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_4029956.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4029956.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4029956.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.39, per 1000 atoms: 0.36 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.720 distance_ideal: 2.720 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 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: 2.754 distance_ideal: 2.710 ideal - model: -0.044 slack: 0.000 delta_slack: -0.044 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 209.2 milliseconds Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 1125 1.05 - 1.28: 2319 1.28 - 1.51: 1549 1.51 - 1.73: 923 1.73 - 1.96: 18 Bond restraints: 5934 Sorted by residual: bond pdb=" N THR B 16 " pdb=" CA THR B 16 " ideal model delta sigma weight residual 1.459 1.712 -0.253 1.17e-02 7.31e+03 4.67e+02 bond pdb=" N ALA B 57 " pdb=" CA ALA B 57 " ideal model delta sigma weight residual 1.456 1.237 0.220 1.04e-02 9.25e+03 4.46e+02 bond pdb=" NE1 TRP A 139 " pdb=" HE1 TRP A 139 " ideal model delta sigma weight residual 0.860 1.249 -0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.448 1.616 -0.168 9.00e-03 1.23e+04 3.48e+02 bond pdb=" CA LYS B 142 " pdb=" C LYS B 142 " ideal model delta sigma weight residual 1.523 1.743 -0.220 1.21e-02 6.83e+03 3.31e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 6153 4.68 - 9.36: 3508 9.36 - 14.04: 1019 14.04 - 18.71: 124 18.71 - 23.39: 6 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE A 76 " pdb=" C ILE A 76 " pdb=" O ILE A 76 " ideal model delta sigma weight residual 121.17 135.65 -14.48 1.06e+00 8.90e-01 1.86e+02 angle pdb=" O LYS A 167 " pdb=" C LYS A 167 " pdb=" N ILE A 168 " ideal model delta sigma weight residual 122.27 138.64 -16.37 1.23e+00 6.61e-01 1.77e+02 angle pdb=" C VAL A 114 " pdb=" N PRO A 115 " pdb=" CA PRO A 115 " ideal model delta sigma weight residual 119.05 133.60 -14.55 1.11e+00 8.12e-01 1.72e+02 angle pdb=" CA PHE B 82 " pdb=" CB PHE B 82 " pdb=" CG PHE B 82 " ideal model delta sigma weight residual 113.80 126.78 -12.98 1.00e+00 1.00e+00 1.68e+02 angle pdb=" O LEU A 87 " pdb=" C LEU A 87 " pdb=" N LEU A 88 " ideal model delta sigma weight residual 122.15 107.40 14.75 1.14e+00 7.69e-01 1.67e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.35: 1847 16.35 - 32.69: 134 32.69 - 49.04: 45 49.04 - 65.38: 19 65.38 - 81.72: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLU A 17 " pdb=" C GLU A 17 " pdb=" N ALA A 18 " pdb=" CA ALA A 18 " ideal model delta harmonic sigma weight residual -180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CG TRP A 146 " pdb=" CD2 TRP A 146 " pdb=" CE3 TRP A 146 " pdb=" HE3 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 -23.27 23.27 0 5.00e+00 4.00e-02 2.17e+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 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.214: 195 0.214 - 0.427: 162 0.427 - 0.639: 98 0.639 - 0.852: 27 0.852 - 1.065: 10 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -1.52 -1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" CA ASP A 163 " pdb=" N ASP A 163 " pdb=" C ASP A 163 " pdb=" CB ASP A 163 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CA SER B 155 " pdb=" N SER B 155 " pdb=" C SER B 155 " pdb=" CB SER B 155 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.071 2.00e-02 2.50e+03 6.59e-02 1.74e+02 pdb=" CG TRP A 146 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.054 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.090 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.083 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.059 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.038 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.054 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.079 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.096 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.068 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.055 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.142 2.00e-02 2.50e+03 7.07e-02 1.50e+02 pdb=" CG PHE B 164 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.081 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.038 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.072 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.047 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG TYR A 194 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " -0.089 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.112 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " -0.043 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " 0.064 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " -0.084 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " -0.100 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 24 1.61 - 2.36: 2373 2.36 - 3.11: 22199 3.11 - 3.85: 33008 3.85 - 4.60: 52641 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110245 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.863 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.921 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.079 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.088 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.145 2.620 ... (remaining 110240 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_4029956_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= 0.2031 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.298934 | | target function (ml) not normalized (work): 805246.222660 | | target function (ml) not normalized (free): 16562.097065 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2132 0.1875 6.7005 6.3017| | 2: 2.94 - 2.33 1.00 7339 128 0.1613 0.1729 5.54 5.6299| | 3: 2.33 - 2.04 0.96 6939 150 0.1635 0.1669 5.1481 5.1787| | 4: 2.04 - 1.85 1.00 7170 155 0.1769 0.1661 4.977 5.0256| | 5: 1.85 - 1.72 0.99 7113 159 0.1920 0.1907 4.8047 4.8908| | 6: 1.72 - 1.62 0.99 7102 142 0.1986 0.2057 4.6624 4.7305| | 7: 1.62 - 1.54 0.99 7104 148 0.2011 0.1713 4.5543 4.5509| | 8: 1.54 - 1.47 0.96 6798 152 0.2009 0.2006 4.4527 4.4268| | 9: 1.47 - 1.41 0.98 6938 155 0.2044 0.2153 4.375 4.4453| | 10: 1.41 - 1.36 0.99 7022 150 0.2121 0.2095 4.3017 4.3141| | 11: 1.36 - 1.32 0.99 6997 151 0.2113 0.2217 4.2285 4.2698| | 12: 1.32 - 1.28 0.98 6976 149 0.2069 0.1956 4.1723 4.2319| | 13: 1.28 - 1.25 0.98 6907 166 0.2024 0.2521 4.1257 4.2763| | 14: 1.25 - 1.22 0.98 7015 113 0.2078 0.2390 4.0775 4.2818| | 15: 1.22 - 1.19 0.98 6957 137 0.2089 0.1747 4.0351 3.9556| | 16: 1.19 - 1.17 0.93 6604 132 0.2122 0.2320 4.0068 4.0692| | 17: 1.17 - 1.14 0.98 6941 135 0.2153 0.2011 3.9491 4.0386| | 18: 1.14 - 1.12 0.98 6875 142 0.2213 0.2307 3.9203 3.919| | 19: 1.12 - 1.10 0.97 6949 106 0.2303 0.2402 3.8853 3.9658| | 20: 1.10 - 1.08 0.97 6884 147 0.2338 0.2231 3.8255 3.8574| | 21: 1.08 - 1.07 0.97 6852 152 0.2438 0.2709 3.7889 3.8345| | 22: 1.07 - 1.05 0.97 6838 135 0.2546 0.2305 3.7508 3.7274| | 23: 1.05 - 1.03 0.97 6829 159 0.2691 0.2567 3.7175 3.8097| | 24: 1.03 - 1.02 0.96 6785 133 0.2913 0.2619 3.7074 3.7091| | 25: 1.02 - 1.01 0.93 6552 130 0.3061 0.2910 3.6758 3.7293| | 26: 1.01 - 0.99 0.96 6767 158 0.3221 0.3254 3.6328 3.6443| | 27: 0.99 - 0.98 0.94 6648 