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_4251871.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4251871.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4251871.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.92, per 1000 atoms: 0.29 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: 2.702 distance_ideal: 2.720 ideal - model: 0.018 slack: 0.000 delta_slack: 0.018 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: 2.688 distance_ideal: 2.710 ideal - model: 0.022 slack: 0.000 delta_slack: 0.022 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 119.1 milliseconds Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 1061 1.05 - 1.28: 2386 1.28 - 1.51: 1536 1.51 - 1.73: 932 1.73 - 1.96: 19 Bond restraints: 5934 Sorted by residual: bond pdb=" C ILE A 70 " pdb=" O ILE A 70 " ideal model delta sigma weight residual 1.237 1.484 -0.247 1.11e-02 8.12e+03 4.96e+02 bond pdb=" N ILE B 105 " pdb=" CA ILE B 105 " ideal model delta sigma weight residual 1.457 1.679 -0.222 1.15e-02 7.56e+03 3.73e+02 bond pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " ideal model delta sigma weight residual 1.326 1.115 0.211 1.10e-02 8.26e+03 3.67e+02 bond pdb=" N TYR B 194 " pdb=" H TYR B 194 " ideal model delta sigma weight residual 0.860 1.225 -0.365 2.00e-02 2.50e+03 3.34e+02 bond pdb=" N LEU A 54 " pdb=" H LEU A 54 " ideal model delta sigma weight residual 0.860 1.221 -0.361 2.00e-02 2.50e+03 3.25e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 5997 4.53 - 9.05: 3540 9.05 - 13.58: 1097 13.58 - 18.11: 165 18.11 - 22.63: 11 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 121.71 110.29 11.42 6.40e-01 2.44e+00 3.19e+02 angle pdb=" CA LEU A 54 " pdb=" C LEU A 54 " pdb=" O LEU A 54 " ideal model delta sigma weight residual 120.46 139.30 -18.84 1.07e+00 8.73e-01 3.10e+02 angle pdb=" O LEU B 171 " pdb=" C LEU B 171 " pdb=" N LEU B 172 " ideal model delta sigma weight residual 122.43 142.41 -19.98 1.34e+00 5.57e-01 2.22e+02 angle pdb=" O ASP A 141 " pdb=" C ASP A 141 " pdb=" N LYS A 142 " ideal model delta sigma weight residual 122.64 138.18 -15.54 1.06e+00 8.90e-01 2.15e+02 angle pdb=" CA CYS B 81 " pdb=" C CYS B 81 " pdb=" O CYS B 81 " ideal model delta sigma weight residual 120.90 106.73 14.17 1.07e+00 8.73e-01 1.75e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.58: 1836 16.58 - 33.15: 139 33.15 - 49.72: 42 49.72 - 66.29: 28 66.29 - 82.86: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA VAL A 32 " pdb=" C VAL A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CG TRP A 146 " pdb=" CD2 TRP A 146 " pdb=" CE3 TRP A 146 " pdb=" HE3 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 21.39 -21.39 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.264: 250 0.264 - 0.526: 168 0.526 - 0.789: 53 0.789 - 1.051: 20 1.051 - 1.314: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 1.12 1.31 2.00e-01 2.50e+01 4.31e+01 chirality pdb=" CA CYS B 106 " pdb=" N CYS B 106 " pdb=" C CYS B 106 " pdb=" CB CYS B 106 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" CA LEU A 9 " pdb=" N LEU A 9 " pdb=" C LEU A 9 " pdb=" CB LEU A 9 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.164 2.00e-02 2.50e+03 8.79e-02 3.09e+02 pdb=" CG TRP A 146 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.061 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.054 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.156 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.044 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.053 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.084 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.138 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.049 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.087 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " 0.065 2.00e-02 2.50e+03 5.87e-02 1.38e+02 pdb=" CG TRP B 146 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.057 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.031 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.054 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.087 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.033 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.119 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.079 2.00e-02 2.50e+03 6.59e-02 1.30e+02 pdb=" CG TYR A 194 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " -0.107 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.141 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " 0.061 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " 0.034 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.65: 30 1.65 - 2.38: 2785 2.38 - 3.12: 22478 3.12 - 3.86: 32887 3.86 - 4.60: 52086 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110266 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.908 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 0.930 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.054 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.170 2.620 ... (remaining 110261 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_4251871_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= 0.2042 r_free= 0.2016 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303583 | | target function (ml) not normalized (work): 806116.952735 | | target function (ml) not normalized (free): 16609.259767 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2148 0.1946 6.6882 6.3044| | 2: 2.94 - 2.33 1.00 7339 128 0.1616 0.1610 5.5396 5.5916| | 3: 2.33 - 2.04 0.96 6939 150 0.1635 0.1656 5.1482 5.1745| | 4: 2.04 - 1.85 1.00 7170 155 0.1757 0.1684 4.9678 5.0678| | 5: 1.85 - 1.72 0.99 7113 159 0.1938 0.1813 4.7985 4.8964| | 6: 1.72 - 1.62 0.99 7102 142 0.1985 0.2051 4.679 4.763| | 7: 1.62 - 1.54 0.99 7104 148 0.2015 0.1658 4.5659 4.5238| | 8: 1.54 - 1.47 0.96 6798 152 0.2047 0.2395 4.4728 4.5894| | 9: 1.47 - 1.41 0.98 6938 155 0.2129 0.2244 4.4062 4.5022| | 10: 1.41 - 1.36 0.99 7022 150 0.2146 0.2067 4.3223 4.3108| | 11: 1.36 - 1.32 0.99 6997 151 0.2108 0.1999 4.2264 4.2542| | 12: 1.32 - 1.28 0.98 6976 149 0.2107 0.2051 4.1882 4.2452| | 13: 1.28 - 1.25 0.98 6907 166 0.2045 0.2309 4.1333 4.2104| | 14: 1.25 - 1.22 0.98 7015 113 0.2118 0.2433 4.0909 4.283| | 15: 1.22 - 1.19 0.98 6957 137 0.2115 0.2034 4.0516 4.049| | 16: 1.19 - 1.17 0.93 6604 132 0.2134 0.2279 4.0073 4.066| | 17: 1.17 - 1.14 0.98 6941 135 0.2158 0.1982 3.9527 4.0149| | 18: 1.14 - 1.12 0.98 6875 142 0.2213 0.2233 3.924 3.8929| | 19: 1.12 - 1.10 0.97 6949 106 0.2259 0.2264 3.8637 3.8985| | 20: 1.10 - 1.08 0.97 6884 147 0.2347 0.2441 3.8352 3.9082| | 21: 1.08 - 1.07 0.97 6852 152 0.2445 0.2868 3.7962 3.8744| | 22: 1.07 - 1.05 0.97 6838 135 0.2569 0.2702 3.7644 3.7716| | 23: 1.05 - 1.03 0.97 6829 159 0.2750 0.2675 3.7361 3.8059| | 24: 1.03 - 1.02 0.96 6785 133 0.2838 0.2722 3.6942 3.726| | 25: 1.02 - 1.01 0.93 6552 130 0.3055 0.2907 3.6691 3.7339| | 26: 1.01 - 0.99 0.96 6767 158 0.3208 0.3328 3.6272 3.6546| | 27: 0.99 - 0.98 0.94 6648 131 0.3385 0.3216 3.6328 3.5981| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.44 0.91 0.97 35395.87| | 2: 2.94 - 2.33 7339 128 0.85 21.31 1.09 1.01 15172.70| | 3: 2.33 - 2.04 6939 150 0.93 13.01 1.11 1.05 4369.49| | 4: 2.04 - 1.85 7170 155 0.92 