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_1760590.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1760590.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1760590.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } 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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.55, per 1000 atoms: 0.23 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.781 distance_ideal: 2.720 ideal - model: -0.061 slack: 0.000 delta_slack: -0.061 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: 2.670 distance_ideal: 2.710 ideal - model: 0.040 slack: 0.000 delta_slack: 0.040 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: 1.00 Conformation dependent library (CDL) restraints added in 151.0 milliseconds Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.03: 789 1.03 - 1.26: 2519 1.26 - 1.48: 1494 1.48 - 1.71: 1104 1.71 - 1.94: 28 Bond restraints: 5934 Sorted by residual: bond pdb=" C ALA A 136 " pdb=" O ALA A 136 " ideal model delta sigma weight residual 1.236 1.464 -0.228 1.15e-02 7.56e+03 3.93e+02 bond pdb=" N LEU A 54 " pdb=" H LEU A 54 " ideal model delta sigma weight residual 0.860 1.239 -0.379 2.00e-02 2.50e+03 3.60e+02 bond pdb=" N GLY B 78 " pdb=" H GLY B 78 " ideal model delta sigma weight residual 0.860 1.228 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" CB ARG B 27 " pdb=" HB3 ARG B 27 " ideal model delta sigma weight residual 0.970 1.332 -0.362 2.00e-02 2.50e+03 3.28e+02 bond pdb=" N GLY A 159 " pdb=" H GLY A 159 " ideal model delta sigma weight residual 0.860 1.221 -0.361 2.00e-02 2.50e+03 3.27e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 6084 4.51 - 9.02: 3453 9.02 - 13.52: 1121 13.52 - 18.03: 143 18.03 - 22.54: 9 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 97 " pdb=" CZ ARG B 97 " pdb=" NH2 ARG B 97 " ideal model delta sigma weight residual 119.20 136.17 -16.97 9.00e-01 1.23e+00 3.55e+02 angle pdb=" O ALA B 57 " pdb=" C ALA B 57 " pdb=" N PRO B 58 " ideal model delta sigma weight residual 121.83 134.42 -12.59 7.80e-01 1.64e+00 2.61e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.22 112.96 9.26 6.50e-01 2.37e+00 2.03e+02 angle pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" O SER B 155 " ideal model delta sigma weight residual 121.38 136.23 -14.85 1.06e+00 8.90e-01 1.96e+02 angle pdb=" O VAL A 89 " pdb=" C VAL A 89 " pdb=" N GLU A 90 " ideal model delta sigma weight residual 121.87 135.00 -13.13 9.70e-01 1.06e+00 1.83e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 1840 17.56 - 35.12: 150 35.12 - 52.68: 41 52.68 - 70.24: 15 70.24 - 87.80: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CG TRP B 139 " pdb=" CD2 TRP B 139 " pdb=" CE3 TRP B 139 " pdb=" HE3 TRP B 139 " ideal model delta harmonic sigma weight residual 0.00 24.80 -24.80 0 5.00e+00 4.00e-02 2.46e+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 -155.57 -24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 194 0.200 - 0.400: 149 0.400 - 0.600: 89 0.600 - 0.800: 44 0.800 - 1.000: 16 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 173 " pdb=" N VAL A 173 " pdb=" C VAL A 173 " pdb=" CB VAL A 173 " both_signs ideal model delta sigma weight residual False 2.44 1.44 1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA ALA A 148 " pdb=" N ALA A 148 " pdb=" C ALA A 148 " pdb=" CB ALA A 148 " both_signs ideal model delta sigma weight residual False 2.48 3.47 -0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CB VAL B 144 " pdb=" CA VAL B 144 " pdb=" CG1 VAL B 144 " pdb=" CG2 VAL B 144 " both_signs ideal model delta sigma weight residual False -2.63 -1.72 -0.91 2.00e-01 2.50e+01 2.06e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.003 2.00e-02 2.50e+03 6.62e-02 1.75e+02 pdb=" CG TRP B 139 " -0.099 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.065 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.020 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.078 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " 0.106 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " 0.075 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.030 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.048 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.070 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.099 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.022 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 67 " -0.086 2.00e-02 2.50e+03 7.45e-02 1.67e+02 pdb=" CG TYR A 67 " -0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 67 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 67 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 67 " 0.118 2.00e-02 2.50e+03 pdb=" CZ TYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" OH TYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" HD1 TYR A 67 " 0.081 2.00e-02 2.50e+03 pdb=" HD2 TYR A 67 " 0.088 2.00e-02 2.50e+03 pdb=" HE1 TYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" HE2 TYR A 67 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.017 2.00e-02 2.50e+03 6.00e-02 1.44e+02 pdb=" CG TRP B 146 " -0.112 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.119 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.041 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.037 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.065 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.042 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.060 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.54: 17 1.54 - 2.30: 1755 2.30 - 3.07: 21570 3.07 - 3.83: 33218 3.83 - 4.60: 53648 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110208 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.770 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.989 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.102 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.138 2.620 nonbonded pdb="HG22 VAL A 181 " pdb=" O HOH S1566 " model vdw 1.145 2.620 ... (remaining 110203 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_1760590_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= 0.2034 r_free= 0.2008 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.301318 | | target function (ml) not normalized (work): 805692.724649 | | target function (ml) not normalized (free): 16568.305317 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2139 0.1943 6.6971 6.3028| | 2: 2.94 - 2.33 1.00 7339 128 0.1609 0.1722 5.5354 5.5963| | 3: 2.33 - 2.04 0.96 6939 150 0.1645 0.1543 5.1519 5.1367| | 4: 2.04 - 1.85 1.00 7170 155 0.1763 0.1709 4.9741 5.1208| | 5: 1.85 - 1.72 0.99 7113 159 0.1898 0.1762 4.7888 4.8534| | 6: 1.72 - 1.62 0.99 7102 142 0.1967 0.1920 4.6698 4.7375| | 7: 1.62 - 1.54 0.99 7104 148 0.2016 0.1858 4.5668 4.5657| | 8: 1.54 - 1.47 0.96 6798 152 0.2078 0.2229 4.4872 4.5183| | 9: 1.47 - 1.41 0.98 6938 155 0.2075 0.2246 4.4027 4.484| | 10: 1.41 - 1.36 0.99 7022 150 0.2117 0.2246 4.3127 4.3593| | 11: 1.36 - 1.32 0.99 6997 151 0.2115 0.2317 4.2374 4.3411| | 12: 1.32 - 1.28 0.98 6976 149 0.2050 0.2093 4.1643 4.2716| | 13: 1.28 - 1.25 0.98 6907 166 0.2033 0.2010 4.1234 4.1252| | 14: 1.25 - 1.22 0.98 7015 113 0.2057 0.2319 4.0705 4.2237| | 15: 1.22 - 1.19 0.98 6957 137 0.2097 0.2104 4.043 4.0394| | 16: 1.19 - 1.17 0.93 6604 132 0.2139 0.2214 4.009 4.0535| | 17: 1.17 - 1.14 0.98 6941 135 0.2180 0.1918 3.9648 