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_1750626.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1750626.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1750626.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.71, per 1000 atoms: 0.26 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: 2.695 distance_ideal: 2.720 ideal - model: 0.025 slack: 0.000 delta_slack: 0.025 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: 2.723 distance_ideal: 2.710 ideal - model: -0.013 slack: 0.000 delta_slack: -0.013 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: 0.89 Conformation dependent library (CDL) restraints added in 114.5 milliseconds Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.03: 812 1.03 - 1.25: 2439 1.25 - 1.48: 1507 1.48 - 1.70: 1148 1.70 - 1.93: 28 Bond restraints: 5934 Sorted by residual: bond pdb=" N GLY B 12 " pdb=" H GLY B 12 " ideal model delta sigma weight residual 0.860 1.265 -0.405 2.00e-02 2.50e+03 4.09e+02 bond pdb=" N ALA B 57 " pdb=" CA ALA B 57 " ideal model delta sigma weight residual 1.456 1.654 -0.198 1.04e-02 9.25e+03 3.63e+02 bond pdb=" CA VAL A 69 " pdb=" HA VAL A 69 " ideal model delta sigma weight residual 0.970 1.351 -0.381 2.00e-02 2.50e+03 3.62e+02 bond pdb=" N LYS B 151 " pdb=" H LYS B 151 " ideal model delta sigma weight residual 0.860 1.233 -0.373 2.00e-02 2.50e+03 3.48e+02 bond pdb=" CA LEU B 72 " pdb=" C LEU B 72 " ideal model delta sigma weight residual 1.523 1.709 -0.186 1.00e-02 1.00e+04 3.45e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 6413 4.84 - 9.68: 3439 9.68 - 14.51: 870 14.51 - 19.35: 84 19.35 - 24.19: 4 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 119.20 134.23 -15.03 9.00e-01 1.23e+00 2.79e+02 angle pdb=" O LYS A 93 " pdb=" C LYS A 93 " pdb=" N GLN A 94 " ideal model delta sigma weight residual 122.09 105.59 16.50 1.04e+00 9.25e-01 2.52e+02 angle pdb=" CA GLY B 174 " pdb=" C GLY B 174 " pdb=" O GLY B 174 " ideal model delta sigma weight residual 122.45 111.43 11.02 7.20e-01 1.93e+00 2.34e+02 angle pdb=" O ILE B 70 " pdb=" C ILE B 70 " pdb=" N VAL B 71 " ideal model delta sigma weight residual 123.18 108.15 15.03 1.05e+00 9.07e-01 2.05e+02 angle pdb=" CA TYR A 192 " pdb=" C TYR A 192 " pdb=" O TYR A 192 " ideal model delta sigma weight residual 120.69 136.38 -15.69 1.14e+00 7.69e-01 1.89e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 1815 16.48 - 32.96: 160 32.96 - 49.43: 48 49.43 - 65.91: 22 65.91 - 82.39: 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 -153.10 -26.90 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CG TRP A 139 " pdb=" CD2 TRP A 139 " pdb=" CE3 TRP A 139 " pdb=" HE3 TRP A 139 " ideal model delta harmonic sigma weight residual 0.00 26.66 -26.66 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 173 0.191 - 0.382: 141 0.382 - 0.573: 106 0.573 - 0.763: 50 0.763 - 0.954: 22 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 114 " pdb=" N VAL B 114 " pdb=" C VAL B 114 " pdb=" CB VAL B 114 " both_signs ideal model delta sigma weight residual False 2.44 1.49 0.95 2.00e-01 2.50e+01 2.28e+01 chirality pdb=" CA ALA B 5 " pdb=" N ALA B 5 " pdb=" C ALA B 5 " pdb=" CB ALA B 5 " both_signs ideal model delta sigma weight residual False 2.48 3.42 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CA PHE B 82 " pdb=" N PHE B 82 " pdb=" C PHE B 82 " pdb=" CB PHE B 82 " both_signs ideal model delta sigma weight residual False 2.51 3.42 -0.91 2.00e-01 2.50e+01 2.07e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.006 2.00e-02 2.50e+03 7.61e-02 2.32e+02 pdb=" CG TRP A 139 " 0.108 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.105 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.025 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.093 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.050 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.063 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.045 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.144 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.176 2.00e-02 2.50e+03 8.35e-02 2.09e+02 pdb=" CG PHE B 164 " -0.113 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.073 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.129 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.064 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.036 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.080 2.00e-02 2.50e+03 8.00e-02 1.92e+02 pdb=" CG TYR A 194 " 0.114 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " 0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.075 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " 0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " -0.053 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.107 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " -0.052 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " -0.112 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " 0.082 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " 0.061 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.59: 26 1.59 - 2.34: 2224 2.34 - 3.10: 22025 3.10 - 3.85: 33053 3.85 - 4.60: 53011 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110339 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.841 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.960 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.984 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.026 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.088 2.620 ... (remaining 110334 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_1750626_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= 0.2031 r_free= 0.1990 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.297595 | | target function (ml) not normalized (work): 804995.342476 | | target function (ml) not normalized (free): 16560.572269 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2134 0.2035 6.6583 6.3289| | 2: 2.94 - 2.33 1.00 7339 128 0.1615 0.1593 5.5475 5.5909| | 3: 2.33 - 2.04 0.96 6939 150 0.1632 0.1556 5.138 5.1082| | 4: 2.04 - 1.85 1.00 7170 155 0.1764 0.1610 4.97 5.0737| | 5: 1.85 - 1.72 0.99 7113 159 0.1949 0.1793 4.8059 4.8736| | 6: 1.72 - 1.62 0.99 7102 142 0.1985 0.1906 4.6537 4.6624| | 7: 1.62 - 1.54 0.99 7104 148 0.1987 0.1535 4.5567 4.4736| | 8: 1.54 - 1.47 0.96 6798 152 0.2043 0.2355 4.472 4.5939| | 9: 1.47 - 1.41 0.98 6938 155 0.2044 0.2171 4.3807 4.4368| | 10: 1.41 - 1.36 0.99 7022 150 0.2090 0.2181 4.3107 4.3594| | 11: 1.36 - 1.32 0.99 6997 151 0.2107 0.2107 4.2342 4.2764| | 12: 1.32 - 1.28 0.98 6976 149 0.2091 0.1820 4.1733 4.1603| | 13: 1.28 - 1.25 0.98 6907 166 0.2028 0.2140 4.1171 4.1838| | 14: 1.25 - 1.22 0.98 7015 113 0.2092 0.2364 4.0677 4.1944| | 15: 1.22 - 1.19 0.98 6957 137 0.2090 0.1924 4.0341 3.9903| | 16: 1.19 - 1.17 0.93 6604 132 0.2118 0.2082 4.0077 3.9847| | 17: 1.17 - 1.14 0.98 6941 135 0.2159 0.1994 3.9585 4.0504| | 18: 1.14 - 1.12 0.98 6875 142 0.2208 0.2507 3.9245 3.9707| | 19: 1.12 - 1.10 0.97 6949 106 0.2251 0.2662 3.8685 4.0498| | 20: 1.10 - 1.08 0.97 6884 147 0.2296 0.2197 3.8191 3.8116| | 21: 1.08 - 1.07 0.97 6852 152 0.2454 0.2693 3.7928 3.8053| | 22: 1.07 - 1.05 0.97 6838 135 0.2559 0.2580 3.7534 3.7794| | 