14.35 1.11 1.06 3057.51| | 5: 1.85 - 1.72 7113 159 0.90 16.69 1.12 1.07 2311.16| | 6: 1.72 - 1.62 7102 142 0.89 17.49 1.11 1.07 1779.69| | 7: 1.62 - 1.54 7104 148 0.89 18.17 1.10 1.07 1406.11| | 8: 1.54 - 1.47 6798 152 0.88 18.95 1.11 1.05 1206.09| | 9: 1.47 - 1.41 6938 155 0.88 19.40 1.10 1.04 1010.28| | 10: 1.41 - 1.36 7022 150 0.87 20.35 1.09 1.03 859.65| | 11: 1.36 - 1.32 6997 151 0.87 19.99 1.08 1.03 728.57| | 12: 1.32 - 1.28 6976 149 0.87 20.33 1.08 1.03 672.94| | 13: 1.28 - 1.25 6907 166 0.87 20.34 1.07 1.04 637.35| | 14: 1.25 - 1.22 7015 113 0.86 21.56 1.08 1.03 609.18| | 15: 1.22 - 1.19 6957 137 0.86 21.61 1.08 1.03 577.05| | 16: 1.19 - 1.17 6604 132 0.86 21.22 1.08 1.02 514.78| | 17: 1.17 - 1.14 6941 135 0.86 21.31 1.08 1.02 449.57| | 18: 1.14 - 1.12 6875 142 0.87 20.81 1.08 0.99 383.65| | 19: 1.12 - 1.10 6949 106 0.86 21.90 1.07 0.99 368.37| | 20: 1.10 - 1.08 6884 147 0.84 23.39 1.06 0.98 365.60| | 21: 1.08 - 1.07 6852 152 0.82 25.37 1.06 0.98 370.55| | 22: 1.07 - 1.05 6838 135 0.81 26.71 1.06 0.96 352.78| | 23: 1.05 - 1.03 6829 159 0.79 28.02 1.06 0.97 337.01| | 24: 1.03 - 1.02 6785 133 0.78 29.19 1.05 0.97 325.48| | 25: 1.02 - 1.01 6552 130 0.77 30.70 1.03 0.93 309.14| | 26: 1.01 - 0.99 6767 158 0.75 32.28 1.02 0.90 289.44| | 27: 0.99 - 0.98 6648 131 0.76 31.78 1.03 0.89 264.46| |alpha: min = 0.89 max = 1.07 mean = 1.01| |beta: min = 264.46 max = 35395.87 mean = 2873.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.02| |phase err.(test): min = 0.00 max = 89.58 mean = 22.13| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.274 2950 Z= 5.541 Angle : 5.330 19.976 4018 Z= 3.790 Chirality : 0.379 1.314 492 Planarity : 0.032 0.142 512 Dihedral : 12.773 82.860 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.08 % Rotamer: Outliers : 0.32 % Allowed : 5.81 % Favored : 93.87 % Cbeta Deviations : 32.30 % 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: -2.47 (0.37), residues: 386 helix: -3.00 (0.29), residues: 144 sheet: -0.87 (0.59), residues: 66 loop : -0.46 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.126 0.021 ARG A 83 TYR 0.112 0.035 TYR A 67 PHE 0.136 0.035 PHE B 119 TRP 0.157 0.046 TRP A 146 HIS 0.079 0.031 HIS B 179 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= 0.2042 r_free= 0.2016 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303583 | | target function (ml) not normalized (work): 806116.952735 | | target function (ml) not normalized (free): 16609.259767 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2040 0.2042 0.2016 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2040 0.2042 0.2016 n_refl.: 191155 remove outliers: r(all,work,free)=0.2040 0.2042 0.2016 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2040 0.2041 0.2015 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1809 0.1806 0.1957 n_refl.: 191145 remove outliers: r(all,work,free)=0.1808 0.1805 0.1957 n_refl.: 191140 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4242 400.535 295.425 0.438 0.912 0.305 13.296-10.522 99.01 99 1 0.2524 528.187 519.379 0.787 0.913 0.260 10.503-8.327 99.45 178 3 0.2501 565.118 557.768 0.971 0.913 0.237 8.318-6.595 100.00 360 8 0.2509 414.736 403.295 0.972 0.913 0.165 6.588-5.215 100.00 711 7 0.2285 381.101 365.985 0.958 0.913 0.150 5.214-4.128 98.38 1367 28 0.1489 557.435 549.599 1.077 0.913 0.080 4.126-3.266 94.74 2603 46 0.1360 508.132 499.381 1.145 0.913 0.009 3.266-2.585 99.86 5447 97 0.1456 342.774 337.606 1.121 0.912 0.000 2.585-2.046 97.45 10613 204 0.1391 258.603 254.173 1.127 0.912 0.000 2.046-1.619 99.39 21536 464 0.1616 153.054 149.766 1.146 0.910 0.000 1.619-1.281 98.00 42464 925 0.1931 82.395 80.180 1.129 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2325 44.203 41.683 1.115 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0046 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1805 r_free=0.1957 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1805 r_free=0.1957 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.527671 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.755675 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 0.1510 0.0238 0.040 1.2 10.9 0.0 0.0 0 11.264 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.10 2.38 1.117 13.109 577.756 0.018 13.01 15.84 2.84 1.288 13.397 577.756 0.017 Individual atomic B min max mean iso aniso Overall: 5.13 73.04 15.12 1.43 435 3274 Protein: 5.13 40.33 11.04 1.43 0 2902 Water: 6.29 73.04 29.80 N/A 435 370 Other: 15.95 30.37 23.16 N/A 0 2 Chain A: 5.32 59.48 13.11 N/A 0 1626 Chain B: 5.13 73.04 12.83 N/A 0 1648 Chain S: 11.65 66.82 31.28 N/A 435 0 Histogram: Values Number of atoms 5.13 - 11.92 2155 11.92 - 18.71 636 18.71 - 25.50 313 25.50 - 32.29 265 32.29 - 39.08 159 39.08 - 45.88 111 45.88 - 52.67 44 52.67 - 59.46 20 59.46 - 66.25 4 66.25 - 73.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1301 r_free=0.1585 r_work=0.1300 r_free=0.1579 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1300 r_free = 0.1579 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1285 r_free = 0.1567 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1285 r_free= 0.1567 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015683 | | target function (ls_wunit_k1) not normalized (work): 2937.470833 | | target function (ls_wunit_k1) not normalized (free): 120.450724 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1285 0.1567 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1477 0.1475 0.1644 n_refl.: 191140 remove outliers: r(all,work,free)=0.1477 0.1475 0.1644 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1500 0.1498 0.1654 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1278 0.1556 n_refl.: 191140 remove outliers: r(all,work,free)=0.1283 0.1277 0.1555 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3588 402.814 374.516 0.488 0.962 0.285 13.296-10.522 99.01 99 1 0.2087 528.187 524.820 0.743 0.963 0.244 10.503-8.327 99.45 178 3 0.1773 565.118 564.784 0.891 0.963 0.230 8.318-6.595 100.00 360 8 0.1705 414.736 412.140 0.909 0.963 0.150 6.588-5.215 100.00 711 7 0.1533 381.101 373.132 0.888 0.963 0.150 5.214-4.128 98.38 1367 28 0.0906 557.435 555.020 0.977 0.964 0.049 4.126-3.266 94.74 2603 46 0.0831 508.132 504.120 1.044 0.964 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.281 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.277 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1094 153.054 151.352 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1285 82.395 81.413 1.048 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.188 1.025 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0361 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1555 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1555 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1555 | n_water=805 | time (s): 2.130 (total time: 2.130) Filter (dist) r_work=0.1283 r_free=0.1564 | n_water=794 | time (s): 98.440 (total time: 100.570) Filter (q & B) r_work=0.1283 r_free=0.1564 | n_water=789 | time (s): 4.760 (total time: 105.330) Compute maps r_work=0.1283 r_free=0.1564 | n_water=789 | time (s): 2.130 (total time: 107.460) Filter (map) r_work=0.1310 r_free=0.1548 | n_water=648 | time (s): 5.570 (total time: 113.030) Find peaks r_work=0.1310 r_free=0.1548 | n_water=648 | time (s): 0.850 (total time: 113.880) Add new water r_work=0.1334 r_free=0.1587 | n_water=956 | time (s): 5.550 (total time: 119.430) Refine new water occ: r_work=0.1290 r_free=0.1536 adp: r_work=0.1277 r_free=0.1529 occ: r_work=0.1279 r_free=0.1526 adp: r_work=0.1272 r_free=0.1523 occ: r_work=0.1274 r_free=0.1520 adp: r_work=0.1271 r_free=0.1521 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1521 r_work=0.1271 r_free=0.1521 | n_water=956 | time (s): 82.490 (total time: 201.920) Filter (q & B) r_work=0.1274 r_free=0.1527 | n_water=888 | time (s): 5.660 (total time: 207.580) Filter (dist only) r_work=0.1275 r_free=0.1526 | n_water=887 | time (s): 113.580 (total time: 321.