4.0205| | 18: 1.14 - 1.12 0.98 6875 142 0.2250 0.2210 3.9266 3.8757| | 19: 1.12 - 1.10 0.97 6949 106 0.2306 0.2347 3.8758 3.8881| | 20: 1.10 - 1.08 0.97 6884 147 0.2322 0.2226 3.8176 3.8348| | 21: 1.08 - 1.07 0.97 6852 152 0.2403 0.2767 3.7828 3.8299| | 22: 1.07 - 1.05 0.97 6838 135 0.2575 0.2626 3.7556 3.7896| | 23: 1.05 - 1.03 0.97 6829 159 0.2680 0.2578 3.7223 3.7723| | 24: 1.03 - 1.02 0.96 6785 133 0.2893 0.2787 3.6933 3.7945| | 25: 1.02 - 1.01 0.93 6552 130 0.3089 0.2765 3.6809 3.6821| | 26: 1.01 - 0.99 0.96 6767 158 0.3204 0.3350 3.6292 3.6197| | 27: 0.99 - 0.98 0.94 6648 131 0.3436 0.3240 3.639 3.597| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.18 0.91 0.97 34532.09| | 2: 2.94 - 2.33 7339 128 0.86 21.11 1.08 1.01 14920.64| | 3: 2.33 - 2.04 6939 150 0.93 13.01 1.11 1.05 4324.59| | 4: 2.04 - 1.85 7170 155 0.92 14.11 1.11 1.06 2948.72| | 5: 1.85 - 1.72 7113 159 0.90 16.24 1.11 1.07 2188.36| | 6: 1.72 - 1.62 7102 142 0.90 17.19 1.11 1.07 1744.75| | 7: 1.62 - 1.54 7104 148 0.89 18.12 1.11 1.08 1411.60| | 8: 1.54 - 1.47 6798 152 0.88 18.82 1.11 1.07 1210.56| | 9: 1.47 - 1.41 6938 155 0.88 19.38 1.10 1.06 1041.34| | 10: 1.41 - 1.36 7022 150 0.86 21.03 1.10 1.05 928.33| | 11: 1.36 - 1.32 6997 151 0.86 21.03 1.08 1.04 803.14| | 12: 1.32 - 1.28 6976 149 0.86 20.78 1.08 1.04 703.43| | 13: 1.28 - 1.25 6907 166 0.88 19.75 1.08 1.05 612.21| | 14: 1.25 - 1.22 7015 113 0.87 20.42 1.08 1.06 564.46| | 15: 1.22 - 1.19 6957 137 0.86 20.80 1.08 1.05 538.33| | 16: 1.19 - 1.17 6604 132 0.87 20.58 1.08 1.03 488.24| | 17: 1.17 - 1.14 6941 135 0.87 20.91 1.07 1.02 438.63| | 18: 1.14 - 1.12 6875 142 0.87 20.30 1.08 1.00 373.11| | 19: 1.12 - 1.10 6949 106 0.86 21.42 1.08 1.02 360.69| | 20: 1.10 - 1.08 6884 147 0.85 22.62 1.06 0.99 345.22| | 21: 1.08 - 1.07 6852 152 0.83 24.34 1.05 0.98 348.76| | 22: 1.07 - 1.05 6838 135 0.81 26.29 1.05 0.97 341.74| | 23: 1.05 - 1.03 6829 159 0.80 27.67 1.04 0.97 334.74| | 24: 1.03 - 1.02 6785 133 0.78 29.80 1.05 0.96 325.77| | 25: 1.02 - 1.01 6552 130 0.77 30.53 1.03 0.91 300.21| | 26: 1.01 - 0.99 6767 158 0.75 32.25 1.03 0.89 286.30| | 27: 0.99 - 0.98 6648 131 0.75 32.50 1.03 0.90 275.26| |alpha: min = 0.89 max = 1.08 mean = 1.01| |beta: min = 275.26 max = 34532.09 mean = 2817.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.81| |phase err.(test): min = 0.00 max = 89.65 mean = 21.98| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.257 2950 Z= 5.434 Angle : 5.171 16.967 4018 Z= 3.675 Chirality : 0.382 1.000 492 Planarity : 0.032 0.138 512 Dihedral : 12.899 87.795 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 1.29 % Allowed : 4.84 % Favored : 93.87 % Cbeta Deviations : 30.62 % 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: -1.67 (0.38), residues: 386 helix: -2.09 (0.35), residues: 144 sheet: -0.70 (0.61), residues: 66 loop : -0.13 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.091 0.018 ARG A 49 TYR 0.110 0.034 TYR B 194 PHE 0.127 0.035 PHE B 164 TRP 0.104 0.043 TRP A 146 HIS 0.070 0.025 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2034 r_free= 0.2008 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.301318 | | target function (ml) not normalized (work): 805692.724649 | | target function (ml) not normalized (free): 16568.305317 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2034 0.2008 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2034 0.2008 n_refl.: 191155 remove outliers: r(all,work,free)=0.2033 0.2034 0.2008 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2033 0.2035 0.2008 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1802 0.1952 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1800 0.1952 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4236 400.535 294.735 0.435 0.913 0.303 13.296-10.522 99.01 99 1 0.2485 528.187 520.641 0.784 0.914 0.251 10.503-8.327 98.90 177 3 0.2466 564.205 558.551 0.976 0.914 0.213 8.318-6.595 100.00 360 8 0.2517 414.736 403.266 0.970 0.914 0.166 6.588-5.215 100.00 711 7 0.2279 381.101 365.089 0.952 0.914 0.130 5.214-4.128 98.38 1367 28 0.1503 557.435 549.425 1.073 0.914 0.080 4.126-3.266 94.74 2603 46 0.1332 508.132 499.542 1.142 0.914 0.014 3.266-2.585 99.86 5447 97 0.1450 342.774 337.816 1.118 0.913 0.000 2.585-2.046 97.45 10613 204 0.1389 258.603 254.519 1.126 0.913 0.000 2.046-1.619 99.39 21536 464 0.1623 153.054 149.739 1.141 0.911 0.000 1.619-1.281 98.00 42464 925 0.1916 82.395 80.263 1.131 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2324 44.203 41.642 1.112 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0032 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1952 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 r_work=0.1804 r_free=0.1959 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.857064 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.015455 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1503 0.0230 0.038 1.2 11.2 0.0 0.3 0 11.929 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.03 2.30 1.118 13.112 577.015 0.018 12.97 15.68 2.71 1.248 13.362 577.015 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.05 15.05 1.41 435 3274 Protein: 5.16 40.42 11.01 1.41 0 2902 Water: 6.29 73.05 29.61 N/A 435 370 Other: 15.88 30.20 23.04 N/A 0 2 Chain A: 5.33 60.33 13.07 N/A 0 1626 Chain B: 5.16 73.05 12.79 N/A 0 1648 Chain S: 11.43 63.81 31.06 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2164 11.95 - 18.74 636 18.74 - 25.53 313 25.53 - 32.32 263 32.32 - 39.10 160 39.10 - 45.89 108 45.89 - 52.68 42 52.68 - 59.47 17 59.47 - 66.26 5 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1568 r_work=0.1296 r_free=0.1562 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1562 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 = 0.1281 r_free = 0.1549 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1549 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015572 | | target function (ls_wunit_k1) not normalized (work): 2916.673220 | | target function (ls_wunit_k1) not normalized (free): 115.626498 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1549 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1474 0.1472 0.1622 n_refl.: 191139 remove outliers: r(all,work,free)=0.1474 0.1472 0.1622 n_refl.: 191139 overall B=0.15 to atoms: r(all,work,free)=0.1496 0.1494 0.1631 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1538 n_refl.: 191139 remove outliers: r(all,work,free)=0.1279 0.1274 0.1537 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 0.3635 402.814 361.313 0.451 1.001 0.287 13.296-10.522 99.01 99 1 0.2077 528.187 519.493 0.705 1.002 0.238 10.503-8.327 98.90 177 3 0.1746 564.205 564.189 0.859 1.002 0.210 8.318-6.595 100.00 360 8 0.1704 414.736 412.284 0.872 1.002 0.144 6.588-5.215 100.00 711 7 0.1549 381.101 374.180 0.853 1.002 0.130 5.214-4.128 98.38 1367 28 0.0909 557.435 554.621 0.938 1.003 0.049 4.126-3.266 94.74 2603 46 0.0833 508.132 504.230 1.004 1.003 0.014 3.266-2.585 99.86 5447 97 0.0918 342.774 340.550 0.988 1.003 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.365 0.998 1.003 0.000 2.046-1.619 99.39 21536 464 0.1086 153.054 151.443 1.015 1.003 0.000 1.619-1.281 98.00 42464 925 0.1277 82.395 81.391 1.007 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.227 0.985 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0351 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1537 | n_water=805 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1278 r_free=0.1539 | n_water=793 | time (s): 100.140 (total time: 102.850) Filter (q & B) r_work=0.1278 r_free=0.1539 | n_water=788 | time (s): 4.200 (total time: 107.050) Compute maps r_work=0.1278 r_free=0.1539 | n_water=788 | time (s): 1.920 (total time: 108.970) Filter (map) r_work=0.1304 r_free=0.1530 | n_water=653 | time (s): 5.000 (total time: 113.970) Find peaks r_work=0.1304 r_free=0.1530 | n_water=653 | time (s): 0.620 (total time: 114.590) Add new water r_work=0.1325 r_free=0.1555 | n_water=948 | time (s): 4.850 (total time: 119.440) Refine new water occ: r_work=0.1283 r_free=0.1508 adp: r_work=0.1272 r_free=0.1506 occ: r_work=0.1274 r_free=0.1502 adp: r_work=0.1268 r_free=0.1502 occ: r_work=0.1270 r_free=0.1499 adp: r_work=0.1266 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1502 r_work=0.1266 r_free=0.1502 | n_water=948 | time (s): 83.400 (total time: 202.840) Filter (q & B) r_work=0.1270 r_free=0.1502 | n_water=876 | time (s): 4.380 (total time: 207.220) Filter (dist only) r_work=0.1270 r_free=0.1501 | n_water=875 | time (s): 109.100 (total time: 316.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.053125 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 597.340745 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1254 0.1522 0.0267 0.041 1.1 16.3 0.0 0.3 0 12.027 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.22 2.67 2.048 15.103 597.341 0.015 12.32 15.10 2.77 2.411 15.178 597.341 0.014 Individual atomic B min max mean iso aniso Overall: 5.37 69.06 16.23 1.22 507 3272 Protein: 5.37 40.56 10.99 1.22 0 2902 Water: 6.52 69.06 33.58 N/A 507 368 Other: 16.12 34.11 25.11 N/A 0 2 Chain A: 5.48 56.02 13.04 N/A 0 1624 Chain B: 5.37 68.20 12.87 N/A 0 1648 Chain S: 10.35 69.06 37.38 N/A 507 0 Histogram: Values Number of atoms 5.37 - 11.74 2062 11.74 - 18.11 712 18.11 - 24.47 262 24.47 - 30.84 207 30.84 - 37.21 191 37.21 - 43.58 166 43.58 - 49.95 89 49.95 - 56.32 64 56.32 - 62.69 17 62.69 - 69.06 9 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1510 r_work=0.1233 r_free=0.1511 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1511 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 = 0.1509 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1509 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013514 | | target function (ls_wunit_k1) not normalized (work): 2531.148714 | | target function (ls_wunit_k1) not normalized (free): 102.274583 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1509 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1440 0.1437 0.1600 n_refl.: 191137 remove outliers: r(all,work,free)=0.1440 0.1437 0.1600 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1436 0.1434 0.1598 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1515 n_refl.: 191137 remove outliers: r(all,work,free)=0.1238 0.1233 0.1515 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 0.3352 402.814 377.394 0.478 0.962 0.267 13.296-10.522 99.01 99 1 0.1945 528.187 521.821 0.760 0.963 0.250 10.503-8.327 98.90 177 3 0.1461 564.205 565.913 0.919 0.963 0.169 8.318-6.595 100.00 360 8 0.1559 414.736 414.786 0.934 0.963 0.145 6.588-5.215 100.00 711 7 0.1357 381.101 376.723 0.913 0.963 0.140 5.214-4.128 98.38 1367 28 0.0827 557.435 556.108 0.994 0.963 0.070 4.126-3.266 94.74 2603 46 0.0758 508.132 505.714 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0859 342.774 341.388 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.783 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.632 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1252 82.395 81.362 1.075 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.217 1.061 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0541 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1515 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1515 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1515 | n_water=875 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1235 r_free=0.1517 | n_water=870 | time (s): 106.740 (total time: 109.270) Filter (q & B) r_work=0.1235 r_free=0.1517 | n_water=865 | time (s): 4.710 (total time: 113.980) Compute maps r_work=0.1235 r_free=0.1517 | n_water=865 | time (s): 1.620 (total time: 115.600) Filter (map) r_work=0.1276 r_free=0.1522 | n_water=681 | time (s): 5.240 (total time: 120.840) Find peaks r_work=0.1276 r_free=0.1522 | n_water=681 | time (s): 0.780 (total time: 121.620) Add new water r_work=0.1297 r_free=0.1544 | n_water=997 | time (s): 4.660 (total time: 126.280) Refine new water occ: r_work=0.1251 r_free=0.1501 adp: r_work=0.1252 r_free=0.1501 occ: r_work=0.1248 r_free=0.1499 adp: r_work=0.1247 r_free=0.1499 occ: r_work=0.1244 r_free=0.1496 adp: r_work=0.1244 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1496 r_work=0.1244 r_free=0.1496 | n_water=997 | time (s): 276.710 (total time: 402.990) Filter (q & B) r_work=0.1249 r_free=0.1498 | n_water=868 | time (s): 5.870 (total time: 408.860) Filter (dist only) r_work=0.1249 r_free=0.1498 | n_water=867 | time (s): 112.830 (total time: 521.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.682453 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.132200 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 0.1237 0.1427 0.0190 0.036 1.1 7.3 0.0 0.0 0 0.841 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.27 1.90 1.940 14.516 16.132 3.937 12.34 13.89 1.55 2.267 14.416 16.132 3.897 Individual atomic B min max mean iso aniso Overall: 5.53 67.74 15.12 1.05 502 3269 Protein: 5.53 36.51 10.74 1.05 0 2902 Water: 6.70 67.74 29.77 N/A 502 365 Other: 14.01 29.59 21.80 N/A 0 2 Chain A: 5.59 54.94 12.76 N/A 0 1623 Chain B: 5.53 67.74 12.54 N/A 0 1646 Chain S: 14.22 66.34 31.18 N/A 502 0 Histogram: Values Number of atoms 5.53 - 11.75 2128 11.75 - 17.97 689 17.97 - 24.19 306 24.19 - 30.41 248 30.41 - 36.64 173 36.64 - 42.86 125 42.86 - 49.08 66 49.08 - 55.30 28 55.30 - 61.52 6 61.52 - 67.74 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1390 r_work=0.1235 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1391 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1386 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1386 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891095 | | target function (ml) not normalized (work): 728786.570654 | | target function (ml) not normalized (free): 15214.181900 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1230 0.1386 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1448 0.1448 0.1485 n_refl.: 191137 remove outliers: r(all,work,free)=0.1448 0.1448 0.1485 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1442 0.1442 0.1481 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1226 0.1381 n_refl.: 191137 remove outliers: r(all,work,free)=0.1228 0.1225 0.1381 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3745 393.525 362.541 0.418 0.946 0.245 13.296-10.522 98.02 98 1 0.2460 530.665 504.760 0.705 0.947 0.215 10.503-8.327 97.80 175 3 0.2034 554.286 557.316 0.880 0.947 0.168 8.318-6.595 100.00 360 8 0.2123 414.736 410.647 0.893 0.947 0.120 6.588-5.215 100.00 711 7 0.1850 381.101 370.330 0.887 0.947 0.110 5.214-4.128 98.38 1367 28 0.1166 557.435 552.226 0.971 0.947 0.070 4.126-3.266 94.74 2603 46 0.1088 508.132 501.544 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1083 