Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4016894.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4016894.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4016894.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.54, per 1000 atoms: 0.38 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: 2.755 distance_ideal: 2.720 ideal - model: -0.035 slack: 0.000 delta_slack: -0.035 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: 2.670 distance_ideal: 2.710 ideal - model: 0.040 slack: 0.000 delta_slack: 0.040 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: 1.13 Conformation dependent library (CDL) restraints added in 223.1 milliseconds Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 1.00: 467 1.00 - 1.24: 2717 1.24 - 1.48: 1589 1.48 - 1.72: 1141 1.72 - 1.97: 20 Bond restraints: 5934 Sorted by residual: bond pdb=" C LEU B 113 " pdb=" N VAL B 114 " ideal model delta sigma weight residual 1.329 1.592 -0.263 1.13e-02 7.83e+03 5.41e+02 bond pdb=" C GLU A 80 " pdb=" O GLU A 80 " ideal model delta sigma weight residual 1.237 1.490 -0.253 1.17e-02 7.31e+03 4.68e+02 bond pdb=" N LEU A 53 " pdb=" CA LEU A 53 " ideal model delta sigma weight residual 1.454 1.199 0.255 1.19e-02 7.06e+03 4.60e+02 bond pdb=" N SER B 48 " pdb=" H SER B 48 " ideal model delta sigma weight residual 0.860 1.279 -0.419 2.00e-02 2.50e+03 4.39e+02 bond pdb=" C LEU B 24 " pdb=" N LEU B 25 " ideal model delta sigma weight residual 1.334 1.081 0.253 1.27e-02 6.20e+03 3.98e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 5655 4.22 - 8.43: 3586 8.43 - 12.65: 1320 12.65 - 16.86: 232 16.86 - 21.08: 17 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.22 134.50 -12.28 6.50e-01 2.37e+00 3.57e+02 angle pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " ideal model delta sigma weight residual 119.98 133.43 -13.45 8.50e-01 1.38e+00 2.50e+02 angle pdb=" O MET A 187 " pdb=" C MET A 187 " pdb=" N ALA A 188 " ideal model delta sigma weight residual 122.94 140.63 -17.69 1.12e+00 7.97e-01 2.50e+02 angle pdb=" O THR B 91 " pdb=" C THR B 91 " pdb=" N VAL B 92 " ideal model delta sigma weight residual 122.09 138.95 -16.86 1.08e+00 8.57e-01 2.44e+02 angle pdb=" CA GLY B 41 " pdb=" C GLY B 41 " pdb=" O GLY B 41 " ideal model delta sigma weight residual 119.10 135.83 -16.73 1.09e+00 8.42e-01 2.36e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 1825 16.42 - 32.85: 148 32.85 - 49.27: 51 49.27 - 65.69: 20 65.69 - 82.11: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual 180.00 -156.73 -23.27 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.218: 197 0.218 - 0.436: 165 0.436 - 0.653: 92 0.653 - 0.871: 33 0.871 - 1.088: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA GLU A 61 " pdb=" N GLU A 61 " pdb=" C GLU A 61 " pdb=" CB GLU A 61 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA PRO B 158 " pdb=" N PRO B 158 " pdb=" C PRO B 158 " pdb=" CB PRO B 158 " both_signs ideal model delta sigma weight residual False 2.72 1.72 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA GLU A 196 " pdb=" N GLU A 196 " pdb=" C GLU A 196 " pdb=" CB GLU A 196 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.24e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.074 2.00e-02 2.50e+03 6.19e-02 1.53e+02 pdb=" CG TRP B 139 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.108 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.080 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " 0.049 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.111 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.047 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.044 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.084 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 82 " -0.105 2.00e-02 2.50e+03 7.01e-02 1.47e+02 pdb=" CG PHE B 82 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 82 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE B 82 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 PHE B 82 " 0.052 2.00e-02 2.50e+03 pdb=" CE2 PHE B 82 " -0.097 2.00e-02 2.50e+03 pdb=" CZ PHE B 82 " -0.074 2.00e-02 2.50e+03 pdb=" HD1 PHE B 82 " 0.082 2.00e-02 2.50e+03 pdb=" HD2 PHE B 82 " 0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE B 82 " 0.033 2.00e-02 2.50e+03 pdb=" HE2 PHE B 82 " 0.108 2.00e-02 2.50e+03 pdb=" HZ PHE B 82 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " 0.030 2.00e-02 2.50e+03 6.82e-02 1.40e+02 pdb=" CG TYR B 67 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " 0.068 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " -0.137 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " 0.088 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " -0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " -0.110 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " 0.004 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.62: 24 1.62 - 2.36: 2443 2.36 - 3.11: 22272 3.11 - 3.85: 32945 3.85 - 4.60: 52615 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110299 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.871 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.056 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.057 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.160 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.175 2.620 ... (remaining 110294 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_4016894_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= 0.2039 r_free= 0.2010 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.305478 | | target function (ml) not normalized (work): 806471.955642 | | target function (ml) not normalized (free): 16610.921367 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2132 0.1865 6.7133 6.2897| | 2: 2.94 - 2.33 1.00 7339 128 0.1628 0.1650 5.5308 5.5985| | 3: 2.33 - 2.04 0.96 6939 150 0.1629 0.1626 5.1391 5.1496| | 4: 2.04 - 1.85 1.00 7170 155 0.1773 0.1752 4.9685 5.1152| | 5: 1.85 - 1.72 0.99 7113 159 0.1933 0.1754 4.8129 4.8306| | 6: 1.72 - 1.62 0.99 7102 142 0.1973 0.2046 4.6707 