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.471371 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 595.432428 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1257 0.1534 0.0276 0.042 1.1 18.7 0.0 0.3 0 11.736 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.34 2.76 2.061 15.239 595.432 0.015 12.36 15.19 2.84 2.451 15.257 595.432 0.014 Individual atomic B min max mean iso aniso Overall: 5.43 68.20 16.32 1.21 519 3272 Protein: 5.43 40.75 11.01 1.21 0 2902 Water: 6.66 68.20 33.69 N/A 519 368 Other: 16.28 32.29 24.29 N/A 0 2 Chain A: 5.49 55.62 13.03 N/A 0 1624 Chain B: 5.43 68.20 12.87 N/A 0 1648 Chain S: 11.82 66.78 37.61 N/A 519 0 Histogram: Values Number of atoms 5.43 - 11.70 2056 11.70 - 17.98 716 17.98 - 24.26 259 24.26 - 30.54 211 30.54 - 36.81 179 36.81 - 43.09 175 43.09 - 49.37 100 49.37 - 55.65 52 55.65 - 61.92 33 61.92 - 68.20 10 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1520 r_work=0.1236 r_free=0.1521 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1521 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1515 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1515 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013516 | | target function (ls_wunit_k1) not normalized (work): 2531.417116 | | target function (ls_wunit_k1) not normalized (free): 105.141311 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1515 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1438 0.1435 0.1601 n_refl.: 191138 remove outliers: r(all,work,free)=0.1438 0.1435 0.1601 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1432 0.1599 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1521 n_refl.: 191138 remove outliers: r(all,work,free)=0.1241 0.1236 0.1521 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3285 402.814 375.775 0.489 0.963 0.271 13.296-10.522 99.01 99 1 0.1940 528.187 518.931 0.757 0.964 0.228 10.503-8.327 99.45 178 3 0.1441 565.118 566.988 0.919 0.964 0.178 8.318-6.595 100.00 360 8 0.1508 414.736 414.766 0.938 0.964 0.150 6.588-5.215 100.00 711 7 0.1359 381.101 376.260 0.912 0.964 0.150 5.214-4.128 98.38 1367 28 0.0828 557.435 556.160 0.993 0.964 0.070 4.126-3.266 94.74 2603 46 0.0762 508.132 505.675 1.058 0.964 0.009 3.266-2.585 99.86 5447 97 0.0857 342.774 341.276 1.045 0.963 0.000 2.585-2.046 97.45 10613 204 0.0900 258.603 256.672 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1048 153.054 151.612 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1261 82.395 81.344 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.219 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0542 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1521 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1521 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1521 | n_water=887 | time (s): 3.490 (total time: 3.490) Filter (dist) r_work=0.1237 r_free=0.1523 | n_water=885 | time (s): 109.520 (total time: 113.010) Filter (q & B) r_work=0.1237 r_free=0.1523 | n_water=882 | time (s): 5.390 (total time: 118.400) Compute maps r_work=0.1237 r_free=0.1523 | n_water=882 | time (s): 1.750 (total time: 120.150) Filter (map) r_work=0.1276 r_free=0.1525 | n_water=683 | time (s): 4.270 (total time: 124.420) Find peaks r_work=0.1276 r_free=0.1525 | n_water=683 | time (s): 0.600 (total time: 125.020) Add new water r_work=0.1299 r_free=0.1553 | n_water=1000 | time (s): 4.680 (total time: 129.700) Refine new water occ: r_work=0.1254 r_free=0.1512 adp: r_work=0.1254 r_free=0.1512 occ: r_work=0.1250 r_free=0.1510 adp: r_work=0.1250 r_free=0.1510 occ: r_work=0.1247 r_free=0.1508 adp: r_work=0.1246 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1246 r_free=0.1508 r_work=0.1246 r_free=0.1508 | n_water=1000 | time (s): 302.060 (total time: 431.760) Filter (q & B) r_work=0.1251 r_free=0.1519 | n_water=870 | time (s): 4.920 (total time: 436.680) Filter (dist only) r_work=0.1251 r_free=0.1519 | n_water=869 | time (s): 111.370 (total time: 548.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.697161 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.471407 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1241 0.1443 0.0201 0.036 1.1 7.1 0.0 0.0 0 0.849 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.43 2.01 1.941 14.590 16.471 3.942 12.34 13.99 1.66 2.220 14.501 16.471 3.898 Individual atomic B min max mean iso aniso Overall: 5.54 67.87 15.26 1.08 503 3270 Protein: 5.54 37.18 10.78 1.08 0 2902 Water: 6.70 67.87 30.22 N/A 503 366 Other: 13.94 28.10 21.02 N/A 0 2 Chain A: 5.54 54.81 12.79 N/A 0 1623 Chain B: 5.55 67.87 12.59 N/A 0 1647 Chain S: 13.84 63.59 31.98 N/A 503 0 Histogram: Values Number of atoms 5.54 - 11.77 2133 11.77 - 18.01 680 18.01 - 24.24 288 24.24 - 30.47 243 30.47 - 36.71 179 36.71 - 42.94 146 42.94 - 49.17 71 49.17 - 55.41 24 55.41 - 61.64 5 61.64 - 67.87 4 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1400 r_work=0.1234 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1400 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1395 target_work(ml) = 3.892 | | 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892423 | | target function (ml) not normalized (work): 729039.175133 | | target function (ml) not normalized (free): 15227.259197 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1229 0.1395 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1446 0.1446 0.1496 n_refl.: 191138 remove outliers: r(all,work,free)=0.1446 0.1446 0.1496 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1439 0.1493 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1226 0.1390 n_refl.: 191138 remove outliers: r(all,work,free)=0.1228 0.1225 0.1390 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3796 398.895 357.658 0.415 0.946 0.243 13.296-10.522 99.01 99 1 0.2517 528.187 506.914 0.711 0.948 0.230 10.503-8.327 98.90 177 3 0.2055 557.261 556.054 0.879 0.948 0.230 8.318-6.595 100.00 360 8 0.2049 414.736 410.413 0.899 0.947 0.141 6.588-5.215 100.00 711 7 0.1833 381.101 370.617 0.885 0.947 0.117 5.214-4.128 98.38 1367 28 0.1168 557.435 551.879 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1096 508.132 501.301 1.033 0.948 0.014 3.266-2.585 99.86 5447 97 0.1084 342.774 339.095 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0966 258.603 255.767 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0976 153.054 151.419 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.490 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.321 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1013 