342.774 339.182 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0972 258.603 255.763 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.410 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.497 1.054 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.315 1.041 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1041 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1381 | n_water=867 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1225 r_free=0.1380 | n_water=866 | time (s): 104.810 (total time: 107.470) Filter (q & B) r_work=0.1226 r_free=0.1379 | n_water=852 | time (s): 4.620 (total time: 112.090) Compute maps r_work=0.1226 r_free=0.1379 | n_water=852 | time (s): 1.870 (total time: 113.960) Filter (map) r_work=0.1247 r_free=0.1389 | n_water=722 | time (s): 4.300 (total time: 118.260) Find peaks r_work=0.1247 r_free=0.1389 | n_water=722 | time (s): 0.580 (total time: 118.840) Add new water r_work=0.1260 r_free=0.1403 | n_water=953 | time (s): 4.030 (total time: 122.870) Refine new water occ: r_work=0.1213 r_free=0.1362 adp: r_work=0.1205 r_free=0.1357 occ: r_work=0.1202 r_free=0.1357 adp: r_work=0.1202 r_free=0.1357 occ: r_work=0.1202 r_free=0.1357 adp: r_work=0.1202 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1357 r_work=0.1202 r_free=0.1357 | n_water=953 | time (s): 194.800 (total time: 317.670) Filter (q & B) r_work=0.1207 r_free=0.1363 | n_water=850 | time (s): 5.210 (total time: 322.880) Filter (dist only) r_work=0.1208 r_free=0.1363 | n_water=849 | time (s): 107.120 (total time: 430.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565355 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.772978 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 0.1207 0.1368 0.0162 0.036 1.1 5.1 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.68 1.62 1.826 14.086 14.773 3.874 12.02 13.66 1.64 1.913 14.052 14.773 3.867 Individual atomic B min max mean iso aniso Overall: 5.54 67.37 14.78 0.99 484 3269 Protein: 5.54 33.46 10.66 0.99 0 2902 Water: 5.88 67.37 28.84 N/A 484 365 Other: 13.95 28.44 21.20 N/A 0 2 Chain A: 5.54 53.98 12.64 N/A 0 1623 Chain B: 5.54 67.37 12.46 N/A 0 1646 Chain S: 5.88 66.16 29.87 N/A 484 0 Histogram: Values Number of atoms 5.54 - 11.72 2125 11.72 - 17.90 719 17.90 - 24.09 327 24.09 - 30.27 221 30.27 - 36.45 148 36.45 - 42.64 115 42.64 - 48.82 64 48.82 - 55.00 27 55.00 - 61.19 5 61.19 - 67.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1366 r_work=0.1202 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1366 target_work(ml) = 3.868 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1364 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865635 | | target function (ml) not normalized (work): 723998.715987 | | target function (ml) not normalized (free): 15147.814655 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1364 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1428 0.1428 0.1473 n_refl.: 191132 remove outliers: r(all,work,free)=0.1428 0.1428 0.1473 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1420 0.1420 0.1468 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1362 n_refl.: 191132 remove outliers: r(all,work,free)=0.1202 0.1198 0.1362 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 91.09 89 3 0.3514 347.545 310.485 0.394 0.947 0.229 13.296-10.522 97.03 97 1 0.2457 481.398 456.662 0.701 0.948 0.193 10.503-8.327 97.80 175 3 0.2095 502.120 495.362 0.859 0.948 0.160 8.315-6.595 100.00 359 8 0.2185 374.758 369.556 0.888 0.948 0.114 6.588-5.215 100.00 711 7 0.1918 345.234 335.834 0.885 0.948 0.093 5.214-4.128 98.38 1367 28 0.1208 504.973 500.143 0.973 0.948 0.060 4.126-3.266 94.74 2603 46 0.1124 460.310 454.013 1.035 0.949 0.000 3.266-2.585 99.86 5447 97 0.1085 310.514 307.461 1.022 0.948 0.000 2.585-2.046 97.45 10613 204 0.0937 234.265 231.894 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0919 138.650 137.359 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0992 74.641 73.929 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.042 38.385 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1285 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1362 | n_water=849 | time (s): 2.820 (total time: 2.820) Filter (dist) r_work=0.1199 r_free=0.1363 | n_water=848 | time (s): 105.850 (total time: 108.670) Filter (q & B) r_work=0.1199 r_free=0.1364 | n_water=842 | time (s): 4.300 (total time: 112.970) Compute maps r_work=0.1199 r_free=0.1364 | n_water=842 | time (s): 1.680 (total time: 114.650) Filter (map) r_work=0.1225 r_free=0.1380 | n_water=709 | time (s): 4.630 (total time: 119.280) Find peaks r_work=0.1225 r_free=0.1380 | n_water=709 | time (s): 0.550 (total time: 119.830) Add new water r_work=0.1236 r_free=0.1384 | n_water=934 | time (s): 4.850 (total time: 124.680) Refine new water occ: r_work=0.1197 r_free=0.1352 adp: r_work=0.1197 r_free=0.1352 occ: r_work=0.1195 r_free=0.1350 adp: r_work=0.1195 r_free=0.1350 occ: r_work=0.1193 r_free=0.1349 adp: r_work=0.1193 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1349 r_work=0.1193 r_free=0.1349 | n_water=934 | time (s): 265.390 (total time: 390.070) Filter (q & B) r_work=0.1196 r_free=0.1358 | n_water=868 | time (s): 4.520 (total time: 394.590) Filter (dist only) r_work=0.1196 r_free=0.1357 | n_water=867 | time (s): 114.600 (total time: 509.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.614711 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.970002 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1358 0.0159 0.036 1.1 6.3 0.0 0.3 0 0.807 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.58 1.59 1.789 14.065 14.970 3.766 12.02 13.61 1.59 1.906 14.018 14.970 3.762 Individual atomic B min max mean iso aniso Overall: 5.53 66.79 14.80 0.94 502 3269 Protein: 5.53 31.16 10.56 0.94 0 2902 Water: 6.03 66.79 28.97 N/A 502 365 Other: 13.82 26.59 20.21 N/A 0 2 Chain A: 5.58 53.36 12.50 N/A 0 1623 Chain B: 5.53 66.79 12.33 N/A 0 1646 Chain S: 6.03 65.92 30.35 N/A 502 0 Histogram: Values Number of atoms 5.53 - 11.65 2123 11.65 - 17.78 739 17.78 - 23.91 304 23.91 - 30.03 218 30.03 - 36.16 166 36.16 - 42.28 125 42.28 - 48.41 62 48.41 - 54.54 27 54.54 - 60.66 4 60.66 - 66.79 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1361 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761057 | | target function (ml) not normalized (work): 704397.134663 | | target function (ml) not normalized (free): 14743.596962 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1361 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1417 0.1417 0.1476 n_refl.: 191128 remove outliers: r(all,work,free)=0.1417 0.1417 0.1476 n_refl.: 191128 overall B=-0.04 to atoms: r(all,work,free)=0.1409 0.1408 0.1471 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1360 n_refl.: 191128 remove outliers: r(all,work,free)=0.1202 0.1199 0.1360 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 91.09 89 3 0.3403 347.545 323.481 0.417 0.949 0.241 13.296-10.522 97.03 97 1 0.2445 481.398 462.584 0.697 0.950 0.170 10.503-8.327 97.80 175 3 0.2133 502.120 494.472 0.855 0.950 0.142 8.315-6.595 100.00 359 8 0.2168 374.758 370.216 0.885 0.950 0.110 6.588-5.215 100.00 711 7 0.1939 345.234 335.523 0.883 0.950 0.093 5.214-4.128 98.38 1367 28 0.1209 504.973 499.972 0.973 0.950 0.070 4.126-3.266 94.74 2603 46 0.1140 460.310 453.730 1.034 0.951 0.000 3.266-2.585 99.86 