Starting phenix.refine on Sun Jan 12 15:15:38 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4824775.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" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4824775.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4824775.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.17, per 1000 atoms: 0.32 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: 2.789 distance_ideal: 2.720 ideal - model: -0.069 slack: 0.000 delta_slack: -0.069 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: 2.652 distance_ideal: 2.710 ideal - model: 0.058 slack: 0.000 delta_slack: 0.058 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 170.3 milliseconds Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.03: 902 1.03 - 1.27: 2518 1.27 - 1.51: 1529 1.51 - 1.75: 973 1.75 - 1.98: 12 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.455 1.245 0.210 7.00e-03 2.04e+04 8.97e+02 bond pdb=" N HIS B 179 " pdb=" CA HIS B 179 " ideal model delta sigma weight residual 1.459 1.190 0.269 1.21e-02 6.83e+03 4.96e+02 bond pdb=" C CYS B 81 " pdb=" O CYS B 81 " ideal model delta sigma weight residual 1.236 1.009 0.227 1.16e-02 7.43e+03 3.83e+02 bond pdb=" N PRO A 11 " pdb=" CD PRO A 11 " ideal model delta sigma weight residual 1.473 1.742 -0.269 1.40e-02 5.10e+03 3.70e+02 bond pdb=" C ALA B 44 " pdb=" O ALA B 44 " ideal model delta sigma weight residual 1.233 1.475 -0.242 1.26e-02 6.30e+03 3.69e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 5215 3.81 - 7.63: 3540 7.63 - 11.44: 1601 11.44 - 15.25: 396 15.25 - 19.07: 58 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O THR A 91 " pdb=" C THR A 91 " pdb=" N VAL A 92 " ideal model delta sigma weight residual 122.12 139.10 -16.98 1.06e+00 8.90e-01 2.57e+02 angle pdb=" NE ARG A 97 " pdb=" CZ ARG A 97 " pdb=" NH1 ARG A 97 " ideal model delta sigma weight residual 121.50 136.41 -14.91 1.00e+00 1.00e+00 2.22e+02 angle pdb=" CA ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 117.59 132.06 -14.47 9.90e-01 1.02e+00 2.14e+02 angle pdb=" O LYS A 131 " pdb=" C LYS A 131 " pdb=" N ASP A 132 " ideal model delta sigma weight residual 122.12 106.74 15.38 1.06e+00 8.90e-01 2.10e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 106.75 12.45 9.00e-01 1.23e+00 1.91e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 1801 15.99 - 31.97: 174 31.97 - 47.96: 46 47.96 - 63.95: 23 63.95 - 79.93: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA VAL B 69 " pdb=" C VAL B 69 " pdb=" N ILE B 70 " pdb=" CA ILE B 70 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 152.35 27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " pdb=" CA PRO B 11 " ideal model delta harmonic sigma weight residual 180.00 153.56 26.44 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 215 0.249 - 0.497: 164 0.497 - 0.746: 83 0.746 - 0.994: 28 0.994 - 1.243: 2 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ARG B 49 " pdb=" N ARG B 49 " pdb=" C ARG B 49 " pdb=" CB ARG B 49 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.86e+01 chirality pdb=" CA ASP A 84 " pdb=" N ASP A 84 " pdb=" C ASP A 84 " pdb=" CB ASP A 84 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CA TYR A 194 " pdb=" N TYR A 194 " pdb=" C TYR A 194 " pdb=" CB TYR A 194 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.44e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.073 2.00e-02 2.50e+03 9.25e-02 2.57e+02 pdb=" CG PHE A 119 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.098 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.117 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.102 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.142 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.092 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.148 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.072 2.00e-02 2.50e+03 7.22e-02 1.56e+02 pdb=" CG PHE B 164 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.081 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.035 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.034 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.106 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.025 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " 0.020 2.00e-02 2.50e+03 7.03e-02 1.48e+02 pdb=" CG PHE A 127 " -0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " 0.099 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " 0.087 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " 0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " -0.091 2.00e-02 2.50e+03 pdb=" HD1 PHE A 127 " -0.055 2.00e-02 2.50e+03 pdb=" HD2 PHE A 127 " -0.072 2.00e-02 2.50e+03 pdb=" HE1 PHE A 127 " -0.055 2.00e-02 2.50e+03 pdb=" HE2 PHE A 127 " -0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 127 " 0.038 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.66: 33 1.66 - 2.40: 2980 2.40 - 3.13: 22516 3.13 - 3.87: 32764 3.87 - 4.60: 51983 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110276 Sorted by model distance: nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.926 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.981 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.983 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.105 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.153 2.620 ... (remaining 110271 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_4824775_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= 0.2040 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.304371 | | target function (ml) not normalized (work): 806264.555459 | | target function (ml) not normalized (free): 16551.681134 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2139 0.1853 6.7 6.3033| | 2: 2.94 - 2.33 1.00 7339 128 0.1629 0.1514 5.5287 5.552| | 3: 2.33 - 2.04 0.96 6939 150 0.1643 0.1391 5.14 5.0927| | 4: 2.04 - 1.85 1.00 7170 155 0.1752 0.1566 4.9641 4.9795| | 5: 1.85 - 1.72 0.99 7113 159 0.1925 0.1804 4.8068 4.866| | 6: 1.72 - 1.62 0.99 7102 142 0.1978 0.1910 4.6666 4.6896| | 7: 1.62 - 1.54 0.99 7104 148 0.2045 0.1703 4.5776 4.5459| | 8: 1.54 - 1.47 0.96 6798 152 0.2064 0.2343 4.4743 4.5512| | 9: 1.47 - 1.41 0.98 6938 155 0.2083 0.2251 4.406 4.4658| | 10: 1.41 - 1.36 0.99 7022 150 0.2097 0.2437 4.3262 4.4903| | 11: 1.36 - 1.32 0.99 6997 151 0.2130 0.2067 4.2493 4.2245| | 12: 1.32 - 1.28 0.98 6976 149 0.2081 0.2010 4.1813 4.2274| | 13: 1.28 - 1.25 0.98 6907 166 0.2052 0.2049 4.1311 4.1713| | 14: 1.25 - 1.22 0.98 7015 113 0.2090 0.2077 4.0829 4.1665| | 15: 1.22 - 1.19 0.98 6957 137 0.2133 0.2063 4.0526 4.0996| | 16: 1.19 - 1.17 0.93 6604 132 0.2122 0.2391 4.009 4.1279| | 17: 1.17 - 1.14 0.98 6941 135 0.2184 0.2092 3.9718 4.0559| | 18: 1.14 - 1.12 0.98 6875 142 0.2196 0.2518 3.9221 3.9367| | 19: 1.12 - 1.10 0.97 6949 106 0.2277 0.2575 3.8702 4.0035| | 20: 1.10 - 1.08 0.97 6884 147 0.2347 0.1935 3.8328 3.7612| | 21: 1.08 - 1.07 0.97 6852 152 0.2405 0.2702 3.7766 3.8081| | 22: 1.07 - 1.05 0.97 6838 135 0.2552 0.2398 3.7525 3.7117| | 23: 1.05 - 1.03 0.97 6829 159 0.2733 0.2536 3.7326 3.7408| | 24: 1.03 - 1.02 0.96 6785 133 0.2880 0.2954 3.6989 3.7869| | 25: 1.02 - 1.01 0.93 6552 130 0.3062 0.2874 3.6795 3.7339| | 26: 1.01 - 0.99 0.96 6767 158 0.3259 0.3191 3.6404 3.6305| | 