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_2303751.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2303751.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2303751.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } 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: 1.53, per 1000 atoms: 0.23 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: 2.596 distance_ideal: 2.720 ideal - model: 0.124 slack: 0.000 delta_slack: 0.124 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: 2.745 distance_ideal: 2.710 ideal - model: -0.035 slack: 0.000 delta_slack: -0.035 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: 0.68 Conformation dependent library (CDL) restraints added in 157.5 milliseconds Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.01: 636 1.01 - 1.24: 2610 1.24 - 1.47: 1439 1.47 - 1.71: 1225 1.71 - 1.94: 24 Bond restraints: 5934 Sorted by residual: bond pdb=" C VAL B 7 " pdb=" O VAL B 7 " ideal model delta sigma weight residual 1.237 1.012 0.225 1.08e-02 8.57e+03 4.35e+02 bond pdb=" N SER A 13 " pdb=" H SER A 13 " ideal model delta sigma weight residual 0.860 1.247 -0.387 2.00e-02 2.50e+03 3.74e+02 bond pdb=" CA ASP B 56 " pdb=" HA ASP B 56 " ideal model delta sigma weight residual 0.970 1.356 -0.386 2.00e-02 2.50e+03 3.72e+02 bond pdb=" C VAL A 19 " pdb=" O VAL A 19 " ideal model delta sigma weight residual 1.236 1.473 -0.237 1.23e-02 6.61e+03 3.71e+02 bond pdb=" CD2 LEU B 171 " pdb="HD21 LEU B 171 " ideal model delta sigma weight residual 0.970 1.329 -0.359 2.00e-02 2.50e+03 3.21e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.91: 6485 4.91 - 9.81: 3446 9.81 - 14.72: 800 14.72 - 19.63: 76 19.63 - 24.53: 3 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ASP B 170 " pdb=" C ASP B 170 " pdb=" N LEU B 171 " ideal model delta sigma weight residual 122.12 139.39 -17.27 1.06e+00 8.90e-01 2.66e+02 angle pdb=" O THR B 21 " pdb=" C THR B 21 " pdb=" N ILE B 22 " ideal model delta sigma weight residual 122.09 138.41 -16.32 1.04e+00 9.25e-01 2.46e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.22 131.96 -9.74 6.50e-01 2.37e+00 2.25e+02 angle pdb=" O PHE B 127 " pdb=" C PHE B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 121.47 132.66 -11.19 7.80e-01 1.64e+00 2.06e+02 angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 119.20 131.99 -12.79 9.00e-01 1.23e+00 2.02e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1849 16.75 - 33.50: 131 33.50 - 50.25: 44 50.25 - 67.00: 22 67.00 - 83.74: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP A 139 " pdb=" C TRP A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+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 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 157.77 22.23 0 5.00e+00 4.00e-02 1.98e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.256: 224 0.256 - 0.511: 172 0.511 - 0.765: 69 0.765 - 1.020: 21 1.020 - 1.275: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB VAL A 112 " pdb=" CA VAL A 112 " pdb=" CG1 VAL A 112 " pdb=" CG2 VAL A 112 " both_signs ideal model delta sigma weight residual False -2.63 -1.35 -1.28 2.00e-01 2.50e+01 4.07e+01 chirality pdb=" CA ALA A 10 " pdb=" N ALA A 10 " pdb=" C ALA A 10 " pdb=" CB ALA A 10 " both_signs ideal model delta sigma weight residual False 2.48 3.65 -1.16 2.00e-01 2.50e+01 3.38e+01 chirality pdb=" CA VAL A 112 " pdb=" N VAL A 112 " pdb=" C VAL A 112 " pdb=" CB VAL A 112 " both_signs ideal model delta sigma weight residual False 2.44 1.35 1.09 2.00e-01 2.50e+01 2.99e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.021 2.00e-02 2.50e+03 7.51e-02 1.69e+02 pdb=" CG PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.100 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.046 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.163 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 82 " -0.040 2.00e-02 2.50e+03 6.90e-02 1.43e+02 pdb=" CG PHE A 82 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A 82 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE A 82 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 PHE A 82 " -0.112 2.00e-02 2.50e+03 pdb=" CE2 PHE A 82 " 0.072 2.00e-02 2.50e+03 pdb=" CZ PHE A 82 " -0.056 2.00e-02 2.50e+03 pdb=" HD1 PHE A 82 " 0.126 2.00e-02 2.50e+03 pdb=" HD2 PHE A 82 " 0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 82 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 82 " 0.060 2.00e-02 2.50e+03 pdb=" HZ PHE A 82 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 195 " 0.082 2.00e-02 2.50e+03 6.75e-02 1.37e+02 pdb=" CG TYR A 195 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 195 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR A 195 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR A 195 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR A 195 " -0.080 2.00e-02 2.50e+03 pdb=" CZ TYR A 195 " -0.062 2.00e-02 2.50e+03 pdb=" OH TYR A 195 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 TYR A 195 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 TYR A 195 " -0.064 2.00e-02 2.50e+03 pdb=" HE1 TYR A 195 " 0.114 2.00e-02 2.50e+03 pdb=" HE2 TYR A 195 " 0.106 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.79 - 1.55: 18 1.55 - 2.31: 1829 2.31 - 3.08: 21717 3.08 - 3.84: 33250 3.84 - 4.60: 53466 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110280 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.788 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.927 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.942 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.109 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.112 2.620 ... (remaining 110275 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_2303751_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= 0.2037 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299131 | | target function (ml) not normalized (work): 805283.218192 | | target function (ml) not normalized (free): 16492.644813 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2136 0.1860 6.6893 6.2941| | 2: 2.94 - 2.33 1.00 7339 128 0.1622 0.1612 5.5172 5.5579| | 3: 2.33 - 2.04 0.96 6939 150 0.1638 0.1417 5.142 5.0211| | 4: 2.04 - 1.85 1.00 7170 155 0.1771 0.1475 4.973 4.9454| | 5: 1.85 - 1.72 0.99 7113 159 0.1929 0.1710 4.7996 4.8034| | 6: 1.72 - 1.62 0.99 7102 142 0.1988 0.1890 4.6655 4.69| | 7: 1.62 - 1.54 0.99 7104 148 0.2018 0.1847 4.5584 4.5626| | 8: 1.54 - 1.47 0.96 6798 152 0.2058 0.2143 4.4782 4.484| | 9: 1.47 - 1.41 0.98 6938 155 0.2092 0.2151 4.3934 4.3878| | 10: 1.41 - 1.36 0.99 7022 150 0.2116 0.1898 4.2943 4.2653| | 11: 1.36 - 1.32 0.99 6997 151 0.2109 0.2184 4.232 4.2991| | 12: 1.32 - 1.28 0.98 6976 149 0.2073 0.2210 4.1732 4.2455| | 13: 1.28 - 1.25 0.98 6907 166 0.2061 0.2283 4.1393 4.2202| | 14: 1.25 - 1.22 0.98 7015 113 0.2124 0.2449 4.1016 4.3909| | 15: 1.22 - 1.19 0.98 6957 137 0.2111 0.1907 4.0617 3.9866| | 16: 1.19 - 1.17 0.93 6604 132 0.2098 0.2189 4.0073 4.0639| | 17: 1.17 - 1.14 0.98 6941 135 0.2158 0.1994 3.9463 4.0054| | 18: 1.14 - 1.12 0.98 6875 142 0.2211 0.2341 3.9109 3.9301| | 19: 1.12 - 1.10 0.97 6949 106 0.2262 0.2243 3.8614 3.9221| | 20: 1.10 - 1.08 0.97 6884 147 0.2310 0.2241 3.818 3.8317| | 21: 1.08 - 1.07 0.97 6852 152 0.2432 0.2369 3.7893 3.7169| | 22: 1.07 - 1.05 0.97 6838 135 0.2521 0.2287 3.7422 3.6876| | 23: 1.05 - 1.03 0.97 6829 159 0.2693 0.2564 