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1390 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1390 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1390 | n_water=869 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1225 r_free=0.1387 | n_water=867 | time (s): 109.680 (total time: 112.410) Filter (q & B) r_work=0.1226 r_free=0.1385 | n_water=854 | time (s): 4.270 (total time: 116.680) Compute maps r_work=0.1226 r_free=0.1385 | n_water=854 | time (s): 2.600 (total time: 119.280) Filter (map) r_work=0.1246 r_free=0.1367 | n_water=713 | time (s): 4.310 (total time: 123.590) Find peaks r_work=0.1246 r_free=0.1367 | n_water=713 | time (s): 0.820 (total time: 124.410) Add new water r_work=0.1263 r_free=0.1388 | n_water=958 | time (s): 4.460 (total time: 128.870) Refine new water occ: r_work=0.1215 r_free=0.1364 adp: r_work=0.1207 r_free=0.1359 occ: r_work=0.1204 r_free=0.1362 adp: r_work=0.1204 r_free=0.1360 occ: r_work=0.1203 r_free=0.1363 adp: r_work=0.1202 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1361 | n_water=958 | time (s): 335.470 (total time: 464.340) Filter (q & B) r_work=0.1207 r_free=0.1363 | n_water=873 | time (s): 5.110 (total time: 469.450) Filter (dist only) r_work=0.1207 r_free=0.1362 | n_water=872 | time (s): 112.880 (total time: 582.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.518401 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.188179 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 0.1369 0.0164 0.036 1.1 6.6 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.69 1.64 1.846 14.272 15.188 3.874 12.00 13.65 1.66 1.962 14.227 15.188 3.867 Individual atomic B min max mean iso aniso Overall: 5.52 67.44 15.04 1.00 507 3269 Protein: 5.52 33.82 10.69 1.00 0 2902 Water: 5.85 67.44 29.52 N/A 507 365 Other: 13.98 27.16 20.57 N/A 0 2 Chain A: 5.54 53.81 12.63 N/A 0 1622 Chain B: 5.52 67.44 12.48 N/A 0 1647 Chain S: 5.85 63.51 31.06 N/A 507 0 Histogram: Values Number of atoms 5.52 - 11.71 2125 11.71 - 17.91 718 17.91 - 24.10 291 24.10 - 30.29 232 30.29 - 36.48 180 36.48 - 42.67 135 42.67 - 48.86 63 48.86 - 55.05 24 55.05 - 61.25 5 61.25 - 67.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1366 r_work=0.1200 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1366 target_work(ml) = 3.868 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1366 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865465 | | target function (ml) not normalized (work): 723978.315569 | | target function (ml) not normalized (free): 15138.123600 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1366 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1486 n_refl.: 191135 remove outliers: r(all,work,free)=0.1406 0.1404 0.1486 n_refl.: 191135 overall B=-0.04 to atoms: r(all,work,free)=0.1398 0.1397 0.1481 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1196 0.1365 n_refl.: 191135 remove outliers: r(all,work,free)=0.1199 0.1196 0.1365 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3809 361.208 322.313 0.411 0.950 0.241 13.296-10.522 98.02 98 1 0.2566 478.929 453.037 0.702 0.952 0.215 10.503-8.327 98.90 177 3 0.2113 504.611 498.258 0.865 0.952 0.210 8.318-6.595 100.00 360 8 0.2097 375.552 371.492 0.890 0.952 0.110 6.588-5.215 100.00 711 7 0.1855 345.095 335.689 0.883 0.952 0.110 5.214-4.128 98.38 1367 28 0.1173 504.769 499.800 0.969 0.952 0.080 4.126-3.266 94.74 2603 46 0.1111 460.124 453.552 1.029 0.953 0.005 3.266-2.585 99.86 5447 97 0.1081 310.389 307.258 1.016 0.952 0.000 2.585-2.046 97.45 10613 204 0.0937 234.170 231.767 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0918 138.594 137.306 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0992 74.611 73.892 1.048 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1666 40.025 38.358 1.034 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1239 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1365 | n_water=872 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1196 r_free=0.1365 | n_water=871 | time (s): 108.380 (total time: 111.070) Filter (q & B) r_work=0.1197 r_free=0.1364 | n_water=861 | time (s): 5.670 (total time: 116.740) Compute maps r_work=0.1197 r_free=0.1364 | n_water=861 | time (s): 2.240 (total time: 118.980) Filter (map) r_work=0.1217 r_free=0.1348 | n_water=743 | time (s): 5.210 (total time: 124.190) Find peaks r_work=0.1217 r_free=0.1348 | n_water=743 | time (s): 0.600 (total time: 124.790) Add new water r_work=0.1230 r_free=0.1365 | n_water=963 | time (s): 3.890 (total time: 128.680) Refine new water occ: r_work=0.1194 r_free=0.1346 adp: r_work=0.1194 r_free=0.1346 occ: r_work=0.1192 r_free=0.1344 adp: r_work=0.1191 r_free=0.1344 occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1342 r_work=0.1189 r_free=0.1342 | n_water=963 | time (s): 266.790 (total time: 395.470) Filter (q & B) r_work=0.1193 r_free=0.1347 | n_water=900 | time (s): 4.230 (total time: 399.700) Filter (dist only) r_work=0.1193 r_free=0.1347 | n_water=899 | time (s): 114.470 (total time: 514.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.559840 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.713652 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1356 0.0161 0.037 1.1 7.2 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.56 1.61 1.799 14.218 15.714 3.765 11.98 13.58 1.60 1.897 14.181 15.714 3.760 Individual atomic B min max mean iso aniso Overall: 5.55 66.93 15.06 0.97 535 3268 Protein: 5.55 32.02 10.60 0.97 0 2902 Water: 6.02 66.93 29.44 N/A 535 364 Other: 13.83 25.58 19.71 N/A 0 2 Chain A: 5.55 52.74 12.51 N/A 0 1622 Chain B: 5.56 66.93 12.35 N/A 0 1646 Chain S: 6.02 63.37 31.09 N/A 535 0 Histogram: Values Number of atoms 5.55 - 11.68 2127 11.68 - 17.82 732 17.82 - 23.96 295 23.96 - 30.10 227 30.10 - 36.24 185 36.24 - 42.37 138 42.37 - 48.51 63 48.51 - 54.65 28 54.65 - 60.79 5 60.79 - 66.93 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1358 r_work=0.1198 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1358 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759401 | | target function (ml) not normalized (work): 704109.510619 | | target function (ml) not normalized (free): 14741.948555 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1491 n_refl.: 191134 remove outliers: r(all,work,free)=0.1400 0.1398 0.1491 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1394 0.1392 0.1486 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1357 n_refl.: 191134 remove outliers: r(all,work,free)=0.1194 0.1191 0.1357 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 0.3756 361.208 325.546 0.390 0.974 0.225 13.296-10.522 98.02 98 1 0.2529 478.929 459.097 0.675 0.976 0.176 10.503-8.327 98.35 176 3 0.2153 502.804 497.195 0.845 0.976 0.150 8.318-6.595 100.00 360 8 0.2102 375.552 371.841 0.864 0.975 0.103 6.588-5.215 100.00 711 7 0.1872 345.095 335.674 0.858 0.975 0.083 5.214-4.128 98.38 1367 28 0.1170 504.769 499.804 0.945 0.974 0.080 4.126-3.266 94.74 2603 46 0.1128 460.124 453.474 1.003 0.973 0.000 3.266-2.585 99.86 5447 97 0.1098 310.389 307.101 0.994 0.970 0.000 2.585-2.046 97.45 10613 204 0.0947 234.170 231.696 1.009 0.967 0.000 2.046-1.619 99.39 21536 464 0.0913 138.594 137.247 1.038 0.960 0.000 1.619-1.281 98.00 42464 925 0.0974 74.611 