27: 0.99 - 0.98 0.94 6648 131 0.3405 0.3433 3.6298 3.6339| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.17 0.91 0.97 34607.14| | 2: 2.94 - 2.33 7339 128 0.86 20.76 1.08 1.02 14422.26| | 3: 2.33 - 2.04 6939 150 0.94 11.63 1.11 1.06 3725.17| | 4: 2.04 - 1.85 7170 155 0.93 12.79 1.11 1.06 2540.51| | 5: 1.85 - 1.72 7113 159 0.91 15.13 1.11 1.07 1978.98| | 6: 1.72 - 1.62 7102 142 0.90 16.30 1.11 1.07 1575.89| | 7: 1.62 - 1.54 7104 148 0.89 17.46 1.11 1.07 1315.06| | 8: 1.54 - 1.47 6798 152 0.88 18.87 1.11 1.06 1208.41| | 9: 1.47 - 1.41 6938 155 0.87 20.16 1.10 1.06 1093.36| | 10: 1.41 - 1.36 7022 150 0.86 21.36 1.09 1.06 968.73| | 11: 1.36 - 1.32 6997 151 0.87 20.66 1.08 1.05 789.30| | 12: 1.32 - 1.28 6976 149 0.87 20.02 1.08 1.04 663.42| | 13: 1.28 - 1.25 6907 166 0.87 19.86 1.07 1.03 598.05| | 14: 1.25 - 1.22 7015 113 0.87 20.71 1.07 1.03 572.17| | 15: 1.22 - 1.19 6957 137 0.86 21.50 1.08 1.03 558.90| | 16: 1.19 - 1.17 6604 132 0.86 21.40 1.08 1.02 530.47| | 17: 1.17 - 1.14 6941 135 0.85 22.29 1.08 1.01 487.92| | 18: 1.14 - 1.12 6875 142 0.86 21.95 1.08 0.99 420.99| | 19: 1.12 - 1.10 6949 106 0.86 21.92 1.07 0.99 368.80| | 20: 1.10 - 1.08 6884 147 0.86 21.65 1.07 0.99 318.24| | 21: 1.08 - 1.07 6852 152 0.85 22.37 1.06 0.99 306.27| | 22: 1.07 - 1.05 6838 135 0.84 24.21 1.05 0.99 303.71| | 23: 1.05 - 1.03 6829 159 0.81 26.89 1.06 0.97 317.18| | 24: 1.03 - 1.02 6785 133 0.78 29.30 1.05 0.98 327.41| | 25: 1.02 - 1.01 6552 130 0.77 30.79 1.02 0.94 316.85| | 26: 1.01 - 0.99 6767 158 0.74 33.09 1.03 0.92 306.75| | 27: 0.99 - 0.98 6648 131 0.73 33.66 1.04 0.91 297.79| |alpha: min = 0.91 max = 1.07 mean = 1.01| |beta: min = 297.79 max = 34607.14 mean = 2749.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.65| |phase err.(test): min = 0.00 max = 89.32 mean = 21.77| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.269 2950 Z= 5.593 Angle : 5.213 16.984 4018 Z= 3.721 Chirality : 0.402 1.243 492 Planarity : 0.034 0.163 512 Dihedral : 12.897 79.932 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.78 % Allowed : 2.59 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Cbeta Deviations : 31.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.40), residues: 386 helix: -1.94 (0.34), residues: 144 sheet: -0.98 (0.52), residues: 86 loop : -0.35 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.074 0.016 ARG B 49 TYR 0.091 0.031 TYR B 67 PHE 0.119 0.044 PHE A 164 TRP 0.124 0.039 TRP B 139 HIS 0.093 0.031 HIS B 116 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= 0.2040 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.304371 | | target function (ml) not normalized (work): 806264.555459 | | target function (ml) not normalized (free): 16551.681134 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2038 0.2040 0.1947 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2038 0.2040 0.1947 n_refl.: 191155 remove outliers: r(all,work,free)=0.2038 0.2040 0.1947 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2035 0.2038 0.1947 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1807 0.1885 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1805 0.1885 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 0.4059 398.008 291.221 0.420 0.936 0.300 13.296-10.522 99.01 99 1 0.2514 528.187 517.436 0.762 0.937 0.254 10.503-8.327 99.45 178 3 0.2466 565.118 554.549 0.938 0.937 0.234 8.318-6.595 100.00 360 8 0.2486 414.736 403.258 0.943 0.937 0.179 6.588-5.215 100.00 711 7 0.2222 381.101 365.852 0.925 0.937 0.160 5.214-4.128 98.38 1367 28 0.1477 557.435 549.354 1.042 0.938 0.080 4.126-3.266 94.74 2603 46 0.1346 508.132 498.765 1.106 0.938 0.014 3.266-2.585 99.86 5447 97 0.1445 342.774 337.127 1.080 0.938 0.000 2.585-2.046 97.45 10613 204 0.1413 258.603 254.334 1.087 0.938 0.000 2.046-1.619 99.39 21536 464 0.1631 153.054 149.959 1.103 0.937 0.000 1.619-1.281 98.00 42464 925 0.1928 82.395 80.528 1.091 0.937 0.000 1.281-0.980 96.53 101826 2056 0.2322 44.203 41.971 1.078 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0493 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1805 r_free=0.1885 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.1805 r_free=0.1885 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.284751 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.777989 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 0.1272 0.1482 0.0210 0.036 1.2 11.9 0.0 0.3 0 11.642 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 14.82 2.10 1.118 13.093 570.778 0.019 13.04 15.55 2.51 1.293 13.397 570.778 0.018 Individual atomic B min max mean iso aniso Overall: 5.22 73.03 15.13 1.42 435 3274 Protein: 5.22 40.60 11.07 1.42 0 2902 Water: 6.51 73.03 29.77 N/A 435 370 Other: 16.10 31.12 23.61 N/A 0 2 Chain A: 5.36 60.54 13.16 N/A 0 1626 Chain B: 5.22 73.03 12.87 N/A 0 1648 Chain S: 11.54 67.28 31.08 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.00 2171 12.00 - 18.78 622 18.78 - 25.56 312 25.56 - 32.34 262 32.34 - 39.12 162 39.12 - 45.90 105 45.90 - 52.68 51 52.68 - 59.47 18 59.47 - 66.25 4 66.25 - 73.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1305 r_free=0.1556 r_work=0.1303 r_free=0.1551 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1303 r_free = 0.1551 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1288 r_free = 0.1537 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1288 r_free= 0.1537 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015756 | | target function (ls_wunit_k1) not normalized (work): 2950.969031 | | target function (ls_wunit_k1) not normalized (free): 112.021759 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1288 0.1537 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1480 0.1478 0.1621 n_refl.: 191138 remove outliers: r(all,work,free)=0.1480 0.1478 0.1621 n_refl.: 191138 overall B=0.14 to atoms: r(all,work,free)=0.1500 0.1498 0.1630 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1285 0.1280 0.1531 n_refl.: 191138 remove outliers: r(all,work,free)=0.1285 0.1280 0.1530 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3659 398.008 363.248 0.472 0.962 0.287 13.296-10.522 99.01 99 1 0.2090 528.187 521.425 0.747 0.964 0.270 10.503-8.327 99.45 178 3 0.1744 565.118 564.148 0.892 0.964 0.218 8.318-6.595 100.00 360 8 0.1725 414.736 411.358 0.910 0.963 0.160 6.588-5.215 100.00 711 7 0.1561 381.101 373.934 0.888 0.964 0.150 5.214-4.128 98.38 1367 28 0.0923 557.435 554.137 0.978 0.964 0.080 4.126-3.266 94.74 2603 46 0.0855 508.132 504.075 1.045 0.965 0.014 3.266-2.585 99.86 5447 97 0.0930 342.774 340.382 1.027 0.965 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.337 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.385 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1284 82.395 81.360 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1883 44.202 42.203 1.024 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0309 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1280 r_free=0.1530 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1280 r_free=0.1530 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1280 r_free=0.1530 | n_water=805 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1283 r_free=0.1535 | n_water=799 | time (s): 107.800 (total time: 110.470) Filter (q & B) r_work=0.1283 r_free=0.1536 | n_water=793 | time (s): 3.950 (total time: 114.420) Compute maps r_work=0.1283 r_free=0.1536 | n_water=793 | time (s): 1.570 (total time: 115.990) Filter (map) r_work=0.1305 r_free=0.1535 | n_water=666 | time (s): 4.730 (total time: 120.720) Find peaks r_work=0.1305 r_free=0.1535 | n_water=666 | time (s): 0.700 (total time: 121.420) Add new water r_work=0.1329 r_free=0.1570 | n_water=978 | time (s): 4.050 (total time: 125.470) Refine new water occ: r_work=0.1285 r_free=0.1513 adp: r_work=0.1273 r_free=0.1506 occ: r_work=0.1276 r_free=0.1503 adp: r_work=0.1270 r_free=0.1502 occ: r_work=0.1271 r_free=0.1500 adp: r_work=0.1268 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1500 r_work=0.1268 r_free=0.1500 | n_water=978 | time (s): 69.840 (total time: 195.310) Filter (q & B) r_work=0.1272 r_free=0.1508 | n_water=898 | time (s): 5.000 (total time: 200.310) Filter (dist only) r_work=0.1272 r_free=0.1508 | n_water=897 | time (s): 116.130 (total time: 316.