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_2484050.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_2484050.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2484050.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.41, per 1000 atoms: 0.36 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: 2.634 distance_ideal: 2.720 ideal - model: 0.086 slack: 0.000 delta_slack: 0.086 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: 2.814 distance_ideal: 2.710 ideal - model: -0.104 slack: 0.000 delta_slack: -0.104 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 138.0 milliseconds Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.03: 790 1.03 - 1.26: 2548 1.26 - 1.49: 1493 1.49 - 1.72: 1091 1.72 - 1.95: 12 Bond restraints: 5934 Sorted by residual: bond pdb=" CA ALA B 10 " pdb=" CB ALA B 10 " ideal model delta sigma weight residual 1.535 1.276 0.259 1.21e-02 6.83e+03 4.58e+02 bond pdb=" N ARG B 83 " pdb=" CA ARG B 83 " ideal model delta sigma weight residual 1.459 1.712 -0.253 1.23e-02 6.61e+03 4.22e+02 bond pdb=" CD2 PHE A 119 " pdb=" HD2 PHE A 119 " ideal model delta sigma weight residual 0.930 1.336 -0.406 2.00e-02 2.50e+03 4.12e+02 bond pdb=" CG HIS B 116 " pdb=" ND1 HIS B 116 " ideal model delta sigma weight residual 1.378 1.597 -0.219 1.10e-02 8.26e+03 3.97e+02 bond pdb=" N LYS A 151 " pdb=" H LYS A 151 " ideal model delta sigma weight residual 0.860 1.250 -0.390 2.00e-02 2.50e+03 3.81e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 5673 4.13 - 8.26: 3506 8.26 - 12.40: 1347 12.40 - 16.53: 259 16.53 - 20.66: 25 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.19 106.48 12.71 6.50e-01 2.37e+00 3.82e+02 angle pdb=" O ILE B 168 " pdb=" C ILE B 168 " pdb=" N ILE B 169 " ideal model delta sigma weight residual 121.94 105.49 16.45 1.00e+00 1.00e+00 2.71e+02 angle pdb=" CA TRP B 146 " pdb=" C TRP B 146 " pdb=" O TRP B 146 " ideal model delta sigma weight residual 120.30 137.82 -17.52 1.07e+00 8.73e-01 2.68e+02 angle pdb=" O SER B 48 " pdb=" C SER B 48 " pdb=" N ARG B 49 " ideal model delta sigma weight residual 122.12 138.27 -16.15 1.06e+00 8.90e-01 2.32e+02 angle pdb=" CA LEU B 171 " pdb=" C LEU B 171 " pdb=" O LEU B 171 " ideal model delta sigma weight residual 119.79 102.28 17.51 1.18e+00 7.18e-01 2.20e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.59: 1855 17.59 - 35.17: 130 35.17 - 52.75: 47 52.75 - 70.33: 14 70.33 - 87.91: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -154.36 -25.64 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+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 -157.94 -22.06 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.213: 209 0.213 - 0.424: 146 0.424 - 0.636: 97 0.636 - 0.847: 32 0.847 - 1.059: 8 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB THR B 21 " pdb=" CA THR B 21 " pdb=" OG1 THR B 21 " pdb=" CG2 THR B 21 " both_signs ideal model delta sigma weight residual False 2.55 3.61 -1.06 2.00e-01 2.50e+01 2.80e+01 chirality pdb=" CA GLU A 137 " pdb=" N GLU A 137 " pdb=" C GLU A 137 " pdb=" CB GLU A 137 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CB ILE B 162 " pdb=" CA ILE B 162 " pdb=" CG1 ILE B 162 " pdb=" CG2 ILE B 162 " both_signs ideal model delta sigma weight residual False 2.64 3.65 -1.00 2.00e-01 2.50e+01 2.50e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.191 2.00e-02 2.50e+03 9.68e-02 2.81e+02 pdb=" CG PHE B 164 " -0.134 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.078 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.116 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.089 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.034 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.002 2.00e-02 2.50e+03 5.26e-02 1.11e+02 pdb=" CG TRP A 139 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.098 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.114 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.068 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.043 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.038 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.024 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " -0.011 2.00e-02 2.50e+03 5.24e-02 1.10e+02 pdb=" CG TRP A 146 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.049 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.072 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.072 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.058 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.006 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " 0.054 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.077 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.060 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.012 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.65: 33 1.65 - 2.39: 2833 2.39 - 3.13: 22626 3.13 - 3.86: 32804 3.86 - 4.60: 52062 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110358 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.917 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.994 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.005 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.063 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.113 2.620 ... (remaining 110353 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_2484050_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.300291 | | target function (ml) not normalized (work): 805500.454917 | | target function (ml) not normalized (free): 16566.779086 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2146 0.2018 6.6645 6.3157| | 2: 2.94 - 2.33 1.00 7339 128 0.1623 0.1556 5.5359 5.5769| | 3: 2.33 - 2.04 0.96 6939 150 0.1655 0.1505 5.1485 5.0947| | 4: 2.04 - 1.85 1.00 7170 155 0.1740 0.1542 4.9493 4.9762| | 5: 1.85 - 1.72 0.99 7113 159 0.1921 0.1813 4.8073 4.899| | 6: 1.72 - 1.62 0.99 7102 142 0.1968 0.1972 4.6537 4.7122| | 7: 1.62 - 1.54 0.99 7104 148 0.2005 0.1726 4.5594 4.537| | 8: 1.54 - 1.47 0.96 6798 152 0.2054 0.2295 4.4799 4.5662| | 9: 1.47 - 1.41 0.98 6938 155 0.2085 0.2164 4.3835 4.4743| | 10: 1.41 - 1.36 0.99 7022 150 0.2124 0.2116 4.3035 4.3364| | 11: 1.36 - 1.32 0.99 6997 151 0.2122 0.2017 4.2248 4.2056| | 12: 1.32 - 1.28 0.98 6976 149 0.2047 0.1853 4.1568 4.141| | 13: 1.28 - 1.25 0.98 6907 166 0.2007 0.2164 4.1148 4.1607| | 14: 1.25 - 1.22 0.98 7015 113 0.2096 0.2278 4.0784 4.1868| | 15: 1.22 - 1.19 0.98 6957 137 0.2097 0.2140 4.0456 4.0849| | 16: 1.19 - 1.17 0.93 6604 132 0.2131 0.2188 4.0007 4.1075| | 17: 1.17 - 1.14 0.98 6941 135 0.2167 0.2031 3.9623 4.0068| | 18: 1.14 - 1.12 0.98 6875 142 0.2219 0.2361 3.9416 3.9524| | 19: 1.12 - 1.10 0.97 6949 106 0.2283 0.2625 3.8844 4.0505| | 20: 1.10 - 1.08 0.97 6884 147 0.2328 0.2226 3.8337 3.8567| | 21: 1.08 - 1.07 0.97 6852 152 0.2473 0.2994 3.816 3.9014| | 22: 1.07 - 1.05 0.97 6838 135 0.2548 0.2691 3.7581 3.8391| | 23: 1.05 - 1.03 0.97 6829 159 0.2714 0.2630 3.7296 3.8201| | 24: 1.03 - 1.02 0.96 6785 133 0.2894 0.2576 3.7067 3.7233| | 25: 1.02 - 1.01 0.93 6552 130 0.3087 0.2920 3.6841 3.7682| | 26: 1.01 - 0.99 0.96 6767 158 0.3189 0.2999 3.6354 3.6035| | 27: 0.99 - 0.98 0.94 6648 131 0.3422 0.3085 3.6401 