351 occ: r_work=0.1184 r_free=0.1349 adp: r_work=0.1184 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1349 r_work=0.1184 r_free=0.1349 | n_water=995 | time (s): 395.960 (total time: 524.890) Filter (q & B) r_work=0.1188 r_free=0.1355 | n_water=917 | time (s): 4.670 (total time: 529.560) Filter (dist only) r_work=0.1188 r_free=0.1355 | n_water=915 | time (s): 117.210 (total time: 646.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.583515 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.006681 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 0.1191 0.1360 0.0169 0.039 1.1 6.0 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.60 1.69 1.689 13.845 14.007 3.755 11.90 13.62 1.72 1.697 13.841 14.007 3.753 Individual atomic B min max mean iso aniso Overall: 5.63 63.40 14.74 0.86 548 3271 Protein: 5.63 28.02 10.42 0.86 0 2902 Water: 6.05 63.40 28.46 N/A 548 367 Other: 13.89 22.02 17.95 N/A 0 2 Chain A: 5.72 49.66 12.22 N/A 0 1624 Chain B: 5.63 63.40 12.09 N/A 0 1647 Chain S: 6.05 62.51 30.19 N/A 548 0 Histogram: Values Number of atoms 5.63 - 11.40 2065 11.40 - 17.18 823 17.18 - 22.96 278 22.96 - 28.74 220 28.74 - 34.51 182 34.51 - 40.29 125 40.29 - 46.07 79 46.07 - 51.84 31 51.84 - 57.62 11 57.62 - 63.40 5 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1362 r_work=0.1191 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1362 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1363 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752836 | | target function (ml) not normalized (work): 702853.556988 | | target function (ml) not normalized (free): 14730.528340 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1363 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1410 0.1408 0.1511 n_refl.: 191127 remove outliers: r(all,work,free)=0.1410 0.1408 0.1511 n_refl.: 191127 overall B=-0.12 to atoms: r(all,work,free)=0.1390 0.1388 0.1496 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1361 n_refl.: 191127 remove outliers: r(all,work,free)=0.1192 0.1189 0.1361 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3630 356.856 326.035 0.382 0.974 0.187 13.296-10.522 95.05 95 1 0.2296 479.669 465.922 0.692 0.976 0.138 10.503-8.327 98.35 176 3 0.2219 502.936 494.927 0.841 0.976 0.117 8.315-6.595 100.00 359 8 0.2118 374.705 369.322 0.865 0.976 0.098 6.588-5.215 100.00 711 7 0.1968 345.186 334.874 0.863 0.977 0.083 5.214-4.128 98.38 1367 28 0.1247 504.902 498.650 0.953 0.978 0.034 4.126-3.266 94.74 2603 46 0.1162 460.246 452.809 1.014 0.979 0.000 3.266-2.585 99.86 5447 97 0.1122 310.471 306.817 0.997 0.981 0.000 2.585-2.046 97.45 10613 204 0.0961 234.232 231.545 1.004 0.983 0.000 2.046-1.619 99.39 21536 464 0.0906 138.630 137.263 1.019 0.988 0.000 1.619-1.281 98.00 42464 925 0.0941 74.631 73.988 1.008 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.036 38.326 0.975 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0265 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1361 After: r_work=0.1190 r_free=0.1362 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1362 | n_water=915 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1190 r_free=0.1362 | n_water=915 | time (s): 114.010 (total time: 116.420) Filter (q & B) r_work=0.1191 r_free=0.1359 | n_water=900 | time (s): 4.110 (total time: 120.530) Compute maps r_work=0.1191 r_free=0.1359 | n_water=900 | time (s): 1.980 (total time: 122.510) Filter (map) r_work=0.1212 r_free=0.1358 | n_water=794 | time (s): 4.590 (total time: 127.100) Find peaks r_work=0.1212 r_free=0.1358 | n_water=794 | time (s): 0.580 (total time: 127.680) Add new water r_work=0.1218 r_free=0.1371 | n_water=1002 | time (s): 5.050 (total time: 132.730) Refine new water occ: r_work=0.1187 r_free=0.1346 adp: r_work=0.1187 r_free=0.1347 occ: r_work=0.1185 r_free=0.1345 adp: r_work=0.1185 r_free=0.1346 occ: r_work=0.1184 r_free=0.1344 adp: r_work=0.1184 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1345 r_work=0.1184 r_free=0.1345 | n_water=1002 | time (s): 221.360 (total time: 354.090) Filter (q & B) r_work=0.1188 r_free=0.1354 | n_water=921 | time (s): 5.290 (total time: 359.380) Filter (dist only) r_work=0.1188 r_free=0.1353 | n_water=920 | time (s): 118.130 (total time: 477.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.487126 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.751589 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1358 0.0165 0.039 1.2 8.0 0.0 0.3 0 0.744 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.58 1.65 1.685 13.741 13.752 3.757 11.93 13.60 1.67 1.675 13.746 13.752 3.756 Individual atomic B min max mean iso aniso Overall: 5.55 63.13 14.66 0.85 553 3271 Protein: 5.55 27.88 10.32 0.85 0 2902 Water: 5.98 63.13 28.35 N/A 553 367 Other: 13.81 21.92 17.87 N/A 0 2 Chain A: 5.62 49.50 12.11 N/A 0 1624 Chain B: 5.55 63.13 11.98 N/A 0 1647 Chain S: 5.98 62.41 30.15 N/A 553 0 Histogram: Values Number of atoms 5.55 - 11.30 2061 11.30 - 17.06 831 17.06 - 22.82 281 22.82 - 28.58 217 28.58 - 34.34 181 34.34 - 40.09 123 40.09 - 45.85 82 45.85 - 51.61 31 51.61 - 57.37 12 57.37 - 63.13 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1360 r_work=0.1194 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1360 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1361 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755893 | | target function (ml) not normalized (work): 703426.139497 | | target function (ml) not normalized (free): 14736.274392 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1355 0.1479 5.6874 5.7725| | 2: 2.94 - 2.33 1.00 7339 128 0.1069 0.1362 5.0813 5.1801| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1180 4.6593 4.7482| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1058 4.3944 4.5739| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.0993 4.1545 4.2474| | 6: 1.72 - 1.62 0.99 7102 142 0.0901 0.1098 3.9517 4.0831| | 7: 1.62 - 1.54 0.99 7104 148 0.0895 0.0971 3.8049 3.9412| | 8: 1.54 - 1.47 0.96 6798 152 0.0892 0.1331 3.7038 3.9121| | 9: 1.47 - 1.41 0.98 6938 155 0.0926 0.1129 3.6232 3.7489| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1205 3.5577 3.6805| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1133 3.486 3.5905| | 12: 1.32 - 1.28 0.98 6975 149 0.1032 0.1122 3.4605 3.5796| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1242 3.4379 3.5645| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1586 3.4337 3.6812| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1237 3.4488 3.4883| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1543 3.4662 3.6551| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1225 3.4339 3.4419| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1706 3.4397 3.5343| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1761 