Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9286674.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9286674.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9286674.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.88, 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: 2.742 distance_ideal: 2.720 ideal - model: -0.022 slack: 0.000 delta_slack: -0.022 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: 2.721 distance_ideal: 2.710 ideal - model: -0.011 slack: 0.000 delta_slack: -0.011 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: 0.74 Conformation dependent library (CDL) restraints added in 179.0 milliseconds Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.03: 841 1.03 - 1.27: 2534 1.27 - 1.51: 1622 1.51 - 1.74: 921 1.74 - 1.98: 16 Bond restraints: 5934 Sorted by residual: bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.461 1.726 -0.266 1.19e-02 7.06e+03 4.99e+02 bond pdb=" N GLY A 190 " pdb=" CA GLY A 190 " ideal model delta sigma weight residual 1.453 1.223 0.230 1.06e-02 8.90e+03 4.72e+02 bond pdb=" NH2 ARG B 27 " pdb="HH21 ARG B 27 " ideal model delta sigma weight residual 0.860 1.257 -0.397 2.00e-02 2.50e+03 3.94e+02 bond pdb=" C TRP A 139 " pdb=" O TRP A 139 " ideal model delta sigma weight residual 1.235 0.995 0.240 1.22e-02 6.72e+03 3.88e+02 bond pdb=" CA LEU A 152 " pdb=" C LEU A 152 " ideal model delta sigma weight residual 1.521 1.745 -0.224 1.17e-02 7.31e+03 3.66e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 5599 4.10 - 8.20: 3515 8.20 - 12.30: 1378 12.30 - 16.40: 285 16.40 - 20.50: 33 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O GLU A 180 " pdb=" C GLU A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 122.07 142.28 -20.21 1.03e+00 9.43e-01 3.85e+02 angle pdb=" O ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 121.32 106.27 15.05 8.50e-01 1.38e+00 3.14e+02 angle pdb=" CA MET B 124 " pdb=" C MET B 124 " pdb=" O MET B 124 " ideal model delta sigma weight residual 121.23 140.08 -18.85 1.07e+00 8.73e-01 3.10e+02 angle pdb=" O VAL B 37 " pdb=" C VAL B 37 " pdb=" N ALA B 38 " ideal model delta sigma weight residual 122.05 106.40 15.65 1.05e+00 9.07e-01 2.22e+02 angle pdb=" NE ARG B 83 " pdb=" CZ ARG B 83 " pdb=" NH2 ARG B 83 " ideal model delta sigma weight residual 119.20 131.92 -12.72 9.00e-01 1.23e+00 2.00e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 1801 15.32 - 30.64: 176 30.64 - 45.96: 37 45.96 - 61.28: 30 61.28 - 76.60: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual 180.00 -146.55 -33.45 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual 180.00 -153.33 -26.67 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA LEU A 185 " pdb=" C LEU A 185 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " ideal model delta harmonic sigma weight residual -180.00 -155.23 -24.77 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.236: 230 0.236 - 0.470: 160 0.470 - 0.705: 75 0.705 - 0.940: 22 0.940 - 1.175: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA PRO B 128 " pdb=" N PRO B 128 " pdb=" C PRO B 128 " pdb=" CB PRO B 128 " both_signs ideal model delta sigma weight residual False 2.72 1.54 1.17 2.00e-01 2.50e+01 3.45e+01 chirality pdb=" CB ILE A 22 " pdb=" CA ILE A 22 " pdb=" CG1 ILE A 22 " pdb=" CG2 ILE A 22 " both_signs ideal model delta sigma weight residual False 2.64 1.64 1.01 2.00e-01 2.50e+01 2.54e+01 chirality pdb=" CB ILE A 45 " pdb=" CA ILE A 45 " pdb=" CG1 ILE A 45 " pdb=" CG2 ILE A 45 " both_signs ideal model delta sigma weight residual False 2.64 1.64 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 127 " -0.019 2.00e-02 2.50e+03 7.43e-02 1.66e+02 pdb=" CG PHE B 127 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 PHE B 127 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE B 127 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 PHE B 127 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE B 127 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 127 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE B 127 " -0.119 2.00e-02 2.50e+03 pdb=" HD2 PHE B 127 " -0.074 2.00e-02 2.50e+03 pdb=" HE1 PHE B 127 " 0.077 2.00e-02 2.50e+03 pdb=" HE2 PHE B 127 " 0.055 2.00e-02 2.50e+03 pdb=" HZ PHE B 127 " -0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 194 " -0.095 2.00e-02 2.50e+03 7.38e-02 1.63e+02 pdb=" CG TYR B 194 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR B 194 " 0.053 2.00e-02 2.50e+03 pdb=" CD2 TYR B 194 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR B 194 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 194 " 0.118 2.00e-02 2.50e+03 pdb=" CZ TYR B 194 " 0.094 2.00e-02 2.50e+03 pdb=" OH TYR B 194 " -0.100 2.00e-02 2.50e+03 pdb=" HD1 TYR B 194 " 0.056 2.00e-02 2.50e+03 pdb=" HD2 TYR B 194 " -0.089 2.00e-02 2.50e+03 pdb=" HE1 TYR B 194 " -0.073 2.00e-02 2.50e+03 pdb=" HE2 TYR B 194 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " 0.043 2.00e-02 2.50e+03 6.09e-02 1.48e+02 pdb=" CG TRP B 139 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.104 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.123 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.051 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.061 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.046 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.088 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " 0.080 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.044 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.034 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.58: 24 1.58 - 2.33: 2087 2.33 - 3.09: 22022 3.09 - 3.84: 32982 3.84 - 4.60: 53143 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110258 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.823 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.936 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.992 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.032 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.221 2.620 ... (remaining 110253 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_9286674_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= 0.1996 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300862 | | target function (ml) not normalized (work): 805607.346937 | | target function (ml) not normalized (free): 16568.922092 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2147 0.2040 6.6712 6.3348| | 2: 2.94 - 2.33 1.00 7339 128 0.1615 0.1571 5.5476 5.5705| | 3: 2.33 - 2.04 0.96 6939 150 0.1627 0.1626 5.1444 5.1677| | 4: 2.04 - 1.85 1.00 7170 155 0.1779 0.1577 4.966 5.0445| | 5: 1.85 - 1.72 0.99 7113 159 0.1904 0.1764 4.7906 4.8412| | 6: 1.72 - 1.62 0.99 7102 142 0.2011 0.1999 4.6723 4.7183| | 7: 1.62 - 1.54 0.99 7104 148 0.2029 0.1550 4.5633 4.4884| | 8: 1.54 - 1.47 0.96 6798 152 0.2048 0.2294 4.47 4.5657| | 9: 1.47 - 1.41 0.98 6938 155 0.2112 0.2263 4.4029 4.4713| | 10: 1.41 - 1.36 0.99 7022 150 0.2112 0.2032 4.3073 4.2971| | 11: 1.36 - 1.32 0.99 6997 151 0.2120 0.2033 4.238 4.2298| | 12: 1.32 - 1.28 0.98 6976 149 0.2075 0.1883 4.1779 4.2358| | 13: 1.28 - 1.25 0.98 6907 166 0.2018 0.2202 4.1101 4.1756| | 14: 1.25 - 1.22 0.98 7015 113 0.2052 0.2174 4.0743 4.1563| | 15: 1.22 - 1.19 0.98 6957 137 0.2089 0.2121 4.0443 4.0583| | 16: 1.19 - 1.17 0.93 6604 132 0.2142 0.2533 4.02 4.2056| | 17: 1.17 - 1.14 0.98 6941 135 0.2163 0.2079 3.9724 4.0041| | 18: 1.14 - 1.12 0.98 6875 142 0.2227 0.2400 3.9232 