73.892 1.045 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1644 40.025 38.344 1.048 0.932 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1025 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1357 | n_water=899 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1191 r_free=0.1356 | n_water=897 | time (s): 120.960 (total time: 123.470) Filter (q & B) r_work=0.1192 r_free=0.1356 | n_water=887 | time (s): 5.680 (total time: 129.150) Compute maps r_work=0.1192 r_free=0.1356 | n_water=887 | time (s): 2.230 (total time: 131.380) Filter (map) r_work=0.1213 r_free=0.1346 | n_water=770 | time (s): 4.300 (total time: 135.680) Find peaks r_work=0.1213 r_free=0.1346 | n_water=770 | time (s): 0.570 (total time: 136.250) Add new water r_work=0.1224 r_free=0.1358 | n_water=975 | time (s): 4.790 (total time: 141.040) Refine new water occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1190 r_free=0.1341 occ: r_work=0.1188 r_free=0.1341 adp: r_work=0.1188 r_free=0.1340 occ: r_work=0.1186 r_free=0.1340 adp: r_work=0.1186 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1340 r_work=0.1186 r_free=0.1340 | n_water=975 | time (s): 190.110 (total time: 331.150) Filter (q & B) r_work=0.1189 r_free=0.1345 | n_water=911 | time (s): 4.440 (total time: 335.590) Filter (dist only) r_work=0.1189 r_free=0.1344 | n_water=910 | time (s): 117.110 (total time: 452.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550914 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.044413 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 0.1350 0.0157 0.038 1.1 5.5 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.50 1.57 1.765 14.110 15.044 3.759 11.95 13.50 1.55 1.890 14.066 15.044 3.756 Individual atomic B min max mean iso aniso Overall: 5.58 65.83 14.95 0.91 547 3267 Protein: 5.58 29.55 10.50 0.91 0 2902 Water: 5.99 65.83 29.13 N/A 547 363 Other: 13.86 22.89 18.38 N/A 0 2 Chain A: 5.62 52.25 12.37 N/A 0 1622 Chain B: 5.58 65.83 12.22 N/A 0 1645 Chain S: 5.99 63.18 30.81 N/A 547 0 Histogram: Values Number of atoms 5.58 - 11.60 2113 11.60 - 17.63 772 17.63 - 23.65 288 23.65 - 29.68 215 29.68 - 35.71 182 35.71 - 41.73 128 41.73 - 47.76 76 47.76 - 53.78 32 53.78 - 59.81 5 59.81 - 65.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1350 r_work=0.1195 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1351 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1350 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755386 | | target function (ml) not normalized (work): 703353.804691 | | target function (ml) not normalized (free): 14725.180804 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1399 0.1397 0.1495 n_refl.: 191133 remove outliers: r(all,work,free)=0.1399 0.1397 0.1495 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1392 0.1391 0.1490 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191133 remove outliers: r(all,work,free)=0.1194 0.1191 0.1348 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3644 360.904 312.968 0.375 0.974 0.209 13.296-10.522 97.03 97 1 0.2485 481.203 455.811 0.668 0.976 0.156 10.503-8.327 98.35 176 3 0.2182 502.804 495.401 0.840 0.976 0.130 8.318-6.595 100.00 360 8 0.2112 375.552 372.102 0.860 0.975 0.093 6.588-5.215 100.00 711 7 0.1888 345.095 335.934 0.858 0.975 0.077 5.214-4.128 98.38 1367 28 0.1182 504.769 499.830 0.946 0.974 0.070 4.126-3.266 94.74 2603 46 0.1139 460.124 453.425 1.004 0.973 0.000 3.266-2.585 99.86 5447 97 0.1109 310.389 307.140 0.994 0.971 0.000 2.585-2.046 97.45 10613 204 0.0951 234.170 231.721 1.009 0.967 0.000 2.046-1.619 99.39 21536 464 0.0909 138.594 137.318 1.038 0.961 0.000 1.619-1.281 98.00 42464 925 0.0965 74.611 73.927 1.045 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1640 40.025 38.352 1.049 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1145 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1348 | n_water=910 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1192 r_free=0.1348 | n_water=909 | time (s): 115.740 (total time: 118.240) Filter (q & B) r_work=0.1193 r_free=0.1348 | n_water=897 | time (s): 5.690 (total time: 123.930) Compute maps r_work=0.1193 r_free=0.1348 | n_water=897 | time (s): 2.430 (total time: 126.360) Filter (map) r_work=0.1212 r_free=0.1348 | n_water=787 | time (s): 5.330 (total time: 131.690) Find peaks r_work=0.1212 r_free=0.1348 | n_water=787 | time (s): 0.700 (total time: 132.390) Add new water r_work=0.1221 r_free=0.1357 | n_water=974 | time (s): 4.130 (total time: 136.520) Refine new water occ: r_work=0.1191 r_free=0.1338 adp: r_work=0.1191 r_free=0.1338 occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1189 r_free=0.1338 occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1187 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1338 r_work=0.1187 r_free=0.1338 | n_water=974 | time (s): 243.660 (total time: 380.180) Filter (q & B) r_work=0.1190 r_free=0.1345 | n_water=913 | time (s): 4.460 (total time: 384.640) Filter (dist only) r_work=0.1191 r_free=0.1344 | n_water=912 | time (s): 118.190 (total time: 502.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544769 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.882313 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1351 0.0157 0.038 1.1 6.1 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.51 1.57 1.725 13.988 14.882 3.757 11.95 13.53 1.58 1.775 13.968 14.882 3.754 Individual atomic B min max mean iso aniso Overall: 5.60 64.71 14.89 0.89 549 3267 Protein: 5.60 28.85 10.45 0.89 0 2902 Water: 5.96 64.71 29.00 N/A 549 363 Other: 13.86 22.14 18.00 N/A 0 2 Chain A: 5.64 51.88 12.29 N/A 0 1622 Chain B: 5.60 64.71 12.14 N/A 0 1645 Chain S: 5.96 63.20 30.81 N/A 549 0 Histogram: Values Number of atoms 5.60 - 11.51 2092 11.51 - 17.42 789 17.42 - 23.33 284 23.33 - 29.24 216 29.24 - 35.15 184 35.15 - 41.06 122 41.06 - 46.97 88 46.97 - 52.89 31 52.89 - 58.80 7 58.80 - 64.71 3 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1353 r_work=0.1195 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.753852 | | target function (ml) not normalized (work): 703058.973650 | | target function (ml) not normalized (free): 14725.591062 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1353 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1496 n_refl.: 191131 remove outliers: r(all,work,free)=0.1391 0.1389 0.1496 n_refl.: 191131 overall B=-0.01 to atoms: r(all,work,free)=0.1389 0.1387 0.1495 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1186 0.1340 n_refl.: 191131 remove outliers: r(all,work,free)=0.1189 0.1186 0.1340 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 91.09 89 3 0.3645 356.324 330.288 0.350 0.988 0.123 13.296-10.522 97.03 97 1 0.2499 481.203 459.789 0.663 0.989 0.100 10.503-8.327 98.35 176 3 0.2218 502.804 493.522 0.848 0.989 0.098 8.318-6.595 100.00 360 8 0.2112 375.552 371.355 0.867 0.989 0.083 6.588-5.215 100.00 711 7 0.1919 345.095 335.359 0.867 0.990 0.077 5.214-4.128 98.38 1367 28 0.1198 504.769 499.132 0.956 0.990 0.060 4.126-3.266 94.74 2603 46 0.1151 460.124 452.548 1.014 0.991 0.000 3.266-2.585 99.86 5447 97 0.1113 310.389 306.753 1.000 0.991 0.000 2.585-2.046 97.45 10613 204 0.0960 234.170 231.448 1.011 0.992 0.000 2.046-1.619 99.39 21536 464 0.0904 138.594 137.169 