131 0.3395 0.2941 3.641 3.5923| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.22 0.91 0.98 34865.43| | 2: 2.94 - 2.33 7339 128 0.86 21.09 1.08 1.03 15094.88| | 3: 2.33 - 2.04 6939 150 0.93 13.03 1.11 1.07 4458.93| | 4: 2.04 - 1.85 7170 155 0.92 13.97 1.11 1.07 2952.43| | 5: 1.85 - 1.72 7113 159 0.90 16.35 1.11 1.08 2264.12| | 6: 1.72 - 1.62 7102 142 0.90 17.13 1.12 1.06 1690.30| | 7: 1.62 - 1.54 7104 148 0.89 17.59 1.11 1.06 1320.81| | 8: 1.54 - 1.47 6798 152 0.89 17.64 1.11 1.04 1045.32| | 9: 1.47 - 1.41 6938 155 0.89 18.09 1.10 1.06 907.61| | 10: 1.41 - 1.36 7022 150 0.87 19.69 1.09 1.05 824.34| | 11: 1.36 - 1.32 6997 151 0.87 20.43 1.08 1.03 749.92| | 12: 1.32 - 1.28 6976 149 0.86 21.21 1.08 1.01 719.18| | 13: 1.28 - 1.25 6907 166 0.86 21.22 1.07 1.02 668.91| | 14: 1.25 - 1.22 7015 113 0.86 21.63 1.08 1.02 612.05| | 15: 1.22 - 1.19 6957 137 0.87 20.53 1.08 1.03 524.34| | 16: 1.19 - 1.17 6604 132 0.88 19.98 1.07 1.03 470.81| | 17: 1.17 - 1.14 6941 135 0.86 20.97 1.08 1.02 441.76| | 18: 1.14 - 1.12 6875 142 0.86 21.55 1.08 1.00 414.65| | 19: 1.12 - 1.10 6949 106 0.85 22.90 1.07 1.00 398.36| | 20: 1.10 - 1.08 6884 147 0.84 23.16 1.06 1.00 365.35| | 21: 1.08 - 1.07 6852 152 0.84 24.01 1.06 0.99 341.43| | 22: 1.07 - 1.05 6838 135 0.83 24.69 1.05 0.99 317.40| | 23: 1.05 - 1.03 6829 159 0.81 26.36 1.05 0.98 308.59| | 24: 1.03 - 1.02 6785 133 0.79 28.53 1.05 0.99 312.36| | 25: 1.02 - 1.01 6552 130 0.78 29.88 1.03 0.95 299.77| | 26: 1.01 - 0.99 6767 158 0.76 31.21 1.03 0.93 279.83| | 27: 0.99 - 0.98 6648 131 0.78 30.09 1.04 0.92 242.87| |alpha: min = 0.92 max = 1.08 mean = 1.01| |beta: min = 242.87 max = 34865.43 mean = 2825.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.53| |phase err.(test): min = 0.00 max = 89.43 mean = 21.52| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.254 2950 Z= 5.484 Angle : 5.239 20.310 4018 Z= 3.739 Chirality : 0.375 1.065 492 Planarity : 0.033 0.150 512 Dihedral : 12.507 81.724 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.37 % Favored : 95.85 % Rotamer: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Cbeta Deviations : 32.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.38), residues: 386 helix: -2.58 (0.30), residues: 146 sheet: -0.56 (0.56), residues: 78 loop : -0.38 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.016 ARG A 100 TYR 0.124 0.036 TYR B 67 PHE 0.111 0.039 PHE B 164 TRP 0.110 0.035 TRP A 146 HIS 0.074 0.032 HIS A 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2031 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.298934 | | target function (ml) not normalized (work): 805246.222660 | | target function (ml) not normalized (free): 16562.097065 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2030 0.2031 0.1996 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2030 0.2031 0.1996 n_refl.: 191155 remove outliers: r(all,work,free)=0.2030 0.2031 0.1996 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2029 0.2031 0.1996 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1801 0.1799 0.1933 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1796 0.1931 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 0.4031 402.814 294.118 0.435 0.914 0.299 13.296-10.522 99.01 99 1 0.2561 528.187 518.390 0.786 0.915 0.249 10.503-8.327 99.45 178 3 0.2525 565.118 556.417 0.970 0.915 0.226 8.318-6.595 100.00 360 8 0.2499 414.736 404.647 0.973 0.915 0.159 6.588-5.215 100.00 711 7 0.2277 381.101 365.474 0.959 0.915 0.140 5.214-4.128 98.38 1367 28 0.1473 557.435 550.288 1.072 0.915 0.100 4.126-3.266 94.74 2603 46 0.1339 508.132 499.799 1.144 0.916 0.024 3.266-2.585 99.86 5447 97 0.1444 342.774 337.805 1.117 0.915 0.005 2.585-2.046 97.45 10613 204 0.1400 258.603 254.271 1.123 0.914 0.000 2.046-1.619 99.39 21536 464 0.1632 153.054 149.729 1.142 0.913 0.000 1.619-1.281 98.00 42464 925 0.1899 82.395 80.316 1.128 0.911 0.000 1.281-0.980 96.53 101826 2055 0.2315 44.202 41.686 1.111 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0041 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1796 r_free=0.1931 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1796 r_free=0.1931 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.654182 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 567.991484 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1270 0.1500 0.0230 0.039 1.2 11.2 0.0 0.3 0 11.327 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.00 2.30 1.117 13.109 567.991 0.018 12.96 15.67 2.71 1.212 13.286 567.991 0.017 Individual atomic B min max mean iso aniso Overall: 5.19 73.04 14.92 1.39 435 3274 Protein: 5.19 40.31 10.96 1.39 0 2902 Water: 6.31 73.04 29.16 N/A 435 370 Other: 15.87 30.50 23.18 N/A 0 2 Chain A: 5.40 60.10 12.98 N/A 0 1626 Chain B: 5.19 73.04 12.71 N/A 0 1648 Chain S: 12.29 61.89 30.55 N/A 435 0 Histogram: Values Number of atoms 5.19 - 11.97 2169 11.97 - 18.76 643 18.76 - 25.54 324 25.54 - 32.33 258 32.33 - 39.11 154 39.11 - 45.90 103 45.90 - 52.69 35 52.69 - 59.47 18 59.47 - 66.26 4 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1567 r_work=0.1296 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1563 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1281 r_free = 0.1552 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 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= 0.1281 r_free= 0.1552 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015570 | | target function (ls_wunit_k1) not normalized (work): 2916.170374 | | target function (ls_wunit_k1) not normalized (free): 116.261326 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1552 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1465 0.1462 0.1628 n_refl.: 191138 remove outliers: r(all,work,free)=0.1465 0.1462 0.1628 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1489 0.1487 0.1638 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1278 0.1273 0.1542 n_refl.: 191138 remove outliers: r(all,work,free)=0.1278 0.1273 0.1542 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3614 402.814 376.774 0.488 0.963 0.285 13.296-10.522 99.01 99 1 0.2078 528.187 520.227 0.735 0.965 0.240 10.503-8.327 99.45 178 3 0.1762 565.118 562.571 0.886 0.965 0.217 8.318-6.595 100.00 360 8 0.1715 414.736 412.894 0.911 0.964 0.150 6.588-5.215 100.00 711 7 0.1540 381.101 373.493 0.888 0.965 0.140 5.214-4.128 98.38 1367 28 0.0905 557.435 554.250 0.976 0.965 0.080 4.126-3.266 94.74 2603 46 0.0832 508.132 504.424 1.044 0.966 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.411 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.417 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1086 153.054 151.394 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1276 82.395 81.412 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.155 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0383 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1542 | n_water=805 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1278 r_free=0.1549 | n_water=793 | time (s): 103.480 (total time: 105.960) Filter (q & B) r_work=0.1279 r_free=0.1548 | n_water=788 | time (s): 5.280 (total time: 111.240) Compute maps r_work=0.1279 r_free=0.1548 | n_water=788 | time (s): 1.870 (total time: 113.110) Filter (map) r_work=0.1302 r_free=0.1527 | n_water=656 | time (s): 4.880 (total time: 117.990) Find peaks r_work=0.1302 r_free=0.1527 | n_water=656 | time (s): 0.760 (total time: 118.750) Add new water r_work=0.1325 r_free=0.1554 | n_water=958 | time (s): 5.250 (total time: 124.000) Refine new water occ: r_work=0.1281 r_free=0.1516 adp: r_work=0.1269 r_free=0.1512 occ: r_work=0.1272 r_free=0.1511 adp: r_work=0.1265 r_free=0.1510 occ: r_work=0.1267 r_free=0.1508 adp: r_work=0.1264 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1264 r_free=0.1509 r_work=0.1264 r_free=0.1509 | n_water=958 | time (s): 88.480 (total time: 212.480) Filter (q & B) r_work=0.1268 r_free=0.1511 | n_water=893 | time (s): 4.690 (total time: 217.170) Filter (dist only) r_work=0.1268 r_free=0.1510 | n_water=892 | time (s): 114.440 (total time: 331.