5447 97 0.1100 310.514 307.392 1.020 0.950 0.000 2.585-2.046 97.45 10613 204 0.0953 234.265 231.784 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0919 138.650 137.323 1.054 0.950 0.000 1.619-1.281 98.00 42464 925 0.0978 74.641 73.932 1.050 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.042 38.380 1.036 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1375 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1360 | n_water=867 | time (s): 3.170 (total time: 3.170) Filter (dist) r_work=0.1200 r_free=0.1362 | n_water=865 | time (s): 106.660 (total time: 109.830) Filter (q & B) r_work=0.1200 r_free=0.1361 | n_water=856 | time (s): 5.010 (total time: 114.840) Compute maps r_work=0.1200 r_free=0.1361 | n_water=856 | time (s): 2.460 (total time: 117.300) Filter (map) r_work=0.1223 r_free=0.1368 | n_water=737 | time (s): 4.390 (total time: 121.690) Find peaks r_work=0.1223 r_free=0.1368 | n_water=737 | time (s): 0.700 (total time: 122.390) Add new water r_work=0.1233 r_free=0.1373 | n_water=965 | time (s): 4.680 (total time: 127.070) Refine new water occ: r_work=0.1196 r_free=0.1344 adp: r_work=0.1196 r_free=0.1343 occ: r_work=0.1194 r_free=0.1343 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1343 adp: r_work=0.1191 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1342 r_work=0.1191 r_free=0.1342 | n_water=965 | time (s): 392.880 (total time: 519.950) Filter (q & B) r_work=0.1195 r_free=0.1347 | n_water=892 | time (s): 5.690 (total time: 525.640) Filter (dist only) r_work=0.1195 r_free=0.1347 | n_water=891 | time (s): 111.060 (total time: 636.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.545928 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.175320 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1354 0.0155 0.037 1.1 8.7 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.54 1.55 1.749 14.002 15.175 3.762 11.99 13.55 1.56 1.840 13.970 15.175 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 65.72 14.83 0.91 526 3269 Protein: 5.57 29.54 10.48 0.91 0 2902 Water: 5.96 65.72 29.00 N/A 526 365 Other: 13.82 23.78 18.80 N/A 0 2 Chain A: 5.59 52.93 12.38 N/A 0 1623 Chain B: 5.57 65.72 12.22 N/A 0 1646 Chain S: 5.96 65.51 30.60 N/A 526 0 Histogram: Values Number of atoms 5.57 - 11.59 2108 11.59 - 17.60 776 17.60 - 23.62 284 23.62 - 29.63 214 29.63 - 35.65 176 35.65 - 41.66 126 41.66 - 47.68 70 47.68 - 53.69 33 53.69 - 59.71 5 59.71 - 65.72 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1355 r_work=0.1199 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1355 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757396 | | target function (ml) not normalized (work): 703711.392980 | | target function (ml) not normalized (free): 14729.242675 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1355 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1475 n_refl.: 191128 remove outliers: r(all,work,free)=0.1409 0.1408 0.1475 n_refl.: 191128 overall B=-0.04 to atoms: r(all,work,free)=0.1401 0.1400 0.1469 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1354 n_refl.: 191128 remove outliers: r(all,work,free)=0.1198 0.1195 0.1354 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 0.3368 348.232 317.100 0.402 0.950 0.225 13.296-10.522 97.03 97 1 0.2418 481.398 463.576 0.694 0.952 0.161 10.503-8.327 97.80 175 3 0.2126 502.120 495.009 0.855 0.952 0.133 8.315-6.595 100.00 359 8 0.2154 374.758 371.228 0.880 0.952 0.090 6.588-5.215 100.00 711 7 0.1923 345.234 335.216 0.881 0.952 0.090 5.214-4.128 98.38 1367 28 0.1201 504.973 499.973 0.970 0.952 0.039 4.126-3.266 94.74 2603 46 0.1138 460.310 453.802 1.033 0.952 0.005 3.266-2.585 99.86 5447 97 0.1104 310.514 307.366 1.019 0.952 0.000 2.585-2.046 97.45 10613 204 0.0953 234.265 231.801 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0914 138.650 137.335 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0970 74.641 73.941 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.042 38.380 1.039 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1373 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1354 | n_water=891 | time (s): 2.960 (total time: 2.960) Filter (dist) r_work=0.1195 r_free=0.1354 | n_water=891 | time (s): 105.780 (total time: 108.740) Filter (q & B) r_work=0.1195 r_free=0.1352 | n_water=880 | time (s): 5.320 (total time: 114.060) Compute maps r_work=0.1195 r_free=0.1352 | n_water=880 | time (s): 2.430 (total time: 116.490) Filter (map) r_work=0.1218 r_free=0.1363 | n_water=770 | time (s): 5.070 (total time: 121.560) Find peaks r_work=0.1218 r_free=0.1363 | n_water=770 | time (s): 0.830 (total time: 122.390) Add new water r_work=0.1226 r_free=0.1369 | n_water=966 | time (s): 5.470 (total time: 127.860) Refine new water occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1343 occ: r_work=0.1192 r_free=0.1344 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1189 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1342 r_work=0.1189 r_free=0.1342 | n_water=966 | time (s): 201.570 (total time: 329.430) Filter (q & B) r_work=0.1193 r_free=0.1347 | n_water=901 | time (s): 4.430 (total time: 333.860) Filter (dist only) r_work=0.1194 r_free=0.1347 | n_water=900 | time (s): 117.930 (total time: 451.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507636 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.859523 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1355 0.0158 0.038 1.1 7.2 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.55 1.58 1.719 13.929 14.860 3.759 11.99 13.56 1.57 1.763 13.911 14.860 3.757 Individual atomic B min max mean iso aniso Overall: 5.57 65.04 14.82 0.89 535 3269 Protein: 5.57 28.77 10.43 0.89 0 2902 Water: 6.00 65.04 28.95 N/A 535 365 Other: 13.87 22.37 18.12 N/A 0 2 Chain A: 5.61 52.62 12.29 N/A 0 1623 Chain B: 5.57 64.66 12.14 N/A 0 1646 Chain S: 6.00 65.04 30.72 N/A 535 0 Histogram: Values Number of atoms 5.57 - 11.52 2095 11.52 - 17.47 794 17.47 - 23.41 275 23.41 - 29.36 215 29.36 - 35.31 182 35.31 - 41.25 126 41.25 - 47.20 76 47.20 - 53.15 31 53.15 - 59.10 6 59.10 - 65.04 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1357 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1356 target_work(ml) = 3.756 | | 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.