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_5431505.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5431505.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5431505.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 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: 2.06, per 1000 atoms: 0.31 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.762 distance_ideal: 2.720 ideal - model: -0.042 slack: 0.000 delta_slack: -0.042 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: 2.753 distance_ideal: 2.710 ideal - model: -0.043 slack: 0.000 delta_slack: -0.043 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: 1.05 Conformation dependent library (CDL) restraints added in 226.2 milliseconds Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.76 - 0.99: 488 0.99 - 1.23: 2603 1.23 - 1.47: 1537 1.47 - 1.70: 1276 1.70 - 1.94: 30 Bond restraints: 5934 Sorted by residual: bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.448 1.264 0.184 8.80e-03 1.29e+04 4.36e+02 bond pdb=" N TYR A 67 " pdb=" H TYR A 67 " ideal model delta sigma weight residual 0.860 1.275 -0.415 2.00e-02 2.50e+03 4.30e+02 bond pdb=" C LEU A 172 " pdb=" N VAL A 173 " ideal model delta sigma weight residual 1.332 1.159 0.173 8.70e-03 1.32e+04 3.95e+02 bond pdb=" NZ LYS A 142 " pdb=" HZ3 LYS A 142 " ideal model delta sigma weight residual 0.890 1.272 -0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" CA PRO A 128 " pdb=" HA PRO A 128 " ideal model delta sigma weight residual 0.970 1.351 -0.381 2.00e-02 2.50e+03 3.62e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 5399 3.95 - 7.90: 3536 7.90 - 11.85: 1488 11.85 - 15.80: 352 15.80 - 19.74: 35 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 103.52 15.68 9.00e-01 1.23e+00 3.04e+02 angle pdb=" CA GLY B 174 " pdb=" C GLY B 174 " pdb=" O GLY B 174 " ideal model delta sigma weight residual 122.45 133.67 -11.22 7.20e-01 1.93e+00 2.43e+02 angle pdb=" O LEU A 25 " pdb=" C LEU A 25 " pdb=" N VAL A 26 " ideal model delta sigma weight residual 122.12 137.92 -15.80 1.06e+00 8.90e-01 2.22e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 135.56 -14.06 1.00e+00 1.00e+00 1.98e+02 angle pdb=" CD2 TRP A 146 " pdb=" CE2 TRP A 146 " pdb=" CZ2 TRP A 146 " ideal model delta sigma weight residual 122.40 108.37 14.03 1.00e+00 1.00e+00 1.97e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 1871 17.84 - 35.67: 117 35.67 - 53.50: 46 53.50 - 71.34: 13 71.34 - 89.17: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N ILE A 70 " pdb=" CA ILE A 70 " ideal model delta harmonic sigma weight residual 180.00 155.49 24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -155.79 -24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL A 112 " pdb=" C VAL A 112 " pdb=" N LEU A 113 " pdb=" CA LEU A 113 " ideal model delta harmonic sigma weight residual 180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.222: 224 0.222 - 0.445: 153 0.445 - 0.667: 92 0.667 - 0.889: 20 0.889 - 1.111: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.48 -1.11 2.00e-01 2.50e+01 3.08e+01 chirality pdb=" CA MET B 124 " pdb=" N MET B 124 " pdb=" C MET B 124 " pdb=" CB MET B 124 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CA ILE A 76 " pdb=" N ILE A 76 " pdb=" C ILE A 76 " pdb=" CB ILE A 76 " both_signs ideal model delta sigma weight residual False 2.43 1.45 0.98 2.00e-01 2.50e+01 2.42e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.136 2.00e-02 2.50e+03 6.67e-02 1.33e+02 pdb=" CG PHE B 164 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.114 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.061 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.061 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.052 2.00e-02 2.50e+03 5.75e-02 1.32e+02 pdb=" CG TRP B 146 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.138 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.074 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.065 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.031 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.032 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.015 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.070 2.00e-02 2.50e+03 6.36e-02 1.21e+02 pdb=" CG PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.094 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.122 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 26 1.61 - 2.36: 2377 2.36 - 3.10: 22292 3.10 - 3.85: 32962 3.85 - 4.60: 52602 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110259 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.862 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.980 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.992 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.045 2.620 nonbonded pdb="HG22 VAL A 181 " pdb=" O HOH S1566 " model vdw 1.227 2.620 ... (remaining 110254 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_5431505_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= 0.2030 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300025 | | target function (ml) not normalized (work): 805450.549385 | | target function (ml) not normalized (free): 16572.891793 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2139 0.1970 6.6891 6.306| | 2: 2.94 - 2.33 1.00 7339 128 0.1617 0.1658 5.5389 5.6003| | 3: 2.33 - 2.04 0.96 6939 150 0.1633 0.1506 5.14 5.1082| | 4: 2.04 - 1.85 1.00 7170 155 0.1729 0.1673 4.9559 5.0548| | 5: 1.85 - 1.72 0.99 7113 159 0.1910 0.1527 4.7843 4.7013| | 6: 1.72 - 1.62 0.99 7102 142 0.1971 0.1898 4.6519 4.6458| | 7: 1.62 - 1.54 0.99 7104 148 0.2014 0.1798 4.556 4.5998| | 8: 1.54 - 1.47 0.96 6798 152 0.2047 0.2230 4.4775 4.5051| | 9: 1.47 - 1.41 0.98 6938 155 0.2100 0.2299 4.4146 4.5017| | 10: 1.41 - 1.36 0.99 7022 150 0.2087 0.2245 4.3009 4.372| | 11: 1.36 - 1.32 0.99 6997 151 0.2107 0.2013 4.2386 4.2402| | 12: 1.32 - 1.28 0.98 6976 149 0.2075 0.1662 4.1597 4.0976| | 13: 1.28 - 1.25 0.98 6907 166 0.2017 0.2107 4.105 4.2232| | 14: 1.25 - 1.22 0.98 7015 113 0.2073 0.2277 4.0762 4.3033| | 15: 1.22 - 1.19 0.98 6957 137 0.2119 0.2307 4.0712 4.1481| | 16: 1.19 - 1.17 0.93 6604 132 0.2135 0.2507 4.024 4.18| | 17: 1.17 - 1.14 0.98 6941 135 0.2182 0.2032 3.9715 4.0672| | 18: 1.14 - 1.12 0.98 6875 142 0.2202 0.2435 3.9226 3.9385| | 19: 1.12 - 1.10 0.97 6949 106 0.2279 0.2445 3.8792 4.0607| | 20: 1.10 - 1.08 0.97 6884 147 0.2317 0.2209 3.8228 3.8232| | 21: 1.08 - 1.07 0.97 6852 152 0.2441 0.2650 3.7953 3.8056| | 22: 1.07 - 1.05 0.97 6838 135 0.2539 0.2652 3.7471 3.7508| | 23: 1.05 - 1.03 0.97 6829 159 0.2708 0.2454 3.7255 3.7752| | 24: 1.03 - 1.02 0.96 6785 133 0.2870 0.2875 3.705 3.7873| | 25: 1.02 - 1.01 0.93 6552 130 0.3070 0.2889 3.6775 3.7185| | 26: 1.01 - 0.99 0.96 6767 158 0.3174 0.3340 3.6252 3.6309| | 27: 0.99 - 0.98 0.94 6648 131 0.3396 0.3364 3.6336 3.6207| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.47 0.91 0.98 35604.25| | 2: 2.94 - 2.33 7339 128 0.85 21.34 1.09 1.01 15133.94| | 3: 2.33 - 2.04 6939 150 0.93 12.45 1.11 1.05 4069.12| | 4: 2.04 - 1.85 7170 155 0.93 12.94 1.11 1.06 2589.35| | 5: 1.85 - 1.72 7113 159 0.92 14.78 1.11 1.06 1874.05| | 6: 1.72 - 1.62 7102 142 0.91 16.03 1.12 1.07 1502.15| | 7: 1.62 - 1.54 7104 148 0.89 17.28 1.11 1.07 1291.87| | 8: 