1.031 0.994 0.000 1.619-1.281 98.00 42464 925 0.0944 74.611 73.950 1.028 0.997 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.025 38.337 1.005 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0312 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1340 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1186 r_free=0.1340 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1340 | n_water=912 | time (s): 2.870 (total time: 2.870) Filter (dist) r_work=0.1186 r_free=0.1341 | n_water=911 | time (s): 118.630 (total time: 121.500) Filter (q & B) r_work=0.1187 r_free=0.1341 | n_water=900 | time (s): 5.410 (total time: 126.910) Compute maps r_work=0.1187 r_free=0.1341 | n_water=900 | time (s): 2.500 (total time: 129.410) Filter (map) r_work=0.1208 r_free=0.1342 | n_water=787 | time (s): 5.410 (total time: 134.820) Find peaks r_work=0.1208 r_free=0.1342 | n_water=787 | time (s): 0.880 (total time: 135.700) Add new water r_work=0.1215 r_free=0.1352 | n_water=981 | time (s): 5.370 (total time: 141.070) Refine new water occ: r_work=0.1185 r_free=0.1327 adp: r_work=0.1185 r_free=0.1327 occ: r_work=0.1183 r_free=0.1328 adp: r_work=0.1183 r_free=0.1328 occ: r_work=0.1182 r_free=0.1328 adp: r_work=0.1182 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1328 r_work=0.1182 r_free=0.1328 | n_water=981 | time (s): 253.360 (total time: 394.430) Filter (q & B) r_work=0.1186 r_free=0.1337 | n_water=911 | time (s): 4.590 (total time: 399.020) Filter (dist only) r_work=0.1186 r_free=0.1339 | n_water=909 | time (s): 115.390 (total time: 514.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.525878 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.722215 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 0.1343 0.0153 0.039 1.1 4.8 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.43 1.53 1.706 13.923 14.722 3.754 11.91 13.46 1.55 1.731 13.912 14.722 3.752 Individual atomic B min max mean iso aniso Overall: 5.62 63.55 14.83 0.88 546 3267 Protein: 5.62 28.35 10.44 0.88 0 2902 Water: 5.98 63.55 28.83 N/A 546 363 Other: 13.91 22.12 18.01 N/A 0 2 Chain A: 5.69 51.48 12.24 N/A 0 1622 Chain B: 5.62 63.55 12.10 N/A 0 1645 Chain S: 5.98 63.42 30.73 N/A 546 0 Histogram: Values Number of atoms 5.62 - 11.41 2063 11.41 - 17.20 827 17.20 - 23.00 263 23.00 - 28.79 220 28.79 - 34.58 175 34.58 - 40.38 120 40.38 - 46.17 100 46.17 - 51.97 31 51.97 - 57.76 10 57.76 - 63.55 4 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1346 r_work=0.1191 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1346 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1345 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751640 | | target function (ml) not normalized (work): 702640.907797 | | target function (ml) not normalized (free): 14715.352773 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1402 0.1400 0.1508 n_refl.: 191130 remove outliers: r(all,work,free)=0.1402 0.1400 0.1508 n_refl.: 191130 overall B=-0.02 to atoms: r(all,work,free)=0.1398 0.1396 0.1505 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1348 n_refl.: 191130 remove outliers: r(all,work,free)=0.1191 0.1188 0.1348 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 91.09 89 3 0.3589 356.324 327.968 0.391 0.975 0.194 13.296-10.522 97.03 97 1 0.2488 481.203 459.911 0.683 0.976 0.141 10.503-8.327 98.35 176 3 0.2204 502.804 494.221 0.855 0.976 0.112 8.318-6.595 100.00 360 8 0.2148 375.552 370.345 0.876 0.976 0.089 6.588-5.215 100.00 711 7 0.1946 345.095 335.319 0.877 0.977 0.080 5.214-4.128 98.38 1367 28 0.1213 504.769 498.928 0.968 0.978 0.070 4.126-3.266 94.74 2603 46 0.1155 460.124 452.652 1.028 0.979 0.000 3.266-2.585 99.86 5447 97 0.1121 310.389 306.739 1.014 0.980 0.000 2.585-2.046 97.45 10613 204 0.0963 234.170 231.478 1.023 0.982 0.000 2.046-1.619 99.39 21536 464 0.0906 138.594 137.217 1.043 0.985 0.000 1.619-1.281 98.00 42464 925 0.0941 74.611 73.958 1.038 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.025 38.309 1.013 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0518 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1348 | n_water=909 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1188 r_free=0.1348 | n_water=909 | time (s): 114.100 (total time: 116.540) Filter (q & B) r_work=0.1189 r_free=0.1348 | n_water=898 | time (s): 4.250 (total time: 120.790) Compute maps r_work=0.1189 r_free=0.1348 | n_water=898 | time (s): 1.700 (total time: 122.490) Filter (map) r_work=0.1206 r_free=0.1349 | n_water=801 | time (s): 4.450 (total time: 126.940) Find peaks r_work=0.1206 r_free=0.1349 | n_water=801 | time (s): 0.600 (total time: 127.540) Add new water r_work=0.1214 r_free=0.1362 | n_water=986 | time (s): 4.840 (total time: 132.380) Refine new water occ: r_work=0.1186 r_free=0.1339 adp: r_work=0.1186 r_free=0.1339 occ: r_work=0.1184 r_free=0.1340 adp: r_work=0.1184 r_free=0.1340 occ: r_work=0.1183 r_free=0.1340 adp: r_work=0.1182 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1340 r_work=0.1182 r_free=0.1340 | n_water=986 | time (s): 227.990 (total time: 360.370) Filter (q & B) r_work=0.1186 r_free=0.1349 | n_water=922 | time (s): 4.990 (total time: 365.360) Filter (dist only) r_work=0.1186 r_free=0.1349 | n_water=921 | time (s): 117.550 (total time: 482.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.572200 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.092910 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 0.1189 0.1357 0.0167 0.039 1.1 5.3 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.57 1.67 1.697 13.902 14.093 3.753 11.91 13.62 1.71 1.701 13.896 14.093 3.753 Individual atomic B min max mean iso aniso Overall: 5.60 63.47 14.82 0.87 558 3267 Protein: 5.60 28.14 10.43 0.87 0 2902 Water: 6.01 63.47 28.64 N/A 558 363 Other: 13.89 22.10 17.99 N/A 0 2 Chain A: 5.72 51.30 12.21 N/A 0 1622 Chain B: 5.60 63.05 12.07 N/A 0 1645 Chain S: 6.01 63.47 30.52 N/A 558 0 Histogram: Values Number of atoms 5.60 - 11.39 2058 11.39 - 17.17 835 17.17 - 22.96 269 22.96 - 28.75 220 28.75 - 34.54 185 34.54 - 40.32 116 40.32 - 46.11 96 46.11 - 51.90 31 51.90 - 57.68 11 57.68 - 63.47 4 =========================== 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) = 3.752 | | 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.