23: 1.05 - 1.03 0.97 6829 159 0.2725 0.2708 3.7359 3.8685| | 24: 1.03 - 1.02 0.96 6785 133 0.2865 0.2898 3.7043 3.8175| | 25: 1.02 - 1.01 0.93 6552 130 0.3058 0.2954 3.6727 3.7477| | 26: 1.01 - 0.99 0.96 6767 158 0.3206 0.3398 3.6274 3.6177| | 27: 0.99 - 0.98 0.94 6648 131 0.3409 0.3310 3.6389 3.6057| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 21.13 0.91 0.97 37549.24| | 2: 2.94 - 2.33 7339 128 0.85 21.39 1.08 1.03 15536.67| | 3: 2.33 - 2.04 6939 150 0.93 12.08 1.11 1.06 3943.02| | 4: 2.04 - 1.85 7170 155 0.92 13.57 1.11 1.07 2834.81| | 5: 1.85 - 1.72 7113 159 0.91 15.76 1.12 1.06 2080.20| | 6: 1.72 - 1.62 7102 142 0.90 16.54 1.12 1.06 1568.50| | 7: 1.62 - 1.54 7104 148 0.90 16.81 1.10 1.05 1220.65| | 8: 1.54 - 1.47 6798 152 0.89 17.85 1.10 1.05 1088.60| | 9: 1.47 - 1.41 6938 155 0.88 18.83 1.10 1.06 965.37| | 10: 1.41 - 1.36 7022 150 0.88 19.60 1.09 1.06 848.50| | 11: 1.36 - 1.32 6997 151 0.88 19.71 1.08 1.04 716.31| | 12: 1.32 - 1.28 6976 149 0.88 19.58 1.08 1.03 622.97| | 13: 1.28 - 1.25 6907 166 0.88 19.42 1.07 1.03 577.02| | 14: 1.25 - 1.22 7015 113 0.87 20.40 1.08 1.04 548.80| | 15: 1.22 - 1.19 6957 137 0.87 20.08 1.08 1.04 510.83| | 16: 1.19 - 1.17 6604 132 0.88 19.87 1.07 1.04 471.58| | 17: 1.17 - 1.14 6941 135 0.86 21.32 1.08 1.02 455.20| | 18: 1.14 - 1.12 6875 142 0.85 22.15 1.08 0.99 428.50| | 19: 1.12 - 1.10 6949 106 0.84 23.23 1.07 0.98 407.71| | 20: 1.10 - 1.08 6884 147 0.85 22.91 1.06 0.98 358.49| | 21: 1.08 - 1.07 6852 152 0.83 24.20 1.07 0.98 342.87| | 22: 1.07 - 1.05 6838 135 0.81 26.32 1.06 0.97 340.57| | 23: 1.05 - 1.03 6829 159 0.78 28.91 1.05 0.96 356.05| | 24: 1.03 - 1.02 6785 133 0.76 30.85 1.05 0.97 357.08| | 25: 1.02 - 1.01 6552 130 0.76 31.60 1.03 0.93 329.52| | 26: 1.01 - 0.99 6767 158 0.74 33.17 1.02 0.90 304.75| | 27: 0.99 - 0.98 6648 131 0.73 33.68 1.03 0.87 287.37| |alpha: min = 0.87 max = 1.07 mean = 1.01| |beta: min = 287.37 max = 37549.24 mean = 2912.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 21.80| |phase err.(test): min = 0.00 max = 89.44 mean = 21.85| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.241 2950 Z= 5.421 Angle : 5.213 17.979 4018 Z= 3.705 Chirality : 0.389 0.954 492 Planarity : 0.033 0.156 512 Dihedral : 12.942 82.385 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.29 % Allowed : 4.19 % Favored : 94.52 % Cbeta Deviations : 32.58 % 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: -2.15 (0.39), residues: 386 helix: -2.54 (0.31), residues: 144 sheet: -0.85 (0.62), residues: 66 loop : -0.41 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.120 0.026 ARG B 143 TYR 0.130 0.034 TYR A 194 PHE 0.153 0.038 PHE B 164 TRP 0.113 0.048 TRP B 139 HIS 0.057 0.026 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2031 r_free= 0.1990 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.297595 | | target function (ml) not normalized (work): 804995.342476 | | target function (ml) not normalized (free): 16560.572269 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2029 0.2031 0.1990 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2029 0.2031 0.1990 n_refl.: 191155 remove outliers: r(all,work,free)=0.2030 0.2031 0.1990 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2029 0.2031 0.1990 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1802 0.1799 0.1932 n_refl.: 191145 remove outliers: r(all,work,free)=0.1800 0.1797 0.1932 n_refl.: 191141 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4230 400.535 295.515 0.435 0.911 0.299 13.296-10.522 100.00 100 1 0.2543 534.497 521.247 0.787 0.913 0.251 10.503-8.327 99.45 178 3 0.2553 565.118 554.969 0.979 0.913 0.230 8.318-6.595 100.00 360 8 0.2519 414.736 402.471 0.974 0.912 0.175 6.588-5.215 100.00 711 7 0.2280 381.101 365.557 0.959 0.913 0.160 5.214-4.128 98.38 1367 28 0.1487 557.435 549.985 1.074 0.913 0.080 4.126-3.266 94.74 2603 46 0.1327 508.132 498.931 1.147 0.913 0.028 3.266-2.585 99.86 5447 97 0.1449 342.774 337.596 1.120 0.912 0.010 2.585-2.046 97.45 10613 204 0.1389 258.603 254.371 1.127 0.912 0.000 2.046-1.619 99.39 21536 464 0.1627 153.054 149.677 1.148 0.910 0.000 1.619-1.281 98.00 42464 925 0.1912 82.395 80.232 1.126 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2315 44.203 41.724 1.114 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0007 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1932 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1797 r_free=0.1932 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.497008 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 576.274998 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1271 0.1499 0.0228 0.040 1.2 11.0 0.0 0.3 0 11.249 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 14.99 2.28 1.117 13.110 576.275 0.019 12.98 15.72 2.74 1.235 13.324 576.275 0.017 Individual atomic B min max mean iso aniso Overall: 5.17 73.04 14.99 1.40 435 3274 Protein: 5.17 40.32 10.99 1.40 0 2902 Water: 6.40 73.04 29.36 N/A 435 370 Other: 16.09 29.97 23.03 N/A 0 2 Chain A: 5.33 59.52 13.02 N/A 0 1626 Chain B: 5.17 73.04 12.76 N/A 0 1648 Chain S: 11.73 63.73 30.75 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2161 11.96 - 18.75 641 18.75 - 25.53 316 25.53 - 32.32 271 32.32 - 39.11 154 39.11 - 45.89 106 45.89 - 52.68 36 52.68 - 59.47 19 59.47 - 66.26 4 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1572 r_work=0.1297 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1566 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1555 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015653 | | target function (ls_wunit_k1) not normalized (work): 2931.707896 | | target function (ls_wunit_k1) not normalized (free): 116.253535 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1555 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1472 0.1469 0.1637 n_refl.: 191141 remove outliers: r(all,work,free)=0.1472 0.1469 0.1637 n_refl.: 191141 overall B=0.17 to atoms: r(all,work,free)=0.1496 0.1493 0.1647 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1548 n_refl.: 191141 remove outliers: r(all,work,free)=0.1280 0.1275 0.1547 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3632 402.814 371.327 0.482 0.962 0.281 13.296-10.522 100.00 100 1 0.2130 534.497 530.007 0.752 0.963 0.249 10.503-8.327 99.45 178 3 0.1764 565.118 561.851 0.891 0.963 0.203 8.318-6.595 100.00 360 8 0.1711 414.736 412.249 0.912 0.963 0.160 6.588-5.215 100.00 711 7 0.1539 381.101 373.335 0.888 0.963 0.150 5.214-4.128 98.38 1367 28 0.0907 557.435 554.863 0.977 0.964 0.055 4.126-3.266 94.74 2603 46 0.0830 508.132 504.361 1.045 0.964 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.353 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.349 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.369 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.414 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.179 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=0.0377 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1547 | n_water=805 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1280 r_free=0.1553 | n_water=793 | time (s): 98.530 (total time: 100.940) Filter (q & B) r_work=0.1280 r_free=0.1553 | n_water=788 | time (s): 4.590 (total time: 105.530) Compute maps r_work=0.1280 r_free=0.1553 | n_water=788 | time (s): 1.870 (total time: 107.400) Filter (map) r_work=0.1306 r_free=0.1539 | n_water=648 | time (s): 5.200 (total time: 112.600) Find peaks r_work=0.1306 r_free=0.1539 | n_water=648 | time (s): 0.910 (total time: 113.510) Add new water r_work=0.1328 r_free=0.1566 | n_water=950 | time (s): 5.300 (total time: 118.810) Refine new water occ: r_work=0.1284 r_free=0.1520 adp: r_work=0.1272 r_free=0.1517 occ: r_work=0.1274 r_free=0.1516 adp: r_work=0.1268 r_free=0.1516 occ: r_work=0.1269 r_free=0.1514 adp: r_work=0.1267 r_free=0.1515 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1515 r_work=0.1267 r_free=0.1515 | n_water=950 | time (s): 80.010 (total time: 198.820) Filter (q & B) r_work=0.1271 r_free=0.1520 | n_water=875 | time (s): 4.470 (total time: 203.290) Filter (dist only) r_work=0.1271 r_free=0.1518 | n_water=873 | time (s): 111.010 (total time: 314.