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_2021531.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2021531.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2021531.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.72, per 1000 atoms: 0.26 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.619 distance_ideal: 2.720 ideal - model: 0.101 slack: 0.000 delta_slack: 0.101 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: 2.713 distance_ideal: 2.710 ideal - model: -0.003 slack: 0.000 delta_slack: -0.003 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: 0.88 Conformation dependent library (CDL) restraints added in 167.5 milliseconds Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.04: 1047 1.04 - 1.27: 2347 1.27 - 1.50: 1537 1.50 - 1.73: 984 1.73 - 1.96: 19 Bond restraints: 5934 Sorted by residual: bond pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " ideal model delta sigma weight residual 1.326 1.070 0.256 1.10e-02 8.26e+03 5.43e+02 bond pdb=" NE ARG A 175 " pdb=" CZ ARG A 175 " ideal model delta sigma weight residual 1.326 1.552 -0.226 1.10e-02 8.26e+03 4.23e+02 bond pdb=" N LYS B 52 " pdb=" H LYS B 52 " ideal model delta sigma weight residual 0.860 1.265 -0.405 2.00e-02 2.50e+03 4.09e+02 bond pdb=" CA ALA B 104 " pdb=" C ALA B 104 " ideal model delta sigma weight residual 1.520 1.756 -0.236 1.20e-02 6.94e+03 3.87e+02 bond pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta sigma weight residual 1.460 1.628 -0.167 8.60e-03 1.35e+04 3.79e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 5371 3.93 - 7.86: 3505 7.86 - 11.79: 1524 11.79 - 15.73: 369 15.73 - 19.66: 41 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O VAL B 51 " pdb=" C VAL B 51 " pdb=" N LYS B 52 " ideal model delta sigma weight residual 122.79 106.36 16.43 9.70e-01 1.06e+00 2.87e+02 angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N ALA A 182 " ideal model delta sigma weight residual 121.87 136.26 -14.39 9.70e-01 1.06e+00 2.20e+02 angle pdb=" O MET A 124 " pdb=" C MET A 124 " pdb=" N THR A 125 " ideal model delta sigma weight residual 123.46 138.12 -14.66 9.90e-01 1.02e+00 2.19e+02 angle pdb=" CA TRP A 146 " pdb=" C TRP A 146 " pdb=" N ASP A 147 " ideal model delta sigma weight residual 116.36 135.02 -18.66 1.28e+00 6.10e-01 2.12e+02 angle pdb=" CA HIS B 96 " pdb=" CB HIS B 96 " pdb=" CG HIS B 96 " ideal model delta sigma weight residual 113.80 99.80 14.00 1.00e+00 1.00e+00 1.96e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 1862 17.79 - 35.57: 126 35.57 - 53.36: 43 53.36 - 71.15: 17 71.15 - 88.93: 2 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CB TRP A 139 " pdb=" CG TRP A 139 " pdb=" CD1 TRP A 139 " pdb=" HD1 TRP A 139 " ideal model delta harmonic sigma weight residual 0.00 -31.49 31.49 0 5.00e+00 4.00e-02 3.97e+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 -150.31 -29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.245: 223 0.245 - 0.489: 170 0.489 - 0.733: 79 0.733 - 0.977: 16 0.977 - 1.222: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE A 101 " pdb=" N ILE A 101 " pdb=" C ILE A 101 " pdb=" CB ILE A 101 " both_signs ideal model delta sigma weight residual False 2.43 3.65 -1.22 2.00e-01 2.50e+01 3.73e+01 chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.45 -1.14 2.00e-01 2.50e+01 3.22e+01 chirality pdb=" CA VAL B 7 " pdb=" N VAL B 7 " pdb=" C VAL B 7 " pdb=" CB VAL B 7 " both_signs ideal model delta sigma weight residual False 2.44 3.51 -1.06 2.00e-01 2.50e+01 2.83e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.144 2.00e-02 2.50e+03 7.36e-02 1.63e+02 pdb=" CG PHE B 164 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.098 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.064 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.069 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.095 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.063 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.024 2.00e-02 2.50e+03 6.36e-02 1.62e+02 pdb=" CG TRP B 139 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.052 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.096 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " -0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " -0.081 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " 0.004 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.119 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.024 2.00e-02 2.50e+03 6.21e-02 1.54e+02 pdb=" CG TRP A 139 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.142 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.054 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.082 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.074 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.042 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.063 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.035 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.003 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.097 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.65: 29 1.65 - 2.39: 2776 2.39 - 3.12: 22421 3.12 - 3.86: 32952 3.86 - 4.60: 52155 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110333 Sorted by model distance: nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.909 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.917 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.038 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.060 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.154 2.620 ... (remaining 110328 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_2021531_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= 0.2041 r_free= 0.1993 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 4.305255 | | target function (ml) not normalized (work): 806430.303588 | | target function (ml) not normalized (free): 16595.972266 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2147 0.1904 6.6889 6.3121| | 2: 2.94 - 2.33 1.00 7339 128 0.1621 0.1489 5.5369 5.5553| | 3: 2.33 - 2.04 0.96 6939 150 0.1637 0.1539 5.145 5.1059| | 4: 2.04 - 1.85 1.00 7170 155 0.1752 0.1595 4.9667 4.9911| | 5: 1.85 - 1.72 0.99 7113 159 0.1936 0.1699 4.8009 4.7659| | 6: 1.72 - 1.62 0.99 7102 142 0.1979 0.1971 4.6667 4.6909| | 7: 1.62 - 1.54 0.99 7104 148 0.2025 0.1900 4.5615 4.6294| | 8: 1.54 - 1.47 0.96 6798 152 0.2017 0.2345 4.4768 4.5816| | 9: 1.47 - 1.41 0.98 6938 155 0.2133 0.2216 4.4093 4.4512| | 10: 1.41 - 1.36 0.99 7022 150 0.2131 0.2131 4.3176 4.3291| | 11: 1.36 - 1.32 0.99 6997 151 0.2143 0.2269 4.2471 4.2877| | 12: 1.32 - 1.28 0.98 6976 149 0.2078 0.2016 4.1753 4.2596| | 13: 1.28 - 1.25 0.98 6907 166 0.2029 0.2067 4.1192 4.1466| | 14: 1.25 - 1.22 0.98 7015 113 0.2063 0.2462 4.079 4.2818| | 15: 1.22 - 1.19 0.98 6957 137 0.2088 0.2038 4.0548 4.0443| | 16: 1.19 - 1.17 0.93 6604 132 0.2106 0.2224 4.0145 4.0254| | 17: 1.17 - 1.14 0.98 6941 135 0.2180 0.2096 3.9625 4.0548| | 18: 1.14 - 1.12 0.98 6875 142 0.2202 0.2771 3.9223 4.0716| | 19: 1.12 - 1.10 0.97 6949 106 0.2284 0.2358 3.8854 3.9072| | 20: 1.10 - 1.08 0.97 6884 147 0.2318 0.2424 3.8228 3.875| | 21: 1.08 - 1.07 0.97 6852 152 0.2428 0.2665 3.7927 3.7939| | 22: 1.07 - 1.05 0.97 6838 135 0.2571 0.2411 3.7623 3.7149| | 23: 1.05 - 1.03 0.97 6829 159 0.2758 