Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5983534.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5983534.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5983534.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.86, 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: 2.790 distance_ideal: 2.720 ideal - model: -0.070 slack: 0.000 delta_slack: -0.070 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: 2.708 distance_ideal: 2.710 ideal - model: 0.002 slack: 0.000 delta_slack: 0.002 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: 0.78 Conformation dependent library (CDL) restraints added in 147.2 milliseconds Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 1.01: 638 1.01 - 1.24: 2571 1.24 - 1.48: 1551 1.48 - 1.72: 1154 1.72 - 1.95: 20 Bond restraints: 5934 Sorted by residual: bond pdb=" NZ LYS B 133 " pdb=" HZ2 LYS B 133 " ideal model delta sigma weight residual 0.890 1.282 -0.392 2.00e-02 2.50e+03 3.84e+02 bond pdb=" N ALA B 188 " pdb=" H ALA B 188 " ideal model delta sigma weight residual 0.860 1.235 -0.375 2.00e-02 2.50e+03 3.52e+02 bond pdb=" N HIS A 96 " pdb=" H HIS A 96 " ideal model delta sigma weight residual 0.860 1.233 -0.373 2.00e-02 2.50e+03 3.48e+02 bond pdb=" CA TYR A 195 " pdb=" C TYR A 195 " ideal model delta sigma weight residual 1.524 1.291 0.232 1.26e-02 6.30e+03 3.40e+02 bond pdb=" CA THR A 154 " pdb=" C THR A 154 " ideal model delta sigma weight residual 1.521 1.740 -0.219 1.20e-02 6.94e+03 3.34e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 5433 3.97 - 7.93: 3473 7.93 - 11.90: 1503 11.90 - 15.87: 365 15.87 - 19.83: 36 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA THR B 33 " pdb=" C THR B 33 " pdb=" N THR B 34 " ideal model delta sigma weight residual 116.37 136.20 -19.83 1.19e+00 7.06e-01 2.78e+02 angle pdb=" O ALA A 108 " pdb=" C ALA A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 120.48 107.58 12.90 8.90e-01 1.26e+00 2.10e+02 angle pdb=" CA PHE B 119 " pdb=" C PHE B 119 " pdb=" N PRO B 120 " ideal model delta sigma weight residual 117.78 132.37 -14.59 1.06e+00 8.90e-01 1.89e+02 angle pdb=" CA ASP B 163 " pdb=" CB ASP B 163 " pdb=" CG ASP B 163 " ideal model delta sigma weight residual 112.60 126.16 -13.56 1.00e+00 1.00e+00 1.84e+02 angle pdb=" CA MET A 187 " pdb=" C MET A 187 " pdb=" O MET A 187 " ideal model delta sigma weight residual 121.44 107.09 14.35 1.08e+00 8.57e-01 1.77e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.56: 1910 22.56 - 45.11: 102 45.11 - 67.66: 33 67.66 - 90.21: 4 90.21 - 112.77: 1 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -146.63 -33.37 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -152.45 -27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.216: 189 0.216 - 0.431: 153 0.431 - 0.646: 113 0.646 - 0.861: 27 0.861 - 1.076: 10 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB THR B 91 " pdb=" CA THR B 91 " pdb=" OG1 THR B 91 " pdb=" CG2 THR B 91 " both_signs ideal model delta sigma weight residual False 2.55 3.63 -1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -3.66 1.03 2.00e-01 2.50e+01 2.68e+01 chirality pdb=" CA LEU B 88 " pdb=" N LEU B 88 " pdb=" C LEU B 88 " pdb=" CB LEU B 88 " both_signs ideal model delta sigma weight residual False 2.51 3.52 -1.01 2.00e-01 2.50e+01 2.56e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " -0.145 2.00e-02 2.50e+03 8.09e-02 1.96e+02 pdb=" CG TYR A 192 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " -0.109 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.143 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " 0.099 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " 0.006 2.00e-02 2.50e+03 7.01e-02 1.47e+02 pdb=" CG TYR B 195 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " 0.123 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " 0.095 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " 0.081 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " -0.020 2.00e-02 2.50e+03 pdb=" HD1 TYR B 195 " -0.104 2.00e-02 2.50e+03 pdb=" HD2 TYR B 195 " -0.061 2.00e-02 2.50e+03 pdb=" HE1 TYR B 195 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR B 195 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 83 " 0.223 9.50e-02 1.11e+02 1.09e-01 1.47e+02 pdb=" NE ARG A 83 " -0.120 2.00e-02 2.50e+03 pdb=" CZ ARG A 83 " -0.036 2.00e-02 2.50e+03 pdb=" NH1 ARG A 83 " 0.083 2.00e-02 2.50e+03 pdb=" NH2 ARG A 83 " 0.060 2.00e-02 2.50e+03 pdb="HH11 ARG A 83 " 0.054 2.00e-02 2.50e+03 pdb="HH12 ARG A 83 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG A 83 " 0.112 2.00e-02 2.50e+03 pdb="HH22 ARG A 83 " -0.112 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.56: 25 1.56 - 2.32: 1944 2.32 - 3.08: 21895 3.08 - 3.84: 33089 3.84 - 4.60: 53342 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110295 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.806 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.915 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.082 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.117 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.139 2.620 ... (remaining 110290 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_5983534_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= 0.2036 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.301971 | | target function (ml) not normalized (work): 805815.009372 | | target function (ml) not normalized (free): 16508.817630 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2143 0.1911 6.6932 6.308| | 2: 2.94 - 2.33 1.00 7339 128 0.1607 0.1570 5.5326 5.5829| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1566 5.1499 5.1464| | 4: 2.04 - 1.85 1.00 7170 155 0.1769 0.1599 4.9738 4.9875| | 5: 1.85 - 1.72 0.99 7113 159 0.1931 0.1846 4.805 4.8653| | 6: 1.72 - 1.62 0.99 7102 142 0.1981 0.1891 4.6726 4.7232| | 7: 1.62 - 1.54 0.99 7104 148 0.1982 0.1760 4.5583 4.581| | 8: 1.54 - 1.47 0.96 6798 152 0.2050 0.2194 4.481 4.4862| | 9: 1.47 - 1.41 0.98 6938 155 0.2105 0.2039 4.4025 4.3876| | 10: 1.41 - 1.36 0.99 7022 150 0.2139 0.1975 4.3145 4.2544| | 11: 1.36 - 1.32 0.99 6997 151 0.2097 0.2250 4.2248 4.3292| | 12: 1.32 - 1.28 0.98 6976 149 0.2088 0.1881 4.1745 4.2347| | 13: 1.28 - 1.25 0.98 6907 166 0.2035 0.2030 4.1104 4.1212| | 14: 1.25 - 1.22 0.98 7015 113 0.2110 0.2382 4.0944 4.2287| | 15: 1.22 - 1.19 0.98 6957 137 0.2096 0.2007 4.0515 4.0085| | 16: 1.19 - 1.17 0.93 6604 132 0.2121 0.2260 4.0078 4.0959| | 17: 1.17 - 1.14 0.98 6941 135 0.2167 0.1813 3.9626 3.9311| | 18: 1.14 - 1.12 0.98 6875 142 0.2215 0.2106 3.9251 3.8435| | 19: 1.12 - 1.10 0.97 6949 106 0.2278 0.2377 3.8674 3.9681| | 20: 1.10 - 1.08 0.97 6884 147 0.2317 0.2338 3.8191 3.8778| | 21: 1.08 - 1.07 0.97 6852 152 0.2484 0.2744 3.802 3.8252| | 22: 1.07 - 1.05 0.97 6838 135 0.2542 0.2437 3.7485 3.7131| | 23: 1.05 - 1.03 0.97 6829 159 0.2690 0.2612 3.7306 3.8082| | 24: 1.03 - 1.02 0.96 6785 133 0.2845 0.2791 3.6931 3.7414| | 25: 1.02 - 1.01 0.93 6552 130 0.3063 0.3111 3.6739 3.7651| | 26: 1.01 - 0.99 0.96 6767 158 0.3220 0.3404 3.6319 3.642| | 27: 0.99 - 0.98 0.94 6648 131 0.3402 0.3216 3.6382 3.5982| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.42 0.91 0.98 35335.09| | 2: 2.94 - 2.33 7339 128 0.86 21.10 1.09 1.01 14863.18| | 3: 2.33 - 2.04 6939 150 0.93 12.29 1.10 1.05 