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.411159 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 591.833011 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 0.1256 0.1532 0.0276 0.042 1.1 15.5 0.0 0.3 0 12.206 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.32 2.76 2.040 15.126 591.833 0.015 12.32 15.18 2.86 2.420 15.190 591.833 0.014 Individual atomic B min max mean iso aniso Overall: 5.37 70.53 16.26 1.21 505 3272 Protein: 5.37 40.72 10.97 1.21 0 2902 Water: 6.57 70.53 33.84 N/A 505 368 Other: 16.36 32.33 24.35 N/A 0 2 Chain A: 5.53 55.50 13.00 N/A 0 1624 Chain B: 5.37 68.21 12.82 N/A 0 1648 Chain S: 13.76 70.53 37.98 N/A 505 0 Histogram: Values Number of atoms 5.37 - 11.88 2111 11.88 - 18.40 685 18.40 - 24.92 257 24.92 - 31.43 209 31.43 - 37.95 180 37.95 - 44.47 163 44.47 - 50.98 94 50.98 - 57.50 44 57.50 - 64.02 28 64.02 - 70.53 6 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1519 r_work=0.1233 r_free=0.1519 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1519 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1514 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1514 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013531 | | target function (ls_wunit_k1) not normalized (work): 2534.415631 | | target function (ls_wunit_k1) not normalized (free): 102.770555 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1514 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1614 n_refl.: 191139 remove outliers: r(all,work,free)=0.1439 0.1436 0.1614 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1436 0.1433 0.1612 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1521 n_refl.: 191139 remove outliers: r(all,work,free)=0.1239 0.1234 0.1521 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3314 402.814 391.930 0.508 0.960 0.265 13.296-10.522 100.00 100 1 0.1891 534.497 529.657 0.778 0.961 0.240 10.503-8.327 99.45 178 3 0.1417 565.118 567.635 0.922 0.961 0.183 8.318-6.595 100.00 360 8 0.1567 414.736 414.167 0.939 0.961 0.150 6.588-5.215 100.00 711 7 0.1355 381.101 376.304 0.912 0.961 0.150 5.214-4.128 98.38 1367 28 0.0840 557.435 555.938 0.996 0.961 0.070 4.126-3.266 94.74 2603 46 0.0763 508.132 505.664 1.062 0.961 0.014 3.266-2.585 99.86 5447 97 0.0863 342.774 341.119 1.048 0.961 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.750 1.060 0.960 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.597 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1252 82.395 81.424 1.072 0.958 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.213 1.054 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0560 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1521 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1521 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1521 | n_water=873 | time (s): 2.810 (total time: 2.810) Filter (dist) r_work=0.1236 r_free=0.1523 | n_water=868 | time (s): 120.630 (total time: 123.440) Filter (q & B) r_work=0.1236 r_free=0.1522 | n_water=866 | time (s): 4.430 (total time: 127.870) Compute maps r_work=0.1236 r_free=0.1522 | n_water=866 | time (s): 2.450 (total time: 130.320) Filter (map) r_work=0.1271 r_free=0.1527 | n_water=694 | time (s): 4.510 (total time: 134.830) Find peaks r_work=0.1271 r_free=0.1527 | n_water=694 | time (s): 0.610 (total time: 135.440) Add new water r_work=0.1293 r_free=0.1561 | n_water=1008 | time (s): 3.940 (total time: 139.380) Refine new water occ: r_work=0.1249 r_free=0.1518 adp: r_work=0.1249 r_free=0.1519 occ: r_work=0.1245 r_free=0.1515 adp: r_work=0.1245 r_free=0.1516 occ: r_work=0.1242 r_free=0.1513 adp: r_work=0.1242 r_free=0.1513 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1513 r_work=0.1242 r_free=0.1513 | n_water=1008 | time (s): 287.630 (total time: 427.010) Filter (q & B) r_work=0.1246 r_free=0.1519 | n_water=875 | time (s): 4.790 (total time: 431.800) Filter (dist only) r_work=0.1246 r_free=0.1519 | n_water=873 | time (s): 114.410 (total time: 546.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.667010 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.141162 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1238 0.1443 0.0205 0.035 1.1 6.6 0.0 0.0 0 0.834 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.43 2.05 1.931 14.544 16.141 3.939 12.37 14.02 1.65 2.269 14.443 16.141 3.899 Individual atomic B min max mean iso aniso Overall: 5.55 67.70 15.19 1.04 506 3271 Protein: 5.55 36.19 10.70 1.04 0 2902 Water: 6.69 67.70 30.11 N/A 506 367 Other: 14.01 28.39 21.20 N/A 0 2 Chain A: 5.58 54.39 12.74 N/A 0 1624 Chain B: 5.55 67.70 12.51 N/A 0 1647 Chain S: 13.34 62.75 31.82 N/A 506 0 Histogram: Values Number of atoms 5.55 - 11.76 2131 11.76 - 17.98 697 17.98 - 24.19 298 24.19 - 30.41 232 30.41 - 36.62 170 36.62 - 42.84 138 42.84 - 49.06 74 49.06 - 55.27 27 55.27 - 61.49 8 61.49 - 67.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1403 r_work=0.1238 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1404 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1396 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1232 r_free= 0.1396 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.893177 | | target function (ml) not normalized (work): 729184.254705 | | target function (ml) not normalized (free): 15231.634379 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1232 0.1396 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1447 0.1447 0.1487 n_refl.: 191139 remove outliers: r(all,work,free)=0.1447 0.1447 0.1487 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1441 0.1440 0.1484 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1227 0.1390 n_refl.: 191139 remove outliers: r(all,work,free)=0.1230 0.1227 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 94.06 92 3 0.3748 398.008 361.705 0.429 0.945 0.250 13.296-10.522 99.01 99 1 0.2354 535.265 512.336 0.720 0.946 0.220 10.503-8.327 98.35 176 3 0.2003 555.265 556.305 0.883 0.946 0.173 8.318-6.595 100.00 360 8 0.2086 414.736 410.431 0.898 0.946 0.125 6.588-5.215 100.00 711 7 0.1857 381.101 370.016 0.887 0.946 0.120 5.214-4.128 98.38 1367 28 0.1169 557.435 552.005 0.972 0.946 0.070 4.126-3.266 94.74 2603 46 0.1095 508.132 501.369 1.035 0.946 0.019 3.266-2.585 99.86 5447 97 0.1091 342.774 339.084 