4.7651| | 7: 1.62 - 1.54 0.99 7104 148 0.2035 0.1860 4.5774 4.6104| | 8: 1.54 - 1.47 0.96 6798 152 0.2034 0.2284 4.4805 4.5341| | 9: 1.47 - 1.41 0.98 6938 155 0.2110 0.2389 4.4085 4.5104| | 10: 1.41 - 1.36 0.99 7022 150 0.2131 0.2081 4.3098 4.2977| | 11: 1.36 - 1.32 0.99 6997 151 0.2107 0.2165 4.2387 4.2688| | 12: 1.32 - 1.28 0.98 6976 149 0.2103 0.1950 4.1853 4.2133| | 13: 1.28 - 1.25 0.98 6907 166 0.2004 0.2113 4.1117 4.1681| | 14: 1.25 - 1.22 0.98 7015 113 0.2118 0.2139 4.0908 4.2262| | 15: 1.22 - 1.19 0.98 6957 137 0.2111 0.2219 4.055 4.0847| | 16: 1.19 - 1.17 0.93 6604 132 0.2134 0.2248 4.0092 4.0981| | 17: 1.17 - 1.14 0.98 6941 135 0.2205 0.1906 3.9701 3.9681| | 18: 1.14 - 1.12 0.98 6875 142 0.2251 0.2552 3.9386 3.9875| | 19: 1.12 - 1.10 0.97 6949 106 0.2281 0.2230 3.8758 3.9299| | 20: 1.10 - 1.08 0.97 6884 147 0.2326 0.2580 3.8298 3.9704| | 21: 1.08 - 1.07 0.97 6852 152 0.2412 0.2791 3.7892 3.8183| | 22: 1.07 - 1.05 0.97 6838 135 0.2565 0.2399 3.7539 3.7212| | 23: 1.05 - 1.03 0.97 6829 159 0.2724 0.2654 3.7293 3.8604| | 24: 1.03 - 1.02 0.96 6785 133 0.2852 0.2723 3.6997 3.7234| | 25: 1.02 - 1.01 0.93 6552 130 0.3091 0.2831 3.6844 3.7257| | 26: 1.01 - 0.99 0.96 6767 158 0.3203 0.3309 3.6268 3.6375| | 27: 0.99 - 0.98 0.94 6648 131 0.3376 0.3256 3.6327 3.6249| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.89 0.91 0.98 33746.91| | 2: 2.94 - 2.33 7339 128 0.86 20.81 1.09 1.02 14623.21| | 3: 2.33 - 2.04 6939 150 0.93 12.83 1.11 1.06 4306.73| | 4: 2.04 - 1.85 7170 155 0.92 14.03 1.12 1.07 2942.61| | 5: 1.85 - 1.72 7113 159 0.90 16.41 1.11 1.06 2237.26| | 6: 1.72 - 1.62 7102 142 0.89 17.65 1.11 1.06 1802.20| | 7: 1.62 - 1.54 7104 148 0.88 18.83 1.11 1.05 1483.01| | 8: 1.54 - 1.47 6798 152 0.88 19.30 1.10 1.06 1267.21| | 9: 1.47 - 1.41 6938 155 0.88 19.62 1.10 1.07 1058.40| | 10: 1.41 - 1.36 7022 150 0.87 20.26 1.09 1.06 874.70| | 11: 1.36 - 1.32 6997 151 0.87 20.02 1.08 1.05 742.87| | 12: 1.32 - 1.28 6976 149 0.87 19.88 1.08 1.04 649.35| | 13: 1.28 - 1.25 6907 166 0.87 19.99 1.07 1.04 607.97| | 14: 1.25 - 1.22 7015 113 0.86 21.04 1.07 1.03 587.22| | 15: 1.22 - 1.19 6957 137 0.86 21.37 1.08 1.04 570.62| | 16: 1.19 - 1.17 6604 132 0.86 21.26 1.08 1.03 522.80| | 17: 1.17 - 1.14 6941 135 0.86 21.52 1.08 1.03 462.44| | 18: 1.14 - 1.12 6875 142 0.86 21.85 1.08 1.00 422.00| | 19: 1.12 - 1.10 6949 106 0.85 22.91 1.07 1.00 402.28| | 20: 1.10 - 1.08 6884 147 0.83 24.23 1.06 0.97 383.33| | 21: 1.08 - 1.07 6852 152 0.83 24.92 1.05 0.96 356.86| | 22: 1.07 - 1.05 6838 135 0.82 26.01 1.05 0.97 334.79| | 23: 1.05 - 1.03 6829 159 0.80 27.25 1.06 0.98 327.58| | 24: 1.03 - 1.02 6785 133 0.79 28.79 1.05 0.99 324.71| | 25: 1.02 - 1.01 6552 130 0.77 30.54 1.03 0.94 311.74| | 26: 1.01 - 0.99 6767 158 0.74 33.11 1.03 0.91 302.51| | 27: 0.99 - 0.98 6648 131 0.73 34.37 1.04 0.87 300.41| |alpha: min = 0.87 max = 1.07 mean = 1.01| |beta: min = 300.41 max = 33746.91 mean = 2787.09| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.09| |phase err.(test): min = 0.00 max = 88.91 mean = 22.19| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.263 2950 Z= 5.526 Angle : 5.196 21.077 4018 Z= 3.696 Chirality : 0.370 1.088 492 Planarity : 0.032 0.145 512 Dihedral : 12.968 82.108 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.63 % Favored : 95.85 % Rotamer: Outliers : 0.65 % Allowed : 5.16 % Favored : 94.19 % Cbeta Deviations : 33.15 % 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: -2.18 (0.39), residues: 386 helix: -2.51 (0.30), residues: 144 sheet: -1.16 (0.47), residues: 86 loop : -0.16 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.079 0.016 ARG A 97 TYR 0.122 0.041 TYR B 194 PHE 0.097 0.042 PHE A 119 TRP 0.131 0.041 TRP B 146 HIS 0.067 0.027 HIS A 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= 0.2039 r_free= 0.2010 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.305478 | | target function (ml) not normalized (work): 806471.955642 | | target function (ml) not normalized (free): 16610.921367 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2038 0.2039 0.2010 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2038 0.2039 0.2010 n_refl.: 191155 remove outliers: r(all,work,free)=0.2038 0.2039 0.2010 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2039 0.2040 0.2010 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1806 0.1803 0.1944 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1800 0.1943 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4064 402.814 293.123 0.424 0.932 0.299 13.296-10.522 99.01 99 1 0.2522 528.187 518.132 0.770 0.933 0.252 10.503-8.327 98.90 177 3 0.2454 564.205 559.041 0.949 0.933 0.230 8.318-6.595 100.00 360 8 0.2504 414.736 402.500 0.946 0.932 0.164 6.588-5.215 100.00 711 7 0.2260 381.101 366.165 0.933 0.932 0.140 5.214-4.128 98.38 1367 28 0.1455 557.435 549.797 1.049 0.931 0.080 4.126-3.266 94.74 2603 46 0.1345 508.132 499.047 1.119 0.931 0.018 3.266-2.585 99.86 5447 97 0.1463 342.774 337.828 1.099 0.928 0.000 2.585-2.046 97.45 10613 204 0.1390 258.603 254.159 1.106 0.925 0.000 2.046-1.619 99.39 21536 464 0.1625 153.054 149.778 1.131 0.919 0.000 1.619-1.281 98.00 42464 925 0.1927 82.395 80.128 1.124 0.910 0.000 1.281-0.980 96.53 101826 2055 0.2318 44.202 41.672 1.124 0.894 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0145 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1943 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1800 r_free=0.1943 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.315059 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.173349 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1267 0.1499 0.0232 0.039 1.1 11.0 0.0 0.3 0 11.158 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.67 14.99 2.32 1.117 13.120 571.173 0.018 12.95 15.66 2.71 1.243 13.371 571.173 0.017 Individual atomic B min max mean iso aniso Overall: 5.18 73.05 15.06 1.40 435 3274 Protein: 5.18 40.67 11.01 1.40 0 2902 Water: 6.37 73.05 29.66 N/A 435 370 Other: 16.09 29.78 22.94 N/A 0 2 Chain A: 5.33 59.78 13.07 N/A 0 1626 Chain B: 5.18 73.05 12.79 N/A 0 1648 Chain S: 12.07 67.12 31.13 N/A 435 0 Histogram: Values Number of atoms 5.18 - 11.96 2167 11.96 - 18.75 632 18.75 - 25.54 313 25.54 - 32.33 264 32.33 - 39.11 159 39.11 - 45.90 104 45.90 - 52.69 45 52.69 - 59.48 21 59.48 - 66.27 2 66.27 - 73.