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_3747331.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3747331.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3747331.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 2.51, per 1000 atoms: 0.38 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: 2.682 distance_ideal: 2.720 ideal - model: 0.038 slack: 0.000 delta_slack: 0.038 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: 2.792 distance_ideal: 2.710 ideal - model: -0.082 slack: 0.000 delta_slack: -0.082 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: 1.15 Conformation dependent library (CDL) restraints added in 217.9 milliseconds Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 1054 1.05 - 1.28: 2400 1.28 - 1.51: 1573 1.51 - 1.75: 891 1.75 - 1.98: 16 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.453 1.640 -0.187 8.30e-03 1.45e+04 5.08e+02 bond pdb=" N HIS A 96 " pdb=" H HIS A 96 " ideal model delta sigma weight residual 0.860 1.257 -0.397 2.00e-02 2.50e+03 3.93e+02 bond pdb=" C GLU A 80 " pdb=" O GLU A 80 " ideal model delta sigma weight residual 1.237 1.005 0.232 1.17e-02 7.31e+03 3.92e+02 bond pdb=" CD1 LEU A 185 " pdb="HD13 LEU A 185 " ideal model delta sigma weight residual 0.970 1.357 -0.387 2.00e-02 2.50e+03 3.74e+02 bond pdb=" N PHE A 119 " pdb=" H PHE A 119 " ideal model delta sigma weight residual 0.860 1.241 -0.381 2.00e-02 2.50e+03 3.63e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 5741 4.28 - 8.56: 3521 8.56 - 12.83: 1299 12.83 - 17.11: 231 17.11 - 21.39: 18 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.20 108.13 11.07 7.30e-01 1.88e+00 2.30e+02 angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" N PRO B 135 " ideal model delta sigma weight residual 119.30 131.17 -11.87 8.10e-01 1.52e+00 2.15e+02 angle pdb=" NE ARG B 83 " pdb=" CZ ARG B 83 " pdb=" NH1 ARG B 83 " ideal model delta sigma weight residual 121.50 107.37 14.13 1.00e+00 1.00e+00 2.00e+02 angle pdb=" NE ARG A 100 " pdb=" CZ ARG A 100 " pdb=" NH2 ARG A 100 " ideal model delta sigma weight residual 119.20 106.59 12.61 9.00e-01 1.23e+00 1.96e+02 angle pdb=" ND1 HIS A 96 " pdb=" CG HIS A 96 " pdb=" CD2 HIS A 96 " ideal model delta sigma weight residual 106.10 120.10 -14.00 1.00e+00 1.00e+00 1.96e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 1846 17.27 - 34.53: 135 34.53 - 51.79: 47 51.79 - 69.06: 18 69.06 - 86.32: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual 180.00 -146.92 -33.08 0 5.00e+00 4.00e-02 4.38e+01 dihedral pdb=" CA ALA A 188 " pdb=" C ALA A 188 " pdb=" N ALA A 189 " pdb=" CA ALA A 189 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -154.07 -25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 194 0.193 - 0.385: 131 0.385 - 0.577: 107 0.577 - 0.769: 47 0.769 - 0.962: 13 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 173 " pdb=" N VAL A 173 " pdb=" C VAL A 173 " pdb=" CB VAL A 173 " both_signs ideal model delta sigma weight residual False 2.44 1.48 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA ALA A 108 " pdb=" N ALA A 108 " pdb=" C ALA A 108 " pdb=" CB ALA A 108 " both_signs ideal model delta sigma weight residual False 2.48 1.54 0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CA THR A 21 " pdb=" N THR A 21 " pdb=" C THR A 21 " pdb=" CB THR A 21 " both_signs ideal model delta sigma weight residual False 2.53 1.61 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.067 2.00e-02 2.50e+03 6.48e-02 1.68e+02 pdb=" CG TRP A 139 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.068 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.043 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.064 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.146 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.011 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.066 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.129 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.044 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 127 " -0.102 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG PHE B 127 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE B 127 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 127 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 127 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 PHE B 127 " -0.108 2.00e-02 2.50e+03 pdb=" CZ PHE B 127 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 PHE B 127 " 0.059 2.00e-02 2.50e+03 pdb=" HD2 PHE B 127 " 0.041 2.00e-02 2.50e+03 pdb=" HE1 PHE B 127 " -0.084 2.00e-02 2.50e+03 pdb=" HE2 PHE B 127 " 0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 127 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.111 2.00e-02 2.50e+03 6.12e-02 1.12e+02 pdb=" CG PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.103 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.088 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.58: 24 1.58 - 2.34: 2074 2.34 - 3.09: 22086 3.09 - 3.85: 33074 3.85 - 4.60: 53044 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110302 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.830 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.938 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.944 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.065 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.090 2.620 ... (remaining 110297 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 12 15.96 2 Mg 2 11.97 3 O 1357 7.97 2 N 488 6.98 3 C 1850 5.99 3 H 2984 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6693 n_use_u_iso = 3419 n_use_u_aniso = 3274 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 6693 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6693 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3419 aniso = 3274) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (1426 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_3747331_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= 0.2032 r_free= 0.1959 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.296253 | | target function (ml) not normalized (work): 804744.046997 | | target function (ml) not normalized (free): 16482.342885 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1874 6.6969 6.2921| | 2: 2.94 - 2.33 1.00 7339 128 0.1627 0.1616 5.5389 5.5992| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1778 5.1396 5.2289| | 4: 2.04 - 1.85 1.00 7170 155 0.1757 0.1465 4.9684 5.008| | 5: 1.85 - 1.72 0.99 7113 159 0.1913 0.1702 4.79 4.7907| | 6: 1.72 - 1.62 0.99 7102 142 0.1941 0.2191 4.6514 4.8485| | 7: 1.62 - 1.54 0.99 7104 148 0.1992 0.1890 4.5589 4.5762| | 8: 1.54 - 1.47 0.96 6798 152 0.2043 0.2069 4.4685 4.4562| | 9: 1.47 - 1.41 0.98 6938 155 0.2109 0.2007 4.3886 4.3853| | 10: 1.41 - 1.36 0.99 7022 150 0.2143 0.2115 4.3173 4.3227| | 11: 1.36 - 1.32 0.99 6997 151 0.2100 0.1993 4.2338 4.1881| | 12: 1.32 - 1.28 0.98 6976 149 0.2081 0.1932 4.1651 4.2097| | 13: 1.28 - 1.25 0.98 6907 166 0.2026 0.2011 4.1119 4.1131| | 14: 1.25 - 1.22 0.98 7015 113 0.2086 0.2258 4.0713 4.1848| | 15: 1.22 - 1.19 0.98 6957 137 0.2079 0.2273 4.0255 4.0625| | 16: 1.19 - 1.17 0.93 6604 132 0.2120 0.2001 3.9967 3.9333| | 17: 1.17 - 1.14 0.98 6941 135 0.2136 0.1895 3.9422 3.9825| | 18: 1.14 - 1.12 0.98 6875 142 0.2204 0.2315 3.9191 3.9117| | 19: 1.12 - 1.10 0.97 6949 