1.021 0.946 0.010 2.585-2.046 97.45 10613 204 0.0972 258.603 255.708 1.034 0.945 0.000 2.046-1.619 99.39 21536 464 0.0977 153.054 151.402 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.489 1.054 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.318 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1011 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1390 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1390 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1390 | n_water=873 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1227 r_free=0.1390 | n_water=873 | time (s): 115.370 (total time: 117.670) Filter (q & B) r_work=0.1228 r_free=0.1388 | n_water=861 | time (s): 4.500 (total time: 122.170) Compute maps r_work=0.1228 r_free=0.1388 | n_water=861 | time (s): 1.950 (total time: 124.120) Filter (map) r_work=0.1250 r_free=0.1391 | n_water=719 | time (s): 5.130 (total time: 129.250) Find peaks r_work=0.1250 r_free=0.1391 | n_water=719 | time (s): 0.720 (total time: 129.970) Add new water r_work=0.1265 r_free=0.1414 | n_water=942 | time (s): 3.910 (total time: 133.880) Refine new water occ: r_work=0.1219 r_free=0.1375 adp: r_work=0.1211 r_free=0.1371 occ: r_work=0.1209 r_free=0.1373 adp: r_work=0.1209 r_free=0.1372 occ: r_work=0.1207 r_free=0.1374 adp: r_work=0.1207 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1372 r_work=0.1207 r_free=0.1372 | n_water=942 | time (s): 423.660 (total time: 557.540) Filter (q & B) r_work=0.1211 r_free=0.1378 | n_water=861 | time (s): 4.800 (total time: 562.340) Filter (dist only) r_work=0.1211 r_free=0.1378 | n_water=860 | time (s): 111.310 (total time: 673.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.594649 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.197635 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 0.1209 0.1378 0.0169 0.036 1.1 6.0 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 13.78 1.69 1.815 14.168 16.198 3.875 11.99 13.72 1.73 1.910 14.130 16.198 3.865 Individual atomic B min max mean iso aniso Overall: 5.50 67.17 14.95 1.00 494 3270 Protein: 5.50 33.14 10.64 1.00 0 2902 Water: 5.89 67.17 29.51 N/A 494 366 Other: 13.99 27.07 20.53 N/A 0 2 Chain A: 5.57 53.20 12.60 N/A 0 1623 Chain B: 5.50 67.17 12.42 N/A 0 1647 Chain S: 5.89 60.64 31.15 N/A 494 0 Histogram: Values Number of atoms 5.50 - 11.67 2104 11.67 - 17.84 740 17.84 - 24.00 293 24.00 - 30.17 220 30.17 - 36.34 180 36.34 - 42.50 126 42.50 - 48.67 70 48.67 - 54.84 24 54.84 - 61.00 6 61.00 - 67.17 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1372 r_work=0.1199 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1372 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1371 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863233 | | target function (ml) not normalized (work): 723560.312495 | | target function (ml) not normalized (free): 15143.133974 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1371 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1427 0.1426 0.1482 n_refl.: 191135 remove outliers: r(all,work,free)=0.1427 0.1426 0.1482 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1419 0.1419 0.1477 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1197 0.1371 n_refl.: 191135 remove outliers: r(all,work,free)=0.1201 0.1197 0.1371 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3865 360.463 319.456 0.414 0.945 0.240 13.296-10.522 99.01 99 1 0.2513 484.773 466.656 0.721 0.946 0.208 10.503-8.327 98.35 176 3 0.2099 502.886 495.652 0.864 0.946 0.161 8.318-6.595 100.00 360 8 0.2178 375.614 370.437 0.894 0.946 0.108 6.588-5.215 100.00 711 7 0.1910 345.152 334.930 0.885 0.946 0.076 5.214-4.128 98.38 1367 28 0.1191 504.852 499.450 0.973 0.947 0.057 4.126-3.266 94.74 2603 46 0.1122 460.200 453.755 1.036 0.947 0.000 3.266-2.585 99.86 5447 97 0.1100 310.440 307.068 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0940 234.209 231.738 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0911 138.616 137.318 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0985 74.623 73.904 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.032 38.369 1.038 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1178 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1371 | n_water=860 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1198 r_free=0.1372 | n_water=859 | time (s): 107.200 (total time: 110.140) Filter (q & B) r_work=0.1198 r_free=0.1371 | n_water=853 | time (s): 4.500 (total time: 114.640) Compute maps r_work=0.1198 r_free=0.1371 | n_water=853 | time (s): 2.400 (total time: 117.040) Filter (map) r_work=0.1219 r_free=0.1364 | n_water=736 | time (s): 4.280 (total time: 121.320) Find peaks r_work=0.1219 r_free=0.1364 | n_water=736 | time (s): 0.730 (total time: 122.050) Add new water r_work=0.1230 r_free=0.1383 | n_water=963 | time (s): 4.230 (total time: 126.280) Refine new water occ: r_work=0.1195 r_free=0.1355 adp: r_work=0.1195 r_free=0.1354 occ: r_work=0.1193 r_free=0.1355 adp: r_work=0.1193 r_free=0.1354 occ: r_work=0.1191 r_free=0.1355 adp: r_work=0.1191 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1355 r_work=0.1191 r_free=0.1355 | n_water=963 | time (s): 226.950 (total time: 353.230) Filter (q & B) r_work=0.1195 r_free=0.1359 | n_water=880 | time (s): 4.360 (total time: 357.590) Filter (dist only) r_work=0.1196 r_free=0.1358 | n_water=879 | time (s): 115.810 (total time: 473.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.499453 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.712236 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1361 0.0162 0.036 1.1 6.3 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.61 1.62 1.784 14.092 14.712 3.764 12.03 13.64 1.61 1.820 14.075 14.712 3.763 Individual atomic B min max mean iso aniso Overall: 5.57 66.96 14.92 0.95 514 3269 Protein: 5.57 32.07 10.58 0.95 0 2902 Water: 5.91 66.96 29.25 N/A 514 365 Other: 13.80 26.46 20.13 N/A 0 2 Chain A: 5.59 52.79 12.52 N/A 0 1623 Chain B: 5.57 66.96 12.34 N/A 0 1646 Chain S: 5.91 60.64 30.80 N/A 514 0 Histogram: Values Number of atoms 5.57 - 11.71 2134 11.71 - 17.85 726 17.85 - 23.98 297 23.98 - 30.12 216 30.12 - 36.26 190 36.26 - 42.40 122 42.40 - 48.54 68 48.54 - 54.68 23 54.68 - 60.82 6 60.82 - 66.96 1 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1364 r_work=0.1204 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1365 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1365 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762558 | | target function (ml) not normalized (work): 704704.526428 | | target function (ml) not normalized (free): 14752.983546 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1365 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1425 0.1424 0.1488 n_refl.: 191135 remove outliers: r(all,work,free)=0.1425 0.1424 0.1488 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1419 0.1418 0.1484 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191135 remove outliers: r(all,work,free)=0.1200 0.1197 0.1362 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 0.3730 360.154 308.817 0.388 0.970 0.235 13.296-10.522 98.02 98 1 0.2421 487.082 465.037 0.692 0.972 0.199 10.503-8.327 98.35 176 3 0.2159 502.886 