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_5857830.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5857830.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5857830.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.05, per 1000 atoms: 0.31 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: 2.774 distance_ideal: 2.720 ideal - model: -0.054 slack: 0.000 delta_slack: -0.054 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: 2.751 distance_ideal: 2.710 ideal - model: -0.041 slack: 0.000 delta_slack: -0.041 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: 0.80 Conformation dependent library (CDL) restraints added in 225.8 milliseconds Time building geometry restraints manager: 1.22 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: 666 1.01 - 1.25: 2573 1.25 - 1.48: 1503 1.48 - 1.71: 1165 1.71 - 1.95: 27 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA B 10 " pdb=" CA ALA B 10 " ideal model delta sigma weight residual 1.453 1.653 -0.200 9.20e-03 1.18e+04 4.73e+02 bond pdb=" C LYS A 133 " pdb=" N ILE A 134 " ideal model delta sigma weight residual 1.324 1.515 -0.190 9.30e-03 1.16e+04 4.18e+02 bond pdb=" N VAL A 51 " pdb=" H VAL A 51 " ideal model delta sigma weight residual 0.860 1.255 -0.395 2.00e-02 2.50e+03 3.90e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.235 1.472 -0.238 1.23e-02 6.61e+03 3.73e+02 bond pdb=" C GLY B 122 " pdb=" O GLY B 122 " ideal model delta sigma weight residual 1.233 1.066 0.167 8.80e-03 1.29e+04 3.61e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 5868 4.32 - 8.63: 3439 8.63 - 12.95: 1278 12.95 - 17.26: 207 17.26 - 21.58: 18 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA SER A 48 " pdb=" C SER A 48 " pdb=" O SER A 48 " ideal model delta sigma weight residual 119.97 101.99 17.98 1.15e+00 7.56e-01 2.45e+02 angle pdb=" O ASP B 56 " pdb=" C ASP B 56 " pdb=" N ALA B 57 " ideal model delta sigma weight residual 122.12 106.33 15.79 1.06e+00 8.90e-01 2.22e+02 angle pdb=" O MET A 187 " pdb=" C MET A 187 " pdb=" N ALA A 188 " ideal model delta sigma weight residual 122.86 106.12 16.74 1.18e+00 7.18e-01 2.01e+02 angle pdb=" NE ARG B 149 " pdb=" CZ ARG B 149 " pdb=" NH2 ARG B 149 " ideal model delta sigma weight residual 119.20 131.88 -12.68 9.00e-01 1.23e+00 1.99e+02 angle pdb=" O LEU B 185 " pdb=" C LEU B 185 " pdb=" N VAL B 186 " ideal model delta sigma weight residual 122.42 140.58 -18.16 1.31e+00 5.83e-01 1.92e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 1843 16.52 - 33.05: 132 33.05 - 49.57: 52 49.57 - 66.09: 18 66.09 - 82.61: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 154.06 25.94 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -155.90 -24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA VAL A 145 " pdb=" C VAL A 145 " pdb=" N TRP A 146 " pdb=" CA TRP A 146 " ideal model delta harmonic sigma weight residual 180.00 158.92 21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.246: 227 0.246 - 0.491: 147 0.491 - 0.737: 88 0.737 - 0.983: 25 0.983 - 1.228: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA LEU A 171 " pdb=" N LEU A 171 " pdb=" C LEU A 171 " pdb=" CB LEU A 171 " both_signs ideal model delta sigma weight residual False 2.51 1.28 1.23 2.00e-01 2.50e+01 3.77e+01 chirality pdb=" CG LEU A 54 " pdb=" CB LEU A 54 " pdb=" CD1 LEU A 54 " pdb=" CD2 LEU A 54 " both_signs ideal model delta sigma weight residual False -2.59 -3.65 1.06 2.00e-01 2.50e+01 2.79e+01 chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.61e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.106 2.00e-02 2.50e+03 6.32e-02 1.60e+02 pdb=" CG TRP B 139 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " 0.106 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.119 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.061 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.078 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.049 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " -0.033 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.020 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " 0.039 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.037 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.113 2.00e-02 2.50e+03 7.10e-02 1.51e+02 pdb=" CG PHE B 164 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.108 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.085 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.053 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " -0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.110 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.023 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " -0.060 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG TYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 TYR A 67 " 0.112 2.00e-02 2.50e+03 pdb=" HD2 TYR A 67 " 0.142 2.00e-02 2.50e+03 pdb=" HE1 TYR A 67 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 TYR A 67 " -0.000 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.55: 20 1.55 - 2.31: 1827 2.31 - 3.07: 21678 3.07 - 3.84: 33187 3.84 - 4.60: 53594 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110306 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.784 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.980 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.057 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.058 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.166 2.620 ... (remaining 110301 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_5857830_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= 0.2044 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.303825 | | target function (ml) not normalized (work): 806162.440808 | | target function (ml) not normalized (free): 16548.312418 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2141 0.1906 6.6921 6.3099| | 2: 2.94 - 2.33 1.00 7339 128 0.1633 0.1500 5.5412 5.5571| | 3: 2.33 - 2.04 0.96 6939 150 0.1635 0.1697 5.146 5.1914| | 4: 2.04 - 1.85 1.00 7170 155 0.1739 0.1615 4.9613 4.9669| | 5: 1.85 - 1.72 0.99 7113 159 0.1939 0.1686 4.8026 4.7617| | 6: 1.72 - 1.62 0.99 7102 142 0.1972 0.1676 4.662 4.5653| | 7: 1.62 - 1.54 0.99 7104 148 0.2038 0.1761 4.5639 4.5666| | 8: 1.54 - 1.47 0.96 6798 152 0.2084 0.2339 4.4918 4.6017| | 9: 1.47 - 1.41 0.98 6938 155 0.2106 0.1950 4.4067 4.3961| | 10: 1.41 - 1.36 0.99 7022 150 0.2125 0.2005 4.3157 4.3303| | 11: 1.36 - 1.32 0.99 6997 151 0.2118 0.2512 4.2399 4.4143| | 12: 1.32 - 1.28 0.98 6976 149 0.2091 0.2037 4.185 4.3058| | 13: 1.28 - 1.25 0.98 6907 166 0.2035 0.2107 4.1187 4.1671| | 14: 1.25 - 1.22 0.98 7015 113 0.2081 0.2304 4.0715 4.2418| | 15: 1.22 - 1.19 0.98 6957 137 0.2165 0.1868 4.0599 3.9673| | 16: 1.19 - 1.17 0.93 6604 132 0.2149 0.2232 4.0171 4.0429| | 17: 1.17 - 1.14 0.98 6941 135 0.2210 0.2092 3.9716 4.08| | 18: 1.14 - 1.12 0.98 6875 142 0.2241 0.2481 3.9269 3.97| | 19: 1.12 - 1.10 0.97 6949 106 0.2284 0.2451 3.8818 3.9478| | 20: 1.10 - 1.08 0.97 6884 147 0.2327 0.2458 3.8227 3.9333| | 21: 1.08 - 1.07 0.97 6852 152 0.2392 0.2615 3.7744 3.8011| | 22: 1.07 - 1.05 0.97 6838 135 0.2557 0.2653 3.7543 3.7373| | 23: 1.05 - 1.03 0.97 6829 159 0.2731 0.2507 3.7306 3.7699| | 24: 1.03 - 1.02 0.96 6785 133 