3.7237 3.7905| | 24: 1.03 - 1.02 0.96 6785 133 0.2884 0.3101 3.7034 3.8824| | 25: 1.02 - 1.01 0.93 6552 130 0.3046 0.3088 3.6757 3.7099| | 26: 1.01 - 0.99 0.96 6767 158 0.3197 0.3578 3.6269 3.6788| | 27: 0.99 - 0.98 0.94 6648 131 0.3451 0.3408 3.6403 3.5989| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.28 0.91 0.96 34301.68| | 2: 2.94 - 2.33 7339 128 0.86 20.30 1.08 1.03 13952.47| | 3: 2.33 - 2.04 6939 150 0.94 10.59 1.11 1.07 3260.37| | 4: 2.04 - 1.85 7170 155 0.93 12.08 1.11 1.07 2356.76| | 5: 1.85 - 1.72 7113 159 0.92 14.78 1.12 1.07 1880.64| | 6: 1.72 - 1.62 7102 142 0.90 16.24 1.11 1.07 1561.42| | 7: 1.62 - 1.54 7104 148 0.89 17.31 1.11 1.06 1292.25| | 8: 1.54 - 1.47 6798 152 0.89 17.71 1.10 1.06 1062.32| | 9: 1.47 - 1.41 6938 155 0.89 18.10 1.10 1.06 893.43| | 10: 1.41 - 1.36 7022 150 0.88 18.97 1.09 1.04 765.80| | 11: 1.36 - 1.32 6997 151 0.88 19.70 1.08 1.04 715.15| | 12: 1.32 - 1.28 6976 149 0.87 20.64 1.08 1.03 688.44| | 13: 1.28 - 1.25 6907 166 0.86 21.36 1.07 1.04 685.17| | 14: 1.25 - 1.22 7015 113 0.85 22.30 1.08 1.03 647.91| | 15: 1.22 - 1.19 6957 137 0.85 21.99 1.07 1.03 593.61| | 16: 1.19 - 1.17 6604 132 0.87 21.05 1.07 1.02 514.02| | 17: 1.17 - 1.14 6941 135 0.86 21.25 1.08 1.02 445.87| | 18: 1.14 - 1.12 6875 142 0.86 20.95 1.08 1.00 389.52| | 19: 1.12 - 1.10 6949 106 0.87 21.09 1.08 1.00 352.19| | 20: 1.10 - 1.08 6884 147 0.86 21.22 1.06 0.99 313.33| | 21: 1.08 - 1.07 6852 152 0.86 21.66 1.06 1.00 291.93| | 22: 1.07 - 1.05 6838 135 0.84 23.55 1.06 0.99 293.35| | 23: 1.05 - 1.03 6829 159 0.81 26.83 1.05 0.98 321.51| | 24: 1.03 - 1.02 6785 133 0.76 30.78 1.05 0.96 350.16| | 25: 1.02 - 1.01 6552 130 0.74 32.72 1.03 0.93 348.45| | 26: 1.01 - 0.99 6767 158 0.72 34.47 1.03 0.90 326.94| | 27: 0.99 - 0.98 6648 131 0.73 33.84 1.03 0.89 295.71| |alpha: min = 0.89 max = 1.07 mean = 1.01| |beta: min = 291.93 max = 34301.68 mean = 2672.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.45| |phase err.(test): min = 0.00 max = 89.00 mean = 21.58| |-----------------------------------------------------------------------------| ----------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 0.248 2950 Z= 5.437 Angle : 5.122 17.272 4018 Z= 3.650 Chirality : 0.400 1.275 492 Planarity : 0.033 0.135 512 Dihedral : 12.859 83.744 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.29 % Allowed : 2.90 % Favored : 95.81 % Cbeta Deviations : 32.87 % 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: -2.60 (0.38), residues: 386 helix: -2.79 (0.31), residues: 144 sheet: -1.37 (0.52), residues: 86 loop : -0.50 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.017 ARG A 143 TYR 0.106 0.041 TYR B 194 PHE 0.121 0.039 PHE B 119 TRP 0.100 0.028 TRP B 139 HIS 0.062 0.028 HIS A 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.1940 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299131 | | target function (ml) not normalized (work): 805283.218192 | | target function (ml) not normalized (free): 16492.644813 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2035 0.2037 0.1940 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2035 0.2037 0.1940 n_refl.: 191155 remove outliers: r(all,work,free)=0.2035 0.2037 0.1940 n_refl.: 191145 overall B=-0.01 to atoms: r(all,work,free)=0.2033 0.2035 0.1939 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1804 0.1870 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1802 0.1869 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.4073 398.008 290.424 0.423 0.934 0.303 13.296-10.522 99.01 99 1 0.2510 528.187 519.100 0.762 0.935 0.256 10.503-8.327 98.90 177 3 0.2421 564.205 558.505 0.941 0.935 0.233 8.318-6.595 100.00 360 8 0.2490 414.736 401.822 0.940 0.935 0.165 6.588-5.215 100.00 711 7 0.2266 381.101 365.393 0.928 0.935 0.150 5.214-4.128 98.38 1367 28 0.1484 557.435 549.020 1.042 0.936 0.090 4.126-3.266 94.74 2603 46 0.1342 508.132 498.701 1.108 0.936 0.033 3.266-2.585 99.86 5447 97 0.1448 342.774 337.127 1.081 0.935 0.010 2.585-2.046 97.45 10613 204 0.1409 258.603 254.195 1.088 0.935 0.000 2.046-1.619 99.39 21536 464 0.1622 153.054 150.010 1.106 0.935 0.000 1.619-1.281 98.00 42464 925 0.1924 82.395 80.399 1.092 0.934 0.000 1.281-0.980 96.53 101826 2055 0.2319 44.202 41.948 1.078 0.932 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0365 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1802 r_free=0.1869 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 r_work=0.1803 r_free=0.1870 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.866937 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.190587 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 0.1267 0.1490 0.0223 0.037 1.2 11.2 0.0 0.0 0 11.433 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.67 14.90 2.23 1.117 13.097 577.191 0.018 12.91 15.58 2.67 1.193 13.284 577.191 0.017 Individual atomic B min max mean iso aniso Overall: 5.27 73.03 14.93 1.39 435 3274 Protein: 5.27 40.47 10.98 1.39 0 2902 Water: 6.34 73.03 29.13 N/A 435 370 Other: 16.10 29.89 22.99 N/A 0 2 Chain A: 5.31 60.24 12.99 N/A 0 1626 Chain B: 5.27 73.03 12.73 N/A 0 1648 Chain S: 12.23 62.95 30.48 N/A 435 0 Histogram: Values Number of atoms 5.27 - 12.04 2184 12.04 - 18.82 632 18.82 - 25.60 317 25.60 - 32.37 266 32.37 - 39.15 149 39.15 - 45.92 104 45.92 - 52.70 35 52.70 - 59.48 18 59.48 - 66.25 3 66.25 - 73.03 1 =========================== Idealize ADP of riding H ========================== r_work=0.1292 r_free=0.1558 r_work=0.1291 r_free=0.1553 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1291 r_free = 0.1553 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 = 0.1277 r_free = 0.1542 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1277 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015477 | | target function (ls_wunit_k1) not normalized (work): 2898.685953 | | target function (ls_wunit_k1) not normalized (free): 113.569644 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1282 0.1277 0.1542 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1466 0.1463 0.1623 n_refl.: 191136 remove outliers: r(all,work,free)=0.1466 0.1463 0.1623 n_refl.: 191136 overall B=0.14 to atoms: r(all,work,free)=0.1487 0.1485 0.1632 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1275 0.1269 0.1534 n_refl.: 191136 remove outliers: r(all,work,free)=0.1275 0.1269 0.1534 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3596 398.008 374.762 0.466 1.002 0.281 13.296-10.522 99.01 99 1 0.2083 528.187 522.594 0.713 1.004 0.255 10.503-8.327 98.90 177 3 0.1716 564.205 561.574 0.851 1.004 0.203 8.318-6.595 100.00 360 8 0.1730 414.736 412.485 0.873 1.003 0.150 6.588-5.215 100.00 711 7 0.1557 381.101 372.944 0.852 1.004 0.140 5.214-4.128 98.38 1367 28 0.0905 557.435 554.836 0.939 1.004 0.059 4.126-3.266 94.74 2603 46 0.0833 508.132 504.151 1.002 1.005 0.018 3.266-2.585 99.86 5447 97 0.0925 342.774 340.292 0.984 1.004 0.000 2.585-2.046 97.45 10613 204 0.0947 258.603 256.393 0.996 1.005 0.000 2.046-1.619 99.39 21536 464 0.1081 153.054 151.414 1.013 1.005 0.000 1.619-1.281 98.00 42464 925 0.1269 82.395 81.428 1.006 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1867 44.202 42.158 0.983 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0326 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1269 r_free=0.1534 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1269 r_free=0.1534 