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.259537 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 586.133016 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 0.1253 0.1519 0.0265 0.039 1.2 16.8 0.0 0.3 0 12.630 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.19 2.65 2.064 15.263 586.133 0.014 12.31 15.06 2.75 2.442 15.287 586.133 0.014 Individual atomic B min max mean iso aniso Overall: 5.46 68.16 16.37 1.21 527 3274 Protein: 5.46 40.48 11.02 1.21 0 2902 Water: 6.61 68.16 33.64 N/A 527 370 Other: 16.46 31.78 24.12 N/A 0 2 Chain A: 5.59 56.77 13.10 N/A 0 1626 Chain B: 5.46 68.16 12.88 N/A 0 1648 Chain S: 13.86 63.89 37.35 N/A 527 0 Histogram: Values Number of atoms 5.46 - 11.73 2065 11.73 - 18.00 702 18.00 - 24.27 267 24.27 - 30.54 222 30.54 - 36.81 186 36.81 - 43.08 156 43.08 - 49.35 103 49.35 - 55.62 50 55.62 - 61.89 44 61.89 - 68.16 6 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1506 r_work=0.1231 r_free=0.1508 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1508 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 = 0.1224 r_free = 0.1500 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1500 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013280 | | target function (ls_wunit_k1) not normalized (work): 2487.237769 | | target function (ls_wunit_k1) not normalized (free): 102.909512 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1224 0.1500 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1435 0.1433 0.1600 n_refl.: 191137 remove outliers: r(all,work,free)=0.1435 0.1433 0.1600 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1598 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1505 n_refl.: 191137 remove outliers: r(all,work,free)=0.1237 0.1231 0.1505 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3208 398.008 374.871 0.492 0.962 0.281 13.296-10.522 99.01 99 1 0.1840 528.187 520.450 0.757 0.963 0.233 10.503-8.327 99.45 178 3 0.1398 565.118 565.392 0.927 0.963 0.179 8.318-6.595 100.00 360 8 0.1505 414.736 413.958 0.934 0.963 0.150 6.588-5.215 100.00 711 7 0.1338 381.101 376.655 0.914 0.963 0.150 5.214-4.128 98.38 1367 28 0.0822 557.435 556.207 0.997 0.963 0.100 4.126-3.266 94.74 2603 46 0.0754 508.132 505.511 1.058 0.963 0.014 3.266-2.585 99.86 5447 97 0.0851 342.774 341.242 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0891 258.603 256.817 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1041 153.054 151.643 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1261 82.395 81.347 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.211 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0568 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1505 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1505 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1505 | n_water=897 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1233 r_free=0.1509 | n_water=894 | time (s): 127.200 (total time: 130.260) Filter (q & B) r_work=0.1233 r_free=0.1509 | n_water=891 | time (s): 5.040 (total time: 135.300) Compute maps r_work=0.1233 r_free=0.1509 | n_water=891 | time (s): 1.730 (total time: 137.030) Filter (map) r_work=0.1270 r_free=0.1510 | n_water=709 | time (s): 5.260 (total time: 142.290) Find peaks r_work=0.1270 r_free=0.1510 | n_water=709 | time (s): 0.630 (total time: 142.920) Add new water r_work=0.1294 r_free=0.1542 | n_water=1021 | time (s): 4.500 (total time: 147.420) Refine new water occ: r_work=0.1251 r_free=0.1508 adp: r_work=0.1251 r_free=0.1509 occ: r_work=0.1247 r_free=0.1506 adp: r_work=0.1246 r_free=0.1506 occ: r_work=0.1244 r_free=0.1504 adp: r_work=0.1243 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1505 r_work=0.1243 r_free=0.1505 | n_water=1021 | time (s): 330.260 (total time: 477.680) Filter (q & B) r_work=0.1247 r_free=0.1507 | n_water=895 | time (s): 5.840 (total time: 483.520) Filter (dist only) r_work=0.1247 r_free=0.1506 | n_water=894 | time (s): 127.000 (total time: 610.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.745202 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.353437 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1238 0.1434 0.0197 0.035 1.1 7.8 0.0 0.0 0 0.873 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.34 1.97 1.943 14.706 16.353 3.942 12.31 13.90 1.59 2.287 14.596 16.353 3.898 Individual atomic B min max mean iso aniso Overall: 5.53 67.67 15.40 1.06 526 3272 Protein: 5.53 36.50 10.75 1.06 0 2902 Water: 6.71 67.67 30.50 N/A 526 368 Other: 14.01 27.88 20.94 N/A 0 2 Chain A: 5.58 55.64 12.82 N/A 0 1625 Chain B: 5.53 67.67 12.55 N/A 0 1647 Chain S: 14.47 63.89 32.34 N/A 526 0 Histogram: Values Number of atoms 5.53 - 11.75 2133 11.75 - 17.96 674 17.96 - 24.17 296 24.17 - 30.39 247 30.39 - 36.60 187 36.60 - 42.82 150 42.82 - 49.03 73 49.03 - 55.24 26 55.24 - 61.46 10 61.46 - 67.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1391 r_work=0.1232 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1391 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1388 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891996 | | target function (ml) not normalized (work): 728955.299150 | | target function (ml) not normalized (free): 15232.597009 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1227 0.1388 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1438 0.1437 0.1490 n_refl.: 191137 remove outliers: r(all,work,free)=0.1438 0.1437 0.1490 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1431 0.1431 0.1486 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1381 n_refl.: 191137 remove outliers: r(all,work,free)=0.1226 0.1223 0.1381 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 0.3871 398.008 358.866 0.416 0.947 0.247 13.296-10.522 99.01 99 1 0.2446 528.187 507.342 0.708 0.948 0.214 10.503-8.327 98.35 176 3 0.1942 555.265 555.228 0.892 0.948 0.169 8.318-6.595 100.00 360 8 0.1997 414.736 410.220 0.901 0.948 0.135 6.588-5.215 100.00 711 7 0.1831 381.101 370.392 0.887 0.948 0.130 5.214-4.128 98.38 1367 28 0.1152 557.435 551.934 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1076 508.132 501.371 1.032 0.949 0.015 3.266-2.585 99.86 5447 97 0.1081 342.774 339.165 1.019 0.948 0.005 2.585-2.046 97.45 10613 204 0.0969 258.603 255.755 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0971 