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_3918332.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3918332.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3918332.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.85, per 1000 atoms: 0.28 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: 2.814 distance_ideal: 2.720 ideal - model: -0.094 slack: 0.000 delta_slack: -0.094 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.753 distance_ideal: 2.710 ideal - model: -0.043 slack: 0.000 delta_slack: -0.043 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 211.7 milliseconds Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 0.99: 474 0.99 - 1.21: 2537 1.21 - 1.43: 1352 1.43 - 1.65: 1462 1.65 - 1.87: 109 Bond restraints: 5934 Sorted by residual: bond pdb=" CA ILE A 134 " pdb=" C ILE A 134 " ideal model delta sigma weight residual 1.523 1.729 -0.206 8.80e-03 1.29e+04 5.50e+02 bond pdb=" ND1 HIS A 179 " pdb=" CE1 HIS A 179 " ideal model delta sigma weight residual 1.321 1.120 0.201 1.00e-02 1.00e+04 4.03e+02 bond pdb=" C GLY A 159 " pdb=" O GLY A 159 " ideal model delta sigma weight residual 1.234 1.482 -0.248 1.25e-02 6.40e+03 3.94e+02 bond pdb=" C LEU B 113 " pdb=" O LEU B 113 " ideal model delta sigma weight residual 1.237 1.468 -0.231 1.19e-02 7.06e+03 3.77e+02 bond pdb=" N ILE A 101 " pdb=" CA ILE A 101 " ideal model delta sigma weight residual 1.458 1.225 0.233 1.24e-02 6.50e+03 3.53e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.56: 6046 4.56 - 9.13: 3488 9.13 - 13.69: 1115 13.69 - 18.25: 154 18.25 - 22.81: 7 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " pdb=" NH1 ARG A 49 " ideal model delta sigma weight residual 121.50 103.27 18.23 1.00e+00 1.00e+00 3.32e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.45 110.08 12.37 7.20e-01 1.93e+00 2.95e+02 angle pdb=" CA LEU B 166 " pdb=" C LEU B 166 " pdb=" O LEU B 166 " ideal model delta sigma weight residual 120.55 138.00 -17.45 1.06e+00 8.90e-01 2.71e+02 angle pdb=" CA LEU B 153 " pdb=" C LEU B 153 " pdb=" O LEU B 153 " ideal model delta sigma weight residual 120.54 105.24 15.30 1.04e+00 9.25e-01 2.16e+02 angle pdb=" CA TYR A 192 " pdb=" C TYR A 192 " pdb=" O TYR A 192 " ideal model delta sigma weight residual 120.81 136.82 -16.01 1.15e+00 7.56e-01 1.94e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 1839 16.90 - 33.80: 141 33.80 - 50.70: 42 50.70 - 67.60: 23 67.60 - 84.50: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 151.50 28.50 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA TRP A 139 " pdb=" C TRP A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 154.35 25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA VAL B 32 " pdb=" C VAL B 32 " pdb=" N THR B 33 " pdb=" CA THR B 33 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.220: 214 0.220 - 0.440: 154 0.440 - 0.660: 86 0.660 - 0.879: 30 0.879 - 1.099: 8 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ARG B 83 " pdb=" N ARG B 83 " pdb=" C ARG B 83 " pdb=" CB ARG B 83 " both_signs ideal model delta sigma weight residual False 2.51 3.61 -1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" CB VAL B 26 " pdb=" CA VAL B 26 " pdb=" CG1 VAL B 26 " pdb=" CG2 VAL B 26 " both_signs ideal model delta sigma weight residual False -2.63 -3.68 1.05 2.00e-01 2.50e+01 2.76e+01 chirality pdb=" CA ARG B 175 " pdb=" N ARG B 175 " pdb=" C ARG B 175 " pdb=" CB ARG B 175 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.67e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 82 " 0.010 2.00e-02 2.50e+03 7.42e-02 1.65e+02 pdb=" CG PHE B 82 " -0.115 2.00e-02 2.50e+03 pdb=" CD1 PHE B 82 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 PHE B 82 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 PHE B 82 " 0.119 2.00e-02 2.50e+03 pdb=" CE2 PHE B 82 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 82 " -0.069 2.00e-02 2.50e+03 pdb=" HD1 PHE B 82 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE B 82 " -0.079 2.00e-02 2.50e+03 pdb=" HE1 PHE B 82 " -0.071 2.00e-02 2.50e+03 pdb=" HE2 PHE B 82 " 0.101 2.00e-02 2.50e+03 pdb=" HZ PHE B 82 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.164 2.00e-02 2.50e+03 7.23e-02 1.57e+02 pdb=" CG PHE A 164 " 0.100 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.079 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.109 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.005 2.00e-02 2.50e+03 6.19e-02 1.53e+02 pdb=" CG TRP A 139 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.064 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.059 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.061 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.013 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.067 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.100 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.106 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.048 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.58: 23 1.58 - 2.34: 2080 2.34 - 3.09: 22043 3.09 - 3.85: 33099 3.85 - 4.60: 53124 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110369 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.826 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.932 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.055 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.130 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.150 2.620 ... (remaining 110364 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_3918332_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= 0.2038 r_free= 0.1985 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.305334 | | target function (ml) not normalized (work): 806444.974073 | | target function (ml) not normalized (free): 16570.317448 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2133 0.1879 6.7012 6.2945| | 2: 2.94 - 2.33 1.00 7339 128 0.1620 0.1600 5.5354 5.5786| | 3: 2.33 - 2.04 0.96 6939 150 0.1628 0.1514 5.1545 5.118| | 4: 2.04 - 1.85 1.00 7170 155 0.1745 0.1696 4.9747 5.1373| | 5: 1.85 - 1.72 0.99 7113 159 0.1944 0.1790 4.8119 4.8329| | 6: 1.72 - 1.62 0.99 7102 142 0.1972 0.1911 4.664 4.6797| | 7: 1.62 - 1.54 0.99 7104 148 0.2036 0.1901 4.571 4.6688| | 8: 1.54 - 1.47 0.96 6798 152 0.2081 0.2211 4.4848 4.5318| | 9: 1.47 - 1.41 0.98 6938 155 0.2110 0.2356 4.4094 4.5406| | 10: 1.41 - 1.36 0.99 7022 150 0.2164 0.2209 4.3237 4.3299| | 11: 1.36 - 1.32 0.99 6997 151 0.2144 0.2080 4.2509 4.2092| | 12: 1.32 - 1.28 0.98 6976 149 0.2076 0.1766 4.1753 4.1291| | 13: 1.28 - 1.25 0.98 6907 166 0.1995 0.2263 4.1104 4.2323| | 14: 1.25 - 1.22 0.98 7015 113 0.2090 0.2154 4.0847 4.1822| | 15: 1.22 - 1.19 0.98 6957 137 0.2087 0.2261 4.0531 4.1377| | 16: 1.19 - 1.17 0.93 6604 132 0.2132 0.2132 4.0157 4.0533| | 17: 1.17 - 1.14 0.98 6941 135 0.2187 0.1807 3.966 3.9115| | 18: 1.14 - 1.12 0.98 6875 142 0.2219 0.2286 3.9283 3.8882| | 19: 1.12 - 1.10 0.97 6949 106 0.2272 0.2681 3.878 4.0523| | 20: 1.10 - 1.08 0.97 6884 147 0.2332 0.2414 3.8316 3.8871| | 21: 1.08 - 1.07 0.97 6852 152 0.2423 0.2718 3.7907 3.836| | 22: 1.07 - 1.05 0.97 6838 135 0.2574 0.2547 3.7568 3.7163| | 23: 1.05 - 1.03 0.97 6829 159 0.2734 0.2575 3.735 3.7625| | 24: 1.03 - 1.02 0.96 6785 133 0.2856 0.2724 3.6914 3.7504| | 25: 1.02 - 1.01 0.93 6552 130 0.3060 