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_4119138.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4119138.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4119138.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.71, per 1000 atoms: 0.40 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: 2.690 distance_ideal: 2.720 ideal - model: 0.030 slack: 0.000 delta_slack: 0.030 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: 2.802 distance_ideal: 2.710 ideal - model: -0.092 slack: 0.000 delta_slack: -0.092 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: 0.73 Conformation dependent library (CDL) restraints added in 115.7 milliseconds Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.73 - 0.98: 338 0.98 - 1.23: 2776 1.23 - 1.47: 1571 1.47 - 1.72: 1231 1.72 - 1.97: 18 Bond restraints: 5934 Sorted by residual: bond pdb=" CA GLY B 174 " pdb=" C GLY B 174 " ideal model delta sigma weight residual 1.516 1.756 -0.240 1.05e-02 9.07e+03 5.22e+02 bond pdb=" C VAL B 26 " pdb=" O VAL B 26 " ideal model delta sigma weight residual 1.237 1.489 -0.253 1.12e-02 7.97e+03 5.08e+02 bond pdb=" NH2 ARG A 27 " pdb="HH22 ARG A 27 " ideal model delta sigma weight residual 0.860 1.270 -0.410 2.00e-02 2.50e+03 4.20e+02 bond pdb=" N CYS A 81 " pdb=" CA CYS A 81 " ideal model delta sigma weight residual 1.459 1.215 0.244 1.21e-02 6.83e+03 4.08e+02 bond pdb=" NZ LYS A 77 " pdb=" HZ1 LYS A 77 " ideal model delta sigma weight residual 0.890 1.284 -0.394 2.00e-02 2.50e+03 3.88e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 5377 3.84 - 7.68: 3447 7.68 - 11.52: 1525 11.52 - 15.36: 407 15.36 - 19.20: 54 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.38 132.26 -12.88 6.80e-01 2.16e+00 3.59e+02 angle pdb=" NE ARG A 97 " pdb=" CZ ARG A 97 " pdb=" NH2 ARG A 97 " ideal model delta sigma weight residual 119.20 106.19 13.01 9.00e-01 1.23e+00 2.09e+02 angle pdb=" N VAL B 26 " pdb=" CA VAL B 26 " pdb=" C VAL B 26 " ideal model delta sigma weight residual 110.53 97.16 13.37 9.40e-01 1.13e+00 2.02e+02 angle pdb=" CA GLU A 80 " pdb=" C GLU A 80 " pdb=" O GLU A 80 " ideal model delta sigma weight residual 120.90 135.65 -14.75 1.07e+00 8.73e-01 1.90e+02 angle pdb=" CA GLU B 176 " pdb=" C GLU B 176 " pdb=" O GLU B 176 " ideal model delta sigma weight residual 120.82 134.59 -13.77 1.05e+00 9.07e-01 1.72e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.70: 1842 16.70 - 33.38: 133 33.38 - 50.07: 49 50.07 - 66.75: 21 66.75 - 83.43: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -143.86 -36.14 0 5.00e+00 4.00e-02 5.23e+01 dihedral pdb=" CA LEU B 72 " pdb=" C LEU B 72 " pdb=" N PRO B 73 " pdb=" CA PRO B 73 " ideal model delta harmonic sigma weight residual 180.00 154.01 25.99 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -157.53 -22.47 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.232: 217 0.232 - 0.465: 172 0.465 - 0.697: 69 0.697 - 0.930: 30 0.930 - 1.162: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA LYS A 131 " pdb=" N LYS A 131 " pdb=" C LYS A 131 " pdb=" CB LYS A 131 " both_signs ideal model delta sigma weight residual False 2.51 3.67 -1.16 2.00e-01 2.50e+01 3.38e+01 chirality pdb=" CA ILE A 162 " pdb=" N ILE A 162 " pdb=" C ILE A 162 " pdb=" CB ILE A 162 " both_signs ideal model delta sigma weight residual False 2.43 3.59 -1.16 2.00e-01 2.50e+01 3.35e+01 chirality pdb=" CB ILE B 45 " pdb=" CA ILE B 45 " pdb=" CG1 ILE B 45 " pdb=" CG2 ILE B 45 " both_signs ideal model delta sigma weight residual False 2.64 1.69 0.96 2.00e-01 2.50e+01 2.28e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.113 2.00e-02 2.50e+03 8.00e-02 1.92e+02 pdb=" CG PHE B 164 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.105 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.046 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.122 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.130 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.029 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.032 2.00e-02 2.50e+03 6.31e-02 1.19e+02 pdb=" CG PHE A 164 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.031 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.097 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 149 " 0.042 9.50e-02 1.11e+02 7.04e-02 1.07e+02 pdb=" NE ARG A 149 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 149 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 149 " 0.071 2.00e-02 2.50e+03 pdb=" NH2 ARG A 149 " -0.139 2.00e-02 2.50e+03 pdb="HH11 ARG A 149 " -0.074 2.00e-02 2.50e+03 pdb="HH12 ARG A 149 " 0.056 2.00e-02 2.50e+03 pdb="HH21 ARG A 149 " 0.057 2.00e-02 2.50e+03 pdb="HH22 ARG A 149 " 0.023 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.63: 32 1.63 - 2.37: 2581 2.37 - 3.11: 22341 3.11 - 3.86: 33060 3.86 - 4.60: 52243 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110257 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.887 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.923 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.026 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.037 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.222 2.620 ... (remaining 110252 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_4119138_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= 0.2029 r_free= 0.2038 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.300988 | | target function (ml) not normalized (work): 805631.031271 | | target function (ml) not normalized (free): 16646.206143 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2128 0.1921 6.6797 6.2977| | 2: 2.94 - 2.33 1.00 7339 128 0.1626 0.1721 5.5449 5.616| | 3: 2.33 - 2.04 0.96 6939 150 0.1607 0.1672 5.1396 5.1675| | 4: 2.04 - 1.85 1.00 7170 155 0.1763 0.1717 4.9659 5.1167| | 5: 1.85 - 1.72 0.99 7113 159 0.1908 0.1838 4.8003 4.8442| | 6: 1.72 - 1.62 0.99 7102 142 0.1974 0.2185 4.6772 4.7352| | 7: 1.62 - 1.54 0.99 7104 148 0.1999 0.1708 4.5589 4.5416| | 8: 1.54 - 1.47 0.96 6798 152 0.2075 0.2192 4.4754 4.5416| | 9: 1.47 - 1.41 0.98 6938 155 0.2071 0.2166 4.3873 4.4601| | 10: 1.41 - 1.36 0.99 7022 150 0.2099 0.2321 4.2977 4.4368| | 11: 1.36 - 1.32 0.99 6997 151 0.2106 0.2106 4.2304 4.2643| | 12: 1.32 - 1.28 0.98 6976 149 0.2080 0.1927 4.181 4.1906| | 13: 1.28 - 1.25 0.98 6907 166 0.2007 0.2136 4.1231 4.1899| | 14: 1.25 - 1.22 0.98 7015 113 0.2065 0.2435 4.0753 4.2856| | 15: 1.22 - 1.19 0.98 6957 137 0.2120 0.2290 4.0473 4.1375| | 16: 1.19 - 1.17 0.93 6604 132 0.2120 0.2112 4.0171 4.0216| | 17: 1.17 - 1.14 0.98 6941 135 0.2167 0.2004 3.9558 3.9849| | 18: 1.14 - 1.12 0.98 6875 142 0.2201 0.2459 3.9233 3.9967| | 19: 1.12 - 1.10 0.97 6949 106 0.2254 0.2677 3.8801 4.0482| | 20: 1.10 - 1.08 0.97 6884 147 0.2324 0.2285 3.835 3.8616| | 21: 1.08 - 1.07 0.97 6852 152 0.2426 0.2856 3.7954 3.856| | 22: 1.07 - 1.05 0.97 6838 135 0.2535 0.2417 3.7467 3.7511| | 23: 1.05 - 1.03 0.97 6829 159 0.2714 0.2617 3.7337 3.8516| | 24: 1.03 - 1.02 0.96 6785 133 0.2897 0.2874 3.7086 3.7944| | 25: 1.02 - 1.01 0.93 6552 130 0.3098 0.2884 3.6722 3.722| | 26: 1.01 - 0.99 0.96 6767 158 0.3221 0.3355 3.6293 3.6612| | 27: 0.99 - 0.98 0.94 6648 131 0.3425 0.3553 3.6327 3.6444| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.53 0.91 0.97 35456.28| | 2: 2.94 - 2.33 