0.2910 0.2735 3.7056 3.7459| | 25: 1.02 - 1.01 0.93 6552 130 0.3051 0.2892 3.6673 3.7104| | 26: 1.01 - 0.99 0.96 6767 158 0.3263 0.3112 3.637 3.629| | 27: 0.99 - 0.98 0.94 6648 131 0.3425 0.3164 3.6426 3.6046| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.39 0.91 0.97 35215.72| | 2: 2.94 - 2.33 7339 128 0.86 21.13 1.08 1.02 15033.72| | 3: 2.33 - 2.04 6939 150 0.93 12.47 1.11 1.06 4109.54| | 4: 2.04 - 1.85 7170 155 0.93 12.74 1.11 1.07 2556.76| | 5: 1.85 - 1.72 7113 159 0.92 14.41 1.11 1.08 1821.03| | 6: 1.72 - 1.62 7102 142 0.91 15.30 1.11 1.08 1426.06| | 7: 1.62 - 1.54 7104 148 0.90 17.02 1.11 1.07 1252.96| | 8: 1.54 - 1.47 6798 152 0.89 18.26 1.10 1.06 1141.17| | 9: 1.47 - 1.41 6938 155 0.88 19.35 1.10 1.06 1022.52| | 10: 1.41 - 1.36 7022 150 0.86 20.93 1.09 1.04 920.28| | 11: 1.36 - 1.32 6997 151 0.86 21.37 1.08 1.03 815.99| | 12: 1.32 - 1.28 6976 149 0.86 21.19 1.08 1.01 719.08| | 13: 1.28 - 1.25 6907 166 0.87 20.15 1.07 1.02 614.45| | 14: 1.25 - 1.22 7015 113 0.87 20.55 1.08 1.04 561.54| | 15: 1.22 - 1.19 6957 137 0.87 20.32 1.08 1.04 516.33| | 16: 1.19 - 1.17 6604 132 0.87 20.49 1.08 1.04 494.75| | 17: 1.17 - 1.14 6941 135 0.86 21.59 1.09 1.02 461.61| | 18: 1.14 - 1.12 6875 142 0.85 22.36 1.08 1.00 436.86| | 19: 1.12 - 1.10 6949 106 0.85 22.97 1.07 1.00 405.84| | 20: 1.10 - 1.08 6884 147 0.84 23.53 1.07 0.99 371.15| | 21: 1.08 - 1.07 6852 152 0.84 23.88 1.07 0.98 338.40| | 22: 1.07 - 1.05 6838 135 0.82 25.36 1.06 0.97 322.66| | 23: 1.05 - 1.03 6829 159 0.81 27.06 1.06 0.97 317.16| | 24: 1.03 - 1.02 6785 133 0.78 29.23 1.05 0.97 324.05| | 25: 1.02 - 1.01 6552 130 0.77 30.33 1.03 0.93 305.24| | 26: 1.01 - 0.99 6767 158 0.75 31.96 1.02 0.92 285.93| | 27: 0.99 - 0.98 6648 131 0.76 31.21 1.04 0.93 264.43| |alpha: min = 0.92 max = 1.08 mean = 1.01| |beta: min = 264.43 max = 35215.72 mean = 2794.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.60| |phase err.(test): min = 0.00 max = 88.58 mean = 21.69| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.265 2950 Z= 5.542 Angle : 5.205 18.896 4018 Z= 3.718 Chirality : 0.402 1.228 492 Planarity : 0.032 0.167 512 Dihedral : 12.742 82.610 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.60 % Rotamer: Outliers : 0.65 % Allowed : 3.87 % Favored : 95.48 % Cbeta Deviations : 30.90 % 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: -2.38 (0.38), residues: 386 helix: -2.99 (0.28), residues: 146 sheet: -1.05 (0.49), residues: 82 loop : -0.06 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.014 ARG A 143 TYR 0.095 0.039 TYR A 192 PHE 0.084 0.035 PHE B 164 TRP 0.126 0.042 TRP B 139 HIS 0.093 0.030 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2044 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.303825 | | target function (ml) not normalized (work): 806162.440808 | | target function (ml) not normalized (free): 16548.312418 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2042 0.2044 0.1961 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2042 0.2044 0.1961 n_refl.: 191155 remove outliers: r(all,work,free)=0.2042 0.2044 0.1961 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2038 0.2041 0.1960 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1810 0.1809 0.1897 n_refl.: 191145 remove outliers: r(all,work,free)=0.1808 0.1806 0.1897 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4102 402.814 292.322 0.420 0.936 0.299 13.296-10.522 99.01 99 1 0.2442 528.187 519.206 0.764 0.937 0.246 10.503-8.327 98.90 177 3 0.2469 564.205 559.536 0.942 0.938 0.220 8.318-6.595 100.00 360 8 0.2502 414.736 402.396 0.935 0.938 0.155 6.588-5.215 100.00 711 7 0.2246 381.101 364.860 0.925 0.938 0.150 5.214-4.128 98.38 1367 28 0.1488 557.435 548.651 1.044 0.938 0.110 4.126-3.266 94.74 2603 46 0.1338 508.132 498.578 1.109 0.939 0.019 3.266-2.585 99.86 5447 97 0.1457 342.774 337.096 1.080 0.938 0.000 2.585-2.046 97.45 10613 204 0.1403 258.603 254.493 1.089 0.938 0.000 2.046-1.619 99.39 21536 464 0.1624 153.054 150.086 1.104 0.938 0.000 1.619-1.281 98.00 42464 925 0.1938 82.395 80.443 1.091 0.937 0.000 1.281-0.980 96.53 101826 2056 0.2326 44.203 41.995 1.081 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0621 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1806 r_free=0.1897 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1806 r_free=0.1897 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.469156 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 574.142806 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 0.1270 0.1500 0.0230 0.040 1.2 11.0 0.0 0.3 0 11.235 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.00 2.30 1.117 13.088 574.143 0.018 12.97 15.65 2.68 1.229 13.352 574.143 0.017 Individual atomic B min max mean iso aniso Overall: 5.25 73.02 15.05 1.40 435 3274 Protein: 5.25 40.58 11.03 1.40 0 2902 Water: 6.38 73.02 29.55 N/A 435 370 Other: 16.09 30.03 23.06 N/A 0 2 Chain A: 5.38 60.17 13.08 N/A 0 1626 Chain B: 5.25 73.02 12.81 N/A 0 1648 Chain S: 11.69 64.91 30.95 N/A 435 0 Histogram: Values Number of atoms 5.25 - 12.02 2171 12.02 - 18.80 635 18.80 - 25.58 313 25.58 - 32.36 266 32.36 - 39.13 154 39.13 - 45.91 105 45.91 - 52.69 39 52.69 - 59.47 20 59.47 - 66.24 5 66.24 - 73.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1566 r_work=0.1297 r_free=0.1560 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1560 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 = 0.1282 r_free = 0.1550 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015552 | | target function (ls_wunit_k1) not normalized (work): 2912.906234 | | target function (ls_wunit_k1) not normalized (free): 115.564549 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1550 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1470 0.1468 0.1629 n_refl.: 191138 remove outliers: r(all,work,free)=0.1470 0.1468 0.1629 n_refl.: 191138 overall B=0.15 to atoms: r(all,work,free)=0.1492 0.1489 0.1638 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1274 0.1541 n_refl.: 191138 remove outliers: r(all,work,free)=0.1280 0.1274 0.1540 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3608 402.814 381.190 0.469 1.003 0.275 13.296-10.522 99.01 99 1 0.2095 528.187 520.573 0.710 1.004 0.250 10.503-8.327 98.90 177 3 0.1709 564.205 561.929 0.850 1.004 0.203 8.318-6.595 100.00 360 8 0.1717 414.736 412.466 0.871 1.004 0.155 6.588-5.215 100.00 711 7 0.1537 381.101 373.496 0.852 1.004 0.150 5.214-4.128 98.38 1367 28 0.0902 557.435 554.199 0.939 1.005 0.090 4.126-3.266 94.74 2603 46 0.0830 508.132 504.311 1.002 1.005 0.014 3.266-2.585 99.86 5447 97 0.0922 342.774 340.414 0.983 1.005 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.441 0.996 1.006 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.435 1.013 1.006 0.000 1.619-1.281 98.00 42464 925 0.1277 82.395 81.426 1.005 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.132 0.982 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0338 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1540 | n_water=805 | time (s): 3.390 (total time: 3.390) Filter (dist) r_work=0.1279 r_free=0.1541 | n_water=794 | time (s): 105.070 (total time: 108.460) Filter (q & B) r_work=0.1279 r_free=0.1540 | n_water=790 | time (s): 4.850 (total time: 113.310) Compute maps r_work=0.1279 r_free=0.1540 | n_water=790 | time (s): 2.060 (total time: 115.370) Filter (map) r_work=0.1303 r_free=0.1523 | n_water=653 | time (s): 4.060 (total time: 119.430) Find peaks r_work=0.1303 r_free=0.1523 | n_water=653 | time (s): 0.600 (total time: 120.030) Add new water r_work=0.1328 r_free=0.1552 | n_water=960 | time (s): 4.140 (total time: 124.170) Refine new water occ: r_work=0.1285 r_free=0.1512 adp: r_work=0.1272 r_free=0.1506 occ: r_work=0.1274 r_free=0.1504 adp: r_work=0.1268 r_free=0.1503 occ: r_work=0.1269 r_free=0.1499 adp: r_work=0.1267 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1499 r_work=0.1267 r_free=0.1499 | n_water=960 | time (s): 80.290 (total time: 204.460) Filter (q & B) r_work=0.1270 r_free=0.1503 | n_water=891 | time (s): 5.570 (total time: 210.030) Filter (dist only) r_work=0.1271 r_free=0.1502 | n_water=890 | time (s): 117.300 (total time: 327.