1.54 - 1.47 6798 152 0.89 18.16 1.11 1.09 1152.06| | 9: 1.47 - 1.41 6938 155 0.88 19.13 1.10 1.09 1023.67| | 10: 1.41 - 1.36 7022 150 0.87 20.20 1.09 1.07 873.72| | 11: 1.36 - 1.32 6997 151 0.87 19.69 1.08 1.04 713.26| | 12: 1.32 - 1.28 6976 149 0.88 18.93 1.08 1.02 588.69| | 13: 1.28 - 1.25 6907 166 0.88 19.31 1.07 1.02 560.88| | 14: 1.25 - 1.22 7015 113 0.86 21.58 1.08 1.03 611.50| | 15: 1.22 - 1.19 6957 137 0.85 22.85 1.07 1.03 638.92| | 16: 1.19 - 1.17 6604 132 0.84 23.05 1.08 1.03 602.91| | 17: 1.17 - 1.14 6941 135 0.84 23.13 1.09 1.03 523.92| | 18: 1.14 - 1.12 6875 142 0.85 22.44 1.08 1.00 441.58| | 19: 1.12 - 1.10 6949 106 0.85 22.86 1.07 1.00 403.39| | 20: 1.10 - 1.08 6884 147 0.85 22.93 1.06 0.97 352.05| | 21: 1.08 - 1.07 6852 152 0.84 23.72 1.06 0.98 335.38| | 22: 1.07 - 1.05 6838 135 0.83 25.14 1.05 0.97 317.83| | 23: 1.05 - 1.03 6829 159 0.81 27.02 1.05 0.98 319.80| | 24: 1.03 - 1.02 6785 133 0.79 28.74 1.04 0.98 321.27| | 25: 1.02 - 1.01 6552 130 0.77 30.35 1.02 0.95 310.22| | 26: 1.01 - 0.99 6767 158 0.75 32.34 1.02 0.92 297.31| | 27: 0.99 - 0.98 6648 131 0.75 32.72 1.04 0.89 279.50| |alpha: min = 0.89 max = 1.09 mean = 1.01| |beta: min = 279.50 max = 35604.25 mean = 2820.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 21.75| |phase err.(test): min = 0.00 max = 89.65 mean = 21.82| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.246 2950 Z= 5.364 Angle : 5.231 19.727 4018 Z= 3.710 Chirality : 0.355 1.111 492 Planarity : 0.031 0.093 512 Dihedral : 12.803 89.169 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 0.65 % Allowed : 4.52 % Favored : 94.84 % Cbeta Deviations : 27.25 % 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: -2.08 (0.38), residues: 386 helix: -2.36 (0.34), residues: 144 sheet: -0.36 (0.55), residues: 86 loop : -0.72 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.018 ARG A 149 TYR 0.121 0.040 TYR A 192 PHE 0.122 0.034 PHE B 164 TRP 0.135 0.031 TRP B 146 HIS 0.067 0.026 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2030 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300025 | | target function (ml) not normalized (work): 805450.549385 | | target function (ml) not normalized (free): 16572.891793 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2028 0.2030 0.1982 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2028 0.2030 0.1982 n_refl.: 191155 remove outliers: r(all,work,free)=0.2029 0.2030 0.1982 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2026 0.2027 0.1981 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1800 0.1798 0.1910 n_refl.: 191145 remove outliers: r(all,work,free)=0.1798 0.1796 0.1910 n_refl.: 191140 ======================== 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 0.4234 400.535 290.861 0.419 0.913 0.293 13.296-10.522 99.01 99 1 0.2511 528.187 518.895 0.783 0.914 0.252 10.503-8.327 99.45 178 3 0.2512 565.118 554.527 0.965 0.914 0.233 8.318-6.595 100.00 360 8 0.2470 414.736 402.353 0.968 0.914 0.200 6.588-5.215 100.00 711 7 0.2270 381.101 365.531 0.949 0.915 0.150 5.214-4.128 98.38 1367 28 0.1471 557.435 548.624 1.066 0.916 0.090 4.126-3.266 94.74 2603 46 0.1374 508.132 498.678 1.131 0.917 0.014 3.266-2.585 99.86 5447 97 0.1435 342.774 337.357 1.109 0.918 0.000 2.585-2.046 97.45 10613 204 0.1391 258.603 254.239 1.109 0.920 0.000 2.046-1.619 99.39 21536 464 0.1599 153.054 150.039 1.122 0.923 0.000 1.619-1.281 98.00 42464 925 0.1923 82.395 80.459 1.101 0.929 0.000 1.281-0.980 96.53 101826 2056 0.2318 44.203 42.024 1.075 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0539 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1796 r_free=0.1910 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 r_work=0.1797 r_free=0.1914 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.313968 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.500764 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 0.1274 0.1505 0.0231 0.039 1.2 10.9 0.0 0.0 0 11.657 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.74 15.05 2.31 1.118 13.091 571.501 0.019 13.05 15.79 2.74 1.264 13.355 571.501 0.018 Individual atomic B min max mean iso aniso Overall: 5.19 73.02 15.06 1.40 435 3274 Protein: 5.19 40.30 11.03 1.40 0 2902 Water: 6.37 73.02 29.54 N/A 435 370 Other: 16.24 31.48 23.86 N/A 0 2 Chain A: 5.34 60.29 13.08 N/A 0 1626 Chain B: 5.19 73.02 12.80 N/A 0 1648 Chain S: 11.74 62.75 30.98 N/A 435 0 Histogram: Values Number of atoms 5.19 - 11.97 2158 11.97 - 18.75 644 18.75 - 25.54 313 25.54 - 32.32 267 32.32 - 39.11 152 39.11 - 45.89 111 45.89 - 52.67 40 52.67 - 59.46 19 59.46 - 66.24 4 66.24 - 73.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1305 r_free=0.1579 r_work=0.1304 r_free=0.1574 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1304 r_free = 0.1574 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 = 0.1289 r_free = 0.1563 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1289 r_free= 0.1563 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015682 | | target function (ls_wunit_k1) not normalized (work): 2937.154058 | | target function (ls_wunit_k1) not normalized (free): 117.351807 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1294 0.1289 0.1563 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1481 0.1478 0.1638 n_refl.: 191140 remove outliers: r(all,work,free)=0.1481 0.1478 0.1638 n_refl.: 191140 overall B=0.15 to atoms: r(all,work,free)=0.1503 0.1500 0.1648 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1285 0.1280 0.1550 n_refl.: 191140 remove outliers: r(all,work,free)=0.1285 0.1280 0.1549 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3562 402.814 378.119 0.481 0.962 0.270 13.296-10.522 99.01 99 1 0.2092 528.187 520.044 0.738 0.964 0.240 10.503-8.327 99.45 178 3 0.1747 565.118 562.226 0.889 0.964 0.209 8.318-6.595 100.00 360 8 0.1693 414.736 412.968 0.912 0.963 0.164 6.588-5.215 100.00 711 7 0.1524 381.101 373.912 0.887 0.964 0.150 5.214-4.128 98.38 1367 28 0.0896 557.435 554.210 0.977 0.964 0.080 4.126-3.266 94.74 2603 46 0.0829 508.132 504.333 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0920 342.774 340.382 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0954 258.603 256.437 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1095 153.054 151.413 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1290 82.395 81.421 1.047 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1884 44.202 42.146 1.023 0.967 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0340 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1280 r_free=0.1549 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1280 r_free=0.1549 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1549 | n_water=805 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1285 r_free=0.1554 | n_water=793 | time (s): 104.950 (total time: 107.960) Filter (q & B) r_work=0.1286 r_free=0.1553 | n_water=788 | time (s): 4.200 (total time: 112.160) Compute maps r_work=0.1286 r_free=0.1553 | n_water=788 | time (s): 1.750 (total time: 113.910) Filter (map) r_work=0.1311 r_free=0.1536 | n_water=653 | time (s): 4.300 (total time: 118.210) Find peaks r_work=0.1311 r_free=0.1536 | n_water=653 | time (s): 0.800 (total time: 119.010) Add new water r_work=0.1335 r_free=0.1560 | n_water=953 | time (s): 5.120 (total time: 124.130) Refine new water occ: r_work=0.1291 r_free=0.1508 adp: r_work=0.1279 r_free=0.1506 occ: r_work=0.1281 r_free=0.1502 adp: r_work=0.1274 r_free=0.1503 occ: r_work=0.1275 r_free=0.1501 adp: r_work=0.1273 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1273 r_free=0.1502 r_work=0.1273 r_free=0.1502 | n_water=953 | time (s): 83.500 (total time: 207.630) Filter (q & B) r_work=0.1277 r_free=0.1509 | n_water=883 | time (s): 5.560 (total time: 213.190) Filter (dist only) r_work=0.1277 r_free=0.1508 | n_water=881 | time (s): 110.290 (total time: 323.