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_4574008.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4574008.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4574008.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" } 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 2 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: 1.61, per 1000 atoms: 0.24 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: 2.746 distance_ideal: 2.720 ideal - model: -0.026 slack: 0.000 delta_slack: -0.026 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: 2.756 distance_ideal: 2.710 ideal - model: -0.046 slack: 0.000 delta_slack: -0.046 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 186.1 milliseconds Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.03: 765 1.03 - 1.25: 2478 1.25 - 1.46: 1371 1.46 - 1.68: 1266 1.68 - 1.90: 54 Bond restraints: 5934 Sorted by residual: bond pdb=" C LEU B 24 " pdb=" O LEU B 24 " ideal model delta sigma weight residual 1.236 0.984 0.252 1.15e-02 7.56e+03 4.81e+02 bond pdb=" C GLY B 190 " pdb=" O GLY B 190 " ideal model delta sigma weight residual 1.234 1.483 -0.250 1.14e-02 7.69e+03 4.79e+02 bond pdb=" N GLU A 180 " pdb=" CA GLU A 180 " ideal model delta sigma weight residual 1.459 1.215 0.245 1.19e-02 7.06e+03 4.22e+02 bond pdb=" CB VAL B 51 " pdb=" HB VAL B 51 " ideal model delta sigma weight residual 0.970 1.352 -0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" N GLY B 126 " pdb=" H GLY B 126 " ideal model delta sigma weight residual 0.860 1.242 -0.382 2.00e-02 2.50e+03 3.64e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.78: 6252 4.78 - 9.55: 3496 9.55 - 14.33: 961 14.33 - 19.10: 96 19.10 - 23.88: 5 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ASP B 147 " pdb=" C ASP B 147 " pdb=" O ASP B 147 " ideal model delta sigma weight residual 120.40 137.20 -16.80 1.05e+00 9.07e-01 2.56e+02 angle pdb=" CD2 TRP A 139 " pdb=" CE2 TRP A 139 " pdb=" CZ2 TRP A 139 " ideal model delta sigma weight residual 122.40 108.27 14.13 1.00e+00 1.00e+00 2.00e+02 angle pdb=" O TRP B 146 " pdb=" C TRP B 146 " pdb=" N ASP B 147 " ideal model delta sigma weight residual 123.12 141.77 -18.65 1.32e+00 5.74e-01 2.00e+02 angle pdb=" N ILE B 169 " pdb=" CA ILE B 169 " pdb=" CB ILE B 169 " ideal model delta sigma weight residual 110.51 126.06 -15.55 1.11e+00 8.12e-01 1.96e+02 angle pdb=" O ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " ideal model delta sigma weight residual 123.00 108.10 14.90 1.07e+00 8.73e-01 1.94e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1845 17.96 - 35.93: 145 35.93 - 53.89: 43 53.89 - 71.85: 14 71.85 - 89.81: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: 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 180.00 154.77 25.23 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CG TRP B 146 " pdb=" CD2 TRP B 146 " pdb=" CE3 TRP B 146 " pdb=" HE3 TRP B 146 " ideal model delta harmonic sigma weight residual 0.00 -23.34 23.34 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.238: 220 0.238 - 0.476: 153 0.476 - 0.713: 82 0.713 - 0.950: 36 0.950 - 1.187: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.40 -1.19 2.00e-01 2.50e+01 3.52e+01 chirality pdb=" CA ALA A 189 " pdb=" N ALA A 189 " pdb=" C ALA A 189 " pdb=" CB ALA A 189 " both_signs ideal model delta sigma weight residual False 2.48 3.43 -0.95 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" CA GLN A 156 " pdb=" N GLN A 156 " pdb=" C GLN A 156 " pdb=" CB GLN A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " 0.021 2.00e-02 2.50e+03 6.58e-02 1.73e+02 pdb=" CG TRP B 146 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.064 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.081 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.073 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.100 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.082 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.044 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.033 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.090 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.088 2.00e-02 2.50e+03 6.28e-02 1.58e+02 pdb=" CG TRP A 139 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.141 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.015 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.096 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.023 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.006 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.114 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.012 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " 0.025 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " 0.030 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR B 195 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " -0.126 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TYR B 195 " -0.076 2.00e-02 2.50e+03 pdb=" HD2 TYR B 195 " -0.094 2.00e-02 2.50e+03 pdb=" HE1 TYR B 195 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR B 195 " 0.052 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 25 1.60 - 2.35: 2270 2.35 - 3.10: 22261 3.10 - 3.85: 32906 3.85 - 4.60: 52840 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110302 Sorted by model distance: nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.853 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.857 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.960 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.067 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.172 2.620 ... (remaining 110297 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_4574008_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= 0.2036 r_free= 0.1981 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.298591 | | target function (ml) not normalized (work): 805181.886938 | | target function (ml) not normalized (free): 16521.710199 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2129 0.2022 6.6747 6.3202| | 2: 2.94 - 2.33 1.00 7339 128 0.1620 0.1563 5.5484 5.5696| | 3: 2.33 - 2.04 0.96 6939 150 0.1635 0.1627 5.143 5.1757| | 4: 2.04 - 1.85 1.00 7170 155 0.1772 0.1707 4.9707 5.0798| | 5: 1.85 - 1.72 0.99 7113 159 0.1904 0.1585 4.7903 4.7153| | 6: 1.72 - 1.62 0.99 7102 142 0.1993 0.2111 4.67 4.7864| | 7: 1.62 - 1.54 0.99 7104 148 0.2046 0.1725 4.5713 4.5772| | 8: 1.54 - 1.47 0.96 6798 152 0.2031 0.2103 4.4785 4.5443| | 9: 1.47 - 1.41 0.98 6938 155 0.2100 0.2381 4.4019 4.4893| | 10: 1.41 - 1.36 0.99 7022 150 0.2157 0.2243 4.3207 4.3914| | 11: 1.36 - 1.32 0.99 6997 151 0.2108 0.1929 4.2303 4.2474| | 12: 1.32 - 1.28 0.98 6976 149 0.2084 0.1895 4.1714 4.1814| | 13: 1.28 - 1.25 0.98 6907 166 0.2043 0.2170 4.1252 4.2017| | 14: 1.25 - 1.22 0.98 7015 113 0.2068 0.2103 4.0736 4.1344| | 15: 1.22 - 1.19 0.98 6957 137 0.2123 0.2012 4.0375 4.0128| | 16: 1.19 - 1.17 0.93 6604 132 0.2138 0.2044 4.009 3.9997| | 17: 1.17 - 1.14 0.98 6941 135 0.2158 0.1773 3.9457 3.8771| | 18: 1.14 - 1.12 0.98 6875 142 0.2227 0.2307 3.914 3.9118| | 19: 1.12 - 1.10 0.97 6949 106 0.2276 0.2520 3.8658 3.9738| | 20: 1.10 - 1.08 0.97 6884 147 0.2309 0.2337 3.812 3.869| | 21: 1.08 - 1.07 0.97 6852 152 0.2412 0.2561 3.7776 3.756| | 22: 1.07 - 