106 0.2244 0.2608 3.8626 4.0227| | 20: 1.10 - 1.08 0.97 6884 147 0.2318 0.2304 3.8162 3.8649| | 21: 1.08 - 1.07 0.97 6852 152 0.2455 0.2447 3.799 3.7611| | 22: 1.07 - 1.05 0.97 6838 135 0.2537 0.2588 3.7452 3.7291| | 23: 1.05 - 1.03 0.97 6829 159 0.2735 0.2534 3.7325 3.8004| | 24: 1.03 - 1.02 0.96 6785 133 0.2854 0.2611 3.6963 3.6843| | 25: 1.02 - 1.01 0.93 6552 130 0.3088 0.3160 3.6774 3.8164| | 26: 1.01 - 0.99 0.96 6767 158 0.3200 0.2896 3.6273 3.5477| | 27: 0.99 - 0.98 0.94 6648 131 0.3409 0.3074 3.6444 3.5745| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.31 0.91 0.98 35105.28| | 2: 2.94 - 2.33 7339 128 0.85 21.17 1.08 1.03 15068.87| | 3: 2.33 - 2.04 6939 150 0.93 12.62 1.11 1.05 4197.88| | 4: 2.04 - 1.85 7170 155 0.92 13.48 1.11 1.05 2760.56| | 5: 1.85 - 1.72 7113 159 0.91 15.89 1.12 1.06 2117.17| | 6: 1.72 - 1.62 7102 142 0.89 17.58 1.11 1.06 1761.30| | 7: 1.62 - 1.54 7104 148 0.89 18.04 1.11 1.06 1391.61| | 8: 1.54 - 1.47 6798 152 0.89 17.98 1.11 1.06 1109.03| | 9: 1.47 - 1.41 6938 155 0.89 18.01 1.11 1.07 887.06| | 10: 1.41 - 1.36 7022 150 0.88 18.78 1.09 1.06 767.66| | 11: 1.36 - 1.32 6997 151 0.89 18.64 1.08 1.04 656.35| | 12: 1.32 - 1.28 6976 149 0.88 18.93 1.08 1.03 587.30| | 13: 1.28 - 1.25 6907 166 0.88 19.25 1.07 1.03 562.00| | 14: 1.25 - 1.22 7015 113 0.87 20.41 1.08 1.04 551.75| | 15: 1.22 - 1.19 6957 137 0.87 20.52 1.08 1.04 520.11| | 16: 1.19 - 1.17 6604 132 0.87 20.04 1.08 1.03 468.25| | 17: 1.17 - 1.14 6941 135 0.87 20.62 1.08 1.02 427.23| | 18: 1.14 - 1.12 6875 142 0.86 21.43 1.08 1.00 403.35| | 19: 1.12 - 1.10 6949 106 0.85 22.30 1.07 1.00 384.34| | 20: 1.10 - 1.08 6884 147 0.85 22.78 1.06 0.98 349.30| | 21: 1.08 - 1.07 6852 152 0.84 23.37 1.06 0.98 323.46| | 22: 1.07 - 1.05 6838 135 0.83 24.57 1.06 0.98 308.15| | 23: 1.05 - 1.03 6829 159 0.81 26.69 1.06 0.97 311.69| | 24: 1.03 - 1.02 6785 133 0.79 28.16 1.05 0.98 308.95| | 25: 1.02 - 1.01 6552 130 0.78 29.63 1.03 0.94 293.18| | 26: 1.01 - 0.99 6767 158 0.77 30.39 1.03 0.94 269.15| | 27: 0.99 - 0.98 6648 131 0.77 30.19 1.04 0.94 250.59| |alpha: min = 0.94 max = 1.07 mean = 1.02| |beta: min = 250.59 max = 35105.28 mean = 2798.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.10| |phase err.(test): min = 0.00 max = 89.51 mean = 21.43| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.242 2950 Z= 5.516 Angle : 5.235 17.527 4018 Z= 3.739 Chirality : 0.369 0.962 492 Planarity : 0.032 0.145 512 Dihedral : 12.782 86.320 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.37 % Favored : 96.37 % Rotamer: Outliers : 0.32 % Allowed : 5.48 % Favored : 94.19 % Cbeta Deviations : 30.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.38), residues: 386 helix: -2.26 (0.33), residues: 144 sheet: -1.06 (0.50), residues: 86 loop : -0.12 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.105 0.026 ARG B 100 TYR 0.112 0.035 TYR A 192 PHE 0.100 0.037 PHE A 119 TRP 0.116 0.031 TRP A 146 HIS 0.080 0.031 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2032 r_free= 0.1959 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.296253 | | target function (ml) not normalized (work): 804744.046997 | | target function (ml) not normalized (free): 16482.342885 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2029 0.2032 0.1959 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2029 0.2032 0.1959 n_refl.: 191155 remove outliers: r(all,work,free)=0.2029 0.2032 0.1959 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2029 0.2031 0.1959 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1800 0.1798 0.1911 n_refl.: 191145 remove outliers: r(all,work,free)=0.1798 0.1796 0.1911 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 0.4068 402.814 292.466 0.436 0.912 0.301 13.296-10.522 99.01 99 1 0.2517 528.187 519.649 0.787 0.913 0.251 10.503-8.327 98.90 177 3 0.2499 564.205 557.433 0.973 0.913 0.227 8.318-6.595 100.00 360 8 0.2499 414.736 404.575 0.975 0.913 0.165 6.588-5.215 100.00 711 7 0.2296 381.101 365.569 0.960 0.913 0.160 5.214-4.128 98.38 1367 28 0.1489 557.435 549.577 1.080 0.913 0.090 4.126-3.266 94.74 2603 46 0.1324 508.132 500.003 1.146 0.913 0.028 3.266-2.585 99.86 5447 97 0.1453 342.774 336.939 1.122 0.912 0.000 2.585-2.046 97.45 10613 204 0.1397 258.603 254.370 1.126 0.912 0.000 2.046-1.619 99.39 21536 464 0.1606 153.054 149.895 1.146 0.911 0.000 1.619-1.281 98.00 42464 925 0.1925 82.395 80.196 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2310 44.203 41.692 1.116 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0106 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1796 r_free=0.1911 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1797 r_free=0.1913 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.659346 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.216186 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1270 0.1506 0.0236 0.039 1.2 11.4 0.0 0.3 0 11.330 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.06 2.36 1.117 13.107 577.216 0.018 12.98 15.72 2.74 1.236 13.307 577.216 0.017 Individual atomic B min max mean iso aniso Overall: 5.18 73.04 14.96 1.39 435 3274 Protein: 5.18 40.33 10.98 1.39 0 2902 Water: 6.34 73.04 29.28 N/A 435 370 Other: 15.98 30.36 23.17 N/A 0 2 Chain A: 5.25 60.42 13.00 N/A 0 1626 Chain B: 5.18 73.04 12.74 N/A 0 1648 Chain S: 11.84 61.84 30.69 N/A 435 0 Histogram: Values Number of atoms 5.18 - 11.97 2167 11.97 - 18.75 642 18.75 - 25.54 311 25.54 - 32.32 267 32.32 - 39.11 155 39.11 - 45.90 104 45.90 - 52.68 39 52.68 - 59.47 18 59.47 - 66.25 5 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1572 r_work=0.1297 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1567 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1554 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015494 | | target function (ls_wunit_k1) not normalized (work): 2901.881249 | | target function (ls_wunit_k1) not normalized (free): 116.444570 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1554 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1465 0.1463 0.1629 n_refl.: 191138 remove outliers: r(all,work,free)=0.1465 0.1463 0.1629 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1489 0.1487 0.1639 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1545 n_refl.: 191138 remove outliers: r(all,work,free)=0.1280 0.1275 0.1544 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3598 402.814 381.121 0.469 1.001 0.275 13.296-10.522 99.01 99 1 0.2091 528.187 521.836 0.712 1.003 0.245 10.503-8.327 98.90 177 3 0.1721 564.205 561.641 0.854 1.003 0.198 8.318-6.595 100.00 360 8 0.1701 414.736 412.480 0.876 1.002 0.160 6.588-5.215 100.00 711 7 0.1532 381.101 373.358 0.855 1.003 0.160 5.214-4.128 98.38 1367 28 0.0900 557.435 555.195 0.941 1.003 0.059 4.126-3.266 94.74 2603 46 0.0826 508.132 504.389 1.004 1.004 0.018 3.266-2.585 99.86 5447 97 0.0918 342.774 340.349 0.987 1.003 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.359 0.998 1.004 0.000 2.046-1.619 99.39 21536 464 0.1091 153.054 151.382 1.015 1.004 0.000 1.619-1.281 98.00 42464 925 0.1283 82.395 81.403 1.006 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.169 0.984 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0386 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1544 | n_water=805 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1280 r_free=0.1551 | n_water=793 | time (s): 99.050 (total time: 101.710) Filter (q & B) r_work=0.1281 r_free=0.1550 | n_water=788 | time (s): 5.530 (total time: 107.240) Compute maps r_work=0.1281 r_free=0.1550 | n_water=788 | time (s): 2.420 (total time: 109.660) Filter (map) r_work=0.1307 r_free=0.1529 | n_water=653 | time (s): 5.320 (total time: 114.980) Find peaks r_work=0.1307 r_free=0.1529 | n_water=653 | time (s): 0.550 (total time: 115.530) Add new water r_work=0.1330 r_free=0.1554 | n_water=954 | time (s): 4.780 (total time: 120.310) Refine new water occ: r_work=0.1286 r_free=0.1512 adp: r_work=0.1274 r_free=0.1508 occ: r_work=0.1276 r_free=0.1508 adp: r_work=0.1269 r_free=0.1506 occ: r_work=0.1270 r_free=0.1505 adp: r_work=0.1268 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1506 r_work=0.1268 r_free=0.1506 | n_water=954 | time (s): 78.470 (total time: 198.780) Filter (q & B) r_work=0.1271 r_free=0.1506 | n_water=884 | time (s): 5.490 (total time: 204.270) Filter (dist only) r_work=0.1272 r_free=0.1506 | n_water=883 | time (s): 110.730 (total time: 315.