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.197372 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 590.484693 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 0.1254 0.1520 0.0266 0.041 1.1 17.2 0.0 0.3 0 11.599 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.20 2.66 2.028 15.171 590.485 0.015 12.33 15.13 2.80 2.385 15.257 590.485 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.21 16.41 1.19 524 3272 Protein: 5.38 40.09 10.97 1.19 0 2902 Water: 6.58 68.21 34.08 N/A 524 368 Other: 16.30 33.60 24.95 N/A 0 2 Chain A: 5.56 55.87 12.98 N/A 0 1624 Chain B: 5.38 68.21 12.80 N/A 0 1648 Chain S: 12.69 67.89 38.38 N/A 524 0 Histogram: Values Number of atoms 5.38 - 11.66 2052 11.66 - 17.94 722 17.94 - 24.23 262 24.23 - 30.51 203 30.51 - 36.79 179 36.79 - 43.08 166 43.08 - 49.36 100 49.36 - 55.64 59 55.64 - 61.93 34 61.93 - 68.21 19 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1513 r_work=0.1233 r_free=0.1514 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1514 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1510 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013428 | | target function (ls_wunit_k1) not normalized (work): 2514.968527 | | target function (ls_wunit_k1) not normalized (free): 101.976594 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1510 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1601 n_refl.: 191138 remove outliers: r(all,work,free)=0.1435 0.1432 0.1601 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1600 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1232 0.1515 n_refl.: 191138 remove outliers: r(all,work,free)=0.1238 0.1232 0.1515 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 0.3286 402.814 378.364 0.492 0.962 0.277 13.296-10.522 99.01 99 1 0.1882 528.187 521.149 0.757 0.963 0.228 10.503-8.327 99.45 178 3 0.1452 565.118 567.453 0.920 0.963 0.174 8.318-6.595 100.00 360 8 0.1524 414.736 414.936 0.937 0.963 0.150 6.588-5.215 100.00 711 7 0.1336 381.101 376.286 0.913 0.963 0.150 5.214-4.128 98.38 1367 28 0.0827 557.435 556.349 0.996 0.963 0.100 4.126-3.266 94.74 2603 46 0.0762 508.132 505.494 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0861 342.774 341.326 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0895 258.603 256.738 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.620 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.345 1.073 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.215 1.059 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0478 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1515 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1515 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1515 | n_water=892 | time (s): 3.360 (total time: 3.360) Filter (dist) r_work=0.1234 r_free=0.1521 | n_water=885 | time (s): 110.500 (total time: 113.860) Filter (q & B) r_work=0.1234 r_free=0.1521 | n_water=884 | time (s): 5.070 (total time: 118.930) Compute maps r_work=0.1234 r_free=0.1521 | n_water=884 | time (s): 2.070 (total time: 121.000) Filter (map) r_work=0.1271 r_free=0.1525 | n_water=697 | time (s): 4.110 (total time: 125.110) Find peaks r_work=0.1271 r_free=0.1525 | n_water=697 | time (s): 0.560 (total time: 125.670) Add new water r_work=0.1296 r_free=0.1559 | n_water=1007 | time (s): 5.030 (total time: 130.700) Refine new water occ: r_work=0.1243 r_free=0.1508 adp: r_work=0.1238 r_free=0.1503 occ: r_work=0.1234 r_free=0.1500 adp: r_work=0.1234 r_free=0.1500 occ: r_work=0.1231 r_free=0.1497 adp: r_work=0.1231 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1231 r_free=0.1497 r_work=0.1231 r_free=0.1497 | n_water=1007 | time (s): 368.810 (total time: 499.510) Filter (q & B) r_work=0.1236 r_free=0.1501 | n_water=874 | time (s): 4.350 (total time: 503.860) Filter (dist only) r_work=0.1237 r_free=0.1502 | n_water=872 | time (s): 112.010 (total time: 615.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.715761 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.233248 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 0.1222 0.1416 0.0194 0.035 1.1 8.8 0.0 0.0 0 0.858 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 14.16 1.94 1.924 14.550 16.233 3.928 12.14 13.82 1.69 2.219 14.453 16.233 3.883 Individual atomic B min max mean iso aniso Overall: 5.54 67.74 15.22 1.05 505 3271 Protein: 5.54 36.32 10.73 1.05 0 2902 Water: 5.67 67.74 30.14 N/A 505 367 Other: 14.01 29.23 21.62 N/A 0 2 Chain A: 5.54 54.94 12.74 N/A 0 1624 Chain B: 5.56 67.74 12.51 N/A 0 1647 Chain S: 5.67 63.12 31.99 N/A 505 0 Histogram: Values Number of atoms 5.54 - 11.76 2133 11.76 - 17.98 684 17.98 - 24.20 290 24.20 - 30.42 241 30.42 - 36.64 190 36.64 - 42.86 139 42.86 - 49.08 62 49.08 - 55.30 28 55.30 - 61.52 6 61.52 - 67.74 3 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1383 r_work=0.1215 r_free=0.1383 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1383 target_work(ml) = 3.884 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1374 target_work(ml) = 3.877 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1208 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.877456 | | target function (ml) not normalized (work): 726235.859373 | | target function (ml) not normalized (free): 15177.336853 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1208 0.1373 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1426 0.1425 0.1462 n_refl.: 191138 remove outliers: r(all,work,free)=0.1426 0.1425 0.1462 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1420 0.1419 0.1459 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1204 0.1368 n_refl.: 191138 remove outliers: r(all,work,free)=0.1207 0.1204 0.1368 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3804 398.895 353.497 0.423 0.946 0.258 13.296-10.522 98.02 98 1 0.2389 528.900 508.888 0.709 0.947 0.223 10.503-8.327 98.35 176 3 0.1996 555.265 558.338 0.886 0.947 0.179 8.318-6.595 100.00 360 8 0.2141 414.736 408.747 0.901 0.947 0.139 6.588-5.215 100.00 711 7 0.1815 381.101 370.714 0.888 0.947 0.120 5.214-4.128 98.38 1367 28 0.1145 557.435 552.287 0.974 0.947 0.080 4.126-3.266 94.74 2603 46 0.1077 508.132 501.027 1.032 0.947 0.005 3.266-2.585 99.86 5447 97 0.1067 342.774 339.153 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0943 258.603 255.775 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0943 153.054 151.492 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1023 82.395 81.521 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1676 