0.2814 3.7439 3.8789| | 24: 1.03 - 1.02 0.96 6785 133 0.2910 0.3029 3.709 3.7868| | 25: 1.02 - 1.01 0.93 6552 130 0.3122 0.2881 3.6865 3.7574| | 26: 1.01 - 0.99 0.96 6767 158 0.3268 0.3541 3.6437 3.7168| | 27: 0.99 - 0.98 0.94 6648 131 0.3432 0.3376 3.6388 3.6307| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.45 0.91 0.97 35487.38| | 2: 2.94 - 2.33 7339 128 0.86 21.00 1.08 1.02 14802.61| | 3: 2.33 - 2.04 6939 150 0.94 11.83 1.11 1.05 3787.65| | 4: 2.04 - 1.85 7170 155 0.93 12.64 1.11 1.08 2538.56| | 5: 1.85 - 1.72 7113 159 0.91 14.89 1.11 1.09 1911.59| | 6: 1.72 - 1.62 7102 142 0.91 16.09 1.11 1.08 1549.90| | 7: 1.62 - 1.54 7104 148 0.89 18.12 1.11 1.06 1381.64| | 8: 1.54 - 1.47 6798 152 0.88 19.32 1.10 1.06 1258.37| | 9: 1.47 - 1.41 6938 155 0.87 20.44 1.11 1.06 1111.65| | 10: 1.41 - 1.36 7022 150 0.86 20.81 1.09 1.06 916.72| | 11: 1.36 - 1.32 6997 151 0.86 20.76 1.08 1.04 774.88| | 12: 1.32 - 1.28 6976 149 0.87 20.21 1.08 1.03 667.60| | 13: 1.28 - 1.25 6907 166 0.87 20.35 1.07 1.02 624.95| | 14: 1.25 - 1.22 7015 113 0.86 21.00 1.07 1.04 585.76| | 15: 1.22 - 1.19 6957 137 0.86 21.06 1.07 1.05 559.02| | 16: 1.19 - 1.17 6604 132 0.87 21.01 1.07 1.04 520.57| | 17: 1.17 - 1.14 6941 135 0.85 22.37 1.08 1.03 493.65| | 18: 1.14 - 1.12 6875 142 0.84 23.12 1.09 1.00 464.35| | 19: 1.12 - 1.10 6949 106 0.84 23.84 1.07 0.98 428.25| | 20: 1.10 - 1.08 6884 147 0.84 23.79 1.06 0.97 374.62| | 21: 1.08 - 1.07 6852 152 0.83 24.25 1.06 0.96 341.49| | 22: 1.07 - 1.05 6838 135 0.82 25.82 1.05 0.95 328.81| | 23: 1.05 - 1.03 6829 159 0.78 28.88 1.05 0.95 349.34| | 24: 1.03 - 1.02 6785 133 0.75 31.63 1.04 0.95 365.83| | 25: 1.02 - 1.01 6552 130 0.73 33.62 1.03 0.91 360.84| | 26: 1.01 - 0.99 6767 158 0.72 35.15 1.03 0.88 331.15| | 27: 0.99 - 0.98 6648 131 0.72 34.65 1.04 0.85 290.96| |alpha: min = 0.85 max = 1.09 mean = 1.01| |beta: min = 290.96 max = 35487.38 mean = 2814.95| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.38| |phase err.(test): min = 0.00 max = 89.61 mean = 22.48| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.256 2950 Z= 5.643 Angle : 5.225 18.658 4018 Z= 3.728 Chirality : 0.377 1.222 492 Planarity : 0.033 0.142 512 Dihedral : 12.736 88.932 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 0.65 % Allowed : 5.81 % Favored : 93.55 % Cbeta Deviations : 26.97 % 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: -2.36 (0.38), residues: 386 helix: -2.78 (0.29), residues: 148 sheet: -0.52 (0.54), residues: 82 loop : -0.58 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.123 0.016 ARG B 100 TYR 0.112 0.036 TYR A 192 PHE 0.115 0.038 PHE A 95 TRP 0.114 0.042 TRP B 139 HIS 0.059 0.018 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2041 r_free= 0.1993 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 4.305255 | | target function (ml) not normalized (work): 806430.303588 | | target function (ml) not normalized (free): 16595.972266 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2039 0.2041 0.1993 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2039 0.2041 0.1993 n_refl.: 191155 remove outliers: r(all,work,free)=0.2039 0.2041 0.1993 n_refl.: 191145 overall B=-0.01 to atoms: r(all,work,free)=0.2037 0.2039 0.1992 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1812 0.1810 0.1921 n_refl.: 191145 remove outliers: r(all,work,free)=0.1810 0.1808 0.1921 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 0.4136 402.814 290.694 0.418 0.935 0.299 13.296-10.522 99.01 99 1 0.2518 528.187 517.441 0.760 0.936 0.250 10.503-8.327 98.90 177 3 0.2463 564.205 556.981 0.939 0.936 0.227 8.318-6.595 100.00 360 8 0.2472 414.736 402.975 0.939 0.936 0.170 6.588-5.215 100.00 711 7 0.2231 381.101 365.899 0.930 0.936 0.160 5.214-4.128 98.38 1367 28 0.1493 557.435 549.967 1.041 0.937 0.090 4.126-3.266 94.74 2603 46 0.1356 508.132 498.473 1.108 0.937 0.040 3.266-2.585 99.86 5447 97 0.1464 342.774 337.624 1.079 0.936 0.000 2.585-2.046 97.45 10613 204 0.1404 258.603 254.314 1.087 0.936 0.000 2.046-1.619 99.39 21536 464 0.1627 153.054 149.876 1.104 0.936 0.000 1.619-1.281 98.00 42464 925 0.1932 82.395 80.361 1.091 0.935 0.000 1.281-0.980 96.53 101826 2056 0.2326 44.203 41.910 1.075 0.933 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0306 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1808 r_free=0.1920 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1808 r_free=0.1920 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.138958 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 574.288215 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 0.1500 0.0231 0.039 1.2 10.9 0.0 0.0 0 11.069 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.69 15.00 2.31 1.117 13.099 574.288 0.018 12.98 15.75 2.77 1.234 13.323 574.288 0.017 Individual atomic B min max mean iso aniso Overall: 5.21 73.03 14.99 1.39 435 3274 Protein: 5.21 40.45 11.01 1.39 0 2902 Water: 6.41 73.03 29.32 N/A 435 370 Other: 16.10 30.30 23.20 N/A 0 2 Chain A: 5.34 60.03 13.05 N/A 0 1626 Chain B: 5.21 73.03 12.77 N/A 0 1648 Chain S: 11.80 63.19 30.69 N/A 435 0 Histogram: Values Number of atoms 5.21 - 12.00 2168 12.00 - 18.78 642 18.78 - 25.56 309 25.56 - 32.34 271 32.34 - 39.12 155 39.12 - 45.90 101 45.90 - 52.69 39 52.69 - 59.47 19 59.47 - 66.25 4 66.25 - 73.03 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1575 r_work=0.1297 r_free=0.1570 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1570 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1560 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1560 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015538 | | target function (ls_wunit_k1) not normalized (work): 2910.149175 | | target function (ls_wunit_k1) not normalized (free): 117.241203 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1560 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1469 0.1466 0.1640 n_refl.: 191138 remove outliers: r(all,work,free)=0.1469 0.1466 0.1640 n_refl.: 191138 overall B=0.15 to atoms: r(all,work,free)=0.1490 0.1488 0.1648 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1549 n_refl.: 191138 remove outliers: r(all,work,free)=0.1280 0.1275 0.1549 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3611 402.814 381.118 0.488 0.963 0.275 13.296-10.522 99.01 99 1 0.2078 528.187 523.105 0.739 0.964 0.239 10.503-8.327 98.90 177 3 0.1725 564.205 565.240 0.888 0.964 0.230 8.318-6.595 100.00 360 8 0.1717 414.736 412.003 0.908 0.964 0.155 6.588-5.215 100.00 711 7 0.1533 381.101 373.481 0.888 0.964 0.150 5.214-4.128 98.38 1367 28 0.0904 557.435 554.705 0.976 0.965 0.055 4.126-3.266 94.74 2603 46 0.0829 508.132 504.250 1.044 0.966 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.297 1.024 0.965 0.000 2.585-2.046 97.45 10613 204 0.0950 258.603 256.359 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.411 1.054 0.966 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.424 1.045 0.967 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.151 1.021 0.968 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0338 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1549 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1549 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1549 | n_water=805 | time (s): 3.320 (total time: 3.320) Filter (dist) r_work=0.1279 r_free=0.1554 | n_water=795 | time (s): 98.960 (total time: 102.280) Filter (q & B) r_work=0.1279 r_free=0.1554 | n_water=792 | time (s): 5.850 (total time: 108.130) Compute maps r_work=0.1279 r_free=0.1554 | n_water=792 | time (s): 2.370 (total time: 110.500) Filter (map) r_work=0.1305 r_free=0.1539 | n_water=658 | time (s): 4.330 (total time: 114.830) Find peaks r_work=0.1305 r_free=0.1539 | n_water=658 | time (s): 0.650 (total time: 115.480) Add new water r_work=0.1329 r_free=0.1566 | n_water=967 | time (s): 4.350 (total time: 119.830) Refine new water occ: r_work=0.1285 r_free=0.1516 adp: r_work=0.1272 r_free=0.1512 occ: r_work=0.1275 r_free=0.1509 adp: r_work=0.1268 r_free=0.1510 occ: r_work=0.1269 r_free=0.1507 adp: r_work=0.1268 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1507 r_work=0.1268 r_free=0.1507 | n_water=967 | time (s): 82.740 (total time: 202.570) Filter (q & B) r_work=0.1271 r_free=0.1510 | n_water=897 | time (s): 4.740 (total time: 207.310) Filter (dist only) r_work=0.1271 r_free=0.1509 | n_water=896 | time (s): 117.470 (total time: 324.