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.576514 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 593.987208 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 0.1253 0.1507 0.0254 0.042 1.2 17.3 0.0 0.3 0 11.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.07 2.54 2.045 15.252 593.987 0.014 12.32 15.02 2.70 2.434 15.318 593.987 0.014 Individual atomic B min max mean iso aniso Overall: 5.45 69.30 16.46 1.21 522 3272 Protein: 5.45 40.60 10.99 1.21 0 2902 Water: 6.71 69.30 34.29 N/A 522 368 Other: 16.38 34.17 25.27 N/A 0 2 Chain A: 5.55 56.11 13.01 N/A 0 1624 Chain B: 5.45 68.17 12.85 N/A 0 1648 Chain S: 8.42 69.30 38.60 N/A 522 0 Histogram: Values Number of atoms 5.45 - 11.84 2089 11.84 - 18.22 697 18.22 - 24.61 255 24.61 - 30.99 210 30.99 - 37.38 171 37.38 - 43.76 163 43.76 - 50.15 114 50.15 - 56.53 44 56.53 - 62.92 36 62.92 - 69.30 15 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1503 r_work=0.1233 r_free=0.1504 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1504 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 = 0.1226 r_free = 0.1501 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1501 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013352 | | target function (ls_wunit_k1) not normalized (work): 2500.833332 | | target function (ls_wunit_k1) not normalized (free): 99.671005 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1501 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1595 n_refl.: 191137 remove outliers: r(all,work,free)=0.1439 0.1436 0.1595 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1433 0.1593 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1509 n_refl.: 191137 remove outliers: r(all,work,free)=0.1238 0.1233 0.1509 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3226 402.814 379.535 0.495 0.962 0.271 13.296-10.522 99.01 99 1 0.1849 528.187 523.134 0.765 0.963 0.250 10.503-8.327 98.90 177 3 0.1418 564.205 566.750 0.920 0.963 0.183 8.318-6.595 100.00 360 8 0.1535 414.736 414.881 0.933 0.963 0.151 6.588-5.215 100.00 711 7 0.1305 381.101 377.064 0.914 0.963 0.137 5.214-4.128 98.38 1367 28 0.0826 557.435 555.950 0.996 0.963 0.110 4.126-3.266 94.74 2603 46 0.0758 508.132 505.560 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0858 342.774 341.454 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.787 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.629 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.348 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.213 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=-0.0580 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1509 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1509 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1509 | n_water=890 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1235 r_free=0.1511 | n_water=884 | time (s): 119.570 (total time: 122.590) Filter (q & B) r_work=0.1235 r_free=0.1511 | n_water=882 | time (s): 5.660 (total time: 128.250) Compute maps r_work=0.1235 r_free=0.1511 | n_water=882 | time (s): 2.060 (total time: 130.310) Filter (map) r_work=0.1273 r_free=0.1522 | n_water=680 | time (s): 4.520 (total time: 134.830) Find peaks r_work=0.1273 r_free=0.1522 | n_water=680 | time (s): 0.550 (total time: 135.380) Add new water r_work=0.1297 r_free=0.1553 | n_water=989 | time (s): 5.080 (total time: 140.460) Refine new water occ: r_work=0.1252 r_free=0.1517 adp: r_work=0.1253 r_free=0.1518 occ: r_work=0.1248 r_free=0.1513 adp: r_work=0.1248 r_free=0.1514 occ: r_work=0.1245 r_free=0.1509 adp: r_work=0.1245 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1509 r_work=0.1245 r_free=0.1509 | n_water=989 | time (s): 309.010 (total time: 449.470) Filter (q & B) r_work=0.1250 r_free=0.1510 | n_water=874 | time (s): 4.590 (total time: 454.060) Filter (dist only) r_work=0.1250 r_free=0.1509 | n_water=872 | time (s): 110.700 (total time: 564.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.716082 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.116514 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 0.1239 0.1438 0.0198 0.036 1.1 7.6 0.0 0.0 0 0.858 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.38 1.98 1.933 14.513 16.117 3.940 12.37 13.97 1.60 2.268 14.414 16.117 3.898 Individual atomic B min max mean iso aniso Overall: 5.58 67.71 15.13 1.04 505 3271 Protein: 5.58 36.41 10.72 1.04 0 2902 Water: 6.71 67.71 29.77 N/A 505 367 Other: 13.74 29.52 21.63 N/A 0 2 Chain A: 5.60 55.08 12.76 N/A 0 1624 Chain B: 5.58 67.71 12.54 N/A 0 1647 Chain S: 12.94 63.40 31.20 N/A 505 0 Histogram: Values Number of atoms 5.58 - 11.79 2135 11.79 - 18.00 689 18.00 - 24.22 316 24.22 - 30.43 234 30.43 - 36.64 171 36.64 - 42.86 131 42.86 - 49.07 66 49.07 - 55.29 24 55.29 - 61.50 6 61.50 - 67.71 4 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1397 r_work=0.1238 r_free=0.1398 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1398 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1233 r_free = 0.1387 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1233 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892257 | | target function (ml) not normalized (work): 729004.214600 | | target function (ml) not normalized (free): 15226.537391 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1233 0.1387 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1447 0.1447 0.1477 n_refl.: 191137 remove outliers: r(all,work,free)=0.1447 0.1447 0.1477 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1441 0.1441 0.1473 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1232 0.1229 0.1377 n_refl.: 191137 remove outliers: r(all,work,free)=0.1231 0.1228 0.1377 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3781 393.525 360.700 0.419 0.945 0.245 13.296-10.522 97.03 97 1 0.2433 531.410 503.489 0.705 0.946 0.209 10.503-8.327 97.80 175 3 0.2001 554.286 558.248 0.879 0.946 0.173 8.318-6.595 100.00 360 8 0.2137 414.736 408.784 0.895 0.946 0.125 6.588-5.215 100.00 711 7 0.1827 381.101 371.658 0.887 0.946 0.104 5.214-4.128 98.38 1367 28 0.1163 557.435 551.979 0.973 0.946 0.070 4.126-3.266 94.74 2603 46 0.1102 508.132 501.216 1.035 0.947 0.009 3.266-2.585 99.86 5447 97 0.1089 342.774 339.224 1.022 0.946 0.000 2.585-2.046 97.45 10613 204 0.0976 258.603 255.730 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0978 