4007.80| | 4: 2.04 - 1.85 7170 155 0.92 13.67 1.11 1.05 2765.80| | 5: 1.85 - 1.72 7113 159 0.91 16.09 1.12 1.07 2191.10| | 6: 1.72 - 1.62 7102 142 0.90 17.08 1.12 1.07 1702.76| | 7: 1.62 - 1.54 7104 148 0.89 17.51 1.10 1.08 1354.05| | 8: 1.54 - 1.47 6798 152 0.89 17.53 1.10 1.08 1085.42| | 9: 1.47 - 1.41 6938 155 0.89 18.11 1.10 1.08 912.45| | 10: 1.41 - 1.36 7022 150 0.88 19.01 1.09 1.06 783.13| | 11: 1.36 - 1.32 6997 151 0.88 19.66 1.09 1.04 704.92| | 12: 1.32 - 1.28 6976 149 0.88 19.38 1.08 1.03 619.04| | 13: 1.28 - 1.25 6907 166 0.88 19.02 1.07 1.04 568.72| | 14: 1.25 - 1.22 7015 113 0.88 19.33 1.07 1.06 522.25| | 15: 1.22 - 1.19 6957 137 0.87 19.85 1.07 1.07 513.68| | 16: 1.19 - 1.17 6604 132 0.88 19.74 1.07 1.04 468.13| | 17: 1.17 - 1.14 6941 135 0.87 20.18 1.08 1.01 420.84| | 18: 1.14 - 1.12 6875 142 0.87 20.28 1.08 0.99 369.00| | 19: 1.12 - 1.10 6949 106 0.86 21.93 1.07 0.99 367.27| | 20: 1.10 - 1.08 6884 147 0.85 22.75 1.06 0.98 349.92| | 21: 1.08 - 1.07 6852 152 0.84 24.04 1.06 0.99 342.48| | 22: 1.07 - 1.05 6838 135 0.83 24.67 1.05 0.99 312.26| | 23: 1.05 - 1.03 6829 159 0.81 26.62 1.05 1.00 321.46| | 24: 1.03 - 1.02 6785 133 0.78 29.02 1.06 1.00 327.34| | 25: 1.02 - 1.01 6552 130 0.76 31.12 1.03 0.95 322.84| | 26: 1.01 - 0.99 6767 158 0.75 32.42 1.04 0.93 300.57| | 27: 0.99 - 0.98 6648 131 0.76 31.64 1.04 0.94 275.57| |alpha: min = 0.93 max = 1.08 mean = 1.02| |beta: min = 275.57 max = 35335.09 mean = 2797.12| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.20| |phase err.(test): min = 0.00 max = 89.93 mean = 21.46| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.254 2950 Z= 5.375 Angle : 5.288 19.833 4018 Z= 3.743 Chirality : 0.381 1.076 492 Planarity : 0.034 0.172 512 Dihedral : 13.195 112.767 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.32 % Allowed : 4.84 % Favored : 94.84 % Cbeta Deviations : 30.90 % 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: -2.30 (0.36), residues: 386 helix: -2.39 (0.29), residues: 144 sheet: -0.57 (0.53), residues: 82 loop : -0.94 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.017 ARG B 97 TYR 0.115 0.044 TYR A 192 PHE 0.127 0.036 PHE B 164 TRP 0.105 0.042 TRP A 146 HIS 0.096 0.033 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2036 r_free= 0.1957 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.301971 | | target function (ml) not normalized (work): 805815.009372 | | target function (ml) not normalized (free): 16508.817630 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2036 0.1957 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2036 0.1957 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2036 0.1957 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2033 0.2036 0.1957 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1804 0.1802 0.1897 n_refl.: 191145 remove outliers: r(all,work,free)=0.1801 0.1799 0.1897 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4072 402.814 291.960 0.434 0.913 0.299 13.296-10.522 99.01 99 1 0.2464 528.187 519.482 0.788 0.914 0.250 10.503-8.327 98.90 177 3 0.2435 564.205 559.701 0.970 0.914 0.227 8.318-6.595 100.00 360 8 0.2493 414.736 402.459 0.965 0.914 0.159 6.588-5.215 100.00 711 7 0.2245 381.101 365.599 0.954 0.914 0.140 5.214-4.128 98.38 1367 28 0.1530 557.435 549.685 1.079 0.914 0.100 4.126-3.266 94.74 2603 46 0.1342 508.132 499.031 1.147 0.914 0.023 3.266-2.585 99.86 5447 97 0.1424 342.774 337.719 1.119 0.914 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 254.118 1.123 0.913 0.000 2.046-1.619 99.39 21536 464 0.1626 153.054 149.852 1.145 0.912 0.000 1.619-1.281 98.00 42464 925 0.1919 82.395 80.237 1.127 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2318 44.203 41.693 1.113 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0076 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1799 r_free=0.1897 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1799 r_free=0.1897 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.413704 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.510102 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 0.1267 0.1481 0.0213 0.034 1.2 11.9 0.0 0.3 0 11.207 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.67 14.81 2.13 1.117 13.108 575.510 0.019 12.95 15.46 2.51 1.221 13.298 575.510 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.04 14.94 1.40 435 3274 Protein: 5.16 40.61 10.98 1.40 0 2902 Water: 6.26 73.04 29.21 N/A 435 370 Other: 15.94 30.67 23.31 N/A 0 2 Chain A: 5.40 60.51 13.01 N/A 0 1626 Chain B: 5.16 73.04 12.74 N/A 0 1648 Chain S: 11.23 61.68 30.53 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2167 11.95 - 18.74 638 18.74 - 25.53 325 25.53 - 32.31 260 32.31 - 39.10 154 39.10 - 45.89 103 45.89 - 52.68 41 52.68 - 59.47 15 59.47 - 66.25 5 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1295 r_free=0.1546 r_work=0.1294 r_free=0.1540 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1294 r_free = 0.1540 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1279 r_free = 0.1526 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1279 r_free= 0.1526 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015670 | | target function (ls_wunit_k1) not normalized (work): 2934.882645 | | target function (ls_wunit_k1) not normalized (free): 112.473076 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1283 0.1279 0.1526 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1465 0.1463 0.1601 n_refl.: 191138 remove outliers: r(all,work,free)=0.1465 0.1463 0.1601 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1488 0.1486 0.1611 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1275 0.1271 0.1517 n_refl.: 191138 remove outliers: r(all,work,free)=0.1275 0.1271 0.1516 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 0.3659 402.814 367.524 0.455 0.997 0.281 13.296-10.522 99.01 99 1 0.2132 528.187 520.107 0.715 0.999 0.260 10.503-8.327 98.90 177 3 0.1722 564.205 565.298 0.860 0.999 0.208 8.318-6.595 100.00 360 8 0.1769 414.736 411.412 0.875 0.999 0.150 6.588-5.215 100.00 711 7 0.1587 381.101 373.377 0.857 0.999 0.140 5.214-4.128 98.38 1367 28 0.0930 557.435 554.042 0.945 0.999 0.080 4.126-3.266 94.74 2603 46 0.0855 508.132 503.940 1.009 1.000 0.024 3.266-2.585 99.86 5447 97 0.0927 342.774 340.451 0.991 1.000 0.010 2.585-2.046 97.45 10613 204 0.0940 258.603 256.376 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1070 153.054 151.433 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1266 82.395 81.385 1.009 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.225 0.989 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0362 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1516 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1271 r_free=0.1516 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1516 | n_water=805 | time (s): 2.990 (total time: 2.990) Filter (dist) r_work=0.1273 r_free=0.1522 | n_water=798 | time (s): 100.980 (total time: 103.970) Filter (q & B) r_work=0.1274 r_free=0.1522 | n_water=793 | time (s): 5.250 (total time: 109.220) Compute maps r_work=0.1274 r_free=0.1522 | n_water=793 | time (s): 1.970 (total time: 111.190) Filter (map) r_work=0.1297 r_free=0.1514 | n_water=662 | time (s): 4.420 (total time: 115.610) Find peaks r_work=0.1297 r_free=0.1514 | n_water=662 | time (s): 0.730 (total time: 116.340) Add new water r_work=0.1321 r_free=0.1547 | n_water=962 | time (s): 5.030 (total time: 121.370) Refine new water occ: r_work=0.1278 r_free=0.1503 adp: r_work=0.1266 r_free=0.1493 occ: r_work=0.1268 r_free=0.1491 adp: r_work=0.1262 r_free=0.1489 occ: r_work=0.1263 r_free=0.1484 adp: r_work=0.1261 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1261 r_free=0.1484 r_work=0.1261 r_free=0.1484 | n_water=962 | time (s): 71.650 (total time: 193.020) Filter (q & B) r_work=0.1264 r_free=0.1485 | n_water=895 | time (s): 5.280 (total time: 198.300) Filter (dist only) r_work=0.1265 r_free=0.1485 | n_water=894 | time (s): 114.660 (total time: 312.