44.202 42.336 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0954 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1204 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1369 | n_water=872 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1204 r_free=0.1369 | n_water=872 | time (s): 104.800 (total time: 107.180) Filter (q & B) r_work=0.1204 r_free=0.1367 | n_water=860 | time (s): 5.140 (total time: 112.320) Compute maps r_work=0.1204 r_free=0.1367 | n_water=860 | time (s): 1.700 (total time: 114.020) Filter (map) r_work=0.1224 r_free=0.1376 | n_water=726 | time (s): 4.810 (total time: 118.830) Find peaks r_work=0.1224 r_free=0.1376 | n_water=726 | time (s): 0.650 (total time: 119.480) Add new water r_work=0.1240 r_free=0.1395 | n_water=974 | time (s): 4.540 (total time: 124.020) Refine new water occ: r_work=0.1202 r_free=0.1357 adp: r_work=0.1202 r_free=0.1357 occ: r_work=0.1199 r_free=0.1356 adp: r_work=0.1199 r_free=0.1356 occ: r_work=0.1197 r_free=0.1356 adp: r_work=0.1197 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1355 r_work=0.1197 r_free=0.1355 | n_water=974 | time (s): 239.050 (total time: 363.070) Filter (q & B) r_work=0.1201 r_free=0.1360 | n_water=888 | time (s): 4.680 (total time: 367.750) Filter (dist only) r_work=0.1202 r_free=0.1359 | n_water=887 | time (s): 122.030 (total time: 489.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550511 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.991985 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 0.1202 0.1367 0.0165 0.036 1.1 7.7 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.67 1.65 1.826 14.265 14.992 3.873 11.99 13.63 1.64 1.933 14.222 14.992 3.866 Individual atomic B min max mean iso aniso Overall: 5.52 67.32 15.08 0.98 520 3271 Protein: 5.52 33.11 10.64 0.98 0 2902 Water: 5.74 67.32 29.60 N/A 520 367 Other: 14.02 28.18 21.10 N/A 0 2 Chain A: 5.57 53.93 12.61 N/A 0 1624 Chain B: 5.52 67.32 12.41 N/A 0 1647 Chain S: 5.74 62.15 31.27 N/A 520 0 Histogram: Values Number of atoms 5.52 - 11.70 2122 11.70 - 17.88 727 17.88 - 24.06 293 24.06 - 30.24 234 30.24 - 36.42 178 36.42 - 42.60 140 42.60 - 48.78 63 48.78 - 54.96 27 54.96 - 61.14 5 61.14 - 67.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1363 r_work=0.1199 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1363 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1362 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864345 | | target function (ml) not normalized (work): 723760.883892 | | target function (ml) not normalized (free): 15141.036725 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1459 n_refl.: 191133 remove outliers: r(all,work,free)=0.1404 0.1403 0.1459 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1397 0.1396 0.1455 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191133 remove outliers: r(all,work,free)=0.1199 0.1195 0.1359 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3811 361.204 321.929 0.405 0.949 0.233 13.296-10.522 97.03 97 1 0.2459 481.198 458.463 0.705 0.951 0.209 10.503-8.327 98.35 176 3 0.2100 502.799 496.696 0.868 0.951 0.164 8.318-6.595 100.00 360 8 0.2161 375.549 369.933 0.893 0.951 0.125 6.588-5.215 100.00 711 7 0.1867 345.091 334.955 0.883 0.951 0.104 5.214-4.128 98.38 1367 28 0.1189 504.764 499.667 0.971 0.951 0.090 4.126-3.266 94.74 2603 46 0.1110 460.120 453.538 1.030 0.952 0.000 3.266-2.585 99.86 5447 97 0.1091 310.386 307.066 1.016 0.951 0.000 2.585-2.046 97.45 10613 204 0.0933 234.168 231.734 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0912 138.592 137.297 1.052 0.950 0.000 1.619-1.281 98.00 42464 925 0.0990 74.610 73.894 1.049 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.025 38.358 1.035 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1184 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1359 | n_water=887 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1196 r_free=0.1360 | n_water=886 | time (s): 113.860 (total time: 116.470) Filter (q & B) r_work=0.1196 r_free=0.1360 | n_water=876 | time (s): 5.570 (total time: 122.040) Compute maps r_work=0.1196 r_free=0.1360 | n_water=876 | time (s): 1.890 (total time: 123.930) Filter (map) r_work=0.1217 r_free=0.1375 | n_water=752 | time (s): 4.110 (total time: 128.040) Find peaks r_work=0.1217 r_free=0.1375 | n_water=752 | time (s): 0.540 (total time: 128.580) Add new water r_work=0.1230 r_free=0.1390 | n_water=983 | time (s): 4.650 (total time: 133.230) Refine new water occ: r_work=0.1194 r_free=0.1354 adp: r_work=0.1194 r_free=0.1354 occ: r_work=0.1191 r_free=0.1352 adp: r_work=0.1191 r_free=0.1352 occ: r_work=0.1189 r_free=0.1350 adp: r_work=0.1189 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1350 r_work=0.1189 r_free=0.1350 | n_water=983 | time (s): 237.150 (total time: 370.380) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=894 | time (s): 3.890 (total time: 374.270) Filter (dist only) r_work=0.1195 r_free=0.1355 | n_water=893 | time (s): 116.840 (total time: 491.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560535 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.951420 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1359 0.0161 0.036 1.1 8.2 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.59 1.61 1.783 14.105 14.951 3.765 12.03 13.65 1.62 1.908 14.061 14.951 3.762 Individual atomic B min max mean iso aniso Overall: 5.53 66.72 14.89 0.93 526 3271 Protein: 5.53 30.78 10.54 0.93 0 2902 Water: 5.75 66.72 29.04 N/A 526 367 Other: 13.87 26.08 19.98 N/A 0 2 Chain A: 5.59 52.52 12.46 N/A 0 1624 Chain B: 5.53 66.72 12.28 N/A 0 1647 Chain S: 5.75 62.26 30.57 N/A 526 0 Histogram: Values Number of atoms 5.53 - 11.65 2125 11.65 - 17.77 747 17.77 - 23.89 291 23.89 - 30.01 230 30.01 - 36.13 182 36.13 - 42.25 126 42.25 - 48.36 64 48.36 - 54.48 24 54.48 - 60.60 6 60.60 - 66.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1365 r_work=0.1203 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1365 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1366 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761288 | | target function (ml) not normalized (work): 704455.320299 | | target function (ml) not normalized (free): 14746.504399 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1201 0.1366 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1405 0.1404 0.1470 n_refl.: 191132 remove outliers: r(all,work,free)=0.1405 0.1404 0.1470 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1397 0.1396 0.1465 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1360 n_refl.: 191132 remove outliers: r(all,work,free)=0.1202 0.1199 0.1360 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3647 360.901 313.685 0.381 0.951 0.203 13.296-10.522 97.03 97 1 0.2452 481.198 461.278 0.689 0.953 0.160 10.503-8.327 98.35 176 3 0.2221 502.799 494.132 0.860 0.953 0.140 8.315-6.595 100.00 359 8 0.2125 374.602 370.571 0.890 0.953 0.113 6.588-5.215 100.00 711 7 0.1907 345.091 334.756 0.880 0.953 0.097 5.214-4.128 98.38 1367 28 0.1218 504.764 499.515 0.968 0.953 0.039 4.126-3.266 94.74 2603 46 0.1134 460.120 453.304 1.030 0.953 0.000 3.266-2.585 99.86 5447 97 0.1106 310.386 307.110 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0953 234.168 231.741 