153.054 151.404 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1054 82.395 81.482 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.312 1.039 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1090 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1228 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1377 | n_water=872 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1228 r_free=0.1377 | n_water=870 | time (s): 105.350 (total time: 108.410) Filter (q & B) r_work=0.1228 r_free=0.1373 | n_water=857 | time (s): 4.930 (total time: 113.340) Compute maps r_work=0.1228 r_free=0.1373 | n_water=857 | time (s): 2.530 (total time: 115.870) Filter (map) r_work=0.1250 r_free=0.1393 | n_water=721 | time (s): 5.390 (total time: 121.260) Find peaks r_work=0.1250 r_free=0.1393 | n_water=721 | time (s): 0.850 (total time: 122.110) Add new water r_work=0.1263 r_free=0.1405 | n_water=974 | time (s): 5.660 (total time: 127.770) Refine new water occ: r_work=0.1214 r_free=0.1355 adp: r_work=0.1207 r_free=0.1352 occ: r_work=0.1204 r_free=0.1352 adp: r_work=0.1204 r_free=0.1351 occ: r_work=0.1202 r_free=0.1351 adp: r_work=0.1202 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1350 r_work=0.1202 r_free=0.1350 | n_water=974 | time (s): 304.570 (total time: 432.340) Filter (q & B) r_work=0.1208 r_free=0.1359 | n_water=879 | time (s): 5.160 (total time: 437.500) Filter (dist only) r_work=0.1208 r_free=0.1358 | n_water=878 | time (s): 111.910 (total time: 549.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.636402 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.985781 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1362 0.0157 0.036 1.1 6.5 0.0 0.3 0 0.818 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.62 1.57 1.821 14.200 15.986 3.873 11.96 13.59 1.64 1.922 14.163 15.986 3.864 Individual atomic B min max mean iso aniso Overall: 5.51 67.19 14.99 1.00 511 3271 Protein: 5.51 33.22 10.65 1.00 0 2902 Water: 6.05 67.19 29.32 N/A 511 367 Other: 13.95 28.20 21.08 N/A 0 2 Chain A: 5.58 53.89 12.63 N/A 0 1624 Chain B: 5.51 67.19 12.45 N/A 0 1647 Chain S: 6.05 63.47 30.71 N/A 511 0 Histogram: Values Number of atoms 5.51 - 11.68 2106 11.68 - 17.84 739 17.84 - 24.01 299 24.01 - 30.18 245 30.18 - 36.35 170 36.35 - 42.52 129 42.52 - 48.69 61 48.69 - 54.85 24 54.85 - 61.02 5 61.02 - 67.19 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1359 r_work=0.1196 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1358 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861902 | | target function (ml) not normalized (work): 723295.685295 | | target function (ml) not normalized (free): 15135.964771 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1193 0.1358 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1417 0.1416 0.1467 n_refl.: 191131 remove outliers: r(all,work,free)=0.1417 0.1416 0.1467 n_refl.: 191131 overall B=-0.03 to atoms: r(all,work,free)=0.1410 0.1409 0.1463 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1191 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1194 0.1191 0.1357 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3485 348.042 307.553 0.403 0.948 0.243 13.296-10.522 97.03 97 1 0.2434 481.135 461.448 0.702 0.950 0.184 10.503-8.327 97.80 175 3 0.2085 501.846 496.806 0.864 0.950 0.157 8.318-6.595 100.00 360 8 0.2126 375.499 370.805 0.885 0.949 0.100 6.588-5.215 100.00 711 7 0.1861 345.046 335.982 0.882 0.949 0.079 5.214-4.128 98.38 1367 28 0.1168 504.697 499.790 0.971 0.950 0.060 4.126-3.266 94.74 2603 46 0.1121 460.059 453.382 1.032 0.950 0.009 3.266-2.585 99.86 5447 97 0.1083 310.344 307.191 1.019 0.949 0.000 2.585-2.046 97.45 10613 204 0.0932 234.137 231.738 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0909 138.574 137.299 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0985 74.600 73.894 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.020 38.360 1.042 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1167 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1357 | n_water=878 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1191 r_free=0.1356 | n_water=876 | time (s): 110.850 (total time: 113.560) Filter (q & B) r_work=0.1192 r_free=0.1358 | n_water=867 | time (s): 5.440 (total time: 119.000) Compute maps r_work=0.1192 r_free=0.1358 | n_water=867 | time (s): 1.690 (total time: 120.690) Filter (map) r_work=0.1217 r_free=0.1365 | n_water=739 | time (s): 4.130 (total time: 124.820) Find peaks r_work=0.1217 r_free=0.1365 | n_water=739 | time (s): 0.630 (total time: 125.450) Add new water r_work=0.1228 r_free=0.1377 | n_water=965 | time (s): 4.560 (total time: 130.010) Refine new water occ: r_work=0.1191 r_free=0.1337 adp: r_work=0.1191 r_free=0.1336 occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1189 r_free=0.1336 occ: r_work=0.1187 r_free=0.1337 adp: r_work=0.1187 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1336 r_work=0.1187 r_free=0.1336 | n_water=965 | time (s): 182.780 (total time: 312.790) Filter (q & B) r_work=0.1192 r_free=0.1347 | n_water=875 | time (s): 5.530 (total time: 318.320) Filter (dist only) r_work=0.1193 r_free=0.1347 | n_water=874 | time (s): 111.810 (total time: 430.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.539732 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.584148 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1351 0.0156 0.036 1.1 6.0 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.51 1.56 1.787 14.087 15.584 3.763 11.98 13.52 1.54 1.833 14.069 15.584 3.760 Individual atomic B min max mean iso aniso Overall: 5.59 66.90 14.90 0.96 507 3271 Protein: 5.59 32.11 10.60 0.96 0 2902 Water: 5.95 66.90 29.17 N/A 507 367 Other: 13.84 27.30 20.57 N/A 0 2 Chain A: 5.60 53.37 12.55 N/A 0 1624 Chain B: 5.59 66.90 12.37 N/A 0 1647 Chain S: 5.95 63.46 30.64 N/A 507 0 Histogram: Values Number of atoms 5.59 - 11.72 2137 11.72 - 17.85 724 17.85 - 23.98 298 23.98 - 30.11 228 30.11 - 36.25 166 36.25 - 42.38 129 42.38 - 48.51 65 48.51 - 54.64 23 54.64 - 60.77 4 60.77 - 66.90 4 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1352 r_work=0.1198 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1353 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1353 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759299 | | target function (ml) not normalized (work): 704067.875795 | | target function (ml) not normalized (free): 14733.936661 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1472 n_refl.: 191128 remove outliers: r(all,work,free)=0.1398 0.1396 0.1472 n_refl.: 191128 overall B=-0.03 to atoms: r(all,work,free)=0.1392 0.1390 0.1468 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1348 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1348 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3516 348.042 321.412 0.394 0.975 0.223 13.296-10.522 97.03 97 1 0.2436 481.135 463.172 0.673 0.977 0.166 10.503-8.327 97.80 175 3 0.2121 501.846 494.373 0.832 0.977 0.140 8.318-6.595 100.00 360 8 0.2126 375.499 371.026 0.859 0.976 0.108 6.588-5.215 100.00 711 7 0.1887 345.046 336.054 0.855 0.976 0.080 5.214-4.128 98.38 1367 28 0.1200 504.697 499.556 0.942 0.975 0.044 4.126-3.266 94.74 2603 46 0.1142 460.059 453.174 1.004 0.974 0.009 3.266-2.585 