0.3128 3.6677 3.7698| | 26: 1.01 - 0.99 0.96 6767 158 0.3249 0.3200 3.6299 3.6139| | 27: 0.99 - 0.98 0.94 6648 131 0.3383 0.3353 3.6324 3.6259| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.16 0.91 0.97 34363.88| | 2: 2.94 - 2.33 7339 128 0.86 21.06 1.09 1.00 14703.63| | 3: 2.33 - 2.04 6939 150 0.93 12.82 1.11 1.03 4155.72| | 4: 2.04 - 1.85 7170 155 0.92 13.90 1.11 1.04 2846.73| | 5: 1.85 - 1.72 7113 159 0.90 16.10 1.11 1.06 2174.51| | 6: 1.72 - 1.62 7102 142 0.90 17.19 1.11 1.07 1731.21| | 7: 1.62 - 1.54 7104 148 0.88 18.51 1.11 1.07 1452.44| | 8: 1.54 - 1.47 6798 152 0.88 19.20 1.11 1.06 1235.69| | 9: 1.47 - 1.41 6938 155 0.87 19.81 1.10 1.07 1071.07| | 10: 1.41 - 1.36 7022 150 0.87 20.00 1.10 1.06 863.73| | 11: 1.36 - 1.32 6997 151 0.88 19.24 1.08 1.06 693.64| | 12: 1.32 - 1.28 6976 149 0.89 18.22 1.08 1.04 563.94| | 13: 1.28 - 1.25 6907 166 0.88 18.80 1.07 1.05 553.71| | 14: 1.25 - 1.22 7015 113 0.87 20.24 1.07 1.05 556.63| | 15: 1.22 - 1.19 6957 137 0.87 20.82 1.07 1.05 548.11| | 16: 1.19 - 1.17 6604 132 0.88 20.09 1.07 1.03 479.25| | 17: 1.17 - 1.14 6941 135 0.87 20.27 1.08 1.02 422.85| | 18: 1.14 - 1.12 6875 142 0.87 20.90 1.07 1.00 389.54| | 19: 1.12 - 1.10 6949 106 0.85 22.52 1.07 0.99 392.44| | 20: 1.10 - 1.08 6884 147 0.84 23.65 1.06 0.98 371.93| | 21: 1.08 - 1.07 6852 152 0.83 24.24 1.05 0.98 350.27| | 22: 1.07 - 1.05 6838 135 0.82 25.19 1.05 0.98 319.08| | 23: 1.05 - 1.03 6829 159 0.81 26.84 1.05 0.98 317.38| | 24: 1.03 - 1.02 6785 133 0.79 28.82 1.06 0.97 317.30| | 25: 1.02 - 1.01 6552 130 0.77 30.87 1.03 0.92 310.71| | 26: 1.01 - 0.99 6767 158 0.74 33.08 1.03 0.89 295.62| | 27: 0.99 - 0.98 6648 131 0.74 32.94 1.04 0.90 281.38| |alpha: min = 0.89 max = 1.07 mean = 1.01| |beta: min = 281.38 max = 34363.88 mean = 2781.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.60| |phase err.(test): min = 0.00 max = 89.80 mean = 21.57| |-----------------------------------------------------------------------------| ----------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 0.270 2950 Z= 5.445 Angle : 5.234 18.228 4018 Z= 3.727 Chirality : 0.373 1.099 492 Planarity : 0.030 0.100 512 Dihedral : 12.928 84.499 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.89 % Favored : 95.60 % Rotamer: Outliers : 0.97 % Allowed : 5.16 % Favored : 93.87 % Cbeta Deviations : 27.53 % 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: -1.96 (0.39), residues: 386 helix: -2.00 (0.33), residues: 144 sheet: -0.77 (0.52), residues: 86 loop : -0.61 (0.50), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.020 ARG B 149 TYR 0.092 0.029 TYR A 67 PHE 0.147 0.041 PHE A 119 TRP 0.103 0.037 TRP A 146 HIS 0.056 0.027 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2038 r_free= 0.1985 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.305334 | | target function (ml) not normalized (work): 806444.974073 | | target function (ml) not normalized (free): 16570.317448 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2038 0.1985 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2038 0.1985 n_refl.: 191155 remove outliers: r(all,work,free)=0.2036 0.2038 0.1985 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2038 0.2040 0.1985 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1807 0.1805 0.1934 n_refl.: 191145 remove outliers: r(all,work,free)=0.1805 0.1803 0.1934 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4067 402.814 292.935 0.434 0.913 0.301 13.296-10.522 99.01 99 1 0.2491 528.187 519.810 0.784 0.914 0.250 10.503-8.327 99.45 178 3 0.2522 565.118 555.634 0.967 0.914 0.223 8.318-6.595 100.00 360 8 0.2457 414.736 403.502 0.966 0.913 0.160 6.588-5.215 100.00 711 7 0.2268 381.101 365.500 0.956 0.914 0.160 5.214-4.128 98.38 1367 28 0.1471 557.435 549.957 1.072 0.914 0.080 4.126-3.266 94.74 2603 46 0.1341 508.132 499.381 1.145 0.914 0.029 3.266-2.585 99.86 5447 97 0.1439 342.774 337.586 1.118 0.913 0.020 2.585-2.046 97.45 10613 204 0.1390 258.603 254.602 1.125 0.912 0.000 2.046-1.619 99.39 21536 464 0.1621 153.054 149.847 1.142 0.911 0.000 1.619-1.281 98.00 42464 925 0.1940 82.395 80.149 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2327 44.203 41.627 1.109 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0156 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1803 r_free=0.1934 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1803 r_free=0.1934 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.633974 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.757610 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 0.1273 0.1504 0.0231 0.040 1.2 11.2 0.0 0.3 0 11.317 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.04 2.31 1.118 13.120 575.758 0.018 12.97 15.70 2.73 1.229 13.334 575.758 0.017 Individual atomic B min max mean iso aniso Overall: 5.18 73.05 15.00 1.40 435 3274 Protein: 5.18 40.44 10.98 1.40 0 2902 Water: 6.36 73.05 29.45 N/A 435 370 Other: 15.95 29.89 22.92 N/A 0 2 Chain A: 5.35 59.87 13.03 N/A 0 1626 Chain B: 5.18 73.05 12.75 N/A 0 1648 Chain S: 11.92 62.70 30.87 N/A 435 0 Histogram: Values Number of atoms 5.18 - 11.97 2172 11.97 - 18.75 637 18.75 - 25.54 312 25.54 - 32.33 266 32.33 - 39.12 155 39.12 - 45.90 101 45.90 - 52.69 42 52.69 - 59.48 20 59.48 - 66.27 3 66.27 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1570 r_work=0.1297 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1566 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 = 0.1282 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015589 | | target function (ls_wunit_k1) not normalized (work): 2919.790624 | | target function (ls_wunit_k1) not normalized (free): 117.711941 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1556 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1466 0.1463 0.1635 n_refl.: 191139 remove outliers: r(all,work,free)=0.1466 0.1463 0.1635 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1490 0.1488 0.1644 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1274 0.1547 n_refl.: 191139 remove outliers: r(all,work,free)=0.1279 0.1274 0.1546 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 0.3615 402.814 379.136 0.473 0.997 0.281 13.296-10.522 99.01 99 1 0.2066 528.187 518.613 0.707 0.999 0.233 10.503-8.327 99.45 178 3 0.1772 565.118 562.913 0.857 0.999 0.210 8.318-6.595 100.00 360 8 0.1714 414.736 412.141 0.879 0.999 0.155 6.588-5.215 100.00 711 7 0.1526 381.101 373.887 0.857 0.999 0.150 5.214-4.128 98.38 1367 28 0.0897 557.435 554.937 0.942 0.999 0.055 4.126-3.266 94.74 2603 46 0.0829 508.132 504.420 1.008 1.000 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.338 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.332 1.002 1.000 0.000 2.046-1.619 99.39 21536 464 0.1090 153.054 151.363 1.019 0.999 0.000 1.619-1.281 98.00 42464 925 0.1278 82.395 81.417 1.012 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.175 0.989 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0392 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1546 | n_water=805 | time (s): 3.250 (total time: 3.250) Filter (dist) r_work=0.1279 r_free=0.1552 | n_water=793 | time (s): 99.100 (total time: 102.350) Filter (q & B) r_work=0.1280 r_free=0.1552 | n_water=788 | time (s): 4.720 (total time: 107.070) Compute maps r_work=0.1280 r_free=0.1552 | n_water=788 | time (s): 2.030 (total time: 109.100) Filter (map) r_work=0.1306 r_free=0.1534 | n_water=650 | time (s): 4.550 (total time: 113.650) Find peaks r_work=0.1306 r_free=0.1534 | n_water=650 | time (s): 0.850 (total time: 114.500) Add new water r_work=0.1328 r_free=0.1564 | n_water=957 | time (s): 5.010 (total time: 119.510) Refine new water occ: r_work=0.1284 r_free=0.1512 adp: r_work=0.1272 r_free=0.1509 occ: r_work=0.1274 r_free=0.1505 adp: r_work=0.1268 r_free=0.1505 occ: r_work=0.1270 r_free=0.1502 adp: r_work=0.1267 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1503 r_work=0.1267 r_free=0.1503 | n_water=957 | time (s): 86.150 (total time: 205.660) Filter (q & B) r_work=0.1271 r_free=0.1507 | n_water=880 | time (s): 5.740 (total time: 211.400) Filter (dist only) r_work=0.1271 r_free=0.1506 | n_water=879 | time (s): 110.160 (total time: 321.