7339 128 0.85 21.35 1.08 1.02 15261.88| | 3: 2.33 - 2.04 6939 150 0.93 12.92 1.10 1.05 4379.93| | 4: 2.04 - 1.85 7170 155 0.92 14.08 1.11 1.07 2934.58| | 5: 1.85 - 1.72 7113 159 0.91 15.89 1.12 1.08 2190.97| | 6: 1.72 - 1.62 7102 142 0.90 16.91 1.11 1.09 1694.40| | 7: 1.62 - 1.54 7104 148 0.89 17.37 1.11 1.08 1332.44| | 8: 1.54 - 1.47 6798 152 0.88 18.49 1.11 1.06 1144.48| | 9: 1.47 - 1.41 6938 155 0.88 19.19 1.10 1.06 999.07| | 10: 1.41 - 1.36 7022 150 0.87 20.59 1.10 1.04 886.08| | 11: 1.36 - 1.32 6997 151 0.87 20.29 1.08 1.04 748.68| | 12: 1.32 - 1.28 6976 149 0.87 19.99 1.07 1.03 653.07| | 13: 1.28 - 1.25 6907 166 0.87 20.15 1.06 1.04 618.12| | 14: 1.25 - 1.22 7015 113 0.86 21.29 1.08 1.04 603.68| | 15: 1.22 - 1.19 6957 137 0.86 21.65 1.08 1.04 576.75| | 16: 1.19 - 1.17 6604 132 0.87 20.78 1.07 1.03 513.44| | 17: 1.17 - 1.14 6941 135 0.86 21.64 1.08 1.02 463.04| | 18: 1.14 - 1.12 6875 142 0.85 22.01 1.08 0.99 428.24| | 19: 1.12 - 1.10 6949 106 0.84 23.61 1.07 0.98 420.88| | 20: 1.10 - 1.08 6884 147 0.83 24.24 1.07 0.95 383.90| | 21: 1.08 - 1.07 6852 152 0.82 25.19 1.06 0.95 359.90| | 22: 1.07 - 1.05 6838 135 0.81 26.36 1.05 0.97 344.92| | 23: 1.05 - 1.03 6829 159 0.79 28.29 1.05 0.97 347.75| | 24: 1.03 - 1.02 6785 133 0.77 30.43 1.06 0.97 351.00| | 25: 1.02 - 1.01 6552 130 0.75 32.34 1.04 0.93 336.47| | 26: 1.01 - 0.99 6767 158 0.72 34.57 1.02 0.90 327.22| | 27: 0.99 - 0.98 6648 131 0.70 36.07 1.03 0.86 321.18| |alpha: min = 0.86 max = 1.09 mean = 1.01| |beta: min = 321.18 max = 35456.28 mean = 2871.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.95 mean = 22.36| |phase err.(test): min = 0.00 max = 89.84 mean = 22.33| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.253 2950 Z= 5.546 Angle : 5.211 17.760 4018 Z= 3.701 Chirality : 0.374 1.162 492 Planarity : 0.031 0.087 512 Dihedral : 13.029 83.434 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.60 % Rotamer: Outliers : 1.29 % Allowed : 4.84 % Favored : 93.87 % Cbeta Deviations : 27.25 % 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: -2.08 (0.38), residues: 386 helix: -2.27 (0.32), residues: 142 sheet: -0.82 (0.54), residues: 86 loop : -0.53 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.020 ARG B 49 TYR 0.119 0.037 TYR B 195 PHE 0.118 0.036 PHE B 164 TRP 0.119 0.030 TRP A 139 HIS 0.082 0.029 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= 0.2029 r_free= 0.2038 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.300988 | | target function (ml) not normalized (work): 805631.031271 | | target function (ml) not normalized (free): 16646.206143 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2028 0.2029 0.2038 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2028 0.2029 0.2038 n_refl.: 191155 remove outliers: r(all,work,free)=0.2028 0.2029 0.2038 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2028 0.2029 0.2038 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1800 0.1797 0.1961 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1795 0.1961 n_refl.: 191141 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4199 400.535 296.841 0.434 0.913 0.299 13.296-10.522 100.00 100 1 0.2572 534.497 521.541 0.783 0.914 0.248 10.503-8.327 99.45 178 3 0.2557 565.118 555.336 0.973 0.914 0.223 8.318-6.595 100.00 360 8 0.2467 414.736 403.433 0.974 0.914 0.179 6.588-5.215 100.00 711 7 0.2241 381.101 366.024 0.957 0.914 0.147 5.214-4.128 98.38 1367 28 0.1478 557.435 549.939 1.077 0.914 0.080 4.126-3.266 94.74 2603 46 0.1331 508.132 499.948 1.145 0.914 0.028 3.266-2.585 99.86 5447 97 0.1441 342.774 337.745 1.117 0.914 0.010 2.585-2.046 97.45 10613 204 0.1394 258.603 254.413 1.122 0.913 0.000 2.046-1.619 99.39 21536 464 0.1620 153.054 149.748 1.143 0.912 0.000 1.619-1.281 98.00 42464 925 0.1913 82.395 80.219 1.129 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2316 44.203 41.687 1.111 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0012 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1795 r_free=0.1961 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 r_work=0.1798 r_free=0.1962 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.472176 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 579.277400 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 0.1271 0.1503 0.0233 0.038 1.2 11.2 0.0 0.0 0 11.236 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.03 2.33 1.117 13.111 579.277 0.019 12.98 15.73 2.75 1.256 13.344 579.277 0.018 Individual atomic B min max mean iso aniso Overall: 5.19 73.04 15.02 1.41 435 3274 Protein: 5.19 40.33 11.01 1.41 0 2902 Water: 6.24 73.04 29.48 N/A 435 370 Other: 16.10 30.11 23.10 N/A 0 2 Chain A: 5.35 59.82 13.06 N/A 0 1626 Chain B: 5.19 73.04 12.78 N/A 0 1648 Chain S: 11.86 65.03 30.86 N/A 435 0 Histogram: Values Number of atoms 5.19 - 11.97 2169 11.97 - 18.76 637 18.76 - 25.54 314 25.54 - 32.33 258 32.33 - 39.12 163 39.12 - 45.90 104 45.90 - 52.69 41 52.69 - 59.47 19 59.47 - 66.26 3 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1573 r_work=0.1298 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1568 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1557 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1557 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015689 | | target function (ls_wunit_k1) not normalized (work): 2938.455963 | | target function (ls_wunit_k1) not normalized (free): 117.247398 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1557 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1472 0.1469 0.1636 n_refl.: 191141 remove outliers: r(all,work,free)=0.1472 0.1469 0.1636 n_refl.: 191141 overall B=0.16 to atoms: r(all,work,free)=0.1495 0.1493 0.1646 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1548 n_refl.: 191141 remove outliers: r(all,work,free)=0.1280 0.1275 0.1547 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3594 402.814 377.445 0.463 1.000 0.269 13.296-10.522 100.00 100 1 0.2145 534.497 525.821 0.715 1.002 0.240 10.503-8.327 99.45 178 3 0.1762 565.118 561.520 0.856 1.002 0.203 8.318-6.595 100.00 360 8 0.1705 414.736 412.222 0.877 1.001 0.160 6.588-5.215 100.00 711 7 0.1534 381.101 373.656 0.855 1.002 0.150 5.214-4.128 98.38 1367 28 0.0904 557.435 555.081 0.941 1.002 0.049 4.126-3.266 94.74 2603 46 0.0834 508.132 504.237 1.005 1.003 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.294 0.987 1.002 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.298 0.998 1.003 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.379 1.015 1.003 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.416 1.007 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.172 0.985 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0376 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 r_work=0.1276 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1547 | n_water=805 | time (s): 3.120 (total time: 3.120) Filter (dist) r_work=0.1281 r_free=0.1552 | n_water=794 | time (s): 108.620 (total time: 111.740) Filter (q & B) r_work=0.1281 r_free=0.1552 | n_water=790 | time (s): 4.790 (total time: 116.530) Compute maps r_work=0.1281 r_free=0.1552 | n_water=790 | time (s): 2.350 (total time: 118.880) Filter (map) r_work=0.1309 r_free=0.1538 | n_water=649 | time (s): 5.250 (total time: 124.130) Find peaks r_work=0.1309 r_free=0.1538 | n_water=649 | time (s): 0.710 (total time: 124.840) Add new water r_work=0.1332 r_free=0.1564 | n_water=962 | time (s): 5.200 (total time: 130.040) Refine new water occ: r_work=0.1286 r_free=0.1518 adp: r_work=0.1274 r_free=0.1516 occ: r_work=0.1276 r_free=0.1512 adp: r_work=0.1270 r_free=0.1514 occ: r_work=0.1271 r_free=0.1509 adp: r_work=0.1268 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1512 r_work=0.1268 r_free=0.1512 | n_water=962 | time (s): 91.510 (total time: 221.550) Filter (q & B) r_work=0.1272 r_free=0.1509 | n_water=890 | time (s): 4.300 (total time: 225.850) Filter (dist only) r_work=0.1272 r_free=0.1508 | n_water=888 | time (s): 114.530 (total time: 340.