153.054 151.425 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1057 82.395 81.472 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.311 1.038 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1381 | n_water=894 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1224 r_free=0.1383 | n_water=892 | time (s): 117.600 (total time: 120.260) Filter (q & B) r_work=0.1224 r_free=0.1383 | n_water=887 | time (s): 4.440 (total time: 124.700) Compute maps r_work=0.1224 r_free=0.1383 | n_water=887 | time (s): 1.810 (total time: 126.510) Filter (map) r_work=0.1247 r_free=0.1382 | n_water=738 | time (s): 5.600 (total time: 132.110) Find peaks r_work=0.1247 r_free=0.1382 | n_water=738 | time (s): 0.690 (total time: 132.800) Add new water r_work=0.1261 r_free=0.1397 | n_water=972 | time (s): 4.740 (total time: 137.540) Refine new water occ: r_work=0.1215 r_free=0.1365 adp: r_work=0.1208 r_free=0.1362 occ: r_work=0.1206 r_free=0.1364 adp: r_work=0.1206 r_free=0.1362 occ: r_work=0.1204 r_free=0.1363 adp: r_work=0.1204 r_free=0.1362 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1362 r_work=0.1204 r_free=0.1362 | n_water=972 | time (s): 297.240 (total time: 434.780) Filter (q & B) r_work=0.1208 r_free=0.1369 | n_water=873 | time (s): 4.970 (total time: 439.750) Filter (dist only) r_work=0.1209 r_free=0.1371 | n_water=871 | time (s): 108.490 (total time: 548.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570520 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.726479 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 0.1209 0.1367 0.0158 0.036 1.1 6.6 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 13.67 1.58 1.835 14.247 15.726 3.876 12.01 13.64 1.63 1.933 14.211 15.726 3.867 Individual atomic B min max mean iso aniso Overall: 5.48 67.20 15.04 1.00 503 3272 Protein: 5.48 33.40 10.68 1.00 0 2902 Water: 5.83 67.20 29.56 N/A 503 368 Other: 13.97 26.96 20.46 N/A 0 2 Chain A: 5.55 54.51 12.69 N/A 0 1625 Chain B: 5.48 67.20 12.47 N/A 0 1647 Chain S: 5.83 63.81 31.09 N/A 503 0 Histogram: Values Number of atoms 5.48 - 11.65 2098 11.65 - 17.83 733 17.83 - 24.00 292 24.00 - 30.17 252 30.17 - 36.34 170 36.34 - 42.51 132 42.51 - 48.68 66 48.68 - 54.86 25 54.86 - 61.03 5 61.03 - 67.20 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1364 r_work=0.1201 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1364 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1359 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864761 | | target function (ml) not normalized (work): 723846.590887 | | target function (ml) not normalized (free): 15143.083357 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1359 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1427 0.1427 0.1482 n_refl.: 191135 remove outliers: r(all,work,free)=0.1427 0.1427 0.1482 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1420 0.1419 0.1477 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1196 0.1356 n_refl.: 191135 remove outliers: r(all,work,free)=0.1199 0.1195 0.1356 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 0.3601 356.204 314.186 0.413 0.947 0.245 13.296-10.522 97.03 97 1 0.2307 481.494 453.037 0.704 0.948 0.209 10.503-8.327 98.35 176 3 0.2033 503.108 496.255 0.874 0.948 0.169 8.318-6.595 100.00 360 8 0.2139 375.779 369.836 0.897 0.948 0.130 6.588-5.215 100.00 711 7 0.1917 345.304 335.033 0.886 0.948 0.120 5.214-4.128 98.38 1367 28 0.1199 505.074 499.811 0.973 0.948 0.090 4.126-3.266 94.74 2603 46 0.1117 460.402 453.889 1.032 0.948 0.000 3.266-2.585 99.86 5447 97 0.1091 310.576 307.320 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0935 234.312 231.935 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0911 138.677 137.414 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.0989 74.656 73.945 1.055 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.050 38.389 1.043 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1205 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1356 | n_water=871 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1195 r_free=0.1356 | n_water=871 | time (s): 114.950 (total time: 117.840) Filter (q & B) r_work=0.1196 r_free=0.1356 | n_water=863 | time (s): 4.620 (total time: 122.460) Compute maps r_work=0.1196 r_free=0.1356 | n_water=863 | time (s): 1.980 (total time: 124.440) Filter (map) r_work=0.1217 r_free=0.1359 | n_water=745 | time (s): 4.840 (total time: 129.280) Find peaks r_work=0.1217 r_free=0.1359 | n_water=745 | time (s): 0.890 (total time: 130.170) Add new water r_work=0.1231 r_free=0.1377 | n_water=963 | time (s): 5.210 (total time: 135.380) Refine new water occ: r_work=0.1196 r_free=0.1348 adp: r_work=0.1196 r_free=0.1347 occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1191 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1346 r_work=0.1191 r_free=0.1346 | n_water=963 | time (s): 236.420 (total time: 371.800) Filter (q & B) r_work=0.1194 r_free=0.1354 | n_water=885 | time (s): 4.360 (total time: 376.160) Filter (dist only) r_work=0.1195 r_free=0.1354 | n_water=884 | time (s): 115.410 (total time: 491.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.542636 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.609636 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 0.1355 0.0159 0.036 1.1 6.3 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.55 1.59 1.797 14.193 14.610 3.765 12.01 13.60 1.59 1.857 14.168 14.610 3.764 Individual atomic B min max mean iso aniso Overall: 5.57 66.90 15.04 0.96 517 3271 Protein: 5.57 32.26 10.61 0.96 0 2902 Water: 5.94 66.90 29.56 N/A 517 367 Other: 13.82 26.05 19.93 N/A 0 2 Chain A: 5.60 53.85 12.58 N/A 0 1624 Chain B: 5.57 66.90 12.38 N/A 0 1647 Chain S: 5.94 63.76 31.23 N/A 517 0 Histogram: Values Number of atoms 5.57 - 11.70 2134 11.70 - 17.84 719 17.84 - 23.97 288 23.97 - 30.10 242 30.10 - 36.24 168 36.24 - 42.37 128 42.37 - 48.50 76 48.50 - 54.63 26 54.63 - 60.77 5 60.77 - 66.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1360 r_work=0.1201 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1360 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1362 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.763208 | | target function (ml) not normalized (work): 704811.141877 | | target function (ml) not normalized (free): 14753.035582 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1362 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1414 0.1413 0.1494 n_refl.: 191131 remove outliers: r(all,work,free)=0.1414 0.1413 0.1494 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1406 0.1405 0.1488 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1360 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 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 0.3562 356.204 330.937 0.422 0.948 0.228 13.296-10.522 97.03 97 1 0.2359 481.494 459.393 0.704 0.949 0.190 10.503-8.327 98.35 176 3 0.2059 503.108 495.797 0.872 0.950 0.148 8.318-6.595 100.00 360 8 0.2142 375.779 370.161 0.894 0.949 0.110 6.588-5.215 100.00 711 7 0.1897 345.304 334.529 0.886 0.949 0.110 5.214-4.128 98.38 1367 28 0.1205 505.074 500.112 0.973 0.950 0.070 4.126-3.266 94.74 2603 46 0.1135 460.402 453.540 1.032 0.950 0.005 3.266-2.585 99.86 5447 97 0.1105 310.576 307.296 1.019 0.950 0.000 