495.740 0.836 0.972 0.143 8.318-6.595 100.00 360 8 0.2182 375.614 371.284 0.862 0.971 0.095 6.588-5.215 100.00 711 7 0.1940 345.152 334.446 0.862 0.971 0.090 5.214-4.128 98.38 1367 28 0.1190 504.852 499.594 0.948 0.970 0.080 4.126-3.266 94.74 2603 46 0.1146 460.200 453.391 1.009 0.969 0.000 3.266-2.585 99.86 5447 97 0.1109 310.440 307.145 0.997 0.966 0.000 2.585-2.046 97.45 10613 204 0.0948 234.209 231.770 1.013 0.962 0.000 2.046-1.619 99.39 21536 464 0.0915 138.616 137.327 1.042 0.956 0.000 1.619-1.281 98.00 42464 925 0.0974 74.623 73.924 1.049 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1645 40.032 38.358 1.053 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0949 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1362 | n_water=879 | time (s): 2.970 (total time: 2.970) Filter (dist) r_work=0.1197 r_free=0.1362 | n_water=878 | time (s): 109.710 (total time: 112.680) Filter (q & B) r_work=0.1197 r_free=0.1362 | n_water=867 | time (s): 4.650 (total time: 117.330) Compute maps r_work=0.1197 r_free=0.1362 | n_water=867 | time (s): 2.180 (total time: 119.510) Filter (map) r_work=0.1219 r_free=0.1356 | n_water=743 | time (s): 5.650 (total time: 125.160) Find peaks r_work=0.1219 r_free=0.1356 | n_water=743 | time (s): 0.710 (total time: 125.870) Add new water r_work=0.1229 r_free=0.1377 | n_water=952 | time (s): 4.050 (total time: 129.920) Refine new water occ: r_work=0.1195 r_free=0.1348 adp: r_work=0.1195 r_free=0.1348 occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1191 r_free=0.1346 adp: r_work=0.1191 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1346 r_work=0.1191 r_free=0.1346 | n_water=952 | time (s): 198.830 (total time: 328.750) Filter (q & B) r_work=0.1195 r_free=0.1348 | n_water=887 | time (s): 4.960 (total time: 333.710) Filter (dist only) r_work=0.1196 r_free=0.1348 | n_water=885 | time (s): 115.980 (total time: 449.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.563283 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.145022 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1355 0.0156 0.037 1.1 6.1 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.55 1.56 1.760 14.035 15.145 3.762 12.00 13.57 1.58 1.841 14.001 15.145 3.759 Individual atomic B min max mean iso aniso Overall: 5.56 66.29 14.85 0.92 520 3269 Protein: 5.56 30.24 10.52 0.92 0 2902 Water: 5.93 66.29 29.06 N/A 520 365 Other: 13.80 24.64 19.22 N/A 0 2 Chain A: 5.62 52.49 12.42 N/A 0 1623 Chain B: 5.56 66.29 12.25 N/A 0 1646 Chain S: 5.93 60.70 30.68 N/A 520 0 Histogram: Values Number of atoms 5.56 - 11.63 2120 11.63 - 17.70 761 17.70 - 23.78 287 23.78 - 29.85 214 29.85 - 35.92 171 35.92 - 42.00 134 42.00 - 48.07 69 48.07 - 54.14 26 54.14 - 60.22 4 60.22 - 66.29 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757915 | | target function (ml) not normalized (work): 703827.407891 | | target function (ml) not normalized (free): 14738.307647 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1416 0.1415 0.1481 n_refl.: 191133 remove outliers: r(all,work,free)=0.1416 0.1415 0.1481 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1409 0.1408 0.1477 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1350 n_refl.: 191133 remove outliers: r(all,work,free)=0.1199 0.1196 0.1350 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3635 360.154 329.826 0.414 0.971 0.236 13.296-10.522 98.02 98 1 0.2390 487.082 468.018 0.684 0.973 0.162 10.503-8.327 98.35 176 3 0.2217 502.886 494.565 0.832 0.973 0.133 8.315-6.595 100.00 359 8 0.2168 374.668 370.206 0.865 0.972 0.116 6.588-5.215 100.00 711 7 0.1959 345.152 334.466 0.862 0.972 0.100 5.214-4.128 98.38 1367 28 0.1209 504.852 499.163 0.944 0.971 0.039 4.126-3.266 94.74 2603 46 0.1164 460.200 453.001 1.009 0.970 0.000 3.266-2.585 99.86 5447 97 0.1116 310.440 307.046 0.997 0.968 0.000 2.585-2.046 97.45 10613 204 0.0953 234.209 231.634 1.012 0.964 0.000 2.046-1.619 99.39 21536 464 0.0910 138.616 137.304 1.041 0.958 0.000 1.619-1.281 98.00 42464 925 0.0966 74.623 73.919 1.047 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1639 40.032 38.362 1.051 0.932 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1097 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1350 | n_water=885 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1196 r_free=0.1350 | n_water=884 | time (s): 113.770 (total time: 116.970) Filter (q & B) r_work=0.1197 r_free=0.1350 | n_water=875 | time (s): 4.450 (total time: 121.420) Compute maps r_work=0.1197 r_free=0.1350 | n_water=875 | time (s): 1.810 (total time: 123.230) Filter (map) r_work=0.1218 r_free=0.1343 | n_water=755 | time (s): 4.800 (total time: 128.030) Find peaks r_work=0.1218 r_free=0.1343 | n_water=755 | time (s): 0.670 (total time: 128.700) Add new water r_work=0.1227 r_free=0.1361 | n_water=967 | time (s): 4.880 (total time: 133.580) Refine new water occ: r_work=0.1193 r_free=0.1340 adp: r_work=0.1194 r_free=0.1340 occ: r_work=0.1191 r_free=0.1339 adp: r_work=0.1191 r_free=0.1339 occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1190 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1338 r_work=0.1190 r_free=0.1338 | n_water=967 | time (s): 191.410 (total time: 324.990) Filter (q & B) r_work=0.1194 r_free=0.1345 | n_water=899 | time (s): 5.530 (total time: 330.520) Filter (dist only) r_work=0.1194 r_free=0.1345 | n_water=898 | time (s): 122.590 (total time: 453.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544895 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.372957 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1349 0.0152 0.038 1.1 7.8 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.49 1.52 1.732 13.971 14.373 3.759 12.00 13.53 1.53 1.799 13.944 14.373 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 65.29 14.83 0.89 533 3269 Protein: 5.57 28.97 10.45 0.89 0 2902 Water: 6.03 65.29 28.94 N/A 533 365 Other: 13.83 22.85 18.34 N/A 0 2 Chain A: 5.63 52.11 12.32 N/A 0 1623 Chain B: 5.57 65.29 12.16 N/A 0 1646 Chain S: 6.03 60.77 30.66 N/A 533 0 Histogram: Values Number of atoms 5.57 - 11.55 2101 11.55 - 17.52 784 17.52 - 23.49 276 23.49 - 29.46 220 29.46 - 35.43 174 35.43 - 41.40 133 41.40 - 47.37 75 47.37 - 53.34 28 53.34 - 59.31 8 59.31 - 65.29 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1353 r_work=0.1200 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1353 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1354 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757173 | | target function (ml) not normalized (work): 703684.705023 | | target function (ml) not normalized (free): 14738.280862 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1354 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1416 0.1415 0.1494 n_refl.: 191132 remove outliers: r(all,work,free)=0.1416 0.1415 0.1494 n_refl.: 191132 overall B=-0.20 to atoms: r(all,work,free)=0.1383 0.1381 0.1471 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1354 n_refl.: 191132 remove outliers: r(all,work,free)=0.1200 0.1197 0.1354 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3612 356.047 328.719 0.422 0.971 0.236 13.296-10.522 97.03 97 1 0.2387 481.282 465.182 0.702 0.972 0.163 10.503-8.327 98.35 176 3 0.2211 502.886 