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.149139 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 568.457537 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 0.1251 0.1512 0.0261 0.038 1.1 19.9 0.0 0.3 0 11.575 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.51 15.12 2.61 2.038 15.084 568.458 0.014 12.34 15.05 2.71 2.377 15.142 568.458 0.014 Individual atomic B min max mean iso aniso Overall: 5.36 68.29 16.18 1.18 525 3273 Protein: 5.36 39.79 10.99 1.18 0 2902 Water: 6.48 68.29 33.00 N/A 525 369 Other: 16.39 33.74 25.06 N/A 0 2 Chain A: 5.53 57.22 13.01 N/A 0 1625 Chain B: 5.36 68.29 12.79 N/A 0 1648 Chain S: 11.91 66.26 36.62 N/A 525 0 Histogram: Values Number of atoms 5.36 - 11.65 2041 11.65 - 17.94 727 17.94 - 24.23 280 24.23 - 30.53 227 30.53 - 36.82 180 36.82 - 43.11 157 43.11 - 49.41 100 49.41 - 55.70 53 55.70 - 61.99 25 61.99 - 68.29 8 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1505 r_work=0.1235 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1507 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1502 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= 0.1229 r_free= 0.1502 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013472 | | target function (ls_wunit_k1) not normalized (work): 2523.340905 | | target function (ls_wunit_k1) not normalized (free): 98.053965 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1501 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1602 n_refl.: 191137 remove outliers: r(all,work,free)=0.1439 0.1436 0.1602 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1436 0.1433 0.1600 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1506 n_refl.: 191137 remove outliers: r(all,work,free)=0.1241 0.1236 0.1506 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 0.3191 402.814 381.884 0.488 0.963 0.271 13.296-10.522 99.01 99 1 0.1937 528.187 518.282 0.754 0.964 0.223 10.503-8.327 98.90 177 3 0.1430 564.205 566.660 0.920 0.964 0.181 8.318-6.595 100.00 360 8 0.1560 414.736 413.953 0.930 0.964 0.146 6.588-5.215 100.00 711 7 0.1353 381.101 376.792 0.911 0.964 0.130 5.214-4.128 98.38 1367 28 0.0827 557.435 556.163 0.995 0.964 0.100 4.126-3.266 94.74 2603 46 0.0765 508.132 505.474 1.059 0.964 0.024 3.266-2.585 99.86 5447 97 0.0866 342.774 341.287 1.046 0.963 0.005 2.585-2.046 97.45 10613 204 0.0898 258.603 256.810 1.057 0.962 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.647 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.352 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.210 1.058 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0491 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1506 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1506 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1506 | n_water=894 | time (s): 2.740 (total time: 2.740) Filter (dist) r_work=0.1239 r_free=0.1512 | n_water=888 | time (s): 120.700 (total time: 123.440) Filter (q & B) r_work=0.1239 r_free=0.1511 | n_water=886 | time (s): 5.780 (total time: 129.220) Compute maps r_work=0.1239 r_free=0.1511 | n_water=886 | time (s): 2.230 (total time: 131.450) Filter (map) r_work=0.1275 r_free=0.1518 | n_water=705 | time (s): 5.610 (total time: 137.060) Find peaks r_work=0.1275 r_free=0.1518 | n_water=705 | time (s): 0.820 (total time: 137.880) Add new water r_work=0.1298 r_free=0.1548 | n_water=1010 | time (s): 4.880 (total time: 142.760) Refine new water occ: r_work=0.1246 r_free=0.1496 adp: r_work=0.1240 r_free=0.1489 occ: r_work=0.1236 r_free=0.1488 adp: r_work=0.1236 r_free=0.1489 occ: r_work=0.1233 r_free=0.1488 adp: r_work=0.1232 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1488 r_work=0.1232 r_free=0.1488 | n_water=1010 | time (s): 290.600 (total time: 433.360) Filter (q & B) r_work=0.1239 r_free=0.1498 | n_water=874 | time (s): 4.830 (total time: 438.190) Filter (dist only) r_work=0.1239 r_free=0.1499 | n_water=872 | time (s): 124.250 (total time: 562.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.606428 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.999449 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 0.1226 0.1428 0.0202 0.034 1.1 7.5 0.0 0.0 0 0.803 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.28 2.02 1.928 14.537 15.999 3.933 12.17 13.87 1.70 2.240 14.442 15.999 3.884 Individual atomic B min max mean iso aniso Overall: 5.52 67.78 15.17 1.06 505 3271 Protein: 5.52 36.22 10.74 1.06 0 2902 Water: 5.73 67.78 29.89 N/A 505 367 Other: 13.81 28.96 21.39 N/A 0 2 Chain A: 5.52 56.23 12.76 N/A 0 1625 Chain B: 5.56 67.78 12.49 N/A 0 1646 Chain S: 5.73 61.58 31.64 N/A 505 0 Histogram: Values Number of atoms 5.52 - 11.75 2131 11.75 - 17.97 682 17.97 - 24.20 302 24.20 - 30.43 240 30.43 - 36.65 187 36.65 - 42.88 142 42.88 - 49.10 59 49.10 - 55.33 24 55.33 - 61.56 7 61.56 - 67.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1388 r_work=0.1218 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1218 r_free = 0.1389 target_work(ml) = 3.885 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1211 r_free = 0.1390 target_work(ml) = 3.879 | | 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= 0.1211 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.879135 | | target function (ml) not normalized (work): 726546.387639 | | target function (ml) not normalized (free): 15191.818586 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1211 0.1390 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1428 0.1427 0.1488 n_refl.: 191137 remove outliers: r(all,work,free)=0.1428 0.1427 0.1488 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1422 0.1421 0.1484 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1208 0.1383 n_refl.: 191137 remove outliers: r(all,work,free)=0.1211 0.1207 0.1383 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 0.3889 398.008 361.059 0.426 0.947 0.251 13.296-10.522 99.01 99 1 0.2451 528.187 508.257 0.707 0.948 0.214 10.503-8.327 97.80 175 3 0.1987 554.286 556.153 0.882 0.948 0.169 8.318-6.595 100.00 360 8 0.2074 414.736 408.841 0.895 0.948 0.125 6.588-5.215 100.00 711 7 0.1822 381.101 370.806 0.886 0.948 0.110 5.214-4.128 98.38 1367 28 0.1151 557.435 552.386 0.973 0.948 0.080 4.126-3.266 94.74 2603 46 0.1085 508.132 501.026 1.032 0.948 0.009 3.266-2.585 99.86 5447 97 0.1074 342.774 339.196 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 255.673 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0943 153.054 151.449 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1026 82.395 81.496 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1677 44.202 42.316 1.038 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1024 