2.585-2.046 97.45 10613 204 0.0948 234.312 231.825 1.032 0.950 0.000 2.046-1.619 99.39 21536 464 0.0917 138.677 137.363 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0983 74.656 73.932 1.049 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1658 40.050 38.380 1.035 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1408 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1360 | n_water=884 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1200 r_free=0.1360 | n_water=883 | time (s): 110.980 (total time: 113.560) Filter (q & B) r_work=0.1200 r_free=0.1361 | n_water=876 | time (s): 5.510 (total time: 119.070) Compute maps r_work=0.1200 r_free=0.1361 | n_water=876 | time (s): 1.650 (total time: 120.720) Filter (map) r_work=0.1221 r_free=0.1364 | n_water=759 | time (s): 5.030 (total time: 125.750) Find peaks r_work=0.1221 r_free=0.1364 | n_water=759 | time (s): 0.910 (total time: 126.660) Add new water r_work=0.1232 r_free=0.1376 | n_water=968 | time (s): 4.710 (total time: 131.370) Refine new water occ: r_work=0.1198 r_free=0.1349 adp: r_work=0.1198 r_free=0.1349 occ: r_work=0.1195 r_free=0.1348 adp: r_work=0.1195 r_free=0.1348 occ: r_work=0.1194 r_free=0.1347 adp: r_work=0.1194 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1348 r_work=0.1194 r_free=0.1348 | n_water=968 | time (s): 262.540 (total time: 393.910) Filter (q & B) r_work=0.1198 r_free=0.1353 | n_water=894 | time (s): 5.090 (total time: 399.000) Filter (dist only) r_work=0.1198 r_free=0.1353 | n_water=892 | time (s): 112.980 (total time: 511.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.491536 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.600731 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1356 0.0154 0.037 1.1 6.5 0.0 0.3 0 0.746 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.56 1.54 1.768 14.088 14.601 3.765 12.03 13.59 1.56 1.895 14.046 14.601 3.761 Individual atomic B min max mean iso aniso Overall: 5.56 65.87 14.91 0.91 525 3271 Protein: 5.56 29.83 10.51 0.91 0 2902 Water: 6.00 65.87 29.22 N/A 525 367 Other: 13.85 23.86 18.85 N/A 0 2 Chain A: 5.64 52.92 12.44 N/A 0 1624 Chain B: 5.56 65.87 12.26 N/A 0 1647 Chain S: 6.00 59.08 30.88 N/A 525 0 Histogram: Values Number of atoms 5.56 - 11.59 2109 11.59 - 17.62 765 17.62 - 23.65 282 23.65 - 29.68 221 29.68 - 35.71 182 35.71 - 41.75 122 41.75 - 47.78 80 47.78 - 53.81 28 53.81 - 59.84 6 59.84 - 65.87 1 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1360 r_work=0.1204 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1360 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1356 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760459 | | target function (ml) not normalized (work): 704296.439909 | | target function (ml) not normalized (free): 14740.119734 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1356 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1415 0.1413 0.1490 n_refl.: 191131 remove outliers: r(all,work,free)=0.1415 0.1413 0.1490 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1407 0.1405 0.1484 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1354 n_refl.: 191131 remove outliers: r(all,work,free)=0.1203 0.1200 0.1354 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 91.09 89 3 0.3517 356.978 325.769 0.410 0.949 0.217 13.296-10.522 97.03 97 1 0.2387 481.494 459.592 0.697 0.950 0.175 10.503-8.327 98.35 176 3 0.2098 503.108 496.211 0.869 0.950 0.149 8.318-6.595 100.00 360 8 0.2156 375.779 370.227 0.893 0.950 0.113 6.588-5.215 100.00 711 7 0.1920 345.304 334.789 0.883 0.950 0.097 5.214-4.128 98.38 1367 28 0.1214 505.074 499.966 0.973 0.950 0.070 4.126-3.266 94.74 2603 46 0.1153 460.402 453.380 1.033 0.951 0.000 3.266-2.585 99.86 5447 97 0.1111 310.576 307.262 1.020 0.950 0.000 2.585-2.046 97.45 10613 204 0.0954 234.312 231.817 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0915 138.677 137.374 1.054 0.950 0.000 1.619-1.281 98.00 42464 925 0.0976 74.656 73.944 1.051 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.050 38.385 1.037 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1435 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1354 | n_water=892 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1200 r_free=0.1354 | n_water=891 | time (s): 113.530 (total time: 116.030) Filter (q & B) r_work=0.1201 r_free=0.1355 | n_water=883 | time (s): 5.350 (total time: 121.380) Compute maps r_work=0.1201 r_free=0.1355 | n_water=883 | time (s): 2.110 (total time: 123.490) Filter (map) r_work=0.1219 r_free=0.1356 | n_water=774 | time (s): 4.760 (total time: 128.250) Find peaks r_work=0.1219 r_free=0.1356 | n_water=774 | time (s): 0.910 (total time: 129.160) Add new water r_work=0.1231 r_free=0.1368 | n_water=982 | time (s): 4.300 (total time: 133.460) Refine new water occ: r_work=0.1197 r_free=0.1346 adp: r_work=0.1197 r_free=0.1346 occ: r_work=0.1195 r_free=0.1347 adp: r_work=0.1195 r_free=0.1347 occ: r_work=0.1195 r_free=0.1347 adp: r_work=0.1195 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1347 r_work=0.1195 r_free=0.1347 | n_water=982 | time (s): 135.530 (total time: 268.990) Filter (q & B) r_work=0.1200 r_free=0.1353 | n_water=891 | time (s): 4.850 (total time: 273.840) Filter (dist only) r_work=0.1200 r_free=0.1352 | n_water=890 | time (s): 113.620 (total time: 387.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.595747 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.321662 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1357 0.0154 0.038 1.1 5.3 0.0 0.3 0 0.798 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.57 1.54 1.726 13.909 14.322 3.761 12.05 13.62 1.57 1.804 13.876 14.322 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 64.47 14.73 0.88 523 3271 Protein: 5.58 28.61 10.43 0.88 0 2902 Water: 6.04 64.47 28.72 N/A 523 367 Other: 13.85 22.37 18.11 N/A 0 2 Chain A: 5.63 52.72 12.32 N/A 0 1624 Chain B: 5.58 64.47 12.15 N/A 0 1647 Chain S: 6.04 59.21 30.30 N/A 523 0 Histogram: Values Number of atoms 5.58 - 11.47 2088 11.47 - 17.36 787 17.36 - 23.25 282 23.25 - 29.14 217 29.14 - 35.03 186 35.03 - 40.91 111 40.91 - 46.80 81 46.80 - 52.69 34 52.69 - 58.58 5 58.58 - 64.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1362 r_work=0.1205 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1362 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1364 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758537 | | target function (ml) not normalized (work): 703932.556440 | | target function (ml) not normalized (free): 14743.319570 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1364 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1505 n_refl.: 191130 remove outliers: r(all,work,free)=0.1401 0.1399 0.1505 n_refl.: 191130 overall B=-0.01 to atoms: r(all,work,free)=0.1399 0.1397 0.1503 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1351 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1192 0.1351 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 91.09 89 3 0.3615 356.978 329.972 0.405 0.973 0.207 13.296-10.522 97.03 97 1 0.2407 481.494 457.640 0.685 0.974 0.159 10.503-8.327 98.35 176 3 0.2153 503.108 493.919 0.863 0.975 0.131 8.318-6.595 100.00 360 8 0.2204 375.779 369.220 0.885 0.975 0.100 6.588-5.215 100.00 711 7 0.1950 345.304 