4.0175| | 19: 1.12 - 1.10 0.97 6949 106 0.2269 0.2367 3.8797 3.9871| | 20: 1.10 - 1.08 0.97 6884 147 0.2357 0.2234 3.837 3.7724| | 21: 1.08 - 1.07 0.97 6852 152 0.2419 0.2661 3.7852 3.7781| | 22: 1.07 - 1.05 0.97 6838 135 0.2565 0.2605 3.7545 3.7936| | 23: 1.05 - 1.03 0.97 6829 159 0.2720 0.2623 3.7278 3.8077| | 24: 1.03 - 1.02 0.96 6785 133 0.2864 0.2856 3.7032 3.7534| | 25: 1.02 - 1.01 0.93 6552 130 0.3064 0.2895 3.6714 3.7417| | 26: 1.01 - 0.99 0.96 6767 158 0.3186 0.3255 3.6259 3.6262| | 27: 0.99 - 0.98 0.94 6648 131 0.3383 0.3403 3.63 3.636| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.95 0.91 0.97 37100.21| | 2: 2.94 - 2.33 7339 128 0.85 21.67 1.09 1.02 15656.75| | 3: 2.33 - 2.04 6939 150 0.93 12.66 1.11 1.05 4180.42| | 4: 2.04 - 1.85 7170 155 0.92 13.77 1.12 1.06 2817.43| | 5: 1.85 - 1.72 7113 159 0.91 15.41 1.11 1.07 2050.59| | 6: 1.72 - 1.62 7102 142 0.90 16.23 1.12 1.08 1572.93| | 7: 1.62 - 1.54 7104 148 0.90 17.03 1.11 1.07 1263.65| | 8: 1.54 - 1.47 6798 152 0.89 18.19 1.10 1.05 1121.17| | 9: 1.47 - 1.41 6938 155 0.88 19.13 1.10 1.05 979.80| | 10: 1.41 - 1.36 7022 150 0.87 19.96 1.09 1.04 846.50| | 11: 1.36 - 1.32 6997 151 0.88 19.63 1.08 1.04 711.68| | 12: 1.32 - 1.28 6976 149 0.88 19.45 1.08 1.04 632.64| | 13: 1.28 - 1.25 6907 166 0.88 19.69 1.07 1.03 591.12| | 14: 1.25 - 1.22 7015 113 0.87 20.69 1.07 1.04 576.68| | 15: 1.22 - 1.19 6957 137 0.86 21.62 1.08 1.04 573.55| | 16: 1.19 - 1.17 6604 132 0.86 21.63 1.08 1.03 540.97| | 17: 1.17 - 1.14 6941 135 0.85 22.41 1.08 1.02 495.84| | 18: 1.14 - 1.12 6875 142 0.85 22.20 1.08 1.00 431.45| | 19: 1.12 - 1.10 6949 106 0.85 22.39 1.07 0.99 389.69| | 20: 1.10 - 1.08 6884 147 0.85 22.45 1.05 0.99 346.63| | 21: 1.08 - 1.07 6852 152 0.84 23.49 1.06 0.98 328.61| | 22: 1.07 - 1.05 6838 135 0.82 25.41 1.05 0.98 326.94| | 23: 1.05 - 1.03 6829 159 0.80 27.60 1.05 0.97 330.89| | 24: 1.03 - 1.02 6785 133 0.78 29.54 1.04 0.98 337.39| | 25: 1.02 - 1.01 6552 130 0.76 31.44 1.03 0.93 323.39| | 26: 1.01 - 0.99 6767 158 0.73 33.93 1.02 0.90 319.62| | 27: 0.99 - 0.98 6648 131 0.71 35.64 1.03 0.86 317.62| |alpha: min = 0.86 max = 1.08 mean = 1.01| |beta: min = 317.62 max = 37100.21 mean = 2916.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.92| |phase err.(test): min = 0.00 max = 89.15 mean = 22.14| |-----------------------------------------------------------------------------| ----------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 0.266 2950 Z= 5.440 Angle : 5.232 20.208 4018 Z= 3.737 Chirality : 0.372 1.175 492 Planarity : 0.031 0.144 512 Dihedral : 12.788 76.598 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 1.29 % Allowed : 3.87 % Favored : 94.84 % Cbeta Deviations : 28.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.39), residues: 386 helix: -2.95 (0.28), residues: 146 sheet: -1.11 (0.53), residues: 82 loop : -0.19 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.103 0.021 ARG A 100 TYR 0.125 0.047 TYR B 67 PHE 0.112 0.036 PHE A 82 TRP 0.097 0.038 TRP B 139 HIS 0.101 0.036 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2038 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300862 | | target function (ml) not normalized (work): 805607.346937 | | target function (ml) not normalized (free): 16568.922092 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2038 0.1996 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2038 0.1996 n_refl.: 191155 remove outliers: r(all,work,free)=0.2036 0.2038 0.1996 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2037 0.2039 0.1996 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1805 0.1948 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1803 0.1948 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4228 400.535 295.834 0.436 0.911 0.301 13.296-10.522 99.01 99 1 0.2464 528.187 518.354 0.784 0.912 0.250 10.503-8.327 98.90 177 3 0.2451 564.205 559.310 0.972 0.912 0.223 8.318-6.595 100.00 360 8 0.2503 414.736 403.928 0.965 0.912 0.155 6.588-5.215 100.00 711 7 0.2298 381.101 366.201 0.959 0.912 0.150 5.214-4.128 98.38 1367 28 0.1475 557.435 550.210 1.073 0.912 0.100 4.126-3.266 94.74 2603 46 0.1359 508.132 499.002 1.149 0.913 0.045 3.266-2.585 99.86 5447 97 0.1448 342.774 337.694 1.119 0.912 0.040 2.585-2.046 97.45 10613 204 0.1402 258.603 254.219 1.125 0.911 0.000 2.046-1.619 99.39 21536 464 0.1617 153.054 149.878 1.147 0.910 0.000 1.619-1.281 98.00 42464 925 0.1932 82.395 80.239 1.128 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2317 44.203 41.686 1.112 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0080 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1803 r_free=0.1948 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1803 r_free=0.1948 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.056497 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 567.660860 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 0.1276 0.1489 0.0213 0.037 1.2 12.1 0.0 0.0 0 11.528 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.76 14.89 2.13 1.117 13.116 567.661 0.019 13.04 15.60 2.56 1.230 13.317 567.661 0.018 Individual atomic B min max mean iso aniso Overall: 5.13 73.05 14.97 1.40 435 3274 Protein: 5.13 40.37 10.99 1.40 0 2902 Water: 6.29 73.05 29.28 N/A 435 370 Other: 16.07 31.65 23.86 N/A 0 2 Chain A: 5.41 60.06 13.03 N/A 0 1626 Chain B: 5.13 73.05 12.76 N/A 0 1648 Chain S: 11.39 62.56 30.58 N/A 435 0 Histogram: Values Number of atoms 5.13 - 11.92 2154 11.92 - 18.71 652 18.71 - 25.50 316 25.50 - 32.30 266 32.30 - 39.09 151 39.09 - 45.88 107 45.88 - 52.67 41 52.67 - 59.46 16 59.46 - 66.26 5 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1304 r_free=0.1560 r_work=0.1303 r_free=0.1556 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1303 r_free = 0.1556 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1287 r_free = 0.1544 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1287 r_free= 0.1544 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015823 | | target function (ls_wunit_k1) not normalized (work): 2963.519893 | | target function (ls_wunit_k1) not normalized (free): 113.731667 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1287 0.1544 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1479 0.1477 0.1617 n_refl.: 191139 remove outliers: r(all,work,free)=0.1479 0.1477 0.1617 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1504 0.1501 0.1627 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1285 0.1280 0.1537 n_refl.: 191139 remove outliers: r(all,work,free)=0.1285 0.1280 0.1536 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3678 402.814 370.964 0.458 0.998 0.281 13.296-10.522 99.01 99 1 0.2122 528.187 522.218 0.715 0.999 0.255 10.503-8.327 98.90 177 3 0.1739 564.205 559.832 0.855 0.999 0.198 8.318-6.595 100.00 360 8 0.1733 414.736 412.334 0.874 0.999 0.145 6.588-5.215 100.00 711 7 0.1583 381.101 373.266 0.856 0.999 0.140 5.214-4.128 98.38 1367 28 0.0929 557.435 554.096 0.942 1.000 0.090 4.126-3.266 94.74 2603 46 0.0854 508.132 504.111 1.010 1.000 0.050 3.266-2.585 99.86 5447 97 0.0930 342.774 340.354 0.990 1.000 0.020 2.585-2.046 97.45 10613 204 0.0948 258.603 256.458 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1082 153.054 151.423 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.403 1.010 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1882 44.202 42.135 0.988 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0381 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1280 