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.228449 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 590.442650 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1253 0.1526 0.0272 0.041 1.1 17.7 0.0 0.3 0 11.614 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.26 2.72 2.040 15.106 590.443 0.014 12.29 15.04 2.76 2.406 15.234 590.443 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 76.76 16.33 1.22 528 3272 Protein: 5.38 40.51 10.97 1.22 0 2902 Water: 6.55 76.76 33.65 N/A 528 368 Other: 16.33 32.43 24.38 N/A 0 2 Chain A: 5.49 56.26 13.02 N/A 0 1624 Chain B: 5.38 68.18 12.85 N/A 0 1648 Chain S: 10.57 76.76 37.38 N/A 528 0 Histogram: Values Number of atoms 5.38 - 12.52 2229 12.52 - 19.65 625 19.65 - 26.79 277 26.79 - 33.93 227 33.93 - 41.07 186 41.07 - 48.21 145 48.21 - 55.34 65 55.34 - 62.48 31 62.48 - 69.62 11 69.62 - 76.76 4 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1505 r_work=0.1229 r_free=0.1506 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1506 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 = 0.1224 r_free = 0.1505 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013355 | | target function (ls_wunit_k1) not normalized (work): 2501.370735 | | target function (ls_wunit_k1) not normalized (free): 101.595836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1224 0.1505 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1432 0.1429 0.1594 n_refl.: 191137 remove outliers: r(all,work,free)=0.1432 0.1429 0.1594 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1429 0.1426 0.1593 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1512 n_refl.: 191137 remove outliers: r(all,work,free)=0.1237 0.1231 0.1512 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3189 402.814 393.020 0.507 0.961 0.271 13.296-10.522 99.01 99 1 0.1902 528.187 527.501 0.765 0.962 0.229 10.503-8.327 98.90 177 3 0.1438 564.205 567.172 0.919 0.962 0.210 8.318-6.595 100.00 360 8 0.1555 414.736 414.316 0.939 0.961 0.150 6.588-5.215 100.00 711 7 0.1337 381.101 376.512 0.915 0.962 0.150 5.214-4.128 98.38 1367 28 0.0817 557.435 555.849 0.995 0.962 0.070 4.126-3.266 94.74 2603 46 0.0754 508.132 505.543 1.061 0.962 0.009 3.266-2.585 99.86 5447 97 0.0857 342.774 341.208 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.774 1.059 0.962 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.611 1.079 0.961 0.000 1.619-1.281 98.00 42464 925 0.1252 82.395 81.434 1.071 0.960 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.190 1.052 0.958 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0600 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1513 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1513 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1513 | n_water=896 | time (s): 3.350 (total time: 3.350) Filter (dist) r_work=0.1234 r_free=0.1516 | n_water=889 | time (s): 115.490 (total time: 118.840) Filter (q & B) r_work=0.1234 r_free=0.1517 | n_water=887 | time (s): 6.080 (total time: 124.920) Compute maps r_work=0.1234 r_free=0.1517 | n_water=887 | time (s): 2.090 (total time: 127.010) Filter (map) r_work=0.1276 r_free=0.1512 | n_water=686 | time (s): 4.440 (total time: 131.450) Find peaks r_work=0.1276 r_free=0.1512 | n_water=686 | time (s): 0.620 (total time: 132.070) Add new water r_work=0.1298 r_free=0.1534 | n_water=998 | time (s): 4.990 (total time: 137.060) Refine new water occ: r_work=0.1253 r_free=0.1502 adp: r_work=0.1253 r_free=0.1504 occ: r_work=0.1249 r_free=0.1502 adp: r_work=0.1248 r_free=0.1503 occ: r_work=0.1246 r_free=0.1501 adp: r_work=0.1245 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1503 r_work=0.1245 r_free=0.1503 | n_water=998 | time (s): 309.630 (total time: 446.690) Filter (q & B) r_work=0.1250 r_free=0.1504 | n_water=874 | time (s): 4.700 (total time: 451.390) Filter (dist only) r_work=0.1250 r_free=0.1504 | n_water=873 | time (s): 109.510 (total time: 560.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.730427 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.304289 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 0.1434 0.0197 0.036 1.1 6.8 0.0 0.0 0 0.865 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.34 1.97 1.936 14.581 16.304 3.936 12.33 13.98 1.65 2.228 14.492 16.304 3.896 Individual atomic B min max mean iso aniso Overall: 5.55 67.81 15.27 1.06 507 3270 Protein: 5.55 36.84 10.74 1.06 0 2902 Water: 6.70 67.81 30.29 N/A 507 366 Other: 14.09 28.61 21.35 N/A 0 2 Chain A: 5.55 55.39 12.79 N/A 0 1624 Chain B: 5.55 67.81 12.55 N/A 0 1646 Chain S: 13.10 64.76 32.02 N/A 507 0 Histogram: Values Number of atoms 5.55 - 11.78 2138 11.78 - 18.00 683 18.00 - 24.23 291 24.23 - 30.46 241 30.46 - 36.68 175 36.68 - 42.91 132 42.91 - 49.13 77 49.13 - 55.36 29 55.36 - 61.59 8 61.59 - 67.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1398 r_work=0.1234 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1399 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1390 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889718 | | target function (ml) not normalized (work): 728528.529777 | | target function (ml) not normalized (free): 15210.649659 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1389 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1442 0.1442 0.1480 n_refl.: 191137 remove outliers: r(all,work,free)=0.1442 0.1442 0.1480 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1435 0.1476 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1384 n_refl.: 191137 remove outliers: r(all,work,free)=0.1226 0.1222 0.1384 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 0.3601 398.008 366.745 0.432 0.946 0.250 13.296-10.522 99.01 99 1 0.2533 528.187 506.167 0.708 0.947 0.215 10.503-8.327 97.80 175 3 0.1877 554.286 558.533 0.882 0.947 0.184 8.318-6.595 100.00 360 8 0.2078 414.736 410.522 0.900 0.947 0.136 6.588-5.215 100.00 711 7 0.1843 381.101 370.768 0.888 0.947 0.113 5.214-4.128 98.38 1367 28 0.1159 557.435 552.216 0.972 0.947 0.070 4.126-3.266 94.74 2603 46 0.1090 508.132 501.340 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1086 342.774 339.049 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0963 258.603 255.805 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.386 