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756034 | | target function (ml) not normalized (work): 703452.566136 | | target function (ml) not normalized (free): 14731.830428 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1356 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1392 0.1391 0.1477 n_refl.: 191127 remove outliers: r(all,work,free)=0.1392 0.1391 0.1477 n_refl.: 191127 overall B=-0.01 to atoms: r(all,work,free)=0.1391 0.1389 0.1475 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1344 n_refl.: 191127 remove outliers: r(all,work,free)=0.1191 0.1188 0.1344 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 0.3453 348.232 319.770 0.393 0.974 0.207 13.296-10.522 97.03 97 1 0.2407 481.398 463.538 0.682 0.976 0.136 10.503-8.327 97.80 175 3 0.2135 502.120 493.824 0.851 0.976 0.107 8.315-6.595 100.00 359 8 0.2140 374.758 370.971 0.875 0.976 0.093 6.588-5.215 100.00 711 7 0.1938 345.234 335.133 0.878 0.977 0.080 5.214-4.128 98.38 1367 28 0.1214 504.973 499.205 0.968 0.977 0.060 4.126-3.266 94.74 2603 46 0.1145 460.310 452.913 1.028 0.979 0.009 3.266-2.585 99.86 5447 97 0.1118 310.514 306.946 1.013 0.979 0.000 2.585-2.046 97.45 10613 204 0.0960 234.265 231.600 1.023 0.981 0.000 2.046-1.619 99.39 21536 464 0.0909 138.650 137.221 1.042 0.984 0.000 1.619-1.281 98.00 42464 925 0.0947 74.641 73.987 1.035 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.042 38.344 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0253 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1345 | n_water=900 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1188 r_free=0.1344 | n_water=899 | time (s): 112.140 (total time: 114.790) Filter (q & B) r_work=0.1188 r_free=0.1344 | n_water=887 | time (s): 4.360 (total time: 119.150) Compute maps r_work=0.1188 r_free=0.1344 | n_water=887 | time (s): 1.850 (total time: 121.000) Filter (map) r_work=0.1210 r_free=0.1352 | n_water=772 | time (s): 4.480 (total time: 125.480) Find peaks r_work=0.1210 r_free=0.1352 | n_water=772 | time (s): 0.850 (total time: 126.330) Add new water r_work=0.1218 r_free=0.1357 | n_water=974 | time (s): 5.460 (total time: 131.790) Refine new water occ: r_work=0.1186 r_free=0.1337 adp: r_work=0.1186 r_free=0.1337 occ: r_work=0.1184 r_free=0.1336 adp: r_work=0.1184 r_free=0.1336 occ: r_work=0.1182 r_free=0.1336 adp: r_work=0.1182 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1335 r_work=0.1182 r_free=0.1335 | n_water=974 | time (s): 235.720 (total time: 367.510) Filter (q & B) r_work=0.1186 r_free=0.1338 | n_water=907 | time (s): 4.190 (total time: 371.700) Filter (dist only) r_work=0.1186 r_free=0.1339 | n_water=904 | time (s): 117.530 (total time: 489.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.496642 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.900554 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1341 0.0152 0.039 1.1 7.7 0.0 0.3 0 0.748 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.41 1.52 1.701 13.882 13.901 3.755 11.91 13.44 1.53 1.707 13.875 13.901 3.754 Individual atomic B min max mean iso aniso Overall: 5.58 64.86 14.79 0.87 539 3269 Protein: 5.58 28.49 10.43 0.87 0 2902 Water: 6.01 64.86 28.76 N/A 539 365 Other: 13.87 22.33 18.10 N/A 0 2 Chain A: 5.65 52.51 12.26 N/A 0 1623 Chain B: 5.58 64.28 12.12 N/A 0 1646 Chain S: 6.01 64.86 30.54 N/A 539 0 Histogram: Values Number of atoms 5.58 - 11.51 2089 11.51 - 17.43 807 17.43 - 23.36 273 23.36 - 29.29 216 29.29 - 35.22 179 35.22 - 41.15 127 41.15 - 47.08 78 47.08 - 53.01 30 53.01 - 58.93 5 58.93 - 64.86 4 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1344 r_work=0.1192 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1344 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1347 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753969 | | target function (ml) not normalized (work): 703065.833140 | | target function (ml) not normalized (free): 14728.942260 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1347 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1477 n_refl.: 191127 remove outliers: r(all,work,free)=0.1401 0.1400 0.1477 n_refl.: 191127 overall B=-0.02 to atoms: r(all,work,free)=0.1398 0.1397 0.1475 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1346 n_refl.: 191127 remove outliers: r(all,work,free)=0.1193 0.1190 0.1346 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 0.3519 348.232 318.913 0.406 0.918 0.193 13.296-10.522 97.03 97 1 0.2432 481.398 462.402 0.725 0.919 0.140 10.503-8.327 97.80 175 3 0.2137 502.120 494.351 0.902 0.920 0.109 8.315-6.595 100.00 359 8 0.2147 374.758 370.042 0.927 0.920 0.088 6.588-5.215 100.00 711 7 0.1956 345.234 335.045 0.932 0.920 0.080 5.214-4.128 98.38 1367 28 0.1223 504.973 499.219 1.028 0.921 0.070 4.126-3.266 94.74 2603 46 0.1155 460.310 452.989 1.092 0.922 0.009 3.266-2.585 99.86 5447 97 0.1124 310.514 306.931 1.076 0.923 0.000 2.585-2.046 97.45 10613 204 0.0963 234.265 231.597 1.086 0.925 0.000 2.046-1.619 99.39 21536 464 0.0911 138.650 137.245 1.106 0.928 0.000 1.619-1.281 98.00 42464 925 0.0944 74.641 73.996 1.100 0.933 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.042 38.331 1.073 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0475 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1346 | n_water=904 | time (s): 2.640 (total time: 2.640) Filter (dist) r_work=0.1190 r_free=0.1346 | n_water=904 | time (s): 106.500 (total time: 109.140) Filter (q & B) r_work=0.1190 r_free=0.1346 | n_water=893 | time (s): 5.160 (total time: 114.300) Compute maps r_work=0.1190 r_free=0.1346 | n_water=893 | time (s): 2.040 (total time: 116.340) Filter (map) r_work=0.1212 r_free=0.1354 | n_water=782 | time (s): 4.100 (total time: 120.440) Find peaks r_work=0.1212 r_free=0.1354 | n_water=782 | time (s): 0.550 (total time: 120.990) Add new water r_work=0.1219 r_free=0.1358 | n_water=988 | time (s): 3.580 (total time: 124.570) Refine new water occ: r_work=0.1187 r_free=0.1335 adp: r_work=0.1187 r_free=0.1335 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1334 occ: r_work=0.1184 r_free=0.1334 adp: r_work=0.1183 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1334 r_work=0.1183 r_free=0.1334 | n_water=988 | time (s): 230.100 (total time: 354.670) Filter (q & B) r_work=0.1187 r_free=0.1340 | n_water=918 | time (s): 4.960 (total time: 359.630) Filter (dist only) r_work=0.1188 r_free=0.1340 | n_water=916 | time (s): 118.270 (total time: 477.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570435 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.120947 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1343 0.0153 0.039 1.1 7.5 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.43 1.53 1.693 13.879 14.121 3.754 11.90 13.46 1.56 1.704 13.872 14.121 3.752 Individual atomic B min max mean iso aniso Overall: 5.63 64.48 14.79 0.86 551 3269 Protein: 5.63 28.24 10.42 0.86 0 2902 Water: 6.05 64.48 28.61 N/A 551 365 Other: 13.89 22.25 18.07 N/A 0 2 Chain A: 5.67 52.20 12.22 N/A 0 1623 Chain B: 5.63 63.53 12.09 N/A 0 1646 Chain S: 6.05 64.48 30.42 N/A 551 0 Histogram: Values Number of atoms 5.63 - 11.52 2092 11.52 - 17.40 812 17.40 - 23.29 268 23.29 - 29.17 219 29.17 - 35.05 185 35.05 - 40.94 130 40.94 - 46.82 72 46.82 - 52.71 33 52.71 - 58.59 5 58.59 - 64.48 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1346 r_work=0.1190 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1346 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1346 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752157 | | target function (ml) not normalized (work): 702726.469729 | | target function (ml) not normalized (free): 14725.483071 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1346 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1486 n_refl.: 191127 remove outliers: r(all,work,free)=0.1404 0.1402 0.1486 n_refl.: 191127 overall B=-0.11 to atoms: r(all,work,free)=0.1385 0.1383 0.1472 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1345 n_refl.: 191127 remove outliers: r(all,work,free)=0.1191 0.1188 0.1345 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 0.3529 348.232 318.343 0.366 0.994 0.187 13.296-10.522 97.03 97 1 0.2423 481.398 463.770 0.658 0.996 0.137 10.503-8.327 97.80 175 3 0.2147 502.120 494.073 0.820 0.996 0.108 8.315-6.595 100.00 359 8 0.2131 374.758 370.476 0.844 0.996 0.088 6.588-5.215 100.00 711 7 0.1971 345.234 334.674 0.847 0.997 0.080 5.214-4.128 98.38 1367 28 0.1227 504.973 499.405 