494.813 0.853 0.972 0.130 8.315-6.595 100.00 359 8 0.2137 374.668 369.888 0.884 0.972 0.108 6.588-5.215 100.00 711 7 0.1973 345.152 334.179 0.884 0.972 0.090 5.214-4.128 98.38 1367 28 0.1217 504.852 499.294 0.969 0.971 0.034 4.126-3.266 94.74 2603 46 0.1165 460.200 453.047 1.036 0.970 0.000 3.266-2.585 99.86 5447 97 0.1125 310.440 307.104 1.020 0.968 0.000 2.585-2.046 97.45 10613 204 0.0955 234.209 231.618 1.032 0.964 0.000 2.046-1.619 99.39 21536 464 0.0910 138.616 137.297 1.055 0.959 0.000 1.619-1.281 98.00 42464 925 0.0963 74.623 73.917 1.054 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1639 40.032 38.354 1.042 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0443 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1354 | n_water=898 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1198 r_free=0.1354 | n_water=896 | time (s): 113.310 (total time: 115.880) Filter (q & B) r_work=0.1198 r_free=0.1354 | n_water=884 | time (s): 5.220 (total time: 121.100) Compute maps r_work=0.1198 r_free=0.1354 | n_water=884 | time (s): 1.750 (total time: 122.850) Filter (map) r_work=0.1222 r_free=0.1354 | n_water=747 | time (s): 5.410 (total time: 128.260) Find peaks r_work=0.1222 r_free=0.1354 | n_water=747 | time (s): 0.880 (total time: 129.140) Add new water r_work=0.1231 r_free=0.1369 | n_water=964 | time (s): 5.310 (total time: 134.450) Refine new water occ: r_work=0.1196 r_free=0.1347 adp: r_work=0.1197 r_free=0.1347 occ: r_work=0.1194 r_free=0.1346 adp: r_work=0.1194 r_free=0.1346 occ: r_work=0.1193 r_free=0.1346 adp: r_work=0.1192 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1346 r_work=0.1192 r_free=0.1346 | n_water=964 | time (s): 225.960 (total time: 360.410) Filter (q & B) r_work=0.1196 r_free=0.1356 | n_water=896 | time (s): 5.030 (total time: 365.440) Filter (dist only) r_work=0.1197 r_free=0.1355 | n_water=894 | time (s): 116.410 (total time: 481.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.571057 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.949948 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1361 0.0162 0.038 1.1 7.8 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.61 1.62 1.707 13.697 13.950 3.759 12.02 13.64 1.62 1.743 13.680 13.950 3.758 Individual atomic B min max mean iso aniso Overall: 5.43 64.02 14.56 0.87 529 3269 Protein: 5.43 28.08 10.24 0.87 0 2902 Water: 5.82 64.02 28.58 N/A 529 365 Other: 13.69 22.13 17.91 N/A 0 2 Chain A: 5.47 51.57 12.08 N/A 0 1623 Chain B: 5.43 64.02 11.93 N/A 0 1646 Chain S: 5.82 60.69 30.38 N/A 529 0 Histogram: Values Number of atoms 5.43 - 11.29 2077 11.29 - 17.15 805 17.15 - 23.01 280 23.01 - 28.87 207 28.87 - 34.73 171 34.73 - 40.59 133 40.59 - 46.44 85 46.44 - 52.30 30 52.30 - 58.16 7 58.16 - 64.02 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1364 r_work=0.1202 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1365 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757454 | | target function (ml) not normalized (work): 703729.786806 | | target function (ml) not normalized (free): 14741.287981 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1363 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1485 n_refl.: 191130 remove outliers: r(all,work,free)=0.1395 0.1393 0.1485 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1395 0.1393 0.1485 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3650 356.047 324.081 0.405 0.970 0.221 13.296-10.522 97.03 97 1 0.2411 481.282 460.571 0.691 0.972 0.155 10.503-8.327 98.35 176 3 0.2207 502.886 494.125 0.847 0.972 0.129 8.315-6.595 100.00 359 8 0.2158 374.668 369.604 0.877 0.972 0.100 6.588-5.215 100.00 711 7 0.1991 345.152 333.749 0.880 0.973 0.100 5.214-4.128 98.38 1367 28 0.1233 504.852 498.932 0.964 0.973 0.034 4.126-3.266 94.74 2603 46 0.1172 460.200 452.768 1.028 0.975 0.005 3.266-2.585 99.86 5447 97 0.1129 310.440 306.898 1.010 0.975 0.000 2.585-2.046 97.45 10613 204 0.0961 234.209 231.552 1.016 0.977 0.000 2.046-1.619 99.39 21536 464 0.0911 138.616 137.240 1.031 0.981 0.000 1.619-1.281 98.00 42464 925 0.0950 74.623 73.955 1.017 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.032 38.337 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0864 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1356 | n_water=894 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1195 r_free=0.1356 | n_water=893 | time (s): 116.090 (total time: 118.600) Filter (q & B) r_work=0.1195 r_free=0.1355 | n_water=882 | time (s): 5.290 (total time: 123.890) Compute maps r_work=0.1195 r_free=0.1355 | n_water=882 | time (s): 1.750 (total time: 125.640) Filter (map) r_work=0.1219 r_free=0.1351 | n_water=757 | time (s): 4.600 (total time: 130.240) Find peaks r_work=0.1219 r_free=0.1351 | n_water=757 | time (s): 0.650 (total time: 130.890) Add new water r_work=0.1227 r_free=0.1366 | n_water=963 | time (s): 4.960 (total time: 135.850) Refine new water occ: r_work=0.1194 r_free=0.1345 adp: r_work=0.1194 r_free=0.1345 occ: r_work=0.1192 r_free=0.1344 adp: r_work=0.1192 r_free=0.1344 occ: r_work=0.1191 r_free=0.1345 adp: r_work=0.1191 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1344 r_work=0.1191 r_free=0.1344 | n_water=963 | time (s): 188.130 (total time: 323.980) Filter (q & B) r_work=0.1194 r_free=0.1350 | n_water=897 | time (s): 4.170 (total time: 328.150) Filter (dist only) r_work=0.1195 r_free=0.1349 | n_water=895 | time (s): 117.390 (total time: 445.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.563287 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.181916 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1358 0.0160 0.039 1.1 5.8 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.58 1.60 1.669 13.643 14.182 3.758 11.98 13.58 1.60 1.682 13.636 14.182 3.755 Individual atomic B min max mean iso aniso Overall: 5.47 62.85 14.53 0.86 530 3269 Protein: 5.47 27.85 10.25 0.86 0 2902 Water: 5.88 62.85 28.40 N/A 530 365 Other: 13.71 22.03 17.87 N/A 0 2 Chain A: 5.50 51.10 12.06 N/A 0 1623 Chain B: 5.47 62.85 11.92 N/A 0 1646 Chain S: 5.88 60.77 30.26 N/A 530 0 Histogram: Values Number of atoms 5.47 - 11.21 2055 11.21 - 16.94 826 16.94 - 22.68 275 22.68 - 28.42 203 28.42 - 34.16 175 34.16 - 39.90 133 39.90 - 45.63 89 45.63 - 51.37 32 51.37 - 57.11 8 57.11 - 62.85 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1359 r_work=0.1199 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1359 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1360 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755233 | | target function (ml) not normalized (work): 703313.910708 | | target function (ml) not normalized (free): 14738.083855 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1360 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1493 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1401 0.1493 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1403 0.1401 0.1493 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3723 356.047 322.159 0.394 0.971 0.217 13.296-10.522 97.03 97 1 0.2454 481.282 460.920 0.683 0.972 0.158 10.503-8.327 98.35 176 3 0.2215 502.886 494.011 0.839 0.973 0.133 8.315-6.595 100.00 359 8 0.2181 374.668 370.027 0.868 0.972 0.090 6.588-5.215 100.00 711 7 