1.05 0.97 6838 135 0.2525 0.2418 3.7429 3.728| | 23: 1.05 - 1.03 0.97 6829 159 0.2761 0.2492 3.7371 3.7853| | 24: 1.03 - 1.02 0.96 6785 133 0.2877 0.2922 3.7021 3.7818| | 25: 1.02 - 1.01 0.93 6552 130 0.3059 0.2974 3.6733 3.7812| | 26: 1.01 - 0.99 0.96 6767 158 0.3175 0.3081 3.6194 3.6085| | 27: 0.99 - 0.98 0.94 6648 131 0.3420 0.3384 3.6422 3.6179| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.76 0.91 0.97 36538.82| | 2: 2.94 - 2.33 7339 128 0.85 21.46 1.08 1.03 15538.17| | 3: 2.33 - 2.04 6939 150 0.93 12.57 1.11 1.06 4162.19| | 4: 2.04 - 1.85 7170 155 0.92 13.44 1.11 1.07 2749.18| | 5: 1.85 - 1.72 7113 159 0.91 15.00 1.11 1.09 1965.11| | 6: 1.72 - 1.62 7102 142 0.90 16.64 1.11 1.08 1637.19| | 7: 1.62 - 1.54 7104 148 0.89 17.97 1.11 1.07 1381.70| | 8: 1.54 - 1.47 6798 152 0.88 19.20 1.10 1.06 1253.05| | 9: 1.47 - 1.41 6938 155 0.87 19.83 1.10 1.07 1067.06| | 10: 1.41 - 1.36 7022 150 0.86 20.65 1.09 1.05 893.53| | 11: 1.36 - 1.32 6997 151 0.87 20.04 1.08 1.04 730.42| | 12: 1.32 - 1.28 6976 149 0.87 19.88 1.08 1.03 638.98| | 13: 1.28 - 1.25 6907 166 0.88 19.63 1.07 1.04 590.93| | 14: 1.25 - 1.22 7015 113 0.87 20.05 1.08 1.04 542.78| | 15: 1.22 - 1.19 6957 137 0.88 19.54 1.08 1.05 482.81| | 16: 1.19 - 1.17 6604 132 0.89 18.68 1.08 1.04 422.02| | 17: 1.17 - 1.14 6941 135 0.88 19.10 1.09 1.04 379.88| | 18: 1.14 - 1.12 6875 142 0.88 19.83 1.09 1.01 357.87| | 19: 1.12 - 1.10 6949 106 0.86 21.24 1.07 1.00 355.66| | 20: 1.10 - 1.08 6884 147 0.85 22.45 1.07 0.98 337.54| | 21: 1.08 - 1.07 6852 152 0.84 23.47 1.06 0.97 322.41| | 22: 1.07 - 1.05 6838 135 0.83 25.01 1.05 0.97 315.36| | 23: 1.05 - 1.03 6829 159 0.80 27.57 1.05 0.96 324.70| | 24: 1.03 - 1.02 6785 133 0.78 29.80 1.05 0.96 332.55| | 25: 1.02 - 1.01 6552 130 0.76 31.28 1.03 0.93 319.52| | 26: 1.01 - 0.99 6767 158 0.74 32.94 1.03 0.90 298.13| | 27: 0.99 - 0.98 6648 131 0.74 33.29 1.04 0.86 279.71| |alpha: min = 0.86 max = 1.09 mean = 1.01| |beta: min = 279.71 max = 36538.82 mean = 2879.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.97 mean = 21.45| |phase err.(test): min = 0.00 max = 89.43 mean = 21.48| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.252 2950 Z= 5.555 Angle : 5.301 18.651 4018 Z= 3.782 Chirality : 0.392 1.187 492 Planarity : 0.033 0.156 512 Dihedral : 13.017 89.815 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.40 % Favored : 95.08 % Rotamer: Outliers : 1.61 % Allowed : 3.23 % Favored : 95.16 % Cbeta Deviations : 34.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.41), residues: 386 helix: -2.69 (0.31), residues: 144 sheet: -0.73 (0.53), residues: 86 loop : -0.15 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.025 ARG B 100 TYR 0.136 0.041 TYR A 194 PHE 0.124 0.038 PHE A 119 TRP 0.098 0.046 TRP A 139 HIS 0.069 0.032 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2036 r_free= 0.1981 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.298591 | | target function (ml) not normalized (work): 805181.886938 | | target function (ml) not normalized (free): 16521.710199 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2035 0.2036 0.1981 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2035 0.2036 0.1981 n_refl.: 191155 remove outliers: r(all,work,free)=0.2035 0.2037 0.1981 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2035 0.2037 0.1981 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1803 0.1801 0.1913 n_refl.: 191145 remove outliers: r(all,work,free)=0.1801 0.1798 0.1913 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4095 402.814 290.895 0.425 0.932 0.303 13.296-10.522 100.00 100 1 0.2492 534.497 523.628 0.770 0.933 0.256 10.503-8.327 98.90 177 3 0.2433 564.205 559.045 0.946 0.933 0.233 8.318-6.595 100.00 360 8 0.2469 414.736 403.970 0.950 0.933 0.165 6.588-5.215 100.00 711 7 0.2266 381.101 366.608 0.935 0.933 0.150 5.214-4.128 98.38 1367 28 0.1457 557.435 551.039 1.052 0.932 0.090 4.126-3.266 94.74 2603 46 0.1351 508.132 499.389 1.120 0.931 0.014 3.266-2.585 99.86 5447 97 0.1440 342.774 337.601 1.098 0.929 0.000 2.585-2.046 97.45 10613 204 0.1399 258.603 254.234 1.107 0.926 0.000 2.046-1.619 99.39 21536 464 0.1621 153.054 149.743 1.130 0.920 0.000 1.619-1.281 98.00 42464 925 0.1932 82.395 80.147 1.124 0.911 0.000 1.281-0.980 96.53 101826 2056 0.2311 44.203 41.690 1.125 0.894 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0089 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1798 r_free=0.1913 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1800 r_free=0.1914 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.939549 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 582.577586 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 0.1269 0.1499 0.0229 0.038 1.2 11.2 0.0 0.3 0 11.470 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.69 14.99 2.29 1.118 13.116 582.578 0.018 12.97 15.69 2.72 1.271 13.375 582.578 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.05 15.07 1.42 435 3274 Protein: 5.16 40.32 11.03 1.42 0 2902 Water: 6.35 73.05 29.61 N/A 435 370 Other: 16.09 30.66 23.38 N/A 0 2 Chain A: 5.39 60.02 13.09 N/A 0 1626 Chain B: 5.16 73.05 12.81 N/A 0 1648 Chain S: 11.32 64.88 31.05 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2157 11.95 - 18.74 642 18.74 - 25.52 313 25.52 - 32.31 263 32.31 - 39.10 160 39.10 - 45.89 108 45.89 - 52.68 42 52.68 - 59.47 19 59.47 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1569 r_work=0.1296 r_free=0.1564 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1564 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1282 r_free = 0.1553 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015552 | | target function (ls_wunit_k1) not normalized (work): 2912.884744 | | target function (ls_wunit_k1) not normalized (free): 116.256638 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1553 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1471 0.1468 0.1634 n_refl.: 191139 remove outliers: r(all,work,free)=0.1471 0.1468 0.1634 n_refl.: 191139 overall B=0.15 to atoms: r(all,work,free)=0.1493 0.1491 0.1644 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1543 n_refl.: 191139 remove outliers: r(all,work,free)=0.1281 0.1276 0.1542 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3597 402.814 381.697 0.471 0.997 0.275 13.296-10.522 100.00 100 1 0.2113 534.497 528.422 0.720 0.999 0.245 10.503-8.327 98.90 177 3 0.1722 564.205 565.481 0.856 0.999 0.240 8.318-6.595 100.00 360 8 0.1710 414.736 412.536 0.877 0.998 0.155 6.588-5.215 100.00 711 7 0.1532 381.101 373.620 0.857 0.999 0.150 5.214-4.128 98.38 1367 28 0.0901 557.435 554.203 0.943 0.999 0.080 4.126-3.266 94.74 2603 46 0.0826 508.132 504.320 1.007 1.000 0.014 3.266-2.585 99.86 5447 97 0.0919 342.774 340.312 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.422 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1093 153.054 151.371 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1284 82.395 81.398 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.159 0.989 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0348 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1542 | n_water=805 | time (s): 2.850 (total time: 2.850) Filter (dist) r_work=0.1280 r_free=0.1547 | n_water=794 | time (s): 99.380 (total time: 102.230) Filter (q & B) r_work=0.1281 r_free=0.1546 | n_water=790 | time (s): 5.530 (total time: 107.760) Compute maps r_work=0.1281 r_free=0.1546 | n_water=790 | time (s): 2.090 (total time: 109.850) Filter (map) r_work=0.1307 r_free=0.1530 | n_water=654 | time (s): 4.350 (total time: 114.200) Find peaks r_work=0.1307 r_free=0.1530 | n_water=654 | time (s): 0.570 (total time: 114.770) Add new water r_work=0.1330 r_free=0.1564 | n_water=961 | time (s): 5.300 (total time: 120.070) Refine new water occ: r_work=0.1287 r_free=0.1516 adp: r_work=0.1275 r_free=0.1515 occ: r_work=0.1277 r_free=0.1513 adp: r_work=0.1270 r_free=0.1513 occ: r_work=0.1271 r_free=0.1511 adp: r_work=0.1269 r_free=0.1511 ADP+occupancy (water only), MIN, final r_work=0.1269 r_free=0.1511 r_work=0.1269 r_free=0.1511 | n_water=961 | time (s): 78.240 (total time: 198.310) Filter (q & B) r_work=0.1273 r_free=0.1512 | n_water=886 | time (s): 6.010 (total time: 204.320) Filter (dist only) r_work=0.1273 r_free=0.1511 | n_water=884 | time (s): 116.260 (total time: 320.