99.86 5447 97 0.1100 310.344 307.149 0.993 0.971 0.000 2.585-2.046 97.45 10613 204 0.0948 234.137 231.642 1.008 0.968 0.000 2.046-1.619 99.39 21536 464 0.0912 138.574 137.248 1.036 0.962 0.000 1.619-1.281 98.00 42464 925 0.0973 74.600 73.897 1.044 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1645 40.020 38.346 1.047 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1348 | n_water=874 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1193 r_free=0.1348 | n_water=873 | time (s): 107.330 (total time: 109.680) Filter (q & B) r_work=0.1194 r_free=0.1348 | n_water=866 | time (s): 4.900 (total time: 114.580) Compute maps r_work=0.1194 r_free=0.1348 | n_water=866 | time (s): 2.130 (total time: 116.710) Filter (map) r_work=0.1214 r_free=0.1355 | n_water=756 | time (s): 5.450 (total time: 122.160) Find peaks r_work=0.1214 r_free=0.1355 | n_water=756 | time (s): 0.690 (total time: 122.850) Add new water r_work=0.1224 r_free=0.1361 | n_water=977 | time (s): 4.280 (total time: 127.130) Refine new water occ: r_work=0.1190 r_free=0.1336 adp: r_work=0.1191 r_free=0.1335 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1334 occ: r_work=0.1186 r_free=0.1334 adp: r_work=0.1186 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1333 r_work=0.1186 r_free=0.1333 | n_water=977 | time (s): 228.670 (total time: 355.800) Filter (q & B) r_work=0.1191 r_free=0.1340 | n_water=889 | time (s): 4.410 (total time: 360.210) Filter (dist only) r_work=0.1191 r_free=0.1340 | n_water=888 | time (s): 110.720 (total time: 470.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.555872 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.807811 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1343 0.0149 0.037 1.1 5.6 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.43 1.49 1.763 14.039 15.808 3.759 11.95 13.45 1.50 1.881 14.002 15.808 3.755 Individual atomic B min max mean iso aniso Overall: 5.57 65.75 14.84 0.92 522 3270 Protein: 5.57 29.75 10.51 0.92 0 2902 Water: 5.97 65.75 28.98 N/A 522 366 Other: 13.88 24.18 19.03 N/A 0 2 Chain A: 5.66 52.72 12.41 N/A 0 1623 Chain B: 5.57 65.75 12.26 N/A 0 1647 Chain S: 5.97 63.59 30.55 N/A 522 0 Histogram: Values Number of atoms 5.57 - 11.59 2102 11.59 - 17.61 780 17.61 - 23.62 280 23.62 - 29.64 212 29.64 - 35.66 188 35.66 - 41.68 129 41.68 - 47.70 64 47.70 - 53.71 28 53.71 - 59.73 4 59.73 - 65.75 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1346 r_work=0.1195 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1346 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1345 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.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.754985 | | target function (ml) not normalized (work): 703259.909022 | | target function (ml) not normalized (free): 14723.329321 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1345 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1397 0.1396 0.1477 n_refl.: 191128 remove outliers: r(all,work,free)=0.1397 0.1396 0.1477 n_refl.: 191128 overall B=-0.24 to atoms: r(all,work,free)=0.1361 0.1359 0.1455 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1348 n_refl.: 191128 remove outliers: r(all,work,free)=0.1199 0.1196 0.1348 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3525 348.042 320.895 0.409 0.952 0.215 13.296-10.522 97.03 97 1 0.2443 481.135 462.484 0.709 0.953 0.161 10.503-8.327 97.80 175 3 0.2139 501.846 494.933 0.877 0.954 0.137 8.318-6.595 100.00 360 8 0.2147 375.499 371.322 0.904 0.953 0.090 6.588-5.215 100.00 711 7 0.1905 345.046 336.417 0.901 0.954 0.075 5.214-4.128 98.38 1367 28 0.1211 504.697 499.539 0.992 0.954 0.040 4.126-3.266 94.74 2603 46 0.1152 460.059 453.016 1.055 0.954 0.009 3.266-2.585 99.86 5447 97 0.1112 310.344 307.036 1.038 0.954 0.000 2.585-2.046 97.45 10613 204 0.0950 234.137 231.614 1.046 0.954 0.000 2.046-1.619 99.39 21536 464 0.0910 138.574 137.292 1.063 0.953 0.000 1.619-1.281 98.00 42464 925 0.0969 74.600 73.902 1.051 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.020 38.349 1.021 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0526 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1348 | n_water=888 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1197 r_free=0.1350 | n_water=887 | time (s): 120.150 (total time: 122.530) Filter (q & B) r_work=0.1197 r_free=0.1350 | n_water=879 | time (s): 5.600 (total time: 128.130) Compute maps r_work=0.1197 r_free=0.1350 | n_water=879 | time (s): 2.400 (total time: 130.530) Filter (map) r_work=0.1219 r_free=0.1356 | n_water=765 | time (s): 4.120 (total time: 134.650) Find peaks r_work=0.1219 r_free=0.1356 | n_water=765 | time (s): 0.690 (total time: 135.340) Add new water r_work=0.1227 r_free=0.1361 | n_water=978 | time (s): 4.600 (total time: 139.940) Refine new water occ: r_work=0.1194 r_free=0.1339 adp: r_work=0.1194 r_free=0.1339 occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1192 r_free=0.1339 occ: r_work=0.1191 r_free=0.1339 adp: r_work=0.1190 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1338 r_work=0.1190 r_free=0.1338 | n_water=978 | time (s): 184.820 (total time: 324.760) Filter (q & B) r_work=0.1194 r_free=0.1348 | n_water=897 | time (s): 4.070 (total time: 328.830) Filter (dist only) r_work=0.1195 r_free=0.1347 | n_water=896 | time (s): 116.200 (total time: 445.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540121 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.828446 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 0.1353 0.0155 0.038 1.1 7.2 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.53 1.55 1.727 13.737 13.828 3.758 12.02 13.57 1.55 1.751 13.724 13.828 3.759 Individual atomic B min max mean iso aniso Overall: 5.37 65.12 14.61 0.88 530 3270 Protein: 5.37 28.96 10.27 0.88 0 2902 Water: 5.81 65.12 28.66 N/A 530 366 Other: 13.67 23.21 18.44 N/A 0 2 Chain A: 5.44 52.28 12.13 N/A 0 1623 Chain B: 5.37 65.12 12.00 N/A 0 1647 Chain S: 5.81 63.38 30.31 N/A 530 0 Histogram: Values Number of atoms 5.37 - 11.34 2103 11.34 - 17.32 781 17.32 - 23.29 287 23.29 - 29.27 209 29.27 - 35.24 183 35.24 - 41.22 131 41.22 - 47.20 69 47.20 - 53.17 28 53.17 - 59.15 4 59.15 - 65.12 5 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1357 r_work=0.1202 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1357 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758197 | | target function (ml) not normalized (work): 703861.373388 | | target function (ml) not normalized (free): 14736.769565 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1360 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1369 0.1367 0.1466 n_refl.: 191128 remove outliers: r(all,work,free)=0.1369 0.1367 0.1466 n_refl.: 191128 overall B=0.06 to atoms: r(all,work,free)=0.1376 0.1374 0.1470 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1352 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1352 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3533 348.042 319.968 0.400 0.975 0.213 13.296-10.522 97.03 97 1 0.2406 481.135 462.508 0.694 0.976 0.154 10.503-8.327 97.80 175 3 0.2157 501.846 494.734 0.864 0.977 0.127 8.318-6.595 100.00 360 8 0.2158 375.499 370.503 0.891 0.977 0.089 6.588-5.215 100.00 711 7 0.1930 345.046 335.905 0.888 