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1207 r_free=0.1383 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1207 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1207 r_free=0.1383 | n_water=872 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1208 r_free=0.1385 | n_water=871 | time (s): 107.490 (total time: 110.030) Filter (q & B) r_work=0.1209 r_free=0.1381 | n_water=860 | time (s): 4.350 (total time: 114.380) Compute maps r_work=0.1209 r_free=0.1381 | n_water=860 | time (s): 1.610 (total time: 115.990) Filter (map) r_work=0.1233 r_free=0.1379 | n_water=715 | time (s): 4.160 (total time: 120.150) Find peaks r_work=0.1233 r_free=0.1379 | n_water=715 | time (s): 0.660 (total time: 120.810) Add new water r_work=0.1249 r_free=0.1405 | n_water=975 | time (s): 4.010 (total time: 124.820) Refine new water occ: r_work=0.1208 r_free=0.1369 adp: r_work=0.1208 r_free=0.1369 occ: r_work=0.1205 r_free=0.1368 adp: r_work=0.1205 r_free=0.1367 occ: r_work=0.1203 r_free=0.1367 adp: r_work=0.1202 r_free=0.1366 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1366 r_work=0.1202 r_free=0.1366 | n_water=975 | time (s): 253.580 (total time: 378.400) Filter (q & B) r_work=0.1208 r_free=0.1369 | n_water=876 | time (s): 4.260 (total time: 382.660) Filter (dist only) r_work=0.1208 r_free=0.1368 | n_water=875 | time (s): 115.650 (total time: 498.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.596141 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.008307 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 0.1207 0.1364 0.0157 0.035 1.1 6.3 0.0 0.0 0 0.798 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.64 1.57 1.833 14.196 16.008 3.872 12.00 13.61 1.61 1.933 14.155 16.008 3.865 Individual atomic B min max mean iso aniso Overall: 5.49 67.34 14.95 1.01 509 3270 Protein: 5.49 33.27 10.67 1.01 0 2902 Water: 5.65 67.34 29.13 N/A 509 366 Other: 14.02 27.86 20.94 N/A 0 2 Chain A: 5.49 55.19 12.63 N/A 0 1625 Chain B: 5.52 67.34 12.38 N/A 0 1645 Chain S: 5.65 61.63 30.62 N/A 509 0 Histogram: Values Number of atoms 5.49 - 11.67 2108 11.67 - 17.86 728 17.86 - 24.04 314 24.04 - 30.23 239 30.23 - 36.41 177 36.41 - 42.60 130 42.60 - 48.78 53 48.78 - 54.97 22 54.97 - 61.16 6 61.16 - 67.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1361 r_work=0.1200 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1362 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1354 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862644 | | target function (ml) not normalized (work): 723446.137880 | | target function (ml) not normalized (free): 15136.957699 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1354 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1423 0.1423 0.1457 n_refl.: 191134 remove outliers: r(all,work,free)=0.1423 0.1423 0.1457 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1416 0.1416 0.1453 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1348 n_refl.: 191134 remove outliers: r(all,work,free)=0.1198 0.1195 0.1348 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3633 360.374 313.282 0.403 0.948 0.238 13.296-10.522 97.03 97 1 0.2416 481.576 454.954 0.683 0.950 0.176 10.503-8.327 97.80 175 3 0.2093 502.306 496.800 0.862 0.950 0.150 8.318-6.595 100.00 360 8 0.2175 375.843 369.488 0.886 0.949 0.105 6.588-5.215 100.00 711 7 0.1911 345.362 334.759 0.882 0.949 0.100 5.214-4.128 98.38 1367 28 0.1198 505.160 500.255 0.971 0.949 0.070 4.126-3.266 94.74 2603 46 0.1123 460.480 453.769 1.032 0.950 0.000 3.266-2.585 99.86 5447 97 0.1094 310.629 307.468 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0937 234.352 231.959 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0910 138.701 137.413 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.0982 74.669 73.976 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.056 38.399 1.042 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1096 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1348 | n_water=875 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1195 r_free=0.1348 | n_water=875 | time (s): 102.750 (total time: 105.050) Filter (q & B) r_work=0.1195 r_free=0.1348 | n_water=867 | time (s): 5.400 (total time: 110.450) Compute maps r_work=0.1195 r_free=0.1348 | n_water=867 | time (s): 1.970 (total time: 112.420) Filter (map) r_work=0.1218 r_free=0.1357 | n_water=745 | time (s): 4.520 (total time: 116.940) Find peaks r_work=0.1218 r_free=0.1357 | n_water=745 | time (s): 0.870 (total time: 117.810) Add new water r_work=0.1229 r_free=0.1374 | n_water=972 | time (s): 4.070 (total time: 121.880) Refine new water occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1341 occ: r_work=0.1188 r_free=0.1339 adp: r_work=0.1188 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1339 r_work=0.1188 r_free=0.1339 | n_water=972 | time (s): 172.590 (total time: 294.470) Filter (q & B) r_work=0.1193 r_free=0.1342 | n_water=888 | time (s): 5.120 (total time: 299.590) Filter (dist only) r_work=0.1193 r_free=0.1342 | n_water=886 | time (s): 111.870 (total time: 411.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.599883 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.786522 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 0.1195 0.1349 0.0154 0.035 1.1 6.3 0.0 0.3 0 0.800 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.49 1.54 1.795 14.068 14.787 3.763 11.99 13.51 1.53 1.830 14.055 14.787 3.762 Individual atomic B min max mean iso aniso Overall: 5.56 67.15 14.85 0.97 521 3269 Protein: 5.56 32.70 10.62 0.97 0 2902 Water: 5.66 67.15 28.69 N/A 521 365 Other: 13.79 27.35 20.57 N/A 0 2 Chain A: 5.60 54.79 12.56 N/A 0 1624 Chain B: 5.56 67.15 12.32 N/A 0 1645 Chain S: 5.66 61.63 29.98 N/A 521 0 Histogram: Values Number of atoms 5.56 - 11.72 2135 11.72 - 17.88 711 17.88 - 24.04 322 24.04 - 30.20 251 30.20 - 36.36 174 36.36 - 42.52 118 42.52 - 48.68 48 48.68 - 54.83 22 54.83 - 60.99 7 60.99 - 67.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1351 r_work=0.1199 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1352 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1353 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760994 | | target function (ml) not normalized (work): 704396.498764 | | target function (ml) not normalized (free): 14742.795095 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1353 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1414 0.1413 0.1475 n_refl.: 191131 remove outliers: r(all,work,free)=0.1414 0.1413 0.1475 n_refl.: 191131 overall B=-0.03 to atoms: r(all,work,free)=0.1408 0.1407 0.1471 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1347 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1347 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3699 360.374 331.224 0.410 0.973 0.234 13.296-10.522 97.03 97 1 0.2406 481.576 460.565 0.672 0.974 0.169 10.503-8.327 97.80 175 3 0.2152 502.306 496.376 0.833 0.974 0.143 8.318-6.595 100.00 360 8 0.2202 375.843 369.429 0.861 0.973 0.100 6.588-5.215 100.00 711 7 0.1930 345.362 334.626 0.859 0.972 0.090 5.214-4.128 98.38 1367 28 0.1211 505.160 499.816 0.945 0.972 0.060 4.126-3.266 94.74 2603 46 0.1127 460.480 453.461 1.008 0.971 0.000 3.266-2.585 99.86 5447 97 0.1098 310.629 307.197 0.996 0.968 0.000 2.585-2.046 97.45 