0.2007 345.152 333.533 0.869 0.973 0.075 5.214-4.128 98.38 1367 28 0.1258 504.852 498.615 0.958 0.974 0.039 4.126-3.266 94.74 2603 46 0.1181 460.200 452.595 1.022 0.975 0.005 3.266-2.585 99.86 5447 97 0.1133 310.440 306.851 1.003 0.976 0.000 2.585-2.046 97.45 10613 204 0.0965 234.209 231.525 1.010 0.978 0.000 2.046-1.619 99.39 21536 464 0.0908 138.616 137.266 1.025 0.982 0.000 1.619-1.281 98.00 42464 925 0.0946 74.623 73.963 1.012 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.032 38.328 0.978 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0503 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1196 r_free=0.1361 After: r_work=0.1197 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1197 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1361 | n_water=895 | time (s): 2.860 (total time: 2.860) Filter (dist) r_work=0.1197 r_free=0.1362 | n_water=894 | time (s): 120.350 (total time: 123.210) Filter (q & B) r_work=0.1197 r_free=0.1361 | n_water=886 | time (s): 4.580 (total time: 127.790) Compute maps r_work=0.1197 r_free=0.1361 | n_water=886 | time (s): 1.850 (total time: 129.640) Filter (map) r_work=0.1222 r_free=0.1357 | n_water=757 | time (s): 5.030 (total time: 134.670) Find peaks r_work=0.1222 r_free=0.1357 | n_water=757 | time (s): 0.660 (total time: 135.330) Add new water r_work=0.1229 r_free=0.1370 | n_water=966 | time (s): 4.330 (total time: 139.660) Refine new water occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1195 r_free=0.1349 occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1193 r_free=0.1350 occ: r_work=0.1191 r_free=0.1350 adp: r_work=0.1191 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1350 r_work=0.1191 r_free=0.1350 | n_water=966 | time (s): 274.260 (total time: 413.920) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=902 | time (s): 4.410 (total time: 418.330) Filter (dist only) r_work=0.1195 r_free=0.1355 | n_water=899 | time (s): 116.100 (total time: 534.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.534307 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.582558 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1359 0.0163 0.039 1.1 9.5 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.59 1.63 1.666 13.634 14.583 3.757 11.96 13.60 1.65 1.659 13.635 14.583 3.755 Individual atomic B min max mean iso aniso Overall: 5.46 62.46 14.53 0.86 534 3269 Protein: 5.46 27.90 10.28 0.86 0 2902 Water: 5.93 62.46 28.24 N/A 534 365 Other: 13.71 22.06 17.89 N/A 0 2 Chain A: 5.56 50.94 12.05 N/A 0 1623 Chain B: 5.46 62.46 11.92 N/A 0 1646 Chain S: 5.93 60.79 30.08 N/A 534 0 Histogram: Values Number of atoms 5.46 - 11.16 2035 11.16 - 16.86 837 16.86 - 22.56 289 22.56 - 28.26 201 28.26 - 33.96 171 33.96 - 39.66 138 39.66 - 45.36 86 45.36 - 51.06 35 51.06 - 56.76 8 56.76 - 62.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1360 r_work=0.1196 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1361 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754510 | | target function (ml) not normalized (work): 703178.415298 | | target function (ml) not normalized (free): 14729.461226 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1370 0.1515 5.7003 5.8106| | 2: 2.94 - 2.33 1.00 7339 128 0.1078 0.1348 5.094 5.1825| | 3: 2.33 - 2.04 0.96 6939 150 0.0903 0.1169 4.6558 4.7437| | 4: 2.04 - 1.85 1.00 7170 155 0.0896 0.1051 4.3901 4.5616| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0995 4.1506 4.2496| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1062 3.9459 4.0677| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0966 3.7962 3.9259| | 8: 1.54 - 1.47 0.96 6798 152 0.0891 0.1331 3.6985 3.9014| | 9: 1.47 - 1.41 0.98 6938 155 0.0924 0.1128 3.6202 3.7511| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1169 3.5547 3.6738| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1122 3.4828 3.5876| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1128 3.459 3.5778| | 13: 1.28 - 1.25 0.98 6907 166 0.1043 0.1254 3.4372 3.5662| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1595 3.432 3.6844| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1243 3.4479 3.4892| | 16: 1.19 - 1.17 0.93 6604 132 0.1252 0.1551 3.4653 3.6595| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1232 3.433 3.4441| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1707 3.4384 3.5321| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1742 3.4189 3.5935| | 20: 1.10 - 1.08 0.97 6884 147 0.1580 0.1575 3.409 3.4326| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2125 3.4174 3.5042| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1942 3.4124 3.4115| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2014 3.4323 3.482| | 24: 1.03 - 1.02 0.96 6784 133 0.2329 0.2249 3.4351 3.5088| | 25: 1.02 - 1.01 0.93 6552 130 0.2610 0.2515 3.4483 3.5258| | 26: 1.01 - 0.99 0.96 6767 158 0.2754 0.2859 3.415 3.4221| | 27: 0.99 - 0.98 0.94 6647 131 0.3036 0.2787 3.4684 3.394| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.92 12.34 1.00 0.97 12123.06| | 2: 2.94 - 2.33 7339 128 0.92 13.28 0.99 0.97 5430.49| | 3: 2.33 - 2.04 6939 150 0.96 7.60 1.01 0.97 1695.26| | 4: 2.04 - 1.85 7170 155 0.96 7.61 1.00 0.98 998.41| | 5: 1.85 - 1.72 7113 159 0.96 8.07 1.00 0.98 633.68| | 6: 1.72 - 1.62 7102 142 0.96 7.97 1.00 0.98 440.44| | 7: 1.62 - 1.54 7104 148 0.96 8.13 1.01 0.99 334.95| | 8: 1.54 - 1.47 6798 152 0.96 8.25 1.01 0.99 277.87| | 9: 1.47 - 1.41 6938 155 0.96 8.42 1.00 1.00 230.20| | 10: 1.41 - 1.36 7022 150 0.96 8.87 1.00 0.99 201.63| | 11: 1.36 - 1.32 6997 151 0.96 8.88 0.99 0.98 173.95| | 12: 1.32 - 1.28 6975 149 0.96 8.94 0.98 0.97 159.88| | 13: 1.28 - 1.25 6907 166 0.96 9.51 1.01 0.98 157.67| | 14: 1.25 - 1.22 7015 112 0.95 10.71 1.01 0.99 162.89| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 1.00 166.81| | 16: 1.19 - 1.17 6604 132 0.95 11.45 1.01 0.98 160.59| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.98 154.38| | 18: 1.14 - 1.12 6875 142 0.94 12.75 1.01 0.97 147.77| | 19: 1.12 - 1.10 6948 106 0.93 14.12 1.00 0.97 150.90| | 20: 1.10 - 1.08 6884 147 0.92 15.17 1.00 0.96 149.66| | 21: 1.08 - 1.07 6852 152 0.91 16.57 1.00 0.95 152.39| | 22: 1.07 - 1.05 6836 135 0.90 18.19 0.99 0.95 153.79| | 23: 1.05 - 1.03 6827 159 0.88 20.39 0.99 0.94 163.62| | 24: 1.03 - 1.02 6784 133 0.85 23.07 0.99 0.95 178.28| | 25: 1.02 - 1.01 6552 130 0.83 25.07 0.97 0.92 181.44| | 26: 1.01 - 0.99 6767 158 0.81 26.52 0.98 0.90 175.80| | 27: 0.99 - 0.98 6647 131 0.82 26.13 0.98 0.89 159.75| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 147.77 max = 12123.06 mean = 972.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.30| |phase err.