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.083707 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 597.944622 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1257 0.1519 0.0262 0.042 1.1 19.7 0.0 0.0 0 11.542 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.19 2.62 2.054 15.213 597.945 0.015 12.31 14.98 2.67 2.442 15.259 597.945 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 70.08 16.34 1.22 516 3272 Protein: 5.38 40.76 10.99 1.22 0 2902 Water: 6.65 70.08 33.90 N/A 516 368 Other: 16.58 32.19 24.39 N/A 0 2 Chain A: 5.50 55.90 13.02 N/A 0 1624 Chain B: 5.38 68.20 12.84 N/A 0 1648 Chain S: 9.71 70.08 37.99 N/A 516 0 Histogram: Values Number of atoms 5.38 - 11.85 2097 11.85 - 18.32 700 18.32 - 24.79 264 24.79 - 31.26 207 31.26 - 37.73 169 37.73 - 44.20 167 44.20 - 50.67 95 50.67 - 57.14 39 57.14 - 63.61 38 63.61 - 70.08 12 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1498 r_work=0.1232 r_free=0.1499 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1499 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 = 0.1503 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1503 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013479 | | target function (ls_wunit_k1) not normalized (work): 2524.625712 | | target function (ls_wunit_k1) not normalized (free): 99.852163 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1503 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1438 0.1435 0.1586 n_refl.: 191138 remove outliers: r(all,work,free)=0.1438 0.1435 0.1586 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1432 0.1584 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1509 n_refl.: 191138 remove outliers: r(all,work,free)=0.1238 0.1233 0.1509 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3274 402.814 377.458 0.484 0.962 0.261 13.296-10.522 100.00 100 1 0.1885 534.497 527.099 0.768 0.963 0.229 10.503-8.327 98.90 177 3 0.1436 564.205 566.715 0.919 0.963 0.194 8.318-6.595 100.00 360 8 0.1541 414.736 413.669 0.939 0.963 0.165 6.588-5.215 100.00 711 7 0.1329 381.101 376.957 0.915 0.963 0.160 5.214-4.128 98.38 1367 28 0.0844 557.435 555.834 0.995 0.963 0.090 4.126-3.266 94.74 2603 46 0.0760 508.132 505.623 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0862 342.774 341.307 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.792 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.615 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1251 82.395 81.366 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.223 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0599 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1510 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1510 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1510 | n_water=884 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1235 r_free=0.1511 | n_water=877 | time (s): 111.640 (total time: 114.310) Filter (q & B) r_work=0.1235 r_free=0.1511 | n_water=875 | time (s): 5.610 (total time: 119.920) Compute maps r_work=0.1235 r_free=0.1511 | n_water=875 | time (s): 2.550 (total time: 122.470) Filter (map) r_work=0.1276 r_free=0.1515 | n_water=678 | time (s): 4.040 (total time: 126.510) Find peaks r_work=0.1276 r_free=0.1515 | n_water=678 | time (s): 0.670 (total time: 127.180) Add new water r_work=0.1300 r_free=0.1547 | n_water=1002 | time (s): 4.580 (total time: 131.760) Refine new water occ: r_work=0.1253 r_free=0.1497 adp: r_work=0.1253 r_free=0.1500 occ: r_work=0.1249 r_free=0.1495 adp: r_work=0.1249 r_free=0.1497 occ: r_work=0.1246 r_free=0.1494 adp: r_work=0.1245 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1496 r_work=0.1245 r_free=0.1496 | n_water=1002 | time (s): 317.550 (total time: 449.310) Filter (q & B) r_work=0.1248 r_free=0.1501 | n_water=882 | time (s): 4.960 (total time: 454.270) Filter (dist only) r_work=0.1248 r_free=0.1501 | n_water=881 | time (s): 115.790 (total time: 570.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.702251 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.831341 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 0.1431 0.0194 0.036 1.1 10.2 0.0 0.0 0 0.851 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.31 1.94 1.938 14.597 16.831 3.937 12.31 13.91 1.60 2.216 14.514 16.831 3.896 Individual atomic B min max mean iso aniso Overall: 5.55 67.85 15.30 1.07 515 3270 Protein: 5.55 37.19 10.76 1.07 0 2902 Water: 6.70 67.85 30.21 N/A 515 366 Other: 14.13 28.16 21.15 N/A 0 2 Chain A: 5.56 55.06 12.80 N/A 0 1624 Chain B: 5.55 67.85 12.56 N/A 0 1646 Chain S: 13.44 65.80 31.92 N/A 515 0 Histogram: Values Number of atoms 5.55 - 11.78 2133 11.78 - 18.01 685 18.01 - 24.24 299 24.24 - 30.47 240 30.47 - 36.70 180 36.70 - 42.93 136 42.93 - 49.16 77 49.16 - 55.39 25 55.39 - 61.62 7 61.62 - 67.85 3 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1391 r_work=0.1232 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1392 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1381 target_work(ml) = 3.890 | | 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1381 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889801 | | target function (ml) not normalized (work): 728548.073259 | | target function (ml) not normalized (free): 15213.810604 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1226 0.1380 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1443 0.1443 0.1473 n_refl.: 191138 remove outliers: r(all,work,free)=0.1443 0.1443 0.1473 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1437 0.1469 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1222 0.1376 n_refl.: 191138 remove outliers: r(all,work,free)=0.1224 0.1221 0.1376 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3817 398.008 362.133 0.428 0.945 0.250 13.296-10.522 99.01 99 1 0.2544 528.187 512.188 0.711 0.947 0.215 10.503-8.327 97.80 175 3 0.1958 554.286 558.026 0.884 0.947 0.210 8.318-6.595 100.00 360 8 0.2059 414.736 409.497 0.899 0.946 0.140 6.588-5.215 100.00 711 7 0.1817 381.101 370.474 0.889 0.946 0.114 5.214-4.128 98.38 1367 28 0.1170 557.435 551.683 0.974 0.946 0.100 4.126-3.266 94.74 2603 46 0.1085 508.132 501.517 1.035 0.947 0.014 3.266-2.585 99.86 5447 97 0.1082 342.774 