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.976717 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 589.834276 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 0.1257 0.1535 0.0277 0.041 1.1 17.2 0.0 0.3 0 11.488 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.35 2.77 2.048 15.245 589.834 0.015 12.34 15.22 2.88 2.427 15.298 589.834 0.014 Individual atomic B min max mean iso aniso Overall: 5.41 70.18 16.43 1.21 520 3272 Protein: 5.41 40.57 10.98 1.21 0 2902 Water: 6.57 70.18 34.25 N/A 520 368 Other: 16.43 32.79 24.61 N/A 0 2 Chain A: 5.51 55.61 13.01 N/A 0 1624 Chain B: 5.41 68.21 12.83 N/A 0 1648 Chain S: 10.39 70.18 38.58 N/A 520 0 Histogram: Values Number of atoms 5.41 - 11.89 2114 11.89 - 18.36 681 18.36 - 24.84 259 24.84 - 31.32 211 31.32 - 37.79 171 37.79 - 44.27 159 44.27 - 50.75 98 50.75 - 57.22 54 57.22 - 63.70 36 63.70 - 70.18 9 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1522 r_work=0.1234 r_free=0.1523 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1523 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1518 target_work(ls_wunit_k1) = 0.014 | | 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.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1518 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013520 | | target function (ls_wunit_k1) not normalized (work): 2532.211344 | | target function (ls_wunit_k1) not normalized (free): 101.096323 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1228 0.1518 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1436 0.1432 0.1616 n_refl.: 191139 remove outliers: r(all,work,free)=0.1436 0.1432 0.1616 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1429 0.1614 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1234 0.1525 n_refl.: 191139 remove outliers: r(all,work,free)=0.1240 0.1234 0.1525 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3315 402.814 376.842 0.485 0.963 0.261 13.296-10.522 100.00 100 1 0.1942 534.497 527.801 0.766 0.964 0.224 10.503-8.327 99.45 178 3 0.1417 565.118 567.230 0.919 0.964 0.190 8.318-6.595 100.00 360 8 0.1571 414.736 414.600 0.939 0.963 0.170 6.588-5.215 100.00 711 7 0.1343 381.101 376.587 0.914 0.963 0.160 5.214-4.128 98.38 1367 28 0.0826 557.435 556.098 0.995 0.963 0.084 4.126-3.266 94.74 2603 46 0.0765 508.132 505.561 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0860 342.774 341.373 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.715 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.606 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.354 1.072 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.217 1.058 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0500 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1525 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1525 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1525 | n_water=888 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1236 r_free=0.1524 | n_water=883 | time (s): 116.800 (total time: 119.100) Filter (q & B) r_work=0.1236 r_free=0.1524 | n_water=882 | time (s): 5.580 (total time: 124.680) Compute maps r_work=0.1236 r_free=0.1524 | n_water=882 | time (s): 2.250 (total time: 126.930) Filter (map) r_work=0.1274 r_free=0.1523 | n_water=693 | time (s): 5.570 (total time: 132.500) Find peaks r_work=0.1274 r_free=0.1523 | n_water=693 | time (s): 0.630 (total time: 133.130) Add new water r_work=0.1299 r_free=0.1565 | n_water=1019 | time (s): 4.600 (total time: 137.730) Refine new water occ: r_work=0.1253 r_free=0.1523 adp: r_work=0.1253 r_free=0.1522 occ: r_work=0.1249 r_free=0.1519 adp: r_work=0.1249 r_free=0.1519 occ: r_work=0.1246 r_free=0.1517 adp: r_work=0.1245 r_free=0.1516 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1516 r_work=0.1245 r_free=0.1516 | n_water=1019 | time (s): 359.620 (total time: 497.350) Filter (q & B) r_work=0.1251 r_free=0.1523 | n_water=875 | time (s): 4.600 (total time: 501.950) Filter (dist only) r_work=0.1251 r_free=0.1523 | n_water=874 | time (s): 112.550 (total time: 614.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.736555 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.768888 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1240 0.1444 0.0204 0.035 1.1 8.7 0.0 0.0 0 0.868 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.44 2.04 1.934 14.585 16.769 3.941 12.34 14.00 1.66 2.221 14.494 16.769 3.897 Individual atomic B min max mean iso aniso Overall: 5.53 67.85 15.27 1.07 508 3270 Protein: 5.53 36.95 10.75 1.07 0 2902 Water: 6.70 67.85 30.29 N/A 508 366 Other: 14.06 28.94 21.50 N/A 0 2 Chain A: 5.54 54.80 12.78 N/A 0 1624 Chain B: 5.53 67.85 12.53 N/A 0 1646 Chain S: 12.62 62.09 32.12 N/A 508 0 Histogram: Values Number of atoms 5.53 - 11.77 2131 11.77 - 18.00 688 18.00 - 24.23 297 24.23 - 30.46 231 30.46 - 36.69 180 36.69 - 42.93 132 42.93 - 49.16 80 49.16 - 55.39 27 55.39 - 61.62 10 61.62 - 67.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1401 r_work=0.1235 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1401 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1393 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891655 | | target function (ml) not normalized (work): 728899.286752 | | target function (ml) not normalized (free): 15234.491461 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1393 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1443 0.1442 0.1489 n_refl.: 191139 remove outliers: r(all,work,free)=0.1443 0.1442 0.1489 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1436 0.1486 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1225 0.1390 n_refl.: 191139 remove outliers: r(all,work,free)=0.1228 0.1225 0.1390 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 94.06 92 3 0.3917 398.008 362.788 0.432 0.945 0.265 13.296-10.522 100.00 100 1 0.2479 534.497 518.123 0.717 0.947 0.226 10.503-8.327 99.45 178 3 0.2092 565.118 561.260 0.879 0.947 0.203 8.318-6.595 100.00 360 8 0.2089 414.736 410.509 0.896 0.946 0.130 6.588-5.215 100.00 711 7 0.1821 381.101 371.033 0.888 0.946 0.130 5.214-4.128 98.38 1367 28 0.1170 557.435 552.264 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1094 508.132 501.290 1.033 0.947 0.019 3.266-2.585 99.86 5447 97 0.1088 342.774 339.050 1.021 0.946 0.005 2.585-2.046 97.45 10613 204 0.0967 258.603 255.774 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0976 153.054 151.404 1.056 0.944 0.000 1.619-1.281 98.00 42464 925 0.1049 82.395 81.495 1.053 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.319 