10613 204 0.0945 234.352 231.858 1.012 0.964 0.000 2.046-1.619 99.39 21536 464 0.0912 138.701 137.359 1.040 0.958 0.000 1.619-1.281 98.00 42464 925 0.0971 74.669 73.965 1.047 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1646 40.056 38.388 1.051 0.930 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1011 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1348 | n_water=886 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1194 r_free=0.1349 | n_water=885 | time (s): 108.800 (total time: 111.890) Filter (q & B) r_work=0.1194 r_free=0.1349 | n_water=874 | time (s): 4.830 (total time: 116.720) Compute maps r_work=0.1194 r_free=0.1349 | n_water=874 | time (s): 1.560 (total time: 118.280) Filter (map) r_work=0.1216 r_free=0.1356 | n_water=754 | time (s): 4.190 (total time: 122.470) Find peaks r_work=0.1216 r_free=0.1356 | n_water=754 | time (s): 0.630 (total time: 123.100) Add new water r_work=0.1226 r_free=0.1370 | n_water=982 | time (s): 4.750 (total time: 127.850) Refine new water occ: r_work=0.1189 r_free=0.1336 adp: r_work=0.1189 r_free=0.1336 occ: r_work=0.1187 r_free=0.1336 adp: r_work=0.1187 r_free=0.1335 occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1186 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1335 r_work=0.1186 r_free=0.1335 | n_water=982 | time (s): 190.910 (total time: 318.760) Filter (q & B) r_work=0.1190 r_free=0.1341 | n_water=896 | time (s): 4.400 (total time: 323.160) Filter (dist only) r_work=0.1190 r_free=0.1341 | n_water=895 | time (s): 114.570 (total time: 437.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.505357 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.475339 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1348 0.0154 0.036 1.1 6.1 0.0 0.3 0 0.753 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.48 1.54 1.774 14.046 15.475 3.762 11.96 13.49 1.54 1.856 14.017 15.475 3.758 Individual atomic B min max mean iso aniso Overall: 5.55 66.55 14.84 0.94 530 3269 Protein: 5.55 30.78 10.56 0.94 0 2902 Water: 5.75 66.55 28.70 N/A 530 365 Other: 13.83 25.60 19.71 N/A 0 2 Chain A: 5.62 53.28 12.46 N/A 0 1624 Chain B: 5.55 66.55 12.24 N/A 0 1645 Chain S: 5.75 59.45 30.19 N/A 530 0 Histogram: Values Number of atoms 5.55 - 11.65 2116 11.65 - 17.75 749 17.75 - 23.85 310 23.85 - 29.95 234 29.95 - 36.05 181 36.05 - 42.15 126 42.15 - 48.25 51 48.25 - 54.35 25 54.35 - 60.45 6 60.45 - 66.55 1 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1349 r_work=0.1196 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1350 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1348 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756802 | | target function (ml) not normalized (work): 703611.427324 | | target function (ml) not normalized (free): 14733.469474 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1413 0.1412 0.1477 n_refl.: 191131 remove outliers: r(all,work,free)=0.1413 0.1412 0.1477 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1405 0.1404 0.1471 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1352 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1352 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3659 360.374 332.191 0.418 0.950 0.229 13.296-10.522 97.03 97 1 0.2404 481.576 460.687 0.690 0.951 0.158 10.503-8.327 97.80 175 3 0.2173 502.306 496.779 0.855 0.951 0.129 8.318-6.595 100.00 360 8 0.2194 375.843 369.865 0.884 0.951 0.090 6.588-5.215 100.00 711 7 0.1920 345.362 334.961 0.882 0.951 0.080 5.214-4.128 98.38 1367 28 0.1215 505.160 499.739 0.971 0.951 0.070 4.126-3.266 94.74 2603 46 0.1142 460.480 453.510 1.033 0.951 0.000 3.266-2.585 99.86 5447 97 0.1110 310.629 307.309 1.019 0.951 0.000 2.585-2.046 97.45 10613 204 0.0950 234.352 231.831 1.031 0.951 0.000 2.046-1.619 99.39 21536 464 0.0910 138.701 137.404 1.054 0.950 0.000 1.619-1.281 98.00 42464 925 0.0969 74.669 73.966 1.052 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.056 38.388 1.040 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1422 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1352 | n_water=895 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1197 r_free=0.1351 | n_water=893 | time (s): 112.970 (total time: 115.600) Filter (q & B) r_work=0.1197 r_free=0.1349 | n_water=885 | time (s): 5.410 (total time: 121.010) Compute maps r_work=0.1197 r_free=0.1349 | n_water=885 | time (s): 2.240 (total time: 123.250) Filter (map) r_work=0.1218 r_free=0.1364 | n_water=770 | time (s): 5.180 (total time: 128.430) Find peaks r_work=0.1218 r_free=0.1364 | n_water=770 | time (s): 0.700 (total time: 129.130) Add new water r_work=0.1227 r_free=0.1380 | n_water=983 | time (s): 4.930 (total time: 134.060) Refine new water occ: r_work=0.1196 r_free=0.1344 adp: r_work=0.1196 r_free=0.1344 occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1341 adp: r_work=0.1191 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1341 r_work=0.1191 r_free=0.1341 | n_water=983 | time (s): 189.380 (total time: 323.440) Filter (q & B) r_work=0.1196 r_free=0.1348 | n_water=900 | time (s): 5.440 (total time: 328.880) Filter (dist only) r_work=0.1196 r_free=0.1347 | n_water=899 | time (s): 113.800 (total time: 442.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.571913 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.795798 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 0.1353 0.0155 0.036 1.1 7.5 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.53 1.55 1.745 13.966 14.796 3.759 12.02 13.59 1.57 1.859 13.928 14.796 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 65.27 14.76 0.89 534 3269 Protein: 5.57 28.79 10.46 0.89 0 2902 Water: 5.86 65.27 28.64 N/A 534 365 Other: 13.85 22.80 18.32 N/A 0 2 Chain A: 5.62 51.02 12.32 N/A 0 1624 Chain B: 5.57 65.27 12.12 N/A 0 1645 Chain S: 5.86 59.59 30.30 N/A 534 0 Histogram: Values Number of atoms 5.57 - 11.54 2097 11.54 - 17.51 780 17.51 - 23.48 289 23.48 - 29.45 224 29.45 - 35.42 184 35.42 - 41.39 130 41.39 - 47.36 64 47.36 - 53.33 28 53.33 - 59.30 5 59.30 - 65.27 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1359 r_work=0.1202 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1360 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1359 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757697 | | target function (ml) not normalized (work): 703779.136277 | | target function (ml) not normalized (free): 14743.298404 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1359 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1482 n_refl.: 191131 remove outliers: r(all,work,free)=0.1415 0.1414 0.1482 n_refl.: 191131 overall B=-0.24 to atoms: r(all,work,free)=0.1379 0.1378 0.1461 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1203 0.1200 0.1358 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 0.3676 361.184 326.120 0.422 0.949 0.222 13.296-10.522 97.03 97 1 0.2395 481.576 461.500 0.709 0.950 0.150 10.503-8.327 97.80 175 3 0.2172 502.306 497.165 0.878 0.950 0.120 8.318-6.595 100.00 360 8 0.2203 375.843 369.820 0.908 0.950 0.095 6.588-5.215 100.00 711 7 0.1959 345.362 335.031 0.906 0.950 0.077 5.214-4.128 98.38 1367 28 0.1227 505.160 499.577 0.997 0.950 0.060 4.126-3.266 94.74 2603 46 0.1156 460.480 453.414 1.060 0.951 0.000 3.266-2.585 99.86 5447 97 0.1121 310.629 307.309 1.042 0.950 0.000 2.585-2.046 