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1280 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1536 | n_water=805 | time (s): 3.070 (total time: 3.070) Filter (dist) r_work=0.1281 r_free=0.1539 | n_water=800 | time (s): 100.320 (total time: 103.390) Filter (q & B) r_work=0.1282 r_free=0.1538 | n_water=794 | time (s): 5.240 (total time: 108.630) Compute maps r_work=0.1282 r_free=0.1538 | n_water=794 | time (s): 1.760 (total time: 110.390) Filter (map) r_work=0.1304 r_free=0.1529 | n_water=669 | time (s): 4.800 (total time: 115.190) Find peaks r_work=0.1304 r_free=0.1529 | n_water=669 | time (s): 0.700 (total time: 115.890) Add new water r_work=0.1330 r_free=0.1555 | n_water=964 | time (s): 4.190 (total time: 120.080) Refine new water occ: r_work=0.1286 r_free=0.1512 adp: r_work=0.1274 r_free=0.1510 occ: r_work=0.1277 r_free=0.1505 adp: r_work=0.1270 r_free=0.1506 occ: r_work=0.1272 r_free=0.1504 adp: r_work=0.1269 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1269 r_free=0.1504 r_work=0.1269 r_free=0.1504 | n_water=964 | time (s): 83.240 (total time: 203.320) Filter (q & B) r_work=0.1272 r_free=0.1504 | n_water=895 | time (s): 5.040 (total time: 208.360) Filter (dist only) r_work=0.1272 r_free=0.1503 | n_water=894 | time (s): 115.300 (total time: 323.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.822116 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 572.731798 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 0.1255 0.1520 0.0265 0.040 1.1 18.5 0.0 0.3 0 11.411 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.20 2.65 2.039 15.164 572.732 0.014 12.33 15.08 2.75 2.377 15.207 572.732 0.014 Individual atomic B min max mean iso aniso Overall: 5.47 69.33 16.28 1.20 525 3273 Protein: 5.47 40.11 11.00 1.20 0 2902 Water: 6.58 69.33 33.40 N/A 525 369 Other: 16.40 33.40 24.90 N/A 0 2 Chain A: 5.48 56.18 13.03 N/A 0 1625 Chain B: 5.47 68.21 12.81 N/A 0 1648 Chain S: 12.66 69.33 37.24 N/A 525 0 Histogram: Values Number of atoms 5.47 - 11.86 2090 11.86 - 18.24 700 18.24 - 24.63 275 24.63 - 31.02 210 31.02 - 37.40 178 37.40 - 43.79 161 43.79 - 50.17 94 50.17 - 56.56 50 56.56 - 62.95 33 62.95 - 69.33 7 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1508 r_work=0.1233 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1509 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1503 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1503 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013447 | | target function (ls_wunit_k1) not normalized (work): 2518.482894 | | target function (ls_wunit_k1) not normalized (free): 101.742321 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1228 0.1502 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1605 n_refl.: 191137 remove outliers: r(all,work,free)=0.1434 0.1431 0.1605 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1603 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1234 0.1508 n_refl.: 191137 remove outliers: r(all,work,free)=0.1240 0.1234 0.1508 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3245 402.814 380.523 0.480 0.963 0.261 13.296-10.522 99.01 99 1 0.1967 528.187 518.356 0.742 0.964 0.202 10.503-8.327 98.90 177 3 0.1467 564.205 564.533 0.920 0.964 0.160 8.318-6.595 100.00 360 8 0.1503 414.736 413.745 0.937 0.963 0.150 6.588-5.215 100.00 711 7 0.1350 381.101 377.172 0.914 0.963 0.130 5.214-4.128 98.38 1367 28 0.0828 557.435 555.730 0.995 0.963 0.100 4.126-3.266 94.74 2603 46 0.0764 508.132 505.506 1.061 0.963 0.050 3.266-2.585 99.86 5447 97 0.0860 342.774 341.226 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0899 258.603 256.721 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.648 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.352 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.210 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0556 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1508 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1508 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1508 | n_water=894 | time (s): 3.520 (total time: 3.520) Filter (dist) r_work=0.1236 r_free=0.1511 | n_water=889 | time (s): 115.490 (total time: 119.010) Filter (q & B) r_work=0.1236 r_free=0.1512 | n_water=887 | time (s): 4.460 (total time: 123.470) Compute maps r_work=0.1236 r_free=0.1512 | n_water=887 | time (s): 1.860 (total time: 125.330) Filter (map) r_work=0.1274 r_free=0.1517 | n_water=703 | time (s): 4.000 (total time: 129.330) Find peaks r_work=0.1274 r_free=0.1517 | n_water=703 | time (s): 0.910 (total time: 130.240) Add new water r_work=0.1301 r_free=0.1553 | n_water=1020 | time (s): 4.430 (total time: 134.670) Refine new water occ: r_work=0.1253 r_free=0.1501 adp: r_work=0.1253 r_free=0.1503 occ: r_work=0.1248 r_free=0.1499 adp: r_work=0.1248 r_free=0.1499 occ: r_work=0.1245 r_free=0.1498 adp: r_work=0.1244 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1498 r_work=0.1244 r_free=0.1498 | n_water=1020 | time (s): 334.570 (total time: 469.240) Filter (q & B) r_work=0.1248 r_free=0.1500 | n_water=891 | time (s): 5.910 (total time: 475.150) Filter (dist only) r_work=0.1249 r_free=0.1500 | n_water=890 | time (s): 113.130 (total time: 588.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.732742 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.090659 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 0.1238 0.1426 0.0188 0.035 1.1 7.7 0.0 0.0 0 0.866 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.26 1.88 1.935 14.624 16.091 3.939 12.32 13.89 1.57 2.238 14.523 16.091 3.896 Individual atomic B min max mean iso aniso Overall: 5.53 67.84 15.30 1.06 522 3272 Protein: 5.53 36.49 10.75 1.06 0 2902 Water: 6.69 67.84 30.14 N/A 522 368 Other: 14.17 28.84 21.51 N/A 0 2 Chain A: 5.53 55.26 12.78 N/A 0 1625 Chain B: 5.55 67.84 12.52 N/A 0 1647 Chain S: 13.98 62.73 31.93 N/A 522 0 Histogram: Values Number of atoms 5.53 - 11.76 2136 11.76 - 17.99 678 17.99 - 24.22 303 24.22 - 30.45 245 30.45 - 36.68 183 36.68 - 42.92 143 42.92 - 49.15 71 49.15 - 55.38 25 55.38 - 61.61 7 61.61 - 67.84 3 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1390 r_work=0.1233 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1391 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1390 target_work(ml) = 3.891 | | 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.