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0935 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1390 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1390 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1390 | n_water=874 | time (s): 3.380 (total time: 3.380) Filter (dist) r_work=0.1225 r_free=0.1388 | n_water=872 | time (s): 110.590 (total time: 113.970) Filter (q & B) r_work=0.1226 r_free=0.1383 | n_water=860 | time (s): 4.330 (total time: 118.300) Compute maps r_work=0.1226 r_free=0.1383 | n_water=860 | time (s): 1.830 (total time: 120.130) Filter (map) r_work=0.1251 r_free=0.1385 | n_water=701 | time (s): 5.260 (total time: 125.390) Find peaks r_work=0.1251 r_free=0.1385 | n_water=701 | time (s): 0.570 (total time: 125.960) Add new water r_work=0.1269 r_free=0.1408 | n_water=959 | time (s): 4.400 (total time: 130.360) Refine new water occ: r_work=0.1215 r_free=0.1363 adp: r_work=0.1208 r_free=0.1359 occ: r_work=0.1204 r_free=0.1359 adp: r_work=0.1204 r_free=0.1359 occ: r_work=0.1202 r_free=0.1359 adp: r_work=0.1202 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1359 r_work=0.1202 r_free=0.1359 | n_water=959 | time (s): 354.670 (total time: 485.030) Filter (q & B) r_work=0.1206 r_free=0.1362 | n_water=884 | time (s): 5.560 (total time: 490.590) Filter (dist only) r_work=0.1206 r_free=0.1361 | n_water=883 | time (s): 112.230 (total time: 602.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570869 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.173445 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1361 0.0156 0.033 1.1 6.6 0.0 0.0 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.61 1.56 1.836 14.254 16.173 3.874 11.97 13.58 1.61 1.927 14.218 16.173 3.865 Individual atomic B min max mean iso aniso Overall: 5.53 67.42 15.05 1.02 517 3270 Protein: 5.53 33.92 10.68 1.02 0 2902 Water: 5.91 67.42 29.42 N/A 517 366 Other: 13.97 27.85 20.91 N/A 0 2 Chain A: 5.55 53.85 12.66 N/A 0 1624 Chain B: 5.53 67.42 12.45 N/A 0 1646 Chain S: 5.91 62.17 30.86 N/A 517 0 Histogram: Values Number of atoms 5.53 - 11.72 2121 11.72 - 17.90 724 17.90 - 24.09 288 24.09 - 30.28 250 30.28 - 36.47 178 36.47 - 42.66 128 42.66 - 48.85 65 48.85 - 55.04 24 55.04 - 61.23 7 61.23 - 67.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1358 r_work=0.1197 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1359 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1359 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862856 | | target function (ml) not normalized (work): 723501.320244 | | target function (ml) not normalized (free): 15135.770585 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1421 0.1420 0.1470 n_refl.: 191138 remove outliers: r(all,work,free)=0.1421 0.1420 0.1470 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1414 0.1413 0.1466 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191138 remove outliers: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3863 360.086 323.409 0.413 0.947 0.247 13.296-10.522 99.01 99 1 0.2533 477.862 461.306 0.701 0.948 0.191 10.503-8.327 98.35 176 3 0.2125 502.360 502.697 0.878 0.948 0.163 8.318-6.595 100.00 360 8 0.2107 375.220 370.283 0.890 0.948 0.114 6.588-5.215 100.00 711 7 0.1834 344.790 335.780 0.885 0.948 0.093 5.214-4.128 98.38 1367 28 0.1185 504.323 499.759 0.971 0.948 0.070 4.126-3.266 94.74 2603 46 0.1114 459.718 453.305 1.033 0.948 0.009 3.266-2.585 99.86 5447 97 0.1081 310.115 306.784 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0930 233.964 231.433 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0914 138.471 137.113 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0984 74.545 73.801 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1663 39.990 38.303 1.037 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1126 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1358 | n_water=883 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1193 r_free=0.1358 | n_water=883 | time (s): 109.480 (total time: 112.090) Filter (q & B) r_work=0.1193 r_free=0.1358 | n_water=871 | time (s): 5.150 (total time: 117.240) Compute maps r_work=0.1193 r_free=0.1358 | n_water=871 | time (s): 1.710 (total time: 118.950) Filter (map) r_work=0.1219 r_free=0.1359 | n_water=730 | time (s): 5.400 (total time: 124.350) Find peaks r_work=0.1219 r_free=0.1359 | n_water=730 | time (s): 0.640 (total time: 124.990) Add new water r_work=0.1232 r_free=0.1379 | n_water=971 | time (s): 3.910 (total time: 128.900) Refine new water occ: r_work=0.1192 r_free=0.1347 adp: r_work=0.1192 r_free=0.1347 occ: r_work=0.1190 r_free=0.1348 adp: r_work=0.1190 r_free=0.1347 occ: r_work=0.1188 r_free=0.1348 adp: r_work=0.1188 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1347 r_work=0.1188 r_free=0.1347 | n_water=971 | time (s): 293.050 (total time: 421.950) Filter (q & B) r_work=0.1192 r_free=0.1356 | n_water=894 | time (s): 4.280 (total time: 426.230) Filter (dist only) r_work=0.1192 r_free=0.1356 | n_water=892 | time (s): 114.470 (total time: 540.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.556554 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.971469 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 0.1360 0.0165 0.035 1.1 8.2 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.60 1.65 1.801 14.172 14.971 3.763 11.98 13.62 1.64 1.831 14.159 14.971 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 67.25 15.02 0.98 527 3269 Protein: 5.57 33.30 10.64 0.98 0 2902 Water: 5.86 67.25 29.28 N/A 527 365 Other: 13.79 27.41 20.60 N/A 0 2 Chain A: 5.62 53.50 12.60 N/A 0 1624 Chain B: 5.57 67.25 12.38 N/A 0 1645 Chain S: 5.86 62.17 30.74 N/A 527 0 Histogram: Values Number of atoms 5.57 - 11.74 2139 11.74 - 17.91 716 17.91 - 24.08 293 24.08 - 30.24 237 30.24 - 36.41 187 36.41 - 42.58 131 42.58 - 48.74 62 48.74 - 54.91 22 54.91 - 61.08 7 61.08 - 67.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1362 r_work=0.1198 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1363 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1368 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.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760797 | | target function (ml) not normalized (work): 704374.758737 | | target function (ml) not normalized (free): 14750.315841 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1368 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1423 0.1422 0.1496 n_refl.: 191135 remove outliers: r(all,work,free)=0.1423 0.1422 0.1496 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1416 0.1414 0.1491 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1366 n_refl.: 191135 remove outliers: r(all,work,free)=0.1197 0.1194 0.1366 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 92.08 90 3 0.3659 360.585 309.545 0.401 0.947 0.241 13.296-10.522 97.03 97 1 0.2475 477.729 448.844 0.699 0.949 0.209 10.503-8.327 98.35 176 3 0.2087 502.360 496.924 0.863 0.949 0.164 8.318-6.595 100.00 360 8 0.2103 375.220 370.932 0.886 0.949 0.108 6.588-5.215 100.00 711 7 0.1837 344.790 336.319 0.885 0.949 0.087 5.214-4.128 98.38 1367 28 0.1173 504.323 499.955 0.974 0.949 0.070 4.126-3.266 94.74 2603 46 0.1134 459.718 453.240 1.033 0.949 0.005 3.266-2.585 99.86 5447 97 0.1099 310.115 306.941 