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.288402 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 592.373099 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1256 0.1527 0.0270 0.042 1.1 17.3 0.0 0.3 0 11.644 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.27 2.70 2.038 15.156 592.373 0.015 12.35 15.14 2.79 2.414 15.212 592.373 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.23 16.31 1.20 511 3272 Protein: 5.38 40.45 10.97 1.20 0 2902 Water: 6.67 68.23 33.90 N/A 511 368 Other: 16.39 32.31 24.35 N/A 0 2 Chain A: 5.54 56.10 12.99 N/A 0 1624 Chain B: 5.38 68.23 12.82 N/A 0 1648 Chain S: 13.70 66.67 38.10 N/A 511 0 Histogram: Values Number of atoms 5.38 - 11.67 2056 11.67 - 17.95 716 17.95 - 24.24 260 24.24 - 30.52 210 30.52 - 36.81 170 36.81 - 43.09 169 43.09 - 49.37 99 49.37 - 55.66 51 55.66 - 61.94 41 61.94 - 68.23 11 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1514 r_work=0.1236 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1515 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1516 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1516 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013554 | | target function (ls_wunit_k1) not normalized (work): 2538.676668 | | target function (ls_wunit_k1) not normalized (free): 101.248707 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1516 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1437 0.1608 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1437 0.1608 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1437 0.1434 0.1606 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1523 n_refl.: 191138 remove outliers: r(all,work,free)=0.1241 0.1236 0.1523 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 0.3269 402.814 388.762 0.502 0.961 0.261 13.296-10.522 99.01 99 1 0.1933 528.187 524.142 0.765 0.962 0.219 10.503-8.327 99.45 178 3 0.1447 565.118 568.525 0.922 0.962 0.200 8.318-6.595 100.00 360 8 0.1531 414.736 414.882 0.941 0.961 0.160 6.588-5.215 100.00 711 7 0.1349 381.101 375.998 0.913 0.962 0.160 5.214-4.128 98.38 1367 28 0.0836 557.435 555.768 0.996 0.962 0.080 4.126-3.266 94.74 2603 46 0.0764 508.132 505.509 1.062 0.962 0.019 3.266-2.585 99.86 5447 97 0.0862 342.774 341.156 1.047 0.961 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.737 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.581 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1259 82.395 81.423 1.071 0.959 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.232 1.054 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0548 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1523 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1523 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1523 | n_water=879 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1237 r_free=0.1524 | n_water=874 | time (s): 113.430 (total time: 116.440) Filter (q & B) r_work=0.1237 r_free=0.1524 | n_water=870 | time (s): 5.670 (total time: 122.110) Compute maps r_work=0.1237 r_free=0.1524 | n_water=870 | time (s): 2.470 (total time: 124.580) Filter (map) r_work=0.1276 r_free=0.1526 | n_water=689 | time (s): 5.150 (total time: 129.730) Find peaks r_work=0.1276 r_free=0.1526 | n_water=689 | time (s): 0.570 (total time: 130.300) Add new water r_work=0.1300 r_free=0.1563 | n_water=1008 | time (s): 4.270 (total time: 134.570) Refine new water occ: r_work=0.1253 r_free=0.1525 adp: r_work=0.1254 r_free=0.1526 occ: r_work=0.1249 r_free=0.1522 adp: r_work=0.1249 r_free=0.1523 occ: r_work=0.1246 r_free=0.1519 adp: r_work=0.1245 r_free=0.1520 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1520 r_work=0.1245 r_free=0.1520 | n_water=1008 | time (s): 298.860 (total time: 433.430) Filter (q & B) r_work=0.1250 r_free=0.1521 | n_water=878 | time (s): 4.520 (total time: 437.950) Filter (dist only) r_work=0.1251 r_free=0.1521 | n_water=876 | time (s): 111.870 (total time: 549.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.694694 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.209944 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1240 0.1441 0.0201 0.035 1.1 9.0 0.0 0.0 0 0.847 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.41 2.01 1.929 14.588 16.210 3.940 12.31 13.97 1.66 2.167 14.508 16.210 3.898 Individual atomic B min max mean iso aniso Overall: 5.49 67.88 15.31 1.07 509 3271 Protein: 5.49 37.18 10.77 1.07 0 2902 Water: 6.66 67.88 30.35 N/A 509 367 Other: 14.20 28.87 21.53 N/A 0 2 Chain A: 5.52 55.46 12.79 N/A 0 1624 Chain B: 5.49 67.88 12.57 N/A 0 1647 Chain S: 13.50 62.48 32.21 N/A 509 0 Histogram: Values Number of atoms 5.49 - 11.73 2117 11.73 - 17.97 692 17.97 - 24.21 304 24.21 - 30.45 238 30.45 - 36.69 171 36.69 - 42.92 141 42.92 - 49.16 78 49.16 - 55.40 26 55.40 - 61.64 11 61.64 - 67.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1398 r_work=0.1232 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1399 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1390 target_work(ml) = 3.892 | | 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= 0.1228 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892027 | | target function (ml) not normalized (work): 728965.031649 | | target function (ml) not normalized (free): 15224.145854 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1390 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1439 0.1492 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1439 0.1492 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1434 0.1489 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1385 n_refl.: 191138 remove outliers: r(all,work,free)=0.1226 0.1223 0.1385 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3805 398.008 361.113 0.419 0.946 0.241 13.296-10.522 99.01 99 1 0.2490 528.187 506.513 0.702 0.947 0.204 10.503-8.327 98.35 176 3 0.1957 555.265 558.222 0.887 0.947 0.190 8.318-6.595 100.00 360 8 0.2079 414.736 410.341 0.900 0.947 0.126 6.588-5.215 100.00 711 7 0.1827 381.101 369.672 0.884 0.947 0.107 5.214-4.128 98.38 1367 28 0.1176 557.435 551.885 0.971 0.947 0.070 4.126-3.266 94.74 2603 46 0.1093 508.132 501.101 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1081 342.774 339.080 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0958 258.603 255.811 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0971 153.054 151.411 1.056 0.944 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.484 