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1269 r_free=0.1534 | n_water=805 | time (s): 3.350 (total time: 3.350) Filter (dist) r_work=0.1274 r_free=0.1540 | n_water=795 | time (s): 97.800 (total time: 101.150) Filter (q & B) r_work=0.1274 r_free=0.1539 | n_water=791 | time (s): 4.950 (total time: 106.100) Compute maps r_work=0.1274 r_free=0.1539 | n_water=791 | time (s): 1.680 (total time: 107.780) Filter (map) r_work=0.1298 r_free=0.1523 | n_water=661 | time (s): 4.220 (total time: 112.000) Find peaks r_work=0.1298 r_free=0.1523 | n_water=661 | time (s): 0.920 (total time: 112.920) Add new water r_work=0.1321 r_free=0.1552 | n_water=960 | time (s): 4.490 (total time: 117.410) Refine new water occ: r_work=0.1279 r_free=0.1516 adp: r_work=0.1266 r_free=0.1506 occ: r_work=0.1269 r_free=0.1507 adp: r_work=0.1262 r_free=0.1502 occ: r_work=0.1263 r_free=0.1500 adp: r_work=0.1260 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1260 r_free=0.1500 r_work=0.1260 r_free=0.1500 | n_water=960 | time (s): 97.590 (total time: 215.000) Filter (q & B) r_work=0.1264 r_free=0.1502 | n_water=893 | time (s): 4.570 (total time: 219.570) Filter (dist only) r_work=0.1265 r_free=0.1501 | n_water=892 | time (s): 115.300 (total time: 334.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.897773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 596.415049 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 0.1249 0.1520 0.0272 0.040 1.1 18.5 0.0 0.0 0 11.949 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.49 15.20 2.72 2.031 15.192 596.415 0.014 12.29 15.09 2.80 2.374 15.300 596.415 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 69.99 16.49 1.20 524 3272 Protein: 5.38 40.77 10.97 1.20 0 2902 Water: 6.59 69.99 34.41 N/A 524 368 Other: 16.41 32.40 24.40 N/A 0 2 Chain A: 5.51 56.56 12.99 N/A 0 1624 Chain B: 5.38 68.17 12.83 N/A 0 1648 Chain S: 12.54 69.99 38.86 N/A 524 0 Histogram: Values Number of atoms 5.38 - 11.84 2095 11.84 - 18.30 705 18.30 - 24.76 255 24.76 - 31.22 215 31.22 - 37.68 165 37.68 - 44.15 157 44.15 - 50.61 101 50.61 - 57.07 47 57.07 - 63.53 39 63.53 - 69.99 17 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1509 r_work=0.1229 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1510 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 = 0.1222 r_free = 0.1512 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1222 r_free= 0.1512 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013291 | | target function (ls_wunit_k1) not normalized (work): 2489.402482 | | target function (ls_wunit_k1) not normalized (free): 102.599814 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1228 0.1222 0.1512 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1432 0.1429 0.1596 n_refl.: 191136 remove outliers: r(all,work,free)=0.1432 0.1429 0.1596 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1429 0.1426 0.1595 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1229 0.1521 n_refl.: 191136 remove outliers: r(all,work,free)=0.1235 0.1229 0.1521 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3186 398.008 373.207 0.485 0.963 0.271 13.296-10.522 99.01 99 1 0.1814 528.187 523.532 0.767 0.964 0.250 10.503-8.327 98.90 177 3 0.1388 564.205 565.231 0.918 0.964 0.174 8.318-6.595 100.00 360 8 0.1529 414.736 414.132 0.934 0.963 0.145 6.588-5.215 100.00 711 7 0.1346 381.101 376.589 0.912 0.963 0.140 5.214-4.128 98.38 1367 28 0.0816 557.435 555.815 0.994 0.964 0.070 4.126-3.266 94.74 2603 46 0.0764 508.132 505.460 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0856 342.774 341.296 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0897 258.603 256.784 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1041 153.054 151.613 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1251 82.395 81.353 1.074 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.220 1.060 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0588 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1521 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1229 r_free=0.1521 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1521 | n_water=892 | time (s): 3.550 (total time: 3.550) Filter (dist) r_work=0.1231 r_free=0.1521 | n_water=887 | time (s): 119.290 (total time: 122.840) Filter (q & B) r_work=0.1231 r_free=0.1521 | n_water=886 | time (s): 5.370 (total time: 128.210) Compute maps r_work=0.1231 r_free=0.1521 | n_water=886 | time (s): 1.680 (total time: 129.890) Filter (map) r_work=0.1272 r_free=0.1524 | n_water=690 | time (s): 3.920 (total time: 133.810) Find peaks r_work=0.1272 r_free=0.1524 | n_water=690 | time (s): 0.590 (total time: 134.400) Add new water r_work=0.1294 r_free=0.1554 | n_water=1006 | time (s): 4.890 (total time: 139.290) Refine new water occ: r_work=0.1251 r_free=0.1521 adp: r_work=0.1252 r_free=0.1522 occ: r_work=0.1248 r_free=0.1520 adp: r_work=0.1247 r_free=0.1521 occ: r_work=0.1244 r_free=0.1519 adp: r_work=0.1243 r_free=0.1520 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1520 r_work=0.1243 r_free=0.1520 | n_water=1006 | time (s): 332.500 (total time: 471.790) Filter (q & B) r_work=0.1248 r_free=0.1526 | n_water=873 | time (s): 4.100 (total time: 475.890) Filter (dist only) r_work=0.1248 r_free=0.1525 | n_water=871 | time (s): 119.220 (total time: 595.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.680492 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.087762 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 0.1240 0.1444 0.0204 0.035 1.1 7.0 0.0 0.0 0 0.840 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.44 2.04 1.928 14.579 16.088 3.938 12.34 14.05 1.71 2.168 14.499 16.088 3.897 Individual atomic B min max mean iso aniso Overall: 5.53 67.87 15.29 1.07 504 3271 Protein: 5.53 37.34 10.77 1.07 0 2902 Water: 6.71 67.87 30.35 N/A 504 367 Other: 14.12 28.67 21.39 N/A 0 2 Chain A: 5.53 55.88 12.79 N/A 0 1624 Chain B: 5.54 67.87 12.58 N/A 0 1647 Chain S: 14.38 63.34 32.22 N/A 504 0 Histogram: Values Number of atoms 5.53 - 11.77 2122 11.77 - 18.00 698 18.00 - 24.24 296 24.24 - 30.47 227 30.47 - 36.70 182 36.70 - 42.94 139 42.94 - 49.17 70 49.17 - 55.41 27 55.41 - 61.64 11 61.64 - 67.87 3 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1406 r_work=0.1234 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1406 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1397 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1397 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891371 | | target function (ml) not normalized (work): 728834.395541 | | target function (ml) not normalized (free): 15219.443251 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1396 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1446 0.1446 0.1503 n_refl.: 191136 remove outliers: r(all,work,free)=0.1446 0.1446 0.1503 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1439 0.1500 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1391 n_refl.: 191136 remove outliers: r(all,work,free)=0.1228 0.1225 0.1391 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3771 398.008 356.041 0.422 0.946 0.257 13.296-10.522 99.01 99 1 0.2474 528.187 508.081 0.706 0.947 0.219 10.503-8.327 97.80 175 3 0.1966 554.286 557.696 0.884 0.947 0.178 8.318-6.595 100.00 360 8 0.2102 414.736 409.664 0.896 0.946 0.138 6.588-5.215 100.00 711 7 0.1847 381.101 370.518 0.885 0.947 0.118 