0.977 0.070 5.214-4.128 98.38 1367 28 0.1221 504.697 498.985 0.979 0.978 0.045 4.126-3.266 94.74 2603 46 0.1165 460.059 452.403 1.041 0.979 0.014 3.266-2.585 99.86 5447 97 0.1118 310.344 306.748 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0956 234.137 231.498 1.031 0.981 0.000 2.046-1.619 99.39 21536 464 0.0913 138.574 137.191 1.047 0.984 0.000 1.619-1.281 98.00 42464 925 0.0953 74.600 73.935 1.035 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1631 40.020 38.323 1.000 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0633 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1352 | n_water=896 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1192 r_free=0.1352 | n_water=896 | time (s): 112.720 (total time: 115.060) Filter (q & B) r_work=0.1193 r_free=0.1351 | n_water=887 | time (s): 5.280 (total time: 120.340) Compute maps r_work=0.1193 r_free=0.1351 | n_water=887 | time (s): 1.950 (total time: 122.290) Filter (map) r_work=0.1214 r_free=0.1350 | n_water=778 | time (s): 4.200 (total time: 126.490) Find peaks r_work=0.1214 r_free=0.1350 | n_water=778 | time (s): 0.590 (total time: 127.080) Add new water r_work=0.1222 r_free=0.1357 | n_water=983 | time (s): 4.070 (total time: 131.150) Refine new water occ: r_work=0.1189 r_free=0.1332 adp: r_work=0.1189 r_free=0.1332 occ: r_work=0.1187 r_free=0.1332 adp: r_work=0.1187 r_free=0.1331 occ: r_work=0.1186 r_free=0.1332 adp: r_work=0.1185 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1331 r_work=0.1185 r_free=0.1331 | n_water=983 | time (s): 235.040 (total time: 366.190) Filter (q & B) r_work=0.1189 r_free=0.1340 | n_water=907 | time (s): 5.890 (total time: 372.080) Filter (dist only) r_work=0.1190 r_free=0.1340 | n_water=905 | time (s): 114.360 (total time: 486.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.541249 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.027269 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 0.1192 0.1346 0.0153 0.039 1.1 5.8 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.46 1.53 1.683 13.767 14.027 3.756 11.93 13.46 1.54 1.715 13.756 14.027 3.754 Individual atomic B min max mean iso aniso Overall: 5.50 64.29 14.67 0.87 539 3270 Protein: 5.50 28.39 10.32 0.87 0 2902 Water: 5.92 64.29 28.61 N/A 539 366 Other: 13.75 22.23 17.99 N/A 0 2 Chain A: 5.57 51.90 12.15 N/A 0 1623 Chain B: 5.50 64.29 12.03 N/A 0 1647 Chain S: 5.92 63.52 30.33 N/A 539 0 Histogram: Values Number of atoms 5.50 - 11.38 2087 11.38 - 17.26 803 17.26 - 23.14 280 23.14 - 29.02 209 29.02 - 34.89 188 34.89 - 40.77 125 40.77 - 46.65 74 46.65 - 52.53 33 52.53 - 58.41 5 58.41 - 64.29 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1347 r_work=0.1193 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1347 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1349 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753947 | | target function (ml) not normalized (work): 703065.492929 | | target function (ml) not normalized (free): 14725.134316 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1349 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1382 0.1381 0.1474 n_refl.: 191128 remove outliers: r(all,work,free)=0.1382 0.1381 0.1474 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1384 0.1383 0.1475 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1348 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1190 0.1348 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3544 348.042 319.708 0.389 0.995 0.211 13.296-10.522 97.03 97 1 0.2429 481.135 461.928 0.676 0.996 0.147 10.503-8.327 97.80 175 3 0.2148 501.846 494.783 0.845 0.997 0.117 8.318-6.595 100.00 360 8 0.2164 375.499 370.766 0.870 0.997 0.084 6.588-5.215 100.00 711 7 0.1936 345.046 336.100 0.868 0.997 0.063 5.214-4.128 98.38 1367 28 0.1226 504.697 498.822 0.958 0.998 0.040 4.126-3.266 94.74 2603 46 0.1168 460.059 452.240 1.019 0.999 0.014 3.266-2.585 99.86 5447 97 0.1120 310.344 306.728 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0957 234.137 231.483 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0912 138.574 137.207 1.027 1.006 0.000 1.619-1.281 98.00 42464 925 0.0947 74.600 73.946 1.017 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.020 38.312 0.985 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0208 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1348 | n_water=905 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1191 r_free=0.1349 | n_water=904 | time (s): 122.930 (total time: 126.130) Filter (q & B) r_work=0.1192 r_free=0.1348 | n_water=891 | time (s): 4.370 (total time: 130.500) Compute maps r_work=0.1192 r_free=0.1348 | n_water=891 | time (s): 1.980 (total time: 132.480) Filter (map) r_work=0.1213 r_free=0.1351 | n_water=779 | time (s): 5.140 (total time: 137.620) Find peaks r_work=0.1213 r_free=0.1351 | n_water=779 | time (s): 0.530 (total time: 138.150) Add new water r_work=0.1220 r_free=0.1359 | n_water=991 | time (s): 4.630 (total time: 142.780) Refine new water occ: r_work=0.1187 r_free=0.1331 adp: r_work=0.1187 r_free=0.1330 occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1186 r_free=0.1330 occ: r_work=0.1184 r_free=0.1330 adp: r_work=0.1184 r_free=0.1330 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1330 r_work=0.1184 r_free=0.1330 | n_water=991 | time (s): 174.450 (total time: 317.230) Filter (q & B) r_work=0.1189 r_free=0.1341 | n_water=903 | time (s): 5.480 (total time: 322.710) Filter (dist only) r_work=0.1189 r_free=0.1342 | n_water=901 | time (s): 117.610 (total time: 440.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.527870 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.253663 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1347 0.0154 0.039 1.1 6.6 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.47 1.54 1.681 13.745 14.254 3.755 11.93 13.50 1.57 1.695 13.745 14.254 3.753 Individual atomic B min max mean iso aniso Overall: 5.55 63.22 14.65 0.87 535 3270 Protein: 5.55 28.15 10.34 0.87 0 2902 Water: 5.97 63.22 28.49 N/A 535 366 Other: 13.81 22.12 17.96 N/A 0 2 Chain A: 5.62 51.42 12.15 N/A 0 1623 Chain B: 5.55 63.22 12.03 N/A 0 1647 Chain S: 5.97 61.52 30.29 N/A 535 0 Histogram: Values Number of atoms 5.55 - 11.32 2062 11.32 - 17.08 827 17.08 - 22.85 271 22.85 - 28.62 202 28.62 - 34.38 193 34.38 - 40.15 125 40.15 - 45.92 76 45.92 - 51.68 38 51.68 - 57.45 7 57.45 - 63.22 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1350 r_work=0.1193 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752851 | | target function (ml) not normalized (work): 702860.142167 | | target function (ml) not normalized (free): 14722.163935 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1393 0.1392 0.1477 n_refl.: 191128 remove outliers: r(all,work,free)=0.1393 0.1392 0.1477 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1393 0.1391 0.1477 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1349 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1349 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3499 348.042 319.794 0.392 0.975 0.203 13.296-10.522 97.03 97 1 0.2432 481.135 461.483 0.686 0.976 0.136 10.503-8.327 97.80 175 3 0.2170 501.846 494.922 0.860 0.977 0.107 8.318-6.595 100.00 360 8 0.2179 375.499 370.058 0.887 0.977 