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1690 44.202 42.318 1.036 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0865 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1386 | n_water=876 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1223 r_free=0.1386 | n_water=875 | time (s): 106.930 (total time: 109.950) Filter (q & B) r_work=0.1224 r_free=0.1385 | n_water=863 | time (s): 4.390 (total time: 114.340) Compute maps r_work=0.1224 r_free=0.1385 | n_water=863 | time (s): 2.460 (total time: 116.800) Filter (map) r_work=0.1246 r_free=0.1396 | n_water=719 | time (s): 4.370 (total time: 121.170) Find peaks r_work=0.1246 r_free=0.1396 | n_water=719 | time (s): 0.550 (total time: 121.720) Add new water r_work=0.1260 r_free=0.1414 | n_water=965 | time (s): 4.650 (total time: 126.370) Refine new water occ: r_work=0.1213 r_free=0.1373 adp: r_work=0.1206 r_free=0.1369 occ: r_work=0.1203 r_free=0.1368 adp: r_work=0.1203 r_free=0.1368 occ: r_work=0.1203 r_free=0.1368 adp: r_work=0.1203 r_free=0.1368 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1368 r_work=0.1203 r_free=0.1368 | n_water=965 | time (s): 178.890 (total time: 305.260) Filter (q & B) r_work=0.1209 r_free=0.1373 | n_water=841 | time (s): 5.080 (total time: 310.340) Filter (dist only) r_work=0.1209 r_free=0.1372 | n_water=840 | time (s): 105.680 (total time: 416.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.619060 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.437413 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 0.1208 0.1372 0.0163 0.033 1.1 6.6 0.0 0.0 0 0.810 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.72 1.63 1.842 14.131 16.437 3.875 12.06 13.67 1.61 2.076 14.055 16.437 3.865 Individual atomic B min max mean iso aniso Overall: 5.48 67.09 14.75 0.99 473 3271 Protein: 5.48 32.88 10.60 0.99 0 2902 Water: 5.94 67.09 29.07 N/A 473 367 Other: 13.78 26.43 20.11 N/A 0 2 Chain A: 5.59 53.52 12.57 N/A 0 1624 Chain B: 5.48 67.09 12.39 N/A 0 1647 Chain S: 5.94 62.21 30.44 N/A 473 0 Histogram: Values Number of atoms 5.48 - 11.65 2115 11.65 - 17.81 736 17.81 - 23.97 317 23.97 - 30.13 207 30.13 - 36.29 145 36.29 - 42.45 123 42.45 - 48.61 66 48.61 - 54.77 26 54.77 - 60.93 6 60.93 - 67.09 3 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1367 r_work=0.1206 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1367 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1364 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862776 | | target function (ml) not normalized (work): 723474.675698 | | target function (ml) not normalized (free): 15126.582562 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1364 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1433 0.1432 0.1474 n_refl.: 191135 remove outliers: r(all,work,free)=0.1433 0.1432 0.1474 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1426 0.1425 0.1469 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1202 0.1362 n_refl.: 191135 remove outliers: r(all,work,free)=0.1204 0.1201 0.1362 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 94.06 92 3 0.3846 360.538 323.788 0.409 0.945 0.237 13.296-10.522 97.03 97 1 0.2412 481.382 454.798 0.691 0.946 0.186 10.503-8.327 98.35 176 3 0.2110 502.991 495.557 0.867 0.947 0.163 8.318-6.595 100.00 360 8 0.2240 375.692 370.347 0.897 0.946 0.124 6.588-5.215 100.00 711 7 0.1941 345.223 334.712 0.883 0.946 0.104 5.214-4.128 98.38 1367 28 0.1235 504.957 499.402 0.974 0.947 0.070 4.126-3.266 94.74 2603 46 0.1142 460.295 453.518 1.036 0.947 0.000 3.266-2.585 99.86 5447 97 0.1094 310.504 307.237 1.022 0.946 0.000 2.585-2.046 97.45 10613 204 0.0945 234.258 231.786 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0915 138.645 137.343 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.0985 74.639 73.937 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1656 40.040 38.389 1.039 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1118 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1362 | n_water=840 | time (s): 3.030 (total time: 3.030) Filter (dist) r_work=0.1201 r_free=0.1362 | n_water=840 | time (s): 112.690 (total time: 115.720) Filter (q & B) r_work=0.1202 r_free=0.1363 | n_water=831 | time (s): 4.250 (total time: 119.970) Compute maps r_work=0.1202 r_free=0.1363 | n_water=831 | time (s): 1.740 (total time: 121.710) Filter (map) r_work=0.1223 r_free=0.1359 | n_water=720 | time (s): 4.850 (total time: 126.560) Find peaks r_work=0.1223 r_free=0.1359 | n_water=720 | time (s): 0.610 (total time: 127.170) Add new water r_work=0.1235 r_free=0.1372 | n_water=931 | time (s): 4.250 (total time: 131.420) Refine new water occ: r_work=0.1198 r_free=0.1346 adp: r_work=0.1199 r_free=0.1347 occ: r_work=0.1196 r_free=0.1345 adp: r_work=0.1196 r_free=0.1346 occ: r_work=0.1194 r_free=0.1345 adp: r_work=0.1194 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1346 r_work=0.1194 r_free=0.1346 | n_water=931 | time (s): 225.680 (total time: 357.100) Filter (q & B) r_work=0.1197 r_free=0.1351 | n_water=864 | time (s): 4.470 (total time: 361.570) Filter (dist only) r_work=0.1197 r_free=0.1350 | n_water=863 | time (s): 114.350 (total time: 475.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.509261 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.592446 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 0.1359 0.0159 0.036 1.1 5.8 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.59 1.59 1.775 14.033 15.592 3.764 12.02 13.66 1.63 1.804 14.019 15.592 3.762 Individual atomic B min max mean iso aniso Overall: 5.54 66.80 14.87 0.95 497 3270 Protein: 5.54 31.67 10.56 0.95 0 2902 Water: 5.96 66.80 29.33 N/A 497 366 Other: 13.77 25.68 19.72 N/A 0 2 Chain A: 5.54 52.86 12.49 N/A 0 1623 Chain B: 5.57 66.80 12.33 N/A 0 1647 Chain S: 5.96 62.10 31.03 N/A 497 0 Histogram: Values Number of atoms 5.54 - 11.67 2132 11.67 - 17.79 727 17.79 - 23.92 294 23.92 - 30.05 217 30.05 - 36.17 164 36.17 - 42.30 127 42.30 - 48.42 72 48.42 - 54.55 25 54.55 - 60.67 6 60.67 - 66.80 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1366 r_work=0.1203 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 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) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (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): 3.761666 | | target function (ml) not normalized (work): 704529.984230 | | target function (ml) not normalized (free): 14753.880299 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1367 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1424 0.1423 0.1480 n_refl.: 191133 remove outliers: r(all,work,free)=0.1424 0.1423 0.1480 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1416 0.1476 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1199 0.1366 n_refl.: 191133 remove outliers: r(all,work,free)=0.1203 0.1199 0.1366 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 94.06 92 3 0.3850 360.538 321.211 0.402 0.948 0.232 13.296-10.522 97.03 97 1 0.2483 481.382 460.940 0.697 0.949 0.178 10.503-8.327 98.35 176 3 0.2111 502.991 496.155 0.864 0.949 0.157 8.318-6.595 100.00 360 8 0.2189 375.692 370.728 0.891 0.949 0.109 6.588-5.215 100.00 711 7 0.1919 345.223 335.270 0.882 0.949 0.090 5.214-4.128 98.38 1367 28 0.1218 504.957 499.377 0.970 0.949 0.044 4.126-3.266 94.74 2603 46 