5.214-4.128 98.38 1367 28 0.1173 557.435 551.835 0.974 0.947 0.080 4.126-3.266 94.74 2603 46 0.1102 508.132 501.026 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1080 342.774 338.960 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0967 258.603 255.764 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0971 153.054 151.410 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.489 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.312 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1063 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1391 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1391 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1391 | n_water=871 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1225 r_free=0.1392 | n_water=870 | time (s): 117.330 (total time: 120.350) Filter (q & B) r_work=0.1225 r_free=0.1391 | n_water=858 | time (s): 4.750 (total time: 125.100) Compute maps r_work=0.1225 r_free=0.1391 | n_water=858 | time (s): 2.350 (total time: 127.450) Filter (map) r_work=0.1248 r_free=0.1385 | n_water=716 | time (s): 4.020 (total time: 131.470) Find peaks r_work=0.1248 r_free=0.1385 | n_water=716 | time (s): 0.770 (total time: 132.240) Add new water r_work=0.1263 r_free=0.1407 | n_water=955 | time (s): 4.270 (total time: 136.510) Refine new water occ: r_work=0.1225 r_free=0.1376 adp: r_work=0.1225 r_free=0.1376 occ: r_work=0.1222 r_free=0.1375 adp: r_work=0.1222 r_free=0.1374 occ: r_work=0.1220 r_free=0.1374 adp: r_work=0.1220 r_free=0.1373 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1373 r_work=0.1220 r_free=0.1373 | n_water=955 | time (s): 192.210 (total time: 328.720) Filter (q & B) r_work=0.1224 r_free=0.1373 | n_water=871 | time (s): 3.890 (total time: 332.610) Filter (dist only) r_work=0.1224 r_free=0.1372 | n_water=870 | time (s): 113.340 (total time: 445.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.609568 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.975462 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 0.1223 0.1376 0.0153 0.036 1.1 6.3 0.0 0.3 0 0.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.23 13.76 1.53 1.839 14.292 15.975 3.885 12.19 13.73 1.54 1.982 14.233 15.975 3.878 Individual atomic B min max mean iso aniso Overall: 5.53 67.41 15.07 1.00 503 3271 Protein: 5.53 33.78 10.65 1.00 0 2902 Water: 6.69 67.41 29.77 N/A 503 367 Other: 14.02 27.57 20.80 N/A 0 2 Chain A: 5.56 54.75 12.62 N/A 0 1624 Chain B: 5.53 67.41 12.45 N/A 0 1647 Chain S: 14.42 63.20 31.52 N/A 503 0 Histogram: Values Number of atoms 5.53 - 11.72 2125 11.72 - 17.91 721 17.91 - 24.10 298 24.10 - 30.28 217 30.28 - 36.47 177 36.47 - 42.66 134 42.66 - 48.85 65 48.85 - 55.04 24 55.04 - 61.22 10 61.22 - 67.41 3 =========================== Idealize ADP of riding H ========================== r_work=0.1219 r_free=0.1373 r_work=0.1219 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1374 target_work(ml) = 3.879 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1216 r_free = 0.1373 target_work(ml) = 3.876 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1216 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.876212 | | target function (ml) not normalized (work): 725987.320901 | | target function (ml) not normalized (free): 15171.520249 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1216 0.1373 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1441 0.1441 0.1485 n_refl.: 191134 remove outliers: r(all,work,free)=0.1441 0.1441 0.1485 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1433 0.1433 0.1480 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1215 0.1370 n_refl.: 191134 remove outliers: r(all,work,free)=0.1217 0.1214 0.1370 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 94.06 92 3 0.3837 360.339 322.794 0.420 0.946 0.253 13.296-10.522 97.03 97 1 0.2364 478.065 451.181 0.702 0.947 0.206 10.503-8.327 97.80 175 3 0.1978 501.826 498.249 0.870 0.947 0.183 8.318-6.595 100.00 360 8 0.2143 375.484 370.653 0.891 0.947 0.125 6.588-5.215 100.00 711 7 0.1887 345.032 335.311 0.888 0.947 0.120 5.214-4.128 98.38 1367 28 0.1200 504.677 499.871 0.975 0.947 0.080 4.126-3.266 94.74 2603 46 0.1133 460.041 453.427 1.035 0.948 0.009 3.266-2.585 99.86 5447 97 0.1101 310.332 307.167 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0959 234.128 231.729 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0943 138.569 137.195 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.1014 74.597 73.863 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1673 40.018 38.347 1.039 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1258 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1214 r_free=0.1370 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1214 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1214 r_free=0.1370 | n_water=870 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1215 r_free=0.1371 | n_water=869 | time (s): 109.710 (total time: 112.800) Filter (q & B) r_work=0.1215 r_free=0.1371 | n_water=860 | time (s): 4.820 (total time: 117.620) Compute maps r_work=0.1215 r_free=0.1371 | n_water=860 | time (s): 1.920 (total time: 119.540) Filter (map) r_work=0.1235 r_free=0.1363 | n_water=745 | time (s): 4.450 (total time: 123.990) Find peaks r_work=0.1235 r_free=0.1363 | n_water=745 | time (s): 0.810 (total time: 124.800) Add new water r_work=0.1248 r_free=0.1379 | n_water=965 | time (s): 5.440 (total time: 130.240) Refine new water occ: r_work=0.1202 r_free=0.1345 adp: r_work=0.1194 r_free=0.1340 occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1192 r_free=0.1339 occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1192 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1339 r_work=0.1192 r_free=0.1339 | n_water=965 | time (s): 241.710 (total time: 371.950) Filter (q & B) r_work=0.1197 r_free=0.1346 | n_water=865 | time (s): 5.030 (total time: 376.980) Filter (dist only) r_work=0.1197 r_free=0.1345 | n_water=864 | time (s): 109.760 (total time: 486.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.619681 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.384397 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 0.1347 0.0149 0.037 1.1 5.4 0.0 0.3 0 0.810 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.47 1.49 1.789 14.045 15.384 3.764 12.00 13.46 1.47 1.962 14.005 15.384 3.760 Individual atomic B min max mean iso aniso Overall: 5.57 66.23 14.79 0.93 498 3270 Protein: 5.57 30.37 10.53 0.93 0 2902 Water: 6.15 66.23 29.09 N/A 498 366 Other: 13.94 24.47 19.21 N/A 0 2 Chain A: 5.62 52.73 12.46 N/A 0 1624 Chain B: 5.57 66.23 12.28 N/A 0 1646 Chain S: 6.15 63.47 30.68 N/A 498 0 Histogram: Values Number of atoms 5.57 - 11.64 2117 11.64 - 17.70 762 17.70 - 23.77 297 23.77 - 29.83 203 29.83 - 35.90 159 35.90 - 41.97 127 41.97 - 48.03 62 48.03 - 54.10 27 54.10 - 60.16 10 60.16 - 66.23 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1347 r_work=0.1200 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1347 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1347 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758789 | | target function (ml) not normalized (work): 703987.337659 | | target function (ml) not normalized (free): 14729.095432 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1347 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1427 0.1426 0.1468 