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.394473 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 591.720295 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 0.1256 0.1520 0.0265 0.041 1.1 17.3 0.0 0.0 0 11.697 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.20 2.65 2.036 15.143 591.720 0.014 12.34 15.06 2.72 2.370 15.177 591.720 0.014 Individual atomic B min max mean iso aniso Overall: 5.44 68.53 16.24 1.20 515 3272 Protein: 5.44 39.99 10.98 1.20 0 2902 Water: 6.60 68.53 33.52 N/A 515 368 Other: 16.31 32.03 24.17 N/A 0 2 Chain A: 5.51 57.72 12.96 N/A 0 1624 Chain B: 5.44 68.53 12.80 N/A 0 1648 Chain S: 9.35 64.86 37.62 N/A 515 0 Histogram: Values Number of atoms 5.44 - 11.75 2080 11.75 - 18.06 688 18.06 - 24.37 273 24.37 - 30.68 219 30.68 - 36.99 174 36.99 - 43.30 162 43.30 - 49.60 101 49.60 - 55.91 41 55.91 - 62.22 38 62.22 - 68.53 11 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1506 r_work=0.1235 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1507 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 = 0.1501 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1501 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013485 | | target function (ls_wunit_k1) not normalized (work): 2525.682790 | | target function (ls_wunit_k1) not normalized (free): 97.265248 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1501 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1437 0.1435 0.1591 n_refl.: 191137 remove outliers: r(all,work,free)=0.1437 0.1435 0.1591 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1432 0.1590 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1510 n_refl.: 191137 remove outliers: r(all,work,free)=0.1241 0.1236 0.1510 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3249 402.814 379.127 0.493 0.963 0.274 13.296-10.522 99.01 99 1 0.1922 528.187 518.475 0.753 0.964 0.220 10.503-8.327 98.90 177 3 0.1443 564.205 564.933 0.918 0.964 0.181 8.318-6.595 100.00 360 8 0.1537 414.736 414.870 0.937 0.963 0.173 6.588-5.215 100.00 711 7 0.1363 381.101 376.532 0.912 0.963 0.139 5.214-4.128 98.38 1367 28 0.0825 557.435 556.104 0.996 0.963 0.090 4.126-3.266 94.74 2603 46 0.0757 508.132 505.668 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0859 342.774 341.298 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0903 258.603 256.747 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.639 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1258 82.395 81.356 1.072 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.216 1.057 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0438 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1511 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1511 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1511 | n_water=883 | time (s): 3.530 (total time: 3.530) Filter (dist) r_work=0.1237 r_free=0.1513 | n_water=879 | time (s): 110.740 (total time: 114.270) Filter (q & B) r_work=0.1237 r_free=0.1513 | n_water=877 | time (s): 4.350 (total time: 118.620) Compute maps r_work=0.1237 r_free=0.1513 | n_water=877 | time (s): 2.300 (total time: 120.920) Filter (map) r_work=0.1276 r_free=0.1528 | n_water=684 | time (s): 5.890 (total time: 126.810) Find peaks r_work=0.1276 r_free=0.1528 | n_water=684 | time (s): 0.690 (total time: 127.500) Add new water r_work=0.1300 r_free=0.1560 | n_water=1006 | time (s): 4.540 (total time: 132.040) Refine new water occ: r_work=0.1253 r_free=0.1510 adp: r_work=0.1254 r_free=0.1509 occ: r_work=0.1250 r_free=0.1508 adp: r_work=0.1249 r_free=0.1508 occ: r_work=0.1246 r_free=0.1508 adp: r_work=0.1246 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1246 r_free=0.1507 r_work=0.1246 r_free=0.1507 | n_water=1006 | time (s): 388.500 (total time: 520.540) Filter (q & B) r_work=0.1251 r_free=0.1512 | n_water=872 | time (s): 4.300 (total time: 524.840) Filter (dist only) r_work=0.1251 r_free=0.1512 | n_water=871 | time (s): 113.750 (total time: 638.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.741705 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.153875 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 0.1240 0.1428 0.0188 0.035 1.1 7.5 0.0 0.0 0 0.871 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.28 1.88 1.933 14.532 16.154 3.940 12.34 13.89 1.55 2.268 14.428 16.154 3.896 Individual atomic B min max mean iso aniso Overall: 5.55 68.08 15.15 1.05 504 3271 Protein: 5.55 36.09 10.72 1.05 0 2902 Water: 6.69 68.08 29.90 N/A 504 367 Other: 14.00 27.70 20.85 N/A 0 2 Chain A: 5.55 56.67 12.71 N/A 0 1624 Chain B: 5.56 68.08 12.49 N/A 0 1647 Chain S: 13.57 59.96 31.69 N/A 504 0 Histogram: Values Number of atoms 5.55 - 11.81 2148 11.81 - 18.06 686 18.06 - 24.31 299 24.31 - 30.57 238 30.57 - 36.82 169 36.82 - 43.07 140 43.07 - 49.32 62 49.32 - 55.58 21 55.58 - 61.83 11 61.83 - 68.08 1 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1389 r_work=0.1235 r_free=0.1390 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1390 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1383 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890546 | | target function (ml) not normalized (work): 728683.790236 | | target function (ml) not normalized (free): 15219.855750 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1383 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1442 0.1442 0.1477 n_refl.: 191137 remove outliers: r(all,work,free)=0.1442 0.1442 0.1477 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1436 0.1473 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1379 n_refl.: 191137 remove outliers: r(all,work,free)=0.1227 0.1224 0.1379 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 0.3930 398.008 363.000 0.425 0.947 0.249 13.296-10.522 99.01 99 1 0.2477 528.187 509.360 0.705 0.948 0.215 10.503-8.327 97.80 175 3 0.2025 554.286 556.912 0.880 0.948 0.164 8.318-6.595 100.00 360 8 0.2085 414.736 410.700 0.897 0.947 0.130 6.588-5.215 100.00 711 7 0.1817 381.101 370.414 0.886 0.948 0.120 5.214-4.128 98.38 1367 28 0.1154 557.435 552.003 0.973 0.948 0.080 4.126-3.266 94.74 2603 46 0.1089 508.132 501.624 1.033 0.948 0.014 3.266-2.585 99.86 5447 97 0.1092 342.774 339.155 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0965 258.603 255.687 