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0941 233.964 231.574 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0915 138.471 137.198 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0978 74.545 73.853 1.054 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1656 39.990 38.331 1.041 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1223 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1366 | n_water=892 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1194 r_free=0.1366 | n_water=892 | time (s): 106.460 (total time: 109.230) Filter (q & B) r_work=0.1194 r_free=0.1365 | n_water=879 | time (s): 5.980 (total time: 115.210) Compute maps r_work=0.1194 r_free=0.1365 | n_water=879 | time (s): 2.270 (total time: 117.480) Filter (map) r_work=0.1216 r_free=0.1351 | n_water=756 | time (s): 4.790 (total time: 122.270) Find peaks r_work=0.1216 r_free=0.1351 | n_water=756 | time (s): 0.870 (total time: 123.140) Add new water r_work=0.1227 r_free=0.1364 | n_water=960 | time (s): 5.190 (total time: 128.330) Refine new water occ: r_work=0.1193 r_free=0.1346 adp: r_work=0.1193 r_free=0.1346 occ: r_work=0.1191 r_free=0.1346 adp: r_work=0.1191 r_free=0.1346 occ: r_work=0.1189 r_free=0.1348 adp: r_work=0.1189 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1347 r_work=0.1189 r_free=0.1347 | n_water=960 | time (s): 312.230 (total time: 440.560) Filter (q & B) r_work=0.1192 r_free=0.1351 | n_water=900 | time (s): 5.930 (total time: 446.490) Filter (dist only) r_work=0.1193 r_free=0.1352 | n_water=897 | time (s): 117.670 (total time: 564.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565682 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.132389 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1365 0.0169 0.035 1.1 7.2 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.65 1.69 1.781 14.108 15.132 3.761 11.99 13.67 1.67 1.945 14.054 15.132 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 66.18 14.89 0.92 532 3269 Protein: 5.57 30.07 10.51 0.92 0 2902 Water: 5.90 66.18 29.04 N/A 532 365 Other: 13.85 24.47 19.16 N/A 0 2 Chain A: 5.62 52.82 12.44 N/A 0 1624 Chain B: 5.57 66.18 12.23 N/A 0 1645 Chain S: 5.90 62.33 30.58 N/A 532 0 Histogram: Values Number of atoms 5.57 - 11.63 2117 11.63 - 17.69 765 17.69 - 23.75 281 23.75 - 29.82 220 29.82 - 35.88 185 35.88 - 41.94 128 41.94 - 48.00 74 48.00 - 54.06 23 54.06 - 60.12 6 60.12 - 66.18 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1367 r_work=0.1200 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1367 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1369 target_work(ml) = 3.758 | | 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= 0.1197 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757607 | | target function (ml) not normalized (work): 703762.169909 | | target function (ml) not normalized (free): 14741.637523 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1369 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1399 0.1397 0.1505 n_refl.: 191131 remove outliers: r(all,work,free)=0.1399 0.1397 0.1505 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1365 0.1363 0.1479 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1367 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1367 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3707 360.585 332.404 0.421 0.952 0.213 13.296-10.522 97.03 97 1 0.2461 477.729 458.770 0.712 0.953 0.166 10.503-8.327 98.35 176 3 0.2167 502.360 496.503 0.881 0.954 0.143 8.318-6.595 100.00 360 8 0.2144 375.220 370.795 0.905 0.953 0.110 6.588-5.215 100.00 711 7 0.1872 344.790 335.658 0.904 0.953 0.094 5.214-4.128 98.38 1367 28 0.1202 504.323 499.785 0.995 0.954 0.092 4.126-3.266 94.74 2603 46 0.1147 459.718 452.853 1.054 0.954 0.005 3.266-2.585 99.86 5447 97 0.1108 310.115 306.757 1.038 0.953 0.000 2.585-2.046 97.45 10613 204 0.0950 233.964 231.449 1.046 0.953 0.000 2.046-1.619 99.39 21536 464 0.0913 138.471 137.152 1.064 0.952 0.000 1.619-1.281 98.00 42464 925 0.0971 74.545 73.839 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1649 39.990 38.329 1.025 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0473 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1368 | n_water=897 | time (s): 2.840 (total time: 2.840) Filter (dist) r_work=0.1196 r_free=0.1368 | n_water=897 | time (s): 108.160 (total time: 111.000) Filter (q & B) r_work=0.1197 r_free=0.1368 | n_water=888 | time (s): 5.470 (total time: 116.470) Compute maps r_work=0.1197 r_free=0.1368 | n_water=888 | time (s): 1.970 (total time: 118.440) Filter (map) r_work=0.1217 r_free=0.1364 | n_water=769 | time (s): 4.850 (total time: 123.290) Find peaks r_work=0.1217 r_free=0.1364 | n_water=769 | time (s): 0.590 (total time: 123.880) Add new water r_work=0.1229 r_free=0.1379 | n_water=981 | time (s): 3.960 (total time: 127.840) Refine new water occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1194 r_free=0.1350 occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1192 r_free=0.1350 occ: r_work=0.1191 r_free=0.1351 adp: r_work=0.1191 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1351 r_work=0.1191 r_free=0.1351 | n_water=981 | time (s): 336.370 (total time: 464.210) Filter (q & B) r_work=0.1195 r_free=0.1360 | n_water=908 | time (s): 4.840 (total time: 469.050) Filter (dist only) r_work=0.1195 r_free=0.1360 | n_water=907 | time (s): 117.660 (total time: 586.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.618435 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.559062 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 0.1368 0.0169 0.037 1.1 6.8 0.0 0.3 0 0.809 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.68 1.69 1.731 13.745 14.559 3.759 12.01 13.71 1.70 1.791 13.724 14.559 3.757 Individual atomic B min max mean iso aniso Overall: 5.40 65.01 14.58 0.89 542 3269 Protein: 5.40 28.82 10.27 0.89 0 2902 Water: 5.77 65.01 28.37 N/A 542 365 Other: 13.67 22.54 18.11 N/A 0 2 Chain A: 5.45 52.22 12.16 N/A 0 1624 Chain B: 5.40 65.01 11.96 N/A 0 1645 Chain S: 5.77 62.32 29.80 N/A 542 0 Histogram: Values Number of atoms 5.40 - 11.36 2101 11.36 - 17.32 785 17.32 - 23.28 294 23.28 - 29.24 217 29.24 - 35.20 184 35.20 - 41.16 123 41.16 - 47.12 72 47.12 - 53.09 27 53.09 - 59.05 6 59.05 - 65.