3.5766| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.86 0.91 0.96 36554.15| | 2: 2.94 - 2.33 7339 128 0.85 21.30 1.08 1.01 15018.26| | 3: 2.33 - 2.04 6939 150 0.94 11.63 1.11 1.05 3729.11| | 4: 2.04 - 1.85 7170 155 0.93 13.09 1.11 1.05 2633.79| | 5: 1.85 - 1.72 7113 159 0.91 15.89 1.11 1.06 2136.52| | 6: 1.72 - 1.62 7102 142 0.89 17.26 1.12 1.06 1695.30| | 7: 1.62 - 1.54 7104 148 0.89 18.15 1.11 1.07 1400.30| | 8: 1.54 - 1.47 6798 152 0.88 18.79 1.10 1.06 1194.24| | 9: 1.47 - 1.41 6938 155 0.88 19.37 1.10 1.05 1004.42| | 10: 1.41 - 1.36 7022 150 0.87 19.94 1.10 1.04 841.69| | 11: 1.36 - 1.32 6997 151 0.88 19.46 1.09 1.04 689.71| | 12: 1.32 - 1.28 6976 149 0.88 19.25 1.08 1.04 613.59| | 13: 1.28 - 1.25 6907 166 0.88 19.23 1.07 1.04 567.49| | 14: 1.25 - 1.22 7015 113 0.87 20.29 1.08 1.04 556.56| | 15: 1.22 - 1.19 6957 137 0.86 20.85 1.08 1.05 544.99| | 16: 1.19 - 1.17 6604 132 0.87 20.84 1.08 1.03 502.96| | 17: 1.17 - 1.14 6941 135 0.86 21.61 1.08 1.01 462.71| | 18: 1.14 - 1.12 6875 142 0.86 21.84 1.08 0.97 413.19| | 19: 1.12 - 1.10 6949 106 0.84 23.61 1.07 0.97 411.71| | 20: 1.10 - 1.08 6884 147 0.83 24.74 1.07 0.95 390.28| | 21: 1.08 - 1.07 6852 152 0.81 26.36 1.06 0.94 387.27| | 22: 1.07 - 1.05 6838 135 0.80 27.36 1.06 0.95 363.52| | 23: 1.05 - 1.03 6829 159 0.79 28.18 1.06 0.96 340.55| | 24: 1.03 - 1.02 6785 133 0.79 28.37 1.05 1.00 316.61| | 25: 1.02 - 1.01 6552 130 0.79 28.75 1.03 0.97 286.23| | 26: 1.01 - 0.99 6767 158 0.77 30.18 1.03 0.97 273.89| | 27: 0.99 - 0.98 6648 131 0.77 30.91 1.04 0.95 263.56| |alpha: min = 0.94 max = 1.07 mean = 1.01| |beta: min = 263.56 max = 36554.15 mean = 2855.32| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.71| |phase err.(test): min = 0.00 max = 89.92 mean = 21.73| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.259 2950 Z= 5.527 Angle : 5.141 17.957 4018 Z= 3.707 Chirality : 0.370 1.059 492 Planarity : 0.031 0.107 512 Dihedral : 12.815 87.906 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.37 % Favored : 96.37 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % Cbeta Deviations : 26.69 % 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: -2.22 (0.38), residues: 386 helix: -2.30 (0.34), residues: 142 sheet: -1.17 (0.49), residues: 86 loop : -0.50 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.022 ARG A 27 TYR 0.101 0.034 TYR B 194 PHE 0.164 0.040 PHE B 164 TRP 0.119 0.041 TRP A 139 HIS 0.077 0.030 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.300291 | | target function (ml) not normalized (work): 805500.454917 | | target function (ml) not normalized (free): 16566.779086 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2035 0.2037 0.1978 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2035 0.2037 0.1978 n_refl.: 191155 remove outliers: r(all,work,free)=0.2035 0.2037 0.1978 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2035 0.2037 0.1978 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1802 0.1799 0.1924 n_refl.: 191145 remove outliers: r(all,work,free)=0.1800 0.1797 0.1924 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4200 400.535 295.873 0.435 0.912 0.299 13.296-10.522 99.01 99 1 0.2499 528.187 520.353 0.787 0.914 0.253 10.503-8.327 98.90 177 3 0.2463 564.205 558.178 0.971 0.914 0.233 8.318-6.595 100.00 360 8 0.2540 414.736 402.491 0.973 0.914 0.200 6.588-5.215 100.00 711 7 0.2272 381.101 365.922 0.957 0.914 0.160 5.214-4.128 98.38 1367 28 0.1487 557.435 549.519 1.072 0.914 0.080 4.126-3.266 94.74 2603 46 0.1344 508.132 499.157 1.143 0.915 0.014 3.266-2.585 99.86 5447 97 0.1459 342.774 337.423 1.116 0.914 0.000 2.585-2.046 97.45 10613 204 0.1405 258.603 254.459 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1601 153.054 149.880 1.144 0.912 0.000 1.619-1.281 98.00 42464 925 0.1906 82.395 80.285 1.129 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2322 44.203 41.685 1.112 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0021 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1924 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1797 r_free=0.1924 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.008370 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 581.510856 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1270 0.1500 0.0229 0.038 1.2 11.0 0.0 0.3 0 11.504 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.00 2.29 1.118 13.110 581.511 0.018 12.96 15.67 2.71 1.254 13.354 581.511 0.017 Individual atomic B min max mean iso aniso Overall: 5.24 73.04 15.04 1.42 435 3274 Protein: 5.24 40.47 11.03 1.42 0 2902 Water: 6.38 73.04 29.48 N/A 435 370 Other: 15.99 30.35 23.17 N/A 0 2 Chain A: 5.36 60.32 13.07 N/A 0 1626 Chain B: 5.24 73.04 12.79 N/A 0 1648 Chain S: 11.52 62.77 30.91 N/A 435 0 Histogram: Values Number of atoms 5.24 - 12.02 2169 12.02 - 18.80 635 18.80 - 25.58 317 25.58 - 32.36 261 32.36 - 39.14 162 39.14 - 45.92 100 45.92 - 52.70 40 52.70 - 59.48 20 59.48 - 66.26 4 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1567 r_work=0.1295 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1563 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 = 0.1280 r_free = 0.1550 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015549 | | target function (ls_wunit_k1) not normalized (work): 2912.252735 | | target function (ls_wunit_k1) not normalized (free): 116.635842 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1280 0.1550 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1474 0.1472 0.1630 n_refl.: 191139 remove outliers: r(all,work,free)=0.1474 0.1472 0.1630 n_refl.: 191139 overall B=0.15 to atoms: r(all,work,free)=0.1497 0.1495 0.1639 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1277 0.1272 0.1539 n_refl.: 191139 remove outliers: r(all,work,free)=0.1277 0.1272 0.1538 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 0.3553 402.814 377.453 0.489 0.962 0.279 13.296-10.522 99.01 99 1 0.2096 528.187 523.344 0.741 0.963 0.239 10.503-8.327 98.90 177 3 0.1727 564.205 565.431 0.890 0.963 0.230 8.318-6.595 100.00 360 8 0.1709 414.736 412.358 0.910 0.963 0.165 6.588-5.215 100.00 711 7 0.1522 381.101 373.801 0.889 0.963 0.160 5.214-4.128 98.38 1367 28 0.0901 557.435 554.152 0.976 0.964 0.070 4.126-3.266 94.74 2603 46 0.0832 508.132 504.329 1.044 0.964 0.014 3.266-2.585 99.86 5447 97 0.0924 342.774 340.289 1.025 0.964 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.398 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.390 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1273 82.395 81.426 1.049 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1868 44.202 42.176 1.025 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0351 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1272 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1538 | n_water=805 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1277 r_free=0.1545 | n_water=794 | time (s): 101.160 (total time: 103.470) Filter (q & B) r_work=0.1277 r_free=0.1545 | n_water=790 | time (s): 4.720 (total time: 108.190) Compute maps r_work=0.1277 r_free=0.1545 | n_water=790 | time (s): 2.630 (total time: 110.820) Filter (map) r_work=0.1304 r_free=0.1526 | n_water=650 | time (s): 4.340 (total time: 115.160) Find peaks r_work=0.1304 r_free=0.1526 | n_water=650 | time (s): 0.650 (total time: 115.810) Add new water r_work=0.1328 r_free=0.1550 | n_water=964 | time (s): 4.000 (total time: 119.810) Refine new water occ: r_work=0.1283 r_free=0.1512 adp: r_work=0.1270 r_free=0.1508 occ: r_work=0.1273 r_free=0.1506 adp: r_work=0.1266 r_free=0.1505 occ: r_work=0.1267 r_free=0.1503 adp: r_work=0.1265 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1265 r_free=0.1504 r_work=0.1265 r_free=0.1504 | n_water=964 | time (s): 86.600 (total time: 206.410) Filter (q & B) r_work=0.1268 r_free=0.1509 | n_water=894 | time (s): 5.190 (total time: 211.600) Filter (dist only) r_work=0.1269 r_free=0.1506 | n_water=892 | time (s): 110.340 (total time: 321.