3.4214 3.5971| | 20: 1.10 - 1.08 0.97 6884 147 0.1587 0.1586 3.412 3.4362| | 21: 1.08 - 1.07 0.97 6852 152 0.1731 0.2140 3.4197 3.5062| | 22: 1.07 - 1.05 0.97 6836 135 0.1906 0.1950 3.4144 3.4174| | 23: 1.05 - 1.03 0.97 6827 159 0.2122 0.2019 3.4345 3.4881| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2249 3.4362 3.5114| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2525 3.45 3.5245| | 26: 1.01 - 0.99 0.96 6767 158 0.2753 0.2845 3.4158 3.4223| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2800 3.4694 3.3971| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7395 127 0.93 11.79 1.00 0.97 11360.22| | 2: 2.94 - 2.33 7339 128 0.93 12.88 0.99 0.98 5190.96| | 3: 2.33 - 2.04 6939 150 0.96 7.68 1.01 0.98 1709.09| | 4: 2.04 - 1.85 7170 155 0.96 7.66 1.00 0.98 1010.25| | 5: 1.85 - 1.72 7113 159 0.96 8.10 1.00 0.98 637.58| | 6: 1.72 - 1.62 7102 142 0.96 8.10 1.00 0.99 448.27| | 7: 1.62 - 1.54 7104 148 0.96 8.20 1.01 1.00 341.20| | 8: 1.54 - 1.47 6798 152 0.96 8.32 1.01 1.00 282.05| | 9: 1.47 - 1.41 6938 155 0.96 8.47 1.00 1.00 231.70| | 10: 1.41 - 1.36 7022 150 0.96 8.90 1.00 1.00 203.03| | 11: 1.36 - 1.32 6997 151 0.96 8.94 0.99 0.98 174.95| | 12: 1.32 - 1.28 6975 149 0.96 8.98 0.98 0.97 160.68| | 13: 1.28 - 1.25 6907 166 0.96 9.53 1.01 0.98 158.27| | 14: 1.25 - 1.22 7015 112 0.95 10.68 1.01 0.99 162.99| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 1.00 166.42| | 16: 1.19 - 1.17 6604 132 0.95 11.40 1.01 0.99 159.73| | 17: 1.17 - 1.14 6940 135 0.94 12.22 1.01 0.99 153.57| | 18: 1.14 - 1.12 6875 142 0.94 12.75 1.01 0.97 147.68| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.97 151.62| | 20: 1.10 - 1.08 6884 147 0.92 15.28 1.00 0.96 151.01| | 21: 1.08 - 1.07 6852 152 0.91 16.70 1.00 0.96 154.12| | 22: 1.07 - 1.05 6836 135 0.89 18.36 1.00 0.95 155.76| | 23: 1.05 - 1.03 6827 159 0.87 20.55 1.00 0.95 165.47| | 24: 1.03 - 1.02 6784 133 0.85 23.19 1.00 0.95 179.52| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.98 0.92 182.17| | 26: 1.01 - 0.99 6767 158 0.81 26.59 0.99 0.91 176.49| | 27: 0.99 - 0.98 6647 131 0.82 26.26 0.99 0.90 160.86| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 147.68 max = 11360.22 mean = 935.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.82 mean = 13.31| |phase err.(test): min = 0.00 max = 89.82 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1361 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1508 n_refl.: 191127 remove outliers: r(all,work,free)=0.1400 0.1398 0.1508 n_refl.: 191127 overall B=-0.04 to atoms: r(all,work,free)=0.1395 0.1393 0.1504 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191127 remove outliers: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3654 356.856 325.850 0.400 0.915 0.179 13.296-10.522 95.05 95 1 0.2311 479.669 465.069 0.735 0.916 0.131 10.503-8.327 98.35 176 3 0.2193 502.936 495.495 0.898 0.917 0.110 8.315-6.595 100.00 359 8 0.2097 374.705 369.431 0.920 0.917 0.089 6.588-5.215 100.00 711 7 0.1953 345.186 335.108 0.920 0.917 0.074 5.214-4.128 98.38 1367 28 0.1245 504.902 498.825 1.017 0.918 0.029 4.126-3.266 94.74 2603 46 0.1163 460.246 452.903 1.083 0.920 0.000 3.266-2.585 99.86 5447 97 0.1118 310.471 306.942 1.065 0.921 0.000 2.585-2.046 97.45 10613 204 0.0968 234.232 231.558 1.071 0.924 0.000 2.046-1.619 99.39 21536 464 0.0913 138.630 137.263 1.087 0.928 0.000 1.619-1.281 