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0970 153.054 151.398 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.481 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.310 1.037 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0928 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1379 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1379 | n_water=871 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1224 r_free=0.1379 | n_water=871 | time (s): 108.160 (total time: 110.710) Filter (q & B) r_work=0.1225 r_free=0.1380 | n_water=861 | time (s): 4.570 (total time: 115.280) Compute maps r_work=0.1225 r_free=0.1380 | n_water=861 | time (s): 1.900 (total time: 117.180) Filter (map) r_work=0.1245 r_free=0.1387 | n_water=718 | time (s): 5.550 (total time: 122.730) Find peaks r_work=0.1245 r_free=0.1387 | n_water=718 | time (s): 0.860 (total time: 123.590) Add new water r_work=0.1260 r_free=0.1397 | n_water=960 | time (s): 4.740 (total time: 128.330) Refine new water occ: r_work=0.1212 r_free=0.1357 adp: r_work=0.1205 r_free=0.1353 occ: r_work=0.1202 r_free=0.1352 adp: r_work=0.1202 r_free=0.1351 occ: r_work=0.1200 r_free=0.1350 adp: r_work=0.1200 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1349 r_work=0.1200 r_free=0.1349 | n_water=960 | time (s): 297.850 (total time: 426.180) Filter (q & B) r_work=0.1205 r_free=0.1354 | n_water=866 | time (s): 5.710 (total time: 431.890) Filter (dist only) r_work=0.1205 r_free=0.1353 | n_water=865 | time (s): 114.840 (total time: 546.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.561641 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.847065 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1357 0.0153 0.036 1.1 6.0 0.0 0.3 0 0.781 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.57 1.53 1.824 14.155 15.847 3.873 11.96 13.53 1.57 1.952 14.111 15.847 3.864 Individual atomic B min max mean iso aniso Overall: 5.49 67.57 14.90 0.99 498 3271 Protein: 5.49 32.88 10.63 0.99 0 2902 Water: 5.88 67.57 29.19 N/A 498 367 Other: 14.02 26.38 20.20 N/A 0 2 Chain A: 5.54 55.16 12.57 N/A 0 1624 Chain B: 5.49 67.57 12.39 N/A 0 1647 Chain S: 5.88 60.02 30.79 N/A 498 0 Histogram: Values Number of atoms 5.49 - 11.70 2114 11.70 - 17.90 745 17.90 - 24.11 286 24.11 - 30.32 243 30.32 - 36.53 169 36.53 - 42.73 128 42.73 - 48.94 56 48.94 - 55.15 17 55.15 - 61.36 10 61.36 - 67.57 1 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1353 r_work=0.1197 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1354 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1349 target_work(ml) = 3.861 | | 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= 0.1195 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861487 | | target function (ml) not normalized (work): 723229.445505 | | target function (ml) not normalized (free): 15129.476653 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1422 0.1422 0.1450 n_refl.: 191134 remove outliers: r(all,work,free)=0.1422 0.1422 0.1450 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1415 0.1415 0.1446 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1348 n_refl.: 191134 remove outliers: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3668 357.109 322.540 0.415 0.945 0.245 13.296-10.522 96.04 96 1 0.2379 480.435 446.635 0.700 0.946 0.209 10.503-8.327 97.80 175 3 0.2073 501.911 496.087 0.866 0.946 0.158 8.318-6.595 100.00 360 8 0.2143 375.548 371.455 0.897 0.946 0.120 6.588-5.215 100.00 711 7 0.1903 345.091 334.785 0.886 0.946 0.089 5.214-4.128 98.38 1367 28 0.1192 504.763 499.361 0.976 0.946 0.070 4.126-3.266 94.74 2603 46 0.1105 460.119 453.874 1.036 0.947 0.005 3.266-2.585 99.86 5447 97 0.1095 310.385 307.179 1.022 0.946 0.000 2.585-2.046 97.45 10613 204 0.0931 234.168 231.771 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0906 138.592 137.321 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.0984 74.610 73.914 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.025 38.369 1.038 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1134 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1348 | n_water=865 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1192 r_free=0.1348 | n_water=865 | time (s): 103.200 (total time: 105.460) Filter (q & B) r_work=0.1192 r_free=0.1348 | n_water=856 | time (s): 4.820 (total time: 110.280) Compute maps r_work=0.1192 r_free=0.1348 | n_water=856 | time (s): 2.320 (total time: 112.600) Filter (map) r_work=0.1215 r_free=0.1361 | n_water=737 | time (s): 5.960 (total time: 118.560) Find peaks r_work=0.1215 r_free=0.1361 | n_water=737 | time (s): 0.830 (total time: 119.390) Add new water r_work=0.1226 r_free=0.1378 | n_water=958 | time (s): 4.900 (total time: 124.290) Refine new water occ: r_work=0.1192 r_free=0.1340 adp: r_work=0.1192 r_free=0.1339 occ: r_work=0.1189 r_free=0.1339 adp: r_work=0.1189 r_free=0.1339 occ: r_work=0.1187 r_free=0.1338 adp: r_work=0.1187 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1338 r_work=0.1187 r_free=0.1338 | n_water=958 | time (s): 263.240 (total time: 387.530) Filter (q & B) r_work=0.1191 r_free=0.1344 | n_water=884 | time (s): 5.420 (total time: 392.950) Filter (dist only) r_work=0.1191 r_free=0.1344 | n_water=883 | time (s): 111.690 (total time: 504.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.516158 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.249419 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1348 0.0154 0.036 1.1 7.0 0.0 0.3 0 0.758 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.48 1.54 1.783 14.092 15.249 3.762 11.98 13.53 1.55 1.823 14.075 15.249 3.760 Individual atomic B min max mean iso aniso Overall: 5.57 67.32 14.93 0.96 516 3271 Protein: 5.57 31.87 10.58 0.96 0 2902 Water: 5.98 67.32 29.18 N/A 516 367 Other: 13.81 25.64 19.72 N/A 0 2 Chain A: 5.60 54.55 12.50 N/A 0 1624 Chain B: 5.57 67.32 12.32 N/A 0 1647 Chain S: 5.98 60.02 30.87 N/A 516 0 Histogram: Values Number of atoms 5.57 - 11.74 2150 11.74 - 17.92 719 17.92 - 24.09 298 24.09 - 30.27 229 30.27 - 36.44 167 36.44 - 42.62 136 42.62 - 48.80 62 48.80 - 54.97 17 54.97 - 61.15 8 61.15 - 67.32 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1353 r_work=0.1198 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1353 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1353 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759169 | | target function (ml) not normalized (work): 704047.230053 | | target function (ml) not normalized (free): 14742.300154 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1352 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1458 n_refl.: 191129 remove outliers: r(all,work,free)=0.1402 0.1401 0.1458 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1395 0.1394 0.1454 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1349 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3701 352.488 323.772 0.386 0.951 0.209 13.296-10.522 96.04 96 1 0.2377 480.435 462.972 0.695 0.953 0.161 10.503-8.327 97.80 175 3 0.2130 501.911 494.908 0.859 0.953 0.140 8.318-6.595 100.00 360 8 0.2127 375.548 371.027 0.890 0.952 0.118 6.588-5.215 100.00 711 7 0.1913 345.091 335.382 0.880 0.953 0.090 5.214-4.128 98.38 1367 28 0.1201 504.763 499.484 0.970 0.953 0.080 4.126-3.266 94.74 2603 46 0.1127 460.119 453.494 1.031 0.953 0.005 3.266-2.585 99.86 5447 