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.778927 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 593.219061 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 0.1261 0.1524 0.0264 0.041 1.1 17.8 0.0 0.0 0 11.889 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.61 15.24 2.64 2.046 15.202 593.219 0.015 12.35 15.07 2.71 2.419 15.237 593.219 0.014 Individual atomic B min max mean iso aniso Overall: 5.44 68.17 16.32 1.20 513 3272 Protein: 5.44 39.74 11.00 1.20 0 2902 Water: 6.63 68.17 33.81 N/A 513 368 Other: 16.31 33.34 24.82 N/A 0 2 Chain A: 5.52 56.77 13.01 N/A 0 1624 Chain B: 5.44 68.17 12.83 N/A 0 1648 Chain S: 12.69 65.70 38.00 N/A 513 0 Histogram: Values Number of atoms 5.44 - 11.72 2072 11.72 - 17.99 698 17.99 - 24.26 268 24.26 - 30.53 205 30.53 - 36.81 170 36.81 - 43.08 173 43.08 - 49.35 98 49.35 - 55.63 52 55.63 - 61.90 36 61.90 - 68.17 13 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1507 r_work=0.1236 r_free=0.1508 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1508 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 = 0.1229 r_free = 0.1502 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1502 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013512 | | target function (ls_wunit_k1) not normalized (work): 2530.805624 | | target function (ls_wunit_k1) not normalized (free): 97.813373 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1502 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1437 0.1612 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1437 0.1612 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1437 0.1434 0.1610 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1236 0.1511 n_refl.: 191138 remove outliers: r(all,work,free)=0.1242 0.1236 0.1511 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3307 402.814 377.803 0.490 0.962 0.267 13.296-10.522 99.01 99 1 0.1916 528.187 522.958 0.768 0.963 0.250 10.503-8.327 99.45 178 3 0.1464 565.118 567.642 0.922 0.963 0.170 8.318-6.595 100.00 360 8 0.1527 414.736 414.763 0.938 0.963 0.160 6.588-5.215 100.00 711 7 0.1333 381.101 376.384 0.912 0.963 0.133 5.214-4.128 98.38 1367 28 0.0827 557.435 556.079 0.996 0.963 0.100 4.126-3.266 94.74 2603 46 0.0764 508.132 505.371 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0863 342.774 341.371 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.744 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.618 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.346 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.213 1.059 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0574 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1237 r_free=0.1511 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1237 r_free=0.1511 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1237 r_free=0.1511 | n_water=881 | time (s): 3.340 (total time: 3.340) Filter (dist) r_work=0.1240 r_free=0.1513 | n_water=872 | time (s): 112.670 (total time: 116.010) Filter (q & B) r_work=0.1240 r_free=0.1512 | n_water=870 | time (s): 4.410 (total time: 120.420) Compute maps r_work=0.1240 r_free=0.1512 | n_water=870 | time (s): 2.180 (total time: 122.600) Filter (map) r_work=0.1278 r_free=0.1506 | n_water=683 | time (s): 5.130 (total time: 127.730) Find peaks r_work=0.1278 r_free=0.1506 | n_water=683 | time (s): 0.780 (total time: 128.510) Add new water r_work=0.1302 r_free=0.1542 | n_water=1001 | time (s): 4.400 (total time: 132.910) Refine new water occ: r_work=0.1255 r_free=0.1507 adp: r_work=0.1256 r_free=0.1508 occ: r_work=0.1251 r_free=0.1503 adp: r_work=0.1251 r_free=0.1505 occ: r_work=0.1248 r_free=0.1500 adp: r_work=0.1248 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1248 r_free=0.1502 r_work=0.1248 r_free=0.1502 | n_water=1001 | time (s): 254.920 (total time: 387.830) Filter (q & B) r_work=0.1253 r_free=0.1506 | n_water=873 | time (s): 5.230 (total time: 393.060) Filter (dist only) r_work=0.1253 r_free=0.1505 | n_water=872 | time (s): 106.180 (total time: 499.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.684137 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.033349 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 0.1241 0.1430 0.0189 0.035 1.1 7.8 0.0 0.0 0 0.842 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.30 1.89 1.935 14.596 16.033 3.941 12.37 13.92 1.55 2.230 14.497 16.033 3.899 Individual atomic B min max mean iso aniso Overall: 5.54 67.78 15.26 1.06 506 3270 Protein: 5.54 36.30 10.75 1.06 0 2902 Water: 6.69 67.78 30.27 N/A 506 366 Other: 14.02 28.67 21.35 N/A 0 2 Chain A: 5.55 55.93 12.77 N/A 0 1624 Chain B: 5.54 67.78 12.52 N/A 0 1646 Chain S: 12.69 63.77 32.21 N/A 506 0 Histogram: Values Number of atoms 5.54 - 11.76 2135 11.76 - 17.99 683 17.99 - 24.21 291 24.21 - 30.44 237 30.44 - 36.66 183 36.66 - 42.89 137 42.89 - 49.11 73 49.11 - 55.34 23 55.34 - 61.56 12 61.56 - 67.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1392 r_work=0.1238 r_free=0.1393 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1393 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1380 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1232 r_free= 0.1380 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892725 | | target function (ml) not normalized (work): 729095.623959 | | target function (ml) not normalized (free): 15223.990338 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1232 0.1380 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1441 0.1468 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1441 0.1468 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1435 0.1435 0.1465 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1228 0.1371 n_refl.: 191138 remove outliers: r(all,work,free)=0.1230 0.1227 0.1371 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 0.3706 398.008 364.496 0.423 0.947 0.238 13.296-10.522 98.02 98 1 0.2381 528.900 504.899 0.696 0.948 0.185 10.503-8.327 98.35 176 3 0.2015 555.265 557.519 0.885 0.948 0.156 8.318-6.595 100.00 360 8 0.2064 414.736 411.992 0.899 0.948 0.125 6.588-5.215 100.00 711 7 0.1798 381.101 371.138 0.886 0.948 0.110 5.214-4.128 98.38 1367 28 0.1174 557.435 551.847 0.973 0.948 0.080 4.126-3.266 94.74 2603 46 0.1101 508.132 501.001 1.031 0.948 0.009 3.266-2.585 99.86 5447 97 0.1085 342.774 339.250 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0973 258.603 255.781 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0979 153.054 151.409 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1054 82.395 81.487 1.051 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1690 44.202 42.316 1.036 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1035 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1372 