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1295 r_free=0.1566 r_work=0.1294 r_free=0.1560 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1294 r_free = 0.1560 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1279 r_free = 0.1551 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1279 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015469 | | target function (ls_wunit_k1) not normalized (work): 2897.299313 | | target function (ls_wunit_k1) not normalized (free): 116.243223 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1285 0.1279 0.1551 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1467 0.1465 0.1632 n_refl.: 191137 remove outliers: r(all,work,free)=0.1467 0.1465 0.1632 n_refl.: 191137 overall B=0.16 to atoms: r(all,work,free)=0.1490 0.1488 0.1641 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1546 n_refl.: 191137 remove outliers: r(all,work,free)=0.1279 0.1274 0.1546 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3602 402.814 379.047 0.468 1.003 0.281 13.296-10.522 99.01 99 1 0.2078 528.187 525.703 0.714 1.004 0.244 10.503-8.327 98.90 177 3 0.1710 564.205 563.128 0.854 1.004 0.193 8.318-6.595 100.00 360 8 0.1702 414.736 413.007 0.872 1.004 0.150 6.588-5.215 100.00 711 7 0.1534 381.101 373.428 0.851 1.004 0.140 5.214-4.128 98.38 1367 28 0.0901 557.435 554.236 0.937 1.005 0.070 4.126-3.266 94.74 2603 46 0.0826 508.132 504.360 1.001 1.005 0.014 3.266-2.585 99.86 5447 97 0.0919 342.774 340.463 0.985 1.005 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.392 0.996 1.005 0.000 2.046-1.619 99.39 21536 464 0.1091 153.054 151.416 1.013 1.005 0.000 1.619-1.281 98.00 42464 925 0.1278 82.395 81.417 1.005 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.149 0.983 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0366 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1546 | n_water=805 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1278 r_free=0.1549 | n_water=796 | time (s): 99.420 (total time: 101.920) Filter (q & B) r_work=0.1278 r_free=0.1549 | n_water=792 | time (s): 4.860 (total time: 106.780) Compute maps r_work=0.1278 r_free=0.1549 | n_water=792 | time (s): 1.840 (total time: 108.620) Filter (map) r_work=0.1305 r_free=0.1529 | n_water=651 | time (s): 4.150 (total time: 112.770) Find peaks r_work=0.1305 r_free=0.1529 | n_water=651 | time (s): 0.590 (total time: 113.360) Add new water r_work=0.1327 r_free=0.1559 | n_water=961 | time (s): 4.920 (total time: 118.280) Refine new water occ: r_work=0.1284 r_free=0.1517 adp: r_work=0.1272 r_free=0.1511 occ: r_work=0.1275 r_free=0.1509 adp: r_work=0.1269 r_free=0.1506 occ: r_work=0.1270 r_free=0.1506 adp: r_work=0.1267 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1506 r_work=0.1267 r_free=0.1506 | n_water=961 | time (s): 77.570 (total time: 195.850) Filter (q & B) r_work=0.1271 r_free=0.1502 | n_water=881 | time (s): 4.420 (total time: 200.270) Filter (dist only) r_work=0.1271 r_free=0.1501 | n_water=880 | time (s): 109.440 (total time: 309.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.693283 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 591.267666 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 0.1254 0.1515 0.0261 0.041 1.2 17.2 0.0 0.3 0 11.847 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.15 2.61 2.045 15.115 591.268 0.015 12.34 14.99 2.65 2.408 15.146 591.268 0.014 Individual atomic B min max mean iso aniso Overall: 5.47 68.21 16.17 1.20 512 3272 Protein: 5.47 40.57 10.99 1.20 0 2902 Water: 6.63 68.21 33.21 N/A 512 368 Other: 16.24 33.13 24.69 N/A 0 2 Chain A: 5.54 56.08 13.00 N/A 0 1624 Chain B: 5.47 68.21 12.84 N/A 0 1648 Chain S: 12.70 65.43 36.92 N/A 512 0 Histogram: Values Number of atoms 5.47 - 11.74 2072 11.74 - 18.02 703 18.02 - 24.29 255 24.29 - 30.57 227 30.57 - 36.84 177 36.84 - 43.12 166 43.12 - 49.39 99 49.39 - 55.66 54 55.66 - 61.94 24 61.94 - 68.21 7 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1499 r_work=0.1235 r_free=0.1500 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1500 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 = 0.1229 r_free = 0.1497 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1497 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013462 | | target function (ls_wunit_k1) not normalized (work): 2521.441388 | | target function (ls_wunit_k1) not normalized (free): 101.533752 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1497 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1596 n_refl.: 191137 remove outliers: r(all,work,free)=0.1439 0.1436 0.1596 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1436 0.1433 0.1594 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1506 n_refl.: 191137 remove outliers: r(all,work,free)=0.1241 0.1236 0.1506 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3274 402.814 378.159 0.484 0.962 0.269 13.296-10.522 99.01 99 1 0.1884 528.187 523.118 0.765 0.963 0.254 10.503-8.327 98.90 177 3 0.1439 564.205 567.648 0.917 0.963 0.189 8.318-6.595 100.00 360 8 0.1556 414.736 414.503 0.937 0.963 0.155 6.588-5.215 100.00 711 7 0.1337 381.101 376.493 0.913 0.963 0.140 5.214-4.128 98.38 1367 28 0.0820 557.435 555.880 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0765 508.132 505.491 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0860 342.774 341.485 1.047 0.962 0.010 2.585-2.046 97.45 10613 204 0.0902 258.603 256.725 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1049 153.054 151.625 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.346 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.216 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=-0.0538 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1506 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1506 