97 0.1103 310.385 307.083 1.016 0.952 0.000 2.585-2.046 97.45 10613 204 0.0946 234.168 231.657 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0911 138.592 137.260 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0974 74.610 73.897 1.050 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.025 38.356 1.038 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1275 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1349 | n_water=883 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1194 r_free=0.1349 | n_water=883 | time (s): 104.940 (total time: 107.280) Filter (q & B) r_work=0.1195 r_free=0.1349 | n_water=873 | time (s): 4.720 (total time: 112.000) Compute maps r_work=0.1195 r_free=0.1349 | n_water=873 | time (s): 2.470 (total time: 114.470) Filter (map) r_work=0.1214 r_free=0.1355 | n_water=756 | time (s): 4.260 (total time: 118.730) Find peaks r_work=0.1214 r_free=0.1355 | n_water=756 | time (s): 0.730 (total time: 119.460) Add new water r_work=0.1226 r_free=0.1360 | n_water=981 | time (s): 4.860 (total time: 124.320) Refine new water occ: r_work=0.1191 r_free=0.1326 adp: r_work=0.1191 r_free=0.1326 occ: r_work=0.1189 r_free=0.1327 adp: r_work=0.1189 r_free=0.1327 occ: r_work=0.1189 r_free=0.1327 adp: r_work=0.1189 r_free=0.1327 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1327 r_work=0.1189 r_free=0.1327 | n_water=981 | time (s): 202.610 (total time: 326.930) Filter (q & B) r_work=0.1194 r_free=0.1339 | n_water=883 | time (s): 5.460 (total time: 332.390) Filter (dist only) r_work=0.1194 r_free=0.1338 | n_water=882 | time (s): 113.770 (total time: 446.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570205 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.073909 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1345 0.0149 0.037 1.1 5.6 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.45 1.49 1.760 13.917 15.074 3.760 12.00 13.47 1.47 1.885 13.885 15.074 3.758 Individual atomic B min max mean iso aniso Overall: 5.58 66.23 14.65 0.91 515 3271 Protein: 5.58 29.34 10.49 0.91 0 2902 Water: 6.05 66.23 28.35 N/A 515 367 Other: 13.81 23.05 18.43 N/A 0 2 Chain A: 5.63 51.56 12.37 N/A 0 1624 Chain B: 5.58 66.23 12.21 N/A 0 1647 Chain S: 6.05 60.29 29.69 N/A 515 0 Histogram: Values Number of atoms 5.58 - 11.64 2127 11.64 - 17.71 765 17.71 - 23.77 307 23.77 - 29.84 227 29.84 - 35.91 139 35.91 - 41.97 130 41.97 - 48.04 60 48.04 - 54.10 23 54.10 - 60.17 6 60.17 - 66.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1348 r_work=0.1200 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1348 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1348 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.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756887 | | target function (ml) not normalized (work): 703616.177168 | | target function (ml) not normalized (free): 14736.573596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1348 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1405 0.1404 0.1466 n_refl.: 191128 remove outliers: r(all,work,free)=0.1405 0.1404 0.1466 n_refl.: 191128 overall B=-0.22 to atoms: r(all,work,free)=0.1369 0.1368 0.1444 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1348 n_refl.: 191128 remove outliers: r(all,work,free)=0.1200 0.1197 0.1348 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3768 352.488 318.940 0.385 0.951 0.201 13.296-10.522 96.04 96 1 0.2403 480.435 463.222 0.711 0.952 0.148 10.503-8.327 97.80 175 3 0.2187 501.911 494.299 0.877 0.953 0.127 8.318-6.595 100.00 360 8 0.2181 375.548 371.108 0.905 0.952 0.100 6.588-5.215 100.00 711 7 0.1935 345.091 335.555 0.903 0.952 0.090 5.214-4.128 98.38 1367 28 0.1228 504.763 499.389 0.995 0.953 0.080 4.126-3.266 94.74 2603 46 0.1139 460.119 453.258 1.057 0.953 0.005 3.266-2.585 99.86 5447 97 0.1115 310.385 307.072 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0952 234.168 231.639 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0911 138.592 137.282 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0968 74.610 73.907 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.025 38.360 1.025 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0493 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1348 | n_water=882 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1198 r_free=0.1350 | n_water=880 | time (s): 123.490 (total time: 125.790) Filter (q & B) r_work=0.1199 r_free=0.1351 | n_water=871 | time (s): 5.160 (total time: 130.950) Compute maps r_work=0.1199 r_free=0.1351 | n_water=871 | time (s): 2.230 (total time: 133.180) Filter (map) r_work=0.1219 r_free=0.1354 | n_water=757 | time (s): 4.940 (total time: 138.120) Find peaks r_work=0.1219 r_free=0.1354 | n_water=757 | time (s): 0.800 (total time: 138.920) Add new water r_work=0.1229 r_free=0.1362 | n_water=984 | time (s): 4.690 (total time: 143.610) Refine new water occ: r_work=0.1194 r_free=0.1327 adp: r_work=0.1194 r_free=0.1326 occ: r_work=0.1192 r_free=0.1328 adp: r_work=0.1192 r_free=0.1328 occ: r_work=0.1192 r_free=0.1328 adp: r_work=0.1192 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1328 r_work=0.1192 r_free=0.1328 | n_water=984 | time (s): 140.810 (total time: 284.420) Filter (q & B) r_work=0.1197 r_free=0.1341 | n_water=881 | time (s): 4.140 (total time: 288.560) Filter (dist only) r_work=0.1197 r_free=0.1340 | n_water=880 | time (s): 113.640 (total time: 402.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.581819 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.944097 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 0.1351 0.0150 0.038 1.1 5.5 0.0 0.3 0 0.791 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.51 1.50 1.720 13.581 14.944 3.759 12.02 13.52 1.50 1.769 13.573 14.944 3.756 Individual atomic B min max mean iso aniso Overall: 5.40 64.92 14.36 0.89 513 3271 Protein: 5.40 28.42 10.24 0.89 0 2902 Water: 5.79 64.92 27.91 N/A 513 367 Other: 13.66 21.99 17.82 N/A 0 2 Chain A: 5.44 50.75 12.08 N/A 0 1624 Chain B: 5.40 64.92 11.94 N/A 0 1647 Chain S: 5.79 60.28 29.31 N/A 513 0 Histogram: Values Number of atoms 5.40 - 11.35 2102 11.35 - 17.30 787 17.30 - 23.25 296 23.25 - 29.21 239 29.21 - 35.16 142 35.16 - 41.11 112 41.11 - 47.06 71 47.06 - 53.01 26 53.01 - 58.97 6 58.97 - 64.