=191130 (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): 3.752500 | | target function (ml) not normalized (work): 702801.910846 | | target function (ml) not normalized (free): 14728.695058 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1190 0.1363 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1521 n_refl.: 191130 remove outliers: r(all,work,free)=0.1407 0.1405 0.1521 n_refl.: 191130 overall B=-0.31 to atoms: r(all,work,free)=0.1363 0.1361 0.1486 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1367 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1367 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3504 355.752 314.583 0.311 1.003 0.060 13.296-10.522 97.03 97 1 0.2502 481.203 461.218 0.653 1.004 0.087 10.503-8.327 98.35 176 3 0.2229 502.804 494.638 0.840 1.004 0.083 8.318-6.595 100.00 360 8 0.2139 375.552 371.649 0.860 1.004 0.080 6.588-5.215 100.00 711 7 0.1965 345.095 335.496 0.862 1.004 0.080 5.214-4.128 98.38 1367 28 0.1225 504.769 499.654 0.951 1.004 0.060 4.126-3.266 94.74 2603 46 0.1166 460.124 453.093 1.009 1.004 0.000 3.266-2.585 99.86 5447 97 0.1135 310.389 307.056 0.994 1.003 0.000 2.585-2.046 97.45 10613 204 0.0960 234.170 231.637 1.001 1.003 0.000 2.046-1.619 99.39 21536 464 0.0907 138.594 137.352 1.018 1.001 0.000 1.619-1.281 98.00 42464 925 0.0959 74.611 73.938 1.007 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1644 40.025 38.349 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0649 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1200 r_free=0.1367 After: r_work=0.1201 r_free=0.1367 ================================== NQH flips ================================== r_work=0.1201 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1367 | n_water=921 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1201 r_free=0.1367 | n_water=921 | time (s): 117.910 (total time: 120.590) Filter (q & B) r_work=0.1201 r_free=0.1367 | n_water=910 | time (s): 4.610 (total time: 125.200) Compute maps r_work=0.1201 r_free=0.1367 | n_water=910 | time (s): 2.420 (total time: 127.620) Filter (map) r_work=0.1223 r_free=0.1368 | n_water=796 | time (s): 4.570 (total time: 132.190) Find peaks r_work=0.1223 r_free=0.1368 | n_water=796 | time (s): 0.580 (total time: 132.770) Add new water r_work=0.1229 r_free=0.1376 | n_water=981 | time (s): 4.260 (total time: 137.030) Refine new water occ: r_work=0.1198 r_free=0.1351 adp: r_work=0.1198 r_free=0.1351 occ: r_work=0.1196 r_free=0.1352 adp: r_work=0.1196 r_free=0.1352 occ: r_work=0.1195 r_free=0.1353 adp: r_work=0.1195 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1353 r_work=0.1195 r_free=0.1353 | n_water=981 | time (s): 299.050 (total time: 436.080) Filter (q & B) r_work=0.1199 r_free=0.1358 | n_water=915 | time (s): 5.330 (total time: 441.410) Filter (dist only) r_work=0.1199 r_free=0.1358 | n_water=914 | time (s): 120.000 (total time: 561.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.569810 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.480044 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1368 0.0162 0.039 1.2 7.8 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.68 1.62 1.690 13.564 14.480 3.762 12.06 13.72 1.66 1.694 13.566 14.480 3.761 Individual atomic B min max mean iso aniso Overall: 5.35 63.17 14.47 0.86 551 3267 Protein: 5.35 27.79 10.14 0.86 0 2902 Water: 5.81 63.17 28.21 N/A 551 363 Other: 13.64 21.68 17.66 N/A 0 2 Chain A: 5.42 50.70 11.89 N/A 0 1622 Chain B: 5.35 61.75 11.76 N/A 0 1645 Chain S: 5.81 63.17 30.17 N/A 551 0 Histogram: Values Number of atoms 5.35 - 11.13 2064 11.13 - 16.91 833 16.91 - 22.70 272 22.70 - 28.48 212 28.48 - 34.26 188 34.26 - 40.04 111 40.04 - 45.83 93 45.83 - 51.61 31 51.61 - 57.39 10 57.39 - 63.17 4 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1372 r_work=0.1206 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1373 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1371 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1205 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760580 | | target function (ml) not normalized (work): 704307.780442 | | target function (ml) not normalized (free): 14758.778008 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1360 0.1445 5.6915 5.7747| | 2: 2.94 - 2.33 1.00 7339 128 0.1080 0.1383 5.0916 5.2039| | 3: 2.33 - 2.04 0.96 6939 150 0.0908 0.1194 4.6627 4.7615| | 4: 2.04 - 1.85 1.00 7170 155 0.0900 0.1057 4.3978 4.5748| | 5: 1.85 - 1.72 0.99 7113 159 0.0939 0.0989 4.1564 4.2379| | 6: 1.72 - 1.62 0.99 7102 142 0.0903 0.1078 3.9548 4.0687| | 7: 1.62 - 1.54 0.99 7104 148 0.0924 0.1007 3.8106 3.9421| | 8: 1.54 - 1.47 0.96 6798 152 0.0915 0.1360 3.715 3.9281| | 9: 1.47 - 1.41 0.98 6938 155 0.0935 0.1155 3.6318 3.7668| | 10: 1.41 - 1.36 0.99 7022 150 0.0982 0.1196 3.5634 3.6857| | 11: 1.36 - 1.32 0.99 6997 151 0.1013 0.1130 3.4934 3.5854| | 12: 1.32 - 1.28 0.98 6975 149 0.1073 0.1165 3.4716 3.5979| | 13: 1.28 - 1.25 0.98 6907 166 0.1101 0.1374 3.4697 3.624| | 14: 1.25 - 1.22 0.98 7015 112 0.1158 0.1636 3.4448 3.6826| | 15: 1.22 - 1.19 0.98 6956 137 0.1209 0.1275 3.4567 3.4921| | 16: 1.19 - 1.17 0.93 6604 132 0.1269 0.1559 3.4667 3.6549| | 17: 1.17 - 1.14 0.98 6940 135 0.1312 0.1243 3.4354 3.4515| | 18: 1.14 - 1.12 0.98 6875 142 0.1389 0.1717 3.4399 3.5314| | 19: 1.12 - 1.10 0.97 6948 106 0.1473 0.1798 3.4223 3.6065| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1601 3.4105 3.4385| | 21: 1.08 - 1.07 0.97 6852 152 0.1735 0.2166 3.4193 3.5054| | 22: 1.07 - 1.05 0.97 6836 135 0.1919 0.1969 3.4141 3.4145| | 23: 1.05 - 1.03 0.97 6827 159 0.2134 0.2038 3.4335 3.4883| | 24: 1.03 - 1.02 0.96 6784 133 0.2356 0.2285 3.4368 3.5155| | 25: 1.02 - 1.01 0.93 6552 130 0.2653 0.2509 3.4491 3.5223| | 26: 1.01 - 0.99 0.96 6767 158 0.2797 0.2944 3.4149 3.4243| | 27: 0.99 - 0.98 0.94 6647 131 0.3072 0.2834 3.469 3.3947| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7396 127 0.93 12.07 1.00 0.95 11685.21| | 2: 2.94 - 2.33 7339 128 0.92 13.10 0.99 0.95 5333.56| | 3: 2.33 - 2.04 6939 150 0.96 7.75 1.00 0.96 1746.55| | 4: 2.04 - 1.85 7170 155 0.96 7.76 1.00 0.95 1015.60| | 5: 1.85 - 1.72 7113 159 0.96 8.09 1.00 0.96 636.54| | 6: 1.72 - 1.62 7102 142 0.96 8.00 0.99 0.96 446.10| | 7: 1.62 - 1.54 7104 148 0.96 8.33 1.03 0.98 343.77| | 8: 1.54 - 1.47 6798 152 0.96 8.50 1.02 0.98 289.56| | 9: 1.47 - 1.41 6938 155 0.96 8.68 1.01 0.98 238.34| | 10: 1.41 - 1.36 7022 150 0.96 9.05 1.00 0.97 207.12| | 11: 1.36 - 1.32 6997 151 0.96 9.06 0.98 0.95 178.32| | 12: 1.32 - 1.28 6975 149 0.96 9.12 0.97 0.94 165.04| | 13: 1.28 - 1.25 6907 166 0.95 9.97 1.03 0.96 164.96| | 14: 1.25 - 1.22 7015 112 0.95 11.04 1.03 0.98 168.82| | 15: 1.22 - 1.19 6956 137 0.94 11.43 1.03 1.00 170.44| | 16: 1.19 - 1.17 6604 132 0.95 11.48 1.02 0.98 161.37| | 17: 1.17 - 1.14 6940 135 0.94 12.31 1.02 0.97 155.31| | 18: 1.14 - 1.12 6875 142 0.94 12.83 1.01 0.95 149.46| | 19: 1.12 - 1.10 6948 106 0.93 14.25 1.00 0.94 153.10| | 20: 1.10 - 1.08 6884 147 0.92 15.31 0.99 0.93 151.62| | 21: 1.08 - 1.07 6852 152 0.91 16.67 0.98 0.92 154.24| | 22: 1.07 - 1.05 6836 135 0.89 18.32 0.98 0.91 155.42| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.97 0.90 165.42| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.96 0.90 179.62| | 25: 1.02 - 1.01 6552 130 0.83 25.13 0.94 0.87 182.28| | 26: 1.01 - 0.99 6767 158 0.81 26.54 0.94 0.85 175.91| | 27: 0.99 - 0.98 6647 131 0.82 26.08 0.95 0.84 159.30| |alpha: min = 0.84 max = 1.00 mean = 0.94| |beta: min = 149.46 max = 11685.21 mean = 957.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.41| |phase err.