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1506 | n_water=880 | time (s): 3.390 (total time: 3.390) Filter (dist) r_work=0.1237 r_free=0.1509 | n_water=875 | time (s): 106.820 (total time: 110.210) Filter (q & B) r_work=0.1237 r_free=0.1509 | n_water=874 | time (s): 5.570 (total time: 115.780) Compute maps r_work=0.1237 r_free=0.1509 | n_water=874 | time (s): 1.980 (total time: 117.760) Filter (map) r_work=0.1275 r_free=0.1512 | n_water=686 | time (s): 4.980 (total time: 122.740) Find peaks r_work=0.1275 r_free=0.1512 | n_water=686 | time (s): 0.820 (total time: 123.560) Add new water r_work=0.1298 r_free=0.1541 | n_water=1006 | time (s): 4.440 (total time: 128.000) Refine new water occ: r_work=0.1247 r_free=0.1496 adp: r_work=0.1242 r_free=0.1491 occ: r_work=0.1238 r_free=0.1488 adp: r_work=0.1238 r_free=0.1487 occ: r_work=0.1236 r_free=0.1485 adp: r_work=0.1236 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1484 r_work=0.1236 r_free=0.1484 | n_water=1006 | time (s): 297.340 (total time: 425.340) Filter (q & B) r_work=0.1240 r_free=0.1490 | n_water=855 | time (s): 5.480 (total time: 430.820) Filter (dist only) r_work=0.1240 r_free=0.1490 | n_water=854 | time (s): 109.420 (total time: 540.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.653687 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.952438 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1227 0.1423 0.0196 0.035 1.1 6.5 0.0 0.0 0 0.827 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.27 14.23 1.96 1.935 14.483 16.952 3.931 12.19 13.84 1.65 2.323 14.372 16.952 3.883 Individual atomic B min max mean iso aniso Overall: 5.55 67.47 15.04 1.05 487 3271 Protein: 5.55 35.76 10.69 1.05 0 2902 Water: 5.73 67.47 29.81 N/A 487 367 Other: 13.81 28.45 21.13 N/A 0 2 Chain A: 5.63 54.42 12.71 N/A 0 1624 Chain B: 5.55 67.47 12.49 N/A 0 1647 Chain S: 5.73 60.24 31.49 N/A 487 0 Histogram: Values Number of atoms 5.55 - 11.75 2135 11.75 - 17.94 696 17.94 - 24.13 281 24.13 - 30.32 243 30.32 - 36.51 174 36.51 - 42.70 128 42.70 - 48.90 69 48.90 - 55.09 25 55.09 - 61.28 6 61.28 - 67.47 1 =========================== Idealize ADP of riding H ========================== r_work=0.1219 r_free=0.1385 r_work=0.1220 r_free=0.1386 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1220 r_free = 0.1386 target_work(ml) = 3.884 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1213 r_free = 0.1373 target_work(ml) = 3.877 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1213 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.877296 | | target function (ml) not normalized (work): 726202.110469 | | target function (ml) not normalized (free): 15166.341807 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1213 0.1373 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1434 0.1433 0.1475 n_refl.: 191137 remove outliers: r(all,work,free)=0.1434 0.1433 0.1475 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1427 0.1427 0.1471 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1213 0.1210 0.1368 n_refl.: 191137 remove outliers: r(all,work,free)=0.1212 0.1209 0.1368 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3854 398.008 362.394 0.427 0.945 0.255 13.296-10.522 99.01 99 1 0.2558 528.187 506.043 0.704 0.947 0.210 10.503-8.327 97.80 175 3 0.1993 554.286 557.798 0.882 0.947 0.187 8.318-6.595 100.00 360 8 0.2128 414.736 409.057 0.897 0.946 0.120 6.588-5.215 100.00 711 7 0.1827 381.101 370.501 0.888 0.946 0.110 5.214-4.128 98.38 1367 28 0.1161 557.435 551.441 0.973 0.947 0.060 4.126-3.266 94.74 2603 46 0.1093 508.132 501.155 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1080 342.774 339.071 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0955 258.603 255.674 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0943 153.054 151.482 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1024 82.395 81.507 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1676 44.202 42.322 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1043 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1209 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1209 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1209 r_free=0.1368 | n_water=854 | time (s): 3.290 (total time: 3.290) Filter (dist) r_work=0.1210 r_free=0.1370 | n_water=852 | time (s): 104.880 (total time: 108.170) Filter (q & B) r_work=0.1210 r_free=0.1369 | n_water=842 | time (s): 5.130 (total time: 113.300) Compute maps r_work=0.1210 r_free=0.1369 | n_water=842 | time (s): 1.810 (total time: 115.110) Filter (map) r_work=0.1232 r_free=0.1371 | n_water=707 | time (s): 4.350 (total time: 119.460) Find peaks r_work=0.1232 r_free=0.1371 | n_water=707 | time (s): 0.790 (total time: 120.250) Add new water r_work=0.1246 r_free=0.1382 | n_water=952 | time (s): 5.020 (total time: 125.270) Refine new water occ: r_work=0.1207 r_free=0.1350 adp: r_work=0.1207 r_free=0.1350 occ: r_work=0.1204 r_free=0.1349 adp: r_work=0.1204 r_free=0.1348 occ: r_work=0.1202 r_free=0.1349 adp: r_work=0.1202 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1348 r_work=0.1202 r_free=0.1348 | n_water=952 | time (s): 373.190 (total time: 498.460) Filter (q & B) r_work=0.1206 r_free=0.1358 | n_water=883 | time (s): 4.610 (total time: 503.070) Filter (dist only) r_work=0.1206 r_free=0.1357 | n_water=882 | time (s): 112.800 (total time: 615.