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1049 82.395 81.488 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.317 1.037 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1061 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1384 | n_water=873 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1223 r_free=0.1384 | n_water=873 | time (s): 103.720 (total time: 106.610) Filter (q & B) r_work=0.1223 r_free=0.1384 | n_water=865 | time (s): 4.420 (total time: 111.030) Compute maps r_work=0.1223 r_free=0.1384 | n_water=865 | time (s): 1.990 (total time: 113.020) Filter (map) r_work=0.1249 r_free=0.1382 | n_water=718 | time (s): 5.330 (total time: 118.350) Find peaks r_work=0.1249 r_free=0.1382 | n_water=718 | time (s): 0.560 (total time: 118.910) Add new water r_work=0.1263 r_free=0.1393 | n_water=966 | time (s): 4.300 (total time: 123.210) Refine new water occ: r_work=0.1214 r_free=0.1362 adp: r_work=0.1207 r_free=0.1357 occ: r_work=0.1204 r_free=0.1359 adp: r_work=0.1204 r_free=0.1357 occ: r_work=0.1202 r_free=0.1361 adp: r_work=0.1201 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1359 r_work=0.1201 r_free=0.1359 | n_water=966 | time (s): 282.820 (total time: 406.030) Filter (q & B) r_work=0.1206 r_free=0.1365 | n_water=883 | time (s): 4.920 (total time: 410.950) Filter (dist only) r_work=0.1206 r_free=0.1364 | n_water=881 | time (s): 110.050 (total time: 521.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.611869 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.829385 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 0.1204 0.1363 0.0160 0.036 1.1 7.3 0.0 0.3 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.63 1.60 1.831 14.261 15.829 3.872 11.96 13.57 1.61 1.941 14.217 15.829 3.864 Individual atomic B min max mean iso aniso Overall: 5.52 67.36 15.06 1.00 515 3270 Protein: 5.52 33.57 10.66 1.00 0 2902 Water: 5.95 67.36 29.55 N/A 515 366 Other: 14.00 27.56 20.78 N/A 0 2 Chain A: 5.56 54.22 12.65 N/A 0 1624 Chain B: 5.52 67.36 12.45 N/A 0 1646 Chain S: 5.95 64.56 31.01 N/A 515 0 Histogram: Values Number of atoms 5.52 - 11.70 2120 11.70 - 17.89 723 17.89 - 24.07 289 24.07 - 30.26 251 30.26 - 36.44 171 36.44 - 42.62 134 42.62 - 48.81 66 48.81 - 54.99 24 54.99 - 61.18 5 61.18 - 67.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1357 r_work=0.1196 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1357 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1356 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861579 | | target function (ml) not normalized (work): 723246.739195 | | target function (ml) not normalized (free): 15127.204417 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1420 0.1420 0.1460 n_refl.: 191134 remove outliers: r(all,work,free)=0.1420 0.1420 0.1460 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1413 0.1412 0.1456 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1354 n_refl.: 191134 remove outliers: r(all,work,free)=0.1196 0.1192 0.1354 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 0.3692 361.234 322.732 0.404 0.946 0.224 13.296-10.522 97.03 97 1 0.2466 481.238 451.339 0.696 0.947 0.190 10.503-8.327 97.80 175 3 0.1995 501.953 499.223 0.868 0.948 0.190 8.318-6.595 100.00 360 8 0.2130 375.579 370.941 0.891 0.947 0.110 6.588-5.215 100.00 711 7 0.1888 345.120 335.508 0.888 0.947 0.110 5.214-4.128 98.38 1367 28 0.1166 504.805 500.149 0.974 0.948 0.060 4.126-3.266 94.74 2603 46 0.1103 460.157 454.083 1.035 0.948 0.005 3.266-2.585 99.86 5447 97 0.1091 310.411 307.243 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0936 234.187 231.802 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0911 138.604 137.332 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0986 74.616 73.916 1.052 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.028 38.373 1.036 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1233 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1354 | n_water=881 | time (s): 3.460 (total time: 3.460) Filter (dist) r_work=0.1192 r_free=0.1354 | n_water=880 | time (s): 112.800 (total time: 116.260) Filter (q & B) r_work=0.1193 r_free=0.1356 | n_water=871 | time (s): 5.600 (total time: 121.860) Compute maps r_work=0.1193 r_free=0.1356 | n_water=871 | time (s): 2.040 (total time: 123.900) Filter (map) r_work=0.1215 r_free=0.1367 | n_water=745 | time (s): 5.730 (total time: 129.630) Find peaks r_work=0.1215 r_free=0.1367 | n_water=745 | time (s): 0.700 (total time: 130.330) Add new water r_work=0.1228 r_free=0.1384 | n_water=967 | time (s): 5.160 (total time: 135.490) Refine new water occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1344 occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1343 occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1186 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1342 r_work=0.1186 r_free=0.1342 | n_water=967 | time (s): 275.710 (total time: 411.200) Filter (q & B) r_work=0.1191 r_free=0.1349 | n_water=896 | time (s): 5.290 (total time: 416.490) Filter (dist only) r_work=0.1191 r_free=0.1348 | n_water=895 | time (s): 113.860 (total time: 530.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.496808 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.971468 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 0.0162 0.037 1.1 6.0 0.0 0.3 0 0.748 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.57 1.62 1.791 14.176 14.971 3.763 11.99 13.60 1.61 1.842 14.155 14.971 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 67.08 15.04 0.96 530 3269 Protein: 5.57 32.29 10.60 0.96 0 2902 Water: 6.03 67.08 29.44 N/A 530 365 Other: 13.81 26.67 20.24 N/A 0 2 Chain A: 5.57 54.06 12.55 N/A 0 1623 Chain B: 5.58 67.08 12.37 N/A 0 1646 Chain S: 6.03 64.45 30.97 N/A 530 0 Histogram: Values Number of atoms 5.57 - 11.72 2139 11.72 - 17.87 719 17.87 - 24.02 299 24.02 - 30.17 228 30.17 - 36.32 179 36.32 - 42.48 133 42.48 - 48.63 69 48.63 - 54.78 26 54.78 - 60.93 5 60.93 - 67.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1360 r_work=0.1199 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1360 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1360 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760816 | | target function (ml) not normalized (work): 704363.292377 | | target function (ml) not normalized (free): 14744.804121 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1360 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1473 n_refl.: 191131 remove outliers: r(all,work,free)=0.1401 0.1399 0.1473 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1394 0.1392 0.1469 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 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 0.3848 361.234 323.065 0.395 0.952 0.213 13.296-10.522 97.03 97 1 0.2468 481.238 460.113 0.693 0.953 0.170 10.503-8.327 97.80 175 3 0.2044 501.953 498.218 0.861 0.954 0.150 8.318-6.595 100.00 360 8 0.2161 375.579 370.494 0.884 0.953 0.110 6.588-5.215 100.00 711 7 0.1887 345.120 335.690 0.884 0.953 0.110 5.214-4.128 98.38 1367 28 0.1168 504.805 499.852 0.968 0.954 0.035 4.126-3.266 94.74 2603 46 0.1124 460.157 453.783 1.030 0.954 0.009 3.266-2.585 99.86 5447 97 0.1098 310.411 307.111 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0948 234.187 231.712 1.027 0.953 