0.086 6.588-5.215 100.00 711 7 0.1947 345.046 335.751 0.885 0.977 0.071 5.214-4.128 98.38 1367 28 0.1235 504.697 498.806 0.976 0.978 0.034 4.126-3.266 94.74 2603 46 0.1173 460.059 452.228 1.040 0.980 0.005 3.266-2.585 99.86 5447 97 0.1123 310.344 306.674 1.024 0.981 0.000 2.585-2.046 97.45 10613 204 0.0959 234.137 231.490 1.031 0.983 0.000 2.046-1.619 99.39 21536 464 0.0909 138.574 137.216 1.048 0.987 0.000 1.619-1.281 98.00 42464 925 0.0943 74.600 73.952 1.039 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.020 38.303 1.008 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0094 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1349 After: r_work=0.1192 r_free=0.1349 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1349 | n_water=901 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1192 r_free=0.1349 | n_water=901 | time (s): 118.840 (total time: 121.400) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=890 | time (s): 5.140 (total time: 126.540) Compute maps r_work=0.1192 r_free=0.1349 | n_water=890 | time (s): 2.220 (total time: 128.760) Filter (map) r_work=0.1214 r_free=0.1350 | n_water=780 | time (s): 4.800 (total time: 133.560) Find peaks r_work=0.1214 r_free=0.1350 | n_water=780 | time (s): 0.650 (total time: 134.210) Add new water r_work=0.1220 r_free=0.1360 | n_water=1000 | time (s): 4.410 (total time: 138.620) Refine new water occ: r_work=0.1188 r_free=0.1331 adp: r_work=0.1188 r_free=0.1331 occ: r_work=0.1186 r_free=0.1331 adp: r_work=0.1186 r_free=0.1331 occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1185 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1331 r_work=0.1185 r_free=0.1331 | n_water=1000 | time (s): 262.870 (total time: 401.490) Filter (q & B) r_work=0.1190 r_free=0.1343 | n_water=911 | time (s): 4.680 (total time: 406.170) Filter (dist only) r_work=0.1191 r_free=0.1343 | n_water=908 | time (s): 114.330 (total time: 520.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.530230 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 12.830510 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1347 0.0153 0.039 1.2 8.9 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.47 1.53 1.679 13.750 12.831 3.755 11.97 13.51 1.54 1.679 13.748 12.831 3.757 Individual atomic B min max mean iso aniso Overall: 5.57 62.93 14.65 0.84 542 3270 Protein: 5.57 27.94 10.35 0.84 0 2902 Water: 6.03 62.93 28.35 N/A 542 366 Other: 13.83 22.15 17.99 N/A 0 2 Chain A: 5.66 51.32 12.13 N/A 0 1623 Chain B: 5.57 62.93 12.02 N/A 0 1647 Chain S: 6.03 61.48 30.14 N/A 542 0 Histogram: Values Number of atoms 5.57 - 11.31 2057 11.31 - 17.04 837 17.04 - 22.78 269 22.78 - 28.52 204 28.52 - 34.25 198 34.25 - 39.99 124 39.99 - 45.72 74 45.72 - 51.46 37 51.46 - 57.20 8 57.20 - 62.93 4 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1351 r_work=0.1197 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1351 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1351 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756741 | | target function (ml) not normalized (work): 703588.759298 | | target function (ml) not normalized (free): 14729.675731 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1368 0.1432 5.6885 5.7453| | 2: 2.94 - 2.33 1.00 7339 128 0.1071 0.1391 5.0745 5.187| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1169 4.6556 4.7437| | 4: 2.04 - 1.85 1.00 7170 155 0.0904 0.1037 4.3973 4.5585| | 5: 1.85 - 1.72 0.99 7113 159 0.0938 0.0994 4.1579 4.2546| | 6: 1.72 - 1.62 0.99 7102 142 0.0902 0.1093 3.9535 4.0812| | 7: 1.62 - 1.54 0.99 7104 148 0.0894 0.0959 3.804 3.9386| | 8: 1.54 - 1.47 0.96 6798 152 0.0895 0.1310 3.7046 3.8968| | 9: 1.47 - 1.41 0.98 6938 155 0.0934 0.1134 3.6287 3.7584| | 10: 1.41 - 1.36 0.99 7022 150 0.0981 0.1189 3.5629 3.6787| | 11: 1.36 - 1.32 0.99 6997 151 0.0997 0.1139 3.4901 3.5994| | 12: 1.32 - 1.28 0.98 6975 149 0.1038 0.1126 3.4649 3.5832| | 13: 1.28 - 1.25 0.98 6907 166 0.1048 0.1245 3.4423 3.5698| | 14: 1.25 - 1.22 0.98 7015 112 0.1111 0.1573 3.4349 3.6734| | 15: 1.22 - 1.19 0.98 6956 137 0.1172 0.1237 3.449 3.4876| | 16: 1.19 - 1.17 0.93 6604 132 0.1254 0.1547 3.4657 3.6563| | 17: 1.17 - 1.14 0.98 6940 135 0.1303 0.1224 3.4337 3.4361| | 18: 1.14 - 1.12 0.98 6875 142 0.1387 0.1706 3.4398 3.5312| | 19: 1.12 - 1.10 0.97 6948 106 0.1474 0.1749 3.4214 3.5943| | 20: 1.10 - 1.08 0.97 6884 147 0.1588 0.1584 3.4121 3.4378| | 21: 1.08 - 1.07 0.97 6852 152 0.1732 0.2134 3.4194 3.5031| | 22: 1.07 - 1.05 0.97 6836 135 0.1907 0.1954 3.4143 3.4172| | 23: 1.05 - 1.03 0.97 6827 159 0.2123 0.2014 3.4343 3.4858| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2261 3.4364 3.5128| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2518 3.4498 3.5262| | 26: 1.01 - 0.99 0.96 6767 158 0.2759 0.2852 3.4161 3.4206| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2808 3.4692 3.3955| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.44 1.00 0.96 10811.06| | 2: 2.94 - 2.33 7339 128 0.93 12.57 0.99 0.96 5000.94| | 3: 2.33 - 2.04 6939 150 0.96 7.65 1.01 0.96 1703.91| | 4: 2.04 - 1.85 7170 155 0.96 7.68 1.00 0.95 1010.57| | 5: 1.85 - 1.72 7113 159 0.96 8.15 1.00 0.96 641.21| | 6: 1.72 - 1.62 7102 142 0.96 8.09 1.00 0.96 448.25| | 7: 1.62 - 1.54 7104 148 0.96 8.19 1.01 0.97 340.13| | 8: 1.54 - 1.47 6798 152 0.96 8.30 1.01 0.97 281.19| | 9: 1.47 - 1.41 6938 155 0.96 8.54 1.00 0.98 233.56| | 10: 1.41 - 1.36 7022 150 0.96 9.00 1.00 0.97 205.32| | 11: 1.36 - 1.32 6997 151 0.96 9.03 0.99 0.96 177.31| | 12: 1.32 - 1.28 6975 149 0.96 9.07 0.98 0.95 162.68| | 13: 1.28 - 1.25 6907 166 0.96 9.59 1.01 0.96 159.50| | 14: 1.25 - 1.22 7015 112 0.95 10.72 1.01 0.97 163.34| | 15: 1.22 - 1.19 6956 137 0.95 11.21 1.01 0.98 165.93| | 16: 1.19 - 1.17 6604 132 0.95 11.37 1.01 0.96 159.05| | 17: 1.17 - 1.14 6940 135 0.94 12.19 1.01 0.96 152.84| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.95 147.19| | 19: 1.12 - 1.10 6948 106 0.93 14.16 1.00 0.95 151.21| | 20: 1.10 - 1.08 6884 147 0.92 15.27 1.00 0.94 150.84| | 21: 1.08 - 1.07 6852 152 0.91 16.68 1.00 0.93 153.69| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.93 155.27| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.92 164.90| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.93 179.42| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.90 182.29| | 26: 1.01 - 0.99 6767 158 0.81 26.66 0.98 0.89 176.84| | 27: 0.99 - 0.98 6647 131 0.82 26.36 0.99 0.87 161.33| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.19 max = 10811.06 mean = 906.49| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.30| |phase err.