97.45 10613 204 0.0957 234.352 231.805 1.050 0.950 0.000 2.046-1.619 99.39 21536 464 0.0909 138.701 137.397 1.066 0.950 0.000 1.619-1.281 98.00 42464 925 0.0965 74.669 73.973 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.056 38.388 1.023 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0525 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1358 | n_water=899 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1200 r_free=0.1358 | n_water=898 | time (s): 112.000 (total time: 114.310) Filter (q & B) r_work=0.1201 r_free=0.1357 | n_water=888 | time (s): 4.460 (total time: 118.770) Compute maps r_work=0.1201 r_free=0.1357 | n_water=888 | time (s): 1.940 (total time: 120.710) Filter (map) r_work=0.1222 r_free=0.1370 | n_water=767 | time (s): 4.160 (total time: 124.870) Find peaks r_work=0.1222 r_free=0.1370 | n_water=767 | time (s): 0.570 (total time: 125.440) Add new water r_work=0.1231 r_free=0.1381 | n_water=990 | time (s): 3.990 (total time: 129.430) Refine new water occ: r_work=0.1198 r_free=0.1348 adp: r_work=0.1198 r_free=0.1348 occ: r_work=0.1196 r_free=0.1347 adp: r_work=0.1196 r_free=0.1347 occ: r_work=0.1194 r_free=0.1346 adp: r_work=0.1194 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1346 r_work=0.1194 r_free=0.1346 | n_water=990 | time (s): 258.950 (total time: 388.380) Filter (q & B) r_work=0.1199 r_free=0.1351 | n_water=904 | time (s): 4.500 (total time: 392.880) Filter (dist only) r_work=0.1199 r_free=0.1351 | n_water=903 | time (s): 113.730 (total time: 506.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.520404 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.298246 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1356 0.0154 0.037 1.1 6.3 0.0 0.3 0 0.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.56 1.54 1.709 13.646 14.298 3.760 12.05 13.60 1.56 1.752 13.630 14.298 3.759 Individual atomic B min max mean iso aniso Overall: 5.39 63.69 14.50 0.87 538 3269 Protein: 5.39 28.04 10.21 0.87 0 2902 Water: 5.75 63.69 28.29 N/A 538 365 Other: 13.68 21.96 17.82 N/A 0 2 Chain A: 5.44 50.63 12.03 N/A 0 1624 Chain B: 5.39 63.69 11.85 N/A 0 1645 Chain S: 5.75 59.47 30.06 N/A 538 0 Histogram: Values Number of atoms 5.39 - 11.22 2069 11.22 - 17.05 813 17.05 - 22.88 276 22.88 - 28.71 224 28.71 - 34.54 187 34.54 - 40.37 124 40.37 - 46.20 73 46.20 - 52.03 33 52.03 - 57.86 6 57.86 - 63.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1361 r_work=0.1205 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1361 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1357 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757910 | | target function (ml) not normalized (work): 703815.118384 | | target function (ml) not normalized (free): 14742.914401 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1357 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1375 0.1373 0.1472 n_refl.: 191130 remove outliers: r(all,work,free)=0.1375 0.1373 0.1472 n_refl.: 191130 overall B=0.08 to atoms: r(all,work,free)=0.1384 0.1383 0.1477 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1342 n_refl.: 191130 remove outliers: r(all,work,free)=0.1196 0.1193 0.1342 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 0.3698 361.184 330.114 0.401 0.993 0.205 13.296-10.522 97.03 97 1 0.2383 481.576 460.583 0.680 0.994 0.144 10.503-8.327 97.80 175 3 0.2177 502.306 496.408 0.842 0.994 0.120 8.318-6.595 100.00 360 8 0.2217 375.843 368.565 0.873 0.994 0.100 6.588-5.215 100.00 711 7 0.1960 345.362 334.509 0.872 0.994 0.083 5.214-4.128 98.38 1367 28 0.1235 505.160 499.315 0.960 0.994 0.029 4.126-3.266 94.74 2603 46 0.1164 460.480 452.591 1.022 0.994 0.000 3.266-2.585 99.86 5447 97 0.1125 310.629 307.048 1.007 0.994 0.000 2.585-2.046 97.45 10613 204 0.0963 234.352 231.682 1.017 0.993 0.000 2.046-1.619 99.39 21536 464 0.0910 138.701 137.303 1.037 0.992 0.000 1.619-1.281 98.00 42464 925 0.0946 74.669 74.020 1.032 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.056 38.346 1.009 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0651 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1342 | n_water=903 | time (s): 2.810 (total time: 2.810) Filter (dist) r_work=0.1193 r_free=0.1342 | n_water=902 | time (s): 110.890 (total time: 113.700) Filter (q & B) r_work=0.1193 r_free=0.1341 | n_water=893 | time (s): 5.130 (total time: 118.830) Compute maps r_work=0.1193 r_free=0.1341 | n_water=893 | time (s): 2.370 (total time: 121.200) Filter (map) r_work=0.1213 r_free=0.1360 | n_water=779 | time (s): 4.320 (total time: 125.520) Find peaks r_work=0.1213 r_free=0.1360 | n_water=779 | time (s): 0.720 (total time: 126.240) Add new water r_work=0.1221 r_free=0.1371 | n_water=991 | time (s): 4.010 (total time: 130.250) Refine new water occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1190 r_free=0.1338 occ: r_work=0.1188 r_free=0.1337 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1186 r_free=0.1337 adp: r_work=0.1186 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1337 r_work=0.1186 r_free=0.1337 | n_water=991 | time (s): 251.650 (total time: 381.900) Filter (q & B) r_work=0.1190 r_free=0.1343 | n_water=909 | time (s): 4.980 (total time: 386.880) Filter (dist only) r_work=0.1191 r_free=0.1341 | n_water=908 | time (s): 116.360 (total time: 503.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.511284 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.940321 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1346 0.0152 0.037 1.1 6.3 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.46 1.52 1.665 13.685 13.940 3.757 11.95 13.49 1.54 1.669 13.681 13.940 3.756 Individual atomic B min max mean iso aniso Overall: 5.47 63.29 14.58 0.86 543 3269 Protein: 5.47 27.94 10.30 0.86 0 2902 Water: 5.93 63.29 28.27 N/A 543 365 Other: 13.76 22.10 17.93 N/A 0 2 Chain A: 5.54 50.58 12.10 N/A 0 1624 Chain B: 5.47 63.29 11.92 N/A 0 1645 Chain S: 5.93 59.52 30.11 N/A 543 0 Histogram: Values Number of atoms 5.47 - 11.25 2056 11.25 - 17.03 830 17.03 - 22.82 278 22.82 - 28.60 218 28.60 - 34.38 181 34.38 - 40.16 132 40.16 - 45.94 78 45.94 - 51.73 31 51.73 - 57.51 4 57.51 - 63.29 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1349 r_work=0.1195 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1349 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1345 target_work(ml) = 3.755 | | 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= 0.1194 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755205 | | target function (ml) not normalized (work): 703308.634088 | | target function (ml) not normalized (free): 14735.119514 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1194 0.1345 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1475 n_refl.: 191130 remove outliers: r(all,work,free)=0.1391 0.1389 0.1475 n_refl.: 191130 overall B=0.02 to atoms: r(all,work,free)=0.1393 0.1392 0.1476 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1345 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1192 0.1345 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 0.3649 361.184 330.924 0.405 0.992 0.213 13.296-10.522 97.03 97 1 0.2382 481.576 460.878 0.679 0.993 0.146 10.503-8.327 97.80 175 3 0.2192 502.306 496.048 0.841 0.994 0.117 8.318-6.595 100.00 360 8 0.2207 375.843 369.061 0.870 0.993 0.089 