0.1145 460.295 453.412 1.034 0.949 0.005 3.266-2.585 99.86 5447 97 0.1106 310.504 307.197 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0952 234.258 231.759 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0916 138.645 137.318 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0974 74.639 73.927 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.040 38.372 1.040 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1163 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1366 | n_water=863 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1200 r_free=0.1366 | n_water=862 | time (s): 109.910 (total time: 112.400) Filter (q & B) r_work=0.1200 r_free=0.1368 | n_water=854 | time (s): 4.400 (total time: 116.800) Compute maps r_work=0.1200 r_free=0.1368 | n_water=854 | time (s): 1.850 (total time: 118.650) Filter (map) r_work=0.1222 r_free=0.1366 | n_water=733 | time (s): 4.240 (total time: 122.890) Find peaks r_work=0.1222 r_free=0.1366 | n_water=733 | time (s): 0.810 (total time: 123.700) Add new water r_work=0.1232 r_free=0.1377 | n_water=939 | time (s): 4.220 (total time: 127.920) Refine new water 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=0.1356 occ: r_work=0.1195 r_free=0.1356 adp: r_work=0.1195 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1356 r_work=0.1195 r_free=0.1356 | n_water=939 | time (s): 224.910 (total time: 352.830) Filter (q & B) r_work=0.1199 r_free=0.1362 | n_water=869 | time (s): 5.170 (total time: 358.000) Filter (dist only) r_work=0.1199 r_free=0.1361 | n_water=868 | time (s): 114.160 (total time: 472.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.610705 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.129405 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1366 0.0163 0.037 1.1 5.6 0.0 0.3 0 0.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.66 1.63 1.754 13.966 15.129 3.762 12.05 13.68 1.64 1.867 13.923 15.129 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 65.71 14.74 0.91 503 3269 Protein: 5.58 29.18 10.47 0.91 0 2902 Water: 5.99 65.71 29.03 N/A 503 365 Other: 13.83 22.92 18.37 N/A 0 2 Chain A: 5.62 51.21 12.36 N/A 0 1623 Chain B: 5.58 65.71 12.20 N/A 0 1646 Chain S: 5.99 61.68 30.78 N/A 503 0 Histogram: Values Number of atoms 5.58 - 11.59 2117 11.59 - 17.60 765 17.60 - 23.61 282 23.61 - 29.63 204 29.63 - 35.64 173 35.64 - 41.65 116 41.65 - 47.67 74 47.67 - 53.68 29 53.68 - 59.69 8 59.69 - 65.71 4 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1369 r_work=0.1205 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1369 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1368 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759132 | | target function (ml) not normalized (work): 704055.310065 | | target function (ml) not normalized (free): 14740.590602 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1368 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1429 0.1428 0.1489 n_refl.: 191133 remove outliers: r(all,work,free)=0.1429 0.1428 0.1489 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1421 0.1420 0.1483 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1203 0.1367 n_refl.: 191133 remove outliers: r(all,work,free)=0.1206 0.1203 0.1367 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3847 361.342 314.683 0.390 0.944 0.219 13.296-10.522 96.04 96 1 0.2406 480.619 456.633 0.700 0.946 0.171 10.503-8.327 98.35 176 3 0.2131 502.991 496.885 0.864 0.946 0.150 8.318-6.595 100.00 360 8 0.2203 375.692 370.845 0.892 0.946 0.100 6.588-5.215 100.00 711 7 0.1939 345.223 334.859 0.885 0.946 0.085 5.214-4.128 98.38 1367 28 0.1245 504.957 499.353 0.974 0.947 0.049 4.126-3.266 94.74 2603 46 0.1174 460.295 453.085 1.039 0.947 0.009 3.266-2.585 99.86 5447 97 0.1121 310.504 307.183 1.024 0.947 0.000 2.585-2.046 97.45 10613 204 0.0954 234.258 231.776 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0913 138.645 137.356 1.056 0.948 0.000 1.619-1.281 98.00 42464 925 0.0969 74.639 73.942 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.040 38.376 1.035 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1315 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1367 | n_water=868 | time (s): 3.080 (total time: 3.080) Filter (dist) r_work=0.1203 r_free=0.1367 | n_water=868 | time (s): 105.700 (total time: 108.780) Filter (q & B) r_work=0.1203 r_free=0.1365 | n_water=860 | time (s): 5.140 (total time: 113.920) Compute maps r_work=0.1203 r_free=0.1365 | n_water=860 | time (s): 1.680 (total time: 115.600) Filter (map) r_work=0.1223 r_free=0.1357 | n_water=741 | time (s): 3.940 (total time: 119.540) Find peaks r_work=0.1223 r_free=0.1357 | n_water=741 | time (s): 0.550 (total time: 120.090) Add new water r_work=0.1233 r_free=0.1375 | n_water=942 | time (s): 4.550 (total time: 124.640) Refine new water occ: r_work=0.1201 r_free=0.1350 adp: r_work=0.1201 r_free=0.1350 occ: r_work=0.1199 r_free=0.1350 adp: r_work=0.1199 r_free=0.1350 occ: r_work=0.1197 r_free=0.1350 adp: r_work=0.1197 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1350 r_work=0.1197 r_free=0.1350 | n_water=942 | time (s): 244.770 (total time: 369.410) Filter (q & B) r_work=0.1200 r_free=0.1358 | n_water=878 | time (s): 5.510 (total time: 374.920) Filter (dist only) r_work=0.1201 r_free=0.1357 | n_water=877 | time (s): 111.840 (total time: 486.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.549355 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.110959 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 0.1205 0.1362 0.0157 0.037 1.1 5.5 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.62 1.57 1.717 13.847 15.111 3.760 12.05 13.67 1.61 1.765 13.826 15.111 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 64.47 14.68 0.89 512 3269 Protein: 5.59 28.61 10.42 0.89 0 2902 Water: 5.95 64.47 28.77 N/A 512 365 Other: 13.85 22.02 17.93 N/A 0 2 Chain A: 5.61 50.65 12.26 N/A 0 1623 Chain B: 5.59 64.47 12.12 N/A 0 1646 Chain S: 5.95 61.24 30.56 N/A 512 0 Histogram: Values Number of atoms 5.59 - 11.48 2091 11.48 - 17.37 793 17.37 - 23.26 273 23.26 - 29.15 204 29.15 - 35.03 178 35.03 - 40.92 123 40.92 - 46.81 76 46.81 - 52.70 30 52.70 - 58.59 9 58.59 - 64.47 4 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1367 r_work=0.1206 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1366 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757170 | | target function (ml) not normalized (work): 703680.413175 | | target function (ml) not normalized (free): 14735.693565 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1366 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1410 0.1409 0.1483 n_refl.: 191131 remove outliers: r(all,work,free)=0.1410 0.1409 0.1483 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1377 0.1375 0.1463 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1363 n_refl.: 191131 remove outliers: r(all,work,free)=0.1206 0.1203 0.1363 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3845 361.342 321.376 0.396 0.949 0.207 13.296-10.522 96.04 96 1 0.2398 480.619 462.148 0.714 0.951 0.156 10.503-8.327 98.35 176 3 0.2184 502.991 496.857 0.881 0.951 0.133 8.318-6.595 100.00 360 8 0.2222 375.692 370.448 0.911 0.951 0.110 6.588-5.215 100.00 711 7 0.1945 345.223 334.636 0.904 0.951 0.093 5.214-4.128 98.38 1367 28 0.1245 