333.994 0.877 0.975 0.087 5.214-4.128 98.38 1367 28 0.1238 505.074 499.041 0.969 0.976 0.070 4.126-3.266 94.74 2603 46 0.1168 460.402 452.522 1.028 0.978 0.000 3.266-2.585 99.86 5447 97 0.1116 310.576 306.916 1.014 0.979 0.000 2.585-2.046 97.45 10613 204 0.0960 234.312 231.653 1.024 0.981 0.000 2.046-1.619 99.39 21536 464 0.0910 138.677 137.274 1.042 0.984 0.000 1.619-1.281 98.00 42464 925 0.0949 74.656 73.994 1.035 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.050 38.351 1.007 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0314 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1351 | n_water=890 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1192 r_free=0.1351 | n_water=890 | time (s): 107.710 (total time: 110.650) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=883 | time (s): 5.630 (total time: 116.280) Compute maps r_work=0.1192 r_free=0.1349 | n_water=883 | time (s): 2.030 (total time: 118.310) Filter (map) r_work=0.1210 r_free=0.1348 | n_water=780 | time (s): 4.730 (total time: 123.040) Find peaks r_work=0.1210 r_free=0.1348 | n_water=780 | time (s): 0.890 (total time: 123.930) Add new water r_work=0.1220 r_free=0.1361 | n_water=996 | time (s): 4.300 (total time: 128.230) Refine new water occ: r_work=0.1187 r_free=0.1342 adp: r_work=0.1187 r_free=0.1342 occ: r_work=0.1185 r_free=0.1342 adp: r_work=0.1185 r_free=0.1342 occ: r_work=0.1184 r_free=0.1343 adp: r_work=0.1183 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1343 r_work=0.1183 r_free=0.1343 | n_water=996 | time (s): 262.710 (total time: 390.940) Filter (q & B) r_work=0.1188 r_free=0.1345 | n_water=909 | time (s): 4.350 (total time: 395.290) Filter (dist only) r_work=0.1189 r_free=0.1345 | n_water=908 | time (s): 114.290 (total time: 509.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.552504 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.885571 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1350 0.0159 0.039 1.1 5.8 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.50 1.59 1.700 13.912 13.886 3.757 11.93 13.55 1.62 1.733 13.891 13.886 3.756 Individual atomic B min max mean iso aniso Overall: 5.60 63.11 14.81 0.86 541 3271 Protein: 5.60 28.06 10.42 0.86 0 2902 Water: 5.99 63.11 28.85 N/A 541 367 Other: 13.87 22.40 18.14 N/A 0 2 Chain A: 5.69 52.44 12.27 N/A 0 1624 Chain B: 5.60 63.11 12.11 N/A 0 1647 Chain S: 5.99 59.26 30.68 N/A 541 0 Histogram: Values Number of atoms 5.60 - 11.35 2048 11.35 - 17.10 827 17.10 - 22.85 275 22.85 - 28.61 204 28.61 - 34.36 202 34.36 - 40.11 112 40.11 - 45.86 94 45.86 - 51.61 38 51.61 - 57.36 7 57.36 - 63.11 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1355 r_work=0.1194 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1356 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1354 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755201 | | target function (ml) not normalized (work): 703307.907022 | | target function (ml) not normalized (free): 14735.961470 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1511 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1401 0.1511 n_refl.: 191130 overall B=-0.02 to atoms: r(all,work,free)=0.1400 0.1398 0.1508 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1355 n_refl.: 191130 remove outliers: r(all,work,free)=0.1194 0.1191 0.1355 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 91.09 89 3 0.3561 356.978 330.690 0.408 0.974 0.213 13.296-10.522 97.03 97 1 0.2378 481.494 459.693 0.681 0.975 0.146 10.503-8.327 98.35 176 3 0.2168 503.108 494.729 0.863 0.976 0.108 8.318-6.595 100.00 360 8 0.2175 375.779 369.729 0.882 0.976 0.086 6.588-5.215 100.00 711 7 0.1912 345.304 334.561 0.876 0.976 0.073 5.214-4.128 98.38 1367 28 0.1233 505.074 499.065 0.968 0.977 0.060 4.126-3.266 94.74 2603 46 0.1173 460.402 452.495 1.027 0.979 0.000 3.266-2.585 99.86 5447 97 0.1119 310.576 306.942 1.014 0.980 0.000 2.585-2.046 97.45 10613 204 0.0961 234.312 231.644 1.023 0.982 0.000 2.046-1.619 99.39 21536 464 0.0911 138.677 137.306 1.041 0.986 0.000 1.619-1.281 98.00 42464 925 0.0945 74.656 74.002 1.035 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.050 38.335 1.009 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0507 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1355 | n_water=908 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1191 r_free=0.1355 | n_water=907 | time (s): 109.650 (total time: 112.110) Filter (q & B) r_work=0.1192 r_free=0.1354 | n_water=896 | time (s): 5.090 (total time: 117.200) Compute maps r_work=0.1192 r_free=0.1354 | n_water=896 | time (s): 1.840 (total time: 119.040) Filter (map) r_work=0.1212 r_free=0.1359 | n_water=784 | time (s): 3.930 (total time: 122.970) Find peaks r_work=0.1212 r_free=0.1359 | n_water=784 | time (s): 0.600 (total time: 123.570) Add new water r_work=0.1220 r_free=0.1372 | n_water=990 | time (s): 4.000 (total time: 127.570) Refine new water occ: r_work=0.1188 r_free=0.1352 adp: r_work=0.1189 r_free=0.1352 occ: r_work=0.1187 r_free=0.1352 adp: r_work=0.1187 r_free=0.1352 occ: r_work=0.1185 r_free=0.1352 adp: r_work=0.1185 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1352 r_work=0.1185 r_free=0.1352 | n_water=990 | time (s): 209.350 (total time: 336.920) Filter (q & B) r_work=0.1189 r_free=0.1353 | n_water=912 | time (s): 5.660 (total time: 342.580) Filter (dist only) r_work=0.1190 r_free=0.1351 | n_water=909 | time (s): 118.990 (total time: 461.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.527168 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.025735 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 0.1358 0.0165 0.039 1.1 6.1 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.58 1.65 1.688 13.854 14.026 3.757 11.93 13.60 1.67 1.686 13.849 14.026 3.755 Individual atomic B min max mean iso aniso Overall: 5.62 62.62 14.77 0.86 542 3271 Protein: 5.62 28.03 10.42 0.86 0 2902 Water: 6.04 62.62 28.64 N/A 542 367 Other: 13.89 22.37 18.13 N/A 0 2 Chain A: 5.72 52.31 12.24 N/A 0 1624 Chain B: 5.62 62.62 12.09 N/A 0 1647 Chain S: 6.04 59.25 30.49 N/A 542 0 Histogram: Values Number of atoms 5.62 - 11.32 2043 11.32 - 17.02 827 17.02 - 22.72 280 22.72 - 28.42 204 28.42 - 34.12 207 34.12 - 39.82 105 39.82 - 45.52 95 45.52 - 51.22 39 51.22 - 56.92 8 56.92 - 62.62 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1360 r_work=0.1193 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1360 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754328 | | target function (ml) not normalized (work): 703144.413403 | | target function (ml) not normalized (free): 14735.802105 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1359 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1410 0.1408 0.1518 n_refl.: 191130 remove outliers: r(all,work,free)=0.1410 0.1408 0.1518 n_refl.: 191130 overall B=-0.12 to atoms: r(all,work,free)=0.1391 0.1389 0.1503 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1357 n_refl.: 191130 remove outliers: r(all,work,free)=0.1194 0.1190 0.1357 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3527 356.978 329.497 0.399 0.974 0.209 13.296-10.522 96.04 96 1 0.2299 480.613 452.019 0.666 0.975 0.137 10.503-8.327 98.35 176 3 0.2192 503.108 494.693 0.850 0.976 0.103 8.318-6.595 100.00 360 8 0.2166 