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.552582 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.829719 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 0.1204 0.1362 0.0158 0.036 1.1 6.8 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.62 1.58 1.818 14.194 15.830 3.870 11.98 13.60 1.62 1.894 14.164 15.830 3.863 Individual atomic B min max mean iso aniso Overall: 5.52 66.99 15.02 0.99 516 3270 Protein: 5.52 33.12 10.64 0.99 0 2902 Water: 5.70 66.99 29.39 N/A 516 366 Other: 13.86 27.07 20.46 N/A 0 2 Chain A: 5.58 53.22 12.60 N/A 0 1624 Chain B: 5.52 66.99 12.40 N/A 0 1646 Chain S: 5.70 60.01 30.97 N/A 516 0 Histogram: Values Number of atoms 5.52 - 11.67 2107 11.67 - 17.81 739 17.81 - 23.96 291 23.96 - 30.11 242 30.11 - 36.26 177 36.26 - 42.40 127 42.40 - 48.55 70 48.55 - 54.70 27 54.70 - 60.84 5 60.84 - 66.99 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1360 r_work=0.1198 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1361 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.861 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.860871 | | target function (ml) not normalized (work): 723114.032245 | | target function (ml) not normalized (free): 15125.274364 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1423 0.1422 0.1477 n_refl.: 191134 remove outliers: r(all,work,free)=0.1423 0.1422 0.1477 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1415 0.1414 0.1472 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191134 remove outliers: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3698 356.726 318.850 0.407 0.946 0.235 13.296-10.522 97.03 97 1 0.2447 481.265 453.464 0.693 0.948 0.185 10.503-8.327 97.80 175 3 0.2039 501.981 497.309 0.868 0.948 0.163 8.318-6.595 100.00 360 8 0.2153 375.600 371.223 0.893 0.947 0.115 6.588-5.215 100.00 711 7 0.1891 345.139 334.935 0.882 0.947 0.084 5.214-4.128 98.38 1367 28 0.1182 504.833 499.757 0.975 0.948 0.070 4.126-3.266 94.74 2603 46 0.1117 460.183 453.870 1.036 0.948 0.005 3.266-2.585 99.86 5447 97 0.1097 310.428 307.280 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0933 234.200 231.818 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0913 138.611 137.308 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0982 74.620 73.915 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.031 38.370 1.038 0.944 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=0.1194 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1359 | n_water=882 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1194 r_free=0.1359 | n_water=882 | time (s): 104.350 (total time: 106.740) Filter (q & B) r_work=0.1194 r_free=0.1359 | n_water=875 | time (s): 4.330 (total time: 111.070) Compute maps r_work=0.1194 r_free=0.1359 | n_water=875 | time (s): 2.320 (total time: 113.390) Filter (map) r_work=0.1218 r_free=0.1372 | n_water=743 | time (s): 4.990 (total time: 118.380) Find peaks r_work=0.1218 r_free=0.1372 | n_water=743 | time (s): 0.550 (total time: 118.930) Add new water r_work=0.1228 r_free=0.1384 | n_water=970 | time (s): 4.240 (total time: 123.170) Refine new water occ: r_work=0.1191 r_free=0.1346 adp: r_work=0.1191 r_free=0.1346 occ: r_work=0.1189 r_free=0.1345 adp: r_work=0.1189 r_free=0.1344 occ: r_work=0.1187 r_free=0.1344 adp: r_work=0.1187 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1343 r_work=0.1187 r_free=0.1343 | n_water=970 | time (s): 214.230 (total time: 337.400) Filter (q & B) r_work=0.1191 r_free=0.1353 | n_water=889 | time (s): 4.570 (total time: 341.970) Filter (dist only) r_work=0.1192 r_free=0.1352 | n_water=888 | time (s): 113.540 (total time: 455.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560420 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.563831 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1362 0.0166 0.037 1.1 7.0 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.62 1.66 1.785 14.101 14.564 3.762 12.00 13.63 1.63 1.825 14.082 14.564 3.761 Individual atomic B min max mean iso aniso Overall: 5.60 66.73 14.93 0.95 522 3270 Protein: 5.60 31.91 10.59 0.95 0 2902 Water: 5.78 66.73 29.11 N/A 522 366 Other: 13.77 26.40 20.09 N/A 0 2 Chain A: 5.60 52.84 12.52 N/A 0 1624 Chain B: 5.61 66.73 12.33 N/A 0 1646 Chain S: 5.78 59.89 30.64 N/A 522 0 Histogram: Values Number of atoms 5.60 - 11.71 2136 11.71 - 17.83 722 17.83 - 23.94 301 23.94 - 30.05 230 30.05 - 36.17 170 36.17 - 42.28 134 42.28 - 48.39 69 48.39 - 54.51 24 54.51 - 60.62 5 60.62 - 66.73 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1363 r_work=0.1200 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1363 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1364 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759772 | | target function (ml) not normalized (work): 704163.893039 | | target function (ml) not normalized (free): 14739.277916 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1365 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1406 0.1405 0.1486 n_refl.: 191130 remove outliers: r(all,work,free)=0.1406 0.1405 0.1486 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1399 0.1397 0.1481 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3766 356.726 320.623 0.388 0.951 0.209 13.296-10.522 97.03 97 1 0.2470 481.265 460.927 0.694 0.953 0.165 10.503-8.327 97.80 175 3 0.2088 501.981 495.368 0.858 0.953 0.147 8.318-6.595 100.00 360 8 0.2157 375.600 371.099 0.888 0.953 0.110 6.588-5.215 100.00 711 7 0.1932 345.139 334.739 0.878 0.953 0.090 5.214-4.128 98.38 1367 28 0.1196 504.833 499.934 0.969 0.953 0.049 4.126-3.266 94.74 2603 46 0.1135 460.183 453.442 1.032 0.953 0.009 3.266-2.585 99.86 5447 97 0.1111 310.428 307.123 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0940 234.200 231.740 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0912 138.611 137.291 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0976 74.620 73.906 1.050 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1655 40.031 38.358 1.038 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1346 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1361 | n_water=888 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1197 r_free=0.1360 | n_water=884 | time (s): 119.190 (total time: 121.700) Filter (q & B) r_work=0.1197 r_free=0.1362 | n_water=875 | time (s): 5.000 (total time: 126.700) Compute maps r_work=0.1197 r_free=0.1362 | n_water=875 | time (s): 2.090 (total time: 128.790) Filter (map) r_work=0.1221 r_free=0.1361 | n_water=754 | time (s): 5.250 (total time: 134.040) Find peaks r_work=0.1221 r_free=0.1361 | n_water=754 | time (s): 0.540 (total time: 134.580) Add new water r_work=0.1230 r_free=0.1372 | n_water=979 | time (s): 4.900 (total time: 139.480) Refine new water occ: r_work=0.1193 r_free=0.1337 adp: r_work=0.1193 r_free=0.1337 occ: r_work=0.1191 r_free=0.1336 adp: r_work=0.1191 r_free=0.1336 occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1189 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1337 r_work=0.1189 r_free=0.1337 | n_water=979 | time (s): 212.330 (total time: 351.810) Filter (q & B) r_work=0.1194 r_free=0.1346 | n_water=895 | time (s): 5.540 (total time: 357.350) Filter (dist only) r_work=0.1195 r_free=0.1345 | n_water=894 | time (s): 112.250 (total time: 469.