339.039 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0961 258.603 255.803 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0972 153.054 151.389 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.486 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.317 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1044 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1221 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1221 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1376 | n_water=881 | time (s): 3.080 (total time: 3.080) Filter (dist) r_work=0.1221 r_free=0.1377 | n_water=880 | time (s): 106.910 (total time: 109.990) Filter (q & B) r_work=0.1222 r_free=0.1377 | n_water=863 | time (s): 4.400 (total time: 114.390) Compute maps r_work=0.1222 r_free=0.1377 | n_water=863 | time (s): 2.080 (total time: 116.470) Filter (map) r_work=0.1244 r_free=0.1384 | n_water=715 | time (s): 4.500 (total time: 120.970) Find peaks r_work=0.1244 r_free=0.1384 | n_water=715 | time (s): 0.540 (total time: 121.510) Add new water r_work=0.1262 r_free=0.1409 | n_water=964 | time (s): 5.020 (total time: 126.530) Refine new water occ: r_work=0.1214 r_free=0.1363 adp: r_work=0.1206 r_free=0.1359 occ: r_work=0.1203 r_free=0.1360 adp: r_work=0.1203 r_free=0.1359 occ: r_work=0.1201 r_free=0.1361 adp: r_work=0.1200 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1359 r_work=0.1200 r_free=0.1359 | n_water=964 | time (s): 337.820 (total time: 464.350) Filter (q & B) r_work=0.1204 r_free=0.1361 | n_water=880 | time (s): 4.260 (total time: 468.610) Filter (dist only) r_work=0.1205 r_free=0.1359 | n_water=879 | time (s): 113.890 (total time: 582.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.600974 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.423339 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 0.1203 0.1364 0.0161 0.036 1.1 6.3 0.0 0.0 0 0.800 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.64 1.61 1.839 14.278 16.423 3.872 11.96 13.60 1.64 1.980 14.226 16.423 3.863 Individual atomic B min max mean iso aniso Overall: 5.50 67.35 15.05 1.01 514 3269 Protein: 5.50 33.65 10.66 1.01 0 2902 Water: 6.00 67.35 29.55 N/A 514 365 Other: 13.97 26.95 20.46 N/A 0 2 Chain A: 5.58 53.69 12.62 N/A 0 1623 Chain B: 5.50 67.35 12.43 N/A 0 1646 Chain S: 6.00 65.53 31.13 N/A 514 0 Histogram: Values Number of atoms 5.50 - 11.68 2105 11.68 - 17.87 741 17.87 - 24.05 294 24.05 - 30.24 239 30.24 - 36.42 165 36.42 - 42.61 135 42.61 - 48.79 67 48.79 - 54.98 27 54.98 - 61.16 7 61.16 - 67.35 3 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1360 r_work=0.1197 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1360 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1358 target_work(ml) = 3.861 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861007 | | target function (ml) not normalized (work): 723139.502606 | | target function (ml) not normalized (free): 15120.044129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1422 0.1422 0.1459 n_refl.: 191134 remove outliers: r(all,work,free)=0.1422 0.1422 0.1459 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1414 0.1414 0.1455 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1359 n_refl.: 191134 remove outliers: r(all,work,free)=0.1195 0.1192 0.1359 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3807 361.142 319.453 0.411 0.946 0.247 13.296-10.522 97.03 97 1 0.2389 478.065 449.653 0.697 0.948 0.199 10.503-8.327 97.80 175 3 0.2083 501.826 498.231 0.866 0.948 0.173 8.318-6.595 100.00 360 8 0.2139 375.484 370.619 0.891 0.948 0.121 6.588-5.215 100.00 711 7 0.1911 345.032 335.010 0.886 0.948 0.100 5.214-4.128 98.38 1367 28 0.1200 504.677 499.190 0.973 0.948 0.090 4.126-3.266 94.74 2603 46 0.1103 460.041 453.748 1.035 0.948 0.005 3.266-2.585 99.86 5447 97 0.1088 310.332 307.131 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0931 234.128 231.747 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0906 138.569 137.308 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0985 74.597 73.903 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.018 38.365 1.038 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1230 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1359 | n_water=879 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1192 r_free=0.1359 | n_water=879 | time (s): 107.240 (total time: 110.180) Filter (q & B) r_work=0.1192 r_free=0.1359 | n_water=866 | time (s): 4.590 (total time: 114.770) Compute maps r_work=0.1192 r_free=0.1359 | n_water=866 | time (s): 1.640 (total time: 116.410) Filter (map) r_work=0.1214 r_free=0.1356 | n_water=742 | time (s): 4.490 (total time: 120.900) Find peaks r_work=0.1214 r_free=0.1356 | n_water=742 | time (s): 0.700 (total time: 121.600) Add new water r_work=0.1226 r_free=0.1381 | n_water=974 | time (s): 5.220 (total time: 126.820) Refine new water occ: r_work=0.1191 r_free=0.1350 adp: r_work=0.1191 r_free=0.1350 occ: r_work=0.1188 r_free=0.1350 adp: r_work=0.1188 r_free=0.1350 occ: r_work=0.1187 r_free=0.1350 adp: r_work=0.1186 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1350 r_work=0.1186 r_free=0.1350 | n_water=974 | time (s): 210.660 (total time: 337.480) Filter (q & B) r_work=0.1191 r_free=0.1351 | n_water=886 | time (s): 4.720 (total time: 342.200) Filter (dist only) r_work=0.1191 r_free=0.1350 | n_water=885 | time (s): 112.650 (total time: 454.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.553861 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.849872 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1357 0.0161 0.037 1.1 5.8 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.57 1.61 1.793 14.130 14.850 3.762 12.00 13.61 1.61 1.825 14.117 14.850 3.761 Individual atomic B min max mean iso aniso Overall: 5.57 67.17 14.97 0.97 520 3269 Protein: 5.57 32.71 10.61 0.97 0 2902 Water: 5.94 67.17 29.26 N/A 520 365 Other: 13.77 26.37 20.07 N/A 0 2 Chain A: 5.62 53.24 12.56 N/A 0 1623 Chain B: 5.57 67.17 12.37 N/A 0 1646 Chain S: 5.94 65.42 30.74 N/A 520 0 Histogram: Values Number of atoms 5.57 - 11.73 2141 11.73 - 17.89 719 17.89 - 24.05 304 24.05 - 30.21 226 30.21 - 36.37 168 36.37 - 42.53 132 42.53 - 48.69 65 48.69 - 54.85 25 54.85 - 61.01 6 61.01 - 67.17 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1361 r_work=0.1200 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 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 = 0.1198 r_free = 0.1360 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760467 | | target function (ml) not normalized (work): 704297.904179 | | target function (ml) not normalized (free): 14746.349666 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1360 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1471 n_refl.: 191131 remove outliers: r(all,work,free)=0.1409 0.1408 0.1471 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1401 0.1400 0.1466 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3859 361.142 323.405 0.398 0.951 0.227 13.296-10.522 97.03 97 1 0.2423 478.065 460.998 0.705 0.953 0.193 10.503-8.327 97.80 175 3 0.2127 501.826 496.495 0.855 0.953 0.173 8.318-6.595 100.00 360 8 0.2146 375.484 371.494 0.882 0.953 0.105 6.588-5.215 100.00 711 7 0.1943 345.032 335.251 0.882 