n_refl.: 191132 remove outliers: r(all,work,free)=0.1427 0.1426 0.1468 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1419 0.1419 0.1463 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1346 n_refl.: 191132 remove outliers: r(all,work,free)=0.1199 0.1196 0.1346 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3592 360.839 312.177 0.403 0.946 0.231 13.296-10.522 96.04 96 1 0.2347 480.353 459.690 0.714 0.948 0.205 10.503-8.327 97.80 175 3 0.2047 501.826 497.998 0.862 0.948 0.171 8.318-6.595 100.00 360 8 0.2191 375.484 368.950 0.886 0.948 0.121 6.588-5.215 100.00 711 7 0.1876 345.032 336.013 0.887 0.948 0.100 5.214-4.128 98.38 1367 28 0.1202 504.677 499.841 0.974 0.948 0.070 4.126-3.266 94.74 2603 46 0.1143 460.041 453.180 1.034 0.948 0.000 3.266-2.585 99.86 5447 97 0.1091 310.332 307.207 1.022 0.948 0.000 2.585-2.046 97.45 10613 204 0.0952 234.128 231.706 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0915 138.569 137.289 1.058 0.946 0.000 1.619-1.281 98.00 42464 925 0.0975 74.597 73.907 1.055 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.018 38.360 1.043 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1277 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1346 | n_water=864 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1196 r_free=0.1346 | n_water=864 | time (s): 103.550 (total time: 106.790) Filter (q & B) r_work=0.1196 r_free=0.1345 | n_water=858 | time (s): 4.030 (total time: 110.820) Compute maps r_work=0.1196 r_free=0.1345 | n_water=858 | time (s): 2.020 (total time: 112.840) Filter (map) r_work=0.1216 r_free=0.1343 | n_water=762 | time (s): 5.240 (total time: 118.080) Find peaks r_work=0.1216 r_free=0.1343 | n_water=762 | time (s): 0.700 (total time: 118.780) Add new water r_work=0.1227 r_free=0.1358 | n_water=975 | time (s): 4.870 (total time: 123.650) Refine new water occ: r_work=0.1192 r_free=0.1338 adp: r_work=0.1192 r_free=0.1337 occ: r_work=0.1190 r_free=0.1339 adp: r_work=0.1190 r_free=0.1338 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1339 r_work=0.1188 r_free=0.1339 | n_water=975 | time (s): 210.170 (total time: 333.820) Filter (q & B) r_work=0.1193 r_free=0.1341 | n_water=893 | time (s): 5.850 (total time: 339.670) Filter (dist only) r_work=0.1193 r_free=0.1341 | n_water=892 | time (s): 121.360 (total time: 461.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550674 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.879852 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 0.1345 0.0149 0.037 1.1 4.9 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.45 1.49 1.737 13.993 14.880 3.758 11.98 13.47 1.49 1.795 13.967 14.880 3.755 Individual atomic B min max mean iso aniso Overall: 5.58 65.14 14.87 0.90 526 3270 Protein: 5.58 29.25 10.46 0.90 0 2902 Water: 6.02 65.14 29.17 N/A 526 366 Other: 13.90 22.65 18.27 N/A 0 2 Chain A: 5.62 52.27 12.36 N/A 0 1624 Chain B: 5.58 65.14 12.18 N/A 0 1646 Chain S: 6.02 63.72 31.00 N/A 526 0 Histogram: Values Number of atoms 5.58 - 11.54 2095 11.54 - 17.49 785 17.49 - 23.45 276 23.45 - 29.40 211 29.40 - 35.36 184 35.36 - 41.32 124 41.32 - 47.27 77 47.27 - 53.23 31 53.23 - 59.19 9 59.19 - 65.14 4 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1347 r_work=0.1198 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1347 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1352 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.754929 | | target function (ml) not normalized (work): 703253.221507 | | target function (ml) not normalized (free): 14718.619686 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1352 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1395 0.1394 0.1485 n_refl.: 191129 remove outliers: r(all,work,free)=0.1395 0.1394 0.1485 n_refl.: 191129 overall B=-0.23 to atoms: r(all,work,free)=0.1360 0.1358 0.1461 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1196 0.1351 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3581 360.839 334.808 0.432 0.952 0.223 13.296-10.522 96.04 96 1 0.2392 480.353 462.625 0.723 0.954 0.176 10.503-8.327 97.80 175 3 0.2108 501.826 497.639 0.879 0.954 0.153 8.318-6.595 100.00 360 8 0.2181 375.484 369.961 0.906 0.954 0.113 6.588-5.215 100.00 711 7 0.1877 345.032 335.793 0.903 0.954 0.090 5.214-4.128 98.38 1367 28 0.1196 504.677 499.763 0.993 0.954 0.035 4.126-3.266 94.74 2603 46 0.1154 460.041 453.123 1.053 0.954 0.005 3.266-2.585 99.86 5447 97 0.1112 310.332 306.957 1.037 0.954 0.000 2.585-2.046 97.45 10613 204 0.0954 234.128 231.634 1.046 0.954 0.000 2.046-1.619 99.39 21536 464 0.0910 138.569 137.254 1.064 0.953 0.000 1.619-1.281 98.00 42464 925 0.0966 74.597 73.898 1.052 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.018 38.348 1.023 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0499 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1351 | n_water=892 | time (s): 2.960 (total time: 2.960) Filter (dist) r_work=0.1196 r_free=0.1351 | n_water=892 | time (s): 103.980 (total time: 106.940) Filter (q & B) r_work=0.1197 r_free=0.1350 | n_water=886 | time (s): 5.460 (total time: 112.400) Compute maps r_work=0.1197 r_free=0.1350 | n_water=886 | time (s): 2.140 (total time: 114.540) Filter (map) r_work=0.1217 r_free=0.1344 | n_water=769 | time (s): 5.220 (total time: 119.760) Find peaks r_work=0.1217 r_free=0.1344 | n_water=769 | time (s): 0.560 (total time: 120.320) Add new water r_work=0.1227 r_free=0.1357 | n_water=977 | time (s): 4.220 (total time: 124.540) Refine new water occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1341 adp: r_work=0.1192 r_free=0.1341 occ: r_work=0.1190 r_free=0.1340 adp: r_work=0.1190 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1340 r_work=0.1190 r_free=0.1340 | n_water=977 | time (s): 302.940 (total time: 427.480) Filter (q & B) r_work=0.1195 r_free=0.1343 | n_water=901 | time (s): 5.080 (total time: 432.560) Filter (dist only) r_work=0.1195 r_free=0.1342 | n_water=900 | time (s): 117.650 (total time: 550.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.510427 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.224687 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 0.1350 0.0152 0.038 1.1 5.3 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.50 1.52 1.713 13.725 14.225 3.756 12.01 13.54 1.53 1.748 13.701 14.225 3.756 Individual atomic B min max mean iso aniso Overall: 5.40 63.99 14.61 0.88 534 3270 Protein: 5.40 28.33 10.23 0.88 0 2902 Water: 5.84 63.99 28.72 N/A 534 366 Other: 13.72 22.24 17.98 N/A 0 2 Chain A: 5.46 51.72 12.08 N/A 0 1624 Chain B: 5.40 63.99 11.92 N/A 0 1646 Chain S: 5.84 63.75 30.60 N/A 534 0 Histogram: Values Number of atoms 5.40 - 11.26 2070 11.26 - 17.12 817 17.12 - 22.98 274 22.98 - 28.84 205 28.84 - 34.70 186 34.70 - 40.56 121 40.56 - 46.41 84 46.41 - 52.27 34 52.27 - 58.13 7 58.13 - 63.99 6 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1354 r_work=0.1201 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1355 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1355 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755584 | | target function (ml) not normalized (work): 703375.757459 | | target function (ml) not normalized (free): 14726.469201 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1369 0.1367 0.1468 n_refl.: 191129 remove outliers: r(all,work,free)=0.1369 0.1367 0.1468 