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.546477 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.695286 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1357 0.0158 0.038 1.1 6.8 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.57 1.58 1.759 14.016 13.695 3.760 12.03 13.60 1.57 1.888 13.971 13.695 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 65.78 14.80 0.89 529 3269 Protein: 5.58 29.43 10.48 0.89 0 2902 Water: 5.91 65.78 28.80 N/A 529 365 Other: 13.85 23.91 18.88 N/A 0 2 Chain A: 5.65 52.51 12.36 N/A 0 1623 Chain B: 5.58 65.78 12.20 N/A 0 1646 Chain S: 5.91 59.53 30.36 N/A 529 0 Histogram: Values Number of atoms 5.58 - 11.60 2113 11.60 - 17.62 776 17.62 - 23.64 278 23.64 - 29.66 221 29.66 - 35.68 172 35.68 - 41.70 133 41.70 - 47.72 74 47.72 - 53.74 25 53.74 - 59.76 5 59.76 - 65.78 1 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1360 r_work=0.1204 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1361 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-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: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 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): 3.759243 | | target function (ml) not normalized (work): 704064.816247 | | target function (ml) not normalized (free): 14736.311385 | |-----------------------------------------------------------------------------| =========================== 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)=0.1406 0.1405 0.1486 n_refl.: 191130 remove outliers: r(all,work,free)=0.1406 0.1405 0.1486 n_refl.: 191130 overall B=-0.24 to atoms: r(all,work,free)=0.1369 0.1368 0.1464 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1360 n_refl.: 191130 remove outliers: r(all,work,free)=0.1204 0.1201 0.1360 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 0.3805 356.401 313.119 0.353 0.952 0.140 13.296-10.522 97.03 97 1 0.2449 481.265 461.329 0.698 0.953 0.131 10.503-8.327 97.80 175 3 0.2129 501.981 494.747 0.880 0.954 0.123 8.318-6.595 100.00 360 8 0.2133 375.600 370.955 0.909 0.953 0.105 6.588-5.215 100.00 711 7 0.1924 345.139 335.364 0.901 0.954 0.087 5.214-4.128 98.38 1367 28 0.1220 504.833 499.787 0.994 0.954 0.045 4.126-3.266 94.74 2603 46 0.1152 460.183 453.381 1.057 0.954 0.009 3.266-2.585 99.86 5447 97 0.1127 310.428 307.213 1.039 0.954 0.000 2.585-2.046 97.45 10613 204 0.0947 234.200 231.726 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0915 138.611 137.325 1.064 0.953 0.000 1.619-1.281 98.00 42464 925 0.0974 74.620 73.924 1.052 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.031 38.366 1.023 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0521 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1360 | n_water=894 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1201 r_free=0.1360 | n_water=894 | time (s): 110.500 (total time: 113.690) Filter (q & B) r_work=0.1202 r_free=0.1361 | n_water=885 | time (s): 4.010 (total time: 117.700) Compute maps r_work=0.1202 r_free=0.1361 | n_water=885 | time (s): 1.710 (total time: 119.410) Filter (map) r_work=0.1226 r_free=0.1356 | n_water=753 | time (s): 5.210 (total time: 124.620) Find peaks r_work=0.1226 r_free=0.1356 | n_water=753 | time (s): 0.710 (total time: 125.330) Add new water r_work=0.1236 r_free=0.1368 | n_water=976 | time (s): 3.870 (total time: 129.200) Refine new water occ: r_work=0.1200 r_free=0.1343 adp: r_work=0.1200 r_free=0.1343 occ: r_work=0.1198 r_free=0.1342 adp: r_work=0.1197 r_free=0.1342 occ: r_work=0.1196 r_free=0.1342 adp: r_work=0.1196 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1342 r_work=0.1196 r_free=0.1342 | n_water=976 | time (s): 235.140 (total time: 364.340) Filter (q & B) r_work=0.1200 r_free=0.1348 | n_water=900 | time (s): 4.380 (total time: 368.720) Filter (dist only) r_work=0.1200 r_free=0.1348 | n_water=899 | time (s): 111.770 (total time: 480.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.521005 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.738555 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 0.1204 0.1348 0.0144 0.038 1.1 5.8 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.48 1.44 1.715 13.692 14.739 3.760 12.02 13.48 1.47 1.749 13.678 14.739 3.755 Individual atomic B min max mean iso aniso Overall: 5.39 64.51 14.56 0.89 534 3269 Protein: 5.39 28.82 10.25 0.89 0 2902 Water: 5.76 64.51 28.46 N/A 534 365 Other: 13.64 22.20 17.92 N/A 0 2 Chain A: 5.44 52.00 12.09 N/A 0 1623 Chain B: 5.39 64.51 11.94 N/A 0 1646 Chain S: 5.76 58.89 30.13 N/A 534 0 Histogram: Values Number of atoms 5.39 - 11.30 2094 11.30 - 17.21 786 17.21 - 23.13 279 23.13 - 29.04 222 29.04 - 34.95 182 34.95 - 40.86 125 40.86 - 46.78 77 46.78 - 52.69 32 52.69 - 58.60 4 58.60 - 64.51 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1348 r_work=0.1202 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1348 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1348 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.754795 | | target function (ml) not normalized (work): 703228.138909 | | target function (ml) not normalized (free): 14719.877577 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1348 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1364 0.1362 0.1458 n_refl.: 191129 remove outliers: r(all,work,free)=0.1364 0.1362 0.1458 n_refl.: 191129 overall B=0.07 to atoms: r(all,work,free)=0.1372 0.1370 0.1462 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1337 