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0917 138.592 137.290 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0977 74.610 73.913 1.050 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.025 38.367 1.039 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1320 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1360 | n_water=893 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1199 r_free=0.1360 | n_water=892 | time (s): 123.620 (total time: 126.020) Filter (q & B) r_work=0.1200 r_free=0.1360 | n_water=881 | time (s): 5.110 (total time: 131.130) Compute maps r_work=0.1200 r_free=0.1360 | n_water=881 | time (s): 2.090 (total time: 133.220) Filter (map) r_work=0.1219 r_free=0.1370 | n_water=779 | time (s): 4.860 (total time: 138.080) Find peaks r_work=0.1219 r_free=0.1370 | n_water=779 | time (s): 0.550 (total time: 138.630) Add new water r_work=0.1227 r_free=0.1380 | n_water=991 | time (s): 5.210 (total time: 143.840) Refine new water occ: r_work=0.1195 r_free=0.1344 adp: r_work=0.1196 r_free=0.1344 occ: r_work=0.1193 r_free=0.1341 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1192 r_free=0.1340 adp: r_work=0.1192 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1341 r_work=0.1192 r_free=0.1341 | n_water=991 | time (s): 236.980 (total time: 380.820) Filter (q & B) r_work=0.1197 r_free=0.1351 | n_water=904 | time (s): 4.160 (total time: 384.980) Filter (dist only) r_work=0.1197 r_free=0.1350 | n_water=903 | time (s): 116.750 (total time: 501.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550308 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.972536 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 0.1200 0.1358 0.0158 0.037 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 12.00 13.58 1.58 1.741 14.012 14.973 3.761 11.99 13.60 1.60 1.815 13.985 14.973 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 65.75 14.88 0.90 536 3271 Protein: 5.57 29.24 10.47 0.90 0 2902 Water: 5.86 65.75 29.07 N/A 536 367 Other: 13.84 23.68 18.76 N/A 0 2 Chain A: 5.64 52.09 12.35 N/A 0 1624 Chain B: 5.57 65.75 12.19 N/A 0 1647 Chain S: 5.86 62.52 30.84 N/A 536 0 Histogram: Values Number of atoms 5.57 - 11.59 2118 11.59 - 17.61 767 17.61 - 23.63 285 23.63 - 29.64 211 29.64 - 35.66 180 35.66 - 41.68 136 41.68 - 47.70 77 47.70 - 53.72 25 53.72 - 59.73 5 59.73 - 65.75 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1360 r_work=0.1200 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1360 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757217 | | target function (ml) not normalized (work): 703685.331121 | | target function (ml) not normalized (free): 14740.586046 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1359 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1393 0.1392 0.1475 n_refl.: 191130 remove outliers: r(all,work,free)=0.1393 0.1392 0.1475 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1358 0.1357 0.1455 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3594 360.901 332.806 0.418 0.953 0.209 13.296-10.522 97.03 97 1 0.2439 481.198 463.253 0.704 0.954 0.153 10.503-8.327 98.35 176 3 0.2193 502.799 495.522 0.882 0.955 0.114 8.315-6.595 100.00 359 8 0.2111 374.602 370.547 0.906 0.954 0.100 6.588-5.215 100.00 711 7 0.1902 345.091 335.035 0.903 0.954 0.100 5.214-4.128 98.38 1367 28 0.1224 504.764 499.504 0.993 0.955 0.039 4.126-3.266 94.74 2603 46 0.1135 460.120 453.250 1.054 0.955 0.000 3.266-2.585 99.86 5447 97 0.1115 310.386 307.065 1.037 0.954 0.000 2.585-2.046 97.45 10613 204 0.0954 234.168 231.662 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0912 138.592 137.280 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0969 74.610 73.912 1.051 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1647 40.025 38.368 1.022 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0505 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1359 | n_water=903 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1197 r_free=0.1359 | n_water=902 | time (s): 116.050 (total time: 118.490) Filter (q & B) r_work=0.1197 r_free=0.1359 | n_water=892 | time (s): 4.100 (total time: 122.590) Compute maps r_work=0.1197 r_free=0.1359 | n_water=892 | time (s): 1.830 (total time: 124.420) Filter (map) r_work=0.1218 r_free=0.1358 | n_water=779 | time (s): 5.280 (total time: 129.700) Find peaks r_work=0.1218 r_free=0.1358 | n_water=779 | time (s): 0.680 (total time: 130.380) Add new water r_work=0.1227 r_free=0.1363 | n_water=998 | time (s): 5.260 (total time: 135.640) Refine new water occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1344 occ: r_work=0.1192 r_free=0.1343 adp: r_work=0.1191 r_free=0.1344 occ: r_work=0.1189 r_free=0.1344 adp: r_work=0.1189 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1344 r_work=0.1189 r_free=0.1344 | n_water=998 | time (s): 236.680 (total time: 372.320) Filter (q & B) r_work=0.1193 r_free=0.1354 | n_water=919 | time (s): 5.600 (total time: 377.920) Filter (dist only) r_work=0.1194 r_free=0.1354 | n_water=917 | time (s): 120.820 (total time: 498.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554026 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.996332 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1365 0.0167 0.038 1.1 8.2 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.65 1.67 1.714 13.763 14.996 3.759 11.99 13.67 1.67 1.755 13.744 14.996 3.756 Individual atomic B min max mean iso aniso Overall: 5.40 64.50 14.68 0.88 551 3270 Protein: 5.40 28.48 10.23 0.88 0 2902 Water: 5.71 64.50 28.76 N/A 551 366 Other: 13.68 22.21 17.94 N/A 0 2 Chain A: 5.46 51.49 12.06 N/A 0 1623 Chain B: 5.40 64.50 11.92 N/A 0 1647 Chain S: 5.71 62.58 30.63 N/A 551 0 Histogram: Values Number of atoms 5.40 - 11.31 2094 11.31 - 17.22 791 17.22 - 23.13 272 23.13 - 29.04 228 29.04 - 34.95 179 34.95 - 40.86 135 40.86 - 46.77 83 46.77 - 52.68 30 52.68 - 58.59 5 58.59 - 64.50 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1367 r_work=0.1200 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1367 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1368 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756154 | | target function (ml) not normalized (work): 703486.414044 | | target function (ml) not normalized (free): 14743.450387 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1368 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1363 0.1362 0.1474 n_refl.: 191130 remove outliers: r(all,work,free)=0.1363 0.1362 0.1474 n_refl.: 191130 overall B=0.06 to atoms: r(all,work,free)=0.1371 0.1369 0.1478 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1357 n_refl.: 191130 remove outliers: r(all,work,free)=0.1192 0.1188 0.1357 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3652 360.621 320.965 0.399 0.910 0.152 13.296-10.522 97.03 97 1 0.2420 481.198 463.156 0.737 0.911 0.134 10.503-8.327 98.35 176 3 0.2191 502.799 495.180 0.931 0.911 0.122 8.315-6.595 100.00 359 8 0.2127 374.602 369.696 0.959 0.911 0.103 6.588-5.215 100.00 711 7 0.1923 345.091 334.837 0.953 0.912 0.087 5.214-4.128 98.38 1367 28 0.1232 504.764 499.134 1.051 0.912 0.039 4.126-3.266 94.74 2603 46 0.1142 460.120 452.703 1.116 0.913 0.005 3.266-2.585 99.86 5447 97 0.1121 310.386 306.727 1.097 0.914 0.000 2.585-2.046 97.45 10613 204 0.0956 234.168 