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1372 | n_water=872 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1228 r_free=0.1372 | n_water=869 | time (s): 109.790 (total time: 113.020) Filter (q & B) r_work=0.1228 r_free=0.1370 | n_water=859 | time (s): 4.760 (total time: 117.780) Compute maps r_work=0.1228 r_free=0.1370 | n_water=859 | time (s): 2.270 (total time: 120.050) Filter (map) r_work=0.1253 r_free=0.1391 | n_water=707 | time (s): 5.290 (total time: 125.340) Find peaks r_work=0.1253 r_free=0.1391 | n_water=707 | time (s): 0.610 (total time: 125.950) Add new water r_work=0.1268 r_free=0.1404 | n_water=955 | time (s): 5.070 (total time: 131.020) Refine new water occ: r_work=0.1218 r_free=0.1361 adp: r_work=0.1210 r_free=0.1358 occ: r_work=0.1208 r_free=0.1357 adp: r_work=0.1208 r_free=0.1357 occ: r_work=0.1206 r_free=0.1356 adp: r_work=0.1206 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1356 r_work=0.1206 r_free=0.1356 | n_water=955 | time (s): 292.970 (total time: 423.990) Filter (q & B) r_work=0.1210 r_free=0.1360 | n_water=866 | time (s): 4.400 (total time: 428.390) Filter (dist only) r_work=0.1211 r_free=0.1359 | n_water=865 | time (s): 107.460 (total time: 535.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.532599 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.836579 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 0.1363 0.0155 0.035 1.1 7.3 0.0 0.0 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 13.63 1.55 1.836 14.154 14.837 3.875 12.02 13.59 1.56 1.903 14.132 14.837 3.868 Individual atomic B min max mean iso aniso Overall: 5.54 67.48 14.90 1.01 499 3270 Protein: 5.54 33.85 10.70 1.01 0 2902 Water: 6.20 67.48 29.00 N/A 499 366 Other: 13.98 28.31 21.15 N/A 0 2 Chain A: 5.54 55.24 12.67 N/A 0 1624 Chain B: 5.54 67.48 12.45 N/A 0 1646 Chain S: 6.20 63.72 30.25 N/A 499 0 Histogram: Values Number of atoms 5.54 - 11.73 2130 11.73 - 17.93 707 17.93 - 24.12 312 24.12 - 30.32 258 30.32 - 36.51 149 36.51 - 42.70 122 42.70 - 48.90 60 48.90 - 55.09 20 55.09 - 61.29 9 61.29 - 67.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1359 r_work=0.1202 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1359 target_work(ml) = 3.868 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1357 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.866136 | | target function (ml) not normalized (work): 724100.299989 | | target function (ml) not normalized (free): 15132.914540 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1357 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1426 0.1426 0.1465 n_refl.: 191134 remove outliers: r(all,work,free)=0.1426 0.1426 0.1465 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1419 0.1418 0.1460 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1356 n_refl.: 191134 remove outliers: r(all,work,free)=0.1201 0.1198 0.1356 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3790 351.838 323.842 0.400 0.948 0.228 13.296-10.522 97.03 97 1 0.2335 481.302 457.653 0.697 0.950 0.184 10.503-8.327 98.35 176 3 0.2115 502.907 496.248 0.866 0.950 0.153 8.318-6.595 100.00 360 8 0.2199 375.630 371.519 0.890 0.949 0.113 6.588-5.215 100.00 711 7 0.1882 345.166 335.417 0.883 0.950 0.097 5.214-4.128 98.38 1367 28 0.1202 504.873 499.430 0.972 0.950 0.080 4.126-3.266 94.74 2603 46 0.1116 460.219 453.552 1.031 0.950 0.000 3.266-2.585 99.86 5447 97 0.1085 310.453 307.258 1.020 0.949 0.000 2.585-2.046 97.45 10613 204 0.0935 234.219 231.771 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0919 138.622 137.303 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0993 74.626 73.900 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1665 40.034 38.362 1.042 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1189 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1356 | n_water=865 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1199 r_free=0.1356 | n_water=864 | time (s): 112.120 (total time: 114.620) Filter (q & B) r_work=0.1199 r_free=0.1357 | n_water=856 | time (s): 5.140 (total time: 119.760) Compute maps r_work=0.1199 r_free=0.1357 | n_water=856 | time (s): 1.830 (total time: 121.590) Filter (map) r_work=0.1221 r_free=0.1357 | n_water=730 | time (s): 4.310 (total time: 125.900) Find peaks r_work=0.1221 r_free=0.1357 | n_water=730 | time (s): 0.580 (total time: 126.480) Add new water r_work=0.1233 r_free=0.1369 | n_water=963 | time (s): 3.910 (total time: 130.390) Refine new water occ: r_work=0.1196 r_free=0.1340 adp: r_work=0.1196 r_free=0.1339 occ: r_work=0.1194 r_free=0.1339 adp: r_work=0.1194 r_free=0.1339 occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1192 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1339 r_work=0.1192 r_free=0.1339 | n_water=963 | time (s): 296.090 (total time: 426.480) Filter (q & B) r_work=0.1196 r_free=0.1347 | n_water=882 | time (s): 5.560 (total time: 432.040) Filter (dist only) r_work=0.1196 r_free=0.1347 | n_water=881 | time (s): 110.250 (total time: 542.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.490546 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.075259 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 0.1350 0.0151 0.036 1.1 7.1 0.0 0.3 0 0.745 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.50 1.51 1.804 14.147 15.075 3.766 12.03 13.56 1.53 1.965 14.095 15.075 3.763 Individual atomic B min max mean iso aniso Overall: 5.50 66.77 14.90 0.95 515 3270 Protein: 5.50 31.12 10.58 0.95 0 2902 Water: 6.03 66.77 29.12 N/A 515 366 Other: 13.93 25.91 19.92 N/A 0 2 Chain A: 5.57 53.58 12.51 N/A 0 1624 Chain B: 5.50 66.77 12.30 N/A 0 1646 Chain S: 6.03 63.65 30.71 N/A 515 0 Histogram: Values Number of atoms 5.50 - 11.63 2120 11.63 - 17.76 739 17.76 - 23.88 300 23.88 - 30.01 227 30.01 - 36.14 172 36.14 - 42.27 131 42.27 - 48.39 62 48.39 - 54.52 23 54.52 - 60.65 9 60.65 - 66.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1356 r_work=0.1203 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1357 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1356 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761281 | | target function (ml) not normalized (work): 704450.288942 | | target function (ml) not normalized (free): 14736.632208 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1356 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1424 0.1423 0.1468 n_refl.: 191131 remove outliers: r(all,work,free)=0.1424 0.1423 0.1468 n_refl.: 191131 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1417 0.1464 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1351 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1351 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 90.10 88 3 0.3654 343.846 311.013 0.374 0.972 0.221 13.296-10.522 97.03 97 1 0.2360 481.302 463.435 0.672 0.973 0.162 10.503-8.327 98.35 176 3 0.2136 502.907 495.784 0.843 0.973 0.137 8.318-6.595 100.00 360 8 0.2184 375.630 371.731 0.865 0.972 0.105 6.588-5.215 100.00 711 7 0.1885 345.166 335.109 0.862 0.972 0.090 5.214-4.128 98.38 1367 28 0.1205 504.873 499.269 0.948 0.971 0.080 4.126-3.266 94.74 2603 46 0.1142 460.219 453.139 1.008 0.970 0.000 3.266-2.585 99.86 5447 97 0.1100 310.453 307.174 0.998 0.967 0.000 2.585-2.046 97.45 10613 204 0.0956 234.219 231.672 