375.779 369.397 0.869 0.976 0.085 6.588-5.215 100.00 711 7 0.1944 345.304 334.587 0.863 0.976 0.070 5.214-4.128 98.38 1367 28 0.1236 505.074 499.201 0.953 0.977 0.050 4.126-3.266 94.74 2603 46 0.1175 460.402 452.647 1.013 0.979 0.000 3.266-2.585 99.86 5447 97 0.1124 310.576 306.989 0.998 0.980 0.000 2.585-2.046 97.45 10613 204 0.0960 234.312 231.676 1.005 0.983 0.000 2.046-1.619 99.39 21536 464 0.0910 138.677 137.325 1.020 0.987 0.000 1.619-1.281 98.00 42464 925 0.0942 74.656 74.014 1.009 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.050 38.336 0.976 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0260 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1357 After: r_work=0.1192 r_free=0.1358 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1358 | n_water=909 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1192 r_free=0.1358 | n_water=909 | time (s): 115.530 (total time: 117.730) Filter (q & B) r_work=0.1192 r_free=0.1356 | n_water=902 | time (s): 4.610 (total time: 122.340) Compute maps r_work=0.1192 r_free=0.1356 | n_water=902 | time (s): 2.270 (total time: 124.610) Filter (map) r_work=0.1211 r_free=0.1362 | n_water=798 | time (s): 5.630 (total time: 130.240) Find peaks r_work=0.1211 r_free=0.1362 | n_water=798 | time (s): 0.800 (total time: 131.040) Add new water r_work=0.1218 r_free=0.1373 | n_water=1006 | time (s): 5.110 (total time: 136.150) Refine new water occ: r_work=0.1188 r_free=0.1348 adp: r_work=0.1188 r_free=0.1349 occ: r_work=0.1186 r_free=0.1347 adp: r_work=0.1186 r_free=0.1348 occ: r_work=0.1185 r_free=0.1347 adp: r_work=0.1185 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1348 r_work=0.1185 r_free=0.1348 | n_water=1006 | time (s): 253.600 (total time: 389.750) Filter (q & B) r_work=0.1190 r_free=0.1353 | n_water=915 | time (s): 4.520 (total time: 394.270) Filter (dist only) r_work=0.1190 r_free=0.1353 | n_water=912 | time (s): 122.010 (total time: 516.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565389 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.489808 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1354 0.0164 0.039 1.1 7.3 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.54 1.64 1.686 13.746 14.490 3.755 11.90 13.56 1.65 1.680 13.745 14.490 3.753 Individual atomic B min max mean iso aniso Overall: 5.55 61.59 14.66 0.86 545 3271 Protein: 5.55 28.03 10.32 0.86 0 2902 Water: 5.99 61.59 28.45 N/A 545 367 Other: 13.82 22.22 18.02 N/A 0 2 Chain A: 5.64 51.94 12.11 N/A 0 1624 Chain B: 5.55 61.59 11.97 N/A 0 1647 Chain S: 5.99 59.31 30.38 N/A 545 0 Histogram: Values Number of atoms 5.55 - 11.15 2022 11.15 - 16.76 844 16.76 - 22.36 282 22.36 - 27.96 196 27.96 - 33.57 206 33.57 - 39.17 118 39.17 - 44.78 88 44.78 - 50.38 46 50.38 - 55.99 8 55.99 - 61.59 6 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1356 r_work=0.1190 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1356 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1355 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752645 | | target function (ml) not normalized (work): 702825.311990 | | target function (ml) not normalized (free): 14727.321951 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1353 0.1494 5.6857 5.7668| | 2: 2.94 - 2.33 1.00 7339 128 0.1069 0.1308 5.0795 5.1732| | 3: 2.33 - 2.04 0.96 6939 150 0.0898 0.1186 4.6548 4.7538| | 4: 2.04 - 1.85 1.00 7170 155 0.0900 0.1051 4.3922 4.5746| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.1000 4.1511 4.2566| | 6: 1.72 - 1.62 0.99 7102 142 0.0891 0.1079 3.9418 4.0728| | 7: 1.62 - 1.54 0.99 7104 148 0.0884 0.0958 3.7934 3.9211| | 8: 1.54 - 1.47 0.96 6798 152 0.0887 0.1304 3.6935 3.8975| | 9: 1.47 - 1.41 0.98 6938 155 0.0922 0.1111 3.6166 3.7458| | 10: 1.41 - 1.36 0.99 7022 150 0.0974 0.1183 3.5529 3.6719| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1123 3.4831 3.5806| | 12: 1.32 - 1.28 0.98 6975 149 0.1029 0.1128 3.4568 3.5859| | 13: 1.28 - 1.25 0.98 6907 166 0.1034 0.1226 3.4324 3.5523| | 14: 1.25 - 1.22 0.98 7015 112 0.1101 0.1584 3.4308 3.6799| | 15: 1.22 - 1.19 0.98 6956 137 0.1163 0.1243 3.4473 3.4941| | 16: 1.19 - 1.17 0.93 6604 132 0.1245 0.1563 3.4647 3.6655| | 17: 1.17 - 1.14 0.98 6940 135 0.1296 0.1230 3.4333 3.4413| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1716 3.4374 3.5351| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1755 3.4192 3.602| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1571 3.4101 3.431| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2128 3.4184 3.5022| | 22: 1.07 - 1.05 0.97 6836 135 0.1901 0.1955 3.413 3.4162| | 23: 1.05 - 1.03 0.97 6827 159 0.2116 0.2027 3.433 3.4863| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2254 3.4363 3.5102| | 25: 1.02 - 1.01 0.93 6552 130 0.2609 0.2519 3.4492 3.5263| | 26: 1.01 - 0.99 0.96 6767 158 0.2752 0.2857 3.4158 3.4256| | 27: 0.99 - 0.98 0.94 6647 131 0.3036 0.2809 3.4683 3.3964| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7397 127 0.93 11.71 1.00 0.98 11259.20| | 2: 2.94 - 2.33 7339 128 0.93 12.77 0.99 0.98 5147.79| | 3: 2.33 - 2.04 6939 150 0.96 7.66 1.01 0.98 1703.97| | 4: 2.04 - 1.85 7170 155 0.96 7.71 1.00 0.98 1012.23| | 5: 1.85 - 1.72 7113 159 0.96 8.10 1.00 0.98 636.98| | 6: 1.72 - 1.62 7102 142 0.96 7.96 1.00 0.99 438.61| | 7: 1.62 - 1.54 7104 148 0.96 8.05 1.01 1.00 331.51| | 8: 1.54 - 1.47 6798 152 0.96 8.17 1.01 1.00 274.37| | 9: 1.47 - 1.41 6938 155 0.96 8.38 1.00 1.00 227.71| | 10: 1.41 - 1.36 7022 150 0.96 8.84 1.00 1.00 200.51| | 11: 1.36 - 1.32 6997 151 0.96 8.86 0.99 0.98 173.32| | 12: 1.32 - 1.28 6975 149 0.96 8.93 0.98 0.97 159.76| | 13: 1.28 - 1.25 6907 166 0.96 9.44 1.01 0.99 157.03| | 14: 1.25 - 1.22 7015 112 0.95 10.66 1.01 0.99 162.52| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 1.00 166.76| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.00 0.98 161.13| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.99 154.87| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.97 148.17| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.97 151.24| | 20: 1.10 - 1.08 6884 147 0.92 15.18 1.00 0.96 149.96| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.96 153.16| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.95 154.99| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.95 165.21| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.95 179.61| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.92 182.60| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.91 177.10| | 27: 0.99 - 0.98 6647 131 0.82 26.35 0.99 0.90 161.64| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 148.17 max = 11259.20 mean = 928.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.27| |phase err.