6.588-5.215 100.00 711 7 0.1966 345.362 334.460 0.870 0.993 0.070 5.214-4.128 98.38 1367 28 0.1232 505.160 499.176 0.959 0.994 0.024 4.126-3.266 94.74 2603 46 0.1167 460.480 452.722 1.022 0.994 0.000 3.266-2.585 99.86 5447 97 0.1128 310.629 307.054 1.008 0.993 0.000 2.585-2.046 97.45 10613 204 0.0964 234.352 231.641 1.018 0.993 0.000 2.046-1.619 99.39 21536 464 0.0912 138.701 137.278 1.038 0.993 0.000 1.619-1.281 98.00 42464 925 0.0943 74.669 74.013 1.036 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.056 38.345 1.016 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0236 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1345 After: r_work=0.1193 r_free=0.1345 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1345 | n_water=908 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1193 r_free=0.1345 | n_water=907 | time (s): 114.090 (total time: 116.520) Filter (q & B) r_work=0.1194 r_free=0.1345 | n_water=896 | time (s): 4.700 (total time: 121.220) Compute maps r_work=0.1194 r_free=0.1345 | n_water=896 | time (s): 1.680 (total time: 122.900) Filter (map) r_work=0.1216 r_free=0.1368 | n_water=783 | time (s): 4.590 (total time: 127.490) Find peaks r_work=0.1216 r_free=0.1368 | n_water=783 | time (s): 0.550 (total time: 128.040) Add new water r_work=0.1222 r_free=0.1380 | n_water=1000 | time (s): 4.350 (total time: 132.390) Refine new water occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1342 occ: r_work=0.1188 r_free=0.1339 adp: r_work=0.1188 r_free=0.1340 occ: r_work=0.1187 r_free=0.1337 adp: r_work=0.1187 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1338 r_work=0.1187 r_free=0.1338 | n_water=1000 | time (s): 208.400 (total time: 340.790) Filter (q & B) r_work=0.1191 r_free=0.1344 | n_water=915 | time (s): 4.880 (total time: 345.670) Filter (dist only) r_work=0.1191 r_free=0.1343 | n_water=913 | time (s): 119.430 (total time: 465.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.531025 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.458246 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 0.1353 0.0154 0.038 1.2 9.5 0.0 0.3 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.53 1.54 1.672 13.706 14.458 3.761 11.98 13.55 1.57 1.672 13.707 14.458 3.759 Individual atomic B min max mean iso aniso Overall: 5.53 62.29 14.60 0.86 548 3269 Protein: 5.53 28.03 10.33 0.86 0 2902 Water: 6.00 62.29 28.14 N/A 548 365 Other: 13.81 22.04 17.92 N/A 0 2 Chain A: 5.64 50.37 12.10 N/A 0 1624 Chain B: 5.53 62.29 11.93 N/A 0 1645 Chain S: 6.00 59.47 30.02 N/A 548 0 Histogram: Values Number of atoms 5.53 - 11.21 2036 11.21 - 16.89 842 16.89 - 22.56 279 22.56 - 28.24 214 28.24 - 33.91 190 33.91 - 39.59 128 39.59 - 45.26 82 45.26 - 50.94 37 50.94 - 56.62 4 56.62 - 62.29 5 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1355 r_work=0.1198 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1352 target_work(ml) = 3.759 | | 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= 0.1197 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.759058 | | target function (ml) not normalized (work): 704030.251319 | | target function (ml) not normalized (free): 14752.773812 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1360 0.1405 5.6882 5.7416| | 2: 2.94 - 2.33 1.00 7339 128 0.1077 0.1392 5.0745 5.2022| | 3: 2.33 - 2.04 0.96 6939 150 0.0912 0.1150 4.6663 4.7265| | 4: 2.04 - 1.85 1.00 7170 155 0.0906 0.1065 4.4008 4.5939| | 5: 1.85 - 1.72 0.99 7113 159 0.0939 0.1023 4.1622 4.2656| | 6: 1.72 - 1.62 0.99 7102 142 0.0904 0.1090 3.9576 4.0858| | 7: 1.62 - 1.54 0.99 7104 148 0.0899 0.0964 3.812 3.9457| | 8: 1.54 - 1.47 0.96 6798 152 0.0904 0.1337 3.7158 3.9195| | 9: 1.47 - 1.41 0.98 6938 155 0.0935 0.1161 3.6347 3.7831| | 10: 1.41 - 1.36 0.99 7022 150 0.0983 0.1204 3.5662 3.6932| | 11: 1.36 - 1.32 0.99 6997 151 0.0999 0.1132 3.494 3.5945| | 12: 1.32 - 1.28 0.98 6975 149 0.1033 0.1118 3.463 3.5872| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1243 3.4421 3.5725| | 14: 1.25 - 1.22 0.98 7015 112 0.1102 0.1587 3.435 3.6891| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1230 3.4518 3.4853| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1531 3.4671 3.6521| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1224 3.4344 3.4418| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1732 3.4408 3.542| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1784 3.4226 3.6043| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1588 3.4124 3.4378| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2146 3.4193 3.5047| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1955 3.4139 3.4182| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2008 3.434 3.4858| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2263 3.4373 3.5165| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2520 3.4503 3.5256| | 26: 1.01 - 0.99 0.96 6767 158 0.2749 0.2856 3.4159 3.4233| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2786 3.4706 3.3957| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 11.26 1.00 0.96 10643.48| | 2: 2.94 - 2.33 7339 128 0.93 12.55 0.99 0.96 4970.59| | 3: 2.33 - 2.04 6939 150 0.96 7.79 1.01 0.95 1737.30| | 4: 2.04 - 1.85 7170 155 0.96 7.84 1.00 0.95 1037.39| | 5: 1.85 - 1.72 7113 159 0.96 8.29 1.00 0.96 654.87| | 6: 1.72 - 1.62 7102 142 0.96 8.21 1.00 0.96 456.74| | 7: 1.62 - 1.54 7104 148 0.96 8.32 1.01 0.97 348.07| | 8: 1.54 - 1.47 6798 152 0.96 8.52 1.01 0.97 290.09| | 9: 1.47 - 1.41 6938 155 0.96 8.77 1.00 0.98 241.82| | 10: 1.41 - 1.36 7022 150 0.96 9.19 1.00 0.97 210.70| | 11: 1.36 - 1.32 6997 151 0.96 9.14 0.99 0.96 180.06| | 12: 1.32 - 1.28 6975 149 0.96 9.10 0.98 0.95 163.60| | 13: 1.28 - 1.25 6907 166 0.96 9.61 1.00 0.96 160.62| | 14: 1.25 - 1.22 7015 112 0.95 10.78 1.01 0.96 165.04| | 15: 1.22 - 1.19 6956 137 0.95 11.31 1.01 0.98 167.74| | 16: 1.19 - 1.17 6604 132 0.95 11.45 1.00 0.96 160.73| | 17: 1.17 - 1.14 6940 135 0.94 12.29 1.01 0.96 154.61| | 18: 1.14 - 1.12 6875 142 0.94 12.85 1.01 0.95 149.40| | 19: 1.12 - 1.10 6948 106 0.93 14.25 1.00 0.95 153.07| | 20: 1.10 - 1.08 6884 147 0.92 15.32 1.00 0.94 151.84| | 21: 1.08 - 1.07 6852 152 0.91 16.68 1.00 0.93 154.04| | 22: 1.07 - 1.05 6836 135 0.89 18.32 1.00 0.93 155.58| | 23: 1.05 - 1.03 6827 159 0.87 20.51 1.00 0.93 165.38| | 24: 1.03 - 1.02 6784 133 0.85 23.20 1.00 0.93 180.02| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.90 182.72| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.99 0.89 176.86| | 27: 0.99 - 0.98 6647 131 0.82 26.24 0.99 0.88 160.64| |alpha: min = 0.88 max = 0.98 mean = 0.95| |beta: min = 149.40 max = 10643.48 mean = 903.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.95 mean = 13.37| |phase err.