504.957 499.215 0.994 0.951 0.049 4.126-3.266 94.74 2603 46 0.1182 460.295 452.837 1.059 0.952 0.009 3.266-2.585 99.86 5447 97 0.1126 310.504 307.169 1.042 0.951 0.000 2.585-2.046 97.45 10613 204 0.0957 234.258 231.722 1.049 0.951 0.000 2.046-1.619 99.39 21536 464 0.0910 138.645 137.336 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0962 74.639 73.940 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1647 40.040 38.366 1.025 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0472 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1363 | n_water=877 | time (s): 2.880 (total time: 2.880) Filter (dist) r_work=0.1203 r_free=0.1363 | n_water=876 | time (s): 110.320 (total time: 113.200) Filter (q & B) r_work=0.1204 r_free=0.1361 | n_water=867 | time (s): 5.160 (total time: 118.360) Compute maps r_work=0.1204 r_free=0.1361 | n_water=867 | time (s): 1.750 (total time: 120.110) Filter (map) r_work=0.1222 r_free=0.1358 | n_water=756 | time (s): 4.930 (total time: 125.040) Find peaks r_work=0.1222 r_free=0.1358 | n_water=756 | time (s): 0.590 (total time: 125.630) Add new water r_work=0.1230 r_free=0.1369 | n_water=964 | time (s): 4.250 (total time: 129.880) Refine new water occ: r_work=0.1199 r_free=0.1349 adp: r_work=0.1199 r_free=0.1349 occ: r_work=0.1197 r_free=0.1349 adp: r_work=0.1197 r_free=0.1349 occ: r_work=0.1195 r_free=0.1349 adp: r_work=0.1195 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1349 r_work=0.1195 r_free=0.1349 | n_water=964 | time (s): 272.230 (total time: 402.110) Filter (q & B) r_work=0.1199 r_free=0.1352 | n_water=893 | time (s): 4.360 (total time: 406.470) Filter (dist only) r_work=0.1200 r_free=0.1352 | n_water=891 | time (s): 116.370 (total time: 522.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.504009 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.568832 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1360 0.0157 0.038 1.1 5.6 0.0 0.3 0 0.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.60 1.57 1.700 13.591 13.569 3.758 12.06 13.65 1.59 1.709 13.584 13.569 3.759 Individual atomic B min max mean iso aniso Overall: 5.38 63.96 14.44 0.86 526 3269 Protein: 5.38 28.10 10.21 0.86 0 2902 Water: 5.82 63.96 28.23 N/A 526 365 Other: 13.63 21.88 17.76 N/A 0 2 Chain A: 5.43 50.33 12.03 N/A 0 1623 Chain B: 5.38 63.96 11.89 N/A 0 1646 Chain S: 5.82 61.06 29.89 N/A 526 0 Histogram: Values Number of atoms 5.38 - 11.24 2073 11.24 - 17.09 810 17.09 - 22.95 292 22.95 - 28.81 204 28.81 - 34.67 178 34.67 - 40.53 119 40.53 - 46.38 75 46.38 - 52.24 31 52.24 - 58.10 9 58.10 - 63.96 4 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1365 r_work=0.1207 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1365 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1366 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758747 | | target function (ml) not normalized (work): 703975.715941 | | target function (ml) not normalized (free): 14742.955828 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1206 0.1366 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1382 0.1380 0.1474 n_refl.: 191131 remove outliers: r(all,work,free)=0.1382 0.1380 0.1474 n_refl.: 191131 overall B=0.00 to atoms: r(all,work,free)=0.1382 0.1380 0.1474 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1357 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 0.3675 361.038 309.751 0.407 0.907 0.205 13.296-10.522 96.04 96 1 0.2394 480.619 462.086 0.740 0.908 0.151 10.503-8.327 98.35 176 3 0.2202 502.991 496.235 0.915 0.909 0.127 8.318-6.595 100.00 360 8 0.2219 375.692 370.180 0.945 0.909 0.106 6.588-5.215 100.00 711 7 0.1962 345.223 334.566 0.939 0.909 0.089 5.214-4.128 98.38 1367 28 0.1248 504.957 499.066 1.032 0.910 0.044 4.126-3.266 94.74 2603 46 0.1185 460.295 452.565 1.099 0.911 0.005 3.266-2.585 99.86 5447 97 0.1128 310.504 306.938 1.080 0.912 0.000 2.585-2.046 97.45 10613 204 0.0961 234.258 231.690 1.087 0.913 0.000 2.046-1.619 99.39 21536 464 0.0912 138.645 137.276 1.101 0.916 0.000 1.619-1.281 98.00 42464 925 0.0949 74.639 73.989 1.086 0.920 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.040 38.346 1.044 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1357 | n_water=891 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1197 r_free=0.1356 | n_water=890 | time (s): 107.280 (total time: 109.850) Filter (q & B) r_work=0.1197 r_free=0.1356 | n_water=879 | time (s): 5.360 (total time: 115.210) Compute maps r_work=0.1197 r_free=0.1356 | n_water=879 | time (s): 1.890 (total time: 117.100) Filter (map) r_work=0.1215 r_free=0.1354 | n_water=773 | time (s): 4.190 (total time: 121.290) Find peaks r_work=0.1215 r_free=0.1354 | n_water=773 | time (s): 0.550 (total time: 121.840) Add new water r_work=0.1222 r_free=0.1363 | n_water=979 | time (s): 4.540 (total time: 126.380) Refine new water occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1191 r_free=0.1346 occ: r_work=0.1189 r_free=0.1347 adp: r_work=0.1189 r_free=0.1347 occ: r_work=0.1188 r_free=0.1348 adp: r_work=0.1188 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1348 r_work=0.1188 r_free=0.1348 | n_water=979 | time (s): 352.170 (total time: 478.550) Filter (q & B) r_work=0.1192 r_free=0.1355 | n_water=905 | time (s): 4.390 (total time: 482.940) Filter (dist only) r_work=0.1193 r_free=0.1356 | n_water=903 | time (s): 115.640 (total time: 598.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.590633 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.122434 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1359 0.0162 0.039 1.1 6.3 0.0 0.3 0 0.795 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.59 1.62 1.664 13.601 14.122 3.757 11.96 13.60 1.64 1.676 13.599 14.122 3.754 Individual atomic B min max mean iso aniso Overall: 5.44 63.12 14.50 0.86 538 3269 Protein: 5.44 27.79 10.21 0.86 0 2902 Water: 5.84 63.12 28.28 N/A 538 365 Other: 13.66 21.86 17.76 N/A 0 2 Chain A: 5.50 49.93 12.00 N/A 0 1623 Chain B: 5.44 63.12 11.88 N/A 0 1646 Chain S: 5.84 61.19 30.08 N/A 538 0 Histogram: Values Number of atoms 5.44 - 11.21 2068 11.21 - 16.98 821 16.98 - 22.75 280 22.75 - 28.51 204 28.51 - 34.28 183 34.28 - 40.05 121 40.05 - 45.81 81 45.81 - 51.58 34 51.58 - 57.35 10 57.35 - 63.12 5 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1360 r_work=0.1196 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1362 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754278 | | target function (ml) not normalized (work): 703134.908974 | | target function (ml) not normalized (free): 14733.472712 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1362 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1379 0.1377 0.1483 n_refl.: 191130 remove outliers: r(all,work,free)=0.1379 0.1377 0.1483 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1379 0.1377 0.1483 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1194 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 0.3733 361.038 327.566 0.377 0.995 0.180 13.296-10.522 96.04 96 1 0.2411 480.619 461.273 0.671 0.996 0.143 10.503-8.327 98.35 176 3 0.2186 502.991 496.553 0.836 0.997 0.131 8.318-6.595 100.00 360 8 0.2201 375.692 370.385 0.860 0.997 0.099 6.588-5.215 100.00 711 7 0.1971 345.223 334.343 0.855 0.997 0.090 5.214-4.128 98.38 1367 28 0.1243 504.957 499.057 0.942 