(test): min = 0.00 max = 89.78 mean = 13.56| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1205 0.1371 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1364 0.1362 0.1498 n_refl.: 191128 remove outliers: r(all,work,free)=0.1364 0.1362 0.1498 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1364 0.1362 0.1498 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1363 n_refl.: 191128 remove outliers: r(all,work,free)=0.1201 0.1198 0.1363 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3547 355.752 332.721 0.337 0.988 0.060 13.296-10.522 97.03 97 1 0.2521 481.203 458.536 0.669 0.989 0.091 10.503-8.327 98.35 176 3 0.2208 502.804 493.717 0.860 0.989 0.095 8.318-6.595 100.00 360 8 0.2150 375.552 370.749 0.886 0.989 0.092 6.588-5.215 100.00 711 7 0.1961 345.095 334.782 0.884 0.990 0.089 5.214-4.128 98.38 1367 28 0.1235 504.769 498.943 0.978 0.990 0.087 4.126-3.266 94.74 2603 46 0.1170 460.124 452.583 1.036 0.992 0.000 3.266-2.585 99.86 5447 97 0.1126 310.389 306.888 1.018 0.993 0.000 2.585-2.046 97.45 10613 204 0.0969 234.170 231.506 1.023 0.995 0.000 2.046-1.619 99.39 21536 464 0.0913 138.594 137.213 1.034 0.999 0.000 1.619-1.281 98.00 42464 925 0.0955 74.611 73.935 1.018 1.005 0.000 1.281-0.980 96.53 101826 2055 0.1632 40.025 38.315 0.975 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.1349 ================= 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 : 0.2042 0.2016 0.083 5.330 5.2 78.0 14.6 805 0.000 1_bss: 0.1805 0.1957 0.083 5.330 5.2 78.0 14.6 805 0.000 1_settarget: 0.1805 0.1957 0.083 5.330 5.2 78.0 14.6 805 0.000 1_nqh: 0.1805 0.1957 0.083 5.330 5.2 78.0 14.6 805 0.000 1_weight: 0.1805 0.1957 0.083 5.330 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1272 0.1510 0.040 1.168 5.2 78.0 14.6 805 0.158 1_adp: 0.1301 0.1585 0.040 1.168 5.1 73.0 15.1 805 0.158 1_regHadp: 0.1300 0.1579 0.040 1.168 5.1 73.0 15.1 805 0.158 1_occ: 0.1285 0.1567 0.040 1.168 5.1 73.0 15.1 805 0.158 2_bss: 0.1277 0.1555 0.040 1.168 5.3 73.2 15.3 805 0.158 2_settarget: 0.1277 0.1555 0.040 1.168 5.3 73.2 15.3 805 0.158 2_updatecdl: 0.1277 0.1555 0.040 1.174 5.3 73.2 15.3 805 0.158 2_nqh: 0.1277 0.1555 0.040 1.174 5.3 73.2 15.3 805 0.158 2_sol: 0.1275 0.1526 0.040 1.174 5.3 73.2 16.3 887 n/a 2_weight: 0.1275 0.1526 0.040 1.174 5.3 73.2 16.3 887 n/a 2_xyzrec: 0.1257 0.1534 0.042 1.129 5.3 73.2 16.3 887 n/a 2_adp: 0.1236 0.1520 0.042 1.129 5.4 68.2 16.3 887 n/a 2_regHadp: 0.1236 0.1521 0.042 1.129 5.4 68.2 16.3 887 n/a 2_occ: 0.1229 0.1515 0.042 1.129 5.4 68.2 16.3 887 n/a 3_bss: 0.1236 0.1521 0.042 1.129 5.4 68.2 16.3 887 n/a 3_settarget: 0.1236 0.1521 0.042 1.129 5.4 68.2 16.3 887 n/a 3_updatecdl: 0.1236 0.1521 0.042 1.130 5.4 68.2 16.3 887 n/a 3_nqh: 0.1236 0.1521 0.042 1.130 5.4 68.2 16.3 887 n/a 3_sol: 0.1251 0.1519 0.042 1.130 5.4 68.2 15.4 869 n/a 3_weight: 0.1251 0.1519 0.042 1.130 5.4 68.2 15.4 869 n/a 3_xyzrec: 0.1241 0.1443 0.036 1.095 5.4 68.2 15.4 869 n/a 3_adp: 0.1234 0.1400 0.036 1.095 5.5 67.9 15.3 869 n/a 3_regHadp: 0.1234 0.1400 0.036 1.095 5.5 67.9 15.3 869 n/a 3_occ: 0.1229 0.1395 0.036 1.095 5.5 67.9 15.3 869 n/a 4_bss: 0.1225 0.1390 0.036 1.095 5.5 67.8 15.2 869 n/a 4_settarget: 0.1225 0.1390 0.036 1.095 5.5 67.8 15.2 869 n/a 4_updatecdl: 0.1225 0.1390 0.036 1.099 5.5 67.8 15.2 869 n/a 4_nqh: 0.1225 0.1390 0.036 1.099 5.5 67.8 15.2 869 n/a 4_sol: 0.1207 0.1362 0.036 1.099 5.5 67.8 15.1 872 n/a 4_weight: 0.1207 0.1362 0.036 1.099 5.5 67.8 15.1 872 n/a 4_xyzrec: 0.1205 0.1369 0.036 1.118 5.5 67.8 15.1 872 n/a 4_adp: 0.1200 0.1366 0.036 1.118 5.5 67.4 15.0 872 n/a 4_regHadp: 0.1200 0.1366 0.036 1.118 5.5 67.4 15.0 872 n/a 4_occ: 0.1198 0.1366 0.036 1.118 5.5 67.4 15.0 872 n/a 5_bss: 0.1196 0.1365 0.036 1.118 5.5 67.4 15.0 872 n/a 5_settarget: 0.1196 0.1365 0.036 1.118 5.5 67.4 15.0 872 n/a 5_updatecdl: 0.1196 0.1365 0.036 1.118 5.5 67.4 15.0 872 n/a 5_nqh: 0.1196 0.1365 0.036 1.118 5.5 67.4 15.0 872 n/a 5_sol: 0.1193 0.1347 0.036 1.118 5.5 67.4 15.1 899 n/a 5_weight: 0.1193 0.1347 0.036 1.118 5.5 67.4 15.1 899 n/a 5_xyzrec: 0.1195 0.1356 0.037 1.129 5.5 67.4 15.1 899 n/a 5_adp: 0.1198 0.1358 0.037 1.129 5.5 66.9 15.1 899 n/a 5_regHadp: 0.1198 0.1358 0.037 1.129 5.5 66.9 15.1 899 n/a 5_occ: 0.1196 0.1359 0.037 1.129 5.5 66.9 15.1 899 n/a 6_bss: 0.1191 0.1357 0.037 1.129 5.5 66.9 15.0 899 n/a 6_settarget: 0.1191 0.1357 0.037 1.129 5.5 66.9 15.0 899 n/a 6_updatecdl: 0.1191 0.1357 0.037 1.129 5.5 66.9 15.0 899 n/a 6_nqh: 0.1191 0.1357 0.037 1.129 5.5 66.9 15.0 899 n/a 6_sol: 0.1189 0.1344 0.037 1.129 5.5 66.9 15.0 910 n/a 6_weight: 0.1189 0.1344 0.037 1.129 5.5 66.9 15.0 910 n/a 6_xyzrec: 0.1193 0.1350 0.038 1.126 5.5 66.9 15.0 910 n/a 6_adp: 0.1195 0.1350 0.038 1.126 5.6 65.8 14.9 910 n/a 6_regHadp: 0.1195 0.1351 0.038 1.126 5.6 65.8 14.9 910 n/a 6_occ: 0.1192 0.1350 0.038 1.126 5.6 65.8 14.9 910 n/a 7_bss: 0.1191 0.1348 0.038 1.126 5.5 65.8 14.9 910 n/a 7_settarget: 0.1191 0.1348 0.038 1.126 5.5 65.8 14.9 910 n/a 7_updatecdl: 0.1191 0.1348 0.038 1.126 5.5 65.8 14.9 910 n/a 7_nqh: 0.1191 0.1348 0.038 1.126 5.5 65.8 14.9 910 n/a 7_sol: 0.1191 0.1344 0.038 1.126 5.5 65.8 14.9 912 n/a 7_weight: 0.1191 0.1344 0.038 1.126 5.5 65.8 14.9 912 n/a 7_xyzrec: 0.1194 0.1351 0.038 1.127 5.5 65.8 14.9 912 n/a 7_adp: 0.1195 0.1353 0.038 1.127 5.6 64.7 14.9 912 n/a 7_regHadp: 0.1195 0.1353 0.038 1.127 5.6 64.7 14.9 912 n/a 7_occ: 0.1193 0.1353 0.038 1.127 5.6 64.7 14.9 912 n/a 8_bss: 0.1186 0.1340 0.038 1.127 5.6 64.7 14.9 912 n/a 8_settarget: 0.1186 0.1340 0.038 1.127 5.6 64.7 14.9 912 n/a 8_updatecdl: 0.1186 0.1340 0.038 1.127 5.6 64.7 14.9 912 n/a 8_nqh: 0.1186 0.1340 0.038 1.127 5.6 64.7 14.9 912 n/a 8_sol: 0.1186 0.1339 0.038 1.127 5.6 64.7 14.8 909 n/a 8_weight: 0.1186 0.1339 0.038 1.127 5.6 64.7 14.8 909 n/a 8_xyzrec: 0.1190 0.1343 0.039 1.124 5.6 64.7 14.8 909 n/a 8_adp: 0.1191 0.1346 0.039 1.124 5.6 63.6 14.8 909 n/a 8_regHadp: 0.1191 0.1346 0.039 1.124 5.6 63.6 14.8 909 n/a 8_occ: 0.1189 0.1345 0.039 1.124 5.6 63.6 14.8 909 n/a 9_bss: 0.1188 0.1348 0.039 1.124 5.6 63.5 14.8 909 n/a 9_settarget: 0.1188 0.1348 0.039 1.124 5.6 63.5 14.8 909 n/a 9_updatecdl: 0.1188 0.1348 0.039 1.123 5.6 63.5 14.8 909 n/a 9_nqh: 0.1188 0.1348 0.039 1.123 5.6 63.5 14.8 909 n/a 9_sol: 0.1186 0.1349 0.039 1.123 5.6 63.5 14.8 921 n/a 9_weight: 0.1186 0.1349 0.039 1.123 5.6 63.5 14.8 921 n/a 9_xyzrec: 0.1189 0.1357 0.039 1.123 5.6 63.5 14.8 921 n/a 9_adp: 0.1191 0.1362 0.039 1.123 5.6 63.5 14.8 921 n/a 9_regHadp: 0.1191 0.1362 0.039 1.123 5.6 63.5 14.8 921 n/a 9_occ: 0.1190 0.1363 0.039 1.123 5.6 63.5 14.8 921 n/a 10_bss: 0.1200 0.1367 0.039 1.123 5.3 63.2 14.5 921 n/a 10_settarget: 0.1200 0.1367 0.039 1.123 5.3 63.2 14.5 921 n/a 10_updatecdl: 0.1200 0.1367 0.039 1.124 5.3 63.2 14.5 921 n/a 10_setrh: 0.1201 0.1367 0.039 1.124 5.3 63.2 14.5 921 n/a 10_nqh: 0.1201 0.1367 0.039 1.124 5.3 63.2 14.5 921 n/a 10_sol: 0.1199 0.1358 0.039 1.124 5.3 63.2 14.5 914 n/a 10_weight: 0.1199 0.1358 0.039 1.124 5.3 63.2 14.5 914 n/a 10_xyzrec: 0.1206 0.1368 0.039 1.192 5.3 63.2 14.5 914 n/a 10_adp: 0.1206 0.1372 0.039 1.192 5.3 63.2 14.5 914 n/a 10_regHadp: 0.1206 0.1373 0.039 1.192 5.3 63.2 14.5 914 n/a 10_occ: 0.1205 0.1371 0.039 1.192 5.3 63.2 14.5 914 n/a end: 0.1198 0.1363 0.039 1.192 5.3 63.2 14.5 914 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4251871_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4251871_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0000 Refinement macro-cycles (run) : 12294.0400 Write final files (write_after_run_outputs) : 142.6500 Total : 12443.6900 Total CPU time: 3.47 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:42 PST -0800 (1736736282.19 s) Start R-work = 0.1805, R-free = 0.1957 Final R-work = 0.1198, R-free = 0.1363 =============================================================================== Job complete usr+sys time: 12702.65 seconds wall clock time: 212 minutes 46.69 seconds (12766.69 seconds total)