0.935 0.998 0.044 4.126-3.266 94.74 2603 46 0.1153 460.310 452.923 0.994 0.999 0.009 3.266-2.585 99.86 5447 97 0.1124 310.514 306.980 0.978 1.000 0.000 2.585-2.046 97.45 10613 204 0.0961 234.265 231.598 0.985 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.650 137.257 1.001 1.007 0.000 1.619-1.281 98.00 42464 925 0.0940 74.641 73.995 0.991 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.042 38.324 0.959 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0242 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1188 r_free=0.1345 After: r_work=0.1189 r_free=0.1345 ================================== NQH flips ================================== r_work=0.1189 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1345 | n_water=916 | time (s): 3.420 (total time: 3.420) Filter (dist) r_work=0.1189 r_free=0.1345 | n_water=916 | time (s): 115.660 (total time: 119.080) Filter (q & B) r_work=0.1189 r_free=0.1344 | n_water=905 | time (s): 5.580 (total time: 124.660) Compute maps r_work=0.1189 r_free=0.1344 | n_water=905 | time (s): 1.980 (total time: 126.640) Filter (map) r_work=0.1211 r_free=0.1352 | n_water=794 | time (s): 5.340 (total time: 131.980) Find peaks r_work=0.1211 r_free=0.1352 | n_water=794 | time (s): 0.860 (total time: 132.840) Add new water r_work=0.1218 r_free=0.1355 | n_water=989 | time (s): 5.130 (total time: 137.970) Refine new water occ: r_work=0.1187 r_free=0.1333 adp: r_work=0.1187 r_free=0.1333 occ: r_work=0.1185 r_free=0.1333 adp: r_work=0.1185 r_free=0.1333 occ: r_work=0.1183 r_free=0.1332 adp: r_work=0.1183 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1332 r_work=0.1183 r_free=0.1332 | n_water=989 | time (s): 229.480 (total time: 367.450) Filter (q & B) r_work=0.1187 r_free=0.1336 | n_water=921 | time (s): 5.150 (total time: 372.600) Filter (dist only) r_work=0.1188 r_free=0.1337 | n_water=918 | time (s): 119.580 (total time: 492.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.484274 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.244411 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1340 0.0150 0.039 1.1 9.4 0.0 0.3 0 0.742 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.40 1.50 1.688 13.763 14.244 3.754 11.90 13.42 1.51 1.687 13.761 14.244 3.753 Individual atomic B min max mean iso aniso Overall: 5.55 64.04 14.68 0.86 553 3269 Protein: 5.55 28.11 10.33 0.86 0 2902 Water: 5.99 64.04 28.40 N/A 553 365 Other: 13.84 22.16 18.00 N/A 0 2 Chain A: 5.62 51.83 12.10 N/A 0 1623 Chain B: 5.55 62.68 11.97 N/A 0 1646 Chain S: 5.99 64.04 30.27 N/A 553 0 Histogram: Values Number of atoms 5.55 - 11.40 2081 11.40 - 17.25 829 17.25 - 23.10 259 23.10 - 28.95 227 28.95 - 34.80 176 34.80 - 40.64 134 40.64 - 46.49 71 46.49 - 52.34 36 52.34 - 58.19 5 58.19 - 64.04 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1342 r_work=0.1190 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1342 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1340 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1340 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752557 | | target function (ml) not normalized (work): 702801.317108 | | target function (ml) not normalized (free): 14719.403275 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1344 0.1401 5.6776 5.7262| | 2: 2.94 - 2.33 1.00 7339 128 0.1070 0.1353 5.0666 5.1752| | 3: 2.33 - 2.04 0.96 6939 150 0.0907 0.1195 4.6607 4.7724| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1040 4.3941 4.5556| | 5: 1.85 - 1.72 0.99 7113 159 0.0934 0.0975 4.1522 4.2416| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1072 3.9444 4.0717| | 7: 1.62 - 1.54 0.99 7104 148 0.0886 0.0963 3.7978 3.9371| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1279 3.6954 3.8897| | 9: 1.47 - 1.41 0.98 6938 155 0.0921 0.1104 3.6137 3.7377| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1190 3.5509 3.6786| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1135 3.4811 3.5816| | 12: 1.32 - 1.28 0.98 6975 149 0.1029 0.1119 3.458 3.5822| | 13: 1.28 - 1.25 0.98 6907 166 0.1039 0.1229 3.4348 3.5561| | 14: 1.25 - 1.22 0.98 7015 112 0.1100 0.1565 3.4304 3.6759| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1228 3.446 3.4872| | 16: 1.19 - 1.17 0.93 6604 132 0.1246 0.1548 3.4634 3.6584| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1224 3.4341 3.4446| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1697 3.4391 3.5319| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1756 3.4198 3.5983| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1580 3.4112 3.435| | 21: 1.08 - 1.07 0.97 6852 152 0.1731 0.2140 3.4199 3.507| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1954 3.4143 3.4171| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2036 3.4335 3.4879| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2244 3.4364 3.5072| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2526 3.4495 3.5256| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2868 3.4162 3.426| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2803 3.4691 3.3963| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7395 127 0.93 11.12 1.00 0.98 10461.07| | 2: 2.94 - 2.33 7339 128 0.93 12.43 0.99 0.98 4900.13| | 3: 2.33 - 2.04 6939 150 0.96 7.71 1.01 0.98 1720.08| | 4: 2.04 - 1.85 7170 155 0.96 7.70 1.00 0.98 1012.76| | 5: 1.85 - 1.72 7113 159 0.96 8.07 1.00 0.98 635.48| | 6: 1.72 - 1.62 7102 142 0.96 8.00 1.00 0.99 441.20| | 7: 1.62 - 1.54 7104 148 0.96 8.07 1.01 1.00 334.39| | 8: 1.54 - 1.47 6798 152 0.96 8.16 1.01 1.00 274.21| | 9: 1.47 - 1.41 6938 155 0.96 8.31 1.00 1.00 225.12| | 10: 1.41 - 1.36 7022 150 0.96 8.78 1.00 1.00 198.49| | 11: 1.36 - 1.32 6997 151 0.96 8.85 0.99 0.99 172.99| | 12: 1.32 - 1.28 6975 149 0.96 8.94 0.98 0.97 160.16| | 13: 1.28 - 1.25 6907 166 0.96 9.46 1.01 0.99 157.27| | 14: 1.25 - 1.22 7015 112 0.95 10.63 1.01 0.99 161.82| | 15: 1.22 - 1.19 6956 137 0.95 11.17 1.01 1.00 165.34| | 16: 1.19 - 1.17 6604 132 0.95 11.38 1.00 0.98 159.50| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.99 153.61| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.97 147.41| | 19: 1.12 - 1.10 6948 106 0.93 14.15 1.00 0.97 151.15| | 20: 1.10 - 1.08 6884 147 0.92 15.23 1.00 0.96 150.52| | 21: 1.08 - 1.07 6852 152 0.91 16.69 1.00 0.96 154.00| | 22: 1.07 - 1.05 6836 135 0.89 18.33 1.00 0.95 155.44| | 23: 1.05 - 1.03 6827 159 0.87 20.53 1.00 0.95 165.23| | 24: 1.03 - 1.02 6784 133 0.85 23.18 1.00 0.95 179.44| | 25: 1.02 - 1.01 6552 130 0.83 25.19 0.98 0.92 182.57| | 26: 1.01 - 0.99 6767 158 0.81 26.66 0.99 0.91 177.06| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.99 0.90 161.39| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 147.41 max = 10461.07 mean = 887.50| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.96 mean = 13.23| |phase err.