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1191 0.1337 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3726 356.167 320.600 0.331 0.986 0.090 13.296-10.522 97.03 97 1 0.2435 481.265 461.302 0.667 0.987 0.099 10.503-8.327 97.80 175 3 0.2185 501.981 493.449 0.853 0.987 0.099 8.318-6.595 100.00 360 8 0.2140 375.600 370.332 0.882 0.987 0.087 6.588-5.215 100.00 711 7 0.1932 345.139 335.326 0.877 0.988 0.080 5.214-4.128 98.38 1367 28 0.1240 504.833 499.242 0.970 0.988 0.049 4.126-3.266 94.74 2603 46 0.1164 460.183 452.611 1.032 0.989 0.009 3.266-2.585 99.86 5447 97 0.1124 310.428 306.908 1.013 0.990 0.000 2.585-2.046 97.45 10613 204 0.0951 234.200 231.626 1.021 0.992 0.000 2.046-1.619 99.39 21536 464 0.0905 138.611 137.248 1.037 0.994 0.000 1.619-1.281 98.00 42464 925 0.0947 74.620 73.965 1.025 0.998 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.031 38.332 0.991 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0628 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1337 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1337 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1337 | n_water=899 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1191 r_free=0.1337 | n_water=899 | time (s): 103.970 (total time: 107.110) Filter (q & B) r_work=0.1191 r_free=0.1337 | n_water=890 | time (s): 5.000 (total time: 112.110) Compute maps r_work=0.1191 r_free=0.1337 | n_water=890 | time (s): 2.020 (total time: 114.130) Filter (map) r_work=0.1214 r_free=0.1339 | n_water=769 | time (s): 5.470 (total time: 119.600) Find peaks r_work=0.1214 r_free=0.1339 | n_water=769 | time (s): 0.850 (total time: 120.450) Add new water r_work=0.1222 r_free=0.1349 | n_water=986 | time (s): 5.200 (total time: 125.650) Refine new water occ: r_work=0.1187 r_free=0.1323 adp: r_work=0.1187 r_free=0.1323 occ: r_work=0.1185 r_free=0.1323 adp: r_work=0.1185 r_free=0.1323 occ: r_work=0.1184 r_free=0.1323 adp: r_work=0.1183 r_free=0.1324 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1324 r_work=0.1183 r_free=0.1324 | n_water=986 | time (s): 266.860 (total time: 392.510) Filter (q & B) r_work=0.1188 r_free=0.1336 | n_water=908 | time (s): 4.260 (total time: 396.770) Filter (dist only) r_work=0.1188 r_free=0.1337 | n_water=907 | time (s): 112.990 (total time: 509.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568236 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.786735 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 0.1343 0.0152 0.039 1.1 5.3 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.43 1.52 1.681 13.733 14.787 3.753 11.92 13.45 1.53 1.702 13.720 14.787 3.751 Individual atomic B min max mean iso aniso Overall: 5.49 63.66 14.62 0.88 542 3269 Protein: 5.49 28.42 10.31 0.88 0 2902 Water: 5.83 63.66 28.39 N/A 542 365 Other: 13.77 22.15 17.96 N/A 0 2 Chain A: 5.57 51.86 12.12 N/A 0 1623 Chain B: 5.49 63.66 11.98 N/A 0 1646 Chain S: 5.83 58.60 30.11 N/A 542 0 Histogram: Values Number of atoms 5.49 - 11.31 2069 11.31 - 17.13 816 17.13 - 22.94 276 22.94 - 28.76 216 28.76 - 34.58 189 34.58 - 40.39 116 40.39 - 46.21 89 46.21 - 52.03 31 52.03 - 57.84 7 57.84 - 63.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1345 r_work=0.1192 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1345 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1344 target_work(ml) = 3.751 | | 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.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750968 | | target function (ml) not normalized (work): 702507.502386 | | target function (ml) not normalized (free): 14712.979310 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1372 0.1370 0.1475 n_refl.: 191128 remove outliers: r(all,work,free)=0.1372 0.1370 0.1475 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1374 0.1372 0.1476 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1342 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1342 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3720 356.167 326.534 0.332 0.987 0.080 13.296-10.522 97.03 97 1 0.2468 481.265 460.265 0.664 0.988 0.097 10.503-8.327 97.80 175 3 0.2166 501.981 493.531 0.852 0.988 0.097 8.318-6.595 100.00 360 8 0.2150 375.600 369.944 0.878 0.988 0.088 6.588-5.215 100.00 711 7 0.1939 345.139 335.026 0.874 0.989 0.080 5.214-4.128 98.38 1367 28 0.1245 504.833 499.049 0.966 0.990 0.044 4.126-3.266 94.74 2603 46 0.1170 460.183 452.530 1.030 0.991 0.005 3.266-2.585 99.86 5447 97 0.1128 310.428 306.815 1.012 0.992 0.000 2.585-2.046 97.45 10613 204 0.0952 234.200 231.604 1.020 0.994 0.000 2.046-1.619 99.39 21536 464 0.0903 138.611 137.256 1.036 0.997 0.000 1.619-1.281 98.00 42464 925 0.0941 74.620 73.971 1.026 1.002 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.031 38.316 0.994 1.012 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0228 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1342 | n_water=907 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1189 r_free=0.1342 | n_water=907 | time (s): 110.220 (total time: 112.680) Filter (q & B) r_work=0.1189 r_free=0.1343 | n_water=901 | time (s): 4.160 (total time: 116.840) Compute maps r_work=0.1189 r_free=0.1343 | n_water=901 | time (s): 1.690 (total time: 118.530) Filter (map) r_work=0.1213 r_free=0.1341 | n_water=781 | time (s): 5.250 (total time: 123.780) Find peaks r_work=0.1213 r_free=0.1341 | n_water=781 | time (s): 0.690 (total time: 124.470) Add new water r_work=0.1220 r_free=0.1352 | n_water=997 | time (s): 3.920 (total time: 128.390) Refine new water occ: r_work=0.1186 r_free=0.1324 adp: r_work=0.1186 r_free=0.1324 occ: r_work=0.1184 r_free=0.1325 adp: r_work=0.1184 r_free=0.1325 occ: r_work=0.1182 r_free=0.1326 adp: r_work=0.1182 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1325 r_work=0.1182 r_free=0.1325 | n_water=997 | time (s): 259.540 (total time: 387.930) Filter (q & B) r_work=0.1187 r_free=0.1334 | n_water=912 | time (s): 4.560 (total time: 392.490) Filter (dist only) r_work=0.1188 r_free=0.1334 | n_water=911 | time (s): 115.420 (total time: 507.