98.00 42464 925 0.0948 74.631 73.979 1.075 0.936 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.036 38.318 1.040 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0085 ================= 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 : 0.2029 0.1952 0.081 5.210 5.2 78.0 14.6 805 0.000 1_bss: 0.1795 0.1885 0.081 5.210 5.2 78.0 14.6 805 0.000 1_settarget: 0.1795 0.1885 0.081 5.210 5.2 78.0 14.6 805 0.000 1_nqh: 0.1796 0.1889 0.081 5.210 5.2 78.0 14.6 805 0.002 1_weight: 0.1796 0.1889 0.081 5.210 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1272 0.1505 0.039 1.157 5.2 78.0 14.6 805 0.158 1_adp: 0.1298 0.1573 0.039 1.157 5.2 73.0 15.1 805 0.158 1_regHadp: 0.1297 0.1568 0.039 1.157 5.2 73.0 15.1 805 0.158 1_occ: 0.1283 0.1559 0.039 1.157 5.2 73.0 15.1 805 0.158 2_bss: 0.1273 0.1543 0.039 1.157 5.4 73.2 15.2 805 0.158 2_settarget: 0.1273 0.1543 0.039 1.157 5.4 73.2 15.2 805 0.158 2_updatecdl: 0.1273 0.1543 0.039 1.162 5.4 73.2 15.2 805 0.158 2_nqh: 0.1273 0.1543 0.039 1.162 5.4 73.2 15.2 805 0.158 2_sol: 0.1269 0.1507 0.039 1.162 5.4 73.2 16.2 885 n/a 2_weight: 0.1269 0.1507 0.039 1.162 5.4 73.2 16.2 885 n/a 2_xyzrec: 0.1254 0.1530 0.042 1.137 5.4 73.2 16.2 885 n/a 2_adp: 0.1233 0.1515 0.042 1.137 5.4 72.1 16.3 885 n/a 2_regHadp: 0.1233 0.1516 0.042 1.137 5.4 72.1 16.3 885 n/a 2_occ: 0.1227 0.1516 0.042 1.137 5.4 72.1 16.3 885 n/a 3_bss: 0.1234 0.1522 0.042 1.137 5.4 72.0 16.3 885 n/a 3_settarget: 0.1234 0.1522 0.042 1.137 5.4 72.0 16.3 885 n/a 3_updatecdl: 0.1234 0.1522 0.042 1.141 5.4 72.0 16.3 885 n/a 3_nqh: 0.1234 0.1522 0.042 1.141 5.4 72.0 16.3 885 n/a 3_sol: 0.1249 0.1518 0.042 1.141 5.4 68.1 15.5 879 n/a 3_weight: 0.1249 0.1518 0.042 1.141 5.4 68.1 15.5 879 n/a 3_xyzrec: 0.1238 0.1432 0.035 1.106 5.4 68.1 15.5 879 n/a 3_adp: 0.1232 0.1397 0.035 1.106 5.5 67.8 15.3 879 n/a 3_regHadp: 0.1233 0.1398 0.035 1.106 5.5 67.8 15.3 879 n/a 3_occ: 0.1226 0.1384 0.035 1.106 5.5 67.8 15.3 879 n/a 4_bss: 0.1222 0.1381 0.035 1.106 5.5 67.8 15.3 879 n/a 4_settarget: 0.1222 0.1381 0.035 1.106 5.5 67.8 15.3 879 n/a 4_updatecdl: 0.1222 0.1381 0.035 1.106 5.5 67.8 15.3 879 n/a 4_nqh: 0.1222 0.1381 0.035 1.106 5.5 67.8 15.3 879 n/a 4_sol: 0.1208 0.1364 0.035 1.106 5.5 67.8 14.9 844 n/a 4_weight: 0.1208 0.1364 0.035 1.106 5.5 67.8 14.9 844 n/a 4_xyzrec: 0.1205 0.1364 0.036 1.122 5.5 67.8 14.9 844 n/a 4_adp: 0.1200 0.1360 0.036 1.122 5.5 67.4 14.8 844 n/a 4_regHadp: 0.1200 0.1361 0.036 1.122 5.5 67.4 14.8 844 n/a 4_occ: 0.1198 0.1357 0.036 1.122 5.5 67.4 14.8 844 n/a 5_bss: 0.1195 0.1355 0.036 1.122 5.5 67.3 14.8 844 n/a 5_settarget: 0.1195 0.1355 0.036 1.122 5.5 67.3 14.8 844 n/a 5_updatecdl: 0.1195 0.1355 0.036 1.123 5.5 67.3 14.8 844 n/a 5_nqh: 0.1196 0.1358 0.036 1.123 5.5 67.3 14.8 844 n/a 5_sol: 0.1192 0.1350 0.036 1.123 5.5 67.3 15.0 883 n/a 5_weight: 0.1192 0.1350 0.036 1.123 5.5 67.3 15.0 883 n/a 5_xyzrec: 0.1196 0.1353 0.036 1.128 5.5 67.3 15.0 883 n/a 5_adp: 0.1201 0.1355 0.036 1.128 5.5 66.7 14.9 883 n/a 5_regHadp: 0.1201 0.1356 0.036 1.128 5.5 66.7 14.9 883 n/a 5_occ: 0.1198 0.1356 0.036 1.128 5.5 66.7 14.9 883 n/a 6_bss: 0.1197 0.1354 0.036 1.128 5.5 66.7 14.9 883 n/a 6_settarget: 0.1197 0.1354 0.036 1.128 5.5 66.7 14.9 883 n/a 6_updatecdl: 0.1197 0.1354 0.036 1.128 5.5 66.7 14.9 883 n/a 6_nqh: 0.1197 0.1354 0.036 1.128 5.5 66.7 14.9 883 n/a 6_sol: 0.1196 0.1343 0.036 1.128 5.5 