231.579 1.106 0.915 0.000 2.046-1.619 99.39 21536 464 0.0907 138.592 137.240 1.123 0.918 0.000 1.619-1.281 98.00 42464 925 0.0948 74.610 73.965 1.111 0.922 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.025 38.346 1.074 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0576 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1357 | n_water=917 | time (s): 3.280 (total time: 3.280) Filter (dist) r_work=0.1189 r_free=0.1358 | n_water=915 | time (s): 118.580 (total time: 121.860) Filter (q & B) r_work=0.1189 r_free=0.1358 | n_water=902 | time (s): 5.230 (total time: 127.090) Compute maps r_work=0.1189 r_free=0.1358 | n_water=902 | time (s): 1.730 (total time: 128.820) Filter (map) r_work=0.1212 r_free=0.1353 | n_water=781 | time (s): 4.870 (total time: 133.690) Find peaks r_work=0.1212 r_free=0.1353 | n_water=781 | time (s): 0.710 (total time: 134.400) Add new water r_work=0.1220 r_free=0.1360 | n_water=997 | time (s): 4.660 (total time: 139.060) Refine new water occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1187 r_free=0.1342 occ: r_work=0.1185 r_free=0.1341 adp: r_work=0.1185 r_free=0.1341 occ: r_work=0.1183 r_free=0.1341 adp: r_work=0.1183 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1341 r_work=0.1183 r_free=0.1341 | n_water=997 | time (s): 236.990 (total time: 376.050) Filter (q & B) r_work=0.1188 r_free=0.1349 | n_water=920 | time (s): 4.850 (total time: 380.900) Filter (dist only) r_work=0.1188 r_free=0.1349 | n_water=919 | time (s): 117.570 (total time: 498.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.576266 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.368054 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 0.1191 0.1355 0.0164 0.038 1.1 7.8 0.0 0.3 0 0.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.55 1.64 1.673 13.770 13.368 3.755 11.93 13.57 1.64 1.677 13.767 13.368 3.756 Individual atomic B min max mean iso aniso Overall: 5.48 64.29 14.73 0.86 553 3270 Protein: 5.48 28.25 10.30 0.86 0 2902 Water: 5.94 64.29 28.70 N/A 553 366 Other: 13.74 22.27 18.00 N/A 0 2 Chain A: 5.54 51.47 12.11 N/A 0 1623 Chain B: 5.48 64.29 11.98 N/A 0 1647 Chain S: 5.94 62.69 30.60 N/A 553 0 Histogram: Values Number of atoms 5.48 - 11.36 2086 11.36 - 17.24 801 17.24 - 23.12 275 23.12 - 29.00 227 29.00 - 34.89 177 34.89 - 40.77 129 40.77 - 46.65 89 46.65 - 52.53 30 52.53 - 58.41 4 58.41 - 64.29 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1357 r_work=0.1193 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1357 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1360 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755313 | | target function (ml) not normalized (work): 703325.122502 | | target function (ml) not normalized (free): 14738.959299 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1360 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1370 0.1368 0.1482 n_refl.: 191129 remove outliers: r(all,work,free)=0.1370 0.1368 0.1482 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1372 0.1370 0.1483 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1356 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1356 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 89.11 87 3 0.3510 355.748 327.913 0.388 0.916 0.118 13.296-10.522 97.03 97 1 0.2418 481.198 462.868 0.722 0.918 0.115 10.503-8.327 98.35 176 3 0.2193 502.799 494.626 0.924 0.918 0.109 8.315-6.595 100.00 359 8 0.2112 374.602 369.882 0.948 0.918 0.096 6.588-5.215 100.00 711 7 0.1935 345.091 334.619 0.945 0.918 0.089 5.214-4.128 98.38 1367 28 0.1237 504.764 498.908 1.041 0.919 0.034 4.126-3.266 94.74 2603 46 0.1147 460.120 452.688 1.108 0.920 0.000 3.266-2.585 99.86 5447 97 0.1125 310.386 306.716 1.089 0.921 0.000 2.585-2.046 97.45 10613 204 0.0961 234.168 231.529 1.099 0.922 0.000 2.046-1.619 99.39 21536 464 0.0912 138.592 137.235 1.116 0.925 0.000 1.619-1.281 98.00 42464 925 0.0946 74.610 73.966 1.106 0.930 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.025 38.323 1.073 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0204 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1356 | n_water=919 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1190 r_free=0.1356 | n_water=919 | time (s): 112.000 (total time: 114.370) Filter (q & B) r_work=0.1191 r_free=0.1357 | n_water=910 | time (s): 4.140 (total time: 118.510) Compute maps r_work=0.1191 r_free=0.1357 | n_water=910 | time (s): 1.670 (total time: 120.180) Filter (map) r_work=0.1214 r_free=0.1353 | n_water=789 | time (s): 5.430 (total time: 125.610) Find peaks r_work=0.1214 r_free=0.1353 | n_water=789 | time (s): 0.560 (total time: 126.170) Add new water r_work=0.1221 r_free=0.1361 | n_water=1000 | time (s): 4.700 (total time: 130.870) Refine new water occ: r_work=0.1189 r_free=0.1340 adp: r_work=0.1189 r_free=0.1340 occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1187 r_free=0.1341 occ: r_work=0.1185 r_free=0.1341 adp: r_work=0.1185 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1342 r_work=0.1185 r_free=0.1342 | n_water=1000 | time (s): 217.800 (total time: 348.670) Filter (q & B) r_work=0.1189 r_free=0.1349 | n_water=925 | time (s): 4.720 (total time: 353.390) Filter (dist only) r_work=0.1190 r_free=0.1349 | n_water=923 | time (s): 117.970 (total time: 471.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.535758 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.201172 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 0.1361 0.0167 0.039 1.1 8.0 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.61 1.67 1.674 13.787 14.201 3.756 11.92 13.61 1.68 1.682 13.781 14.201 3.754 Individual atomic B min max mean iso aniso Overall: 5.55 63.49 14.73 0.86 557 3270 Protein: 5.55 28.04 10.32 0.86 0 2902 Water: 5.96 63.49 28.56 N/A 557 366 Other: 13.79 22.17 17.98 N/A 0 2 Chain A: 5.62 51.18 12.10 N/A 0 1623 Chain B: 5.55 63.49 11.98 N/A 0 1647 Chain S: 5.96 62.84 30.49 N/A 557 0 Histogram: Values Number of atoms 5.55 - 11.34 2074 11.34 - 17.13 818 17.13 - 22.93 268 22.93 - 28.72 221 28.72 - 34.52 187 34.52 - 40.31 131 40.31 - 46.11 88 46.11 - 51.90 29 51.90 - 57.70 6 57.70 - 63.49 5 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1361 r_work=0.1193 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1362 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753764 | | target function (ml) not normalized (work): 703027.536683 | | target function (ml) not normalized (free): 14739.663642 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1362 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1373 0.1371 0.1492 n_refl.: 191127 remove outliers: r(all,work,free)=0.1373 0.1371 0.1492 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1372 0.1370 0.1492 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1361 n_refl.: 191127 remove outliers: r(all,work,free)=0.1194 0.1191 0.1361 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 89.11 87 3 0.3500 355.748 331.591 0.359 0.983 0.106 13.296-10.522 97.03 97 1 0.2389 481.198 463.173 0.667 0.985 0.102 10.503-8.327 98.35 176 3 0.2217 502.799 494.302 0.858 0.985 0.096 8.315-6.595 100.00 359 8 0.2121 374.602 369.282 0.881 0.985 0.086 6.588-5.215 100.00 711 7 0.1977 345.091 334.570 0.876 0.986 0.080 5.214-4.128 98.38 1367 28 0.1255 504.764 