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.346478 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 598.366637 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 0.1251 0.1518 0.0267 0.042 1.1 21.8 0.0 0.3 0 11.673 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.51 15.18 2.67 2.052 15.224 598.367 0.014 12.33 15.09 2.76 2.385 15.257 598.367 0.014 Individual atomic B min max mean iso aniso Overall: 5.46 68.27 16.34 1.21 524 3272 Protein: 5.46 40.48 11.03 1.21 0 2902 Water: 6.66 68.27 33.63 N/A 524 368 Other: 16.28 32.94 24.61 N/A 0 2 Chain A: 5.60 57.30 13.02 N/A 0 1624 Chain B: 5.46 68.27 12.84 N/A 0 1648 Chain S: 13.04 66.55 37.65 N/A 524 0 Histogram: Values Number of atoms 5.46 - 11.74 2066 11.74 - 18.02 700 18.02 - 24.30 271 24.30 - 30.58 220 30.58 - 36.86 176 36.86 - 43.15 173 43.15 - 49.43 88 49.43 - 55.71 52 55.71 - 61.99 39 61.99 - 68.27 11 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1509 r_work=0.1233 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1510 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1510 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013427 | | target function (ls_wunit_k1) not normalized (work): 2514.862520 | | target function (ls_wunit_k1) not normalized (free): 100.452084 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1510 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1442 0.1440 0.1605 n_refl.: 191137 remove outliers: r(all,work,free)=0.1442 0.1440 0.1605 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1439 0.1436 0.1603 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1517 n_refl.: 191137 remove outliers: r(all,work,free)=0.1239 0.1234 0.1517 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 0.3241 402.814 379.575 0.492 0.962 0.269 13.296-10.522 99.01 99 1 0.1856 528.187 520.738 0.757 0.963 0.226 10.503-8.327 98.90 177 3 0.1432 564.205 567.464 0.919 0.963 0.194 8.318-6.595 100.00 360 8 0.1562 414.736 414.022 0.936 0.963 0.159 6.588-5.215 100.00 711 7 0.1359 381.101 376.644 0.911 0.963 0.139 5.214-4.128 98.38 1367 28 0.0833 557.435 556.238 0.995 0.963 0.090 4.126-3.266 94.74 2603 46 0.0764 508.132 505.189 1.061 0.963 0.030 3.266-2.585 99.86 5447 97 0.0855 342.774 341.334 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.757 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.641 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.352 1.075 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.223 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0600 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1517 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1517 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1517 | n_water=892 | time (s): 2.870 (total time: 2.870) Filter (dist) r_work=0.1236 r_free=0.1518 | n_water=884 | time (s): 127.990 (total time: 130.860) Filter (q & B) r_work=0.1236 r_free=0.1518 | n_water=883 | time (s): 5.720 (total time: 136.580) Compute maps r_work=0.1236 r_free=0.1518 | n_water=883 | time (s): 1.890 (total time: 138.470) Filter (map) r_work=0.1272 r_free=0.1526 | n_water=692 | time (s): 4.780 (total time: 143.250) Find peaks r_work=0.1272 r_free=0.1526 | n_water=692 | time (s): 0.910 (total time: 144.160) Add new water r_work=0.1295 r_free=0.1552 | n_water=1002 | time (s): 5.480 (total time: 149.640) Refine new water occ: r_work=0.1250 r_free=0.1515 adp: r_work=0.1251 r_free=0.1515 occ: r_work=0.1247 r_free=0.1511 adp: r_work=0.1247 r_free=0.1512 occ: r_work=0.1244 r_free=0.1509 adp: r_work=0.1243 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1509 r_work=0.1243 r_free=0.1509 | n_water=1002 | time (s): 356.110 (total time: 505.750) Filter (q & B) r_work=0.1248 r_free=0.1513 | n_water=872 | time (s): 4.900 (total time: 510.650) Filter (dist only) r_work=0.1249 r_free=0.1513 | n_water=871 | time (s): 110.860 (total time: 621.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.640720 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.477422 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1239 0.1437 0.0198 0.036 1.1 6.6 0.0 0.0 0 0.820 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.37 1.98 1.944 14.605 16.477 3.940 12.34 13.94 1.60 2.280 14.497 16.477 3.897 Individual atomic B min max mean iso aniso Overall: 5.54 67.77 15.23 1.06 504 3271 Protein: 5.54 36.37 10.75 1.06 0 2902 Water: 6.71 67.77 30.14 N/A 504 367 Other: 13.93 28.12 21.03 N/A 0 2 Chain A: 5.56 56.25 12.76 N/A 0 1624 Chain B: 5.54 67.77 12.52 N/A 0 1647 Chain S: 13.53 61.81 32.04 N/A 504 0 Histogram: Values Number of atoms 5.54 - 11.77 2138 11.77 - 17.99 677 17.99 - 24.21 294 24.21 - 30.43 239 30.43 - 36.66 177 36.66 - 42.88 149 42.88 - 49.10 69 49.10 - 55.33 22 55.33 - 61.55 8 61.55 - 67.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1394 r_work=0.1235 r_free=0.1395 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1395 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1384 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890995 | | target function (ml) not normalized (work): 728767.719910 | | target function (ml) not normalized (free): 15223.425634 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1383 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1447 0.1446 0.1486 n_refl.: 191137 remove outliers: r(all,work,free)=0.1447 0.1446 0.1486 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1440 0.1482 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1376 n_refl.: 191137 remove outliers: r(all,work,free)=0.1228 0.1225 0.1376 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3758 398.008 361.758 0.427 0.946 0.246 13.296-10.522 99.01 99 1 0.2444 528.187 506.938 0.710 0.948 0.219 10.503-8.327 97.80 175 3 0.1908 554.286 560.343 0.882 0.948 0.178 8.318-6.595 100.00 360 8 0.2095 414.736 410.396 0.902 0.947 0.140 6.588-5.215 100.00 711 7 0.1810 381.101 370.692 0.888 0.947 0.140 5.214-4.128 98.38 1367 28 0.1164 557.435 552.025 0.971 0.947 0.060 4.126-3.266 94.74 2603 46 0.1097 508.132 501.340 1.033 0.948 0.009 3.266-2.585 99.86 5447 97 0.1083 342.774 339.151 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0969 258.603 255.692 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0976 153.054 151.395 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.481 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.313 1.040 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1100 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1376 | n_water=871 