0.998 0.049 4.126-3.266 94.74 2603 46 0.1189 460.295 452.529 1.003 0.999 0.009 3.266-2.585 99.86 5447 97 0.1130 310.504 306.856 0.986 1.000 0.000 2.585-2.046 97.45 10613 204 0.0960 234.258 231.637 0.992 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.645 137.270 1.005 1.006 0.000 1.619-1.281 98.00 42464 925 0.0944 74.639 73.988 0.992 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.040 38.342 0.957 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0815 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1194 r_free=0.1359 After: r_work=0.1195 r_free=0.1360 ================================== NQH flips ================================== r_work=0.1195 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1360 | n_water=903 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1195 r_free=0.1360 | n_water=903 | time (s): 114.950 (total time: 117.620) Filter (q & B) r_work=0.1196 r_free=0.1360 | n_water=888 | time (s): 4.800 (total time: 122.420) Compute maps r_work=0.1196 r_free=0.1360 | n_water=888 | time (s): 1.890 (total time: 124.310) Filter (map) r_work=0.1216 r_free=0.1363 | n_water=778 | time (s): 5.080 (total time: 129.390) Find peaks r_work=0.1216 r_free=0.1363 | n_water=778 | time (s): 0.550 (total time: 129.940) Add new water r_work=0.1224 r_free=0.1373 | n_water=981 | time (s): 4.470 (total time: 134.410) Refine new water occ: r_work=0.1192 r_free=0.1352 adp: r_work=0.1193 r_free=0.1351 occ: r_work=0.1190 r_free=0.1352 adp: r_work=0.1191 r_free=0.1351 occ: r_work=0.1189 r_free=0.1352 adp: r_work=0.1189 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1352 r_work=0.1189 r_free=0.1352 | n_water=981 | time (s): 256.050 (total time: 390.460) Filter (q & B) r_work=0.1193 r_free=0.1360 | n_water=906 | time (s): 5.090 (total time: 395.550) Filter (dist only) r_work=0.1194 r_free=0.1359 | n_water=903 | time (s): 118.610 (total time: 514.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.522557 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.233834 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 0.1363 0.0165 0.039 1.2 8.0 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.63 1.65 1.660 13.597 14.234 3.757 11.98 13.65 1.67 1.661 13.594 14.234 3.756 Individual atomic B min max mean iso aniso Overall: 5.46 62.15 14.49 0.86 538 3269 Protein: 5.46 27.79 10.23 0.86 0 2902 Water: 5.89 62.15 28.17 N/A 538 365 Other: 13.71 21.73 17.72 N/A 0 2 Chain A: 5.57 49.55 12.00 N/A 0 1623 Chain B: 5.46 62.15 11.87 N/A 0 1646 Chain S: 5.89 61.31 30.04 N/A 538 0 Histogram: Values Number of atoms 5.46 - 11.13 2040 11.13 - 16.80 843 16.80 - 22.47 277 22.47 - 28.14 204 28.14 - 33.80 190 33.80 - 39.47 120 39.47 - 45.14 77 45.14 - 50.81 39 50.81 - 56.48 11 56.48 - 62.15 6 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1365 r_work=0.1199 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1365 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1366 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755744 | | target function (ml) not normalized (work): 703409.584106 | | target function (ml) not normalized (free): 14729.914237 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1375 0.1544 5.7011 5.7939| | 2: 2.94 - 2.33 1.00 7339 128 0.1077 0.1341 5.0911 5.1867| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1168 4.6586 4.7432| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1040 4.3948 4.5516| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.1011 4.1545 4.2622| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1102 3.9494 4.0842| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0964 3.7977 3.9208| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1296 3.7001 3.8958| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1125 3.6214 3.7543| | 10: 1.41 - 1.36 0.99 7022 150 0.0977 0.1172 3.5555 3.6643| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1129 3.4838 3.5906| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1121 3.4587 3.5835| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1240 3.4376 3.5623| | 14: 1.25 - 1.22 0.98 7015 112 0.1110 0.1589 3.4324 3.6757| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1230 3.4475 3.4811| | 16: 1.19 - 1.17 0.93 6604 132 0.1253 0.1527 3.4647 3.6523| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1228 3.4331 3.446| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1713 3.4386 3.5314| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1789 3.4208 3.6076| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1582 3.4117 3.4352| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2146 3.4193 3.509| | 22: 1.07 - 1.05 0.97 6836 135 0.1906 0.1957 3.4137 3.415| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2022 3.4335 3.4877| | 24: 1.03 - 1.02 0.96 6784 133 0.2336 0.2244 3.4364 3.5094| | 25: 1.02 - 1.01 0.93 6552 130 0.2618 0.2500 3.4498 3.523| | 26: 1.01 - 0.99 0.96 6767 158 0.2760 0.2877 3.4158 3.4249| | 27: 0.99 - 0.98 0.94 6647 131 0.3045 0.2790 3.4705 3.3936| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7398 127 0.93 12.12 1.00 0.97 11883.59| | 2: 2.94 - 2.33 7339 128 0.92 13.13 0.99 0.97 5348.51| | 3: 2.33 - 2.04 6939 150 0.96 7.61 1.01 0.97 1697.82| | 4: 2.04 - 1.85 7170 155 0.96 7.69 1.00 0.97 1009.94| | 5: 1.85 - 1.72 7113 159 0.96 8.19 1.00 0.97 644.31| | 6: 1.72 - 1.62 7102 142 0.96 8.05 1.00 0.98 446.12| | 7: 1.62 - 1.54 7104 148 0.96 8.12 1.01 0.99 335.33| | 8: 1.54 - 1.47 6798 152 0.96 8.20 1.01 0.99 276.94| | 9: 1.47 - 1.41 6938 155 0.96 8.43 1.00 0.99 229.37| | 10: 1.41 - 1.36 7022 150 0.96 8.88 1.00 0.98 201.60| | 11: 1.36 - 1.32 6997 151 0.96 8.90 0.99 0.97 174.27| | 12: 1.32 - 1.28 6975 149 0.96 8.98 0.98 0.96 160.49| | 13: 1.28 - 1.25 6907 166 0.96 9.50 1.01 0.97 157.36| | 14: 1.25 - 1.22 7015 112 0.95 10.64 1.02 0.98 161.90| | 15: 1.22 - 1.19 6956 137 0.95 11.14 1.01 0.99 164.81| | 16: 1.19 - 1.17 6604 132 0.95 11.36 1.01 0.98 158.98| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.98 153.41| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.96 148.06| | 19: 1.12 - 1.10 6948 106 0.93 14.21 1.00 0.96 152.20| | 20: 1.10 - 1.08 6884 147 0.92 15.28 1.00 0.95 151.23| | 21: 1.08 - 1.07 6852 152 0.91 16.71 1.00 0.94 154.31| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.94 155.38| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.93 165.09| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.94 179.12| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.97 0.91 181.94| | 26: 1.01 - 0.99 6767 158 0.81 26.54 0.98 0.89 175.78| | 27: 0.99 - 0.98 6647 131 0.82 26.07 0.98 0.88 159.10| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 148.06 max = 11883.59 mean = 961.36| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 13.31| |phase err.