(test): min = 0.00 max = 89.94 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1501 n_refl.: 191129 remove outliers: r(all,work,free)=0.1395 0.1393 0.1501 n_refl.: 191129 overall B=-0.03 to atoms: r(all,work,free)=0.1391 0.1389 0.1497 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1188 0.1355 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1188 0.1355 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3503 356.978 328.995 0.427 0.915 0.215 13.296-10.522 96.04 96 1 0.2332 480.613 461.522 0.723 0.916 0.140 10.503-8.327 98.35 176 3 0.2170 503.108 494.985 0.905 0.917 0.105 8.318-6.595 100.00 360 8 0.2150 375.779 369.808 0.928 0.917 0.090 6.588-5.215 100.00 711 7 0.1926 345.304 334.814 0.920 0.917 0.080 5.214-4.128 98.38 1367 28 0.1238 505.074 499.313 1.015 0.918 0.034 4.126-3.266 94.74 2603 46 0.1171 460.402 452.710 1.081 0.920 0.000 3.266-2.585 99.86 5447 97 0.1116 310.576 307.040 1.064 0.921 0.000 2.585-2.046 97.45 10613 204 0.0959 234.312 231.684 1.072 0.924 0.000 2.046-1.619 99.39 21536 464 0.0909 138.677 137.319 1.087 0.928 0.000 1.619-1.281 98.00 42464 925 0.0943 74.656 74.003 1.075 0.936 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.050 38.337 1.040 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0072 ================= 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 : 0.2040 0.1947 0.083 5.213 5.2 78.0 14.6 805 0.000 1_bss: 0.1805 0.1885 0.083 5.213 5.2 78.0 14.6 805 0.000 1_settarget: 0.1805 0.1885 0.083 5.213 5.2 78.0 14.6 805 0.000 1_nqh: 0.1805 0.1885 0.083 5.213 5.2 78.0 14.6 805 0.000 1_weight: 0.1805 0.1885 0.083 5.213 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1272 0.1482 0.036 1.178 5.2 78.0 14.6 805 0.142 1_adp: 0.1305 0.1556 0.036 1.178 5.2 73.0 15.1 805 0.142 1_regHadp: 0.1303 0.1551 0.036 1.178 5.2 73.0 15.1 805 0.142 1_occ: 0.1288 0.1537 0.036 1.178 5.2 73.0 15.1 805 0.142 2_bss: 0.1280 0.1530 0.036 1.178 5.4 73.2 15.3 805 0.142 2_settarget: 0.1280 0.1530 0.036 1.178 5.4 73.2 15.3 805 0.142 2_updatecdl: 0.1280 0.1530 0.036 1.196 5.4 73.2 15.3 805 0.142 2_nqh: 0.1280 0.1530 0.036 1.196 5.4 73.2 15.3 805 0.142 2_sol: 0.1272 0.1508 0.036 1.196 5.4 73.2 16.3 897 n/a 2_weight: 0.1272 0.1508 0.036 1.196 5.4 73.2 16.3 897 n/a 2_xyzrec: 0.1253 0.1519 0.039 1.161 5.4 73.2 16.3 897 n/a 2_adp: 0.1231 0.1506 0.039 1.161 5.5 68.2 16.4 897 n/a 2_regHadp: 0.1231 0.1508 0.039 1.161 5.5 68.2 16.4 897 n/a 2_occ: 0.1224 0.1500 0.039 1.161 5.5 68.2 16.4 897 n/a 3_bss: 0.1231 0.1505 0.039 1.161 5.4 68.1 16.3 897 n/a 3_settarget: 0.1231 0.1505 0.039 1.161 5.4 68.1 16.3 897 n/a 3_updatecdl: 0.1231 0.1505 0.039 1.165 5.4 68.1 16.3 897 n/a 3_nqh: 0.1231 0.1505 0.039 1.165 5.4 68.1 16.3 897 n/a 3_sol: 0.1247 0.1506 0.039 1.165 5.4 68.1 15.6 894 n/a 3_weight: 0.1247 0.1506 0.039 1.165 5.4 68.1 15.6 894 n/a 3_xyzrec: 0.1238 0.1434 0.035 1.116 5.4 68.1 15.6 894 n/a 3_adp: 0.1232 0.1391 0.035 1.116 5.5 67.7 15.4 894 n/a 3_regHadp: 0.1232 0.1391 0.035 1.116 5.5 67.7 15.4 894 n/a 3_occ: 0.1227 0.1388 0.035 1.116 5.5 67.7 15.4 894 n/a 4_bss: 0.1223 0.1381 0.035 1.116 5.5 67.6 15.4 894 n/a 4_settarget: 0.1223 0.1381 0.035 1.116 5.5 67.6 15.4 894 n/a 4_updatecdl: 0.1223 0.1381 0.035 1.116 5.5 67.6 15.4 894 n/a 4_nqh: 0.1223 0.1381 0.035 1.116 5.5 67.6 15.4 894 n/a 4_sol: 0.1209 0.1371 0.035 1.116 5.5 67.6 15.1 871 n/a 4_weight: 0.1209 0.1371 0.035 1.116 5.5 67.6 15.1 871 n/a 4_xyzrec: 0.1209 0.1367 0.036 1.121 5.5 67.6 15.1 871 n/a 4_adp: 0.1201 0.1364 0.036 1.121 5.5 67.2 15.0 871 n/a 4_regHadp: 0.1201 0.1364 0.036 1.121 5.5 67.2 15.0 871 n/a 4_occ: 0.1199 0.1359 0.036 1.121 5.5 67.2 15.0 871 n/a 5_bss: 0.1195 0.1356 0.036 1.121 5.4 67.2 15.0 871 n/a 5_settarget: 0.1195 0.1356 0.036 1.121 5.4 67.2 15.0 871 n/a 5_updatecdl: 0.1195 0.1356 0.036 1.121 5.4 67.2 15.0 871 n/a 5_nqh: 0.1195 0.1356 0.036 1.121 5.4 67.2 15.0 871 n/a 5_sol: 0.1195 0.1354 0.036 1.121 5.4 67.2 15.1 884 n/a 5_weight: 0.1195 0.1354 0.036 1.121 5.4 67.2 15.1 884 n/a 5_xyzrec: 0.1196 0.1355 0.036 1.134 5.4 67.2 15.1 884 n/a 5_adp: 0.1201 0.1360 0.036 1.134 5.6 66.9 15.0 884 n/a 5_regHadp: 0.1201 0.1360 0.036 1.134 5.6 66.9 15.0 884 n/a 5_occ: 0.1200 0.1362 0.036 1.134 5.6 66.9 15.0 884 n/a 6_bss: 0.1199 0.1360 0.036 1.134 5.5 66.9 15.0 884 n/a 6_settarget: 0.1199 0.1360 0.036 1.134 5.5 66.9 15.0 884 n/a 6_updatecdl: 0.1199 0.1360 0.036 1.134 5.5 66.9 15.0 884 n/a 6_nqh: 0.1199 0.1360 0.036 1.134 5.5 66.9 15.0 884 n/a 6_sol: 0.1198 0.1353 0.036 1.134 5.5 66.9 15.0 892 n/a 6_weight: 0.1198 0.1353 0.036 1.134 5.5 66.9 15.0 892 n/a 6_xyzrec: 0.1202 0.1356 0.037 1.130 5.5 66.9 15.0 892 n/a 6_adp: 0.1203 0.1360 0.037 1.130 5.6 65.9 14.9 892 n/a 6_regHadp: 0.1204 0.1360 0.037 1.130 5.6 65.9 14.9 892 n/a 6_occ: 0.1201 0.1356 0.037 1.130 5.6 65.9 14.9 892 n/a 7_bss: 0.1200 0.1354 0.037 1.130 5.5 65.8 14.9 892 n/a 7_settarget: 0.1200 0.1354 0.037 1.130 5.5 65.8 14.9 892 n/a 7_updatecdl: 0.1200 0.1354 0.037 1.130 5.5 65.8 14.9 892 n/a 7_nqh: 0.1200 0.1354 0.037 1.130 5.5 65.8 14.9 892 n/a 7_sol: 0.1200 0.1352 0.037 1.130 5.5 65.8 14.8 890 n/a 7_weight: 0.1200 0.1352 0.037 1.130 5.5 65.8 14.8 890 n/a 7_xyzrec: 0.1203 0.1357 0.038 1.135 5.5 65.8 14.8 890 n/a 7_adp: 0.1205 0.1362 0.038 1.135 5.6 64.5 14.7 890 n/a 7_regHadp: 0.1205 0.1362 0.038 1.135 5.6 64.5 14.7 890 n/a 7_occ: 0.1202 0.1364 0.038 1.135 5.6 64.5 14.7 890 n/a 8_bss: 0.1192 0.1351 0.038 1.135 5.6 64.5 14.7 890 n/a 8_settarget: 0.1192 0.1351 0.038 1.135 5.6 64.5 14.7 890 n/a 8_updatecdl: 0.1192 0.1351 0.038 1.134 5.6 64.5 14.7 890 n/a 8_nqh: 0.1192 0.1351 0.038 1.134 5.6 64.5 14.7 890 n/a 8_sol: 0.1189 0.1345 0.038 1.134 5.6 64.5 14.8 908 n/a 8_weight: 0.1189 0.1345 0.038 1.134 5.6 64.5 14.8 908 n/a 8_xyzrec: 0.1191 0.1350 0.039 1.116 5.6 64.5 14.8 908 n/a 8_adp: 0.1193 0.1355 0.039 1.116 5.6 63.1 14.8 908 n/a 8_regHadp: 0.1194 0.1356 0.039 1.116 5.6 63.1 14.8 908 n/a 8_occ: 0.1192 0.1354 0.039 1.116 5.6 63.1 14.8 908 n/a 9_bss: 0.1191 0.1355 0.039 1.116 5.6 63.1 14.8 908 n/a 9_settarget: 0.1191 0.1355 0.039 1.116 5.6 63.1 14.8 908 n/a 9_updatecdl: 0.1191 0.1355 0.039 1.117 5.6 63.1 14.8 908 n/a 9_nqh: 0.1191 0.1355 0.039 1.117 5.6 63.1 14.8 908 n/a 9_sol: 0.1190 0.1351 0.039 1.117 5.6 63.1 14.8 909 n/a 9_weight: 0.1190 0.1351 0.039 1.117 5.6 63.1 14.8 909 n/a 9_xyzrec: 0.1193 0.1358 0.039 1.113 5.6 63.1 14.8 909 n/a 9_adp: 0.1193 0.1360 0.039 1.113 5.6 62.6 14.8 909 n/a 9_regHadp: 0.1193 0.1360 0.039 1.113 5.6 62.6 14.8 909 n/a 9_occ: 0.1192 0.1359 0.039 1.113 5.6 62.6 14.8 909 n/a 10_bss: 0.1191 0.1357 0.039 1.113 5.5 62.5 14.6 909 n/a 10_settarget: 0.1191 0.1357 0.039 1.113 5.5 62.5 14.6 909 n/a 10_updatecdl: 0.1191 0.1357 0.039 1.113 5.5 62.5 14.6 909 n/a 10_setrh: 0.1192 0.1358 0.039 1.113 5.5 62.5 14.6 909 n/a 10_nqh: 0.1192 0.1358 0.039 1.113 5.5 62.5 14.6 909 n/a 10_sol: 0.1190 0.1353 0.039 1.113 5.5 62.5 14.7 912 n/a 10_weight: 0.1190 0.1353 0.039 1.113 5.5 62.5 14.7 912 n/a 10_xyzrec: 0.1191 0.1354 0.039 1.143 5.5 62.5 14.7 912 n/a 10_adp: 0.1190 0.1356 0.039 1.143 5.5 61.6 14.7 912 n/a 10_regHadp: 0.1190 0.1356 0.039 1.143 5.5 61.6 14.7 912 n/a 10_occ: 0.1189 0.1355 0.039 1.143 5.5 61.6 14.7 912 n/a end: 0.1189 0.1355 0.039 1.143 5.5 61.6 14.6 912 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4824775_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4824775_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2100 Refinement macro-cycles (run) : 11999.2600 Write final files (write_after_run_outputs) : 161.7300 Total : 12167.2000 Total CPU time: 3.39 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:39:55 PST -0800 (1736735995.83 s) Start R-work = 0.1805, R-free = 0.1885 Final R-work = 0.1189, R-free = 0.1355 =============================================================================== Job complete usr+sys time: 12457.20 seconds wall clock time: 208 minutes 36.24 seconds (12516.24 seconds total)