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1225 r_free=0.1377 | n_water=870 | time (s): 119.560 (total time: 122.010) Filter (q & B) r_work=0.1226 r_free=0.1374 | n_water=859 | time (s): 4.220 (total time: 126.230) Compute maps r_work=0.1226 r_free=0.1374 | n_water=859 | time (s): 2.100 (total time: 128.330) Filter (map) r_work=0.1248 r_free=0.1385 | n_water=726 | time (s): 4.880 (total time: 133.210) Find peaks r_work=0.1248 r_free=0.1385 | n_water=726 | time (s): 0.890 (total time: 134.100) Add new water r_work=0.1262 r_free=0.1399 | n_water=981 | time (s): 5.420 (total time: 139.520) Refine new water occ: r_work=0.1215 r_free=0.1360 adp: r_work=0.1207 r_free=0.1356 occ: r_work=0.1204 r_free=0.1355 adp: r_work=0.1204 r_free=0.1355 occ: r_work=0.1204 r_free=0.1355 adp: r_work=0.1204 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1355 r_work=0.1204 r_free=0.1355 | n_water=981 | time (s): 227.610 (total time: 367.130) Filter (q & B) r_work=0.1209 r_free=0.1365 | n_water=866 | time (s): 4.520 (total time: 371.650) Filter (dist only) r_work=0.1210 r_free=0.1364 | n_water=865 | time (s): 109.890 (total time: 481.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.477463 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.865119 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 0.1209 0.1368 0.0159 0.036 1.1 5.8 0.0 0.0 0 0.739 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 13.68 1.59 1.835 14.140 15.865 3.875 12.01 13.63 1.62 1.936 14.111 15.865 3.866 Individual atomic B min max mean iso aniso Overall: 5.51 67.30 14.86 1.01 498 3271 Protein: 5.51 33.33 10.68 1.01 0 2902 Water: 5.98 67.30 28.88 N/A 498 367 Other: 13.97 27.33 20.65 N/A 0 2 Chain A: 5.56 55.12 12.63 N/A 0 1624 Chain B: 5.51 67.30 12.44 N/A 0 1647 Chain S: 5.98 60.95 30.14 N/A 498 0 Histogram: Values Number of atoms 5.51 - 11.69 2105 11.69 - 17.87 735 17.87 - 24.05 330 24.05 - 30.23 228 30.23 - 36.41 147 36.41 - 42.59 134 42.59 - 48.76 63 48.76 - 54.94 19 54.94 - 61.12 7 61.12 - 67.30 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1363 r_work=0.1201 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864446 | | target function (ml) not normalized (work): 723783.627928 | | target function (ml) not normalized (free): 15133.849818 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1199 0.1362 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1429 0.1429 0.1470 n_refl.: 191134 remove outliers: r(all,work,free)=0.1429 0.1429 0.1470 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1421 0.1421 0.1465 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1360 n_refl.: 191134 remove outliers: r(all,work,free)=0.1201 0.1198 0.1360 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3830 361.352 319.033 0.406 0.946 0.239 13.296-10.522 98.02 98 1 0.2492 480.720 453.639 0.690 0.947 0.190 10.503-8.327 97.80 175 3 0.2110 502.117 497.594 0.861 0.947 0.167 8.318-6.595 100.00 360 8 0.2228 375.702 369.686 0.895 0.947 0.123 6.588-5.215 100.00 711 7 0.1941 345.232 334.867 0.883 0.947 0.100 5.214-4.128 98.38 1367 28 0.1206 504.970 499.593 0.972 0.948 0.060 4.126-3.266 94.74 2603 46 0.1115 460.307 454.116 1.035 0.948 0.000 3.266-2.585 99.86 5447 97 0.1080 310.512 307.320 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0936 234.264 231.814 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0915 138.649 137.368 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0989 74.641 73.925 1.054 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.041 38.377 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1268 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1360 | n_water=865 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1198 r_free=0.1360 | n_water=865 | time (s): 106.420 (total time: 109.430) Filter (q & B) r_work=0.1198 r_free=0.1359 | n_water=856 | time (s): 5.880 (total time: 115.310) Compute maps r_work=0.1198 r_free=0.1359 | n_water=856 | time (s): 2.140 (total time: 117.450) Filter (map) r_work=0.1217 r_free=0.1354 | n_water=741 | time (s): 4.340 (total time: 121.790) Find peaks r_work=0.1217 r_free=0.1354 | n_water=741 | time (s): 0.810 (total time: 122.600) Add new water r_work=0.1228 r_free=0.1364 | n_water=956 | time (s): 5.010 (total time: 127.610) Refine new water occ: r_work=0.1194 r_free=0.1341 adp: r_work=0.1194 r_free=0.1340 occ: r_work=0.1192 r_free=0.1341 adp: r_work=0.1192 r_free=0.1340 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1340 r_work=0.1190 r_free=0.1340 | n_water=956 | time (s): 232.760 (total time: 360.370) Filter (q & B) r_work=0.1193 r_free=0.1346 | n_water=888 | time (s): 4.080 (total time: 364.450) Filter (dist only) r_work=0.1193 r_free=0.1345 | n_water=887 | time (s): 117.530 (total time: 481.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.583552 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.945292 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1351 0.0157 0.037 1.1 5.6 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.51 1.57 1.797 14.148 14.945 3.763 11.99 13.55 1.56 1.852 14.124 14.945 3.761 Individual atomic B min max mean iso aniso Overall: 5.61 67.04 14.97 0.96 520 3271 Protein: 5.61 32.31 10.61 0.96 0 2902 Water: 6.09 67.04 29.20 N/A 520 367 Other: 13.79 26.30 20.04 N/A 0 2 Chain A: 5.61 54.48 12.55 N/A 0 1624 Chain B: 5.61 67.04 12.36 N/A 0 1647 Chain S: 6.09 60.94 30.79 N/A 520 0 Histogram: Values Number of atoms 5.61 - 11.75 2151 11.75 - 17.89 711 17.89 - 24.04 308 24.04 - 30.18 223 30.18 - 36.32 162 36.32 - 42.47 145 42.47 - 48.61 65 48.61 - 54.75 19 54.75 - 60.90 5 60.90 - 67.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1355 r_work=0.1199 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1356 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1362 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760820 | | target function (ml) not normalized (work): 704367.704312 | | target function (ml) not normalized (free): 14748.996762 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1362 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1489 n_refl.: 191132 remove outliers: r(all,work,free)=0.1407 0.1405 0.1489 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1399 0.1397 0.1484 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191132 remove outliers: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3823 361.352 321.945 0.408 0.950 0.241 13.296-10.522 96.04 96 1 0.2395 480.632 449.520 0.696 0.952 0.201 10.503-8.327 97.80 175 3 0.2086 502.117 497.984 0.857 0.952 0.180 8.318-6.595 100.00 360 8 0.2182 375.702 370.744 0.888 0.952 0.105 6.588-5.215 100.00 711 7 0.1917 345.232 335.205 0.878 0.952 0.074 5.214-4.128 98.38 1367 28 0.1215 504.970 499.972 0.967 0.952 0.029 4.126-3.266 94.74 2603 46 0.1126 460.307 453.768 1.030 0.953 0.000 3.266-2.585 99.86 5447 97 0.1098 310.512 307.305 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0943 234.264 231.800 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0914 138.649 137.357 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0977 74.641 73.932 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.041 38.375 1.039 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1345 