498.791 0.969 0.987 0.029 4.126-3.266 94.74 2603 46 0.1153 460.120 452.564 1.033 0.988 0.000 3.266-2.585 99.86 5447 97 0.1128 310.386 306.726 1.015 0.989 0.000 2.585-2.046 97.45 10613 204 0.0963 234.168 231.525 1.024 0.991 0.000 2.046-1.619 99.39 21536 464 0.0909 138.592 137.238 1.040 0.995 0.000 1.619-1.281 98.00 42464 925 0.0944 74.610 73.964 1.031 1.001 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.025 38.318 1.002 1.011 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0086 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1361 After: r_work=0.1191 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1361 | n_water=923 | time (s): 3.300 (total time: 3.300) Filter (dist) r_work=0.1192 r_free=0.1362 | n_water=922 | time (s): 120.940 (total time: 124.240) Filter (q & B) r_work=0.1193 r_free=0.1361 | n_water=909 | time (s): 5.070 (total time: 129.310) Compute maps r_work=0.1193 r_free=0.1361 | n_water=909 | time (s): 1.820 (total time: 131.130) Filter (map) r_work=0.1216 r_free=0.1366 | n_water=791 | time (s): 5.330 (total time: 136.460) Find peaks r_work=0.1216 r_free=0.1366 | n_water=791 | time (s): 0.810 (total time: 137.270) Add new water r_work=0.1222 r_free=0.1373 | n_water=1017 | time (s): 5.610 (total time: 142.880) Refine new water occ: r_work=0.1189 r_free=0.1340 adp: r_work=0.1189 r_free=0.1341 occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1187 r_free=0.1340 occ: r_work=0.1185 r_free=0.1339 adp: r_work=0.1185 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1339 r_work=0.1185 r_free=0.1339 | n_water=1017 | time (s): 202.120 (total time: 345.000) Filter (q & B) r_work=0.1191 r_free=0.1347 | n_water=923 | time (s): 4.810 (total time: 349.810) Filter (dist only) r_work=0.1192 r_free=0.1348 | n_water=920 | time (s): 120.120 (total time: 469.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.564871 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.905139 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1351 0.0156 0.039 1.2 10.1 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.51 1.56 1.674 13.752 14.905 3.756 11.93 13.50 1.57 1.666 13.757 14.905 3.753 Individual atomic B min max mean iso aniso Overall: 5.57 62.96 14.68 0.87 554 3270 Protein: 5.57 28.18 10.35 0.87 0 2902 Water: 5.96 62.96 28.33 N/A 554 366 Other: 13.80 22.12 17.96 N/A 0 2 Chain A: 5.65 50.91 12.11 N/A 0 1623 Chain B: 5.57 62.56 11.99 N/A 0 1647 Chain S: 5.96 62.96 30.21 N/A 554 0 Histogram: Values Number of atoms 5.57 - 11.31 2058 11.31 - 17.05 830 17.05 - 22.79 274 22.79 - 28.52 218 28.52 - 34.26 193 34.26 - 40.00 121 40.00 - 45.74 86 45.74 - 51.48 31 51.48 - 57.22 7 57.22 - 62.96 6 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1350 r_work=0.1193 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1347 target_work(ml) = 3.753 | | 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= 0.1192 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752931 | | target function (ml) not normalized (work): 702871.388696 | | target function (ml) not normalized (free): 14729.471355 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1364 0.1415 5.6878 5.7556| | 2: 2.94 - 2.33 1.00 7339 128 0.1071 0.1369 5.0761 5.1843| | 3: 2.33 - 2.04 0.96 6939 150 0.0903 0.1193 4.6563 4.7669| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1051 4.3923 4.5622| | 5: 1.85 - 1.72 0.99 7113 159 0.0928 0.1000 4.1479 4.2481| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1061 3.9431 4.0682| | 7: 1.62 - 1.54 0.99 7104 148 0.0885 0.0950 3.7947 3.9309| | 8: 1.54 - 1.47 0.96 6798 152 0.0891 0.1310 3.6989 3.9004| | 9: 1.47 - 1.41 0.98 6938 155 0.0925 0.1119 3.6214 3.7546| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1185 3.5562 3.677| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1133 3.4848 3.5978| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1134 3.4592 3.5812| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1243 3.4359 3.568| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1574 3.432 3.6862| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1232 3.447 3.4911| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1527 3.4627 3.6514| | 17: 1.17 - 1.14 0.98 6940 135 0.1295 0.1218 3.4296 3.4389| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1692 3.4361 3.527| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1767 3.4183 3.5995| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1579 3.4091 3.4332| | 21: 1.08 - 1.07 0.97 6852 152 0.1725 0.2148 3.4172 3.5058| | 22: 1.07 - 1.05 0.97 6836 135 0.1901 0.1950 3.4122 3.4092| | 23: 1.05 - 1.03 0.97 6827 159 0.2116 0.2014 3.4319 3.4856| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2266 3.435 3.5122| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2500 3.4488 3.5234| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2868 3.4149 3.4227| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2792 3.4696 3.3938| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.49 1.00 0.96 10945.32| | 2: 2.94 - 2.33 7339 128 0.93 12.71 0.99 0.96 5075.60| | 3: 2.33 - 2.04 6939 150 0.96 7.75 1.01 0.95 1733.57| | 4: 2.04 - 1.85 7170 155 0.96 7.68 1.00 0.95 1014.71| | 5: 1.85 - 1.72 7113 159 0.96 8.06 1.00 0.96 634.99| | 6: 1.72 - 1.62 7102 142 0.96 8.01 1.00 0.96 441.00| | 7: 1.62 - 1.54 7104 148 0.96 8.09 1.01 0.97 335.32| | 8: 1.54 - 1.47 6798 152 0.96 8.27 1.01 0.97 279.21| | 9: 1.47 - 1.41 6938 155 0.96 8.52 1.00 0.98 232.66| | 10: 1.41 - 1.36 7022 150 0.96 8.98 1.00 0.97 204.51| | 11: 1.36 - 1.32 6997 151 0.96 8.99 0.99 0.96 176.50| | 12: 1.32 - 1.28 6975 149 0.96 9.02 0.98 0.95 162.11| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.96 159.19| | 14: 1.25 - 1.22 7015 112 0.95 10.76 1.01 0.96 164.15| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 0.98 166.75| | 16: 1.19 - 1.17 6604 132 0.95 11.39 1.01 0.96 159.52| | 17: 1.17 - 1.14 6940 135 0.94 12.17 1.01 0.96 152.56| | 18: 1.14 - 1.12 6875 142 0.94 12.69 1.01 0.95 146.72| | 19: 1.12 - 1.10 6948 106 0.93 14.13 1.00 0.95 150.93| | 20: 1.10 - 1.08 6884 147 0.92 15.22 1.00 0.94 150.24| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.93 153.23| | 22: 1.07 - 1.05 6836 135 0.89 18.26 0.99 0.93 154.49| | 23: 1.05 - 1.03 6827 159 0.87 20.48 0.99 0.92 164.56| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.93 179.07| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.98 0.90 182.13| | 26: 1.01 - 0.99 6767 158 0.81 26.57 0.98 0.88 176.00| | 27: 0.99 - 0.98 6647 131 0.82 26.11 0.99 0.87 159.37| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.72 max = 10945.32 mean = 914.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.28| |phase err.