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1376 0.1374 0.1472 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1344 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1344 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3539 360.839 333.048 0.417 0.995 0.225 13.296-10.522 96.04 96 1 0.2359 480.353 462.329 0.694 0.997 0.169 10.503-8.327 97.80 175 3 0.2123 501.826 496.464 0.847 0.997 0.143 8.318-6.595 100.00 360 8 0.2166 375.484 369.814 0.875 0.997 0.111 6.588-5.215 100.00 711 7 0.1894 345.032 335.281 0.872 0.998 0.093 5.214-4.128 98.38 1367 28 0.1211 504.677 498.912 0.960 0.998 0.044 4.126-3.266 94.74 2603 46 0.1168 460.041 452.377 1.018 0.999 0.005 3.266-2.585 99.86 5447 97 0.1120 310.332 306.650 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0955 234.128 231.552 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.569 137.175 1.025 1.005 0.000 1.619-1.281 98.00 42464 925 0.0948 74.597 73.938 1.014 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.018 38.323 0.980 1.017 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0621 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1344 | n_water=900 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1190 r_free=0.1345 | n_water=899 | time (s): 114.380 (total time: 117.470) Filter (q & B) r_work=0.1190 r_free=0.1347 | n_water=891 | time (s): 5.550 (total time: 123.020) Compute maps r_work=0.1190 r_free=0.1347 | n_water=891 | time (s): 1.870 (total time: 124.890) Filter (map) r_work=0.1211 r_free=0.1340 | n_water=778 | time (s): 4.990 (total time: 129.880) Find peaks r_work=0.1211 r_free=0.1340 | n_water=778 | time (s): 0.580 (total time: 130.460) Add new water r_work=0.1220 r_free=0.1351 | n_water=990 | time (s): 4.230 (total time: 134.690) Refine new water occ: r_work=0.1186 r_free=0.1328 adp: r_work=0.1186 r_free=0.1328 occ: r_work=0.1184 r_free=0.1329 adp: r_work=0.1184 r_free=0.1329 occ: r_work=0.1183 r_free=0.1328 adp: r_work=0.1183 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1329 r_work=0.1183 r_free=0.1329 | n_water=990 | time (s): 282.930 (total time: 417.620) Filter (q & B) r_work=0.1187 r_free=0.1339 | n_water=917 | time (s): 4.630 (total time: 422.250) Filter (dist only) r_work=0.1188 r_free=0.1338 | n_water=916 | time (s): 113.450 (total time: 535.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558369 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.828598 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1339 0.0149 0.037 1.1 6.0 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.39 1.49 1.671 13.763 13.829 3.754 11.91 13.43 1.52 1.684 13.755 13.829 3.752 Individual atomic B min max mean iso aniso Overall: 5.48 64.01 14.71 0.87 550 3270 Protein: 5.48 28.13 10.29 0.87 0 2902 Water: 5.91 64.01 28.70 N/A 550 366 Other: 13.77 22.26 18.01 N/A 0 2 Chain A: 5.57 51.55 12.11 N/A 0 1624 Chain B: 5.48 63.37 11.95 N/A 0 1646 Chain S: 5.91 64.01 30.64 N/A 550 0 Histogram: Values Number of atoms 5.48 - 11.33 2073 11.33 - 17.18 819 17.18 - 23.04 277 23.04 - 28.89 211 28.89 - 34.74 189 34.74 - 40.59 124 40.59 - 46.45 79 46.45 - 52.30 33 52.30 - 58.15 9 58.15 - 64.01 6 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1343 r_work=0.1191 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1343 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1343 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752002 | | target function (ml) not normalized (work): 702704.865253 | | target function (ml) not normalized (free): 14712.789910 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1343 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1380 0.1378 0.1465 n_refl.: 191129 remove outliers: r(all,work,free)=0.1380 0.1378 0.1465 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1382 0.1380 0.1466 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191129 remove outliers: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3692 360.839 329.365 0.403 0.975 0.199 13.296-10.522 96.04 96 1 0.2378 480.353 461.134 0.698 0.977 0.146 10.503-8.327 97.80 175 3 0.2146 501.826 495.927 0.863 0.977 0.118 8.318-6.595 100.00 360 8 0.2164 375.484 369.883 0.890 0.977 0.098 6.588-5.215 100.00 711 7 0.1913 345.032 335.383 0.886 0.978 0.080 5.214-4.128 98.38 1367 28 0.1216 504.677 498.905 0.978 0.978 0.034 4.126-3.266 94.74 2603 46 0.1164 460.041 452.471 1.039 0.980 0.000 3.266-2.585 99.86 5447 97 0.1116 310.332 306.754 1.023 0.981 0.000 2.585-2.046 97.45 10613 204 0.0956 234.128 231.553 1.031 0.983 0.000 2.046-1.619 99.39 21536 464 0.0909 138.569 137.201 1.048 0.986 0.000 1.619-1.281 98.00 42464 925 0.0943 74.597 73.950 1.038 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.018 38.312 1.006 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0202 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1342 | n_water=916 | time (s): 3.300 (total time: 3.300) Filter (dist) r_work=0.1188 r_free=0.1342 | n_water=916 | time (s): 113.930 (total time: 117.230) Filter (q & B) r_work=0.1189 r_free=0.1345 | n_water=903 | time (s): 5.320 (total time: 122.550) Compute maps r_work=0.1189 r_free=0.1345 | n_water=903 | time (s): 2.170 (total time: 124.720) Filter (map) r_work=0.1211 r_free=0.1342 | n_water=791 | time (s): 5.350 (total time: 130.070) Find peaks r_work=0.1211 r_free=0.1342 | n_water=791 | time (s): 0.870 (total time: 130.940) Add new water r_work=0.1218 r_free=0.1353 | n_water=995 | time (s): 4.990 (total time: 135.930) Refine new water occ: r_work=0.1185 r_free=0.1332 adp: r_work=0.1186 r_free=0.1331 occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1184 r_free=0.1332 occ: r_work=0.1183 r_free=0.1333 adp: r_work=0.1183 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1332 r_work=0.1183 r_free=0.1332 | n_water=995 | time (s): 305.670 (total time: 441.600) Filter (q & B) r_work=0.1187 r_free=0.1338 | n_water=915 | time (s): 4.290 (total time: 445.890) Filter (dist only) r_work=0.1188 r_free=0.1338 | n_water=913 | time (s): 118.190 (total time: 564.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533888 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.528433 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1341 0.0152 0.038 1.1 5.3 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.41 1.52 1.673 13.760 13.528 3.754 11.91 13.43 1.52 1.672 13.757 13.528 3.753 Individual atomic B min max mean iso aniso Overall: 5.51 64.09 14.70 0.86 547 3270 Protein: 5.51 28.02 10.32 0.86 0 2902 Water: 5.98 64.09 28.60 N/A 547 366 Other: 13.83 22.26 18.05 N/A 0 2 Chain A: 5.60 51.47 12.11 N/A 0 1624 Chain B: 5.51 63.06 11.96 N/A 0 1646 Chain S: 5.98 64.09 30.60 N/A 547 0 Histogram: Values Number of atoms 5.51 - 11.37 2079 11.37 - 17.23 821 17.23 - 23.09 271 23.09 - 28.94 217 28.94 - 34.80 183 34.80 - 40.66 124 40.66 - 46.52 75 46.52 - 52.38 33 52.38 - 58.24 8 58.24 - 64.09 6 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1344 r_work=0.1191 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1344 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1345 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752448 | | target function (ml) not normalized (work): 702788.549048 | | target function (ml) not normalized (free): 14717.619591 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1345 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1390 0.1389 0.1471 n_refl.: 191129 remove outliers: r(all,work,free)=0.1390 