(test): min = 0.00 max = 89.75 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1388 0.1387 0.1488 n_refl.: 191130 remove outliers: r(all,work,free)=0.1388 0.1387 0.1488 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1388 0.1387 0.1488 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1366 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1366 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 0.3637 361.038 328.543 0.392 0.975 0.195 13.296-10.522 96.04 96 1 0.2421 480.619 462.302 0.678 0.976 0.141 10.503-8.327 98.35 176 3 0.2176 502.991 496.125 0.845 0.977 0.109 8.318-6.595 100.00 360 8 0.2171 375.692 370.210 0.870 0.977 0.088 6.588-5.215 100.00 711 7 0.1966 345.223 334.464 0.864 0.977 0.080 5.214-4.128 98.38 1367 28 0.1254 504.957 498.733 0.954 0.978 0.044 4.126-3.266 94.74 2603 46 0.1193 460.295 452.427 1.017 0.979 0.005 3.266-2.585 99.86 5447 97 0.1129 310.504 306.894 1.000 0.981 0.000 2.585-2.046 97.45 10613 204 0.0964 234.258 231.662 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0913 138.645 137.265 1.020 0.987 0.000 1.619-1.281 98.00 42464 925 0.0947 74.639 73.986 1.008 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.040 38.333 0.973 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0472 ================= 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 : 0.2038 0.1985 0.081 5.234 5.2 78.0 14.6 805 0.000 1_bss: 0.1803 0.1934 0.081 5.234 5.2 78.1 14.6 805 0.000 1_settarget: 0.1803 0.1934 0.081 5.234 5.2 78.1 14.6 805 0.000 1_nqh: 0.1803 0.1934 0.081 5.234 5.2 78.1 14.6 805 0.000 1_weight: 0.1803 0.1934 0.081 5.234 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1273 0.1504 0.040 1.151 5.2 78.1 14.6 805 0.158 1_adp: 0.1298 0.1570 0.040 1.151 5.2 73.1 15.0 805 0.158 1_regHadp: 0.1297 0.1566 0.040 1.151 5.2 73.1 15.0 805 0.158 1_occ: 0.1282 0.1556 0.040 1.151 5.2 73.1 15.0 805 0.158 2_bss: 0.1274 0.1546 0.040 1.151 5.4 73.2 15.2 805 0.158 2_settarget: 0.1274 0.1546 0.040 1.151 5.4 73.2 15.2 805 0.158 2_updatecdl: 0.1274 0.1546 0.040 1.160 5.4 73.2 15.2 805 0.158 2_nqh: 0.1274 0.1546 0.040 1.160 5.4 73.2 15.2 805 0.158 2_sol: 0.1271 0.1506 0.040 1.160 5.4 73.2 16.2 879 n/a 2_weight: 0.1271 0.1506 0.040 1.160 5.4 73.2 16.2 879 n/a 2_xyzrec: 0.1256 0.1527 0.042 1.128 5.4 73.2 16.2 879 n/a 2_adp: 0.1235 0.1514 0.042 1.128 5.4 68.2 16.3 879 n/a 2_regHadp: 0.1236 0.1515 0.042 1.128 5.4 68.2 16.3 879 n/a 2_occ: 0.1229 0.1516 0.042 1.128 5.4 68.2 16.3 879 n/a 3_bss: 0.1236 0.1523 0.042 1.128 5.4 68.2 16.3 879 n/a 3_settarget: 0.1236 0.1523 0.042 1.128 5.4 68.2 16.3 879 n/a 3_updatecdl: 0.1236 0.1523 0.042 1.132 5.4 68.2 16.3 879 n/a 3_nqh: 0.1236 0.1523 0.042 1.132 5.4 68.2 16.3 879 n/a 3_sol: 0.1251 0.1521 0.042 1.132 5.4 68.2 15.5 876 n/a 3_weight: 0.1251 0.1521 0.042 1.132 5.4 68.2 15.5 876 n/a 3_xyzrec: 0.1240 0.1441 0.035 1.097 5.4 68.2 15.5 876 n/a 3_adp: 0.1231 0.1398 0.035 1.097 5.5 67.9 15.3 876 n/a 3_regHadp: 0.1232 0.1399 0.035 1.097 5.5 67.9 15.3 876 n/a 3_occ: 0.1228 0.1390 0.035 1.097 5.5 67.9 15.3 876 n/a 4_bss: 0.1223 0.1386 0.035 1.097 5.5 67.9 15.3 876 n/a 4_settarget: 0.1223 0.1386 0.035 1.097 5.5 67.9 15.3 876 n/a 4_updatecdl: 0.1223 0.1386 0.035 1.102 5.5 67.9 15.3 876 n/a 4_nqh: 0.1223 0.1386 0.035 1.102 5.5 67.9 15.3 876 n/a 4_sol: 0.1209 0.1372 0.035 1.102 5.5 67.9 14.9 840 n/a 4_weight: 0.1209 0.1372 0.035 1.102 5.5 67.9 14.9 840 n/a 4_xyzrec: 0.1208 0.1372 0.033 1.128 5.5 67.9 14.9 840 n/a 4_adp: 0.1206 0.1367 0.033 1.128 5.5 67.1 14.7 840 n/a 4_regHadp: 0.1206 0.1367 0.033 1.128 5.5 67.1 14.7 840 n/a 4_occ: 0.1203 0.1364 0.033 1.128 5.5 67.1 14.7 840 n/a 5_bss: 0.1201 0.1362 0.033 1.128 5.5 67.1 14.7 840 n/a 5_settarget: 0.1201 0.1362 0.033 1.128 5.5 67.1 14.7 840 n/a 5_updatecdl: 0.1201 0.1362 0.033 1.128 5.5 67.1 14.7 840 n/a 5_nqh: 0.1201 0.1362 0.033 1.128 5.5 67.1 14.7 840 n/a 5_sol: 0.1197 0.1350 0.033 1.128 5.5 67.1 14.9 863 n/a 5_weight: 0.1197 0.1350 0.033 1.128 5.5 67.1 14.9 863 n/a 5_xyzrec: 0.1200 0.1359 0.036 1.123 5.5 67.1 14.9 863 n/a 5_adp: 0.1202 0.1366 0.036 1.123 5.5 66.8 14.9 863 n/a 5_regHadp: 0.1203 0.1366 0.036 1.123 5.5 66.8 14.9 863 n/a 5_occ: 0.1201 0.1366 0.036 1.123 5.5 66.8 14.9 863 n/a 6_bss: 0.1199 0.1366 0.036 1.123 5.5 66.8 14.8 863 n/a 6_settarget: 0.1199 0.1366 0.036 1.123 5.5 66.8 14.8 863 n/a 6_updatecdl: 0.1199 0.1366 0.036 1.122 5.5 66.8 14.8 863 n/a 6_nqh: 0.1199 0.1366 0.036 1.122 5.5 66.8 14.8 863 n/a 6_sol: 0.1199 0.1361 0.036 1.122 5.5 66.8 14.8 868 n/a 6_weight: 0.1199 0.1361 0.036 1.122 5.5 66.8 14.8 868 n/a 6_xyzrec: 0.1203 0.1366 0.037 1.128 5.5 66.8 14.8 868 n/a 6_adp: 0.1205 0.1369 0.037 1.128 5.6 65.7 14.7 868 n/a 6_regHadp: 0.1205 0.1369 0.037 1.128 5.6 65.7 14.7 868 n/a 6_occ: 0.1203 0.1368 0.037 1.128 5.6 65.7 14.7 868 n/a 7_bss: 0.1203 0.1367 0.037 1.128 5.5 65.7 14.7 868 n/a 7_settarget: 0.1203 0.1367 0.037 1.128 5.5 65.7 14.7 868 n/a 7_updatecdl: 0.1203 0.1367 0.037 1.128 5.5 65.7 14.7 868 n/a 7_nqh: 0.1203 0.1367 0.037 1.128 5.5 65.7 14.7 868 n/a 7_sol: 0.1201 0.1357 0.037 1.128 5.5 65.7 14.7 877 n/a 7_weight: 0.1201 0.1357 0.037 1.128 5.5 65.7 14.7 877 n/a 7_xyzrec: 0.1205 0.1362 0.037 1.124 5.5 65.7 14.7 877 n/a 7_adp: 0.1205 0.1367 0.037 1.124 5.6 64.5 14.7 877 n/a 7_regHadp: 0.1206 0.1367 0.037 1.124 5.6 64.5 14.7 877 n/a 7_occ: 0.1204 0.1366 0.037 1.124 5.6 64.5 14.7 877 n/a 8_bss: 0.1203 0.1363 0.037 1.124 5.4 64.3 14.5 877 n/a 8_settarget: 0.1203 0.1363 0.037 1.124 5.4 64.3 14.5 877 n/a 8_updatecdl: 0.1203 0.1363 0.037 1.123 5.4 64.3 14.5 877 n/a 8_nqh: 0.1203 0.1363 0.037 1.123 5.4 64.3 14.5 877 n/a 8_sol: 0.1200 0.1352 0.037 1.123 5.4 64.3 14.5 891 n/a 8_weight: 0.1200 0.1352 0.037 1.123 5.4 64.3 14.5 891 n/a 8_xyzrec: 0.1203 0.1360 0.038 1.110 5.4 64.3 14.5 891 n/a 8_adp: 0.1206 0.1365 0.038 1.110 5.4 64.0 14.4 891 n/a 8_regHadp: 0.1207 0.1365 0.038 1.110 5.4 64.0 14.4 891 n/a 8_occ: 0.1206 0.1366 0.038 1.110 5.4 64.0 14.4 891 n/a 9_bss: 0.1197 0.1357 0.038 1.110 5.4 64.0 14.4 891 n/a 9_settarget: 0.1197 0.1357 0.038 1.110 5.4 64.0 14.4 891 n/a 9_updatecdl: 0.1197 0.1357 0.038 1.111 5.4 64.0 14.4 891 n/a 9_nqh: 0.1197 0.1357 0.038 1.111 5.4 64.0 14.4 891 n/a 9_sol: 0.1193 0.1356 0.038 1.111 5.4 64.0 14.5 903 n/a 9_weight: 0.1193 0.1356 0.038 1.111 5.4 64.0 14.5 903 n/a 9_xyzrec: 0.1197 0.1359 0.039 1.123 5.4 64.0 14.5 903 n/a 9_adp: 0.1196 0.1360 0.039 1.123 5.4 63.1 14.5 903 n/a 9_regHadp: 0.1196 0.1360 0.039 1.123 5.4 63.1 14.5 903 n/a 9_occ: 0.1195 0.1362 0.039 1.123 5.4 63.1 14.5 903 n/a 10_bss: 0.1194 0.1359 0.039 1.123 5.4 63.1 14.5 903 n/a 10_settarget: 0.1194 0.1359 0.039 1.123 5.4 63.1 14.5 903 n/a 10_updatecdl: 0.1194 0.1359 0.039 1.123 5.4 63.1 14.5 903 n/a 10_setrh: 0.1195 0.1360 0.039 1.123 5.4 63.1 14.5 903 n/a 10_nqh: 0.1195 0.1360 0.039 1.123 5.4 63.1 14.5 903 n/a 10_sol: 0.1194 0.1359 0.039 1.123 5.4 63.1 14.5 903 n/a 10_weight: 0.1194 0.1359 0.039 1.123 5.4 63.1 14.5 903 n/a 10_xyzrec: 0.1198 0.1363 0.039 1.160 5.4 63.1 14.5 903 n/a 10_adp: 0.1199 0.1365 0.039 1.160 5.5 62.1 14.5 903 n/a 10_regHadp: 0.1199 0.1365 0.039 1.160 5.5 62.1 14.5 903 n/a 10_occ: 0.1198 0.1366 0.039 1.160 5.5 62.1 14.5 903 n/a end: 0.1197 0.1366 0.039 1.160 5.5 62.1 14.5 903 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3918332_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3918332_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.2100 Refinement macro-cycles (run) : 12188.9000 Write final files (write_after_run_outputs) : 147.4000 Total : 12343.5100 Total CPU time: 3.44 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:57 PST -0800 (1736736177.41 s) Start R-work = 0.1803, R-free = 0.1934 Final R-work = 0.1197, R-free = 0.1366 =============================================================================== Job complete usr+sys time: 12599.95 seconds wall clock time: 211 minutes 1.43 seconds (12661.43 seconds total)