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1353 r_work=0.1202 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1353 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1355 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756154 | | target function (ml) not normalized (work): 703478.787001 | | target function (ml) not normalized (free): 14740.221466 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1355 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1378 0.1377 0.1453 n_refl.: 191128 remove outliers: r(all,work,free)=0.1378 0.1377 0.1453 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1378 0.1377 0.1453 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1345 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1345 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3855 352.488 315.796 0.351 0.995 0.181 13.296-10.522 96.04 96 1 0.2438 480.435 463.001 0.669 0.997 0.140 10.503-8.327 97.80 175 3 0.2179 501.911 493.588 0.829 0.998 0.111 8.315-6.595 100.00 359 8 0.2170 374.602 370.449 0.855 0.997 0.095 6.588-5.215 100.00 711 7 0.1953 345.091 334.882 0.854 0.998 0.090 5.214-4.128 98.38 1367 28 0.1249 504.763 498.860 0.941 0.999 0.049 4.126-3.266 94.74 2603 46 0.1164 460.119 452.517 1.001 1.000 0.005 3.266-2.585 99.86 5447 97 0.1125 310.385 306.823 0.984 1.000 0.000 2.585-2.046 97.45 10613 204 0.0955 234.168 231.546 0.990 1.002 0.000 2.046-1.619 99.39 21536 464 0.0906 138.592 137.200 1.004 1.005 0.000 1.619-1.281 98.00 42464 925 0.0948 74.610 73.947 0.990 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.025 38.334 0.953 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1345 | n_water=880 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1191 r_free=0.1345 | n_water=880 | time (s): 118.580 (total time: 120.970) Filter (q & B) r_work=0.1192 r_free=0.1343 | n_water=870 | time (s): 5.090 (total time: 126.060) Compute maps r_work=0.1192 r_free=0.1343 | n_water=870 | time (s): 2.060 (total time: 128.120) Filter (map) r_work=0.1213 r_free=0.1344 | n_water=758 | time (s): 5.470 (total time: 133.590) Find peaks r_work=0.1213 r_free=0.1344 | n_water=758 | time (s): 0.680 (total time: 134.270) Add new water r_work=0.1222 r_free=0.1349 | n_water=985 | time (s): 4.050 (total time: 138.320) Refine new water occ: r_work=0.1186 r_free=0.1317 adp: r_work=0.1187 r_free=0.1316 occ: r_work=0.1184 r_free=0.1318 adp: r_work=0.1184 r_free=0.1317 occ: r_work=0.1183 r_free=0.1318 adp: r_work=0.1183 r_free=0.1317 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1317 r_work=0.1183 r_free=0.1317 | n_water=985 | time (s): 202.630 (total time: 340.950) Filter (q & B) r_work=0.1187 r_free=0.1331 | n_water=903 | time (s): 4.830 (total time: 345.780) Filter (dist only) r_work=0.1187 r_free=0.1330 | n_water=902 | time (s): 115.050 (total time: 460.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.535594 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.315506 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1342 0.0153 0.039 1.1 6.7 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.42 1.53 1.678 13.637 14.316 3.754 11.91 13.44 1.52 1.695 13.626 14.316 3.753 Individual atomic B min max mean iso aniso Overall: 5.43 64.16 14.51 0.87 535 3271 Protein: 5.43 27.98 10.25 0.87 0 2902 Water: 5.85 64.16 28.20 N/A 535 367 Other: 13.69 22.07 17.88 N/A 0 2 Chain A: 5.50 50.40 12.05 N/A 0 1624 Chain B: 5.43 64.16 11.92 N/A 0 1647 Chain S: 5.85 60.45 29.95 N/A 535 0 Histogram: Values Number of atoms 5.43 - 11.31 2082 11.31 - 17.18 813 17.18 - 23.05 271 23.05 - 28.92 231 28.92 - 34.80 173 34.80 - 40.67 116 40.67 - 46.54 82 46.54 - 52.41 28 52.41 - 58.29 7 58.29 - 64.16 3 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1344 r_work=0.1192 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1344 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1347 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752828 | | target function (ml) not normalized (work): 702852.072698 | | target function (ml) not normalized (free): 14730.856751 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1347 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1382 0.1380 0.1467 n_refl.: 191127 remove outliers: r(all,work,free)=0.1382 0.1380 0.1467 n_refl.: 191127 overall B=0.00 to atoms: r(all,work,free)=0.1382 0.1380 0.1467 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191127 remove outliers: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3833 352.488 316.269 0.358 0.976 0.181 13.296-10.522 96.04 96 1 0.2410 480.435 464.381 0.676 0.977 0.124 10.503-8.327 97.80 175 3 0.2166 501.911 493.336 0.847 0.978 0.098 8.315-6.595 100.00 359 8 0.2136 374.602 369.756 0.870 0.978 0.086 6.588-5.215 100.00 711 7 0.1936 345.091 335.353 0.871 0.978 0.077 5.214-4.128 98.38 1367 28 0.1237 504.763 499.194 0.960 0.979 0.039 4.126-3.266 94.74 2603 46 0.1162 460.119 452.552 1.022 0.980 0.005 3.266-2.585 99.86 5447 97 0.1124 310.385 306.844 1.004 0.981 0.000 2.585-2.046 97.45 10613 204 0.0955 234.168 231.577 1.011 0.983 0.000 2.046-1.619 99.39 21536 464 0.0906 138.592 137.226 1.025 0.986 0.000 1.619-1.281 98.00 42464 925 0.0945 74.610 73.957 1.013 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.025 38.324 0.977 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0784 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1190 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1348 | n_water=902 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1190 r_free=0.1349 | n_water=901 | time (s): 122.090 (total time: 124.810) Filter (q & B) r_work=0.1191 r_free=0.1349 | n_water=892 | time (s): 5.110 (total time: 129.920) Compute maps r_work=0.1191 r_free=0.1349 | n_water=892 | time (s): 2.590 (total time: 132.510) Filter (map) r_work=0.1214 r_free=0.1354 | n_water=774 | time (s): 5.580 (total time: 138.090) Find peaks r_work=0.1214 r_free=0.1354 | n_water=774 | time (s): 0.670 (total time: 138.760) Add new water r_work=0.1220 r_free=0.1365 | n_water=972 | time (s): 3.960 (total time: 142.720) Refine new water occ: r_work=0.1188 r_free=0.1336 adp: r_work=0.1188 r_free=0.1335 occ: r_work=0.1187 r_free=0.1336 adp: r_work=0.1187 r_free=0.1336 occ: r_work=0.1185 r_free=0.1337 adp: r_work=0.1185 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1336 r_work=0.1185 r_free=0.1336 | n_water=972 | time (s): 221.010 (total time: 363.730) Filter (q & B) r_work=0.1189 r_free=0.1342 | n_water=900 | time (s): 4.270 (total time: 368.000) Filter (dist only) r_work=0.1189 r_free=0.1341 | n_water=899 | time (s): 113.360 (total time: 481.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.546273 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.319213 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 0.1344 0.0152 0.039 1.1 5.5 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.44 1.52 1.670 13.606 14.319 3.754 11.92 13.45 1.53 1.681 13.605 14.319 3.752 Individual atomic B min max mean iso aniso Overall: 5.47 63.12 14.47 0.87 532 3271 Protein: 5.47 27.83 10.26 0.87 0 2902 Water: 5.87 63.12 28.07 N/A 532 367 Other: 13.72 22.01 17.86 N/A 0 2 Chain A: 5.52 49.89 12.03 N/A 0 1624 Chain B: 5.47 63.12 11.90 N/A 0 1647 Chain S: 5.87 60.61 29.88 N/A 532 0 Histogram: Values Number of atoms 5.47 - 11.23 2063 11.23 - 17.00 829 17.00 - 22.77 275 22.77 - 28.53 220 28.53 - 34.30 173 34.30 - 40.06 127 40.06 - 45.83 73 45.83 - 51.59 31 51.59 - 57.36 8 57.36 - 63.12 4 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1345 r_work=0.1192 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1345 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1346 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752057 | | target function (ml) not normalized (work): 702707.744463 | | target function (ml) not normalized (free): 14723.564849 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1346 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1390 0.1389 0.1468 n_refl.: 191127 remove outliers: r(all,work,free)=0.1390 0.1389 0.1468 n_refl.: 191127 overall B=0.00 to atoms: r(all,work,free)=0.1390 0.1389 0.1468 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1342 n_refl.: 191127 remove outliers: r(all,work,free)=0.1193 0.1190 0.1342 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3986 352.488 314.745 0.345 0.911 0.120 13.296-10.522 96.04 96 1 0.2424 480.435 462.337 0.714 0.912 0.113 10.503-8.327 97.80 175 3 0.2161 501.911 493.667 0.901 