1.013 0.963 0.000 2.046-1.619 99.39 21536 464 0.0919 138.622 137.269 1.042 0.957 0.000 1.619-1.281 98.00 42464 925 0.0974 74.626 73.918 1.049 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1646 40.034 38.357 1.053 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1351 | n_water=881 | time (s): 2.980 (total time: 2.980) Filter (dist) r_work=0.1196 r_free=0.1351 | n_water=881 | time (s): 107.140 (total time: 110.120) Filter (q & B) r_work=0.1197 r_free=0.1352 | n_water=872 | time (s): 5.140 (total time: 115.260) Compute maps r_work=0.1197 r_free=0.1352 | n_water=872 | time (s): 2.230 (total time: 117.490) Filter (map) r_work=0.1217 r_free=0.1354 | n_water=757 | time (s): 4.450 (total time: 121.940) Find peaks r_work=0.1217 r_free=0.1354 | n_water=757 | time (s): 0.590 (total time: 122.530) Add new water r_work=0.1227 r_free=0.1367 | n_water=962 | time (s): 3.950 (total time: 126.480) Refine new water occ: r_work=0.1195 r_free=0.1339 adp: r_work=0.1195 r_free=0.1340 occ: r_work=0.1192 r_free=0.1337 adp: r_work=0.1192 r_free=0.1338 occ: r_work=0.1191 r_free=0.1336 adp: r_work=0.1190 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1337 r_work=0.1190 r_free=0.1337 | n_water=962 | time (s): 282.490 (total time: 408.970) Filter (q & B) r_work=0.1195 r_free=0.1340 | n_water=892 | time (s): 4.620 (total time: 413.590) Filter (dist only) r_work=0.1195 r_free=0.1339 | n_water=890 | time (s): 113.450 (total time: 527.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.534414 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.467939 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1344 0.0147 0.036 1.1 5.8 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.44 1.47 1.753 14.016 14.468 3.760 11.98 13.45 1.47 1.841 13.986 14.468 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 65.81 14.84 0.90 524 3270 Protein: 5.59 29.50 10.50 0.90 0 2902 Water: 6.00 65.81 28.97 N/A 524 366 Other: 13.93 23.80 18.86 N/A 0 2 Chain A: 5.65 51.76 12.40 N/A 0 1624 Chain B: 5.59 65.81 12.21 N/A 0 1646 Chain S: 6.00 63.58 30.68 N/A 524 0 Histogram: Values Number of atoms 5.59 - 11.61 2112 11.61 - 17.63 773 17.63 - 23.66 274 23.66 - 29.68 228 29.68 - 35.70 171 35.70 - 41.72 134 41.72 - 47.74 67 47.74 - 53.76 26 53.76 - 59.79 6 59.79 - 65.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1345 r_work=0.1198 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1346 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1345 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757386 | | target function (ml) not normalized (work): 703713.280945 | | target function (ml) not normalized (free): 14726.082872 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1345 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1405 0.1404 0.1471 n_refl.: 191129 remove outliers: r(all,work,free)=0.1405 0.1404 0.1471 n_refl.: 191129 overall B=-0.21 to atoms: r(all,work,free)=0.1371 0.1369 0.1449 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1343 n_refl.: 191129 remove outliers: r(all,work,free)=0.1198 0.1195 0.1343 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 90.10 88 3 0.3640 343.846 309.361 0.365 0.975 0.194 13.296-10.522 97.03 97 1 0.2402 481.302 462.779 0.679 0.976 0.141 10.503-8.327 98.35 176 3 0.2152 502.907 495.095 0.863 0.976 0.125 8.318-6.595 100.00 360 8 0.2186 375.630 371.781 0.881 0.976 0.086 6.588-5.215 100.00 711 7 0.1907 345.166 335.492 0.879 0.975 0.077 5.214-4.128 98.38 1367 28 0.1202 504.873 499.433 0.970 0.975 0.070 4.126-3.266 94.74 2603 46 0.1148 460.219 453.084 1.030 0.974 0.000 3.266-2.585 99.86 5447 97 0.1109 310.453 307.221 1.017 0.971 0.000 2.585-2.046 97.45 10613 204 0.0958 234.219 231.683 1.028 0.968 0.000 2.046-1.619 99.39 21536 464 0.0915 138.622 137.289 1.052 0.962 0.000 1.619-1.281 98.00 42464 925 0.0966 74.626 73.927 1.052 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1643 40.034 38.351 1.040 0.936 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0461 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1343 | n_water=890 | time (s): 2.760 (total time: 2.760) Filter (dist) r_work=0.1196 r_free=0.1343 | n_water=890 | time (s): 104.760 (total time: 107.520) Filter (q & B) r_work=0.1197 r_free=0.1343 | n_water=881 | time (s): 5.180 (total time: 112.700) Compute maps r_work=0.1197 r_free=0.1343 | n_water=881 | time (s): 1.950 (total time: 114.650) Filter (map) r_work=0.1217 r_free=0.1349 | n_water=769 | time (s): 5.260 (total time: 119.910) Find peaks r_work=0.1217 r_free=0.1349 | n_water=769 | time (s): 0.680 (total time: 120.590) Add new water r_work=0.1225 r_free=0.1361 | n_water=962 | time (s): 5.230 (total time: 125.820) Refine new water occ: r_work=0.1194 r_free=0.1341 adp: r_work=0.1194 r_free=0.1341 occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1192 r_free=0.1340 occ: r_work=0.1191 r_free=0.1338 adp: r_work=0.1190 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1339 r_work=0.1190 r_free=0.1339 | n_water=962 | time (s): 217.590 (total time: 343.410) Filter (q & B) r_work=0.1194 r_free=0.1339 | n_water=901 | time (s): 5.670 (total time: 349.080) Filter (dist only) r_work=0.1194 r_free=0.1339 | n_water=899 | time (s): 111.680 (total time: 460.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.518330 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.416795 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1346 0.0149 0.038 1.1 6.0 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.46 1.49 1.722 13.766 14.417 3.759 11.99 13.49 1.51 1.773 13.748 14.417 3.757 Individual atomic B min max mean iso aniso Overall: 5.40 64.54 14.64 0.88 533 3270 Protein: 5.40 28.52 10.28 0.88 0 2902 Water: 5.84 64.54 28.72 N/A 533 366 Other: 13.75 22.13 17.94 N/A 0 2 Chain A: 5.48 51.18 12.13 N/A 0 1624 Chain B: 5.40 64.54 11.96 N/A 0 1646 Chain S: 5.84 63.40 30.56 N/A 533 0 Histogram: Values Number of atoms 5.40 - 11.32 2084 11.32 - 17.23 796 17.23 - 23.14 267 23.14 - 29.06 228 29.06 - 34.97 176 34.97 - 40.88 139 40.88 - 46.80 75 46.80 - 52.71 28 52.71 - 58.63 6 58.63 - 64.54 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1350 r_work=0.1199 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1350 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1350 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756884 | | target function (ml) not normalized (work): 703619.372650 | | target function (ml) not normalized (free): 14731.916856 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1379 0.1378 0.1452 n_refl.: 191129 remove outliers: r(all,work,free)=0.1379 0.1378 0.1452 n_refl.: 191129 overall B=0.05 to atoms: r(all,work,free)=0.1386 0.1385 0.1456 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1341 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1341 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3705 343.846 307.887 0.355 0.994 0.188 13.296-10.522 97.03 97 1 0.2344 481.302 464.107 0.669 0.995 0.129 10.503-8.327 98.35 176 3 0.2168 502.907 493.393 0.851 0.996 0.103 8.318-6.595 100.00 360 8 0.2176 375.630 371.353 0.872 0.995 0.089 6.588-5.215 100.00 711 7 0.1912 345.166 334.876 0.870 0.995 0.077 5.214-4.128 98.38 1367 28 0.1209 504.873 499.100 0.958 0.996 0.034 4.126-3.266 94.74 2603 46 0.1155 460.219 452.421 1.019 0.996 0.000 3.266-2.585 99.86 