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1361 | n_water=887 | time (s): 3.460 (total time: 3.460) Filter (dist) r_work=0.1196 r_free=0.1362 | n_water=886 | time (s): 110.960 (total time: 114.420) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=875 | time (s): 4.240 (total time: 118.660) Compute maps r_work=0.1196 r_free=0.1362 | n_water=875 | time (s): 1.760 (total time: 120.420) Filter (map) r_work=0.1219 r_free=0.1357 | n_water=756 | time (s): 5.730 (total time: 126.150) Find peaks r_work=0.1219 r_free=0.1357 | n_water=756 | time (s): 0.630 (total time: 126.780) Add new water r_work=0.1227 r_free=0.1369 | n_water=974 | time (s): 4.850 (total time: 131.630) Refine new water occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1194 r_free=0.1350 occ: r_work=0.1192 r_free=0.1351 adp: r_work=0.1192 r_free=0.1351 occ: r_work=0.1191 r_free=0.1353 adp: r_work=0.1190 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1353 r_work=0.1190 r_free=0.1353 | n_water=974 | time (s): 254.810 (total time: 386.440) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=899 | time (s): 4.170 (total time: 390.610) Filter (dist only) r_work=0.1194 r_free=0.1356 | n_water=898 | time (s): 114.150 (total time: 504.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.551493 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.012582 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1355 0.0156 0.038 1.1 5.4 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.55 1.56 1.769 14.052 15.013 3.762 12.01 13.58 1.57 1.918 14.005 15.013 3.759 Individual atomic B min max mean iso aniso Overall: 5.59 65.99 14.83 0.91 532 3270 Protein: 5.59 29.54 10.50 0.91 0 2902 Water: 5.99 65.99 28.83 N/A 532 366 Other: 13.85 23.38 18.61 N/A 0 2 Chain A: 5.61 51.66 12.39 N/A 0 1624 Chain B: 5.59 65.99 12.20 N/A 0 1646 Chain S: 5.99 61.05 30.41 N/A 532 0 Histogram: Values Number of atoms 5.59 - 11.63 2126 11.63 - 17.67 763 17.67 - 23.71 282 23.71 - 29.75 228 29.75 - 35.79 175 35.79 - 41.83 128 41.83 - 47.87 70 47.87 - 53.91 23 53.91 - 59.95 5 59.95 - 65.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1358 r_work=0.1202 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1359 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1364 target_work(ml) = 3.758 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757916 | | target function (ml) not normalized (work): 703816.334436 | | target function (ml) not normalized (free): 14737.717083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1492 n_refl.: 191130 remove outliers: r(all,work,free)=0.1404 0.1403 0.1492 n_refl.: 191130 overall B=-0.24 to atoms: r(all,work,free)=0.1367 0.1365 0.1467 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3909 361.352 320.711 0.404 0.949 0.217 13.296-10.522 96.04 96 1 0.2393 480.632 461.213 0.723 0.951 0.176 10.503-8.327 97.80 175 3 0.2125 502.117 498.281 0.884 0.951 0.157 8.318-6.595 100.00 360 8 0.2196 375.702 370.595 0.912 0.951 0.105 6.588-5.215 100.00 711 7 0.1945 345.232 334.663 0.905 0.951 0.100 5.214-4.128 98.38 1367 28 0.1227 504.970 499.693 0.995 0.951 0.034 4.126-3.266 94.74 2603 46 0.1145 460.307 453.393 1.058 0.952 0.000 3.266-2.585 99.86 5447 97 0.1114 310.512 307.217 1.041 0.952 0.000 2.585-2.046 97.45 10613 204 0.0951 234.264 231.768 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0912 138.649 137.353 1.064 0.953 0.000 1.619-1.281 98.00 42464 925 0.0970 74.641 73.928 1.050 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.041 38.368 1.017 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0522 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1361 | n_water=898 | time (s): 2.760 (total time: 2.760) Filter (dist) r_work=0.1200 r_free=0.1361 | n_water=898 | time (s): 110.400 (total time: 113.160) Filter (q & B) r_work=0.1200 r_free=0.1362 | n_water=890 | time (s): 5.670 (total time: 118.830) Compute maps r_work=0.1200 r_free=0.1362 | n_water=890 | time (s): 2.550 (total time: 121.380) Filter (map) r_work=0.1221 r_free=0.1367 | n_water=776 | time (s): 5.250 (total time: 126.630) Find peaks r_work=0.1221 r_free=0.1367 | n_water=776 | time (s): 0.580 (total time: 127.210) Add new water r_work=0.1230 r_free=0.1373 | n_water=966 | time (s): 3.990 (total time: 131.200) Refine new water occ: r_work=0.1199 r_free=0.1353 adp: r_work=0.1199 r_free=0.1353 occ: r_work=0.1198 r_free=0.1353 adp: r_work=0.1198 r_free=0.1353 occ: r_work=0.1196 r_free=0.1353 adp: r_work=0.1196 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1353 r_work=0.1196 r_free=0.1353 | n_water=966 | time (s): 141.140 (total time: 272.340) Filter (q & B) r_work=0.1199 r_free=0.1355 | n_water=910 | time (s): 5.190 (total time: 277.530) Filter (dist only) r_work=0.1199 r_free=0.1355 | n_water=909 | time (s): 117.200 (total time: 394.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.542054 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.529692 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1361 0.0158 0.039 1.1 6.3 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.61 1.58 1.723 13.732 14.530 3.759 12.04 13.63 1.60 1.766 13.713 14.530 3.758 Individual atomic B min max mean iso aniso Overall: 5.39 64.92 14.60 0.89 543 3270 Protein: 5.39 28.61 10.25 0.89 0 2902 Water: 5.82 64.92 28.49 N/A 543 366 Other: 13.65 22.14 17.89 N/A 0 2 Chain A: 5.44 51.07 12.10 N/A 0 1624 Chain B: 5.39 64.92 11.93 N/A 0 1646 Chain S: 5.82 60.90 30.16 N/A 543 0 Histogram: Values Number of atoms 5.39 - 11.34 2106 11.34 - 17.30 784 17.30 - 23.25 280 23.25 - 29.20 226 29.20 - 35.16 177 35.16 - 41.11 130 41.11 - 47.06 75 47.06 - 53.01 26 53.01 - 58.97 7 58.97 - 64.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1364 r_work=0.1204 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1364 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1365 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757519 | | target function (ml) not normalized (work): 703741.954079 | | target function (ml) not normalized (free): 14742.340179 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1365 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1375 0.1373 0.1477 n_refl.: 191130 remove outliers: r(all,work,free)=0.1375 0.1373 0.1477 n_refl.: 191130 overall B=0.06 to atoms: r(all,work,free)=0.1383 0.1381 0.1482 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1354 n_refl.: 191130 remove outliers: r(all,work,free)=0.1196 0.1193 0.1354 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 93.07 91 3 0.3998 361.352 318.721 0.414 0.907 0.203 13.296-10.522 96.04 96 1 0.2369 480.632 460.936 0.754 0.909 0.154 10.503-8.327 97.80 175 3 0.2195 502.117 495.587 0.930 0.909 0.130 8.315-6.595 100.00 359 8 0.2163 374.755 370.290 0.959 0.909 0.099 6.588-5.215 100.00 711 7 0.1961 345.232 334.280 0.954 0.909 0.080 5.214-4.128 98.38 1367 28 0.1243 504.970 499.216 1.051 0.910 0.034 4.126-3.266 94.74 2603 46 0.1155 460.307 452.814 1.118 0.911 0.000 3.266-2.585 99.86 5447 97 0.1128 310.512 306.900 1.100 0.912 0.000 2.585-2.046 97.45 10613 204 0.0956 234.264 231.639 1.108 0.913 0.000 2.046-1.619 99.39 21536 464 0.0911 138.649 137.261 1.126 0.916 0.000 1.619-1.281 98.00 42464 925 0.0948 74.641 73.968 1.113 0.919 