66.7 14.9 893 n/a 6_weight: 0.1196 0.1343 0.036 1.128 5.5 66.7 14.9 893 n/a 6_xyzrec: 0.1198 0.1349 0.037 1.127 5.5 66.7 14.9 893 n/a 6_adp: 0.1201 0.1354 0.037 1.127 5.6 65.6 14.8 893 n/a 6_regHadp: 0.1201 0.1354 0.037 1.127 5.6 65.6 14.8 893 n/a 6_occ: 0.1199 0.1353 0.037 1.127 5.6 65.6 14.8 893 n/a 7_bss: 0.1199 0.1351 0.037 1.127 5.5 65.6 14.8 893 n/a 7_settarget: 0.1199 0.1351 0.037 1.127 5.5 65.6 14.8 893 n/a 7_updatecdl: 0.1199 0.1351 0.037 1.128 5.5 65.6 14.8 893 n/a 7_nqh: 0.1199 0.1351 0.037 1.128 5.5 65.6 14.8 893 n/a 7_sol: 0.1197 0.1353 0.037 1.128 5.5 65.6 14.8 910 n/a 7_weight: 0.1197 0.1353 0.037 1.128 5.5 65.6 14.8 910 n/a 7_xyzrec: 0.1200 0.1359 0.038 1.128 5.5 65.6 14.8 910 n/a 7_adp: 0.1201 0.1362 0.038 1.128 5.6 64.6 14.8 910 n/a 7_regHadp: 0.1201 0.1363 0.038 1.128 5.6 64.6 14.8 910 n/a 7_occ: 0.1199 0.1364 0.038 1.128 5.6 64.6 14.8 910 n/a 8_bss: 0.1188 0.1350 0.038 1.128 5.6 64.6 14.8 910 n/a 8_settarget: 0.1188 0.1350 0.038 1.128 5.6 64.6 14.8 910 n/a 8_updatecdl: 0.1188 0.1350 0.038 1.128 5.6 64.6 14.8 910 n/a 8_nqh: 0.1188 0.1350 0.038 1.128 5.6 64.6 14.8 910 n/a 8_sol: 0.1187 0.1349 0.038 1.128 5.6 64.6 14.8 913 n/a 8_weight: 0.1187 0.1349 0.038 1.128 5.6 64.6 14.8 913 n/a 8_xyzrec: 0.1190 0.1357 0.038 1.115 5.6 64.6 14.8 913 n/a 8_adp: 0.1192 0.1360 0.038 1.115 5.6 64.3 14.8 913 n/a 8_regHadp: 0.1192 0.1360 0.038 1.115 5.6 64.3 14.8 913 n/a 8_occ: 0.1191 0.1362 0.038 1.115 5.6 64.3 14.8 913 n/a 9_bss: 0.1190 0.1362 0.038 1.115 5.6 64.3 14.8 913 n/a 9_settarget: 0.1190 0.1362 0.038 1.115 5.6 64.3 14.8 913 n/a 9_updatecdl: 0.1190 0.1362 0.038 1.115 5.6 64.3 14.8 913 n/a 9_nqh: 0.1190 0.1362 0.038 1.115 5.6 64.3 14.8 913 n/a 9_sol: 0.1188 0.1355 0.038 1.115 5.6 64.3 14.8 915 n/a 9_weight: 0.1188 0.1355 0.038 1.115 5.6 64.3 14.8 915 n/a 9_xyzrec: 0.1191 0.1360 0.039 1.117 5.6 64.3 14.8 915 n/a 9_adp: 0.1191 0.1362 0.039 1.117 5.6 63.4 14.7 915 n/a 9_regHadp: 0.1191 0.1362 0.039 1.117 5.6 63.4 14.7 915 n/a 9_occ: 0.1190 0.1363 0.039 1.117 5.6 63.4 14.7 915 n/a 10_bss: 0.1189 0.1361 0.039 1.117 5.5 63.3 14.6 915 n/a 10_settarget: 0.1189 0.1361 0.039 1.117 5.5 63.3 14.6 915 n/a 10_updatecdl: 0.1189 0.1361 0.039 1.117 5.5 63.3 14.6 915 n/a 10_setrh: 0.1190 0.1362 0.039 1.117 5.5 63.3 14.6 915 n/a 10_nqh: 0.1190 0.1362 0.039 1.117 5.5 63.3 14.6 915 n/a 10_sol: 0.1188 0.1353 0.039 1.117 5.5 63.3 14.7 920 n/a 10_weight: 0.1188 0.1353 0.039 1.117 5.5 63.3 14.7 920 n/a 10_xyzrec: 0.1193 0.1358 0.039 1.154 5.5 63.3 14.7 920 n/a 10_adp: 0.1193 0.1360 0.039 1.154 5.5 63.1 14.7 920 n/a 10_regHadp: 0.1194 0.1360 0.039 1.154 5.5 63.1 14.7 920 n/a 10_occ: 0.1193 0.1361 0.039 1.154 5.5 63.1 14.7 920 n/a end: 0.1193 0.1360 0.039 1.154 5.5 63.1 14.6 920 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4806716_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4806716_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.9700 Refinement macro-cycles (run) : 12082.4700 Write final files (write_after_run_outputs) : 158.2700 Total : 12246.7100 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:22 PST -0800 (1736736082.74 s) Start R-work = 0.1795, R-free = 0.1885 Final R-work = 0.1193, R-free = 0.1360 =============================================================================== Job complete usr+sys time: 12529.68 seconds wall clock time: 209 minutes 50.40 seconds (12590.40 seconds total)