5447 97 0.1118 310.453 307.005 1.006 0.995 0.000 2.585-2.046 97.45 10613 204 0.0963 234.219 231.538 1.016 0.994 0.000 2.046-1.619 99.39 21536 464 0.0912 138.622 137.207 1.037 0.992 0.000 1.619-1.281 98.00 42464 925 0.0949 74.626 73.963 1.034 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.034 38.329 1.012 0.986 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0597 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1341 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1341 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1341 | n_water=899 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1190 r_free=0.1341 | n_water=899 | time (s): 107.900 (total time: 110.380) Filter (q & B) r_work=0.1191 r_free=0.1342 | n_water=892 | time (s): 4.170 (total time: 114.550) Compute maps r_work=0.1191 r_free=0.1342 | n_water=892 | time (s): 2.160 (total time: 116.710) Filter (map) r_work=0.1213 r_free=0.1346 | n_water=774 | time (s): 5.950 (total time: 122.660) Find peaks r_work=0.1213 r_free=0.1346 | n_water=774 | time (s): 0.770 (total time: 123.430) Add new water r_work=0.1219 r_free=0.1353 | n_water=971 | time (s): 4.330 (total time: 127.760) Refine new water occ: r_work=0.1188 r_free=0.1333 adp: r_work=0.1188 r_free=0.1333 occ: r_work=0.1186 r_free=0.1332 adp: r_work=0.1186 r_free=0.1332 occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1184 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1332 r_work=0.1184 r_free=0.1332 | n_water=971 | time (s): 213.750 (total time: 341.510) Filter (q & B) r_work=0.1188 r_free=0.1340 | n_water=900 | time (s): 5.830 (total time: 347.340) Filter (dist only) r_work=0.1189 r_free=0.1339 | n_water=898 | time (s): 113.470 (total time: 460.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.517603 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.473283 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1344 0.0153 0.038 1.1 6.3 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.44 1.53 1.681 13.748 14.473 3.756 11.92 13.46 1.54 1.701 13.739 14.473 3.754 Individual atomic B min max mean iso aniso Overall: 5.50 63.54 14.64 0.87 532 3270 Protein: 5.50 28.27 10.33 0.87 0 2902 Water: 5.93 63.54 28.55 N/A 532 366 Other: 13.82 22.14 17.98 N/A 0 2 Chain A: 5.59 50.92 12.15 N/A 0 1624 Chain B: 5.50 63.54 11.99 N/A 0 1646 Chain S: 5.93 59.99 30.45 N/A 532 0 Histogram: Values Number of atoms 5.50 - 11.31 2059 11.31 - 17.11 823 17.11 - 22.91 262 22.91 - 28.72 215 28.72 - 34.52 188 34.52 - 40.32 133 40.32 - 46.13 80 46.13 - 51.93 30 51.93 - 57.73 8 57.73 - 63.54 4 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1346 r_work=0.1192 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1346 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1347 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754250 | | target function (ml) not normalized (work): 703126.035903 | | target function (ml) not normalized (free): 14731.634596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1190 0.1347 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1396 0.1395 0.1475 n_refl.: 191129 remove outliers: r(all,work,free)=0.1396 0.1395 0.1475 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1396 0.1395 0.1476 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1346 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1346 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 90.10 88 3 0.3728 343.846 306.964 0.356 0.976 0.181 13.296-10.522 97.03 97 1 0.2388 481.302 463.262 0.683 0.978 0.137 10.503-8.327 98.35 176 3 0.2147 502.907 494.217 0.864 0.978 0.123 8.318-6.595 100.00 360 8 0.2175 375.630 371.288 0.886 0.978 0.087 6.588-5.215 100.00 711 7 0.1917 345.166 335.232 0.886 0.979 0.077 5.214-4.128 98.38 1367 28 0.1210 504.873 499.249 0.976 0.980 0.029 4.126-3.266 94.74 2603 46 0.1165 460.219 452.437 1.038 0.981 0.000 3.266-2.585 99.86 5447 97 0.1122 310.453 306.981 1.022 0.982 0.000 2.585-2.046 97.45 10613 204 0.0963 234.219 231.573 1.030 0.984 0.000 2.046-1.619 99.39 21536 464 0.0911 138.622 137.242 1.047 0.988 0.000 1.619-1.281 98.00 42464 925 0.0946 74.626 73.972 1.038 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.034 38.316 1.007 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0049 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1346 | n_water=898 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1190 r_free=0.1347 | n_water=897 | time (s): 110.920 (total time: 113.480) Filter (q & B) r_work=0.1192 r_free=0.1346 | n_water=884 | time (s): 5.440 (total time: 118.920) Compute maps r_work=0.1192 r_free=0.1346 | n_water=884 | time (s): 1.950 (total time: 120.870) Filter (map) r_work=0.1214 r_free=0.1351 | n_water=770 | time (s): 4.940 (total time: 125.810) Find peaks r_work=0.1214 r_free=0.1351 | n_water=770 | time (s): 0.850 (total time: 126.660) Add new water r_work=0.1220 r_free=0.1358 | n_water=966 | time (s): 4.760 (total time: 131.420) Refine new water occ: r_work=0.1189 r_free=0.1330 adp: r_work=0.1189 r_free=0.1330 occ: r_work=0.1187 r_free=0.1328 adp: r_work=0.1187 r_free=0.1329 occ: r_work=0.1186 r_free=0.1326 adp: r_work=0.1186 r_free=0.1326 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1326 r_work=0.1186 r_free=0.1326 | n_water=966 | time (s): 190.650 (total time: 322.070) Filter (q & B) r_work=0.1190 r_free=0.1340 | n_water=894 | time (s): 4.400 (total time: 326.470) Filter (dist only) r_work=0.1190 r_free=0.1340 | n_water=892 | time (s): 112.960 (total time: 439.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.510246 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.931822 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1346 0.0153 0.039 1.1 6.1 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.46 1.53 1.681 13.692 13.932 3.755 11.95 13.49 1.54 1.685 13.689 13.932 3.755 Individual atomic B min max mean iso aniso Overall: 5.50 63.10 14.54 0.86 527 3269 Protein: 5.50 28.10 10.35 0.86 0 2902 Water: 6.04 63.10 28.18 N/A 527 365 Other: 13.85 22.13 17.99 N/A 0 2 Chain A: 5.61 50.76 12.14 N/A 0 1624 Chain B: 5.50 63.10 11.96 N/A 0 1645 Chain S: 6.04 60.10 30.00 N/A 527 0 Histogram: Values Number of atoms 5.50 - 11.26 2046 11.26 - 17.02 836 17.02 - 22.78 267 22.78 - 28.54 222 28.54 - 34.30 188 34.30 - 40.06 116 40.06 - 45.82 76 45.82 - 51.58 33 51.58 - 57.34 6 57.34 - 63.10 6 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1349 r_work=0.1195 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1349 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1351 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754820 | | target function (ml) not normalized (work): 703232.737332 | | target function (ml) not normalized (free): 14731.481091 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1409 0.1407 0.1484 n_refl.: 191129 remove outliers: r(all,work,free)=0.1409 0.1407 0.1484 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1403 0.1401 0.1480 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1193 0.1350 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3744 343.846 305.733 0.349 0.975 0.188 13.296-10.522 97.03 97 1 0.2353 481.302 463.479 0.665 0.977 0.129 10.503-8.327 98.35 176 3 0.2209 502.907 493.346 0.842 0.977 0.107 8.318-6.595 100.00 360 8 0.2193 375.630 371.218 0.864 0.977 0.080 6.588-5.215 