(test): min = 0.00 max = 88.14 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1340 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1394 0.1393 0.1475 n_refl.: 191127 remove outliers: r(all,work,free)=0.1394 0.1393 0.1475 n_refl.: 191127 overall B=-0.04 to atoms: r(all,work,free)=0.1389 0.1387 0.1471 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1339 n_refl.: 191127 remove outliers: r(all,work,free)=0.1192 0.1189 0.1339 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 0.3540 348.232 317.683 0.396 0.915 0.187 13.296-10.522 97.03 97 1 0.2399 481.398 463.846 0.711 0.917 0.128 10.503-8.327 97.80 175 3 0.2138 502.120 494.940 0.890 0.917 0.102 8.315-6.595 100.00 359 8 0.2115 374.758 370.267 0.917 0.917 0.086 6.588-5.215 100.00 711 7 0.1955 345.234 335.103 0.921 0.918 0.073 5.214-4.128 98.38 1367 28 0.1230 504.973 499.518 1.016 0.919 0.024 4.126-3.266 94.74 2603 46 0.1153 460.310 452.920 1.082 0.920 0.000 3.266-2.585 99.86 5447 97 0.1120 310.514 307.045 1.065 0.921 0.000 2.585-2.046 97.45 10613 204 0.0963 234.265 231.636 1.071 0.924 0.000 2.046-1.619 99.39 21536 464 0.0911 138.650 137.260 1.088 0.928 0.000 1.619-1.281 98.00 42464 925 0.0943 74.641 73.994 1.077 0.934 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.042 38.326 1.042 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0083 ================= 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 : 0.2034 0.2008 0.081 5.171 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1952 0.081 5.171 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1952 0.081 5.171 5.2 78.0 14.6 805 0.000 1_nqh: 0.1804 0.1959 0.081 5.171 5.2 78.0 14.6 805 0.002 1_weight: 0.1804 0.1959 0.081 5.171 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1272 0.1503 0.038 1.193 5.2 78.0 14.6 805 0.155 1_adp: 0.1297 0.1568 0.038 1.193 5.2 73.0 15.1 805 0.155 1_regHadp: 0.1296 0.1562 0.038 1.193 5.2 73.0 15.1 805 0.155 1_occ: 0.1281 0.1549 0.038 1.193 5.2 73.0 15.1 805 0.155 2_bss: 0.1274 0.1537 0.038 1.193 5.3 73.2 15.2 805 0.155 2_settarget: 0.1274 0.1537 0.038 1.193 5.3 73.2 15.2 805 0.155 2_updatecdl: 0.1274 0.1537 0.038 1.192 5.3 73.2 15.2 805 0.155 2_nqh: 0.1274 0.1537 0.038 1.192 5.3 73.2 15.2 805 0.155 2_sol: 0.1270 0.1501 0.038 1.192 5.3 73.2 16.1 875 n/a 2_weight: 0.1270 0.1501 0.038 1.192 5.3 73.2 16.1 875 n/a 2_xyzrec: 0.1254 0.1522 0.041 1.142 5.3 73.2 16.1 875 n/a 2_adp: 0.1233 0.1510 0.041 1.142 5.4 69.1 16.2 875 n/a 2_regHadp: 0.1233 0.1511 0.041 1.142 5.4 69.1 16.2 875 n/a 2_occ: 0.1226 0.1509 0.041 1.142 5.4 69.1 16.2 875 n/a 3_bss: 0.1233 0.1515 0.041 1.142 5.3 69.0 16.2 875 n/a 3_settarget: 0.1233 0.1515 0.041 1.142 5.3 69.0 16.2 875 n/a 3_updatecdl: 0.1233 0.1515 0.041 1.147 5.3 69.0 16.2 875 n/a 3_nqh: 0.1233 0.1515 0.041 1.147 5.3 69.0 16.2 875 n/a 3_sol: 0.1249 0.1498 0.041 1.147 5.3 68.2 15.3 867 n/a 3_weight: 0.1249 0.1498 0.041 1.147 5.3 68.2 15.3 867 n/a 3_xyzrec: 0.1237 0.1427 0.036 1.097 5.3 68.2 15.3 867 n/a 3_adp: 0.1234 0.1390 0.036 1.097 5.5 67.7 15.1 867 n/a 3_regHadp: 0.1235 0.1391 0.036 1.097 5.5 67.7 15.1 867 n/a 3_occ: 0.1230 0.1386 0.036 1.097 5.5 67.7 15.1 867 n/a 4_bss: 0.1225 0.1381 0.036 1.097 5.5 67.7 15.1 867 n/a 4_settarget: 0.1225 0.1381 0.036 1.097 5.5 67.7 15.1 867 n/a 4_updatecdl: 0.1225 0.1381 0.036 1.103 5.5 67.7 15.1 867 n/a 4_nqh: 0.1225 0.1381 0.036 1.103 5.5 67.7 15.1 867 n/a 4_sol: 0.1208 0.1363 0.036 1.103 5.5 67.7 14.8 849 n/a 4_weight: 0.1208 0.1363 0.036 1.103 5.5 67.7 14.8 849 n/a 4_xyzrec: 0.1207 0.1368 0.036 1.119 5.5 67.7 14.8 849 n/a 4_adp: 0.1202 0.1366 0.036 1.119 5.5 67.4 14.8 849 n/a 4_regHadp: 0.1202 0.1366 0.036 1.119 5.5 67.4 14.8 849 n/a 4_occ: 0.1201 0.1364 0.036 1.119 5.5 67.4 14.8 849 n/a 5_bss: 0.1199 0.1362 0.036 1.119 5.5 67.3 14.7 849 n/a 5_settarget: 0.1199 0.1362 0.036 1.119 5.5 67.3 14.7 849 n/a 5_updatecdl: 0.1199 0.1362 0.036 1.119 5.5 67.3 14.7 849 n/a 5_nqh: 0.1199 0.1362 0.036 1.119 5.5 67.3 14.7 849 n/a 5_sol: 0.1196 0.1357 0.036 1.119 5.5 67.3 14.9 867 n/a 5_weight: 0.1196 0.1357 0.036 1.119 5.5 67.3 14.9 867 n/a 5_xyzrec: 0.1199 0.1358 0.036 1.136 5.5 67.3 14.9 867 n/a 5_adp: 0.1202 0.1361 0.036 1.136 5.5 66.8 14.8 867 n/a 5_regHadp: 0.1202 0.1361 0.036 1.136 5.5 66.8 14.8 867 n/a 5_occ: 0.1200 0.1361 0.036 1.136 5.5 66.8 14.8 867 n/a 6_bss: 0.1199 0.1360 0.036 1.136 5.5 66.8 14.8 867 n/a 6_settarget: 0.1199 0.1360 0.036 1.136 5.5 66.8 14.8 867 n/a 6_updatecdl: 0.1199 0.1360 0.036 1.136 5.5 66.8 14.8 867 n/a 6_nqh: 0.1199 0.1360 0.036 1.136 5.5 66.8 14.8 867 n/a 6_sol: 0.1195 0.1347 0.036 1.136 5.5 66.8 14.9 891 n/a 6_weight: 0.1195 0.1347 0.036 1.136 5.5 66.8 14.9 891 n/a 6_xyzrec: 0.1199 0.1354 0.037 1.140 5.5 66.8 14.9 891 n/a 6_adp: 0.1199 0.1355 0.037 1.140 5.6 65.7 14.8 891 n/a 6_regHadp: 0.1199 0.1355 0.037 1.140 5.6 65.7 14.8 891 n/a 6_occ: 0.1197 0.1355 0.037 1.140 5.6 65.7 14.8 891 n/a 7_bss: 0.1195 0.1354 0.037 1.140 5.5 65.7 14.8 891 n/a 7_settarget: 0.1195 0.1354 0.037 1.140 5.5 65.7 14.8 891 n/a 7_updatecdl: 0.1195 0.1354 0.037 1.139 5.5 65.7 14.8 891 n/a 7_nqh: 0.1195 0.1354 0.037 1.139 5.5 65.7 14.8 891 n/a 7_sol: 0.1194 0.1347 0.037 1.139 5.5 65.7 14.8 900 n/a 7_weight: 0.1194 0.1347 0.037 1.139 5.5 65.7 14.8 900 n/a 7_xyzrec: 0.1197 0.1355 0.038 1.122 5.5 65.7 14.8 900 n/a 7_adp: 0.1200 0.1357 0.038 1.122 5.6 65.0 14.8 900 n/a 7_regHadp: 0.1200 0.1357 0.038 1.122 5.6 65.0 14.8 900 n/a 7_occ: 0.1198 0.1356 0.038 1.122 5.6 65.0 14.8 900 n/a 8_bss: 0.1188 0.1345 0.038 1.122 5.6 65.0 14.8 900 n/a 8_settarget: 0.1188 0.1345 0.038 1.122 5.6 65.0 14.8 900 n/a 8_updatecdl: 0.1188 0.1345 0.038 1.123 5.6 65.0 14.8 900 n/a 8_nqh: 0.1188 0.1345 0.038 1.123 5.6 65.0 14.8 900 n/a 8_sol: 0.1186 0.1339 0.038 1.123 5.6 65.0 14.8 904 n/a 8_weight: 0.1186 0.1339 0.038 1.123 5.6 65.0 14.8 904 n/a 8_xyzrec: 0.1189 0.1341 0.039 1.107 5.6 65.0 14.8 904 n/a 8_adp: 0.1191 0.1344 0.039 1.107 5.6 64.9 14.8 904 n/a 8_regHadp: 0.1192 0.1344 0.039 1.107 5.6 64.9 14.8 904 n/a 8_occ: 0.1190 0.1347 0.039 1.107 5.6 64.9 14.8 904 n/a 9_bss: 0.1190 0.1346 0.039 1.107 5.6 64.8 14.8 904 n/a 9_settarget: 0.1190 0.1346 0.039 1.107 5.6 64.8 14.8 904 n/a 9_updatecdl: 0.1190 0.1346 0.039 1.107 5.6 64.8 14.8 904 n/a 9_nqh: 0.1190 0.1346 0.039 1.107 5.6 64.8 14.8 904 n/a 9_sol: 0.1188 0.1340 0.039 1.107 5.6 64.8 14.8 916 n/a 9_weight: 0.1188 0.1340 0.039 1.107 5.6 64.8 14.8 916 n/a 9_xyzrec: 0.1190 0.1343 0.039 1.118 5.6 64.8 14.8 916 n/a 9_adp: 0.1190 0.1346 0.039 1.118 5.6 64.5 14.8 916 n/a 9_regHadp: 0.1190 0.1346 0.039 1.118 5.6 64.5 14.8 916 n/a 9_occ: 0.1189 0.1346 0.039 1.118 5.6 64.5 14.8 916 n/a 10_bss: 0.1188 0.1345 0.039 1.118 5.5 64.4 14.7 916 n/a 10_settarget: 0.1188 0.1345 0.039 1.118 5.5 64.4 14.7 916 n/a 10_updatecdl: 0.1188 0.1345 0.039 1.118 5.5 64.4 14.7 916 n/a 10_setrh: 0.1189 0.1345 0.039 1.118 5.5 64.4 14.7 916 n/a 10_nqh: 0.1189 0.1345 0.039 1.118 5.5 64.4 14.7 916 n/a 10_sol: 0.1188 0.1337 0.039 1.118 5.5 64.4 14.7 918 n/a 10_weight: 0.1188 0.1337 0.039 1.118 5.5 64.4 14.7 918 n/a 10_xyzrec: 0.1189 0.1340 0.039 1.141 5.5 64.4 14.7 918 n/a 10_adp: 0.1190 0.1342 0.039 1.141 5.6 64.0 14.7 918 n/a 10_regHadp: 0.1190 0.1342 0.039 1.141 5.6 64.0 14.7 918 n/a 10_occ: 0.1189 0.1340 0.039 1.141 5.6 64.0 14.7 918 n/a end: 0.1189 0.1339 0.039 1.141 5.5 64.0 14.6 918 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1760590_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1760590_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.4700 Refinement macro-cycles (run) : 12097.8700 Write final files (write_after_run_outputs) : 164.7900 Total : 12269.1300 Total CPU time: 3.42 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:41 PST -0800 (1736736101.12 s) Start R-work = 0.1800, R-free = 0.1952 Final R-work = 0.1189, R-free = 0.1339 =============================================================================== Job complete usr+sys time: 12554.29 seconds wall clock time: 210 minutes 16.46 seconds (12616.46 seconds total)