0.000 2.046-1.619 99.39 21536 464 0.0918 138.604 137.297 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0980 74.616 73.901 1.048 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1655 40.028 38.358 1.036 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1280 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1359 | n_water=895 | time (s): 3.500 (total time: 3.500) Filter (dist) r_work=0.1196 r_free=0.1359 | n_water=895 | time (s): 109.250 (total time: 112.750) Filter (q & B) r_work=0.1196 r_free=0.1359 | n_water=883 | time (s): 5.000 (total time: 117.750) Compute maps r_work=0.1196 r_free=0.1359 | n_water=883 | time (s): 2.450 (total time: 120.200) Filter (map) r_work=0.1217 r_free=0.1375 | n_water=762 | time (s): 5.450 (total time: 125.650) Find peaks r_work=0.1217 r_free=0.1375 | n_water=762 | time (s): 0.580 (total time: 126.230) Add new water r_work=0.1228 r_free=0.1384 | n_water=992 | time (s): 4.270 (total time: 130.500) Refine new water occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1190 r_free=0.1348 adp: r_work=0.1190 r_free=0.1348 occ: r_work=0.1188 r_free=0.1349 adp: r_work=0.1188 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1349 r_work=0.1188 r_free=0.1349 | n_water=992 | time (s): 310.240 (total time: 440.740) Filter (q & B) r_work=0.1193 r_free=0.1358 | n_water=907 | time (s): 4.960 (total time: 445.700) Filter (dist only) r_work=0.1193 r_free=0.1357 | n_water=906 | time (s): 117.010 (total time: 562.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.555082 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.294844 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1359 0.0162 0.037 1.1 6.8 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.59 1.62 1.763 14.108 15.295 3.761 11.96 13.59 1.63 1.850 14.082 15.295 3.757 Individual atomic B min max mean iso aniso Overall: 5.56 66.35 14.98 0.93 541 3269 Protein: 5.56 30.38 10.52 0.93 0 2902 Water: 5.98 66.35 29.27 N/A 541 365 Other: 13.83 24.65 19.24 N/A 0 2 Chain A: 5.63 53.74 12.43 N/A 0 1623 Chain B: 5.56 66.35 12.27 N/A 0 1646 Chain S: 5.98 64.20 30.89 N/A 541 0 Histogram: Values Number of atoms 5.56 - 11.64 2124 11.64 - 17.72 755 17.72 - 23.79 291 23.79 - 29.87 223 29.87 - 35.95 167 35.95 - 42.03 143 42.03 - 48.11 72 48.11 - 54.19 29 54.19 - 60.27 4 60.27 - 66.35 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1359 r_work=0.1196 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1359 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756639 | | target function (ml) not normalized (work): 703580.837545 | | target function (ml) not normalized (free): 14729.000224 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1484 n_refl.: 191131 remove outliers: r(all,work,free)=0.1400 0.1398 0.1484 n_refl.: 191131 overall B=-0.23 to atoms: r(all,work,free)=0.1365 0.1363 0.1464 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1194 0.1360 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 0.3815 361.234 323.321 0.402 0.949 0.211 13.296-10.522 97.03 97 1 0.2407 481.238 461.616 0.711 0.951 0.163 10.503-8.327 97.80 175 3 0.2076 501.953 497.453 0.885 0.952 0.140 8.318-6.595 100.00 360 8 0.2161 375.579 370.347 0.903 0.951 0.090 6.588-5.215 100.00 711 7 0.1896 345.120 336.224 0.908 0.952 0.090 5.214-4.128 98.38 1367 28 0.1178 504.805 500.043 0.996 0.952 0.035 4.126-3.266 94.74 2603 46 0.1129 460.157 453.532 1.057 0.953 0.009 3.266-2.585 99.86 5447 97 0.1099 310.411 307.162 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0951 234.187 231.674 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0913 138.604 137.317 1.064 0.954 0.000 1.619-1.281 98.00 42464 925 0.0971 74.616 73.911 1.049 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.028 38.355 1.016 0.956 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0497 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1361 | n_water=906 | time (s): 3.450 (total time: 3.450) Filter (dist) r_work=0.1194 r_free=0.1361 | n_water=906 | time (s): 108.540 (total time: 111.990) Filter (q & B) r_work=0.1195 r_free=0.1361 | n_water=896 | time (s): 5.120 (total time: 117.110) Compute maps r_work=0.1195 r_free=0.1361 | n_water=896 | time (s): 2.450 (total time: 119.560) Filter (map) r_work=0.1215 r_free=0.1363 | n_water=790 | time (s): 4.550 (total time: 124.110) Find peaks r_work=0.1215 r_free=0.1363 | n_water=790 | time (s): 0.660 (total time: 124.770) Add new water r_work=0.1223 r_free=0.1367 | n_water=1003 | time (s): 5.150 (total time: 129.920) Refine new water occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1341 occ: r_work=0.1189 r_free=0.1340 adp: r_work=0.1189 r_free=0.1341 occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1187 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1340 r_work=0.1187 r_free=0.1340 | n_water=1003 | time (s): 287.450 (total time: 417.370) Filter (q & B) r_work=0.1192 r_free=0.1348 | n_water=922 | time (s): 5.500 (total time: 422.870) Filter (dist only) r_work=0.1192 r_free=0.1347 | n_water=921 | time (s): 117.830 (total time: 540.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.569840 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.821129 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 0.1354 0.0158 0.037 1.1 5.8 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.54 1.58 1.735 13.851 14.821 3.758 11.97 13.56 1.59 1.796 13.829 14.821 3.756 Individual atomic B min max mean iso aniso Overall: 5.38 65.22 14.76 0.90 556 3269 Protein: 5.38 29.07 10.27 0.90 0 2902 Water: 5.81 65.22 28.93 N/A 556 365 Other: 13.66 22.74 18.20 N/A 0 2 Chain A: 5.44 53.22 12.15 N/A 0 1623 Chain B: 5.38 65.22 12.00 N/A 0 1646 Chain S: 5.81 63.71 30.60 N/A 556 0 Histogram: Values Number of atoms 5.38 - 11.36 2107 11.36 - 17.35 782 17.35 - 23.33 278 23.33 - 29.32 217 29.32 - 35.30 179 35.30 - 41.28 149 41.28 - 47.27 75 47.27 - 53.25 30 53.25 - 59.24 6 59.24 - 65.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1356 r_work=0.1197 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1355 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755748 | | target function (ml) not normalized (work): 703413.960962 | | target function (ml) not normalized (free): 14730.654055 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1355 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1370 0.1368 0.1467 n_refl.: 191131 remove outliers: r(all,work,free)=0.1370 0.1368 0.1467 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1378 0.1376 0.1471 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1186 0.1341 n_refl.: 191131 remove outliers: r(all,work,free)=0.1188 0.1185 0.1341 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 91.09 89 3 0.3732 356.381 317.543 0.344 0.980 0.129 13.296-10.522 97.03 97 1 0.2449 481.238 460.641 0.682 0.982 0.125 10.503-8.327 97.80 175 3 0.2071 501.953 496.888 0.864 0.982 0.123 8.318-6.595 100.00 360 8 0.2142 375.579 370.064 0.882 0.982 0.091 6.588-5.215 100.00 711 7 0.1914 345.120 335.400 0.885 0.983 0.070 5.214-4.128 98.38 1367 28 0.1191 504.805 499.391 0.974 0.983 0.035 4.126-3.266 94.74 2603 46 0.1139 460.157 453.136 1.035 0.985 0.009 3.266-2.585 99.86 5447 97 0.1106 310.411 306.879 1.018 0.985 0.000 2.585-2.046 97.45 10613 204 0.0955 234.187 231.549 1.026 0.987 0.000 2.046-1.619 99.39 21536 464 0.0907 