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1371 r_work=0.1201 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1371 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1371 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756558 | | target function (ml) not normalized (work): 703565.741241 | | target function (ml) not normalized (free): 14742.425996 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1199 0.1371 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1373 0.1371 0.1489 n_refl.: 191131 remove outliers: r(all,work,free)=0.1373 0.1371 0.1489 n_refl.: 191131 overall B=0.05 to atoms: r(all,work,free)=0.1380 0.1378 0.1494 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1360 n_refl.: 191131 remove outliers: r(all,work,free)=0.1194 0.1190 0.1360 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 92.08 90 3 0.3722 360.585 331.778 0.411 0.974 0.207 13.296-10.522 97.03 97 1 0.2471 477.729 458.631 0.696 0.975 0.154 10.503-8.327 98.35 176 3 0.2212 502.360 494.950 0.865 0.976 0.125 8.318-6.595 100.00 360 8 0.2158 375.220 370.181 0.890 0.976 0.105 6.588-5.215 100.00 711 7 0.1887 344.790 335.440 0.891 0.976 0.091 5.214-4.128 98.38 1367 28 0.1225 504.323 498.944 0.980 0.977 0.046 4.126-3.266 94.74 2603 46 0.1161 459.718 452.175 1.040 0.978 0.005 3.266-2.585 99.86 5447 97 0.1119 310.115 306.473 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0958 233.964 231.289 1.032 0.980 0.000 2.046-1.619 99.39 21536 464 0.0907 138.471 137.082 1.048 0.983 0.000 1.619-1.281 98.00 42464 925 0.0949 74.545 73.880 1.037 0.987 0.000 1.281-0.980 96.53 101826 2055 0.1628 39.990 38.302 1.003 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0587 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1360 | n_water=907 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1190 r_free=0.1361 | n_water=905 | time (s): 118.010 (total time: 121.200) Filter (q & B) r_work=0.1191 r_free=0.1362 | n_water=896 | time (s): 5.870 (total time: 127.070) Compute maps r_work=0.1191 r_free=0.1362 | n_water=896 | time (s): 2.530 (total time: 129.600) Filter (map) r_work=0.1214 r_free=0.1356 | n_water=766 | time (s): 4.630 (total time: 134.230) Find peaks r_work=0.1214 r_free=0.1356 | n_water=766 | time (s): 0.560 (total time: 134.790) Add new water r_work=0.1223 r_free=0.1369 | n_water=987 | time (s): 3.800 (total time: 138.590) Refine new water occ: r_work=0.1188 r_free=0.1345 adp: r_work=0.1188 r_free=0.1344 occ: r_work=0.1186 r_free=0.1345 adp: r_work=0.1186 r_free=0.1345 occ: r_work=0.1186 r_free=0.1345 adp: r_work=0.1186 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1345 r_work=0.1186 r_free=0.1345 | n_water=987 | time (s): 183.000 (total time: 321.590) Filter (q & B) r_work=0.1191 r_free=0.1354 | n_water=893 | time (s): 4.370 (total time: 325.960) Filter (dist only) r_work=0.1191 r_free=0.1353 | n_water=892 | time (s): 116.320 (total time: 442.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.523169 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.962944 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 0.1357 0.0162 0.037 1.1 4.8 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.57 1.62 1.684 13.660 13.963 3.756 11.96 13.58 1.61 1.722 13.657 13.963 3.754 Individual atomic B min max mean iso aniso Overall: 5.50 63.97 14.50 0.87 527 3269 Protein: 5.50 28.14 10.32 0.87 0 2902 Water: 5.86 63.97 28.08 N/A 527 365 Other: 13.80 22.10 17.95 N/A 0 2 Chain A: 5.54 51.81 12.17 N/A 0 1624 Chain B: 5.50 63.97 11.98 N/A 0 1645 Chain S: 5.86 62.62 29.51 N/A 527 0 Histogram: Values Number of atoms 5.50 - 11.34 2074 11.34 - 17.19 810 17.19 - 23.04 304 23.04 - 28.89 210 28.89 - 34.73 166 34.73 - 40.58 115 40.58 - 46.43 76 46.43 - 52.27 32 52.27 - 58.12 7 58.12 - 63.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1358 r_work=0.1197 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1358 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754104 | | target function (ml) not normalized (work): 703106.087262 | | target function (ml) not normalized (free): 14723.831859 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1392 0.1390 0.1498 n_refl.: 191131 remove outliers: r(all,work,free)=0.1392 0.1390 0.1498 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1394 0.1392 0.1499 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1193 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 0.3645 360.585 331.852 0.414 0.974 0.215 13.296-10.522 97.03 97 1 0.2451 477.729 460.216 0.689 0.975 0.149 10.503-8.327 98.35 176 3 0.2277 502.360 493.794 0.860 0.976 0.117 8.315-6.595 100.00 359 8 0.2177 374.275 370.293 0.887 0.976 0.100 6.588-5.215 100.00 711 7 0.1916 344.790 335.069 0.887 0.976 0.087 5.214-4.128 98.38 1367 28 0.1248 504.323 498.301 0.980 0.977 0.080 4.126-3.266 94.74 2603 46 0.1166 459.718 452.207 1.041 0.978 0.000 3.266-2.585 99.86 5447 97 0.1126 310.115 306.440 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0963 233.964 231.268 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0908 138.471 137.099 1.050 0.984 0.000 1.619-1.281 98.00 42464 925 0.0948 74.545 73.884 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1627 39.990 38.287 1.009 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0177 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1358 | n_water=892 | time (s): 2.380 (total time: 2.380) Filter (dist) r_work=0.1194 r_free=0.1358 | n_water=891 | time (s): 117.260 (total time: 119.640) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=885 | time (s): 4.970 (total time: 124.610) Compute maps r_work=0.1194 r_free=0.1357 | n_water=885 | time (s): 1.790 (total time: 126.400) Filter (map) r_work=0.1214 r_free=0.1353 | n_water=773 | time (s): 4.420 (total time: 130.820) Find peaks r_work=0.1214 r_free=0.1353 | n_water=773 | time (s): 0.720 (total time: 131.540) Add new water r_work=0.1224 r_free=0.1373 | n_water=995 | time (s): 3.900 (total time: 135.440) Refine new water occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1187 r_free=0.1342 adp: r_work=0.1187 r_free=0.1342 occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1185 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1342 r_work=0.1185 r_free=0.1342 | n_water=995 | time (s): 281.170 (total time: 416.610) Filter (q & B) r_work=0.1190 r_free=0.1352 | n_water=913 | time (s): 4.310 (total time: 420.920) Filter (dist only) r_work=0.1191 r_free=0.1352 | n_water=912 | time (s): 120.120 (total time: 541.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.539196 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.736910 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1356 0.0163 0.038 1.1 5.6 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.56 1.63 1.679 13.746 13.737 3.754 11.94 13.61 1.67 1.679 13.743 13.737 3.753 Individual atomic B min max mean iso aniso Overall: 5.52 63.57 14.65 0.86 548 3268 Protein: 5.52 28.08 10.35 0.86 0 2902 Water: 5.97 63.57 28.32 N/A 548 364 Other: 13.80 22.15 17.97 N/A 0 2 Chain A: 5.61 51.67 12.17 N/A 0 1624 Chain B: 5.52 63.57 11.98 N/A 0 1644 Chain S: 5.97 62.72 30.01 N/A 548 0 Histogram: Values Number of atoms 5.52 - 11.32 2063 11.32 - 17.13 824 17.13 - 22.93 278 22.93 - 28.74 222 28.74 - 34.55 183 34.55 - 40.35 126 40.35 - 46.16 77 46.16 - 51.96 32 51.96 - 57.77 9 57.77 - 63.