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891225 | | target function (ml) not normalized (work): 728810.916411 | | target function (ml) not normalized (free): 15226.133275 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1227 0.1390 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1437 0.1436 0.1500 n_refl.: 191137 remove outliers: r(all,work,free)=0.1437 0.1436 0.1500 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1431 0.1430 0.1496 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1387 n_refl.: 191137 remove outliers: r(all,work,free)=0.1226 0.1223 0.1387 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3832 398.008 361.542 0.412 0.947 0.236 13.296-10.522 99.01 99 1 0.2435 528.187 507.290 0.701 0.948 0.205 10.503-8.327 97.80 175 3 0.1994 554.286 556.588 0.882 0.948 0.158 8.318-6.595 100.00 360 8 0.2078 414.736 409.810 0.895 0.948 0.115 6.588-5.215 100.00 711 7 0.1847 381.101 370.990 0.885 0.948 0.100 5.214-4.128 98.38 1367 28 0.1165 557.435 551.664 0.973 0.948 0.090 4.126-3.266 94.74 2603 46 0.1091 508.132 501.056 1.033 0.948 0.030 3.266-2.585 99.86 5447 97 0.1083 342.774 339.044 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0965 258.603 255.746 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0969 153.054 151.401 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.482 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.309 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1014 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1387 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1387 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1387 | n_water=890 | time (s): 2.880 (total time: 2.880) Filter (dist) r_work=0.1224 r_free=0.1390 | n_water=887 | time (s): 108.550 (total time: 111.430) Filter (q & B) r_work=0.1225 r_free=0.1390 | n_water=879 | time (s): 5.480 (total time: 116.910) Compute maps r_work=0.1225 r_free=0.1390 | n_water=879 | time (s): 2.430 (total time: 119.340) Filter (map) r_work=0.1247 r_free=0.1394 | n_water=727 | time (s): 5.500 (total time: 124.840) Find peaks r_work=0.1247 r_free=0.1394 | n_water=727 | time (s): 0.750 (total time: 125.590) Add new water r_work=0.1262 r_free=0.1409 | n_water=973 | time (s): 4.880 (total time: 130.470) Refine new water occ: r_work=0.1226 r_free=0.1375 adp: r_work=0.1226 r_free=0.1375 occ: r_work=0.1224 r_free=0.1373 adp: r_work=0.1224 r_free=0.1373 occ: r_work=0.1222 r_free=0.1372 adp: r_work=0.1222 r_free=0.1372 ADP+occupancy (water only), MIN, final r_work=0.1222 r_free=0.1372 r_work=0.1222 r_free=0.1372 | n_water=973 | time (s): 237.110 (total time: 367.580) Filter (q & B) r_work=0.1226 r_free=0.1382 | n_water=882 | time (s): 4.320 (total time: 371.900) Filter (dist only) r_work=0.1226 r_free=0.1381 | n_water=881 | time (s): 113.150 (total time: 485.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.598842 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.111683 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 0.1227 0.1388 0.0161 0.036 1.1 6.6 0.0 0.0 0 0.799 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 13.88 1.61 1.833 14.240 15.112 3.887 12.24 13.89 1.65 1.922 14.204 15.112 3.881 Individual atomic B min max mean iso aniso Overall: 5.53 67.53 15.03 1.00 513 3272 Protein: 5.53 33.56 10.68 1.00 0 2902 Water: 6.72 67.53 29.37 N/A 513 368 Other: 13.95 28.19 21.07 N/A 0 2 Chain A: 5.55 54.46 12.66 N/A 0 1625 Chain B: 5.53 67.53 12.44 N/A 0 1647 Chain S: 13.57 60.45 30.88 N/A 513 0 Histogram: Values Number of atoms 5.53 - 11.73 2130 11.73 - 17.93 712 17.93 - 24.13 305 24.13 - 30.33 234 30.33 - 36.53 181 36.53 - 42.73 132 42.73 - 48.93 63 48.93 - 55.13 21 55.13 - 61.33 6 61.33 - 67.53 1 =========================== Idealize ADP of riding H ========================== r_work=0.1224 r_free=0.1389 r_work=0.1224 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1224 r_free = 0.1389 target_work(ml) = 3.881 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1222 r_free = 0.1385 target_work(ml) = 3.879 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1222 r_free= 0.1385 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.879130 | | target function (ml) not normalized (work): 726533.969000 | | target function (ml) not normalized (free): 15191.698709 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1225 0.1222 0.1385 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1443 0.1442 0.1519 n_refl.: 191134 remove outliers: r(all,work,free)=0.1443 0.1442 0.1519 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1435 0.1434 0.1513 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1223 0.1220 0.1380 n_refl.: 191134 remove outliers: r(all,work,free)=0.1223 0.1220 0.1380 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3811 361.517 317.899 0.406 0.945 0.236 13.296-10.522 98.02 98 1 0.2479 480.940 454.578 0.691 0.947 0.174 10.503-8.327 97.80 175 3 0.2106 502.347 496.384 0.866 0.947 0.150 8.318-6.595 100.00 360 8 0.2167 375.874 369.957 0.890 0.946 0.115 6.588-5.215 100.00 711 7 0.1922 345.390 335.515 0.887 0.947 0.100 5.214-4.128 98.38 1367 28 0.1211 505.201 500.336 0.973 0.947 0.059 4.126-3.266 94.74 2603 46 0.1129 460.518 453.948 1.037 0.947 0.019 3.266-2.585 99.86 5447 97 0.1116 310.655 307.392 1.022 0.947 0.010 2.585-2.046 97.45 10613 204 0.0963 234.371 231.959 1.035 0.947 0.000 2.046-1.619 99.39 21536 464 0.0947 138.712 137.341 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.1017 74.675 73.929 1.054 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1674 40.060 38.382 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1260 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1220 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1220 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1220 r_free=0.1380 | n_water=881 | time (s): 2.640 (total time: 2.640) Filter (dist) r_work=0.1220 r_free=0.1380 | n_water=879 | time (s): 108.800 (total time: 111.440) Filter (q & B) r_work=0.1220 r_free=0.1379 | n_water=871 | time (s): 5.380 (total time: 116.820) Compute maps r_work=0.1220 r_free=0.1379 | n_water=871 | time (s): 2.450 (total time: 119.270) Filter (map) r_work=0.1242 r_free=0.1381 | n_water=745 | time (s): 5.370 (total time: 124.640) Find peaks r_work=0.1242 r_free=0.1381 | n_water=745 | time (s): 0.680 (total time: 125.320) Add new water r_work=0.1255 r_free=0.1393 | n_water=982 | time (s): 4.890 (total time: 130.210) Refine new water occ: r_work=0.1209 r_free=0.1359 adp: r_work=0.1201 r_free=0.1354 occ: r_work=0.1200 r_free=0.1354 adp: r_work=0.1200 r_free=0.1354 occ: r_work=0.1200 r_free=0.1354 adp: r_work=0.1200 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1354 r_work=0.1200 r_free=0.1354 | n_water=982 | time (s): 120.330 (total time: 250.540) Filter (q & B) r_work=0.1206 r_free=0.1362 | n_water=846 | time (s): 4.760 (total time: 255.300) Filter (dist only) r_work=0.1207 r_free=0.1361 | n_water=845 | time (s): 106.520 (total time: 361.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.579284 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.168539 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 0.1362 0.0154 0.036 1.1 5.3 0.0 0.3 0 0.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.62 1.54 1.795 13.963 15.169 3.769 12.11 13.64 1.53 1.910 13.927 15.169 3.764 Individual atomic B min max mean iso aniso Overall: 5.55 66.94 14.63 0.95 479 3270 Protein: 5.55 31.53 10.58 0.95 0 2902 Water: 5.91 66.94 28.50 N/A 479 366 Other: 13.81 26.40 20.11 N/A 0 2 Chain A: 5.55 53.13 12.52 N/A 0 1624 Chain B: 5.55 66.94 12.30 N/A 0 1646 Chain S: 5.91 60.65 29.76 N/A 479 0 Histogram: Values Number of atoms 5.55 - 11.68 2130 11.68 - 17.82 725 17.82 - 23.96 340 23.96 - 30.10 191 30.10 - 36.24 156 36.24 - 42.38 118 42.38 - 48.52 62 48.52 - 54.66 21 54.66 - 60.80 5 60.80 - 66.94 1 =========================== Idealize ADP of riding H ========================== r_work=0.1211 r_free=0.1364 r_work=0.1211 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1211 r_free = 0.1364 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1361 target_work(ml) = 3.763 | | 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1209 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762966 | | target function (ml) not normalized (work): 704769.616465 | | target function (ml) not normalized (free): 14756.439417 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1209 0.1361 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1424 0.1423 0.1499 n_refl.: 