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.041 38.346 1.077 0.926 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0603 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1354 | n_water=909 | time (s): 3.380 (total time: 3.380) Filter (dist) r_work=0.1193 r_free=0.1355 | n_water=908 | time (s): 112.110 (total time: 115.490) Filter (q & B) r_work=0.1193 r_free=0.1355 | n_water=897 | time (s): 5.070 (total time: 120.560) Compute maps r_work=0.1193 r_free=0.1355 | n_water=897 | time (s): 1.790 (total time: 122.350) Filter (map) r_work=0.1218 r_free=0.1365 | n_water=767 | time (s): 4.270 (total time: 126.620) Find peaks r_work=0.1218 r_free=0.1365 | n_water=767 | time (s): 0.620 (total time: 127.240) Add new water r_work=0.1225 r_free=0.1377 | n_water=971 | time (s): 5.320 (total time: 132.560) Refine new water occ: r_work=0.1192 r_free=0.1350 adp: r_work=0.1192 r_free=0.1350 occ: r_work=0.1190 r_free=0.1349 adp: r_work=0.1190 r_free=0.1349 occ: r_work=0.1188 r_free=0.1348 adp: r_work=0.1188 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1348 r_work=0.1188 r_free=0.1348 | n_water=971 | time (s): 180.460 (total time: 313.020) Filter (q & B) r_work=0.1192 r_free=0.1351 | n_water=906 | time (s): 5.440 (total time: 318.460) Filter (dist only) r_work=0.1192 r_free=0.1350 | n_water=905 | time (s): 115.490 (total time: 433.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.477858 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.257827 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 0.1355 0.0160 0.039 1.1 5.8 0.0 0.3 0 0.739 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.55 1.60 1.679 13.691 14.258 3.756 11.97 13.59 1.62 1.705 13.681 14.258 3.755 Individual atomic B min max mean iso aniso Overall: 5.50 64.09 14.55 0.87 539 3270 Protein: 5.50 28.19 10.31 0.87 0 2902 Water: 5.84 64.09 28.15 N/A 539 366 Other: 13.72 22.09 17.90 N/A 0 2 Chain A: 5.58 50.79 12.13 N/A 0 1624 Chain B: 5.50 64.09 11.97 N/A 0 1646 Chain S: 5.84 61.03 29.75 N/A 539 0 Histogram: Values Number of atoms 5.50 - 11.36 2078 11.36 - 17.22 812 17.22 - 23.08 283 23.08 - 28.94 229 28.94 - 34.80 172 34.80 - 40.66 120 40.66 - 46.51 78 46.51 - 52.37 28 52.37 - 58.23 6 58.23 - 64.09 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1359 r_work=0.1197 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1359 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.755 | | 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= 0.1196 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754880 | | target function (ml) not normalized (work): 703244.034444 | | target function (ml) not normalized (free): 14733.086974 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1394 0.1392 0.1493 n_refl.: 191129 remove outliers: r(all,work,free)=0.1394 0.1392 0.1493 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1396 0.1394 0.1495 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1358 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1358 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 92.08 90 3 0.3754 361.048 308.265 0.387 0.974 0.215 13.296-10.522 96.04 96 1 0.2347 480.632 463.123 0.699 0.975 0.155 10.503-8.327 97.80 175 3 0.2231 502.117 494.748 0.862 0.976 0.127 8.315-6.595 100.00 359 8 0.2178 374.755 369.552 0.890 0.976 0.096 6.588-5.215 100.00 711 7 0.1970 345.232 334.526 0.887 0.976 0.077 5.214-4.128 98.38 1367 28 0.1257 504.970 499.178 0.977 0.977 0.029 4.126-3.266 94.74 2603 46 0.1169 460.307 452.721 1.041 0.978 0.000 3.266-2.585 99.86 5447 97 0.1131 310.512 306.947 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0959 234.264 231.705 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0912 138.649 137.295 1.049 0.985 0.000 1.619-1.281 98.00 42464 925 0.0945 74.641 73.997 1.039 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.041 38.341 1.007 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0202 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1358 | n_water=905 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1195 r_free=0.1358 | n_water=904 | time (s): 129.060 (total time: 131.500) Filter (q & B) r_work=0.1196 r_free=0.1357 | n_water=891 | time (s): 4.990 (total time: 136.490) Compute maps r_work=0.1196 r_free=0.1357 | n_water=891 | time (s): 2.280 (total time: 138.770) Filter (map) r_work=0.1217 r_free=0.1358 | n_water=776 | time (s): 5.020 (total time: 143.790) Find peaks r_work=0.1217 r_free=0.1358 | n_water=776 | time (s): 0.570 (total time: 144.360) Add new water r_work=0.1223 r_free=0.1368 | n_water=966 | time (s): 3.910 (total time: 148.270) Refine new water occ: r_work=0.1192 r_free=0.1352 adp: r_work=0.1192 r_free=0.1351 occ: r_work=0.1190 r_free=0.1352 adp: r_work=0.1190 r_free=0.1351 occ: r_work=0.1189 r_free=0.1352 adp: r_work=0.1189 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1352 r_work=0.1189 r_free=0.1352 | n_water=966 | time (s): 194.350 (total time: 342.620) Filter (q & B) r_work=0.1192 r_free=0.1356 | n_water=909 | time (s): 4.410 (total time: 347.030) Filter (dist only) r_work=0.1193 r_free=0.1355 | n_water=907 | time (s): 113.420 (total time: 460.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.506358 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.955509 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 0.1363 0.0167 0.039 1.1 5.3 0.0 0.3 0 0.753 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.63 1.67 1.679 13.721 14.956 3.756 11.95 13.65 1.70 1.688 13.716 14.956 3.753 Individual atomic B min max mean iso aniso Overall: 5.57 63.09 14.60 0.88 541 3270 Protein: 5.57 28.19 10.34 0.88 0 2902 Water: 6.00 63.09 28.23 N/A 541 366 Other: 13.77 22.06 17.92 N/A 0 2 Chain A: 5.62 50.38 12.12 N/A 0 1624 Chain B: 5.57 63.09 11.97 N/A 0 1646 Chain S: 6.00 61.11 30.05 N/A 541 0 Histogram: Values Number of atoms 5.57 - 11.32 2061 11.32 - 17.08 826 17.08 - 22.83 280 22.83 - 28.58 211 28.58 - 34.33 186 34.33 - 40.08 124 40.08 - 45.84 78 45.84 - 51.59 35 51.59 - 57.34 6 57.34 - 63.09 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1365 r_work=0.1195 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1365 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1365 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752993 | | target function (ml) not normalized (work): 702886.764834 | | target function (ml) not normalized (free): 14735.933484 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1365 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1396 0.1394 0.1504 n_refl.: 191128 remove outliers: r(all,work,free)=0.1396 0.1394 0.1504 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1395 0.1393 0.1503 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1363 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1363 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 92.08 90 3 0.3742 361.048 327.601 0.402 0.994 0.215 13.296-10.522 96.04 96 1 0.2389 480.632 461.943 0.686 0.996 0.159 10.503-8.327 97.80 175 3 0.2220 502.117 495.418 0.843 0.996 0.127 8.315-6.595 100.00 359 8 0.2186 374.755 369.070 0.871 0.996 0.099 6.588-5.215 100.00 711 7 0.1962 345.232 335.002 0.867 0.997 0.078 5.214-4.128 98.38 1367 28 0.1261 504.970 499.172 0.957 0.998 0.029 4.126-3.266 94.74 2603 46 0.1178 460.307 