(test): min = 0.00 max = 89.90 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1361 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1410 0.1409 0.1504 n_refl.: 191130 remove outliers: r(all,work,free)=0.1410 0.1409 0.1504 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1410 0.1409 0.1504 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3678 356.047 324.333 0.418 0.908 0.210 13.296-10.522 97.03 97 1 0.2444 481.282 460.069 0.720 0.910 0.142 10.503-8.327 98.35 176 3 0.2200 502.886 494.712 0.898 0.910 0.115 8.315-6.595 100.00 359 8 0.2137 374.668 369.867 0.929 0.910 0.100 6.588-5.215 100.00 711 7 0.1999 345.152 333.500 0.931 0.910 0.087 5.214-4.128 98.38 1367 28 0.1254 504.852 498.745 1.023 0.911 0.034 4.126-3.266 94.74 2603 46 0.1176 460.200 452.474 1.093 0.913 0.000 3.266-2.585 99.86 5447 97 0.1126 310.440 306.970 1.073 0.914 0.000 2.585-2.046 97.45 10613 204 0.0964 234.209 231.569 1.080 0.916 0.000 2.046-1.619 99.39 21536 464 0.0909 138.616 137.257 1.096 0.921 0.000 1.619-1.281 98.00 42464 925 0.0945 74.623 73.971 1.084 0.927 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.032 38.323 1.048 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0186 ================= 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 : 0.2031 0.1990 0.081 5.213 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1932 0.081 5.213 5.2 78.0 14.6 805 0.000 1_settarget: 0.1797 0.1932 0.081 5.213 5.2 78.0 14.6 805 0.000 1_nqh: 0.1797 0.1932 0.081 5.213 5.2 78.0 14.6 805 0.000 1_weight: 0.1797 0.1932 0.081 5.213 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1499 0.040 1.153 5.2 78.0 14.6 805 0.157 1_adp: 0.1298 0.1572 0.040 1.153 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1297 0.1566 0.040 1.153 5.2 73.0 15.0 805 0.157 1_occ: 0.1283 0.1555 0.040 1.153 5.2 73.0 15.0 805 0.157 2_bss: 0.1275 0.1547 0.040 1.153 5.3 73.2 15.2 805 0.157 2_settarget: 0.1275 0.1547 0.040 1.153 5.3 73.2 15.2 805 0.157 2_updatecdl: 0.1275 0.1547 0.040 1.171 5.3 73.2 15.2 805 0.157 2_nqh: 0.1275 0.1547 0.040 1.171 5.3 73.2 15.2 805 0.157 2_sol: 0.1271 0.1518 0.040 1.171 5.3 73.2 16.1 873 n/a 2_weight: 0.1271 0.1518 0.040 1.171 5.3 73.2 16.1 873 n/a 2_xyzrec: 0.1256 0.1532 0.042 1.141 5.3 73.2 16.1 873 n/a 2_adp: 0.1233 0.1519 0.042 1.141 5.4 70.5 16.3 873 n/a 2_regHadp: 0.1233 0.1519 0.042 1.141 5.4 70.5 16.3 873 n/a 2_occ: 0.1227 0.1514 0.042 1.141 5.4 70.5 16.3 873 n/a 3_bss: 0.1234 0.1521 0.042 1.141 5.3 70.5 16.2 873 n/a 3_settarget: 0.1234 0.1521 0.042 1.141 5.3 70.5 16.2 873 n/a 3_updatecdl: 0.1234 0.1521 0.042 1.145 5.3 70.5 16.2 873 n/a 3_nqh: 0.1234 0.1521 0.042 1.145 5.3 70.5 16.2 873 n/a 3_sol: 0.1246 0.1519 0.042 1.145 5.3 68.2 15.4 873 n/a 3_weight: 0.1246 0.1519 0.042 1.145 5.3 68.2 15.4 873 n/a 3_xyzrec: 0.1238 0.1443 0.035 1.096 5.3 68.2 15.4 873 n/a 3_adp: 0.1237 0.1403 0.035 1.096 5.5 67.7 15.2 873 n/a 3_regHadp: 0.1238 0.1404 0.035 1.096 5.5 67.7 15.2 873 n/a 3_occ: 0.1232 0.1396 0.035 1.096 5.5 67.7 15.2 873 n/a 4_bss: 0.1227 0.1390 0.035 1.096 5.5 67.7 15.2 873 n/a 4_settarget: 0.1227 0.1390 0.035 1.096 5.5 67.7 15.2 873 n/a 4_updatecdl: 0.1227 0.1390 0.035 1.101 5.5 67.7 15.2 873 n/a 4_nqh: 0.1227 0.1390 0.035 1.101 5.5 67.7 15.2 873 n/a 4_sol: 0.1211 0.1378 0.035 1.101 5.5 67.7 15.0 860 n/a 4_weight: 0.1211 0.1378 0.035 1.101 5.5 67.7 15.0 860 n/a 4_xyzrec: 0.1209 0.1378 0.036 1.124 5.5 67.7 15.0 860 n/a 4_adp: 0.1199 0.1372 0.036 1.124 5.5 67.2 15.0 860 n/a 4_regHadp: 0.1199 0.1372 0.036 1.124 5.5 67.2 15.0 860 n/a 4_occ: 0.1198 0.1371 0.036 1.124 5.5 67.2 15.0 860 n/a 5_bss: 0.1197 0.1371 0.036 1.124 5.5 67.1 14.9 860 n/a 5_settarget: 0.1197 0.1371 0.036 1.124 5.5 67.1 14.9 860 n/a 5_updatecdl: 0.1197 0.1371 0.036 1.124 5.5 67.1 14.9 860 n/a 5_nqh: 0.1197 0.1371 0.036 1.124 5.5 67.1 14.9 860 n/a 5_sol: 0.1196 0.1358 0.036 1.124 5.5 67.1 15.0 879 n/a 5_weight: 0.1196 0.1358 0.036 1.124 5.5 67.1 15.0 879 n/a 5_xyzrec: 0.1199 0.1361 0.036 1.117 5.5 67.1 15.0 879 n/a 5_adp: 0.1203 0.1364 0.036 1.117 5.6 67.0 14.9 879 n/a 5_regHadp: 0.1204 0.1365 0.036 1.117 5.6 67.0 14.9 879 n/a 5_occ: 0.1202 0.1365 0.036 1.117 5.6 67.0 14.9 879 n/a 6_bss: 0.1197 0.1362 0.036 1.117 5.5 66.9 14.9 879 n/a 6_settarget: 0.1197 0.1362 0.036 1.117 5.5 66.9 14.9 879 n/a 6_updatecdl: 0.1197 0.1362 0.036 1.117 5.5 66.9 14.9 879 n/a 6_nqh: 0.1197 0.1362 0.036 1.117 5.5 66.9 14.9 879 n/a 6_sol: 0.1196 0.1348 0.036 1.117 5.5 66.9 14.9 885 n/a 6_weight: 0.1196 0.1348 0.036 1.117 5.5 66.9 14.9 885 n/a 6_xyzrec: 0.1198 0.1355 0.037 1.125 5.5 66.9 14.9 885 n/a 6_adp: 0.1200 0.1357 0.037 1.125 5.6 66.3 14.9 885 n/a 6_regHadp: 0.1200 0.1358 0.037 1.125 5.6 66.3 14.9 885 n/a 6_occ: 0.1198 0.1355 0.037 1.125 5.6 66.3 14.9 885 n/a 7_bss: 0.1196 0.1350 0.037 1.125 5.5 66.3 14.8 885 n/a 7_settarget: 0.1196 0.1350 0.037 1.125 5.5 66.3 14.8 885 n/a 7_updatecdl: 0.1196 0.1350 0.037 1.125 5.5 66.3 14.8 885 n/a 7_nqh: 0.1196 0.1350 0.037 1.125 5.5 66.3 14.8 885 n/a 7_sol: 0.1194 0.1345 0.037 1.125 5.5 66.3 14.9 898 n/a 7_weight: 0.1194 0.1345 0.037 1.125 5.5 66.3 14.9 898 n/a 7_xyzrec: 0.1197 0.1349 0.038 1.122 5.5 66.3 14.9 898 n/a 7_adp: 0.1200 0.1353 0.038 1.122 5.6 65.3 14.8 898 n/a 7_regHadp: 0.1200 0.1353 0.038 1.122 5.6 65.3 14.8 898 n/a 7_occ: 0.1198 0.1354 0.038 1.122 5.6 65.3 14.8 898 n/a 8_bss: 0.1197 0.1354 0.038 1.122 5.4 65.1 14.6 898 n/a 8_settarget: 0.1197 0.1354 0.038 1.122 5.4 65.1 14.6 898 n/a 8_updatecdl: 0.1197 0.1354 0.038 1.123 5.4 65.1 14.6 898 n/a 8_nqh: 0.1197 0.1354 0.038 1.123 5.4 65.1 14.6 898 n/a 8_sol: 0.1197 0.1355 0.038 1.123 5.4 65.1 14.6 894 n/a 8_weight: 0.1197 0.1355 0.038 1.123 5.4 65.1 14.6 894 n/a 8_xyzrec: 0.1200 0.1361 0.038 1.118 5.4 65.1 14.6 894 n/a 8_adp: 0.1202 0.1364 0.038 1.118 5.4 64.0 14.6 894 n/a 8_regHadp: 0.1202 0.1365 0.038 1.118 5.4 64.0 14.6 894 n/a 8_occ: 0.1201 0.1363 0.038 1.118 5.4 64.0 14.6 894 n/a 9_bss: 0.1195 0.1356 0.038 1.118 5.4 64.0 14.6 894 n/a 9_settarget: 0.1195 0.1356 0.038 1.118 5.4 64.0 14.6 894 n/a 9_updatecdl: 0.1195 0.1356 0.038 1.118 5.4 64.0 14.6 894 n/a 9_nqh: 0.1195 0.1356 0.038 1.118 5.4 64.0 14.6 894 n/a 9_sol: 0.1195 0.1349 0.038 1.118 5.4 64.0 14.5 895 n/a 9_weight: 0.1195 0.1349 0.038 1.118 5.4 64.0 14.5 895 n/a 9_xyzrec: 0.1198 0.1358 0.039 1.117 5.4 64.0 14.5 895 n/a 9_adp: 0.1199 0.1359 0.039 1.117 5.5 62.8 14.5 895 n/a 9_regHadp: 0.1199 0.1359 0.039 1.117 5.5 62.8 14.5 895 n/a 9_occ: 0.1197 0.1360 0.039 1.117 5.5 62.8 14.5 895 n/a 10_bss: 0.1196 0.1361 0.039 1.117 5.5 62.8 14.5 895 n/a 10_settarget: 0.1196 0.1361 0.039 1.117 5.5 62.8 14.5 895 n/a 10_updatecdl: 0.1196 0.1361 0.039 1.118 5.5 62.8 14.5 895 n/a 10_setrh: 0.1197 0.1361 0.039 1.118 5.5 62.8 14.5 895 n/a 10_nqh: 0.1197 0.1361 0.039 1.118 5.5 62.8 14.5 895 n/a 10_sol: 0.1195 0.1355 0.039 1.118 5.5 62.8 14.5 899 n/a 10_weight: 0.1195 0.1355 0.039 1.118 5.5 62.8 14.5 899 n/a 10_xyzrec: 0.1196 0.1359 0.039 1.147 5.5 62.8 14.5 899 n/a 10_adp: 0.1196 0.1360 0.039 1.147 5.5 62.5 14.5 899 n/a 10_regHadp: 0.1196 0.1360 0.039 1.147 5.5 62.5 14.5 899 n/a 10_occ: 0.1195 0.1361 0.039 1.147 5.5 62.5 14.5 899 n/a end: 0.1194 0.1358 0.039 1.147 5.5 62.5 14.5 899 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1750626_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1750626_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3600 Refinement macro-cycles (run) : 12210.7100 Write final files (write_after_run_outputs) : 152.8300 Total : 12369.9000 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:18 PST -0800 (1736736198.47 s) Start R-work = 0.1797, R-free = 0.1932 Final R-work = 0.1194, R-free = 0.1358 =============================================================================== Job complete usr+sys time: 12633.84 seconds wall clock time: 211 minutes 33.20 seconds (12693.20 seconds total)