191132 remove outliers: r(all,work,free)=0.1424 0.1423 0.1499 n_refl.: 191132 overall B=-0.22 to atoms: r(all,work,free)=0.1386 0.1384 0.1474 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1208 0.1361 n_refl.: 191132 remove outliers: r(all,work,free)=0.1210 0.1207 0.1361 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3553 361.213 314.725 0.416 0.947 0.231 13.296-10.522 97.03 97 1 0.2405 481.615 457.277 0.711 0.948 0.174 10.503-8.327 97.80 175 3 0.2194 502.347 495.753 0.877 0.949 0.150 8.318-6.595 100.00 360 8 0.2259 375.874 368.924 0.907 0.948 0.105 6.588-5.215 100.00 711 7 0.2011 345.390 334.849 0.906 0.949 0.095 5.214-4.128 98.38 1367 28 0.1251 505.201 499.857 0.995 0.949 0.054 4.126-3.266 94.74 2603 46 0.1163 460.518 453.732 1.061 0.950 0.009 3.266-2.585 99.86 5447 97 0.1126 310.655 307.314 1.044 0.949 0.000 2.585-2.046 97.45 10613 204 0.0954 234.371 231.923 1.051 0.949 0.000 2.046-1.619 99.39 21536 464 0.0917 138.712 137.461 1.068 0.949 0.000 1.619-1.281 98.00 42464 925 0.0978 74.675 73.978 1.055 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.060 38.399 1.024 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0489 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1208 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1208 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1208 r_free=0.1361 | n_water=845 | time (s): 2.830 (total time: 2.830) Filter (dist) r_work=0.1208 r_free=0.1361 | n_water=845 | time (s): 105.150 (total time: 107.980) Filter (q & B) r_work=0.1208 r_free=0.1361 | n_water=834 | time (s): 4.330 (total time: 112.310) Compute maps r_work=0.1208 r_free=0.1361 | n_water=834 | time (s): 1.750 (total time: 114.060) Filter (map) r_work=0.1228 r_free=0.1366 | n_water=735 | time (s): 4.930 (total time: 118.990) Find peaks r_work=0.1228 r_free=0.1366 | n_water=735 | time (s): 0.550 (total time: 119.540) Add new water r_work=0.1240 r_free=0.1382 | n_water=967 | time (s): 4.230 (total time: 123.770) Refine new water occ: r_work=0.1201 r_free=0.1352 adp: r_work=0.1201 r_free=0.1352 occ: r_work=0.1199 r_free=0.1351 adp: r_work=0.1199 r_free=0.1351 occ: r_work=0.1197 r_free=0.1351 adp: r_work=0.1197 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1351 r_work=0.1197 r_free=0.1351 | n_water=967 | time (s): 174.760 (total time: 298.530) Filter (q & B) r_work=0.1201 r_free=0.1355 | n_water=893 | time (s): 5.160 (total time: 303.690) Filter (dist only) r_work=0.1201 r_free=0.1355 | n_water=892 | time (s): 117.940 (total time: 421.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.574309 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.449865 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 0.1206 0.1363 0.0157 0.036 1.1 7.2 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.63 1.57 1.756 13.806 15.450 3.763 12.06 13.64 1.58 1.872 13.763 15.450 3.759 Individual atomic B min max mean iso aniso Overall: 5.40 65.54 14.58 0.91 526 3270 Protein: 5.40 28.99 10.30 0.91 0 2902 Water: 5.81 65.54 28.51 N/A 526 366 Other: 13.67 23.45 18.56 N/A 0 2 Chain A: 5.41 51.27 12.20 N/A 0 1624 Chain B: 5.40 65.54 12.00 N/A 0 1646 Chain S: 5.81 60.91 30.04 N/A 526 0 Histogram: Values Number of atoms 5.40 - 11.41 2114 11.41 - 17.42 768 17.42 - 23.44 296 23.44 - 29.45 224 29.45 - 35.47 169 35.47 - 41.48 123 41.48 - 47.50 66 47.50 - 53.51 28 53.51 - 59.53 5 59.53 - 65.54 3 =========================== 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) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1365 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758459 | | target function (ml) not normalized (work): 703918.081754 | | target function (ml) not normalized (free): 14750.206917 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1365 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1370 0.1368 0.1476 n_refl.: 191130 remove outliers: r(all,work,free)=0.1370 0.1368 0.1476 n_refl.: 191130 overall B=0.06 to atoms: r(all,work,free)=0.1378 0.1376 0.1481 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1353 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1194 0.1353 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 0.3770 361.213 327.857 0.434 0.909 0.201 13.296-10.522 97.03 97 1 0.2355 481.615 461.825 0.743 0.911 0.146 10.503-8.327 97.80 175 3 0.2245 502.347 494.067 0.920 0.911 0.123 8.318-6.595 100.00 360 8 0.2228 375.874 369.299 0.948 0.911 0.085 6.588-5.215 100.00 711 7 0.1992 345.390 335.047 0.952 0.912 0.080 5.214-4.128 98.38 1367 28 0.1241 505.201 498.947 1.047 0.912 0.034 4.126-3.266 94.74 2603 46 0.1167 460.518 452.946 1.115 0.913 0.005 3.266-2.585 99.86 5447 97 0.1129 310.655 306.979 1.097 0.914 0.000 2.585-2.046 97.45 10613 204 0.0957 234.371 231.748 1.106 0.915 0.000 2.046-1.619 99.39 21536 464 0.0908 138.712 137.334 1.123 0.917 0.000 1.619-1.281 98.00 42464 925 0.0950 74.675 74.009 1.112 0.920 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.060 38.374 1.075 0.926 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0636 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1353 | n_water=892 | time (s): 3.000 (total time: 3.000) Filter (dist) r_work=0.1194 r_free=0.1354 | n_water=891 | time (s): 112.340 (total time: 115.340) Filter (q & B) r_work=0.1195 r_free=0.1355 | n_water=878 | time (s): 5.010 (total time: 120.350) Compute maps r_work=0.1195 r_free=0.1355 | n_water=878 | time (s): 2.170 (total time: 122.520) Filter (map) r_work=0.1220 r_free=0.1363 | n_water=750 | time (s): 4.790 (total time: 127.310) Find peaks r_work=0.1220 r_free=0.1363 | n_water=750 | time (s): 0.550 (total time: 127.860) Add new water r_work=0.1229 r_free=0.1380 | n_water=971 | time (s): 4.640 (total time: 132.500) Refine new water occ: r_work=0.1194 r_free=0.1346 adp: r_work=0.1194 r_free=0.1346 occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1192 r_free=0.1345 occ: r_work=0.1190 r_free=0.1344 adp: r_work=0.1190 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1345 r_work=0.1190 r_free=0.1345 | n_water=971 | time (s): 213.120 (total time: 345.620) Filter (q & B) r_work=0.1194 r_free=0.1351 | n_water=895 | time (s): 4.090 (total time: 349.710) Filter (dist only) r_work=0.1194 r_free=0.1350 | n_water=894 | time (s): 113.890 (total time: 463.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.520791 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.326214 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 0.1354 0.0157 0.036 1.1 7.0 0.0 0.3 0 0.