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1361 r_work=0.1194 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1361 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1366 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753102 | | target function (ml) not normalized (work): 702914.648087 | | target function (ml) not normalized (free): 14728.345151 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1192 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1509 n_refl.: 191130 remove outliers: r(all,work,free)=0.1397 0.1395 0.1509 n_refl.: 191130 overall B=-0.00 to atoms: r(all,work,free)=0.1397 0.1395 0.1508 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1191 0.1362 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1191 0.1362 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3707 360.585 329.650 0.396 0.974 0.187 13.296-10.522 97.03 97 1 0.2450 477.729 459.638 0.682 0.976 0.126 10.503-8.327 98.35 176 3 0.2246 502.360 494.214 0.861 0.977 0.098 8.315-6.595 100.00 359 8 0.2131 374.275 370.018 0.884 0.977 0.088 6.588-5.215 100.00 711 7 0.1914 344.790 335.207 0.888 0.977 0.080 5.214-4.128 98.38 1367 28 0.1236 504.323 498.639 0.977 0.978 0.044 4.126-3.266 94.74 2603 46 0.1167 459.718 452.366 1.041 0.979 0.005 3.266-2.585 99.86 5447 97 0.1129 310.115 306.450 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0964 233.964 231.284 1.032 0.983 0.000 2.046-1.619 99.39 21536 464 0.0906 138.471 137.098 1.049 0.987 0.000 1.619-1.281 98.00 42464 925 0.0944 74.545 73.892 1.040 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1625 39.990 38.285 1.009 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0135 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1362 After: r_work=0.1192 r_free=0.1363 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1363 | n_water=912 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1192 r_free=0.1363 | n_water=911 | time (s): 122.910 (total time: 125.190) Filter (q & B) r_work=0.1193 r_free=0.1363 | n_water=899 | time (s): 4.230 (total time: 129.420) Compute maps r_work=0.1193 r_free=0.1363 | n_water=899 | time (s): 1.810 (total time: 131.230) Filter (map) r_work=0.1215 r_free=0.1350 | n_water=786 | time (s): 5.210 (total time: 136.440) Find peaks r_work=0.1215 r_free=0.1350 | n_water=786 | time (s): 0.540 (total time: 136.980) Add new water r_work=0.1222 r_free=0.1362 | n_water=993 | time (s): 4.220 (total time: 141.200) 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=0.1339 adp: r_work=0.1188 r_free=0.1339 occ: r_work=0.1186 r_free=0.1340 adp: r_work=0.1186 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1341 r_work=0.1186 r_free=0.1341 | n_water=993 | time (s): 240.470 (total time: 381.670) Filter (q & B) r_work=0.1191 r_free=0.1349 | n_water=912 | time (s): 5.120 (total time: 386.790) Filter (dist only) r_work=0.1191 r_free=0.1349 | n_water=911 | time (s): 121.270 (total time: 508.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.546927 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.235019 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1358 0.0162 0.038 1.2 10.4 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.58 1.62 1.678 13.756 13.235 3.756 11.97 13.60 1.63 1.677 13.755 13.235 3.756 Individual atomic B min max mean iso aniso Overall: 5.56 63.26 14.66 0.85 547 3268 Protein: 5.56 27.98 10.36 0.85 0 2902 Water: 5.99 63.26 28.35 N/A 547 364 Other: 13.83 22.11 17.97 N/A 0 2 Chain A: 5.64 51.57 12.15 N/A 0 1624 Chain B: 5.56 63.26 11.97 N/A 0 1644 Chain S: 5.99 62.77 30.16 N/A 547 0 Histogram: Values Number of atoms 5.56 - 11.33 2062 11.33 - 17.10 836 17.10 - 22.87 263 22.87 - 28.64 222 28.64 - 34.41 184 34.41 - 40.18 121 40.18 - 45.95 80 45.95 - 51.72 35 51.72 - 57.49 10 57.49 - 63.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1360 r_work=0.1197 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1360 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1362 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756302 | | target function (ml) not normalized (work): 703514.123876 | | target function (ml) not normalized (free): 14732.602495 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1358 0.1453 5.6867 5.7368| | 2: 2.94 - 2.33 1.00 7339 128 0.1078 0.1423 5.077 5.198| | 3: 2.33 - 2.04 0.96 6939 150 0.0908 0.1159 4.6577 4.7367| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1067 4.3941 4.5769| | 5: 1.85 - 1.72 0.99 7113 159 0.0936 0.0996 4.1527 4.2417| | 6: 1.72 - 1.62 0.99 7102 142 0.0899 0.1083 3.9495 4.0809| | 7: 1.62 - 1.54 0.99 7104 148 0.0900 0.0967 3.8065 3.9361| | 8: 1.54 - 1.47 0.96 6798 152 0.0899 0.1335 3.7069 3.9121| | 9: 1.47 - 1.41 0.98 6938 155 0.0932 0.1131 3.6274 3.7542| | 10: 1.41 - 1.36 0.99 7022 150 0.0985 0.1204 3.5631 3.6848| | 11: 1.36 - 1.32 0.99 6997 151 0.1000 0.1144 3.4911 3.5947| | 12: 1.32 - 1.28 0.98 6975 149 0.1041 0.1130 3.4648 3.5836| | 13: 1.28 - 1.25 0.98 6907 166 0.1050 0.1255 3.4426 3.5725| | 14: 1.25 - 1.22 0.98 7015 112 0.1110 0.1582 3.4358 3.6794| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1258 3.451 3.4958| | 16: 1.19 - 1.17 0.93 6604 132 0.1256 0.1550 3.4674 3.6558| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1218 3.4337 3.4376| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1725 3.4391 3.5369| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1760 3.4201 3.5883| | 20: 1.10 - 1.08 0.97 6884 147 0.1587 0.1583 3.4107 3.4367| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2138 3.4184 3.5037| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1951 3.4129 3.4161| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2009 3.4328 3.4845| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2266 3.4353 3.5132| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2519 3.4487 3.5212| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2853 3.415 3.4186| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2796 3.4676 3.396| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.36 1.00 0.95 10772.00| | 2: 2.94 - 2.33 7339 128 0.93 12.61 0.99 0.95 5005.88| | 3: 2.33 - 2.04 6939 150 0.96 7.69 1.01 0.95 1719.50| | 4: 2.04 - 1.85 7170 155 0.96 7.70 1.00 0.95 1010.03| | 5: 1.85 - 1.72 7113 159 0.96 8.07 1.00 0.96 634.91| | 6: 1.72 - 1.62 7102 142 0.96 8.07 1.00 0.96 445.52| | 7: 1.62 - 1.54 7104 148 0.96 8.19 1.01 0.97 339.91| | 8: 1.54 - 1.47 6798 152 0.96 8.36 1.01 0.97 282.40| | 9: 1.47 - 1.41 6938 155 0.96 8.54 1.00 0.98 233.33| | 10: 1.41 - 1.36 7022 150 0.96 9.02 1.00 0.97 205.25| | 11: 1.36 - 1.32 6997 151 0.96 9.03 0.99 0.96 176.92| | 12: 1.32 - 1.28 6975 149 0.96 9.08 0.98 0.95 162.48| | 13: 1.28 - 1.25 6907 166 0.96 9.63 1.01 0.96 159.66| | 14: 1.25 - 1.22 7015 112 0.95 10.78 1.01 0.96 164.51| | 15: 1.22 - 1.19 6956 137 0.94 11.32 1.01 0.97 167.78| | 16: 1.19 - 1.17 6604 132 0.95 11.49 1.01 0.96 160.86| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.96 154.13| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.94 148.06| | 19: 1.12 - 1.10 6948 106 0.93 14.17 1.00 0.94 151.36| | 20: 1.10 - 1.08 6884 147 0.92 15.26 1.00 0.94 150.62| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.93 153.25| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.93 155.08| | 23: 1.05 - 1.03 6827 159 0.87 20.50 0.99 0.92 164.67| | 24: 1.03 - 1.02 6784 133 0.85 23.14 0.99 0.93 178.78| | 25: 1.02 - 1.01 6552 130 0.83 25.11 0.98 0.90 181.47| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.88 176.15| | 27: 0.99 - 0.98 6647 131 0.82 26.35 0.99 0.87 161.13| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.06 max = 10772.00 mean = 905.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.31| |phase err.