(test): min = 0.00 max = 88.31 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1347 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1381 0.1379 0.1487 n_refl.: 191127 remove outliers: r(all,work,free)=0.1381 0.1379 0.1487 n_refl.: 191127 overall B=-0.09 to atoms: r(all,work,free)=0.1368 0.1366 0.1479 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1346 n_refl.: 191127 remove outliers: r(all,work,free)=0.1195 0.1192 0.1346 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 89.11 87 3 0.3498 355.748 330.843 0.371 0.910 0.092 13.296-10.522 97.03 97 1 0.2411 481.198 461.893 0.695 0.912 0.079 10.503-8.327 98.35 176 3 0.2271 502.799 494.003 0.902 0.912 0.078 8.315-6.595 100.00 359 8 0.2131 374.602 369.251 0.926 0.913 0.072 6.588-5.215 100.00 711 7 0.1968 345.091 334.463 0.923 0.913 0.070 5.214-4.128 98.38 1367 28 0.1257 504.764 498.705 1.022 0.915 0.034 4.126-3.266 94.74 2603 46 0.1162 460.120 452.374 1.088 0.917 0.000 3.266-2.585 99.86 5447 97 0.1126 310.386 306.784 1.067 0.919 0.000 2.585-2.046 97.45 10613 204 0.0962 234.168 231.529 1.072 0.924 0.000 2.046-1.619 99.39 21536 464 0.0908 138.592 137.303 1.084 0.931 0.000 1.619-1.281 98.00 42464 925 0.0945 74.610 74.036 1.066 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.025 38.399 1.021 0.963 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0206 ================= 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 : 0.2031 0.1996 0.081 5.239 5.2 78.0 14.6 805 0.000 1_bss: 0.1796 0.1931 0.081 5.239 5.2 78.0 14.6 805 0.000 1_settarget: 0.1796 0.1931 0.081 5.239 5.2 78.0 14.6 805 0.000 1_nqh: 0.1796 0.1931 0.081 5.239 5.2 78.0 14.6 805 0.000 1_weight: 0.1796 0.1931 0.081 5.239 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1500 0.039 1.153 5.2 78.0 14.6 805 0.156 1_adp: 0.1296 0.1567 0.039 1.153 5.2 73.0 14.9 805 0.156 1_regHadp: 0.1296 0.1563 0.039 1.153 5.2 73.0 14.9 805 0.156 1_occ: 0.1281 0.1552 0.039 1.153 5.2 73.0 14.9 805 0.156 2_bss: 0.1273 0.1542 0.039 1.153 5.4 73.2 15.1 805 0.156 2_settarget: 0.1273 0.1542 0.039 1.153 5.4 73.2 15.1 805 0.156 2_updatecdl: 0.1273 0.1542 0.039 1.168 5.4 73.2 15.1 805 0.156 2_nqh: 0.1273 0.1542 0.039 1.168 5.4 73.2 15.1 805 0.156 2_sol: 0.1268 0.1510 0.039 1.168 5.4 73.2 16.3 892 n/a 2_weight: 0.1268 0.1510 0.039 1.168 5.4 73.2 16.3 892 n/a 2_xyzrec: 0.1254 0.1520 0.041 1.131 5.4 73.2 16.3 892 n/a 2_adp: 0.1233 0.1513 0.041 1.131 5.4 68.2 16.4 892 n/a 2_regHadp: 0.1233 0.1514 0.041 1.131 5.4 68.2 16.4 892 n/a 2_occ: 0.1226 0.1510 0.041 1.131 5.4 68.2 16.4 892 n/a 3_bss: 0.1232 0.1515 0.041 1.131 5.4 68.2 16.4 892 n/a 3_settarget: 0.1232 0.1515 0.041 1.131 5.4 68.2 16.4 892 n/a 3_updatecdl: 0.1232 0.1515 0.041 1.134 5.4 68.2 16.4 892 n/a 3_nqh: 0.1232 0.1515 0.041 1.134 5.4 68.2 16.4 892 n/a 3_sol: 0.1237 0.1502 0.041 1.134 5.4 68.2 15.4 872 n/a 3_weight: 0.1237 0.1502 0.041 1.134 5.4 68.2 15.4 872 n/a 3_xyzrec: 0.1222 0.1416 0.035 1.109 5.4 68.2 15.4 872 n/a 3_adp: 0.1214 0.1383 0.035 1.109 5.5 67.7 15.2 872 n/a 3_regHadp: 0.1215 0.1383 0.035 1.109 5.5 67.7 15.2 872 n/a 3_occ: 0.1208 0.1374 0.035 1.109 5.5 67.7 15.2 872 n/a 4_bss: 0.1204 0.1369 0.035 1.109 5.5 67.7 15.2 872 n/a 4_settarget: 0.1204 0.1369 0.035 1.109 5.5 67.7 15.2 872 n/a 4_updatecdl: 0.1204 0.1369 0.035 1.114 5.5 67.7 15.2 872 n/a 4_nqh: 0.1204 0.1369 0.035 1.114 5.5 67.7 15.2 872 n/a 4_sol: 0.1202 0.1359 0.035 1.114 5.5 67.7 15.2 887 n/a 4_weight: 0.1202 0.1359 0.035 1.114 5.5 67.7 15.2 887 n/a 4_xyzrec: 0.1202 0.1367 0.036 1.128 5.5 67.7 15.2 887 n/a 4_adp: 0.1199 0.1363 0.036 1.128 5.5 67.3 15.1 887 n/a 4_regHadp: 0.1199 0.1363 0.036 1.128 5.5 67.3 15.1 887 n/a 4_occ: 0.1197 0.1362 0.036 1.128 5.5 67.3 15.1 887 n/a 5_bss: 0.1195 0.1359 0.036 1.128 5.5 67.3 15.0 887 n/a 5_settarget: 0.1195 0.1359 0.036 1.128 5.5 67.3 15.0 887 n/a 5_updatecdl: 0.1195 0.1359 0.036 1.128 5.5 67.3 15.0 887 n/a 5_nqh: 0.1195 0.1359 0.036 1.128 5.5 67.3 15.0 887 n/a 5_sol: 0.1195 0.1355 0.036 1.128 5.5 67.3 15.0 893 n/a 5_weight: 0.1195 0.1355 0.036 1.128 5.5 67.3 15.0 893 n/a 5_xyzrec: 0.1198 0.1359 0.036 1.132 5.5 67.3 15.0 893 n/a 5_adp: 0.1203 0.1365 0.036 1.132 5.5 66.7 14.9 893 n/a 5_regHadp: 0.1203 0.1365 0.036 1.132 5.5 66.7 14.9 893 n/a 5_occ: 0.1201 0.1366 0.036 1.132 5.5 66.7 14.9 893 n/a 6_bss: 0.1199 0.1360 0.036 1.132 5.5 66.7 14.9 893 n/a 6_settarget: 0.1199 0.1360 0.036 1.132 5.5 66.7 14.9 893 n/a 6_updatecdl: 0.1199 0.1360 0.036 1.133 5.5 66.7 14.9 893 n/a 6_nqh: 0.1199 0.1360 0.036 1.133 5.5 66.7 14.9 893 n/a 6_sol: 0.1197 0.1350 0.036 1.133 5.5 66.7 14.9 903 n/a 6_weight: 0.1197 0.1350 0.036 1.133 5.5 66.7 14.9 903 n/a 6_xyzrec: 0.1200 0.1358 0.037 1.130 5.5 66.7 14.9 903 n/a 6_adp: 0.1199 0.1360 0.037 1.130 5.6 65.8 14.9 903 n/a 6_regHadp: 0.1200 0.1360 0.037 1.130 5.6 65.8 14.9 903 n/a 6_occ: 0.1197 0.1360 0.037 1.130 5.6 65.8 14.9 903 n/a 7_bss: 0.1197 0.1359 0.037 1.130 5.3 65.5 14.7 903 n/a 7_settarget: 0.1197 0.1359 0.037 1.130 5.3 65.5 14.7 903 n/a 7_updatecdl: 0.1197 0.1359 0.037 1.130 5.3 65.5 14.7 903 n/a 7_nqh: 0.1197 0.1359 0.037 1.130 5.3 65.5 14.7 903 n/a 7_sol: 0.1194 0.1354 0.037 1.130 5.3 65.5 14.7 917 n/a 7_weight: 0.1194 0.1354 0.037 1.130 5.3 65.5 14.7 917 n/a 7_xyzrec: 0.1198 0.1365 0.038 1.128 5.3 65.5 14.7 917 n/a 7_adp: 0.1199 0.1367 0.038 1.128 5.4 64.5 14.7 917 n/a 7_regHadp: 0.1200 0.1367 0.038 1.128 5.4 64.5 14.7 917 n/a 7_occ: 0.1197 0.1368 0.038 1.128 5.4 64.5 14.7 917 n/a 8_bss: 0.1188 0.1357 0.038 1.128 5.5 64.6 14.7 917 n/a 8_settarget: 0.1188 0.1357 0.038 1.128 5.5 64.6 14.7 917 n/a 8_updatecdl: 0.1188 0.1357 0.038 1.128 5.5 64.6 14.7 917 n/a 8_nqh: 0.1188 0.1357 0.038 1.128 5.5 64.6 14.7 917 n/a 8_sol: 0.1188 0.1349 0.038 1.128 5.5 64.6 14.7 919 n/a 8_weight: 0.1188 0.1349 0.038 1.128 5.5 64.6 14.7 919 n/a 8_xyzrec: 0.1191 0.1355 0.038 1.125 5.5 64.6 14.7 919 n/a 8_adp: 0.1193 0.1357 0.038 1.125 5.5 64.3 14.7 919 n/a 8_regHadp: 0.1193 0.1357 0.038 1.125 5.5 64.3 14.7 919 n/a 8_occ: 0.1192 0.1360 0.038 1.125 5.5 64.3 14.7 919 n/a 9_bss: 0.1190 0.1356 0.038 1.125 5.5 64.3 14.7 919 n/a 9_settarget: 0.1190 0.1356 0.038 1.125 5.5 64.3 14.7 919 n/a 9_updatecdl: 0.1190 0.1356 0.038 1.125 5.5 64.3 14.7 919 n/a 9_nqh: 0.1190 0.1356 0.038 1.125 5.5 64.3 14.7 919 n/a 9_sol: 0.1190 0.1349 0.038 1.125 5.5 64.3 14.7 923 n/a 9_weight: 0.1190 0.1349 0.038 1.125 5.5 64.3 14.7 923 n/a 9_xyzrec: 0.1193 0.1361 0.039 1.120 5.5 64.3 14.7 923 n/a 9_adp: 0.1192 0.1361 0.039 1.120 5.5 63.5 14.7 923 n/a 9_regHadp: 0.1193 0.1361 0.039 1.120 5.5 63.5 14.7 923 n/a 9_occ: 0.1191 0.1362 0.039 1.120 5.5 63.5 14.7 923 n/a 10_bss: 0.1191 0.1361 0.039 1.120 5.5 63.5 14.7 923 n/a 10_settarget: 0.1191 0.1361 0.039 1.120 5.5 63.5 14.7 923 n/a 10_updatecdl: 0.1191 0.1361 0.039 1.121 5.5 63.5 14.7 923 n/a 10_setrh: 0.1191 0.1361 0.039 1.121 5.5 63.5 14.7 923 n/a 10_nqh: 0.1191 0.1361 0.039 1.121 5.5 63.5 14.7 923 n/a 10_sol: 0.1192 0.1348 0.039 1.121 5.5 63.5 14.7 920 n/a 10_weight: 0.1192 0.1348 0.039 1.121 5.5 63.5 14.7 920 n/a 10_xyzrec: 0.1194 0.1351 0.039 1.171 5.5 63.5 14.7 920 n/a 10_adp: 0.1193 0.1350 0.039 1.171 5.6 63.0 14.7 920 n/a 10_regHadp: 0.1193 0.1350 0.039 1.171 5.6 63.0 14.7 920 n/a 10_occ: 0.1192 0.1347 0.039 1.171 5.6 63.0 14.7 920 n/a end: 0.1192 0.1347 0.039 1.171 5.5 62.9 14.6 920 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4029956_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4029956_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.9500 Refinement macro-cycles (run) : 12208.9600 Write final files (write_after_run_outputs) : 159.5500 Total : 12374.4600 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:31 PST -0800 (1736736211.84 s) Start R-work = 0.1796, R-free = 0.1931 Final R-work = 0.1192, R-free = 0.1347 =============================================================================== Job complete usr+sys time: 12656.29 seconds wall clock time: 211 minutes 58.45 seconds (12718.45 seconds total)