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.54 1.57 1.697 13.758 14.326 3.758 11.99 13.56 1.57 1.739 13.738 14.326 3.757 Individual atomic B min max mean iso aniso Overall: 5.49 64.72 14.60 0.88 528 3270 Protein: 5.49 28.32 10.35 0.88 0 2902 Water: 5.91 64.72 28.41 N/A 528 366 Other: 13.77 22.41 18.09 N/A 0 2 Chain A: 5.55 51.28 12.20 N/A 0 1624 Chain B: 5.49 64.72 12.02 N/A 0 1646 Chain S: 5.91 61.31 30.03 N/A 528 0 Histogram: Values Number of atoms 5.49 - 11.41 2090 11.41 - 17.34 792 17.34 - 23.26 291 23.26 - 29.18 217 29.18 - 35.10 177 35.10 - 41.03 124 41.03 - 46.95 71 46.95 - 52.87 28 52.87 - 58.79 4 58.79 - 64.72 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1357 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.756 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756120 | | target function (ml) not normalized (work): 703479.914831 | | target function (ml) not normalized (free): 14735.008313 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1388 0.1386 0.1491 n_refl.: 191130 remove outliers: r(all,work,free)=0.1388 0.1386 0.1491 n_refl.: 191130 overall B=0.01 to atoms: r(all,work,free)=0.1390 0.1388 0.1492 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1353 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1353 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 0.3677 361.213 328.821 0.412 0.974 0.210 13.296-10.522 97.03 97 1 0.2371 481.615 461.170 0.685 0.976 0.130 10.503-8.327 97.80 175 3 0.2276 502.347 493.683 0.856 0.976 0.100 8.318-6.595 100.00 360 8 0.2251 375.874 369.331 0.882 0.976 0.086 6.588-5.215 100.00 711 7 0.1991 345.390 335.047 0.886 0.977 0.073 5.214-4.128 98.38 1367 28 0.1239 505.201 499.251 0.976 0.977 0.029 4.126-3.266 94.74 2603 46 0.1174 460.518 452.783 1.042 0.979 0.000 3.266-2.585 99.86 5447 97 0.1135 310.655 306.967 1.023 0.979 0.000 2.585-2.046 97.45 10613 204 0.0963 234.371 231.719 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0909 138.712 137.344 1.050 0.984 0.000 1.619-1.281 98.00 42464 925 0.0946 74.675 74.013 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.060 38.353 1.009 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0188 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1353 | n_water=894 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1196 r_free=0.1353 | n_water=893 | time (s): 121.940 (total time: 125.030) Filter (q & B) r_work=0.1197 r_free=0.1352 | n_water=884 | time (s): 4.680 (total time: 129.710) Compute maps r_work=0.1197 r_free=0.1352 | n_water=884 | time (s): 1.750 (total time: 131.460) Filter (map) r_work=0.1221 r_free=0.1367 | n_water=764 | time (s): 4.350 (total time: 135.810) Find peaks r_work=0.1221 r_free=0.1367 | n_water=764 | time (s): 0.830 (total time: 136.640) Add new water r_work=0.1228 r_free=0.1381 | n_water=979 | time (s): 5.010 (total time: 141.650) Refine new water occ: r_work=0.1194 r_free=0.1349 adp: r_work=0.1195 r_free=0.1350 occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1348 occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1348 r_work=0.1193 r_free=0.1348 | n_water=979 | time (s): 128.660 (total time: 270.310) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=874 | time (s): 4.990 (total time: 275.300) Filter (dist only) r_work=0.1198 r_free=0.1355 | n_water=873 | time (s): 112.680 (total time: 387.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.610541 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.830074 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1362 0.0161 0.038 1.1 5.1 0.0 0.3 0 0.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.62 1.61 1.689 13.636 14.830 3.758 12.01 13.64 1.63 1.705 13.626 14.830 3.755 Individual atomic B min max mean iso aniso Overall: 5.56 63.82 14.41 0.88 507 3270 Protein: 5.56 28.19 10.37 0.88 0 2902 Water: 5.96 63.82 27.85 N/A 507 366 Other: 13.82 22.21 18.02 N/A 0 2 Chain A: 5.63 51.15 12.19 N/A 0 1624 Chain B: 5.56 63.82 12.02 N/A 0 1646 Chain S: 5.96 61.61 29.30 N/A 507 0 Histogram: Values Number of atoms 5.56 - 11.39 2072 11.39 - 17.21 814 17.21 - 23.04 306 23.04 - 28.87 211 28.87 - 34.69 149 34.69 - 40.52 113 40.52 - 46.35 74 46.35 - 52.17 30 52.17 - 58.00 4 58.00 - 63.82 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1364 r_work=0.1201 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1364 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1363 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754538 | | target function (ml) not normalized (work): 703183.717180 | | target function (ml) not normalized (free): 14739.960452 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1363 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1505 n_refl.: 191130 remove outliers: r(all,work,free)=0.1406 0.1404 0.1505 n_refl.: 191130 overall B=-0.00 to atoms: r(all,work,free)=0.1405 0.1403 0.1505 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1363 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 0.3715 361.213 330.725 0.447 0.914 0.225 13.296-10.522 97.03 97 1 0.2413 481.615 461.179 0.733 0.916 0.157 10.503-8.327 97.80 175 3 0.2290 502.347 494.576 0.907 0.916 0.127 8.318-6.595 100.00 360 8 0.2289 375.874 368.783 0.938 0.916 0.094 6.588-5.215 100.00 711 7 0.2049 345.390 334.186 0.941 0.917 0.073 5.214-4.128 98.38 1367 28 0.1278 505.201 498.818 1.039 0.917 0.024 4.126-3.266 94.74 2603 46 0.1196 460.518 452.758 1.111 0.919 0.000 3.266-2.585 99.86 5447 97 0.1146 310.655 306.912 1.091 0.919 0.000 2.585-2.046 97.45 10613 204 0.0966 234.371 231.696 1.101 0.921 0.000 2.046-1.619 99.39 21536 464 0.0907 138.712 137.332 1.119 0.925 0.000 1.619-1.281 98.00 42464 925 0.0939 74.675 74.018 1.110 0.930 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.060 38.349 1.079 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0129 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1363 | n_water=873 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1200 r_free=0.1363 | n_water=872 | time (s): 121.920 (total time: 124.460) Filter (q & B) r_work=0.1200 r_free=0.1362 | n_water=864 | time (s): 4.560 (total time: 129.020) Compute maps r_work=0.1200 r_free=0.1362 | n_water=864 | time (s): 2.320 (total time: 131.340) Filter (map) r_work=0.1222 r_free=0.1359 | n_water=752 | time (s): 4.990 (total time: 136.330) Find peaks r_work=0.1222 r_free=0.1359 | n_water=752 | time (s): 0.560 (total time: 136.890) Add new water r_work=0.1231 r_free=0.1374 | n_water=984 | time (s): 3.830 (total time: 140.720) Refine new water occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1344 occ: r_work=0.1192 r_free=0.1343 adp: r_work=0.1192 r_free=0.1344 occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1190 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1344 r_work=0.1190 r_free=0.1344 | n_water=984 | time (s): 203.710 (total time: 344.430) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=905 | time (s): 4.920 (total time: 349.350) Filter (dist only) r_work=0.1195 r_free=0.1356 | n_water=903 | time (s): 120.440 (total time: 469.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570911 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.493825 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1358 0.0159 0.038 1.1 8.4 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.58 1.59 1.687 13.745 14.494 3.755 11.99 13.61 1.63 1.688 13.742 14.494 3.754 Individual atomic B min max mean iso aniso Overall: 5.55 63.38 14.61 0.87 537 3270 Protein: 5.55 28.06 10.38 0.87 0 2902 Water: 6.00 63.38 28.20 N/A 537 366 Other: 13.83 22.12 17.98 N/A 0 2 Chain A: 5.63 51.09 12.17 N/A 0 1624 Chain B: 5.55 63.38 12.01 N/A 0 1646 Chain S: 6.00 61.75 29.96 N/A 537 0 Histogram: Values Number of atoms 5.55 - 11.34 2054 11.34 - 17.12 835 17.12 - 22.90 286 22.90 - 28.68 216 28.68 - 34.47 166 34.47 - 40.25 126 40.25 - 46.03 82 46.03 - 51.81 31 51.81 - 57.60 7 57.60 - 63.38 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1361 r_work=0.1199 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1362 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753540 | | target function (ml) not normalized (work): 702996.697611 | | target function (ml) not normalized (free): 14731.602503 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1512 n_refl.: 191130 remove outliers: r(all,work,free)=0.1407 0.1405 0.1512 n_refl.: 191130 overall B=-0.06 to atoms: r(all,work,free)=0.1397 0.1395 0.1504 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3729 