138.604 137.241 1.042 0.990 0.000 1.619-1.281 98.00 42464 925 0.0950 74.616 73.960 1.030 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.028 38.336 0.995 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0605 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1341 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1341 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1341 | n_water=921 | time (s): 3.660 (total time: 3.660) Filter (dist) r_work=0.1185 r_free=0.1341 | n_water=921 | time (s): 112.570 (total time: 116.230) Filter (q & B) r_work=0.1186 r_free=0.1342 | n_water=910 | time (s): 4.200 (total time: 120.430) Compute maps r_work=0.1186 r_free=0.1342 | n_water=910 | time (s): 1.940 (total time: 122.370) Filter (map) r_work=0.1208 r_free=0.1348 | n_water=792 | time (s): 4.750 (total time: 127.120) Find peaks r_work=0.1208 r_free=0.1348 | n_water=792 | time (s): 0.760 (total time: 127.880) Add new water r_work=0.1215 r_free=0.1353 | n_water=992 | time (s): 5.220 (total time: 133.100) Refine new water occ: r_work=0.1184 r_free=0.1326 adp: r_work=0.1184 r_free=0.1326 occ: r_work=0.1182 r_free=0.1327 adp: r_work=0.1182 r_free=0.1327 occ: r_work=0.1180 r_free=0.1329 adp: r_work=0.1180 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1328 r_work=0.1180 r_free=0.1328 | n_water=992 | time (s): 339.460 (total time: 472.560) Filter (q & B) r_work=0.1184 r_free=0.1336 | n_water=921 | time (s): 4.400 (total time: 476.960) Filter (dist only) r_work=0.1184 r_free=0.1335 | n_water=920 | time (s): 121.560 (total time: 598.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.556508 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.991871 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 0.1188 0.1341 0.0153 0.038 1.1 6.1 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.41 1.53 1.687 13.846 14.992 3.754 11.87 13.40 1.53 1.718 13.836 14.992 3.751 Individual atomic B min max mean iso aniso Overall: 5.48 64.24 14.80 0.89 555 3269 Protein: 5.48 28.62 10.33 0.89 0 2902 Water: 5.99 64.24 28.91 N/A 555 365 Other: 13.79 22.08 17.93 N/A 0 2 Chain A: 5.54 52.90 12.17 N/A 0 1623 Chain B: 5.48 64.24 12.03 N/A 0 1646 Chain S: 5.99 63.48 30.72 N/A 555 0 Histogram: Values Number of atoms 5.48 - 11.36 2080 11.36 - 17.23 804 17.23 - 23.11 273 23.11 - 28.99 216 28.99 - 34.86 183 34.86 - 40.74 147 40.74 - 46.61 79 46.61 - 52.49 33 52.49 - 58.37 4 58.37 - 64.24 5 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1340 r_work=0.1188 r_free=0.1341 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1341 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1343 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1186 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751221 | | target function (ml) not normalized (work): 702558.607384 | | target function (ml) not normalized (free): 14717.007472 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1186 0.1343 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1376 0.1375 0.1474 n_refl.: 191129 remove outliers: r(all,work,free)=0.1376 0.1375 0.1474 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1378 0.1377 0.1476 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1185 0.1340 n_refl.: 191129 remove outliers: r(all,work,free)=0.1188 0.1185 0.1340 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3670 356.148 320.674 0.352 0.914 0.080 13.296-10.522 97.03 97 1 0.2449 481.238 459.705 0.720 0.915 0.104 10.503-8.327 97.80 175 3 0.2106 501.953 496.498 0.923 0.915 0.104 8.318-6.595 100.00 360 8 0.2140 375.579 370.489 0.944 0.915 0.083 6.588-5.215 100.00 711 7 0.1943 345.120 335.363 0.948 0.916 0.063 5.214-4.128 98.38 1367 28 0.1201 504.805 499.564 1.044 0.916 0.035 4.126-3.266 94.74 2603 46 0.1146 460.157 452.986 1.111 0.918 0.009 3.266-2.585 99.86 5447 97 0.1112 310.411 306.872 1.092 0.918 0.000 2.585-2.046 97.45 10613 204 0.0954 234.187 231.533 1.101 0.920 0.000 2.046-1.619 99.39 21536 464 0.0904 138.604 137.260 1.119 0.923 0.000 1.619-1.281 98.00 42464 925 0.0943 74.616 73.969 1.108 0.928 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.028 38.317 1.073 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0224 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1340 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1340 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1340 | n_water=920 | time (s): 2.780 (total time: 2.780) Filter (dist) r_work=0.1185 r_free=0.1340 | n_water=920 | time (s): 117.650 (total time: 120.430) Filter (q & B) r_work=0.1186 r_free=0.1343 | n_water=907 | time (s): 4.480 (total time: 124.910) Compute maps r_work=0.1186 r_free=0.1343 | n_water=907 | time (s): 1.790 (total time: 126.700) Filter (map) r_work=0.1208 r_free=0.1344 | n_water=799 | time (s): 4.420 (total time: 131.120) Find peaks r_work=0.1208 r_free=0.1344 | n_water=799 | time (s): 0.550 (total time: 131.670) Add new water r_work=0.1213 r_free=0.1350 | n_water=988 | time (s): 4.860 (total time: 136.530) Refine new water occ: r_work=0.1184 r_free=0.1322 adp: r_work=0.1184 r_free=0.1322 occ: r_work=0.1182 r_free=0.1323 adp: r_work=0.1182 r_free=0.1323 occ: r_work=0.1181 r_free=0.1323 adp: r_work=0.1180 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1323 r_work=0.1180 r_free=0.1323 | n_water=988 | time (s): 198.700 (total time: 335.230) Filter (q & B) r_work=0.1184 r_free=0.1332 | n_water=924 | time (s): 4.590 (total time: 339.820) Filter (dist only) r_work=0.1184 r_free=0.1332 | n_water=922 | time (s): 119.130 (total time: 458.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.604809 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.629065 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 0.1188 0.1338 0.0151 0.038 1.1 7.5 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.38 1.51 1.687 13.845 13.629 3.752 11.90 13.42 1.52 1.687 13.843 13.629 3.753 Individual atomic B min max mean iso aniso Overall: 5.53 64.09 14.80 0.87 557 3269 Protein: 5.53 28.47 10.35 0.87 0 2902 Water: 5.87 64.09 28.80 N/A 557 365 Other: 13.78 22.12 17.95 N/A 0 2 Chain A: 5.61 52.84 12.18 N/A 0 1623 Chain B: 5.53 64.09 12.04 N/A 0 1646 Chain S: 5.87 63.43 30.62 N/A 557 0 Histogram: Values Number of atoms 5.53 - 11.38 2077 11.38 - 17.24 808 17.24 - 23.09 278 23.09 - 28.95 219 28.95 - 34.81 179 34.81 - 40.66 143 40.66 - 46.52 77 46.52 - 52.37 35 52.37 - 58.23 5 58.23 - 64.09 5 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1342 r_work=0.1190 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1342 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1345 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753007 | | target function (ml) not normalized (work): 702889.513231 | | target function (ml) not normalized (free): 14724.367150 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1382 0.1380 0.1484 n_refl.: 191128 remove outliers: r(all,work,free)=0.1382 0.1380 0.1484 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1381 0.1379 0.1483 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1343 n_refl.: 191128 remove outliers: r(all,work,free)=0.1191 0.1188 0.1343 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3674 356.148 327.207 0.352 0.916 0.070 13.296-10.522 97.03 97 1 0.2459 481.238 459.689 0.713 0.918 0.096 10.503-8.327 97.80 175 3 0.2131 501.953 495.561 