(test): min = 0.00 max = 86.42 mean = 13.51| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1509 n_refl.: 191130 remove outliers: r(all,work,free)=0.1407 0.1405 0.1509 n_refl.: 191130 overall B=-0.06 to atoms: r(all,work,free)=0.1397 0.1395 0.1503 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1360 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1360 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3609 356.009 330.229 0.371 0.994 0.172 13.296-10.522 96.04 96 1 0.2398 480.016 457.495 0.649 0.995 0.119 10.503-8.327 98.35 176 3 0.2212 502.360 495.098 0.824 0.996 0.100 8.315-6.595 100.00 359 8 0.2113 374.275 369.768 0.846 0.996 0.085 6.588-5.215 100.00 711 7 0.1910 344.790 335.119 0.848 0.996 0.080 5.214-4.128 98.38 1367 28 0.1240 504.323 498.611 0.935 0.997 0.039 4.126-3.266 94.74 2603 46 0.1170 459.718 452.321 0.996 0.999 0.000 3.266-2.585 99.86 5447 97 0.1125 310.115 306.629 0.980 1.000 0.000 2.585-2.046 97.45 10613 204 0.0969 233.964 231.295 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0913 138.471 137.097 1.001 1.007 0.000 1.619-1.281 98.00 42464 925 0.0953 74.545 73.886 0.991 1.015 0.000 1.281-0.980 96.53 101826 2055 0.1628 39.990 38.276 0.959 1.028 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0132 ================= 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 : 0.2029 0.2038 0.082 5.211 5.2 78.0 14.6 805 0.000 1_bss: 0.1795 0.1961 0.082 5.211 5.2 78.0 14.6 805 0.000 1_settarget: 0.1795 0.1961 0.082 5.211 5.2 78.0 14.6 805 0.000 1_nqh: 0.1798 0.1962 0.082 5.211 5.2 78.0 14.6 805 0.002 1_weight: 0.1798 0.1962 0.082 5.211 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1271 0.1503 0.038 1.161 5.2 78.0 14.6 805 0.157 1_adp: 0.1298 0.1573 0.038 1.161 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1298 0.1568 0.038 1.161 5.2 73.0 15.0 805 0.157 1_occ: 0.1283 0.1557 0.038 1.161 5.2 73.0 15.0 805 0.157 2_bss: 0.1275 0.1547 0.038 1.161 5.4 73.2 15.2 805 0.157 2_settarget: 0.1275 0.1547 0.038 1.161 5.4 73.2 15.2 805 0.157 2_updatecdl: 0.1275 0.1547 0.038 1.169 5.4 73.2 15.2 805 0.157 2_nqh: 0.1276 0.1547 0.038 1.169 5.4 73.2 15.2 805 0.156 2_sol: 0.1272 0.1508 0.038 1.169 5.4 73.2 16.3 888 n/a 2_weight: 0.1272 0.1508 0.038 1.169 5.4 73.2 16.3 888 n/a 2_xyzrec: 0.1257 0.1535 0.041 1.139 5.4 73.2 16.3 888 n/a 2_adp: 0.1234 0.1522 0.041 1.139 5.4 70.2 16.4 888 n/a 2_regHadp: 0.1234 0.1523 0.041 1.139 5.4 70.2 16.4 888 n/a 2_occ: 0.1228 0.1518 0.041 1.139 5.4 70.2 16.4 888 n/a 3_bss: 0.1234 0.1525 0.041 1.139 5.4 70.2 16.4 888 n/a 3_settarget: 0.1234 0.1525 0.041 1.139 5.4 70.2 16.4 888 n/a 3_updatecdl: 0.1234 0.1525 0.041 1.141 5.4 70.2 16.4 888 n/a 3_nqh: 0.1234 0.1525 0.041 1.141 5.4 70.2 16.4 888 n/a 3_sol: 0.1251 0.1523 0.041 1.141 5.4 68.2 15.4 874 n/a 3_weight: 0.1251 0.1523 0.041 1.141 5.4 68.2 15.4 874 n/a 3_xyzrec: 0.1240 0.1444 0.035 1.102 5.4 68.2 15.4 874 n/a 3_adp: 0.1234 0.1401 0.035 1.102 5.5 67.9 15.3 874 n/a 3_regHadp: 0.1235 0.1401 0.035 1.102 5.5 67.9 15.3 874 n/a 3_occ: 0.1229 0.1393 0.035 1.102 5.5 67.9 15.3 874 n/a 4_bss: 0.1225 0.1390 0.035 1.102 5.5 67.8 15.2 874 n/a 4_settarget: 0.1225 0.1390 0.035 1.102 5.5 67.8 15.2 874 n/a 4_updatecdl: 0.1225 0.1390 0.035 1.107 5.5 67.8 15.2 874 n/a 4_nqh: 0.1225 0.1390 0.035 1.107 5.5 67.8 15.2 874 n/a 4_sol: 0.1206 0.1361 0.035 1.107 5.5 67.8 15.1 883 n/a 4_weight: 0.1206 0.1361 0.035 1.107 5.5 67.8 15.1 883 n/a 4_xyzrec: 0.1205 0.1361 0.033 1.114 5.5 67.8 15.1 883 n/a 4_adp: 0.1197 0.1358 0.033 1.114 5.5 67.4 15.1 883 n/a 4_regHadp: 0.1197 0.1359 0.033 1.114 5.5 67.4 15.1 883 n/a 4_occ: 0.1195 0.1359 0.033 1.114 5.5 67.4 15.1 883 n/a 5_bss: 0.1193 0.1358 0.033 1.114 5.5 67.4 15.0 883 n/a 5_settarget: 0.1193 0.1358 0.033 1.114 5.5 67.4 15.0 883 n/a 5_updatecdl: 0.1193 0.1358 0.033 1.114 5.5 67.4 15.0 883 n/a 5_nqh: 0.1193 0.1358 0.033 1.114 5.5 67.4 15.0 883 n/a 5_sol: 0.1192 0.1356 0.033 1.114 5.5 67.4 15.0 892 n/a 5_weight: 0.1192 0.1356 0.033 1.114 5.5 67.4 15.0 892 n/a 5_xyzrec: 0.1195 0.1360 0.035 1.118 5.5 67.4 15.0 892 n/a 5_adp: 0.1198 0.1362 0.035 1.118 5.6 67.2 15.0 892 n/a 5_regHadp: 0.1198 0.1363 0.035 1.118 5.6 67.2 15.0 892 n/a 5_occ: 0.1196 0.1368 0.035 1.118 5.6 67.2 15.0 892 n/a 6_bss: 0.1194 0.1366 0.035 1.118 5.5 67.2 15.0 892 n/a 6_settarget: 0.1194 0.1366 0.035 1.118 5.5 67.2 15.0 892 n/a 6_updatecdl: 0.1194 0.1366 0.035 1.118 5.5 67.2 15.0 892 n/a 6_nqh: 0.1194 0.1366 0.035 1.118 5.5 67.2 15.0 892 n/a 6_sol: 0.1193 0.1352 0.035 1.118 5.5 67.2 15.0 897 n/a 6_weight: 0.1193 0.1352 0.035 1.118 5.5 67.2 15.0 897 n/a 6_xyzrec: 0.1196 0.1365 0.035 1.127 5.5 67.2 15.0 897 n/a 6_adp: 0.1199 0.1367 0.035 1.127 5.6 66.2 14.9 897 n/a 6_regHadp: 0.1200 0.1367 0.035 1.127 5.6 66.2 14.9 897 n/a 6_occ: 0.1197 0.1369 0.035 1.127 5.6 66.2 14.9 897 n/a 7_bss: 0.1196 0.1368 0.035 1.127 5.4 66.0 14.7 897 n/a 7_settarget: 0.1196 0.1368 0.035 1.127 5.4 66.0 14.7 897 n/a 7_updatecdl: 0.1196 0.1368 0.035 1.128 5.4 66.0 14.7 897 n/a 7_nqh: 0.1196 0.1368 0.035 1.128 5.4 66.0 14.7 897 n/a 7_sol: 0.1195 0.1360 0.035 1.128 5.4 66.0 14.6 907 n/a 7_weight: 0.1195 0.1360 0.035 1.128 5.4 66.0 14.6 907 n/a 7_xyzrec: 0.1199 0.1368 0.037 1.131 5.4 66.0 14.6 907 n/a 7_adp: 0.1201 0.1371 0.037 1.131 5.4 65.0 14.6 907 n/a 7_regHadp: 0.1201 0.1371 0.037 1.131 5.4 65.0 14.6 907 n/a 7_occ: 0.1200 0.1371 0.037 1.131 5.4 65.0 14.6 907 n/a 8_bss: 0.1190 0.1360 0.037 1.131 5.5 65.1 14.6 907 n/a 8_settarget: 0.1190 0.1360 0.037 1.131 5.5 65.1 14.6 907 n/a 8_updatecdl: 0.1190 0.1360 0.037 1.131 5.5 65.1 14.6 907 n/a 8_nqh: 0.1190 0.1360 0.037 1.131 5.5 65.1 14.6 907 n/a 8_sol: 0.1191 0.1353 0.037 1.131 5.5 65.1 14.5 892 n/a 8_weight: 0.1191 0.1353 0.037 1.131 5.5 65.1 14.5 892 n/a 8_xyzrec: 0.1195 0.1357 0.037 1.114 5.5 65.1 14.5 892 n/a 8_adp: 0.1196 0.1358 0.037 1.114 5.5 64.0 14.5 892 n/a 8_regHadp: 0.1197 0.1358 0.037 1.114 5.5 64.0 14.5 892 n/a 8_occ: 0.1195 0.1359 0.037 1.114 5.5 64.0 14.5 892 n/a 9_bss: 0.1193 0.1358 0.037 1.114 5.5 64.0 14.5 892 n/a 9_settarget: 0.1193 0.1358 0.037 1.114 5.5 64.0 14.5 892 n/a 9_updatecdl: 0.1193 0.1358 0.037 1.115 5.5 64.0 14.5 892 n/a 9_nqh: 0.1193 0.1358 0.037 1.115 5.5 64.0 14.5 892 n/a 9_sol: 0.1191 0.1352 0.037 1.115 5.5 64.0 14.7 912 n/a 9_weight: 0.1191 0.1352 0.037 1.115 5.5 64.0 14.7 912 n/a 9_xyzrec: 0.1193 0.1356 0.038 1.115 5.5 64.0 14.7 912 n/a 9_adp: 0.1194 0.1361 0.038 1.115 5.5 63.6 14.6 912 n/a 9_regHadp: 0.1194 0.1361 0.038 1.115 5.5 63.6 14.6 912 n/a 9_occ: 0.1192 0.1366 0.038 1.115 5.5 63.6 14.6 912 n/a 10_bss: 0.1191 0.1362 0.038 1.115 5.5 63.6 14.6 912 n/a 10_settarget: 0.1191 0.1362 0.038 1.115 5.5 63.6 14.6 912 n/a 10_updatecdl: 0.1191 0.1362 0.038 1.115 5.5 63.6 14.6 912 n/a 10_setrh: 0.1192 0.1363 0.038 1.115 5.5 63.6 14.6 912 n/a 10_nqh: 0.1192 0.1363 0.038 1.115 5.5 63.6 14.6 912 n/a 10_sol: 0.1191 0.1349 0.038 1.115 5.5 63.6 14.7 911 n/a 10_weight: 0.1191 0.1349 0.038 1.115 5.5 63.6 14.7 911 n/a 10_xyzrec: 0.1196 0.1358 0.038 1.177 5.5 63.6 14.7 911 n/a 10_adp: 0.1197 0.1360 0.038 1.177 5.6 63.3 14.7 911 n/a 10_regHadp: 0.1197 0.1360 0.038 1.177 5.6 63.3 14.7 911 n/a 10_occ: 0.1196 0.1362 0.038 1.177 5.6 63.3 14.7 911 n/a end: 0.1195 0.1360 0.038 1.177 5.5 63.2 14.6 911 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4119138_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4119138_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0600 Refinement macro-cycles (run) : 12478.3100 Write final files (write_after_run_outputs) : 128.2200 Total : 12613.5900 Total CPU time: 3.51 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:47:26 PST -0800 (1736736446.90 s) Start R-work = 0.1795, R-free = 0.1961 Final R-work = 0.1195, R-free = 0.1360 =============================================================================== Job complete usr+sys time: 12862.02 seconds wall clock time: 215 minutes 22.57 seconds (12922.57 seconds total)