361.213 328.720 0.394 0.974 0.200 13.296-10.522 97.03 97 1 0.2371 481.615 462.415 0.663 0.976 0.127 10.503-8.327 97.80 175 3 0.2280 502.347 493.080 0.834 0.976 0.097 8.318-6.595 100.00 360 8 0.2235 375.874 369.685 0.860 0.976 0.076 6.588-5.215 100.00 711 7 0.2008 345.390 334.933 0.861 0.977 0.063 5.214-4.128 98.38 1367 28 0.1261 505.201 498.978 0.953 0.978 0.030 4.126-3.266 94.74 2603 46 0.1188 460.518 452.794 1.017 0.979 0.005 3.266-2.585 99.86 5447 97 0.1144 310.655 306.973 0.998 0.980 0.000 2.585-2.046 97.45 10613 204 0.0967 234.371 231.667 1.007 0.983 0.000 2.046-1.619 99.39 21536 464 0.0907 138.712 137.343 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0937 74.675 74.023 1.012 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.060 38.341 0.980 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0138 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1196 r_free=0.1360 After: r_work=0.1197 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1197 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1361 | n_water=903 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1197 r_free=0.1361 | n_water=902 | time (s): 129.380 (total time: 131.730) Filter (q & B) r_work=0.1197 r_free=0.1361 | n_water=894 | time (s): 5.590 (total time: 137.320) Compute maps r_work=0.1197 r_free=0.1361 | n_water=894 | time (s): 2.220 (total time: 139.540) Filter (map) r_work=0.1222 r_free=0.1368 | n_water=768 | time (s): 5.080 (total time: 144.620) Find peaks r_work=0.1222 r_free=0.1368 | n_water=768 | time (s): 0.580 (total time: 145.200) Add new water r_work=0.1230 r_free=0.1382 | n_water=993 | time (s): 5.070 (total time: 150.270) Refine new water occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1352 occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1193 r_free=0.1352 occ: r_work=0.1192 r_free=0.1350 adp: r_work=0.1192 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1350 r_work=0.1192 r_free=0.1350 | n_water=993 | time (s): 229.920 (total time: 380.190) Filter (q & B) r_work=0.1198 r_free=0.1361 | n_water=893 | time (s): 3.970 (total time: 384.160) Filter (dist only) r_work=0.1198 r_free=0.1359 | n_water=891 | time (s): 116.750 (total time: 500.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.588476 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.429773 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1361 0.0162 0.038 1.2 8.0 0.0 0.3 0 0.794 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.61 1.62 1.684 13.642 14.430 3.755 12.00 13.64 1.64 1.687 13.638 14.430 3.754 Individual atomic B min max mean iso aniso Overall: 5.55 62.42 14.47 0.86 525 3270 Protein: 5.55 27.90 10.33 0.86 0 2902 Water: 6.03 62.42 27.93 N/A 525 366 Other: 13.85 22.06 17.95 N/A 0 2 Chain A: 5.63 50.88 12.10 N/A 0 1624 Chain B: 5.55 62.42 11.94 N/A 0 1646 Chain S: 6.03 61.92 29.71 N/A 525 0 Histogram: Values Number of atoms 5.55 - 11.24 2047 11.24 - 16.93 833 16.93 - 22.61 287 22.61 - 28.30 209 28.30 - 33.99 178 33.99 - 39.67 115 39.67 - 45.36 79 45.36 - 51.05 35 51.05 - 56.73 8 56.73 - 62.42 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1364 r_work=0.1200 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1364 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1363 target_work(ml) = 3.754 | | 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= 0.1199 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754241 | | target function (ml) not normalized (work): 703128.078522 | | target function (ml) not normalized (free): 14729.355156 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1396 0.1531 5.7162 5.8184| | 2: 2.94 - 2.33 1.00 7339 128 0.1086 0.1334 5.1053 5.2007| | 3: 2.33 - 2.04 0.96 6939 150 0.0907 0.1169 4.6586 4.7283| | 4: 2.04 - 1.85 1.00 7170 155 0.0898 0.1060 4.3904 4.5741| | 5: 1.85 - 1.72 0.99 7113 159 0.0928 0.0999 4.1476 4.2368| | 6: 1.72 - 1.62 0.99 7102 142 0.0895 0.1097 3.9444 4.082| | 7: 1.62 - 1.54 0.99 7104 148 0.0882 0.0967 3.7928 3.9209| | 8: 1.54 - 1.47 0.96 6798 152 0.0885 0.1303 3.6952 3.8972| | 9: 1.47 - 1.41 0.98 6938 155 0.0922 0.1122 3.6165 3.7449| | 10: 1.41 - 1.36 0.99 7022 150 0.0969 0.1189 3.5494 3.6798| | 11: 1.36 - 1.32 0.99 6997 151 0.0987 0.1096 3.4783 3.5733| | 12: 1.32 - 1.28 0.98 6975 149 0.1025 0.1102 3.4522 3.5724| | 13: 1.28 - 1.25 0.98 6907 166 0.1034 0.1239 3.4306 3.56| | 14: 1.25 - 1.22 0.98 7015 112 0.1101 0.1596 3.4294 3.6761| | 15: 1.22 - 1.19 0.98 6956 137 0.1164 0.1246 3.4461 3.4923| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1550 3.4639 3.6561| | 17: 1.17 - 1.14 0.98 6940 135 0.1297 0.1236 3.4328 3.4476| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1709 3.4376 3.5343| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1741 3.4191 3.5952| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1574 3.4099 3.4349| | 21: 1.08 - 1.07 0.97 6852 152 0.1725 0.2134 3.4177 3.5035| | 22: 1.07 - 1.05 0.97 6836 135 0.1901 0.1959 3.4127 3.4155| | 23: 1.05 - 1.03 0.97 6827 159 0.2115 0.2028 3.4327 3.4876| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2251 3.4359 3.5095| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2525 3.4496 3.5251| | 26: 1.01 - 0.99 0.96 6767 158 0.2754 0.2857 3.4161 3.4241| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2798 3.4692 3.3971| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.92 12.58 1.00 0.97 12513.59| | 2: 2.94 - 2.33 7339 128 0.92 13.48 0.99 0.97 5571.83| | 3: 2.33 - 2.04 6939 150 0.96 7.65 1.01 0.98 1702.72| | 4: 2.04 - 1.85 7170 155 0.96 7.61 1.00 0.98 1000.96| | 5: 1.85 - 1.72 7113 159 0.96 8.03 1.00 0.98 630.93| | 6: 1.72 - 1.62 7102 142 0.96 7.98 1.00 0.99 441.37| | 7: 1.62 - 1.54 7104 148 0.96 8.03 1.01 1.00 332.65| | 8: 1.54 - 1.47 6798 152 0.96 8.16 1.01 1.00 275.77| | 9: 1.47 - 1.41 6938 155 0.96 8.35 1.00 1.00 227.29| | 10: 1.41 - 1.36 7022 150 0.96 8.81 1.00 0.99 199.89| | 11: 1.36 - 1.32 6997 151 0.96 8.80 0.99 0.98 171.44| | 12: 1.32 - 1.28 6975 149 0.96 8.85 0.98 0.97 157.59| | 13: 1.28 - 1.25 6907 166 0.96 9.40 1.01 0.98 155.58| | 14: 1.25 - 1.22 7015 112 0.95 10.63 1.01 0.99 161.86| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 1.00 166.31| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.99 160.63| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.99 154.48| | 18: 1.14 - 1.12 6875 142 0.94 12.77 1.01 0.97 148.22| | 19: 1.12 - 1.10 6948 106 0.93 14.16 1.00 0.97 151.56| | 20: 1.10 - 1.08 6884 147 0.92 15.22 1.00 0.96 150.58| | 21: 1.08 - 1.07 6852 152 0.91 16.65 1.00 0.96 153.62| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.95 155.22| | 23: 1.05 - 1.03 6827 159 0.87 20.49 0.99 0.94 165.02| | 24: 1.03 - 1.02 6784 133 0.85 23.16 0.99 0.95 179.32| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.98 0.92 182.48| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.91 177.13| | 27: 0.99 - 0.98 6647 131 0.82 26.34 0.99 0.89 161.72| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 148.22 max = 12513.59 mean = 993.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 13.32| |phase err.