0.953 0.100 5.214-4.128 98.38 1367 28 0.1211 504.677 499.164 0.968 0.953 0.060 4.126-3.266 94.74 2603 46 0.1131 460.041 453.303 1.031 0.953 0.009 3.266-2.585 99.86 5447 97 0.1111 310.332 306.967 1.016 0.952 0.000 2.585-2.046 97.45 10613 204 0.0939 234.128 231.691 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0911 138.569 137.250 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0978 74.597 73.881 1.050 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.018 38.343 1.039 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1281 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1358 | n_water=885 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1197 r_free=0.1358 | n_water=885 | time (s): 116.770 (total time: 119.500) Filter (q & B) r_work=0.1197 r_free=0.1356 | n_water=873 | time (s): 5.520 (total time: 125.020) Compute maps r_work=0.1197 r_free=0.1356 | n_water=873 | time (s): 2.450 (total time: 127.470) Filter (map) r_work=0.1218 r_free=0.1362 | n_water=754 | time (s): 5.280 (total time: 132.750) Find peaks r_work=0.1218 r_free=0.1362 | n_water=754 | time (s): 0.650 (total time: 133.400) Add new water r_work=0.1229 r_free=0.1372 | n_water=964 | time (s): 4.140 (total time: 137.540) Refine new water occ: r_work=0.1195 r_free=0.1344 adp: r_work=0.1195 r_free=0.1344 occ: r_work=0.1193 r_free=0.1344 adp: r_work=0.1193 r_free=0.1344 occ: r_work=0.1191 r_free=0.1344 adp: r_work=0.1191 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1344 r_work=0.1191 r_free=0.1344 | n_water=964 | time (s): 217.000 (total time: 354.540) Filter (q & B) r_work=0.1194 r_free=0.1350 | n_water=897 | time (s): 5.390 (total time: 359.930) Filter (dist only) r_work=0.1194 r_free=0.1350 | n_water=896 | time (s): 114.660 (total time: 474.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.530159 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.692152 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1354 0.0156 0.037 1.1 7.0 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.54 1.56 1.769 14.083 14.692 3.761 12.01 13.59 1.58 1.864 14.048 14.692 3.760 Individual atomic B min max mean iso aniso Overall: 5.55 66.53 14.91 0.92 532 3268 Protein: 5.55 30.63 10.53 0.92 0 2902 Water: 5.95 66.53 29.08 N/A 532 364 Other: 13.81 24.49 19.15 N/A 0 2 Chain A: 5.63 52.76 12.44 N/A 0 1623 Chain B: 5.55 66.53 12.25 N/A 0 1645 Chain S: 5.95 65.07 30.67 N/A 532 0 Histogram: Values Number of atoms 5.55 - 11.65 2124 11.65 - 17.75 759 17.75 - 23.84 295 23.84 - 29.94 216 29.94 - 36.04 173 36.04 - 42.14 126 42.14 - 48.24 70 48.24 - 54.34 29 54.34 - 60.44 5 60.44 - 66.53 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1359 r_work=0.1201 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1359 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1358 target_work(ml) = 3.759 | | 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.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758814 | | target function (ml) not normalized (work): 703988.225806 | | target function (ml) not normalized (free): 14738.972563 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1481 n_refl.: 191131 remove outliers: r(all,work,free)=0.1409 0.1408 0.1481 n_refl.: 191131 overall B=-0.23 to atoms: r(all,work,free)=0.1372 0.1370 0.1460 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3838 361.142 321.938 0.408 0.949 0.225 13.296-10.522 97.03 97 1 0.2449 478.065 460.444 0.723 0.950 0.186 10.503-8.327 97.80 175 3 0.2143 501.826 496.249 0.880 0.951 0.163 8.318-6.595 100.00 360 8 0.2124 375.484 371.576 0.906 0.950 0.090 6.588-5.215 100.00 711 7 0.1921 345.032 335.613 0.908 0.951 0.090 5.214-4.128 98.38 1367 28 0.1214 504.677 499.158 0.996 0.951 0.060 4.126-3.266 94.74 2603 46 0.1140 460.041 453.355 1.059 0.952 0.005 3.266-2.585 99.86 5447 97 0.1116 310.332 306.970 1.041 0.952 0.000 2.585-2.046 97.45 10613 204 0.0947 234.128 231.687 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0914 138.569 137.255 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0974 74.597 73.883 1.051 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.018 38.340 1.018 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0511 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1358 | n_water=896 | time (s): 3.180 (total time: 3.180) Filter (dist) r_work=0.1199 r_free=0.1359 | n_water=895 | time (s): 118.470 (total time: 121.650) Filter (q & B) r_work=0.1200 r_free=0.1358 | n_water=887 | time (s): 4.280 (total time: 125.930) Compute maps r_work=0.1200 r_free=0.1358 | n_water=887 | time (s): 1.950 (total time: 127.880) Filter (map) r_work=0.1220 r_free=0.1356 | n_water=779 | time (s): 4.370 (total time: 132.250) Find peaks r_work=0.1220 r_free=0.1356 | n_water=779 | time (s): 0.880 (total time: 133.130) Add new water r_work=0.1229 r_free=0.1366 | n_water=963 | time (s): 4.170 (total time: 137.300) Refine new water occ: r_work=0.1199 r_free=0.1341 adp: r_work=0.1199 r_free=0.1342 occ: r_work=0.1197 r_free=0.1341 adp: r_work=0.1197 r_free=0.1342 occ: r_work=0.1196 r_free=0.1342 adp: r_work=0.1195 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1343 r_work=0.1195 r_free=0.1343 | n_water=963 | time (s): 234.390 (total time: 371.690) Filter (q & B) r_work=0.1198 r_free=0.1352 | n_water=907 | time (s): 4.460 (total time: 376.150) Filter (dist only) r_work=0.1199 r_free=0.1351 | n_water=905 | time (s): 116.520 (total time: 492.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.553425 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.295172 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 0.1201 0.1353 0.0152 0.038 1.1 8.0 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.53 1.52 1.734 13.804 13.295 3.760 12.05 13.58 1.53 1.815 13.777 13.295 3.760 Individual atomic B min max mean iso aniso Overall: 5.40 65.46 14.67 0.88 541 3268 Protein: 5.40 28.78 10.26 0.88 0 2902 Water: 5.82 65.46 28.83 N/A 541 364 Other: 13.64 22.62 18.13 N/A 0 2 Chain A: 5.44 52.16 12.13 N/A 0 1623 Chain B: 5.40 65.46 11.96 N/A 0 1645 Chain S: 5.82 64.42 30.56 N/A 541 0 Histogram: Values Number of atoms 5.40 - 11.40 2117 11.40 - 17.41 776 17.41 - 23.42 282 23.42 - 29.42 208 29.42 - 35.43 183 35.43 - 41.43 129 41.43 - 47.44 76 47.44 - 53.45 30 53.45 - 59.45 5 59.45 - 65.