452.676 1.020 0.999 0.000 3.266-2.585 99.86 5447 97 0.1136 310.512 306.793 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0958 234.264 231.623 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0909 138.649 137.254 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0939 74.641 73.990 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.041 38.334 0.989 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0110 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1193 r_free=0.1363 After: r_work=0.1193 r_free=0.1363 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1363 | n_water=907 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1193 r_free=0.1363 | n_water=907 | time (s): 121.770 (total time: 124.330) Filter (q & B) r_work=0.1194 r_free=0.1362 | n_water=899 | time (s): 4.970 (total time: 129.300) Compute maps r_work=0.1194 r_free=0.1362 | n_water=899 | time (s): 2.330 (total time: 131.630) Filter (map) r_work=0.1214 r_free=0.1366 | n_water=784 | time (s): 5.060 (total time: 136.690) Find peaks r_work=0.1214 r_free=0.1366 | n_water=784 | time (s): 0.720 (total time: 137.410) Add new water r_work=0.1221 r_free=0.1377 | n_water=987 | time (s): 4.490 (total time: 141.900) Refine new water occ: r_work=0.1191 r_free=0.1354 adp: r_work=0.1191 r_free=0.1354 occ: r_work=0.1189 r_free=0.1354 adp: r_work=0.1189 r_free=0.1354 occ: r_work=0.1188 r_free=0.1353 adp: r_work=0.1188 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1354 r_work=0.1188 r_free=0.1354 | n_water=987 | time (s): 265.020 (total time: 406.920) Filter (q & B) r_work=0.1191 r_free=0.1361 | n_water=913 | time (s): 4.500 (total time: 411.420) Filter (dist only) r_work=0.1192 r_free=0.1360 | n_water=912 | time (s): 119.630 (total time: 531.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.500898 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.829353 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 0.1364 0.0169 0.040 1.2 7.3 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.64 1.69 1.681 13.738 14.829 3.756 11.95 13.68 1.72 1.674 13.739 14.829 3.755 Individual atomic B min max mean iso aniso Overall: 5.56 62.88 14.63 0.87 546 3270 Protein: 5.56 28.10 10.36 0.87 0 2902 Water: 6.01 62.88 28.24 N/A 546 366 Other: 13.81 22.08 17.94 N/A 0 2 Chain A: 5.62 50.30 12.12 N/A 0 1624 Chain B: 5.56 62.88 11.97 N/A 0 1646 Chain S: 6.01 61.10 30.13 N/A 546 0 Histogram: Values Number of atoms 5.56 - 11.29 2048 11.29 - 17.02 834 17.02 - 22.75 284 22.75 - 28.49 220 28.49 - 34.22 178 34.22 - 39.95 124 39.95 - 45.68 81 45.68 - 51.42 36 51.42 - 57.15 7 57.15 - 62.88 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1368 r_work=0.1195 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1368 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1367 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754951 | | target function (ml) not normalized (work): 703253.479712 | | target function (ml) not normalized (free): 14737.054102 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1371 0.1528 5.6975 5.7887| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1312 5.0874 5.1705| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1187 4.6551 4.7492| | 4: 2.04 - 1.85 1.00 7170 155 0.0905 0.1054 4.3994 4.5752| | 5: 1.85 - 1.72 0.99 7113 159 0.0937 0.1025 4.1586 4.2699| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1110 3.9507 4.0955| | 7: 1.62 - 1.54 0.99 7104 148 0.0888 0.0959 3.7985 3.9104| | 8: 1.54 - 1.47 0.96 6798 152 0.0885 0.1336 3.6985 3.9138| | 9: 1.47 - 1.41 0.98 6938 155 0.0922 0.1150 3.6212 3.766| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1195 3.5566 3.6846| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1142 3.4837 3.5846| | 12: 1.32 - 1.28 0.98 6975 149 0.1032 0.1126 3.4574 3.581| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1247 3.4354 3.5642| | 14: 1.25 - 1.22 0.98 7015 112 0.1103 0.1584 3.4304 3.6726| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1248 3.4458 3.483| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1537 3.4632 3.6512| | 17: 1.17 - 1.14 0.98 6940 135 0.1296 0.1224 3.4318 3.4423| | 18: 1.14 - 1.12 0.98 6875 142 0.1381 0.1707 3.4378 3.5338| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1757 3.4192 3.5964| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1576 3.4096 3.4318| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2134 3.418 3.5053| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1940 3.4131 3.4141| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2021 3.4334 3.4878| | 24: 1.03 - 1.02 0.96 6784 133 0.2329 0.2255 3.4354 3.5112| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2510 3.4493 3.5209| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2846 3.4156 3.4238| | 27: 0.99 - 0.98 0.94 6647 131 0.3039 0.2804 3.4686 3.396| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.16 1.00 0.94 11783.34| | 2: 2.94 - 2.33 7339 128 0.92 13.09 0.99 0.95 5310.26| | 3: 2.33 - 2.04 6939 150 0.96 7.64 1.01 0.95 1699.61| | 4: 2.04 - 1.85 7170 155 0.96 7.80 1.00 0.95 1028.45| | 5: 1.85 - 1.72 7113 159 0.96 8.30 1.00 0.96 657.56| | 6: 1.72 - 1.62 7102 142 0.96 8.17 1.00 0.96 454.51| | 7: 1.62 - 1.54 7104 148 0.96 8.15 1.01 0.97 338.88| | 8: 1.54 - 1.47 6798 152 0.96 8.29 1.01 0.97 281.58| | 9: 1.47 - 1.41 6938 155 0.96 8.55 1.00 0.98 233.59| | 10: 1.41 - 1.36 7022 150 0.96 9.02 1.00 0.97 205.47| | 11: 1.36 - 1.32 6997 151 0.96 8.96 0.99 0.96 176.04| | 12: 1.32 - 1.28 6975 149 0.96 8.99 0.98 0.95 160.75| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.01 0.96 157.51| | 14: 1.25 - 1.22 7015 112 0.95 10.63 1.01 0.96 161.79| | 15: 1.22 - 1.19 6956 137 0.95 11.15 1.01 0.98 164.95| | 16: 1.19 - 1.17 6604 132 0.95 11.36 1.01 0.96 158.84| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.96 153.19| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.95 147.47| | 19: 1.12 - 1.10 6948 106 0.93 14.13 1.00 0.94 151.00| | 20: 1.10 - 1.08 6884 147 0.92 15.21 1.00 0.94 150.14| | 21: 1.08 - 1.07 6852 152 0.91 16.63 1.00 0.93 153.30| | 22: 1.07 - 1.05 6836 135 0.89 18.30 0.99 0.93 155.13| | 23: 1.05 - 1.03 6827 159 0.87 20.50 0.99 0.92 164.91| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.93 179.08| | 25: 1.02 - 1.01 6552 130 0.83 25.10 0.98 0.90 181.76| | 26: 1.01 - 0.99 6767 158 0.81 26.57 0.98 0.88 176.28| | 27: 0.99 - 0.98 6647 131 0.82 26.26 0.99 0.87 160.89| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.47 max = 11783.34 mean = 957.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.33| |phase err.