0.1389 0.1471 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1390 0.1389 0.1471 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1344 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1344 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3679 360.839 329.207 0.394 0.994 0.197 13.296-10.522 96.04 96 1 0.2370 480.353 461.552 0.684 0.996 0.144 10.503-8.327 97.80 175 3 0.2117 501.826 496.143 0.846 0.996 0.113 8.318-6.595 100.00 360 8 0.2156 375.484 369.842 0.872 0.996 0.090 6.588-5.215 100.00 711 7 0.1913 345.032 335.253 0.868 0.997 0.073 5.214-4.128 98.38 1367 28 0.1217 504.677 498.905 0.959 0.998 0.029 4.126-3.266 94.74 2603 46 0.1168 460.041 452.424 1.019 0.999 0.000 3.266-2.585 99.86 5447 97 0.1121 310.332 306.708 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0959 234.128 231.525 1.012 1.003 0.000 2.046-1.619 99.39 21536 464 0.0911 138.569 137.192 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0942 74.597 73.949 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.018 38.299 0.989 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1344 After: r_work=0.1190 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1344 | n_water=913 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1190 r_free=0.1344 | n_water=912 | time (s): 118.300 (total time: 121.010) Filter (q & B) r_work=0.1191 r_free=0.1345 | n_water=904 | time (s): 4.120 (total time: 125.130) Compute maps r_work=0.1191 r_free=0.1345 | n_water=904 | time (s): 1.950 (total time: 127.080) Filter (map) r_work=0.1213 r_free=0.1351 | n_water=795 | time (s): 4.080 (total time: 131.160) Find peaks r_work=0.1213 r_free=0.1351 | n_water=795 | time (s): 0.600 (total time: 131.760) Add new water r_work=0.1219 r_free=0.1359 | n_water=1002 | time (s): 4.180 (total time: 135.940) Refine new water occ: r_work=0.1186 r_free=0.1334 adp: r_work=0.1186 r_free=0.1334 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1335 occ: r_work=0.1183 r_free=0.1335 adp: r_work=0.1183 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1335 r_work=0.1183 r_free=0.1335 | n_water=1002 | time (s): 247.540 (total time: 383.480) Filter (q & B) r_work=0.1188 r_free=0.1342 | n_water=921 | time (s): 4.500 (total time: 387.980) Filter (dist only) r_work=0.1188 r_free=0.1341 | n_water=919 | time (s): 119.610 (total time: 507.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.495884 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.871004 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1352 0.0156 0.038 1.2 7.3 0.0 0.3 0 0.748 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.52 1.56 1.671 13.764 13.871 3.759 11.96 13.54 1.58 1.669 13.768 13.871 3.758 Individual atomic B min max mean iso aniso Overall: 5.56 64.23 14.70 0.85 553 3270 Protein: 5.56 27.90 10.34 0.85 0 2902 Water: 6.04 64.23 28.50 N/A 553 366 Other: 13.84 22.18 18.01 N/A 0 2 Chain A: 5.64 51.27 12.10 N/A 0 1624 Chain B: 5.56 62.23 11.96 N/A 0 1646 Chain S: 6.04 64.23 30.52 N/A 553 0 Histogram: Values Number of atoms 5.56 - 11.43 2082 11.43 - 17.30 837 17.30 - 23.16 255 23.16 - 29.03 228 29.03 - 34.89 181 34.89 - 40.76 119 40.76 - 46.63 75 46.63 - 52.49 32 52.49 - 58.36 8 58.36 - 64.23 6 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1354 r_work=0.1196 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1354 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1352 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757440 | | target function (ml) not normalized (work): 703723.332063 | | target function (ml) not normalized (free): 14736.633998 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1351 0.1432 5.6788 5.7197| | 2: 2.94 - 2.33 1.00 7339 128 0.1064 0.1339 5.0643 5.1618| | 3: 2.33 - 2.04 0.96 6939 150 0.0911 0.1179 4.6614 4.7403| | 4: 2.04 - 1.85 1.00 7170 155 0.0907 0.1054 4.4008 4.5746| | 5: 1.85 - 1.72 0.99 7113 159 0.0944 0.1009 4.1631 4.2787| | 6: 1.72 - 1.62 0.99 7102 142 0.0904 0.1089 3.956 4.0796| | 7: 1.62 - 1.54 0.99 7104 148 0.0897 0.0972 3.8069 3.939| | 8: 1.54 - 1.47 0.96 6798 152 0.0903 0.1317 3.7101 3.9008| | 9: 1.47 - 1.41 0.98 6938 155 0.0938 0.1148 3.6302 3.7672| | 10: 1.41 - 1.36 0.99 7022 150 0.0984 0.1200 3.5637 3.6825| | 11: 1.36 - 1.32 0.99 6997 151 0.0998 0.1128 3.4899 3.5838| | 12: 1.32 - 1.28 0.98 6975 149 0.1038 0.1129 3.4635 3.5934| | 13: 1.28 - 1.25 0.98 6907 166 0.1047 0.1252 3.4428 3.5788| | 14: 1.25 - 1.22 0.98 7015 112 0.1111 0.1592 3.4371 3.6853| | 15: 1.22 - 1.19 0.98 6956 137 0.1173 0.1242 3.4522 3.493| | 16: 1.19 - 1.17 0.93 6604 132 0.1255 0.1543 3.4679 3.6496| | 17: 1.17 - 1.14 0.98 6940 135 0.1303 0.1231 3.4361 3.4494| | 18: 1.14 - 1.12 0.98 6875 142 0.1389 0.1718 3.4414 3.5344| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1786 3.4218 3.6032| | 20: 1.10 - 1.08 0.97 6884 147 0.1588 0.1594 3.4124 3.4393| | 21: 1.08 - 1.07 0.97 6852 152 0.1731 0.2146 3.4193 3.5058| | 22: 1.07 - 1.05 0.97 6836 135 0.1906 0.1963 3.4139 3.4149| | 23: 1.05 - 1.03 0.97 6827 159 0.2123 0.2004 3.4342 3.4853| | 24: 1.03 - 1.02 0.96 6784 133 0.2337 0.2261 3.4368 3.5132| | 25: 1.02 - 1.01 0.93 6552 130 0.2619 0.2515 3.4503 3.5217| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2865 3.4155 3.4232| | 27: 0.99 - 0.98 0.94 6647 131 0.3046 0.2789 3.4701 3.3958| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7397 127 0.93 11.12 1.00 0.96 10372.27| | 2: 2.94 - 2.33 7339 128 0.93 12.34 0.99 0.95 4841.69| | 3: 2.33 - 2.04 6939 150 0.96 7.62 1.01 0.95 1701.86| | 4: 2.04 - 1.85 7170 155 0.96 7.78 1.00 0.95 1023.99| | 5: 1.85 - 1.72 7113 159 0.96 8.30 1.00 0.96 655.26| | 6: 1.72 - 1.62 7102 142 0.96 8.15 1.00 0.96 451.84| | 7: 1.62 - 1.54 7104 148 0.96 8.21 1.01 0.97 341.44| | 8: 1.54 - 1.47 6798 152 0.96 8.32 1.01 0.97 282.51| | 9: 1.47 - 1.41 6938 155 0.96 8.58 1.00 0.98 234.18| | 10: 1.41 - 1.36 7022 150 0.96 9.01 1.00 0.97 205.40| | 11: 1.36 - 1.32 6997 151 0.96 8.99 0.99 0.96 176.38| | 12: 1.32 - 1.28 6975 149 0.96 9.05 0.98 0.95 162.28| | 13: 1.28 - 1.25 6907 166 0.96 9.62 1.01 0.96 160.24| | 14: 1.25 - 1.22 7015 112 0.95 10.84 1.01 0.96 165.53| | 15: 1.22 - 1.19 6956 137 0.94 11.36 1.01 0.98 168.59| | 16: 1.19 - 1.17 6604 132 0.95 11.49 1.01 0.96 161.43| | 17: 1.17 - 1.14 6940 135 0.94 12.31 1.01 0.96 154.86| | 18: 1.14 - 1.12 6875 142 0.94 12.83 1.01 0.95 148.90| | 19: 1.12 - 1.10 6948 106 0.93 14.25 1.00 0.94 152.83| | 20: 1.10 - 1.08 6884 147 0.92 15.34 1.00 0.94 151.84| | 21: 1.08 - 1.07 6852 152 0.91 16.72 1.00 0.93 154.44| | 22: 1.07 - 1.05 6836 135 0.89 18.36 0.99 0.93 155.44| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 165.03| | 24: 1.03 - 1.02 6784 133 0.85 23.20 0.99 0.93 179.38| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.90 182.17| | 26: 1.01 - 0.99 6767 158 0.81 26.61 0.98 0.88 176.32| | 27: 0.99 - 0.98 6647 131 0.82 26.20 0.99 0.87 160.11| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.90 max = 10372.27 mean = 884.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.32| |phase err.