(test): min = 0.00 max = 89.11 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1352 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1405 0.1403 0.1489 n_refl.: 191130 remove outliers: r(all,work,free)=0.1405 0.1403 0.1489 n_refl.: 191130 overall B=-0.01 to atoms: r(all,work,free)=0.1403 0.1401 0.1488 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1350 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1350 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 0.3642 361.184 330.641 0.415 0.932 0.207 13.296-10.522 97.03 97 1 0.2406 481.576 460.418 0.699 0.933 0.134 10.503-8.327 97.80 175 3 0.2174 502.306 496.704 0.871 0.933 0.105 8.318-6.595 100.00 360 8 0.2186 375.843 369.711 0.900 0.933 0.084 6.588-5.215 100.00 711 7 0.1959 345.362 334.735 0.903 0.933 0.067 5.214-4.128 98.38 1367 28 0.1229 505.160 499.142 0.997 0.934 0.020 4.126-3.266 94.74 2603 46 0.1174 460.480 452.576 1.064 0.934 0.000 3.266-2.585 99.86 5447 97 0.1126 310.629 307.001 1.048 0.934 0.000 2.585-2.046 97.45 10613 204 0.0969 234.352 231.632 1.058 0.934 0.000 2.046-1.619 99.39 21536 464 0.0917 138.701 137.272 1.079 0.934 0.000 1.619-1.281 98.00 42464 925 0.0953 74.669 74.006 1.076 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.056 38.338 1.056 0.936 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0024 ================= 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 : 0.2036 0.1957 0.081 5.288 5.2 78.0 14.6 805 0.000 1_bss: 0.1799 0.1897 0.081 5.288 5.2 78.0 14.6 805 0.000 1_settarget: 0.1799 0.1897 0.081 5.288 5.2 78.0 14.6 805 0.000 1_nqh: 0.1799 0.1897 0.081 5.288 5.2 78.0 14.6 805 0.000 1_weight: 0.1799 0.1897 0.081 5.288 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1267 0.1481 0.034 1.162 5.2 78.0 14.6 805 0.141 1_adp: 0.1295 0.1546 0.034 1.162 5.2 73.0 14.9 805 0.141 1_regHadp: 0.1294 0.1540 0.034 1.162 5.2 73.0 14.9 805 0.141 1_occ: 0.1279 0.1526 0.034 1.162 5.2 73.0 14.9 805 0.141 2_bss: 0.1271 0.1516 0.034 1.162 5.3 73.2 15.1 805 0.141 2_settarget: 0.1271 0.1516 0.034 1.162 5.3 73.2 15.1 805 0.141 2_updatecdl: 0.1271 0.1516 0.034 1.179 5.3 73.2 15.1 805 0.141 2_nqh: 0.1271 0.1516 0.034 1.179 5.3 73.2 15.1 805 0.141 2_sol: 0.1265 0.1485 0.034 1.179 5.3 73.2 16.1 894 n/a 2_weight: 0.1265 0.1485 0.034 1.179 5.3 73.2 16.1 894 n/a 2_xyzrec: 0.1251 0.1512 0.038 1.134 5.3 73.2 16.1 894 n/a 2_adp: 0.1235 0.1505 0.038 1.134 5.4 68.3 16.2 894 n/a 2_regHadp: 0.1235 0.1507 0.038 1.134 5.4 68.3 16.2 894 n/a 2_occ: 0.1229 0.1502 0.038 1.134 5.4 68.3 16.2 894 n/a 3_bss: 0.1236 0.1506 0.038 1.134 5.3 68.3 16.2 894 n/a 3_settarget: 0.1236 0.1506 0.038 1.134 5.3 68.3 16.2 894 n/a 3_updatecdl: 0.1236 0.1506 0.038 1.142 5.3 68.3 16.2 894 n/a 3_nqh: 0.1236 0.1506 0.038 1.142 5.3 68.3 16.2 894 n/a 3_sol: 0.1239 0.1499 0.038 1.142 5.3 68.3 15.3 872 n/a 3_weight: 0.1239 0.1499 0.038 1.142 5.3 68.3 15.3 872 n/a 3_xyzrec: 0.1226 0.1428 0.034 1.096 5.3 68.3 15.3 872 n/a 3_adp: 0.1217 0.1388 0.034 1.096 5.5 67.8 15.2 872 n/a 3_regHadp: 0.1218 0.1389 0.034 1.096 5.5 67.8 15.2 872 n/a 3_occ: 0.1211 0.1390 0.034 1.096 5.5 67.8 15.2 872 n/a 4_bss: 0.1207 0.1383 0.034 1.096 5.5 67.8 15.1 872 n/a 4_settarget: 0.1207 0.1383 0.034 1.096 5.5 67.8 15.1 872 n/a 4_updatecdl: 0.1207 0.1383 0.034 1.093 5.5 67.8 15.1 872 n/a 4_nqh: 0.1207 0.1383 0.034 1.093 5.5 67.8 15.1 872 n/a 4_sol: 0.1208 0.1368 0.034 1.093 5.5 67.8 15.0 875 n/a 4_weight: 0.1208 0.1368 0.034 1.093 5.5 67.8 15.0 875 n/a 4_xyzrec: 0.1207 0.1364 0.035 1.124 5.5 67.8 15.0 875 n/a 4_adp: 0.1200 0.1361 0.035 1.124 5.5 67.3 14.9 875 n/a 4_regHadp: 0.1200 0.1362 0.035 1.124 5.5 67.3 14.9 875 n/a 4_occ: 0.1198 0.1354 0.035 1.124 5.5 67.3 14.9 875 n/a 5_bss: 0.1195 0.1348 0.035 1.124 5.5 67.3 14.9 875 n/a 5_settarget: 0.1195 0.1348 0.035 1.124 5.5 67.3 14.9 875 n/a 5_updatecdl: 0.1195 0.1348 0.035 1.124 5.5 67.3 14.9 875 n/a 5_nqh: 0.1195 0.1348 0.035 1.124 5.5 67.3 14.9 875 n/a 5_sol: 0.1193 0.1342 0.035 1.124 5.5 67.3 14.9 886 n/a 5_weight: 0.1193 0.1342 0.035 1.124 5.5 67.3 14.9 886 n/a 5_xyzrec: 0.1195 0.1349 0.035 1.126 5.5 67.3 14.9 886 n/a 5_adp: 0.1199 0.1351 0.035 1.126 5.6 67.2 14.8 886 n/a 5_regHadp: 0.1199 0.1352 0.035 1.126 5.6 67.2 14.8 886 n/a 5_occ: 0.1198 0.1353 0.035 1.126 5.6 67.2 14.8 886 n/a 6_bss: 0.1193 0.1348 0.035 1.126 5.5 67.1 14.8 886 n/a 6_settarget: 0.1193 0.1348 0.035 1.126 5.5 67.1 14.8 886 n/a 6_updatecdl: 0.1193 0.1348 0.035 1.126 5.5 67.1 14.8 886 n/a 6_nqh: 0.1193 0.1348 0.035 1.126 5.5 67.1 14.8 886 n/a 6_sol: 0.1190 0.1341 0.035 1.126 5.5 67.1 14.9 895 n/a 6_weight: 0.1190 0.1341 0.035 1.126 5.5 67.1 14.9 895 n/a 6_xyzrec: 0.1194 0.1348 0.036 1.117 5.5 67.1 14.9 895 n/a 6_adp: 0.1196 0.1349 0.036 1.117 5.5 66.6 14.8 895 n/a 6_regHadp: 0.1196 0.1350 0.036 1.117 5.5 66.6 14.8 895 n/a 6_occ: 0.1194 0.1348 0.036 1.117 5.5 66.6 14.8 895 n/a 7_bss: 0.1197 0.1352 0.036 1.117 5.5 66.5 14.8 895 n/a 7_settarget: 0.1197 0.1352 0.036 1.117 5.5 66.5 14.8 895 n/a 7_updatecdl: 0.1197 0.1352 0.036 1.117 5.5 66.5 14.8 895 n/a 7_nqh: 0.1197 0.1352 0.036 1.117 5.5 66.5 14.8 895 n/a 7_sol: 0.1196 0.1347 0.036 1.117 5.5 66.5 14.8 899 n/a 7_weight: 0.1196 0.1347 0.036 1.117 5.5 66.5 14.8 899 n/a 7_xyzrec: 0.1199 0.1353 0.036 1.125 5.5 66.5 14.8 899 n/a 7_adp: 0.1202 0.1359 0.036 1.125 5.6 65.3 14.8 899 n/a 7_regHadp: 0.1202 0.1360 0.036 1.125 5.6 65.3 14.8 899 n/a 7_occ: 0.1200 0.1359 0.036 1.125 5.6 65.3 14.8 899 n/a 8_bss: 0.1200 0.1358 0.036 1.125 5.3 65.0 14.5 899 n/a 8_settarget: 0.1200 0.1358 0.036 1.125 5.3 65.0 14.5 899 n/a 8_updatecdl: 0.1200 0.1358 0.036 1.125 5.3 65.0 14.5 899 n/a 8_nqh: 0.1200 0.1358 0.036 1.125 5.3 65.0 14.5 899 n/a 8_sol: 0.1199 0.1351 0.036 1.125 5.3 65.0 14.5 903 n/a 8_weight: 0.1199 0.1351 0.036 1.125 5.3 65.0 14.5 903 n/a 8_xyzrec: 0.1203 0.1356 0.037 1.116 5.3 65.0 14.5 903 n/a 8_adp: 0.1205 0.1361 0.037 1.116 5.4 63.7 14.5 903 n/a 8_regHadp: 0.1205 0.1361 0.037 1.116 5.4 63.7 14.5 903 n/a 8_occ: 0.1203 0.1357 0.037 1.116 5.4 63.7 14.5 903 n/a 9_bss: 0.1193 0.1342 0.037 1.116 5.5 63.8 14.6 903 n/a 9_settarget: 0.1193 0.1342 0.037 1.116 5.5 63.8 14.6 903 n/a 9_updatecdl: 0.1193 0.1342 0.037 1.116 5.5 63.8 14.6 903 n/a 9_nqh: 0.1193 0.1342 0.037 1.116 5.5 63.8 14.6 903 n/a 9_sol: 0.1191 0.1341 0.037 1.116 5.5 63.8 14.6 908 n/a 9_weight: 0.1191 0.1341 0.037 1.116 5.5 63.8 14.6 908 n/a 9_xyzrec: 0.1194 0.1346 0.037 1.107 5.5 63.8 14.6 908 n/a 9_adp: 0.1195 0.1349 0.037 1.107 5.5 63.3 14.6 908 n/a 9_regHadp: 0.1195 0.1349 0.037 1.107 5.5 63.3 14.6 908 n/a 9_occ: 0.1194 0.1345 0.037 1.107 5.5 63.3 14.6 908 n/a 10_bss: 0.1192 0.1345 0.037 1.107 5.5 63.3 14.6 908 n/a 10_settarget: 0.1192 0.1345 0.037 1.107 5.5 63.3 14.6 908 n/a 10_updatecdl: 0.1192 0.1345 0.037 1.107 5.5 63.3 14.6 908 n/a 10_setrh: 0.1193 0.1345 0.037 1.107 5.5 63.3 14.6 908 n/a 10_nqh: 0.1193 0.1345 0.037 1.107 5.5 63.3 14.6 908 n/a 10_sol: 0.1191 0.1343 0.037 1.107 5.5 63.3 14.6 913 n/a 10_weight: 0.1191 0.1343 0.037 1.107 5.5 63.3 14.6 913 n/a 10_xyzrec: 0.1199 0.1353 0.038 1.187 5.5 63.3 14.6 913 n/a 10_adp: 0.1198 0.1355 0.038 1.187 5.5 62.3 14.6 913 n/a 10_regHadp: 0.1198 0.1355 0.038 1.187 5.5 62.3 14.6 913 n/a 10_occ: 0.1197 0.1352 0.038 1.187 5.5 62.3 14.6 913 n/a end: 0.1196 0.1350 0.038 1.187 5.5 62.3 14.6 913 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5983534_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5983534_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.0900 Refinement macro-cycles (run) : 11903.1500 Write final files (write_after_run_outputs) : 165.7900 Total : 12075.0300 Total CPU time: 3.36 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:38:23 PST -0800 (1736735903.47 s) Start R-work = 0.1799, R-free = 0.1897 Final R-work = 0.1196, R-free = 0.1350 =============================================================================== Job complete usr+sys time: 12379.34 seconds wall clock time: 207 minutes 15.82 seconds (12435.82 seconds total)