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1358 r_work=0.1205 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1359 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1357 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759580 | | target function (ml) not normalized (work): 704131.739610 | | target function (ml) not normalized (free): 14733.946970 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1357 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1379 0.1378 0.1462 n_refl.: 191131 remove outliers: r(all,work,free)=0.1379 0.1378 0.1462 n_refl.: 191131 overall B=0.00 to atoms: r(all,work,free)=0.1379 0.1378 0.1462 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1345 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1345 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3707 360.839 312.098 0.394 0.992 0.225 13.296-10.522 97.03 97 1 0.2466 478.065 458.935 0.699 0.993 0.177 10.503-8.327 97.80 175 3 0.2141 501.826 496.507 0.853 0.994 0.151 8.318-6.595 100.00 360 8 0.2133 375.484 371.082 0.876 0.993 0.080 6.588-5.215 100.00 711 7 0.1941 345.032 335.302 0.879 0.993 0.080 5.214-4.128 98.38 1367 28 0.1221 504.677 498.578 0.968 0.993 0.070 4.126-3.266 94.74 2603 46 0.1154 460.041 452.559 1.029 0.993 0.009 3.266-2.585 99.86 5447 97 0.1119 310.332 306.669 1.014 0.992 0.000 2.585-2.046 97.45 10613 204 0.0958 234.128 231.546 1.023 0.991 0.000 2.046-1.619 99.39 21536 464 0.0915 138.569 137.158 1.041 0.989 0.000 1.619-1.281 98.00 42464 925 0.0956 74.597 73.932 1.034 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.018 38.322 1.007 0.981 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.1492 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1345 | n_water=905 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1193 r_free=0.1345 | n_water=905 | time (s): 116.780 (total time: 119.920) Filter (q & B) r_work=0.1193 r_free=0.1347 | n_water=898 | time (s): 5.050 (total time: 124.970) Compute maps r_work=0.1193 r_free=0.1347 | n_water=898 | time (s): 1.900 (total time: 126.870) Filter (map) r_work=0.1211 r_free=0.1346 | n_water=790 | time (s): 4.180 (total time: 131.050) Find peaks r_work=0.1211 r_free=0.1346 | n_water=790 | time (s): 0.540 (total time: 131.590) Add new water r_work=0.1219 r_free=0.1357 | n_water=980 | time (s): 4.340 (total time: 135.930) Refine new water occ: r_work=0.1190 r_free=0.1331 adp: r_work=0.1190 r_free=0.1331 occ: r_work=0.1188 r_free=0.1331 adp: r_work=0.1188 r_free=0.1332 occ: r_work=0.1187 r_free=0.1332 adp: r_work=0.1187 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1332 r_work=0.1187 r_free=0.1332 | n_water=980 | time (s): 235.530 (total time: 371.460) Filter (q & B) r_work=0.1190 r_free=0.1344 | n_water=912 | time (s): 5.400 (total time: 376.860) Filter (dist only) r_work=0.1191 r_free=0.1343 | n_water=910 | time (s): 116.430 (total time: 493.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.526975 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.980039 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1352 0.0159 0.038 1.1 6.3 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.52 1.59 1.678 13.729 13.980 3.758 11.93 13.54 1.61 1.704 13.718 13.980 3.754 Individual atomic B min max mean iso aniso Overall: 5.43 64.58 14.66 0.87 546 3268 Protein: 5.43 28.38 10.26 0.87 0 2902 Water: 5.83 64.58 28.69 N/A 546 364 Other: 13.69 21.99 17.84 N/A 0 2 Chain A: 5.49 51.87 12.10 N/A 0 1623 Chain B: 5.43 64.58 11.93 N/A 0 1645 Chain S: 5.83 63.98 30.49 N/A 546 0 Histogram: Values Number of atoms 5.43 - 11.34 2093 11.34 - 17.26 798 17.26 - 23.17 279 23.17 - 29.09 208 29.09 - 35.00 191 35.00 - 40.92 118 40.92 - 46.84 87 46.84 - 52.75 30 52.75 - 58.67 6 58.67 - 64.58 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1354 r_work=0.1193 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1354 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754028 | | target function (ml) not normalized (work): 703088.173579 | | target function (ml) not normalized (free): 14724.603123 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1377 0.1375 0.1471 n_refl.: 191130 remove outliers: r(all,work,free)=0.1377 0.1375 0.1471 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1377 0.1375 0.1471 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3666 360.839 331.313 0.413 0.973 0.221 13.296-10.522 97.03 97 1 0.2442 478.065 459.411 0.692 0.975 0.165 10.503-8.327 97.80 175 3 0.2166 501.826 496.129 0.848 0.975 0.136 8.318-6.595 100.00 360 8 0.2164 375.484 370.863 0.875 0.975 0.091 6.588-5.215 100.00 711 7 0.1948 345.032 335.186 0.874 0.976 0.070 5.214-4.128 98.38 1367 28 0.1231 504.677 498.610 0.964 0.977 0.070 4.126-3.266 94.74 2603 46 0.1156 460.041 452.581 1.024 0.978 0.009 3.266-2.585 99.86 5447 97 0.1127 310.332 306.586 1.007 0.979 0.000 2.585-2.046 97.45 10613 204 0.0958 234.128 231.502 1.013 0.980 0.000 2.046-1.619 99.39 21536 464 0.0909 138.569 137.201 1.028 0.983 0.000 1.619-1.281 98.00 42464 925 0.0949 74.597 73.933 1.015 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.018 38.315 0.979 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0838 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1192 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1355 | n_water=910 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1192 r_free=0.1356 | n_water=909 | time (s): 119.090 (total time: 121.740) Filter (q & B) r_work=0.1193 r_free=0.1353 | n_water=899 | time (s): 4.850 (total time: 126.590) Compute maps r_work=0.1193 r_free=0.1353 | n_water=899 | time (s): 1.790 (total time: 128.380) Filter (map) r_work=0.1213 r_free=0.1350 | n_water=790 | time (s): 5.290 (total time: 133.670) Find peaks r_work=0.1213 r_free=0.1350 | n_water=790 | time (s): 0.870 (total time: 134.540) Add new water r_work=0.1221 r_free=0.1361 | n_water=1000 | time (s): 4.430 (total time: 138.970) Refine new water occ: r_work=0.1188 r_free=0.1337 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1187 r_free=0.1337 adp: r_work=0.1187 r_free=0.1338 occ: r_work=0.1185 r_free=0.1338 adp: r_work=0.1185 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1338 r_work=0.1185 r_free=0.1338 | n_water=1000 | time (s): 232.380 (total time: 371.350) Filter (q & B) r_work=0.1189 r_free=0.1350 | n_water=920 | time (s): 4.670 (total time: 376.020) Filter (dist only) r_work=0.1190 r_free=0.1350 | n_water=919 | time (s): 115.670 (total time: 491.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.515648 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.361607 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1351 0.0157 0.038 1.1 7.5 0.0 0.3 0 0.758 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.51 1.57 1.673 13.728 14.362 3.756 11.93 13.54 1.61 1.690 13.726 14.362 3.753 Individual atomic B min max mean iso aniso Overall: 5.46 63.48 14.67 0.87 555 3268 Protein: 5.46 28.17 10.27 0.87 0 2902 Water: 5.87 63.48 28.59 N/A 555 364 Other: 13.75 22.09 17.92 N/A 0 2 Chain A: 5.51 51.46 12.07 N/A 0 1623 Chain B: 5.46 63.48 11.92 N/A 0 1645 Chain S: 5.87 63.43 30.45 N/A 555 0 Histogram: Values Number of atoms 5.46 - 11.26 2064 11.26 - 17.07 829 17.07 - 22.87 271 22.87 - 28.67 205 28.67 - 34.47 202 34.47 - 40.27 116 40.27 - 46.07 86 46.07 - 51.87 37 51.87 - 57.68 8 57.68 - 63.48 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1354 r_work=0.1193 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1354 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1353 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752425 | | target function (ml) not normalized (work): 702787.998659 | | target function (ml) not normalized (free): 14715.729749 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1383 0.1381 0.1472 n_refl.: 191130 remove outliers: r(all,work,free)=0.1383 0.1381 0.1472 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1383 0.1381 0.1472 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1350 n_refl.: 191130 remove outliers: r(all,work,free)=0.1193 0.1190 0.1350 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3649 360.839 331.017 0.402 0.973 0.211 13.296-10.522 97.03 97 1 0.2438 478.065 460.340 0.684 0.975 0.159 10.503-8.327 97.80 175 3 0.2165 501.826 496.290 0.840 0.976 0.133 8.315-6.595 