(test): min = 0.00 max = 89.75 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1367 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1522 n_refl.: 191128 remove outliers: r(all,work,free)=0.1404 0.1402 0.1522 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1395 0.1393 0.1515 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1365 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1194 0.1365 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 92.08 90 3 0.3647 361.048 329.210 0.400 0.973 0.213 13.296-10.522 96.04 96 1 0.2394 480.632 461.631 0.680 0.975 0.147 10.503-8.327 97.80 175 3 0.2214 502.117 495.501 0.840 0.975 0.115 8.315-6.595 100.00 359 8 0.2186 374.755 369.131 0.867 0.975 0.095 6.588-5.215 100.00 711 7 0.1969 345.232 334.831 0.865 0.976 0.080 5.214-4.128 98.38 1367 28 0.1264 504.970 499.158 0.955 0.977 0.034 4.126-3.266 94.74 2603 46 0.1172 460.307 452.718 1.018 0.978 0.000 3.266-2.585 99.86 5447 97 0.1130 310.512 306.883 1.001 0.979 0.000 2.585-2.046 97.45 10613 204 0.0961 234.264 231.626 1.007 0.982 0.000 2.046-1.619 99.39 21536 464 0.0914 138.649 137.253 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0942 74.641 73.988 1.012 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.041 38.324 0.979 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0124 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2037 0.1978 0.082 5.141 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1924 0.082 5.141 5.2 78.0 14.6 805 0.000 1_settarget: 0.1797 0.1924 0.082 5.141 5.2 78.0 14.6 805 0.000 1_nqh: 0.1797 0.1924 0.082 5.141 5.2 78.0 14.6 805 0.000 1_weight: 0.1797 0.1924 0.082 5.141 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1500 0.038 1.159 5.2 78.0 14.6 805 0.157 1_adp: 0.1296 0.1567 0.038 1.159 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1295 0.1563 0.038 1.159 5.2 73.0 15.0 805 0.157 1_occ: 0.1280 0.1550 0.038 1.159 5.2 73.0 15.0 805 0.157 2_bss: 0.1272 0.1538 0.038 1.159 5.4 73.2 15.2 805 0.157 2_settarget: 0.1272 0.1538 0.038 1.159 5.4 73.2 15.2 805 0.157 2_updatecdl: 0.1272 0.1538 0.038 1.169 5.4 73.2 15.2 805 0.157 2_nqh: 0.1272 0.1538 0.038 1.169 5.4 73.2 15.2 805 0.157 2_sol: 0.1269 0.1506 0.038 1.169 5.4 73.2 16.3 892 n/a 2_weight: 0.1269 0.1506 0.038 1.169 5.4 73.2 16.3 892 n/a 2_xyzrec: 0.1251 0.1518 0.042 1.139 5.4 73.2 16.3 892 n/a 2_adp: 0.1233 0.1509 0.042 1.139 5.5 68.3 16.3 892 n/a 2_regHadp: 0.1233 0.1510 0.042 1.139 5.5 68.3 16.3 892 n/a 2_occ: 0.1227 0.1510 0.042 1.139 5.5 68.3 16.3 892 n/a 3_bss: 0.1234 0.1517 0.042 1.139 5.4 68.2 16.3 892 n/a 3_settarget: 0.1234 0.1517 0.042 1.139 5.4 68.2 16.3 892 n/a 3_updatecdl: 0.1234 0.1517 0.042 1.145 5.4 68.2 16.3 892 n/a 3_nqh: 0.1234 0.1517 0.042 1.145 5.4 68.2 16.3 892 n/a 3_sol: 0.1249 0.1513 0.042 1.145 5.4 68.2 15.4 871 n/a 3_weight: 0.1249 0.1513 0.042 1.145 5.4 68.2 15.4 871 n/a 3_xyzrec: 0.1239 0.1437 0.036 1.100 5.4 68.2 15.4 871 n/a 3_adp: 0.1234 0.1394 0.036 1.100 5.5 67.8 15.2 871 n/a 3_regHadp: 0.1235 0.1395 0.036 1.100 5.5 67.8 15.2 871 n/a 3_occ: 0.1229 0.1384 0.036 1.100 5.5 67.8 15.2 871 n/a 4_bss: 0.1225 0.1376 0.036 1.100 5.5 67.7 15.2 871 n/a 4_settarget: 0.1225 0.1376 0.036 1.100 5.5 67.7 15.2 871 n/a 4_updatecdl: 0.1225 0.1376 0.036 1.100 5.5 67.7 15.2 871 n/a 4_nqh: 0.1225 0.1376 0.036 1.100 5.5 67.7 15.2 871 n/a 4_sol: 0.1210 0.1364 0.036 1.100 5.5 67.7 14.9 865 n/a 4_weight: 0.1210 0.1364 0.036 1.100 5.5 67.7 14.9 865 n/a 4_xyzrec: 0.1209 0.1368 0.036 1.121 5.5 67.7 14.9 865 n/a 4_adp: 0.1201 0.1363 0.036 1.121 5.5 67.3 14.9 865 n/a 4_regHadp: 0.1201 0.1363 0.036 1.121 5.5 67.3 14.9 865 n/a 4_occ: 0.1199 0.1362 0.036 1.121 5.5 67.3 14.9 865 n/a 5_bss: 0.1198 0.1360 0.036 1.121 5.5 67.3 14.8 865 n/a 5_settarget: 0.1198 0.1360 0.036 1.121 5.5 67.3 14.8 865 n/a 5_updatecdl: 0.1198 0.1360 0.036 1.121 5.5 67.3 14.8 865 n/a 5_nqh: 0.1198 0.1360 0.036 1.121 5.5 67.3 14.8 865 n/a 5_sol: 0.1193 0.1345 0.036 1.121 5.5 67.3 15.0 887 n/a 5_weight: 0.1193 0.1345 0.036 1.121 5.5 67.3 15.0 887 n/a 5_xyzrec: 0.1195 0.1351 0.037 1.131 5.5 67.3 15.0 887 n/a 5_adp: 0.1199 0.1355 0.037 1.131 5.6 67.0 15.0 887 n/a 5_regHadp: 0.1199 0.1356 0.037 1.131 5.6 67.0 15.0 887 n/a 5_occ: 0.1197 0.1362 0.037 1.131 5.6 67.0 15.0 887 n/a 6_bss: 0.1196 0.1361 0.037 1.131 5.6 67.0 14.9 887 n/a 6_settarget: 0.1196 0.1361 0.037 1.131 5.6 67.0 14.9 887 n/a 6_updatecdl: 0.1196 0.1361 0.037 1.131 5.6 67.0 14.9 887 n/a 6_nqh: 0.1196 0.1361 0.037 1.131 5.6 67.0 14.9 887 n/a 6_sol: 0.1194 0.1356 0.037 1.131 5.6 67.0 14.9 898 n/a 6_weight: 0.1194 0.1356 0.037 1.131 5.6 67.0 14.9 898 n/a 6_xyzrec: 0.1199 0.1355 0.038 1.128 5.6 67.0 14.9 898 n/a 6_adp: 0.1201 0.1358 0.038 1.128 5.6 66.0 14.8 898 n/a 6_regHadp: 0.1202 0.1359 0.038 1.128 5.6 66.0 14.8 898 n/a 6_occ: 0.1199 0.1364 0.038 1.128 5.6 66.0 14.8 898 n/a 7_bss: 0.1200 0.1361 0.038 1.128 5.4 65.8 14.6 898 n/a 7_settarget: 0.1200 0.1361 0.038 1.128 5.4 65.8 14.6 898 n/a 7_updatecdl: 0.1200 0.1361 0.038 1.128 5.4 65.8 14.6 898 n/a 7_nqh: 0.1200 0.1361 0.038 1.128 5.4 65.8 14.6 898 n/a 7_sol: 0.1199 0.1355 0.038 1.128 5.4 65.8 14.6 909 n/a 7_weight: 0.1199 0.1355 0.038 1.128 5.4 65.8 14.6 909 n/a 7_xyzrec: 0.1203 0.1361 0.039 1.121 5.4 65.8 14.6 909 n/a 7_adp: 0.1204 0.1364 0.039 1.121 5.4 64.9 14.6 909 n/a 7_regHadp: 0.1204 0.1364 0.039 1.121 5.4 64.9 14.6 909 n/a 7_occ: 0.1203 0.1365 0.039 1.121 5.4 64.9 14.6 909 n/a 8_bss: 0.1193 0.1354 0.039 1.121 5.5 65.0 14.7 909 n/a 8_settarget: 0.1193 0.1354 0.039 1.121 5.5 65.0 14.7 909 n/a 8_updatecdl: 0.1193 0.1354 0.039 1.121 5.5 65.0 14.7 909 n/a 8_nqh: 0.1193 0.1354 0.039 1.121 5.5 65.0 14.7 909 n/a 8_sol: 0.1192 0.1350 0.039 1.121 5.5 65.0 14.6 905 n/a 8_weight: 0.1192 0.1350 0.039 1.121 5.5 65.0 14.6 905 n/a 8_xyzrec: 0.1195 0.1355 0.039 1.110 5.5 65.0 14.6 905 n/a 8_adp: 0.1197 0.1359 0.039 1.110 5.5 64.1 14.6 905 n/a 8_regHadp: 0.1197 0.1359 0.039 1.110 5.5 64.1 14.6 905 n/a 8_occ: 0.1196 0.1360 0.039 1.110 5.5 64.1 14.6 905 n/a 9_bss: 0.1194 0.1358 0.039 1.110 5.5 64.1 14.6 905 n/a 9_settarget: 0.1194 0.1358 0.039 1.110 5.5 64.1 14.6 905 n/a 9_updatecdl: 0.1194 0.1358 0.039 1.110 5.5 64.1 14.6 905 n/a 9_nqh: 0.1194 0.1358 0.039 1.110 5.5 64.1 14.6 905 n/a 9_sol: 0.1193 0.1355 0.039 1.110 5.5 64.1 14.6 907 n/a 9_weight: 0.1193 0.1355 0.039 1.110 5.5 64.1 14.6 907 n/a 9_xyzrec: 0.1196 0.1363 0.039 1.108 5.5 64.1 14.6 907 n/a 9_adp: 0.1195 0.1365 0.039 1.108 5.6 63.1 14.6 907 n/a 9_regHadp: 0.1195 0.1365 0.039 1.108 5.6 63.1 14.6 907 n/a 9_occ: 0.1194 0.1365 0.039 1.108 5.6 63.1 14.6 907 n/a 10_bss: 0.1193 0.1363 0.039 1.108 5.6 63.1 14.6 907 n/a 10_settarget: 0.1193 0.1363 0.039 1.108 5.6 63.1 14.6 907 n/a 10_updatecdl: 0.1193 0.1363 0.039 1.109 5.6 63.1 14.6 907 n/a 10_setrh: 0.1193 0.1363 0.039 1.109 5.6 63.1 14.6 907 n/a 10_nqh: 0.1193 0.1363 0.039 1.109 5.6 63.1 14.6 907 n/a 10_sol: 0.1192 0.1360 0.039 1.109 5.6 63.1 14.6 912 n/a 10_weight: 0.1192 0.1360 0.039 1.109 5.6 63.1 14.6 912 n/a 10_xyzrec: 0.1195 0.1364 0.040 1.155 5.6 63.1 14.6 912 n/a 10_adp: 0.1195 0.1368 0.040 1.155 5.6 62.9 14.6 912 n/a 10_regHadp: 0.1195 0.1368 0.040 1.155 5.6 62.9 14.6 912 n/a 10_occ: 0.1195 0.1367 0.040 1.155 5.6 62.9 14.6 912 n/a end: 0.1194 0.1365 0.040 1.155 5.5 62.8 14.6 912 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2484050_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2484050_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1400 Refinement macro-cycles (run) : 12066.1000 Write final files (write_after_run_outputs) : 157.5100 Total : 12230.7500 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:08 PST -0800 (1736736068.40 s) Start R-work = 0.1797, R-free = 0.1924 Final R-work = 0.1194, R-free = 0.1365 =============================================================================== Job complete usr+sys time: 12512.75 seconds wall clock time: 209 minutes 35.07 seconds (12575.07 seconds total)