0.912 0.105 8.315-6.595 100.00 359 8 0.2149 374.602 369.561 0.924 0.912 0.091 6.588-5.215 100.00 711 7 0.1947 345.091 335.144 0.925 0.913 0.080 5.214-4.128 98.38 1367 28 0.1250 504.763 499.160 1.023 0.914 0.039 4.126-3.266 94.74 2603 46 0.1169 460.119 452.468 1.089 0.915 0.005 3.266-2.585 99.86 5447 97 0.1122 310.385 306.858 1.071 0.916 0.000 2.585-2.046 97.45 10613 204 0.0958 234.168 231.537 1.078 0.918 0.000 2.046-1.619 99.39 21536 464 0.0906 138.592 137.228 1.094 0.921 0.000 1.619-1.281 98.00 42464 925 0.0942 74.610 73.962 1.081 0.927 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.025 38.317 1.045 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0408 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1342 After: r_work=0.1191 r_free=0.1343 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1343 | n_water=899 | time (s): 3.170 (total time: 3.170) Filter (dist) r_work=0.1191 r_free=0.1343 | n_water=899 | time (s): 123.750 (total time: 126.920) Filter (q & B) r_work=0.1192 r_free=0.1344 | n_water=890 | time (s): 5.510 (total time: 132.430) Compute maps r_work=0.1192 r_free=0.1344 | n_water=890 | time (s): 1.770 (total time: 134.200) Filter (map) r_work=0.1215 r_free=0.1354 | n_water=783 | time (s): 4.580 (total time: 138.780) Find peaks r_work=0.1215 r_free=0.1354 | n_water=783 | time (s): 0.750 (total time: 139.530) Add new water r_work=0.1220 r_free=0.1363 | n_water=974 | time (s): 4.330 (total time: 143.860) Refine new water occ: r_work=0.1189 r_free=0.1329 adp: r_work=0.1190 r_free=0.1329 occ: r_work=0.1188 r_free=0.1331 adp: r_work=0.1188 r_free=0.1330 occ: r_work=0.1186 r_free=0.1332 adp: r_work=0.1186 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1332 r_work=0.1186 r_free=0.1332 | n_water=974 | time (s): 218.160 (total time: 362.020) Filter (q & B) r_work=0.1190 r_free=0.1338 | n_water=896 | time (s): 4.680 (total time: 366.700) Filter (dist only) r_work=0.1190 r_free=0.1338 | n_water=895 | time (s): 114.760 (total time: 481.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550025 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.551606 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1339 0.0149 0.039 1.1 7.5 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.39 1.49 1.667 13.584 14.552 3.753 11.90 13.39 1.49 1.659 13.587 14.552 3.751 Individual atomic B min max mean iso aniso Overall: 5.48 62.80 14.44 0.86 528 3271 Protein: 5.48 27.84 10.29 0.86 0 2902 Water: 5.98 62.80 27.90 N/A 528 367 Other: 13.77 22.02 17.90 N/A 0 2 Chain A: 5.57 49.77 12.03 N/A 0 1624 Chain B: 5.48 62.80 11.91 N/A 0 1647 Chain S: 5.98 60.64 29.72 N/A 528 0 Histogram: Values Number of atoms 5.48 - 11.22 2053 11.22 - 16.95 837 16.95 - 22.68 276 22.68 - 28.41 229 28.41 - 34.14 167 34.14 - 39.87 115 39.87 - 45.60 80 45.60 - 51.34 30 51.34 - 57.07 8 57.07 - 62.80 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1339 r_work=0.1190 r_free=0.1340 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1340 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1341 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1341 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751040 | | target function (ml) not normalized (work): 702517.221016 | | target function (ml) not normalized (free): 14716.593639 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1362 0.1425 5.6882 5.7613| | 2: 2.94 - 2.33 1.00 7339 128 0.1069 0.1316 5.0729 5.1643| | 3: 2.33 - 2.04 0.96 6939 150 0.0897 0.1164 4.6454 4.743| | 4: 2.04 - 1.85 1.00 7170 155 0.0892 0.1036 4.3849 4.5474| | 5: 1.85 - 1.72 0.99 7113 159 0.0928 0.0992 4.1465 4.2409| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1094 3.9484 4.0888| | 7: 1.62 - 1.54 0.99 7104 148 0.0887 0.0980 3.7982 3.9375| | 8: 1.54 - 1.47 0.96 6798 152 0.0884 0.1310 3.6957 3.9006| | 9: 1.47 - 1.41 0.98 6938 155 0.0920 0.1106 3.6169 3.7425| | 10: 1.41 - 1.36 0.99 7022 150 0.0971 0.1179 3.5515 3.6815| | 11: 1.36 - 1.32 0.99 6997 151 0.0988 0.1119 3.4796 3.5774| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1129 3.4544 3.5789| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1238 3.4324 3.5545| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1579 3.4274 3.6733| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1238 3.4437 3.4889| | 16: 1.19 - 1.17 0.93 6604 132 0.1246 0.1549 3.4614 3.6557| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1233 3.432 3.4455| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1704 3.4372 3.5338| | 19: 1.12 - 1.10 0.97 6948 106 0.1466 0.1739 3.4172 3.5924| | 20: 1.10 - 1.08 0.97 6884 147 0.1579 0.1577 3.4079 3.4313| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2120 3.4169 3.4989| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1958 3.412 3.4163| | 23: 1.05 - 1.03 0.97 6827 159 0.2115 0.2021 3.4319 3.4842| | 24: 1.03 - 1.02 0.96 6784 133 0.2328 0.2255 3.4347 3.5086| | 25: 1.02 - 1.01 0.93 6552 130 0.2609 0.2502 3.448 3.5233| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2866 3.4152 3.4231| | 27: 0.99 - 0.98 0.94 6647 131 0.3035 0.2800 3.4676 3.3937| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7395 127 0.93 11.61 1.00 0.98 11078.60| | 2: 2.94 - 2.33 7339 128 0.93 12.65 0.99 0.98 5045.88| | 3: 2.33 - 2.04 6939 150 0.96 7.46 1.01 0.98 1653.65| | 4: 2.04 - 1.85 7170 155 0.96 7.53 1.00 0.98 987.03| | 5: 1.85 - 1.72 7113 159 0.96 8.08 1.00 0.98 634.36| | 6: 1.72 - 1.62 7102 142 0.96 8.10 1.00 0.98 448.93| | 7: 1.62 - 1.54 7104 148 0.96 8.21 1.01 0.99 340.66| | 8: 1.54 - 1.47 6798 152 0.96 8.31 1.01 1.00 280.85| | 9: 1.47 - 1.41 6938 155 0.96 8.44 1.00 1.00 230.07| | 10: 1.41 - 1.36 7022 150 0.96 8.88 1.00 0.99 201.29| | 11: 1.36 - 1.32 6997 151 0.96 8.86 0.99 0.98 173.06| | 12: 1.32 - 1.28 6975 149 0.96 8.91 0.98 0.97 159.06| | 13: 1.28 - 1.25 6907 166 0.96 9.45 1.01 0.98 156.25| | 14: 1.25 - 1.22 7015 112 0.95 10.59 1.01 0.99 160.93| | 15: 1.22 - 1.19 6956 137 0.95 11.14 1.01 1.00 164.68| | 16: 1.19 - 1.17 6604 132 0.95 11.37 1.01 0.98 159.13| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.98 153.78| | 18: 1.14 - 1.12 6875 142 0.94 12.75 1.01 0.97 147.64| | 19: 1.12 - 1.10 6948 106 0.93 14.10 1.00 0.97 150.45| | 20: 1.10 - 1.08 6884 147 0.92 15.15 1.00 0.96 149.27| | 21: 1.08 - 1.07 6852 152 0.91 16.57 1.00 0.95 152.21| | 22: 1.07 - 1.05 6836 135 0.89 18.23 0.99 0.95 154.28| | 23: 1.05 - 1.03 6827 159 0.87 20.45 0.99 0.94 164.14| | 24: 1.03 - 1.02 6784 133 0.85 23.11 0.99 0.95 178.58| | 25: 1.02 - 1.01 6552 130 0.83 25.07 0.97 0.92 181.42| | 26: 1.01 - 0.99 6767 158 0.81 26.54 0.98 0.90 175.80| | 27: 0.99 - 0.98 6647 131 0.82 26.16 0.99 0.89 160.02| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 147.64 max = 11078.60 mean = 914.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.23| |phase err.