100.00 359 8 0.2134 374.538 371.042 0.868 0.975 0.098 6.588-5.215 100.00 711 7 0.1951 345.032 335.145 0.869 0.976 0.080 5.214-4.128 98.38 1367 28 0.1230 504.677 498.787 0.956 0.977 0.049 4.126-3.266 94.74 2603 46 0.1164 460.041 452.525 1.018 0.978 0.009 3.266-2.585 99.86 5447 97 0.1123 310.332 306.660 1.001 0.979 0.000 2.585-2.046 97.45 10613 204 0.0961 234.128 231.509 1.007 0.981 0.000 2.046-1.619 99.39 21536 464 0.0907 138.569 137.201 1.022 0.985 0.000 1.619-1.281 98.00 42464 925 0.0945 74.597 73.940 1.010 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.018 38.309 0.976 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0495 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1350 After: r_work=0.1191 r_free=0.1350 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1350 | n_water=919 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1191 r_free=0.1350 | n_water=919 | time (s): 122.720 (total time: 125.290) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=909 | time (s): 5.250 (total time: 130.540) Compute maps r_work=0.1192 r_free=0.1349 | n_water=909 | time (s): 1.620 (total time: 132.160) Filter (map) r_work=0.1213 r_free=0.1354 | n_water=797 | time (s): 4.700 (total time: 136.860) Find peaks r_work=0.1213 r_free=0.1354 | n_water=797 | time (s): 0.580 (total time: 137.440) Add new water r_work=0.1221 r_free=0.1363 | n_water=991 | time (s): 4.280 (total time: 141.720) Refine new water occ: r_work=0.1189 r_free=0.1338 adp: r_work=0.1189 r_free=0.1339 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1340 occ: r_work=0.1186 r_free=0.1341 adp: r_work=0.1186 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1341 r_work=0.1186 r_free=0.1341 | n_water=991 | time (s): 190.050 (total time: 331.770) Filter (q & B) r_work=0.1190 r_free=0.1354 | n_water=920 | time (s): 5.730 (total time: 337.500) Filter (dist only) r_work=0.1191 r_free=0.1354 | n_water=919 | time (s): 123.430 (total time: 460.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.527981 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.333284 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1357 0.0163 0.039 1.2 7.3 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.57 1.63 1.670 13.685 14.333 3.755 11.95 13.61 1.66 1.671 13.688 14.333 3.754 Individual atomic B min max mean iso aniso Overall: 5.48 63.26 14.61 0.86 555 3268 Protein: 5.48 28.00 10.29 0.86 0 2902 Water: 5.94 63.26 28.24 N/A 555 364 Other: 13.74 22.01 17.87 N/A 0 2 Chain A: 5.57 51.23 12.06 N/A 0 1623 Chain B: 5.48 62.77 11.91 N/A 0 1645 Chain S: 5.94 63.26 30.01 N/A 555 0 Histogram: Values Number of atoms 5.48 - 11.26 2058 11.26 - 17.04 840 17.04 - 22.81 274 22.81 - 28.59 218 28.59 - 34.37 194 34.37 - 40.15 104 40.15 - 45.92 86 45.92 - 51.70 35 51.70 - 57.48 9 57.48 - 63.26 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1361 r_work=0.1195 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754226 | | target function (ml) not normalized (work): 703121.487841 | | target function (ml) not normalized (free): 14723.780588 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1361 0.1495 5.6901 5.7726| | 2: 2.94 - 2.33 1.00 7339 128 0.1078 0.1382 5.0838 5.1917| | 3: 2.33 - 2.04 0.96 6939 150 0.0903 0.1155 4.6539 4.7274| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1050 4.3916 4.5647| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.0982 4.1475 4.2374| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1079 3.9427 4.0606| | 7: 1.62 - 1.54 0.99 7104 148 0.0894 0.0949 3.798 3.9142| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1335 3.699 3.9113| | 9: 1.47 - 1.41 0.98 6938 155 0.0926 0.1139 3.6217 3.76| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1180 3.5563 3.6718| | 11: 1.36 - 1.32 0.99 6997 151 0.0994 0.1132 3.4847 3.5862| | 12: 1.32 - 1.28 0.98 6975 149 0.1034 0.1141 3.4601 3.5856| | 13: 1.28 - 1.25 0.98 6907 166 0.1045 0.1251 3.4391 3.5671| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1595 3.4327 3.6775| | 15: 1.22 - 1.19 0.98 6956 137 0.1174 0.1241 3.4494 3.4871| | 16: 1.19 - 1.17 0.93 6604 132 0.1253 0.1547 3.4656 3.6555| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1229 3.4341 3.4473| | 18: 1.14 - 1.12 0.98 6875 142 0.1388 0.1716 3.4397 3.5347| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1768 3.4198 3.5962| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1580 3.41 3.436| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2129 3.4176 3.5016| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1953 3.4127 3.4154| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2029 3.4329 3.4865| | 24: 1.03 - 1.02 0.96 6784 133 0.2335 0.2261 3.4361 3.511| | 25: 1.02 - 1.01 0.93 6552 130 0.2618 0.2507 3.4496 3.5217| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2864 3.4154 3.4235| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2798 3.4688 3.3947| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.87 1.00 0.97 11445.86| | 2: 2.94 - 2.33 7339 128 0.93 12.91 0.99 0.97 5201.97| | 3: 2.33 - 2.04 6939 150 0.96 7.59 1.01 0.98 1688.67| | 4: 2.04 - 1.85 7170 155 0.96 7.64 1.00 0.98 999.25| | 5: 1.85 - 1.72 7113 159 0.96 7.99 1.00 0.98 625.24| | 6: 1.72 - 1.62 7102 142 0.96 7.90 1.00 0.98 434.91| | 7: 1.62 - 1.54 7104 148 0.96 8.03 1.01 0.99 331.91| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 1.00 277.66| | 9: 1.47 - 1.41 6938 155 0.96 8.47 1.00 1.00 231.08| | 10: 1.41 - 1.36 7022 150 0.96 8.92 1.00 0.99 202.86| | 11: 1.36 - 1.32 6997 151 0.96 8.95 0.99 0.98 175.44| | 12: 1.32 - 1.28 6975 149 0.96 9.00 0.98 0.97 161.69| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.98 159.04| | 14: 1.25 - 1.22 7015 112 0.95 10.74 1.01 0.99 163.59| | 15: 1.22 - 1.19 6956 137 0.95 11.25 1.01 1.00 166.81| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.01 0.98 160.51| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.98 154.48| | 18: 1.14 - 1.12 6875 142 0.94 12.80 1.01 0.97 148.29| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.97 151.67| | 20: 1.10 - 1.08 6884 147 0.92 15.24 1.00 0.96 150.44| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.95 153.35| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.95 155.03| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.94 165.04| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.95 179.38| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.97 0.92 182.18| | 26: 1.01 - 0.99 6767 158 0.81 26.60 0.98 0.90 176.38| | 27: 0.99 - 0.98 6647 131 0.82 26.23 0.98 0.89 160.49| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 148.29 max = 11445.86 mean = 936.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.30| |phase err.