100.00 711 7 0.1932 345.166 335.032 0.864 0.978 0.080 5.214-4.128 98.38 1367 28 0.1223 504.873 498.841 0.954 0.979 0.029 4.126-3.266 94.74 2603 46 0.1172 460.219 452.379 1.015 0.980 0.000 3.266-2.585 99.86 5447 97 0.1128 310.453 306.992 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0968 234.219 231.534 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0913 138.622 137.243 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0945 74.626 73.974 1.012 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.034 38.309 0.981 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0083 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1193 r_free=0.1350 After: r_work=0.1194 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1194 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1351 | n_water=892 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1194 r_free=0.1351 | n_water=891 | time (s): 116.370 (total time: 118.720) Filter (q & B) r_work=0.1195 r_free=0.1351 | n_water=882 | time (s): 5.260 (total time: 123.980) Compute maps r_work=0.1195 r_free=0.1351 | n_water=882 | time (s): 1.760 (total time: 125.740) Filter (map) r_work=0.1216 r_free=0.1356 | n_water=773 | time (s): 4.280 (total time: 130.020) Find peaks r_work=0.1216 r_free=0.1356 | n_water=773 | time (s): 0.640 (total time: 130.660) Add new water r_work=0.1222 r_free=0.1370 | n_water=975 | time (s): 4.290 (total time: 134.950) Refine new water occ: r_work=0.1191 r_free=0.1348 adp: r_work=0.1191 r_free=0.1348 occ: r_work=0.1189 r_free=0.1347 adp: r_work=0.1189 r_free=0.1348 occ: r_work=0.1188 r_free=0.1346 adp: r_work=0.1188 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1347 r_work=0.1188 r_free=0.1347 | n_water=975 | time (s): 277.380 (total time: 412.330) Filter (q & B) r_work=0.1191 r_free=0.1353 | n_water=905 | time (s): 5.700 (total time: 418.030) Filter (dist only) r_work=0.1192 r_free=0.1353 | n_water=903 | time (s): 118.040 (total time: 536.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.514045 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.866478 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1362 0.0162 0.039 1.2 11.9 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.62 1.62 1.677 13.697 13.866 3.761 12.01 13.66 1.64 1.685 13.697 13.866 3.761 Individual atomic B min max mean iso aniso Overall: 5.52 61.99 14.58 0.85 538 3269 Protein: 5.52 27.81 10.32 0.85 0 2902 Water: 6.06 61.99 28.26 N/A 538 365 Other: 13.83 21.96 17.90 N/A 0 2 Chain A: 5.62 50.28 12.09 N/A 0 1624 Chain B: 5.52 61.99 11.92 N/A 0 1645 Chain S: 6.06 60.35 30.23 N/A 538 0 Histogram: Values Number of atoms 5.52 - 11.16 2024 11.16 - 16.81 848 16.81 - 22.46 275 22.46 - 28.11 206 28.11 - 33.75 192 33.75 - 39.40 131 39.40 - 45.05 78 45.05 - 50.70 39 50.70 - 56.34 8 56.34 - 61.99 6 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1366 r_work=0.1202 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1366 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1366 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.760749 | | target function (ml) not normalized (work): 704343.186510 | | target function (ml) not normalized (free): 14754.011747 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1361 0.1436 5.6887 5.7499| | 2: 2.94 - 2.33 1.00 7339 128 0.1079 0.1406 5.0788 5.2099| | 3: 2.33 - 2.04 0.96 6939 150 0.0923 0.1189 4.6754 4.7427| | 4: 2.04 - 1.85 1.00 7170 155 0.0909 0.1073 4.4027 4.576| | 5: 1.85 - 1.72 0.99 7113 159 0.0944 0.1013 4.164 4.252| | 6: 1.72 - 1.62 0.99 7102 142 0.0908 0.1101 3.9594 4.0852| | 7: 1.62 - 1.54 0.99 7104 148 0.0906 0.1006 3.8174 3.9671| | 8: 1.54 - 1.47 0.96 6798 152 0.0904 0.1332 3.7167 3.9146| | 9: 1.47 - 1.41 0.98 6938 155 0.0937 0.1142 3.6343 3.7682| | 10: 1.41 - 1.36 0.99 7022 150 0.0987 0.1204 3.5678 3.6893| | 11: 1.36 - 1.32 0.99 6997 151 0.1004 0.1144 3.497 3.5999| | 12: 1.32 - 1.28 0.98 6975 149 0.1044 0.1122 3.4691 3.5936| | 13: 1.28 - 1.25 0.98 6907 166 0.1052 0.1268 3.447 3.5764| | 14: 1.25 - 1.22 0.98 7015 112 0.1111 0.1609 3.4389 3.6921| | 15: 1.22 - 1.19 0.98 6956 137 0.1174 0.1251 3.4537 3.4923| | 16: 1.19 - 1.17 0.93 6604 132 0.1253 0.1523 3.4667 3.6405| | 17: 1.17 - 1.14 0.98 6940 135 0.1304 0.1225 3.4355 3.4445| | 18: 1.14 - 1.12 0.98 6875 142 0.1387 0.1711 3.44 3.5367| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1784 3.4211 3.6072| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1592 3.4111 3.4349| | 21: 1.08 - 1.07 0.97 6852 152 0.1731 0.2138 3.4199 3.5066| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1958 3.4142 3.4161| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2023 3.4341 3.4921| | 24: 1.03 - 1.02 0.96 6784 133 0.2335 0.2273 3.4371 3.5164| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2525 3.4506 3.5222| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2863 3.4161 3.4239| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2791 3.4705 3.3949| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.41 1.00 0.98 10859.29| | 2: 2.94 - 2.33 7339 128 0.93 12.67 0.99 0.98 5059.83| | 3: 2.33 - 2.04 6939 150 0.96 7.85 1.01 0.97 1749.77| | 4: 2.04 - 1.85 7170 155 0.96 7.80 1.00 0.97 1027.62| | 5: 1.85 - 1.72 7113 159 0.96 8.21 1.00 0.98 648.65| | 6: 1.72 - 1.62 7102 142 0.96 8.22 1.00 0.98 456.98| | 7: 1.62 - 1.54 7104 148 0.96 8.36 1.01 0.99 351.02| | 8: 1.54 - 1.47 6798 152 0.96 8.52 1.01 1.00 289.75| | 9: 1.47 - 1.41 6938 155 0.96 8.70 1.00 1.00 238.98| | 10: 1.41 - 1.36 7022 150 0.96 9.13 1.00 0.99 209.01| | 11: 1.36 - 1.32 6997 151 0.96 9.14 0.99 0.98 180.50| | 12: 1.32 - 1.28 6975 149 0.96 9.20 0.98 0.97 165.57| | 13: 1.28 - 1.25 6907 166 0.95 9.71 1.01 0.98 162.18| | 14: 1.25 - 1.22 7015 112 0.95 10.84 1.01 0.99 166.01| | 15: 1.22 - 1.19 6956 137 0.94 11.32 1.01 1.00 167.90| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.98 160.25| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.98 153.93| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.97 148.55| | 19: 1.12 - 1.10 6948 106 0.93 14.22 1.00 0.97 152.55| | 20: 1.10 - 1.08 6884 147 0.92 15.29 1.00 0.96 151.39| | 21: 1.08 - 1.07 6852 152 0.91 16.71 1.00 0.95 154.23| | 22: 1.07 - 1.05 6836 135 0.89 18.36 0.99 0.95 155.95| | 23: 1.05 - 1.03 6827 159 0.87 20.60 0.99 0.94 166.23| | 24: 1.03 - 1.02 6784 133 0.85 23.27 0.99 0.95 180.46| | 25: 1.02 - 1.01 6552 130 0.83 25.22 0.98 0.92 183.01| | 26: 1.01 - 0.99 6767 158 0.81 26.61 0.98 0.91 176.55| | 27: 0.99 - 0.98 6647 131 0.82 26.18 0.99 0.89 159.99| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 148.55 max = 10859.29 mean = 915.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 13.38| |phase err.