(test): min = 0.00 max = 88.58 mean = 13.38| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1341 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1398 0.1397 0.1476 n_refl.: 191127 remove outliers: r(all,work,free)=0.1398 0.1397 0.1476 n_refl.: 191127 overall B=0.00 to atoms: r(all,work,free)=0.1398 0.1397 0.1476 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1343 n_refl.: 191127 remove outliers: r(all,work,free)=0.1191 0.1188 0.1343 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3860 352.488 313.400 0.351 0.975 0.179 13.296-10.522 96.04 96 1 0.2492 480.435 462.826 0.671 0.977 0.133 10.503-8.327 97.80 175 3 0.2158 501.911 492.982 0.840 0.977 0.109 8.315-6.595 100.00 359 8 0.2149 374.602 369.814 0.864 0.977 0.097 6.588-5.215 100.00 711 7 0.1936 345.091 335.385 0.866 0.978 0.095 5.214-4.128 98.38 1367 28 0.1253 504.763 498.845 0.955 0.979 0.063 4.126-3.266 94.74 2603 46 0.1164 460.119 452.575 1.017 0.980 0.005 3.266-2.585 99.86 5447 97 0.1119 310.385 306.887 1.000 0.981 0.000 2.585-2.046 97.45 10613 204 0.0958 234.168 231.542 1.006 0.984 0.000 2.046-1.619 99.39 21536 464 0.0905 138.592 137.228 1.022 0.988 0.000 1.619-1.281 98.00 42464 925 0.0941 74.610 73.961 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.025 38.307 0.979 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0108 ================= 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 : 0.2032 0.1959 0.082 5.235 5.2 78.0 14.6 805 0.000 1_bss: 0.1796 0.1911 0.082 5.235 5.2 78.0 14.6 805 0.000 1_settarget: 0.1796 0.1911 0.082 5.235 5.2 78.0 14.6 805 0.000 1_nqh: 0.1797 0.1913 0.082 5.235 5.2 78.0 14.6 805 0.002 1_weight: 0.1797 0.1913 0.082 5.235 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1270 0.1506 0.039 1.168 5.2 78.0 14.6 805 0.156 1_adp: 0.1298 0.1572 0.039 1.168 5.2 73.0 15.0 805 0.156 1_regHadp: 0.1297 0.1567 0.039 1.168 5.2 73.0 15.0 805 0.156 1_occ: 0.1283 0.1554 0.039 1.168 5.2 73.0 15.0 805 0.156 2_bss: 0.1275 0.1544 0.039 1.168 5.3 73.2 15.1 805 0.156 2_settarget: 0.1275 0.1544 0.039 1.168 5.3 73.2 15.1 805 0.156 2_updatecdl: 0.1275 0.1544 0.039 1.183 5.3 73.2 15.1 805 0.156 2_nqh: 0.1275 0.1544 0.039 1.183 5.3 73.2 15.1 805 0.156 2_sol: 0.1272 0.1506 0.039 1.183 5.3 73.2 16.2 883 n/a 2_weight: 0.1272 0.1506 0.039 1.183 5.3 73.2 16.2 883 n/a 2_xyzrec: 0.1256 0.1520 0.041 1.133 5.3 73.2 16.2 883 n/a 2_adp: 0.1234 0.1506 0.041 1.133 5.4 68.5 16.2 883 n/a 2_regHadp: 0.1235 0.1507 0.041 1.133 5.4 68.5 16.2 883 n/a 2_occ: 0.1229 0.1501 0.041 1.133 5.4 68.5 16.2 883 n/a 3_bss: 0.1236 0.1511 0.041 1.133 5.4 68.5 16.2 883 n/a 3_settarget: 0.1236 0.1511 0.041 1.133 5.4 68.5 16.2 883 n/a 3_updatecdl: 0.1236 0.1511 0.041 1.139 5.4 68.5 16.2 883 n/a 3_nqh: 0.1236 0.1511 0.041 1.139 5.4 68.5 16.2 883 n/a 3_sol: 0.1251 0.1512 0.041 1.139 5.4 68.5 15.3 871 n/a 3_weight: 0.1251 0.1512 0.041 1.139 5.4 68.5 15.3 871 n/a 3_xyzrec: 0.1240 0.1428 0.035 1.098 5.4 68.5 15.3 871 n/a 3_adp: 0.1234 0.1389 0.035 1.098 5.6 68.1 15.1 871 n/a 3_regHadp: 0.1235 0.1390 0.035 1.098 5.6 68.1 15.1 871 n/a 3_occ: 0.1228 0.1383 0.035 1.098 5.6 68.1 15.1 871 n/a 4_bss: 0.1224 0.1379 0.035 1.098 5.5 68.1 15.1 871 n/a 4_settarget: 0.1224 0.1379 0.035 1.098 5.5 68.1 15.1 871 n/a 4_updatecdl: 0.1224 0.1379 0.035 1.103 5.5 68.1 15.1 871 n/a 4_nqh: 0.1224 0.1379 0.035 1.103 5.5 68.1 15.1 871 n/a 4_sol: 0.1205 0.1353 0.035 1.103 5.5 68.1 15.0 865 n/a 4_weight: 0.1205 0.1353 0.035 1.103 5.5 68.1 15.0 865 n/a 4_xyzrec: 0.1204 0.1357 0.036 1.120 5.5 68.1 15.0 865 n/a 4_adp: 0.1196 0.1353 0.036 1.120 5.5 67.6 14.9 865 n/a 4_regHadp: 0.1197 0.1354 0.036 1.120 5.5 67.6 14.9 865 n/a 4_occ: 0.1195 0.1349 0.036 1.120 5.5 67.6 14.9 865 n/a 5_bss: 0.1192 0.1348 0.036 1.120 5.5 67.5 14.9 865 n/a 5_settarget: 0.1192 0.1348 0.036 1.120 5.5 67.5 14.9 865 n/a 5_updatecdl: 0.1192 0.1348 0.036 1.120 5.5 67.5 14.9 865 n/a 5_nqh: 0.1192 0.1348 0.036 1.120 5.5 67.5 14.9 865 n/a 5_sol: 0.1191 0.1344 0.036 1.120 5.5 67.5 15.0 883 n/a 5_weight: 0.1191 0.1344 0.036 1.120 5.5 67.5 15.0 883 n/a 5_xyzrec: 0.1194 0.1348 0.036 1.120 5.5 67.5 15.0 883 n/a 5_adp: 0.1198 0.1353 0.036 1.120 5.6 67.3 14.9 883 n/a 5_regHadp: 0.1198 0.1353 0.036 1.120 5.6 67.3 14.9 883 n/a 5_occ: 0.1196 0.1353 0.036 1.120 5.6 67.3 14.9 883 n/a 6_bss: 0.1194 0.1349 0.036 1.120 5.5 67.3 14.9 883 n/a 6_settarget: 0.1194 0.1349 0.036 1.120 5.5 67.3 14.9 883 n/a 6_updatecdl: 0.1194 0.1349 0.036 1.120 5.5 67.3 14.9 883 n/a 6_nqh: 0.1194 0.1349 0.036 1.120 5.5 67.3 14.9 883 n/a 6_sol: 0.1194 0.1338 0.036 1.120 5.5 67.3 14.7 882 n/a 6_weight: 0.1194 0.1338 0.036 1.120 5.5 67.3 14.7 882 n/a 6_xyzrec: 0.1196 0.1345 0.037 1.119 5.5 67.3 14.7 882 n/a 6_adp: 0.1200 0.1348 0.037 1.119 5.6 66.2 14.7 882 n/a 6_regHadp: 0.1200 0.1348 0.037 1.119 5.6 66.2 14.7 882 n/a 6_occ: 0.1198 0.1348 0.037 1.119 5.6 66.2 14.7 882 n/a 7_bss: 0.1198 0.1348 0.037 1.119 5.4 66.0 14.4 882 n/a 7_settarget: 0.1198 0.1348 0.037 1.119 5.4 66.0 14.4 882 n/a 7_updatecdl: 0.1198 0.1348 0.037 1.119 5.4 66.0 14.4 882 n/a 7_nqh: 0.1198 0.1348 0.037 1.119 5.4 66.0 14.4 882 n/a 7_sol: 0.1197 0.1340 0.037 1.119 5.4 66.0 14.4 880 n/a 7_weight: 0.1197 0.1340 0.037 1.119 5.4 66.0 14.4 880 n/a 7_xyzrec: 0.1201 0.1351 0.038 1.124 5.4 66.0 14.4 880 n/a 7_adp: 0.1202 0.1353 0.038 1.124 5.4 64.9 14.4 880 n/a 7_regHadp: 0.1202 0.1353 0.038 1.124 5.4 64.9 14.4 880 n/a 7_occ: 0.1201 0.1355 0.038 1.124 5.4 64.9 14.4 880 n/a 8_bss: 0.1191 0.1345 0.038 1.124 5.4 64.9 14.4 880 n/a 8_settarget: 0.1191 0.1345 0.038 1.124 5.4 64.9 14.4 880 n/a 8_updatecdl: 0.1191 0.1345 0.038 1.123 5.4 64.9 14.4 880 n/a 8_nqh: 0.1191 0.1345 0.038 1.123 5.4 64.9 14.4 880 n/a 8_sol: 0.1187 0.1330 0.038 1.123 5.4 64.9 14.5 902 n/a 8_weight: 0.1187 0.1330 0.038 1.123 5.4 64.9 14.5 902 n/a 8_xyzrec: 0.1189 0.1342 0.039 1.112 5.4 64.9 14.5 902 n/a 8_adp: 0.1191 0.1344 0.039 1.112 5.4 64.2 14.5 902 n/a 8_regHadp: 0.1192 0.1344 0.039 1.112 5.4 64.2 14.5 902 n/a 8_occ: 0.1190 0.1347 0.039 1.112 5.4 64.2 14.5 902 n/a 9_bss: 0.1189 0.1345 0.039 1.112 5.4 64.2 14.5 902 n/a 9_settarget: 0.1189 0.1345 0.039 1.112 5.4 64.2 14.5 902 n/a 9_updatecdl: 0.1189 0.1345 0.039 1.113 5.4 64.2 14.5 902 n/a 9_nqh: 0.1190 0.1348 0.039 1.113 5.4 64.2 14.5 902 n/a 9_sol: 0.1189 0.1341 0.039 1.113 5.4 64.2 14.5 899 n/a 9_weight: 0.1189 0.1341 0.039 1.113 5.4 64.2 14.5 899 n/a 9_xyzrec: 0.1193 0.1344 0.039 1.119 5.4 64.2 14.5 899 n/a 9_adp: 0.1192 0.1345 0.039 1.119 5.5 63.1 14.5 899 n/a 9_regHadp: 0.1192 0.1345 0.039 1.119 5.5 63.1 14.5 899 n/a 9_occ: 0.1191 0.1346 0.039 1.119 5.5 63.1 14.5 899 n/a 10_bss: 0.1190 0.1342 0.039 1.119 5.5 63.1 14.5 899 n/a 10_settarget: 0.1190 0.1342 0.039 1.119 5.5 63.1 14.5 899 n/a 10_updatecdl: 0.1190 0.1342 0.039 1.119 5.5 63.1 14.5 899 n/a 10_setrh: 0.1191 0.1343 0.039 1.119 5.5 63.1 14.5 899 n/a 10_nqh: 0.1191 0.1343 0.039 1.119 5.5 63.1 14.5 899 n/a 10_sol: 0.1190 0.1338 0.039 1.119 5.5 63.1 14.4 895 n/a 10_weight: 0.1190 0.1338 0.039 1.119 5.5 63.1 14.4 895 n/a 10_xyzrec: 0.1190 0.1339 0.039 1.137 5.5 63.1 14.4 895 n/a 10_adp: 0.1190 0.1339 0.039 1.137 5.5 62.8 14.4 895 n/a 10_regHadp: 0.1190 0.1340 0.039 1.137 5.5 62.8 14.4 895 n/a 10_occ: 0.1190 0.1341 0.039 1.137 5.5 62.8 14.4 895 n/a end: 0.1188 0.1343 0.039 1.137 5.5 62.8 14.4 895 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3747331_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3747331_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3600 Refinement macro-cycles (run) : 12076.5400 Write final files (write_after_run_outputs) : 152.8000 Total : 12235.7000 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:08 PST -0800 (1736736068.94 s) Start R-work = 0.1796, R-free = 0.1911 Final R-work = 0.1188, R-free = 0.1343 =============================================================================== Job complete usr+sys time: 12516.98 seconds wall clock time: 209 minutes 36.04 seconds (12576.04 seconds total)