(test): min = 0.00 max = 89.09 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1351 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1406 0.1405 0.1487 n_refl.: 191128 remove outliers: r(all,work,free)=0.1406 0.1405 0.1487 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1397 0.1396 0.1482 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1350 n_refl.: 191128 remove outliers: r(all,work,free)=0.1199 0.1196 0.1350 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3542 348.042 317.467 0.378 0.974 0.201 13.296-10.522 97.03 97 1 0.2446 481.135 460.830 0.669 0.976 0.142 10.503-8.327 97.80 175 3 0.2164 501.846 495.141 0.836 0.976 0.117 8.315-6.595 100.00 359 8 0.2180 374.553 369.496 0.866 0.976 0.094 6.588-5.215 100.00 711 7 0.1967 345.046 335.158 0.863 0.977 0.077 5.214-4.128 98.38 1367 28 0.1252 504.697 498.583 0.953 0.978 0.029 4.126-3.266 94.74 2603 46 0.1172 460.059 452.395 1.016 0.980 0.000 3.266-2.585 99.86 5447 97 0.1127 310.344 306.760 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0963 234.137 231.471 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0916 138.574 137.200 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0951 74.600 73.943 1.010 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.020 38.293 0.977 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0130 ================= 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 : 0.2044 0.1961 0.083 5.205 5.2 78.0 14.6 805 0.000 1_bss: 0.1806 0.1897 0.083 5.205 5.2 78.0 14.6 805 0.000 1_settarget: 0.1806 0.1897 0.083 5.205 5.2 78.0 14.6 805 0.000 1_nqh: 0.1806 0.1897 0.083 5.205 5.2 78.0 14.6 805 0.000 1_weight: 0.1806 0.1897 0.083 5.205 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1500 0.040 1.169 5.2 78.0 14.6 805 0.157 1_adp: 0.1298 0.1566 0.040 1.169 5.2 73.0 15.1 805 0.157 1_regHadp: 0.1297 0.1560 0.040 1.169 5.2 73.0 15.1 805 0.157 1_occ: 0.1282 0.1550 0.040 1.169 5.2 73.0 15.1 805 0.157 2_bss: 0.1274 0.1540 0.040 1.169 5.4 73.2 15.2 805 0.157 2_settarget: 0.1274 0.1540 0.040 1.169 5.4 73.2 15.2 805 0.157 2_updatecdl: 0.1274 0.1540 0.040 1.182 5.4 73.2 15.2 805 0.157 2_nqh: 0.1274 0.1540 0.040 1.182 5.4 73.2 15.2 805 0.157 2_sol: 0.1271 0.1502 0.040 1.182 5.4 73.2 16.3 890 n/a 2_weight: 0.1271 0.1502 0.040 1.182 5.4 73.2 16.3 890 n/a 2_xyzrec: 0.1253 0.1507 0.042 1.155 5.4 73.2 16.3 890 n/a 2_adp: 0.1232 0.1503 0.042 1.155 5.5 69.3 16.5 890 n/a 2_regHadp: 0.1233 0.1504 0.042 1.155 5.5 69.3 16.5 890 n/a 2_occ: 0.1226 0.1501 0.042 1.155 5.5 69.3 16.5 890 n/a 3_bss: 0.1233 0.1509 0.042 1.155 5.4 69.3 16.4 890 n/a 3_settarget: 0.1233 0.1509 0.042 1.155 5.4 69.3 16.4 890 n/a 3_updatecdl: 0.1233 0.1509 0.042 1.153 5.4 69.3 16.4 890 n/a 3_nqh: 0.1233 0.1509 0.042 1.153 5.4 69.3 16.4 890 n/a 3_sol: 0.1250 0.1509 0.042 1.153 5.4 68.1 15.3 872 n/a 3_weight: 0.1250 0.1509 0.042 1.153 5.4 68.1 15.3 872 n/a 3_xyzrec: 0.1239 0.1438 0.036 1.099 5.4 68.1 15.3 872 n/a 3_adp: 0.1237 0.1397 0.036 1.099 5.6 67.7 15.1 872 n/a 3_regHadp: 0.1238 0.1398 0.036 1.099 5.6 67.7 15.1 872 n/a 3_occ: 0.1233 0.1387 0.036 1.099 5.6 67.7 15.1 872 n/a 4_bss: 0.1228 0.1377 0.036 1.099 5.5 67.7 15.1 872 n/a 4_settarget: 0.1228 0.1377 0.036 1.099 5.5 67.7 15.1 872 n/a 4_updatecdl: 0.1228 0.1377 0.036 1.105 5.5 67.7 15.1 872 n/a 4_nqh: 0.1228 0.1377 0.036 1.105 5.5 67.7 15.1 872 n/a 4_sol: 0.1208 0.1358 0.036 1.105 5.5 67.7 15.1 878 n/a 4_weight: 0.1208 0.1358 0.036 1.105 5.5 67.7 15.1 878 n/a 4_xyzrec: 0.1206 0.1362 0.036 1.127 5.5 67.7 15.1 878 n/a 4_adp: 0.1196 0.1359 0.036 1.127 5.5 67.2 15.0 878 n/a 4_regHadp: 0.1196 0.1359 0.036 1.127 5.5 67.2 15.0 878 n/a 4_occ: 0.1193 0.1358 0.036 1.127 5.5 67.2 15.0 878 n/a 5_bss: 0.1191 0.1357 0.036 1.127 5.5 67.2 15.0 878 n/a 5_settarget: 0.1191 0.1357 0.036 1.127 5.5 67.2 15.0 878 n/a 5_updatecdl: 0.1191 0.1357 0.036 1.127 5.5 67.2 15.0 878 n/a 5_nqh: 0.1191 0.1357 0.036 1.127 5.5 67.2 15.0 878 n/a 5_sol: 0.1193 0.1347 0.036 1.127 5.5 67.2 14.9 874 n/a 5_weight: 0.1193 0.1347 0.036 1.127 5.5 67.2 14.9 874 n/a 5_xyzrec: 0.1195 0.1351 0.036 1.136 5.5 67.2 14.9 874 n/a 5_adp: 0.1198 0.1352 0.036 1.136 5.6 66.9 14.9 874 n/a 5_regHadp: 0.1198 0.1353 0.036 1.136 5.6 66.9 14.9 874 n/a 5_occ: 0.1197 0.1353 0.036 1.136 5.6 66.9 14.9 874 n/a 6_bss: 0.1193 0.1348 0.036 1.136 5.6 66.9 14.9 874 n/a 6_settarget: 0.1193 0.1348 0.036 1.136 5.6 66.9 14.9 874 n/a 6_updatecdl: 0.1193 0.1348 0.036 1.136 5.6 66.9 14.9 874 n/a 6_nqh: 0.1193 0.1348 0.036 1.136 5.6 66.9 14.9 874 n/a 6_sol: 0.1191 0.1340 0.036 1.136 5.6 66.9 14.9 888 n/a 6_weight: 0.1191 0.1340 0.036 1.136 5.6 66.9 14.9 888 n/a 6_xyzrec: 0.1194 0.1343 0.037 1.125 5.6 66.9 14.9 888 n/a 6_adp: 0.1195 0.1346 0.037 1.125 5.6 65.7 14.8 888 n/a 6_regHadp: 0.1195 0.1346 0.037 1.125 5.6 65.7 14.8 888 n/a 6_occ: 0.1193 0.1345 0.037 1.125 5.6 65.7 14.8 888 n/a 7_bss: 0.1196 0.1348 0.037 1.125 5.3 65.5 14.6 888 n/a 7_settarget: 0.1196 0.1348 0.037 1.125 5.3 65.5 14.6 888 n/a 7_updatecdl: 0.1196 0.1348 0.037 1.126 5.3 65.5 14.6 888 n/a 7_nqh: 0.1196 0.1348 0.037 1.126 5.3 65.5 14.6 888 n/a 7_sol: 0.1195 0.1347 0.037 1.126 5.3 65.5 14.6 896 n/a 7_weight: 0.1195 0.1347 0.037 1.126 5.3 65.5 14.6 896 n/a 7_xyzrec: 0.1198 0.1353 0.038 1.118 5.3 65.5 14.6 896 n/a 7_adp: 0.1202 0.1357 0.038 1.118 5.4 65.1 14.6 896 n/a 7_regHadp: 0.1202 0.1357 0.038 1.118 5.4 65.1 14.6 896 n/a 7_occ: 0.1201 0.1360 0.038 1.118 5.4 65.1 14.6 896 n/a 8_bss: 0.1192 0.1352 0.038 1.118 5.4 65.2 14.7 896 n/a 8_settarget: 0.1192 0.1352 0.038 1.118 5.4 65.2 14.7 896 n/a 8_updatecdl: 0.1192 0.1352 0.038 1.118 5.4 65.2 14.7 896 n/a 8_nqh: 0.1192 0.1352 0.038 1.118 5.4 65.2 14.7 896 n/a 8_sol: 0.1190 0.1340 0.038 1.118 5.4 65.2 14.7 905 n/a 8_weight: 0.1190 0.1340 0.038 1.118 5.4 65.2 14.7 905 n/a 8_xyzrec: 0.1192 0.1346 0.039 1.118 5.4 65.2 14.7 905 n/a 8_adp: 0.1193 0.1347 0.039 1.118 5.5 64.3 14.7 905 n/a 8_regHadp: 0.1193 0.1347 0.039 1.118 5.5 64.3 14.7 905 n/a 8_occ: 0.1192 0.1349 0.039 1.118 5.5 64.3 14.7 905 n/a 9_bss: 0.1190 0.1348 0.039 1.118 5.5 64.3 14.7 905 n/a 9_settarget: 0.1190 0.1348 0.039 1.118 5.5 64.3 14.7 905 n/a 9_updatecdl: 0.1190 0.1348 0.039 1.118 5.5 64.3 14.7 905 n/a 9_nqh: 0.1190 0.1348 0.039 1.118 5.5 64.3 14.7 905 n/a 9_sol: 0.1189 0.1342 0.039 1.118 5.5 64.3 14.6 901 n/a 9_weight: 0.1189 0.1342 0.039 1.118 5.5 64.3 14.6 901 n/a 9_xyzrec: 0.1193 0.1347 0.039 1.118 5.5 64.3 14.6 901 n/a 9_adp: 0.1193 0.1350 0.039 1.118 5.6 63.2 14.6 901 n/a 9_regHadp: 0.1193 0.1350 0.039 1.118 5.6 63.2 14.6 901 n/a 9_occ: 0.1192 0.1350 0.039 1.118 5.6 63.2 14.6 901 n/a 10_bss: 0.1191 0.1349 0.039 1.118 5.5 63.2 14.6 901 n/a 10_settarget: 0.1191 0.1349 0.039 1.118 5.5 63.2 14.6 901 n/a 10_updatecdl: 0.1191 0.1349 0.039 1.118 5.5 63.2 14.6 901 n/a 10_setrh: 0.1192 0.1349 0.039 1.118 5.5 63.2 14.6 901 n/a 10_nqh: 0.1192 0.1349 0.039 1.118 5.5 63.2 14.6 901 n/a 10_sol: 0.1191 0.1343 0.039 1.118 5.5 63.2 14.6 908 n/a 10_weight: 0.1191 0.1343 0.039 1.118 5.5 63.2 14.6 908 n/a 10_xyzrec: 0.1194 0.1347 0.039 1.163 5.5 63.2 14.6 908 n/a 10_adp: 0.1197 0.1351 0.039 1.163 5.6 62.9 14.6 908 n/a 10_regHadp: 0.1197 0.1351 0.039 1.163 5.6 62.9 14.6 908 n/a 10_occ: 0.1197 0.1351 0.039 1.163 5.6 62.9 14.6 908 n/a end: 0.1196 0.1351 0.039 1.163 5.5 62.9 14.6 908 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5857830_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5857830_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.9100 Refinement macro-cycles (run) : 11976.2300 Write final files (write_after_run_outputs) : 176.3000 Total : 12160.4400 Total CPU time: 3.39 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:39:55 PST -0800 (1736735995.43 s) Start R-work = 0.1806, R-free = 0.1897 Final R-work = 0.1196, R-free = 0.1351 =============================================================================== Job complete usr+sys time: 12478.98 seconds wall clock time: 209 minutes 0.26 seconds (12540.26 seconds total)