0.919 0.918 0.107 8.318-6.595 100.00 360 8 0.2163 375.579 370.186 0.940 0.918 0.080 6.588-5.215 100.00 711 7 0.1962 345.120 334.834 0.943 0.918 0.060 5.214-4.128 98.38 1367 28 0.1219 504.805 499.343 1.041 0.919 0.035 4.126-3.266 94.74 2603 46 0.1156 460.157 452.677 1.108 0.921 0.009 3.266-2.585 99.86 5447 97 0.1115 310.411 306.898 1.089 0.922 0.000 2.585-2.046 97.45 10613 204 0.0957 234.187 231.500 1.098 0.924 0.000 2.046-1.619 99.39 21536 464 0.0907 138.604 137.248 1.116 0.927 0.000 1.619-1.281 98.00 42464 925 0.0944 74.616 73.960 1.106 0.933 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.028 38.305 1.073 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0059 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1188 r_free=0.1343 After: r_work=0.1189 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1189 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1344 | n_water=922 | time (s): 3.110 (total time: 3.110) Filter (dist) r_work=0.1189 r_free=0.1344 | n_water=922 | time (s): 116.920 (total time: 120.030) Filter (q & B) r_work=0.1189 r_free=0.1345 | n_water=910 | time (s): 4.610 (total time: 124.640) Compute maps r_work=0.1189 r_free=0.1345 | n_water=910 | time (s): 2.070 (total time: 126.710) Filter (map) r_work=0.1212 r_free=0.1350 | n_water=800 | time (s): 5.940 (total time: 132.650) Find peaks r_work=0.1212 r_free=0.1350 | n_water=800 | time (s): 0.680 (total time: 133.330) Add new water r_work=0.1218 r_free=0.1357 | n_water=995 | time (s): 4.320 (total time: 137.650) Refine new water occ: r_work=0.1186 r_free=0.1329 adp: r_work=0.1186 r_free=0.1330 occ: r_work=0.1184 r_free=0.1330 adp: r_work=0.1184 r_free=0.1330 occ: r_work=0.1182 r_free=0.1330 adp: r_work=0.1182 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1331 r_work=0.1182 r_free=0.1331 | n_water=995 | time (s): 250.050 (total time: 387.700) Filter (q & B) r_work=0.1186 r_free=0.1338 | n_water=926 | time (s): 4.320 (total time: 392.020) Filter (dist only) r_work=0.1186 r_free=0.1338 | n_water=924 | time (s): 123.740 (total time: 515.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567954 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.259796 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1347 0.0155 0.039 1.2 10.4 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.47 1.55 1.683 13.850 13.260 3.758 11.95 13.50 1.55 1.699 13.841 13.260 3.758 Individual atomic B min max mean iso aniso Overall: 5.55 63.39 14.79 0.85 559 3269 Protein: 5.55 27.97 10.35 0.85 0 2902 Water: 5.96 63.39 28.73 N/A 559 365 Other: 13.81 22.05 17.93 N/A 0 2 Chain A: 5.64 52.54 12.15 N/A 0 1623 Chain B: 5.55 63.39 12.02 N/A 0 1646 Chain S: 5.96 63.22 30.62 N/A 559 0 Histogram: Values Number of atoms 5.55 - 11.33 2061 11.33 - 17.12 831 17.12 - 22.90 267 22.90 - 28.69 216 28.69 - 34.47 182 34.47 - 40.26 144 40.26 - 46.04 78 46.04 - 51.82 37 51.82 - 57.61 6 57.61 - 63.39 6 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1350 r_work=0.1195 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1350 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1350 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.758225 | | target function (ml) not normalized (work): 703866.595178 | | target function (ml) not normalized (free): 14740.708990 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1345 0.1424 5.6791 5.7696| | 2: 2.94 - 2.33 1.00 7339 128 0.1067 0.1371 5.0806 5.1821| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1156 4.6611 4.747| | 4: 2.04 - 1.85 1.00 7170 155 0.0905 0.1051 4.3999 4.5696| | 5: 1.85 - 1.72 0.99 7113 159 0.0941 0.1014 4.1596 4.2601| | 6: 1.72 - 1.62 0.99 7102 142 0.0904 0.1075 3.9524 4.0775| | 7: 1.62 - 1.54 0.99 7104 148 0.0899 0.0945 3.8052 3.9168| | 8: 1.54 - 1.47 0.96 6798 152 0.0902 0.1330 3.7089 3.9136| | 9: 1.47 - 1.41 0.98 6938 155 0.0935 0.1144 3.6311 3.7671| | 10: 1.41 - 1.36 0.99 7022 150 0.0987 0.1192 3.566 3.6818| | 11: 1.36 - 1.32 0.99 6997 151 0.1004 0.1121 3.4948 3.5955| | 12: 1.32 - 1.28 0.98 6975 149 0.1041 0.1135 3.4663 3.5884| | 13: 1.28 - 1.25 0.98 6907 166 0.1051 0.1250 3.4446 3.5726| | 14: 1.25 - 1.22 0.98 7015 112 0.1111 0.1594 3.4377 3.6886| | 15: 1.22 - 1.19 0.98 6956 137 0.1174 0.1250 3.4527 3.4987| | 16: 1.19 - 1.17 0.93 6604 132 0.1256 0.1540 3.4688 3.6509| | 17: 1.17 - 1.14 0.98 6940 135 0.1304 0.1221 3.4359 3.4411| | 18: 1.14 - 1.12 0.98 6875 142 0.1388 0.1717 3.4404 3.5332| | 19: 1.12 - 1.10 0.97 6948 106 0.1474 0.1772 3.4221 3.6004| | 20: 1.10 - 1.08 0.97 6884 147 0.1587 0.1587 3.4119 3.4387| | 21: 1.08 - 1.07 0.97 6852 152 0.1731 0.2147 3.4197 3.5035| | 22: 1.07 - 1.05 0.97 6836 135 0.1908 0.1954 3.4147 3.416| | 23: 1.05 - 1.03 0.97 6827 159 0.2122 0.2017 3.4342 3.4857| | 24: 1.03 - 1.02 0.96 6784 133 0.2337 0.2257 3.4371 3.5129| | 25: 1.02 - 1.01 0.93 6552 130 0.2618 0.2522 3.4503 3.5241| | 26: 1.01 - 0.99 0.96 6767 158 0.2761 0.2853 3.4161 3.4216| | 27: 0.99 - 0.98 0.94 6647 131 0.3047 0.2800 3.4701 3.3966| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.67 1.00 0.95 11262.90| | 2: 2.94 - 2.33 7339 128 0.93 12.82 0.99 0.95 5160.57| | 3: 2.33 - 2.04 6939 150 0.96 7.71 1.01 0.95 1716.75| | 4: 2.04 - 1.85 7170 155 0.96 7.73 1.00 0.95 1017.71| | 5: 1.85 - 1.72 7113 159 0.96 8.17 1.00 0.96 642.76| | 6: 1.72 - 1.62 7102 142 0.96 8.04 1.00 0.96 445.41| | 7: 1.62 - 1.54 7104 148 0.96 8.14 1.01 0.97 336.05| | 8: 1.54 - 1.47 6798 152 0.96 8.31 1.01 0.97 280.67| | 9: 1.47 - 1.41 6938 155 0.96 8.57 1.00 0.98 234.42| | 10: 1.41 - 1.36 7022 150 0.96 9.06 1.00 0.97 206.55| | 11: 1.36 - 1.32 6997 151 0.96 9.08 0.99 0.96 178.57| | 12: 1.32 - 1.28 6975 149 0.96 9.08 0.98 0.95 163.34| | 13: 1.28 - 1.25 6907 166 0.95 9.68 1.01 0.96 160.95| | 14: 1.25 - 1.22 7015 112 0.95 10.81 1.01 0.96 165.35| | 15: 1.22 - 1.19 6956 137 0.94 11.35 1.01 0.98 168.52| | 16: 1.19 - 1.17 6604 132 0.95 11.48 1.01 0.96 161.23| | 17: 1.17 - 1.14 6940 135 0.94 12.29 1.01 0.96 154.65| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.95 148.35| | 19: 1.12 - 1.10 6948 106 0.93 14.21 1.00 0.94 151.99| | 20: 1.10 - 1.08 6884 147 0.92 15.29 1.00 0.94 151.07| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.89| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.93 155.30| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 165.12| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.93 179.49| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.90 182.40| | 26: 1.01 - 0.99 6767 158 0.81 26.64 0.98 0.88 176.66| | 27: 0.99 - 0.98 6647 131 0.82 26.28 0.99 0.87 160.79| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.35 max = 11262.90 mean = 931.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.35| |phase err.