(test): min = 0.00 max = 88.67 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1366 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1414 0.1413 0.1490 n_refl.: 191129 remove outliers: r(all,work,free)=0.1414 0.1413 0.1490 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1409 0.1407 0.1487 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1365 n_refl.: 191129 remove outliers: r(all,work,free)=0.1203 0.1200 0.1365 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 90.10 88 3 0.3668 343.846 307.368 0.372 0.913 0.186 13.296-10.522 97.03 97 1 0.2333 481.302 464.254 0.704 0.914 0.122 10.503-8.327 98.35 176 3 0.2176 502.907 492.991 0.899 0.915 0.097 8.318-6.595 100.00 360 8 0.2187 375.630 370.885 0.925 0.915 0.083 6.588-5.215 100.00 711 7 0.1932 345.166 334.743 0.922 0.915 0.070 5.214-4.128 98.38 1367 28 0.1232 504.873 498.661 1.019 0.916 0.029 4.126-3.266 94.74 2603 46 0.1172 460.219 452.305 1.086 0.918 0.000 3.266-2.585 99.86 5447 97 0.1135 310.453 307.072 1.068 0.919 0.000 2.585-2.046 97.45 10613 204 0.0977 234.219 231.532 1.074 0.921 0.000 2.046-1.619 99.39 21536 464 0.0921 138.622 137.236 1.090 0.926 0.000 1.619-1.281 98.00 42464 925 0.0958 74.626 73.956 1.079 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.034 38.304 1.045 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0082 ================= 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 : 0.2030 0.1982 0.080 5.231 5.2 78.0 14.6 805 0.000 1_bss: 0.1796 0.1910 0.080 5.231 5.2 78.0 14.6 805 0.000 1_settarget: 0.1796 0.1910 0.080 5.231 5.2 78.0 14.6 805 0.000 1_nqh: 0.1797 0.1914 0.080 5.231 5.2 78.0 14.6 805 0.002 1_weight: 0.1797 0.1914 0.080 5.231 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1274 0.1505 0.039 1.177 5.2 78.0 14.6 805 0.159 1_adp: 0.1305 0.1579 0.039 1.177 5.2 73.0 15.1 805 0.159 1_regHadp: 0.1304 0.1574 0.039 1.177 5.2 73.0 15.1 805 0.159 1_occ: 0.1289 0.1563 0.039 1.177 5.2 73.0 15.1 805 0.159 2_bss: 0.1280 0.1549 0.039 1.177 5.3 73.2 15.2 805 0.159 2_settarget: 0.1280 0.1549 0.039 1.177 5.3 73.2 15.2 805 0.159 2_updatecdl: 0.1280 0.1549 0.039 1.190 5.3 73.2 15.2 805 0.159 2_nqh: 0.1280 0.1549 0.039 1.190 5.3 73.2 15.2 805 0.159 2_sol: 0.1277 0.1508 0.039 1.190 5.3 73.2 16.3 881 n/a 2_weight: 0.1277 0.1508 0.039 1.190 5.3 73.2 16.3 881 n/a 2_xyzrec: 0.1261 0.1524 0.041 1.149 5.3 73.2 16.3 881 n/a 2_adp: 0.1236 0.1507 0.041 1.149 5.4 68.2 16.3 881 n/a 2_regHadp: 0.1236 0.1508 0.041 1.149 5.4 68.2 16.3 881 n/a 2_occ: 0.1229 0.1502 0.041 1.149 5.4 68.2 16.3 881 n/a 3_bss: 0.1237 0.1511 0.041 1.149 5.4 68.2 16.3 881 n/a 3_settarget: 0.1237 0.1511 0.041 1.149 5.4 68.2 16.3 881 n/a 3_updatecdl: 0.1237 0.1511 0.041 1.151 5.4 68.2 16.3 881 n/a 3_nqh: 0.1237 0.1511 0.041 1.151 5.4 68.2 16.3 881 n/a 3_sol: 0.1253 0.1505 0.041 1.151 5.4 68.2 15.4 872 n/a 3_weight: 0.1253 0.1505 0.041 1.151 5.4 68.2 15.4 872 n/a 3_xyzrec: 0.1241 0.1430 0.035 1.107 5.4 68.2 15.4 872 n/a 3_adp: 0.1237 0.1392 0.035 1.107 5.5 67.8 15.3 872 n/a 3_regHadp: 0.1238 0.1393 0.035 1.107 5.5 67.8 15.3 872 n/a 3_occ: 0.1232 0.1380 0.035 1.107 5.5 67.8 15.3 872 n/a 4_bss: 0.1227 0.1372 0.035 1.107 5.5 67.8 15.2 872 n/a 4_settarget: 0.1227 0.1372 0.035 1.107 5.5 67.8 15.2 872 n/a 4_updatecdl: 0.1227 0.1372 0.035 1.108 5.5 67.8 15.2 872 n/a 4_nqh: 0.1227 0.1372 0.035 1.108 5.5 67.8 15.2 872 n/a 4_sol: 0.1211 0.1359 0.035 1.108 5.5 67.8 14.9 865 n/a 4_weight: 0.1211 0.1359 0.035 1.108 5.5 67.8 14.9 865 n/a 4_xyzrec: 0.1209 0.1363 0.035 1.115 5.5 67.8 14.9 865 n/a 4_adp: 0.1202 0.1359 0.035 1.115 5.5 67.5 14.9 865 n/a 4_regHadp: 0.1202 0.1359 0.035 1.115 5.5 67.5 14.9 865 n/a 4_occ: 0.1201 0.1357 0.035 1.115 5.5 67.5 14.9 865 n/a 5_bss: 0.1198 0.1356 0.035 1.115 5.5 67.4 14.9 865 n/a 5_settarget: 0.1198 0.1356 0.035 1.115 5.5 67.4 14.9 865 n/a 5_updatecdl: 0.1198 0.1356 0.035 1.115 5.5 67.4 14.9 865 n/a 5_nqh: 0.1198 0.1356 0.035 1.115 5.5 67.4 14.9 865 n/a 5_sol: 0.1196 0.1347 0.035 1.115 5.5 67.4 15.0 881 n/a 5_weight: 0.1196 0.1347 0.035 1.115 5.5 67.4 15.0 881 n/a 5_xyzrec: 0.1199 0.1350 0.036 1.123 5.5 67.4 15.0 881 n/a 5_adp: 0.1203 0.1356 0.036 1.123 5.5 66.8 14.9 881 n/a 5_regHadp: 0.1203 0.1357 0.036 1.123 5.5 66.8 14.9 881 n/a 5_occ: 0.1201 0.1356 0.036 1.123 5.5 66.8 14.9 881 n/a 6_bss: 0.1196 0.1351 0.036 1.123 5.5 66.7 14.9 881 n/a 6_settarget: 0.1196 0.1351 0.036 1.123 5.5 66.7 14.9 881 n/a 6_updatecdl: 0.1196 0.1351 0.036 1.123 5.5 66.7 14.9 881 n/a 6_nqh: 0.1196 0.1351 0.036 1.123 5.5 66.7 14.9 881 n/a 6_sol: 0.1195 0.1339 0.036 1.123 5.5 66.7 14.9 890 n/a 6_weight: 0.1195 0.1339 0.036 1.123 5.5 66.7 14.9 890 n/a 6_xyzrec: 0.1197 0.1344 0.036 1.128 5.5 66.7 14.9 890 n/a 6_adp: 0.1198 0.1345 0.036 1.128 5.6 65.8 14.8 890 n/a 6_regHadp: 0.1198 0.1346 0.036 1.128 5.6 65.8 14.8 890 n/a 6_occ: 0.1196 0.1345 0.036 1.128 5.6 65.8 14.8 890 n/a 7_bss: 0.1196 0.1343 0.036 1.128 5.4 65.6 14.6 890 n/a 7_settarget: 0.1196 0.1343 0.036 1.128 5.4 65.6 14.6 890 n/a 7_updatecdl: 0.1196 0.1343 0.036 1.128 5.4 65.6 14.6 890 n/a 7_nqh: 0.1196 0.1343 0.036 1.128 5.4 65.6 14.6 890 n/a 7_sol: 0.1194 0.1339 0.036 1.128 5.4 65.6 14.7 899 n/a 7_weight: 0.1194 0.1339 0.036 1.128 5.4 65.6 14.7 899 n/a 7_xyzrec: 0.1197 0.1346 0.038 1.121 5.4 65.6 14.7 899 n/a 7_adp: 0.1199 0.1350 0.038 1.121 5.4 64.5 14.6 899 n/a 7_regHadp: 0.1199 0.1350 0.038 1.121 5.4 64.5 14.6 899 n/a 7_occ: 0.1197 0.1350 0.038 1.121 5.4 64.5 14.6 899 n/a 8_bss: 0.1190 0.1341 0.038 1.121 5.5 64.6 14.7 899 n/a 8_settarget: 0.1190 0.1341 0.038 1.121 5.5 64.6 14.7 899 n/a 8_updatecdl: 0.1190 0.1341 0.038 1.121 5.5 64.6 14.7 899 n/a 8_nqh: 0.1190 0.1341 0.038 1.121 5.5 64.6 14.7 899 n/a 8_sol: 0.1189 0.1339 0.038 1.121 5.5 64.6 14.7 898 n/a 8_weight: 0.1189 0.1339 0.038 1.121 5.5 64.6 14.7 898 n/a 8_xyzrec: 0.1192 0.1344 0.038 1.118 5.5 64.6 14.7 898 n/a 8_adp: 0.1192 0.1346 0.038 1.118 5.5 63.5 14.6 898 n/a 8_regHadp: 0.1192 0.1346 0.038 1.118 5.5 63.5 14.6 898 n/a 8_occ: 0.1190 0.1347 0.038 1.118 5.5 63.5 14.6 898 n/a 9_bss: 0.1190 0.1346 0.038 1.118 5.5 63.5 14.6 898 n/a 9_settarget: 0.1190 0.1346 0.038 1.118 5.5 63.5 14.6 898 n/a 9_updatecdl: 0.1190 0.1346 0.038 1.118 5.5 63.5 14.6 898 n/a 9_nqh: 0.1190 0.1346 0.038 1.118 5.5 63.5 14.6 898 n/a 9_sol: 0.1190 0.1340 0.038 1.118 5.5 63.5 14.5 892 n/a 9_weight: 0.1190 0.1340 0.038 1.118 5.5 63.5 14.5 892 n/a 9_xyzrec: 0.1193 0.1346 0.039 1.113 5.5 63.5 14.5 892 n/a 9_adp: 0.1195 0.1349 0.039 1.113 5.5 63.1 14.5 892 n/a 9_regHadp: 0.1195 0.1349 0.039 1.113 5.5 63.1 14.5 892 n/a 9_occ: 0.1194 0.1351 0.039 1.113 5.5 63.1 14.5 892 n/a 10_bss: 0.1193 0.1350 0.039 1.113 5.5 63.1 14.5 892 n/a 10_settarget: 0.1193 0.1350 0.039 1.113 5.5 63.1 14.5 892 n/a 10_updatecdl: 0.1193 0.1350 0.039 1.113 5.5 63.1 14.5 892 n/a 10_setrh: 0.1194 0.1351 0.039 1.113 5.5 63.1 14.5 892 n/a 10_nqh: 0.1194 0.1351 0.039 1.113 5.5 63.1 14.5 892 n/a 10_sol: 0.1192 0.1353 0.039 1.113 5.5 63.1 14.6 903 n/a 10_weight: 0.1192 0.1353 0.039 1.113 5.5 63.1 14.6 903 n/a 10_xyzrec: 0.1201 0.1362 0.039 1.186 5.5 63.1 14.6 903 n/a 10_adp: 0.1202 0.1366 0.039 1.186 5.5 62.0 14.6 903 n/a 10_regHadp: 0.1202 0.1366 0.039 1.186 5.5 62.0 14.6 903 n/a 10_occ: 0.1201 0.1366 0.039 1.186 5.5 62.0 14.6 903 n/a end: 0.1200 0.1365 0.039 1.186 5.5 62.0 14.5 903 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5431505_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5431505_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.5600 Refinement macro-cycles (run) : 12242.1800 Write final files (write_after_run_outputs) : 154.3000 Total : 12403.0400 Total CPU time: 3.46 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:00 PST -0800 (1736736240.61 s) Start R-work = 0.1796, R-free = 0.1910 Final R-work = 0.1200, R-free = 0.1365 =============================================================================== Job complete usr+sys time: 12666.00 seconds wall clock time: 212 minutes 9.89 seconds (12729.89 seconds total)