(test): min = 0.00 max = 88.55 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1194 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1491 n_refl.: 191129 remove outliers: r(all,work,free)=0.1395 0.1393 0.1491 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1395 0.1393 0.1491 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1359 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1193 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3629 360.839 330.735 0.391 0.994 0.209 13.296-10.522 97.03 97 1 0.2452 478.065 460.263 0.662 0.996 0.147 10.503-8.327 97.80 175 3 0.2195 501.826 495.560 0.819 0.997 0.110 8.315-6.595 100.00 359 8 0.2145 374.538 370.369 0.844 0.997 0.090 6.588-5.215 100.00 711 7 0.1955 345.032 334.792 0.849 0.997 0.080 5.214-4.128 98.38 1367 28 0.1238 504.677 498.536 0.938 0.998 0.080 4.126-3.266 94.74 2603 46 0.1164 460.041 452.402 0.996 1.000 0.000 3.266-2.585 99.86 5447 97 0.1131 310.332 306.673 0.980 1.001 0.000 2.585-2.046 97.45 10613 204 0.0964 234.128 231.500 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0910 138.569 137.186 1.002 1.008 0.000 1.619-1.281 98.00 42464 925 0.0947 74.597 73.948 0.991 1.015 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.018 38.309 0.959 1.028 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0111 ================= 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 : 0.2036 0.1981 0.083 5.301 5.2 78.0 14.6 805 0.000 1_bss: 0.1798 0.1913 0.083 5.301 5.2 78.0 14.6 805 0.000 1_settarget: 0.1798 0.1913 0.083 5.301 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1914 0.083 5.301 5.2 78.0 14.6 805 0.002 1_weight: 0.1800 0.1914 0.083 5.301 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1269 0.1499 0.038 1.164 5.2 78.0 14.6 805 0.158 1_adp: 0.1297 0.1569 0.038 1.164 5.2 73.0 15.1 805 0.158 1_regHadp: 0.1296 0.1564 0.038 1.164 5.2 73.0 15.1 805 0.158 1_occ: 0.1282 0.1553 0.038 1.164 5.2 73.0 15.1 805 0.158 2_bss: 0.1276 0.1542 0.038 1.164 5.3 73.2 15.2 805 0.158 2_settarget: 0.1276 0.1542 0.038 1.164 5.3 73.2 15.2 805 0.158 2_updatecdl: 0.1276 0.1542 0.038 1.183 5.3 73.2 15.2 805 0.158 2_nqh: 0.1276 0.1542 0.038 1.183 5.3 73.2 15.2 805 0.158 2_sol: 0.1273 0.1511 0.038 1.183 5.3 73.2 16.3 884 n/a 2_weight: 0.1273 0.1511 0.038 1.183 5.3 73.2 16.3 884 n/a 2_xyzrec: 0.1257 0.1519 0.042 1.141 5.3 73.2 16.3 884 n/a 2_adp: 0.1231 0.1498 0.042 1.141 5.4 70.1 16.3 884 n/a 2_regHadp: 0.1232 0.1499 0.042 1.141 5.4 70.1 16.3 884 n/a 2_occ: 0.1226 0.1503 0.042 1.141 5.4 70.1 16.3 884 n/a 3_bss: 0.1233 0.1510 0.042 1.141 5.4 70.1 16.3 884 n/a 3_settarget: 0.1233 0.1510 0.042 1.141 5.4 70.1 16.3 884 n/a 3_updatecdl: 0.1233 0.1510 0.042 1.141 5.4 70.1 16.3 884 n/a 3_nqh: 0.1233 0.1510 0.042 1.141 5.4 70.1 16.3 884 n/a 3_sol: 0.1248 0.1501 0.042 1.141 5.4 68.2 15.4 881 n/a 3_weight: 0.1248 0.1501 0.042 1.141 5.4 68.2 15.4 881 n/a 3_xyzrec: 0.1237 0.1431 0.036 1.104 5.4 68.2 15.4 881 n/a 3_adp: 0.1231 0.1391 0.036 1.104 5.6 67.9 15.3 881 n/a 3_regHadp: 0.1232 0.1392 0.036 1.104 5.6 67.9 15.3 881 n/a 3_occ: 0.1226 0.1381 0.036 1.104 5.6 67.9 15.3 881 n/a 4_bss: 0.1221 0.1376 0.036 1.104 5.5 67.8 15.3 881 n/a 4_settarget: 0.1221 0.1376 0.036 1.104 5.5 67.8 15.3 881 n/a 4_updatecdl: 0.1221 0.1376 0.036 1.104 5.5 67.8 15.3 881 n/a 4_nqh: 0.1221 0.1376 0.036 1.104 5.5 67.8 15.3 881 n/a 4_sol: 0.1205 0.1359 0.036 1.104 5.5 67.8 15.1 879 n/a 4_weight: 0.1205 0.1359 0.036 1.104 5.5 67.8 15.1 879 n/a 4_xyzrec: 0.1203 0.1364 0.036 1.122 5.5 67.8 15.1 879 n/a 4_adp: 0.1196 0.1360 0.036 1.122 5.5 67.4 15.1 879 n/a 4_regHadp: 0.1197 0.1360 0.036 1.122 5.5 67.4 15.1 879 n/a 4_occ: 0.1194 0.1358 0.036 1.122 5.5 67.4 15.1 879 n/a 5_bss: 0.1192 0.1359 0.036 1.122 5.5 67.3 15.0 879 n/a 5_settarget: 0.1192 0.1359 0.036 1.122 5.5 67.3 15.0 879 n/a 5_updatecdl: 0.1192 0.1359 0.036 1.123 5.5 67.3 15.0 879 n/a 5_nqh: 0.1192 0.1359 0.036 1.123 5.5 67.3 15.0 879 n/a 5_sol: 0.1191 0.1350 0.036 1.123 5.5 67.3 15.0 885 n/a 5_weight: 0.1191 0.1350 0.036 1.123 5.5 67.3 15.0 885 n/a 5_xyzrec: 0.1195 0.1357 0.037 1.128 5.5 67.3 15.0 885 n/a 5_adp: 0.1200 0.1361 0.037 1.128 5.6 67.2 15.0 885 n/a 5_regHadp: 0.1200 0.1361 0.037 1.128 5.6 67.2 15.0 885 n/a 5_occ: 0.1198 0.1360 0.037 1.128 5.6 67.2 15.0 885 n/a 6_bss: 0.1197 0.1358 0.037 1.128 5.5 67.1 14.9 885 n/a 6_settarget: 0.1197 0.1358 0.037 1.128 5.5 67.1 14.9 885 n/a 6_updatecdl: 0.1197 0.1358 0.037 1.127 5.5 67.1 14.9 885 n/a 6_nqh: 0.1197 0.1358 0.037 1.127 5.5 67.1 14.9 885 n/a 6_sol: 0.1194 0.1350 0.037 1.127 5.5 67.1 15.0 896 n/a 6_weight: 0.1194 0.1350 0.037 1.127 5.5 67.1 15.0 896 n/a 6_xyzrec: 0.1198 0.1354 0.037 1.127 5.5 67.1 15.0 896 n/a 6_adp: 0.1201 0.1359 0.037 1.127 5.5 66.5 14.9 896 n/a 6_regHadp: 0.1201 0.1359 0.037 1.127 5.5 66.5 14.9 896 n/a 6_occ: 0.1199 0.1358 0.037 1.127 5.5 66.5 14.9 896 n/a 7_bss: 0.1199 0.1358 0.037 1.127 5.3 66.3 14.7 896 n/a 7_settarget: 0.1199 0.1358 0.037 1.127 5.3 66.3 14.7 896 n/a 7_updatecdl: 0.1199 0.1358 0.037 1.128 5.3 66.3 14.7 896 n/a 7_nqh: 0.1199 0.1358 0.037 1.128 5.3 66.3 14.7 896 n/a 7_sol: 0.1199 0.1351 0.037 1.128 5.3 66.3 14.7 905 n/a 7_weight: 0.1199 0.1351 0.037 1.128 5.3 66.3 14.7 905 n/a 7_xyzrec: 0.1201 0.1353 0.038 1.135 5.3 66.3 14.7 905 n/a 7_adp: 0.1205 0.1358 0.038 1.135 5.4 65.5 14.7 905 n/a 7_regHadp: 0.1205 0.1359 0.038 1.135 5.4 65.5 14.7 905 n/a 7_occ: 0.1204 0.1357 0.038 1.135 5.4 65.5 14.7 905 n/a 8_bss: 0.1193 0.1345 0.038 1.135 5.4 65.5 14.7 905 n/a 8_settarget: 0.1193 0.1345 0.038 1.135 5.4 65.5 14.7 905 n/a 8_updatecdl: 0.1193 0.1345 0.038 1.135 5.4 65.5 14.7 905 n/a 8_nqh: 0.1193 0.1345 0.038 1.135 5.4 65.5 14.7 905 n/a 8_sol: 0.1191 0.1343 0.038 1.135 5.4 65.5 14.7 910 n/a 8_weight: 0.1191 0.1343 0.038 1.135 5.4 65.5 14.7 910 n/a 8_xyzrec: 0.1194 0.1352 0.038 1.121 5.4 65.5 14.7 910 n/a 8_adp: 0.1193 0.1354 0.038 1.121 5.4 64.6 14.7 910 n/a 8_regHadp: 0.1193 0.1354 0.038 1.121 5.4 64.6 14.7 910 n/a 8_occ: 0.1192 0.1354 0.038 1.121 5.4 64.6 14.7 910 n/a 9_bss: 0.1192 0.1353 0.038 1.121 5.4 64.6 14.7 910 n/a 9_settarget: 0.1192 0.1353 0.038 1.121 5.4 64.6 14.7 910 n/a 9_updatecdl: 0.1192 0.1353 0.038 1.121 5.4 64.6 14.7 910 n/a 9_nqh: 0.1192 0.1355 0.038 1.121 5.4 64.6 14.7 910 n/a 9_sol: 0.1190 0.1350 0.038 1.121 5.4 64.6 14.7 919 n/a 9_weight: 0.1190 0.1350 0.038 1.121 5.4 64.6 14.7 919 n/a 9_xyzrec: 0.1194 0.1351 0.038 1.117 5.4 64.6 14.7 919 n/a 9_adp: 0.1193 0.1354 0.038 1.117 5.5 63.5 14.7 919 n/a 9_regHadp: 0.1193 0.1354 0.038 1.117 5.5 63.5 14.7 919 n/a 9_occ: 0.1192 0.1353 0.038 1.117 5.5 63.5 14.7 919 n/a 10_bss: 0.1190 0.1350 0.038 1.117 5.5 63.5 14.7 919 n/a 10_settarget: 0.1190 0.1350 0.038 1.117 5.5 63.5 14.7 919 n/a 10_updatecdl: 0.1190 0.1350 0.038 1.117 5.5 63.5 14.7 919 n/a 10_setrh: 0.1191 0.1350 0.038 1.117 5.5 63.5 14.7 919 n/a 10_nqh: 0.1191 0.1350 0.038 1.117 5.5 63.5 14.7 919 n/a 10_sol: 0.1191 0.1354 0.038 1.117 5.5 63.5 14.6 919 n/a 10_weight: 0.1191 0.1354 0.038 1.117 5.5 63.5 14.6 919 n/a 10_xyzrec: 0.1194 0.1357 0.039 1.165 5.5 63.5 14.6 919 n/a 10_adp: 0.1195 0.1361 0.039 1.165 5.5 63.3 14.6 919 n/a 10_regHadp: 0.1195 0.1361 0.039 1.165 5.5 63.3 14.6 919 n/a 10_occ: 0.1194 0.1361 0.039 1.165 5.5 63.3 14.6 919 n/a end: 0.1193 0.1359 0.039 1.165 5.5 63.3 14.6 919 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4574008_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4574008_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0200 Refinement macro-cycles (run) : 12007.9400 Write final files (write_after_run_outputs) : 166.9300 Total : 12181.8900 Total CPU time: 3.39 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:14 PST -0800 (1736736014.05 s) Start R-work = 0.1798, R-free = 0.1913 Final R-work = 0.1193, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 12474.68 seconds wall clock time: 208 minutes 55.00 seconds (12535.00 seconds total)