(test): min = 0.00 max = 89.67 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1410 0.1407 0.1524 n_refl.: 191130 remove outliers: r(all,work,free)=0.1410 0.1407 0.1524 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1403 0.1401 0.1519 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1362 n_refl.: 191130 remove outliers: r(all,work,free)=0.1201 0.1198 0.1362 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3749 361.213 327.848 0.419 0.914 0.202 13.296-10.522 97.03 97 1 0.2416 481.615 460.489 0.707 0.916 0.130 10.503-8.327 97.80 175 3 0.2317 502.347 492.674 0.883 0.916 0.100 8.318-6.595 100.00 360 8 0.2240 375.874 369.843 0.914 0.916 0.075 6.588-5.215 100.00 711 7 0.2008 345.390 334.906 0.916 0.917 0.063 5.214-4.128 98.38 1367 28 0.1273 505.201 498.779 1.017 0.918 0.029 4.126-3.266 94.74 2603 46 0.1196 460.518 452.739 1.085 0.919 0.000 3.266-2.585 99.86 5447 97 0.1143 310.655 306.916 1.065 0.920 0.000 2.585-2.046 97.45 10613 204 0.0967 234.371 231.705 1.073 0.923 0.000 2.046-1.619 99.39 21536 464 0.0908 138.712 137.352 1.089 0.927 0.000 1.619-1.281 98.00 42464 925 0.0940 74.675 74.022 1.077 0.934 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.060 38.343 1.042 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0091 ================= 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 0.1996 0.081 5.232 5.2 78.0 14.6 805 0.000 1_bss: 0.1803 0.1948 0.081 5.232 5.2 78.0 14.6 805 0.000 1_settarget: 0.1803 0.1948 0.081 5.232 5.2 78.0 14.6 805 0.000 1_nqh: 0.1803 0.1948 0.081 5.232 5.2 78.0 14.6 805 0.000 1_weight: 0.1803 0.1948 0.081 5.232 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1276 0.1489 0.037 1.180 5.2 78.0 14.6 805 0.142 1_adp: 0.1304 0.1560 0.037 1.180 5.1 73.0 15.0 805 0.142 1_regHadp: 0.1303 0.1556 0.037 1.180 5.1 73.0 15.0 805 0.142 1_occ: 0.1287 0.1544 0.037 1.180 5.1 73.0 15.0 805 0.142 2_bss: 0.1280 0.1536 0.037 1.180 5.3 73.2 15.1 805 0.142 2_settarget: 0.1280 0.1536 0.037 1.180 5.3 73.2 15.1 805 0.142 2_updatecdl: 0.1280 0.1536 0.037 1.188 5.3 73.2 15.1 805 0.142 2_nqh: 0.1280 0.1536 0.037 1.188 5.3 73.2 15.1 805 0.142 2_sol: 0.1272 0.1503 0.037 1.188 5.3 73.2 16.2 894 n/a 2_weight: 0.1272 0.1503 0.037 1.188 5.3 73.2 16.2 894 n/a 2_xyzrec: 0.1255 0.1520 0.040 1.128 5.3 73.2 16.2 894 n/a 2_adp: 0.1233 0.1508 0.040 1.128 5.5 69.3 16.3 894 n/a 2_regHadp: 0.1233 0.1509 0.040 1.128 5.5 69.3 16.3 894 n/a 2_occ: 0.1228 0.1503 0.040 1.128 5.5 69.3 16.3 894 n/a 3_bss: 0.1234 0.1508 0.040 1.128 5.5 69.3 16.3 894 n/a 3_settarget: 0.1234 0.1508 0.040 1.128 5.5 69.3 16.3 894 n/a 3_updatecdl: 0.1234 0.1508 0.040 1.131 5.5 69.3 16.3 894 n/a 3_nqh: 0.1234 0.1508 0.040 1.131 5.5 69.3 16.3 894 n/a 3_sol: 0.1249 0.1500 0.040 1.131 5.5 68.2 15.5 890 n/a 3_weight: 0.1249 0.1500 0.040 1.131 5.5 68.2 15.5 890 n/a 3_xyzrec: 0.1238 0.1426 0.035 1.100 5.5 68.2 15.5 890 n/a 3_adp: 0.1232 0.1390 0.035 1.100 5.5 67.8 15.3 890 n/a 3_regHadp: 0.1233 0.1391 0.035 1.100 5.5 67.8 15.3 890 n/a 3_occ: 0.1227 0.1390 0.035 1.100 5.5 67.8 15.3 890 n/a 4_bss: 0.1223 0.1387 0.035 1.100 5.5 67.8 15.3 890 n/a 4_settarget: 0.1223 0.1387 0.035 1.100 5.5 67.8 15.3 890 n/a 4_updatecdl: 0.1223 0.1387 0.035 1.101 5.5 67.8 15.3 890 n/a 4_nqh: 0.1223 0.1387 0.035 1.101 5.5 67.8 15.3 890 n/a 4_sol: 0.1226 0.1381 0.035 1.101 5.5 67.8 15.1 881 n/a 4_weight: 0.1226 0.1381 0.035 1.101 5.5 67.8 15.1 881 n/a 4_xyzrec: 0.1227 0.1388 0.036 1.111 5.5 67.8 15.1 881 n/a 4_adp: 0.1224 0.1389 0.036 1.111 5.5 67.5 15.0 881 n/a 4_regHadp: 0.1224 0.1389 0.036 1.111 5.5 67.5 15.0 881 n/a 4_occ: 0.1222 0.1385 0.036 1.111 5.5 67.5 15.0 881 n/a 5_bss: 0.1220 0.1380 0.036 1.111 5.5 67.5 15.0 881 n/a 5_settarget: 0.1220 0.1380 0.036 1.111 5.5 67.5 15.0 881 n/a 5_updatecdl: 0.1220 0.1380 0.036 1.111 5.5 67.5 15.0 881 n/a 5_nqh: 0.1220 0.1380 0.036 1.111 5.5 67.5 15.0 881 n/a 5_sol: 0.1207 0.1361 0.036 1.111 5.5 67.5 14.7 845 n/a 5_weight: 0.1207 0.1361 0.036 1.111 5.5 67.5 14.7 845 n/a 5_xyzrec: 0.1208 0.1362 0.036 1.124 5.5 67.5 14.7 845 n/a 5_adp: 0.1211 0.1364 0.036 1.124 5.5 66.9 14.6 845 n/a 5_regHadp: 0.1211 0.1364 0.036 1.124 5.5 66.9 14.6 845 n/a 5_occ: 0.1209 0.1361 0.036 1.124 5.5 66.9 14.6 845 n/a 6_bss: 0.1208 0.1361 0.036 1.124 5.3 66.7 14.4 845 n/a 6_settarget: 0.1208 0.1361 0.036 1.124 5.3 66.7 14.4 845 n/a 6_updatecdl: 0.1208 0.1361 0.036 1.125 5.3 66.7 14.4 845 n/a 6_nqh: 0.1208 0.1361 0.036 1.125 5.3 66.7 14.4 845 n/a 6_sol: 0.1201 0.1355 0.036 1.125 5.3 66.7 14.7 892 n/a 6_weight: 0.1201 0.1355 0.036 1.125 5.3 66.7 14.7 892 n/a 6_xyzrec: 0.1206 0.1363 0.036 1.129 5.3 66.7 14.7 892 n/a 6_adp: 0.1206 0.1365 0.036 1.129 5.4 65.5 14.6 892 n/a 6_regHadp: 0.1207 0.1365 0.036 1.129 5.4 65.5 14.6 892 n/a 6_occ: 0.1204 0.1365 0.036 1.129 5.4 65.5 14.6 892 n/a 7_bss: 0.1194 0.1353 0.036 1.129 5.5 65.6 14.6 892 n/a 7_settarget: 0.1194 0.1353 0.036 1.129 5.5 65.6 14.6 892 n/a 7_updatecdl: 0.1194 0.1353 0.036 1.129 5.5 65.6 14.6 892 n/a 7_nqh: 0.1194 0.1353 0.036 1.129 5.5 65.6 14.6 892 n/a 7_sol: 0.1194 0.1350 0.036 1.129 5.5 65.6 14.6 894 n/a 7_weight: 0.1194 0.1350 0.036 1.129 5.5 65.6 14.6 894 n/a 7_xyzrec: 0.1197 0.1354 0.036 1.122 5.5 65.6 14.6 894 n/a 7_adp: 0.1200 0.1357 0.036 1.122 5.5 64.7 14.6 894 n/a 7_regHadp: 0.1200 0.1357 0.036 1.122 5.5 64.7 14.6 894 n/a 7_occ: 0.1198 0.1355 0.036 1.122 5.5 64.7 14.6 894 n/a 8_bss: 0.1196 0.1353 0.036 1.122 5.5 64.7 14.6 894 n/a 8_settarget: 0.1196 0.1353 0.036 1.122 5.5 64.7 14.6 894 n/a 8_updatecdl: 0.1196 0.1353 0.036 1.122 5.5 64.7 14.6 894 n/a 8_nqh: 0.1196 0.1353 0.036 1.122 5.5 64.7 14.6 894 n/a 8_sol: 0.1198 0.1355 0.036 1.122 5.5 64.7 14.4 873 n/a 8_weight: 0.1198 0.1355 0.036 1.122 5.5 64.7 14.4 873 n/a 8_xyzrec: 0.1201 0.1362 0.038 1.122 5.5 64.7 14.4 873 n/a 8_adp: 0.1201 0.1364 0.038 1.122 5.6 63.8 14.4 873 n/a 8_regHadp: 0.1201 0.1364 0.038 1.122 5.6 63.8 14.4 873 n/a 8_occ: 0.1200 0.1363 0.038 1.122 5.6 63.8 14.4 873 n/a 9_bss: 0.1199 0.1363 0.038 1.122 5.6 63.8 14.4 873 n/a 9_settarget: 0.1199 0.1363 0.038 1.122 5.6 63.8 14.4 873 n/a 9_updatecdl: 0.1199 0.1363 0.038 1.122 5.6 63.8 14.4 873 n/a 9_nqh: 0.1199 0.1363 0.038 1.122 5.6 63.8 14.4 873 n/a 9_sol: 0.1195 0.1356 0.038 1.122 5.6 63.8 14.6 903 n/a 9_weight: 0.1195 0.1356 0.038 1.122 5.6 63.8 14.6 903 n/a 9_xyzrec: 0.1199 0.1358 0.038 1.124 5.6 63.8 14.6 903 n/a 9_adp: 0.1199 0.1361 0.038 1.124 5.6 63.4 14.6 903 n/a 9_regHadp: 0.1199 0.1362 0.038 1.124 5.6 63.4 14.6 903 n/a 9_occ: 0.1197 0.1362 0.038 1.124 5.6 63.4 14.6 903 n/a 10_bss: 0.1196 0.1360 0.038 1.124 5.5 63.3 14.5 903 n/a 10_settarget: 0.1196 0.1360 0.038 1.124 5.5 63.3 14.5 903 n/a 10_updatecdl: 0.1196 0.1360 0.038 1.124 5.5 63.3 14.5 903 n/a 10_setrh: 0.1197 0.1361 0.038 1.124 5.5 63.3 14.5 903 n/a 10_nqh: 0.1197 0.1361 0.038 1.124 5.5 63.3 14.5 903 n/a 10_sol: 0.1198 0.1359 0.038 1.124 5.5 63.3 14.5 891 n/a 10_weight: 0.1198 0.1359 0.038 1.124 5.5 63.3 14.5 891 n/a 10_xyzrec: 0.1199 0.1361 0.038 1.151 5.5 63.3 14.5 891 n/a 10_adp: 0.1200 0.1364 0.038 1.151 5.6 62.4 14.5 891 n/a 10_regHadp: 0.1200 0.1364 0.038 1.151 5.6 62.4 14.5 891 n/a 10_occ: 0.1199 0.1363 0.038 1.151 5.6 62.4 14.5 891 n/a end: 0.1198 0.1362 0.038 1.151 5.5 62.4 14.4 891 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9286674_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9286674_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.9100 Refinement macro-cycles (run) : 11726.1000 Write final files (write_after_run_outputs) : 171.7100 Total : 11905.7200 Total CPU time: 3.32 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:35:38 PST -0800 (1736735738.93 s) Start R-work = 0.1803, R-free = 0.1948 Final R-work = 0.1198, R-free = 0.1362 =============================================================================== Job complete usr+sys time: 12237.16 seconds wall clock time: 204 minutes 59.50 seconds (12299.50 seconds total)