(test): min = 0.00 max = 88.18 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1350 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1499 n_refl.: 191128 remove outliers: r(all,work,free)=0.1393 0.1391 0.1499 n_refl.: 191128 overall B=-0.05 to atoms: r(all,work,free)=0.1386 0.1384 0.1495 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1193 0.1350 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1193 0.1350 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3670 356.148 326.551 0.323 0.986 0.080 13.296-10.522 97.03 97 1 0.2483 481.238 458.959 0.645 0.987 0.094 10.503-8.327 97.80 175 3 0.2126 501.953 495.704 0.833 0.987 0.096 8.318-6.595 100.00 360 8 0.2141 375.579 370.556 0.853 0.987 0.076 6.588-5.215 100.00 711 7 0.1943 345.120 334.715 0.856 0.988 0.060 5.214-4.128 98.38 1367 28 0.1215 504.805 499.402 0.944 0.989 0.035 4.126-3.266 94.74 2603 46 0.1155 460.157 452.713 1.006 0.990 0.009 3.266-2.585 99.86 5447 97 0.1116 310.411 306.974 0.988 0.992 0.000 2.585-2.046 97.45 10613 204 0.0964 234.187 231.488 0.995 0.994 0.000 2.046-1.619 99.39 21536 464 0.0917 138.604 137.226 1.011 0.999 0.000 1.619-1.281 98.00 42464 925 0.0955 74.616 73.947 1.000 1.005 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.028 38.295 0.968 1.018 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0100 ================= 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 : 0.2041 0.1993 0.084 5.225 5.2 78.0 14.6 805 0.000 1_bss: 0.1808 0.1920 0.084 5.225 5.2 78.0 14.6 805 0.000 1_settarget: 0.1808 0.1920 0.084 5.225 5.2 78.0 14.6 805 0.000 1_nqh: 0.1808 0.1920 0.084 5.225 5.2 78.0 14.6 805 0.000 1_weight: 0.1808 0.1920 0.084 5.225 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1269 0.1500 0.039 1.157 5.2 78.0 14.6 805 0.155 1_adp: 0.1298 0.1575 0.039 1.157 5.2 73.0 15.0 805 0.155 1_regHadp: 0.1297 0.1570 0.039 1.157 5.2 73.0 15.0 805 0.155 1_occ: 0.1283 0.1560 0.039 1.157 5.2 73.0 15.0 805 0.155 2_bss: 0.1275 0.1549 0.039 1.157 5.4 73.2 15.1 805 0.155 2_settarget: 0.1275 0.1549 0.039 1.157 5.4 73.2 15.1 805 0.155 2_updatecdl: 0.1275 0.1549 0.039 1.168 5.4 73.2 15.1 805 0.155 2_nqh: 0.1275 0.1549 0.039 1.168 5.4 73.2 15.1 805 0.155 2_sol: 0.1271 0.1509 0.039 1.168 5.4 73.2 16.1 896 n/a 2_weight: 0.1271 0.1509 0.039 1.168 5.4 73.2 16.1 896 n/a 2_xyzrec: 0.1253 0.1526 0.041 1.126 5.4 73.2 16.1 896 n/a 2_adp: 0.1229 0.1505 0.041 1.126 5.4 76.8 16.3 896 n/a 2_regHadp: 0.1229 0.1506 0.041 1.126 5.4 76.8 16.3 896 n/a 2_occ: 0.1224 0.1505 0.041 1.126 5.4 76.8 16.3 896 n/a 3_bss: 0.1231 0.1513 0.041 1.126 5.4 76.7 16.3 896 n/a 3_settarget: 0.1231 0.1513 0.041 1.126 5.4 76.7 16.3 896 n/a 3_updatecdl: 0.1231 0.1513 0.041 1.128 5.4 76.7 16.3 896 n/a 3_nqh: 0.1231 0.1513 0.041 1.128 5.4 76.7 16.3 896 n/a 3_sol: 0.1250 0.1504 0.041 1.128 5.4 68.2 15.4 873 n/a 3_weight: 0.1250 0.1504 0.041 1.128 5.4 68.2 15.4 873 n/a 3_xyzrec: 0.1237 0.1434 0.036 1.101 5.4 68.2 15.4 873 n/a 3_adp: 0.1233 0.1398 0.036 1.101 5.5 67.8 15.3 873 n/a 3_regHadp: 0.1234 0.1399 0.036 1.101 5.5 67.8 15.3 873 n/a 3_occ: 0.1227 0.1390 0.036 1.101 5.5 67.8 15.3 873 n/a 4_bss: 0.1223 0.1384 0.036 1.101 5.5 67.8 15.2 873 n/a 4_settarget: 0.1223 0.1384 0.036 1.101 5.5 67.8 15.2 873 n/a 4_updatecdl: 0.1223 0.1384 0.036 1.106 5.5 67.8 15.2 873 n/a 4_nqh: 0.1223 0.1384 0.036 1.106 5.5 67.8 15.2 873 n/a 4_sol: 0.1206 0.1364 0.036 1.106 5.5 67.8 15.1 881 n/a 4_weight: 0.1206 0.1364 0.036 1.106 5.5 67.8 15.1 881 n/a 4_xyzrec: 0.1204 0.1363 0.036 1.127 5.5 67.8 15.1 881 n/a 4_adp: 0.1196 0.1357 0.036 1.127 5.5 67.4 15.1 881 n/a 4_regHadp: 0.1196 0.1357 0.036 1.127 5.5 67.4 15.1 881 n/a 4_occ: 0.1194 0.1356 0.036 1.127 5.5 67.4 15.1 881 n/a 5_bss: 0.1192 0.1354 0.036 1.127 5.5 67.3 15.0 881 n/a 5_settarget: 0.1192 0.1354 0.036 1.127 5.5 67.3 15.0 881 n/a 5_updatecdl: 0.1192 0.1354 0.036 1.127 5.5 67.3 15.0 881 n/a 5_nqh: 0.1192 0.1354 0.036 1.127 5.5 67.3 15.0 881 n/a 5_sol: 0.1191 0.1348 0.036 1.127 5.5 67.3 15.1 895 n/a 5_weight: 0.1191 0.1348 0.036 1.127 5.5 67.3 15.1 895 n/a 5_xyzrec: 0.1194 0.1357 0.037 1.127 5.5 67.3 15.1 895 n/a 5_adp: 0.1199 0.1360 0.037 1.127 5.6 67.1 15.0 895 n/a 5_regHadp: 0.1199 0.1360 0.037 1.127 5.6 67.1 15.0 895 n/a 5_occ: 0.1197 0.1360 0.037 1.127 5.6 67.1 15.0 895 n/a 6_bss: 0.1196 0.1359 0.037 1.127 5.5 67.0 15.0 895 n/a 6_settarget: 0.1196 0.1359 0.037 1.127 5.5 67.0 15.0 895 n/a 6_updatecdl: 0.1196 0.1359 0.037 1.127 5.5 67.0 15.0 895 n/a 6_nqh: 0.1196 0.1359 0.037 1.127 5.5 67.0 15.0 895 n/a 6_sol: 0.1193 0.1357 0.037 1.127 5.5 67.0 15.0 906 n/a 6_weight: 0.1193 0.1357 0.037 1.127 5.5 67.0 15.0 906 n/a 6_xyzrec: 0.1196 0.1359 0.037 1.136 5.5 67.0 15.0 906 n/a 6_adp: 0.1196 0.1359 0.037 1.136 5.6 66.4 15.0 906 n/a 6_regHadp: 0.1196 0.1360 0.037 1.136 5.6 66.4 15.0 906 n/a 6_occ: 0.1194 0.1359 0.037 1.136 5.6 66.4 15.0 906 n/a 7_bss: 0.1194 0.1361 0.037 1.136 5.3 66.1 14.8 906 n/a 7_settarget: 0.1194 0.1361 0.037 1.136 5.3 66.1 14.8 906 n/a 7_updatecdl: 0.1194 0.1361 0.037 1.136 5.3 66.1 14.8 906 n/a 7_nqh: 0.1194 0.1361 0.037 1.136 5.3 66.1 14.8 906 n/a 7_sol: 0.1192 0.1347 0.037 1.136 5.3 66.1 14.8 921 n/a 7_weight: 0.1192 0.1347 0.037 1.136 5.3 66.1 14.8 921 n/a 7_xyzrec: 0.1195 0.1354 0.037 1.133 5.3 66.1 14.8 921 n/a 7_adp: 0.1197 0.1356 0.037 1.133 5.4 65.2 14.8 921 n/a 7_regHadp: 0.1197 0.1357 0.037 1.133 5.4 65.2 14.8 921 n/a 7_occ: 0.1195 0.1355 0.037 1.133 5.4 65.2 14.8 921 n/a 8_bss: 0.1185 0.1341 0.037 1.133 5.4 65.3 14.8 921 n/a 8_settarget: 0.1185 0.1341 0.037 1.133 5.4 65.3 14.8 921 n/a 8_updatecdl: 0.1185 0.1341 0.037 1.133 5.4 65.3 14.8 921 n/a 8_nqh: 0.1185 0.1341 0.037 1.133 5.4 65.3 14.8 921 n/a 8_sol: 0.1184 0.1335 0.037 1.133 5.4 65.3 14.8 920 n/a 8_weight: 0.1184 0.1335 0.037 1.133 5.4 65.3 14.8 920 n/a 8_xyzrec: 0.1188 0.1341 0.038 1.127 5.4 65.3 14.8 920 n/a 8_adp: 0.1188 0.1340 0.038 1.127 5.5 64.2 14.8 920 n/a 8_regHadp: 0.1188 0.1341 0.038 1.127 5.5 64.2 14.8 920 n/a 8_occ: 0.1186 0.1343 0.038 1.127 5.5 64.2 14.8 920 n/a 9_bss: 0.1185 0.1340 0.038 1.127 5.5 64.3 14.8 920 n/a 9_settarget: 0.1185 0.1340 0.038 1.127 5.5 64.3 14.8 920 n/a 9_updatecdl: 0.1185 0.1340 0.038 1.127 5.5 64.3 14.8 920 n/a 9_nqh: 0.1185 0.1340 0.038 1.127 5.5 64.3 14.8 920 n/a 9_sol: 0.1184 0.1332 0.038 1.127 5.5 64.3 14.8 922 n/a 9_weight: 0.1184 0.1332 0.038 1.127 5.5 64.3 14.8 922 n/a 9_xyzrec: 0.1188 0.1338 0.038 1.133 5.5 64.3 14.8 922 n/a 9_adp: 0.1190 0.1342 0.038 1.133 5.5 64.1 14.8 922 n/a 9_regHadp: 0.1190 0.1342 0.038 1.133 5.5 64.1 14.8 922 n/a 9_occ: 0.1189 0.1345 0.038 1.133 5.5 64.1 14.8 922 n/a 10_bss: 0.1188 0.1343 0.038 1.133 5.5 64.1 14.8 922 n/a 10_settarget: 0.1188 0.1343 0.038 1.133 5.5 64.1 14.8 922 n/a 10_updatecdl: 0.1188 0.1343 0.038 1.133 5.5 64.1 14.8 922 n/a 10_setrh: 0.1189 0.1344 0.038 1.133 5.5 64.1 14.8 922 n/a 10_nqh: 0.1189 0.1344 0.038 1.133 5.5 64.1 14.8 922 n/a 10_sol: 0.1186 0.1338 0.038 1.133 5.5 64.1 14.8 924 n/a 10_weight: 0.1186 0.1338 0.038 1.133 5.5 64.1 14.8 924 n/a 10_xyzrec: 0.1192 0.1347 0.039 1.185 5.5 64.1 14.8 924 n/a 10_adp: 0.1195 0.1350 0.039 1.185 5.5 63.4 14.8 924 n/a 10_regHadp: 0.1195 0.1350 0.039 1.185 5.5 63.4 14.8 924 n/a 10_occ: 0.1194 0.1350 0.039 1.185 5.5 63.4 14.8 924 n/a end: 0.1194 0.1350 0.039 1.185 5.5 63.3 14.7 924 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2021531_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2021531_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.6000 Refinement macro-cycles (run) : 12486.0300 Write final files (write_after_run_outputs) : 130.1000 Total : 12622.7300 Total CPU time: 3.52 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:47:33 PST -0800 (1736736453.65 s) Start R-work = 0.1808, R-free = 0.1920 Final R-work = 0.1194, R-free = 0.1350 =============================================================================== Job complete usr+sys time: 12872.35 seconds wall clock time: 215 minutes 31.60 seconds (12931.60 seconds total)