(test): min = 0.00 max = 89.62 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1352 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1484 n_refl.: 191129 remove outliers: r(all,work,free)=0.1401 0.1399 0.1484 n_refl.: 191129 overall B=-0.06 to atoms: r(all,work,free)=0.1392 0.1391 0.1478 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3696 360.839 328.501 0.382 0.976 0.183 13.296-10.522 96.04 96 1 0.2351 480.353 460.689 0.673 0.977 0.126 10.503-8.327 97.80 175 3 0.2114 501.826 495.783 0.840 0.978 0.095 8.318-6.595 100.00 360 8 0.2142 375.484 370.329 0.864 0.978 0.076 6.588-5.215 100.00 711 7 0.1903 345.032 335.408 0.861 0.978 0.063 5.214-4.128 98.38 1367 28 0.1218 504.677 498.836 0.954 0.979 0.024 4.126-3.266 94.74 2603 46 0.1175 460.041 452.456 1.014 0.981 0.000 3.266-2.585 99.86 5447 97 0.1119 310.332 306.743 0.998 0.982 0.000 2.585-2.046 97.45 10613 204 0.0964 234.128 231.513 1.004 0.985 0.000 2.046-1.619 99.39 21536 464 0.0919 138.569 137.181 1.019 0.990 0.000 1.619-1.281 98.00 42464 925 0.0954 74.597 73.941 1.008 0.997 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.018 38.299 0.975 1.010 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0124 ================= 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 : 0.2037 0.1940 0.081 5.122 5.2 78.0 14.6 805 0.000 1_bss: 0.1802 0.1869 0.081 5.122 5.2 78.0 14.6 805 0.000 1_settarget: 0.1802 0.1869 0.081 5.122 5.2 78.0 14.6 805 0.000 1_nqh: 0.1803 0.1870 0.081 5.122 5.2 78.0 14.6 805 0.002 1_weight: 0.1803 0.1870 0.081 5.122 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1267 0.1490 0.037 1.154 5.2 78.0 14.6 805 0.157 1_adp: 0.1292 0.1558 0.037 1.154 5.3 73.0 14.9 805 0.157 1_regHadp: 0.1291 0.1553 0.037 1.154 5.3 73.0 14.9 805 0.157 1_occ: 0.1277 0.1542 0.037 1.154 5.3 73.0 14.9 805 0.157 2_bss: 0.1269 0.1534 0.037 1.154 5.4 73.2 15.1 805 0.157 2_settarget: 0.1269 0.1534 0.037 1.154 5.4 73.2 15.1 805 0.157 2_updatecdl: 0.1269 0.1534 0.037 1.160 5.4 73.2 15.1 805 0.157 2_nqh: 0.1269 0.1534 0.037 1.160 5.4 73.2 15.1 805 0.157 2_sol: 0.1265 0.1501 0.037 1.160 5.4 73.2 16.3 892 n/a 2_weight: 0.1265 0.1501 0.037 1.160 5.4 73.2 16.3 892 n/a 2_xyzrec: 0.1249 0.1520 0.040 1.133 5.4 73.2 16.3 892 n/a 2_adp: 0.1229 0.1509 0.040 1.133 5.4 70.0 16.5 892 n/a 2_regHadp: 0.1229 0.1510 0.040 1.133 5.4 70.0 16.5 892 n/a 2_occ: 0.1222 0.1512 0.040 1.133 5.4 70.0 16.5 892 n/a 3_bss: 0.1229 0.1521 0.040 1.133 5.4 70.0 16.5 892 n/a 3_settarget: 0.1229 0.1521 0.040 1.133 5.4 70.0 16.5 892 n/a 3_updatecdl: 0.1229 0.1521 0.040 1.147 5.4 70.0 16.5 892 n/a 3_nqh: 0.1229 0.1521 0.040 1.147 5.4 70.0 16.5 892 n/a 3_sol: 0.1248 0.1525 0.040 1.147 5.4 68.2 15.4 871 n/a 3_weight: 0.1248 0.1525 0.040 1.147 5.4 68.2 15.4 871 n/a 3_xyzrec: 0.1240 0.1444 0.035 1.100 5.4 68.2 15.4 871 n/a 3_adp: 0.1234 0.1406 0.035 1.100 5.5 67.9 15.3 871 n/a 3_regHadp: 0.1234 0.1406 0.035 1.100 5.5 67.9 15.3 871 n/a 3_occ: 0.1228 0.1397 0.035 1.100 5.5 67.9 15.3 871 n/a 4_bss: 0.1225 0.1391 0.035 1.100 5.5 67.8 15.3 871 n/a 4_settarget: 0.1225 0.1391 0.035 1.100 5.5 67.8 15.3 871 n/a 4_updatecdl: 0.1225 0.1391 0.035 1.100 5.5 67.8 15.3 871 n/a 4_nqh: 0.1225 0.1391 0.035 1.100 5.5 67.8 15.3 871 n/a 4_sol: 0.1224 0.1372 0.035 1.100 5.5 67.8 15.2 870 n/a 4_weight: 0.1224 0.1372 0.035 1.100 5.5 67.8 15.2 870 n/a 4_xyzrec: 0.1223 0.1376 0.036 1.121 5.5 67.8 15.2 870 n/a 4_adp: 0.1219 0.1373 0.036 1.121 5.5 67.4 15.1 870 n/a 4_regHadp: 0.1219 0.1374 0.036 1.121 5.5 67.4 15.1 870 n/a 4_occ: 0.1216 0.1373 0.036 1.121 5.5 67.4 15.1 870 n/a 5_bss: 0.1214 0.1370 0.036 1.121 5.5 67.4 15.0 870 n/a 5_settarget: 0.1214 0.1370 0.036 1.121 5.5 67.4 15.0 870 n/a 5_updatecdl: 0.1214 0.1370 0.036 1.122 5.5 67.4 15.0 870 n/a 5_nqh: 0.1214 0.1370 0.036 1.122 5.5 67.4 15.0 870 n/a 5_sol: 0.1197 0.1345 0.036 1.122 5.5 67.4 14.9 864 n/a 5_weight: 0.1197 0.1345 0.036 1.122 5.5 67.4 14.9 864 n/a 5_xyzrec: 0.1198 0.1347 0.037 1.138 5.5 67.4 14.9 864 n/a 5_adp: 0.1200 0.1347 0.037 1.138 5.6 66.2 14.8 864 n/a 5_regHadp: 0.1200 0.1347 0.037 1.138 5.6 66.2 14.8 864 n/a 5_occ: 0.1198 0.1347 0.037 1.138 5.6 66.2 14.8 864 n/a 6_bss: 0.1196 0.1346 0.037 1.138 5.5 66.2 14.8 864 n/a 6_settarget: 0.1196 0.1346 0.037 1.138 5.5 66.2 14.8 864 n/a 6_updatecdl: 0.1196 0.1346 0.037 1.138 5.5 66.2 14.8 864 n/a 6_nqh: 0.1196 0.1346 0.037 1.138 5.5 66.2 14.8 864 n/a 6_sol: 0.1193 0.1341 0.037 1.138 5.5 66.2 14.9 892 n/a 6_weight: 0.1193 0.1341 0.037 1.138 5.5 66.2 14.9 892 n/a 6_xyzrec: 0.1196 0.1345 0.037 1.122 5.5 66.2 14.9 892 n/a 6_adp: 0.1198 0.1347 0.037 1.122 5.6 65.1 14.9 892 n/a 6_regHadp: 0.1198 0.1347 0.037 1.122 5.6 65.1 14.9 892 n/a 6_occ: 0.1196 0.1352 0.037 1.122 5.6 65.1 14.9 892 n/a 7_bss: 0.1196 0.1351 0.037 1.122 5.4 64.9 14.6 892 n/a 7_settarget: 0.1196 0.1351 0.037 1.122 5.4 64.9 14.6 892 n/a 7_updatecdl: 0.1196 0.1351 0.037 1.123 5.4 64.9 14.6 892 n/a 7_nqh: 0.1196 0.1351 0.037 1.123 5.4 64.9 14.6 892 n/a 7_sol: 0.1195 0.1342 0.037 1.123 5.4 64.9 14.7 900 n/a 7_weight: 0.1195 0.1342 0.037 1.123 5.4 64.9 14.7 900 n/a 7_xyzrec: 0.1197 0.1350 0.038 1.113 5.4 64.9 14.7 900 n/a 7_adp: 0.1201 0.1354 0.038 1.113 5.4 64.0 14.6 900 n/a 7_regHadp: 0.1201 0.1355 0.038 1.113 5.4 64.0 14.6 900 n/a 7_occ: 0.1199 0.1355 0.038 1.113 5.4 64.0 14.6 900 n/a 8_bss: 0.1190 0.1344 0.038 1.113 5.5 64.0 14.7 900 n/a 8_settarget: 0.1190 0.1344 0.038 1.113 5.5 64.0 14.7 900 n/a 8_updatecdl: 0.1190 0.1344 0.038 1.112 5.5 64.0 14.7 900 n/a 8_nqh: 0.1190 0.1344 0.038 1.112 5.5 64.0 14.7 900 n/a 8_sol: 0.1188 0.1338 0.038 1.112 5.5 64.0 14.7 916 n/a 8_weight: 0.1188 0.1338 0.038 1.112 5.5 64.0 14.7 916 n/a 8_xyzrec: 0.1190 0.1339 0.037 1.120 5.5 64.0 14.7 916 n/a 8_adp: 0.1191 0.1343 0.037 1.120 5.5 64.0 14.7 916 n/a 8_regHadp: 0.1191 0.1343 0.037 1.120 5.5 64.0 14.7 916 n/a 8_occ: 0.1189 0.1343 0.037 1.120 5.5 64.0 14.7 916 n/a 9_bss: 0.1188 0.1342 0.037 1.120 5.5 64.0 14.7 916 n/a 9_settarget: 0.1188 0.1342 0.037 1.120 5.5 64.0 14.7 916 n/a 9_updatecdl: 0.1188 0.1342 0.037 1.121 5.5 64.0 14.7 916 n/a 9_nqh: 0.1188 0.1342 0.037 1.121 5.5 64.0 14.7 916 n/a 9_sol: 0.1188 0.1338 0.037 1.121 5.5 64.0 14.7 913 n/a 9_weight: 0.1188 0.1338 0.037 1.121 5.5 64.0 14.7 913 n/a 9_xyzrec: 0.1190 0.1341 0.038 1.116 5.5 64.0 14.7 913 n/a 9_adp: 0.1191 0.1344 0.038 1.116 5.5 64.1 14.7 913 n/a 9_regHadp: 0.1191 0.1344 0.038 1.116 5.5 64.1 14.7 913 n/a 9_occ: 0.1190 0.1345 0.038 1.116 5.5 64.1 14.7 913 n/a 10_bss: 0.1189 0.1344 0.038 1.116 5.5 64.1 14.7 913 n/a 10_settarget: 0.1189 0.1344 0.038 1.116 5.5 64.1 14.7 913 n/a 10_updatecdl: 0.1189 0.1344 0.038 1.116 5.5 64.1 14.7 913 n/a 10_setrh: 0.1190 0.1344 0.038 1.116 5.5 64.1 14.7 913 n/a 10_nqh: 0.1190 0.1344 0.038 1.116 5.5 64.1 14.7 913 n/a 10_sol: 0.1188 0.1341 0.038 1.116 5.5 64.1 14.7 919 n/a 10_weight: 0.1188 0.1341 0.038 1.116 5.5 64.1 14.7 919 n/a 10_xyzrec: 0.1196 0.1352 0.038 1.178 5.5 64.1 14.7 919 n/a 10_adp: 0.1196 0.1354 0.038 1.178 5.6 64.2 14.7 919 n/a 10_regHadp: 0.1196 0.1354 0.038 1.178 5.6 64.2 14.7 919 n/a 10_occ: 0.1195 0.1352 0.038 1.178 5.6 64.2 14.7 919 n/a end: 0.1194 0.1351 0.038 1.178 5.5 64.2 14.6 919 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2303751_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2303751_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3200 Refinement macro-cycles (run) : 12247.3800 Write final files (write_after_run_outputs) : 153.9200 Total : 12407.6200 Total CPU time: 3.46 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:00 PST -0800 (1736736240.44 s) Start R-work = 0.1802, R-free = 0.1869 Final R-work = 0.1194, R-free = 0.1351 =============================================================================== Job complete usr+sys time: 12677.73 seconds wall clock time: 212 minutes 19.03 seconds (12739.03 seconds total)