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.583766 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.266300 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 0.1190 0.1338 0.0148 0.039 1.1 5.6 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.38 1.48 1.682 13.742 14.266 3.752 11.91 13.41 1.49 1.691 13.736 14.266 3.751 Individual atomic B min max mean iso aniso Overall: 5.53 62.82 14.63 0.87 546 3269 Protein: 5.53 28.18 10.34 0.87 0 2902 Water: 5.93 62.82 28.29 N/A 546 365 Other: 13.81 22.18 18.00 N/A 0 2 Chain A: 5.62 51.63 12.11 N/A 0 1623 Chain B: 5.53 62.82 11.98 N/A 0 1646 Chain S: 5.93 58.36 30.09 N/A 546 0 Histogram: Values Number of atoms 5.53 - 11.26 2046 11.26 - 16.99 838 16.99 - 22.72 275 22.72 - 28.45 219 28.45 - 34.17 186 34.17 - 39.90 122 39.90 - 45.63 85 45.63 - 51.36 33 51.36 - 57.09 8 57.09 - 62.82 3 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1341 r_work=0.1192 r_free=0.1341 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1341 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1340 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1340 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750717 | | target function (ml) not normalized (work): 702460.600377 | | target function (ml) not normalized (free): 14710.034121 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1340 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1382 0.1380 0.1479 n_refl.: 191128 remove outliers: r(all,work,free)=0.1382 0.1380 0.1479 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1381 0.1380 0.1479 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1190 0.1338 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1190 0.1338 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3724 356.167 326.986 0.320 0.995 0.060 13.296-10.522 97.03 97 1 0.2456 481.265 459.292 0.651 0.996 0.080 10.503-8.327 97.80 175 3 0.2180 501.981 492.970 0.842 0.997 0.086 8.318-6.595 100.00 360 8 0.2153 375.600 370.171 0.868 0.997 0.080 6.588-5.215 100.00 711 7 0.1946 345.139 334.751 0.866 0.997 0.073 5.214-4.128 98.38 1367 28 0.1245 504.833 498.995 0.957 0.998 0.040 4.126-3.266 94.74 2603 46 0.1174 460.183 452.533 1.022 0.999 0.009 3.266-2.585 99.86 5447 97 0.1128 310.428 306.844 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0954 234.200 231.605 1.012 1.003 0.000 2.046-1.619 99.39 21536 464 0.0904 138.611 137.252 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0939 74.620 73.975 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.031 38.312 0.989 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0065 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1338 After: r_work=0.1190 r_free=0.1339 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1339 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1339 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1339 | n_water=911 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1190 r_free=0.1339 | n_water=911 | time (s): 113.430 (total time: 116.010) Filter (q & B) r_work=0.1191 r_free=0.1339 | n_water=903 | time (s): 4.290 (total time: 120.300) Compute maps r_work=0.1191 r_free=0.1339 | n_water=903 | time (s): 2.400 (total time: 122.700) Filter (map) r_work=0.1215 r_free=0.1344 | n_water=790 | time (s): 4.660 (total time: 127.360) Find peaks r_work=0.1215 r_free=0.1344 | n_water=790 | time (s): 0.760 (total time: 128.120) Add new water r_work=0.1220 r_free=0.1350 | n_water=984 | time (s): 5.240 (total time: 133.360) Refine new water occ: r_work=0.1188 r_free=0.1325 adp: r_work=0.1188 r_free=0.1325 occ: r_work=0.1186 r_free=0.1325 adp: r_work=0.1187 r_free=0.1325 occ: r_work=0.1185 r_free=0.1326 adp: r_work=0.1185 r_free=0.1326 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1326 r_work=0.1185 r_free=0.1326 | n_water=984 | time (s): 215.080 (total time: 348.440) Filter (q & B) r_work=0.1189 r_free=0.1339 | n_water=907 | time (s): 5.240 (total time: 353.680) Filter (dist only) r_work=0.1190 r_free=0.1338 | n_water=905 | time (s): 113.400 (total time: 467.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.534658 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.183680 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 0.1340 0.0149 0.039 1.2 6.8 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.40 1.49 1.680 13.711 13.184 3.752 11.93 13.43 1.50 1.680 13.709 13.184 3.753 Individual atomic B min max mean iso aniso Overall: 5.56 62.57 14.58 0.85 540 3269 Protein: 5.56 28.05 10.35 0.85 0 2902 Water: 5.94 62.57 28.13 N/A 540 365 Other: 13.83 22.18 18.01 N/A 0 2 Chain A: 5.61 51.56 12.10 N/A 0 1623 Chain B: 5.56 62.57 11.98 N/A 0 1646 Chain S: 5.94 58.28 29.94 N/A 540 0 Histogram: Values Number of atoms 5.56 - 11.26 2048 11.26 - 16.96 836 16.96 - 22.66 281 22.66 - 28.36 209 28.36 - 34.06 197 34.06 - 39.76 112 39.76 - 45.46 81 45.46 - 51.17 32 51.17 - 56.87 10 56.87 - 62.57 3 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1343 r_work=0.1193 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1343 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1345 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753055 | | target function (ml) not normalized (work): 702898.499123 | | target function (ml) not normalized (free): 14713.224205 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1367 0.1463 5.6935 5.7677| | 2: 2.94 - 2.33 1.00 7339 128 0.1067 0.1369 5.0773 5.1846| | 3: 2.33 - 2.04 0.96 6939 150 0.0898 0.1159 4.6475 4.7362| | 4: 2.04 - 1.85 1.00 7170 155 0.0898 0.1007 4.3878 4.5423| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0976 4.145 4.2358| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1059 3.9436 4.0669| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0956 3.7981 3.9312| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1302 3.6962 3.8928| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1083 3.6167 3.7379| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1176 3.5511 3.6763| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1120 3.4817 3.5821| | 12: 1.32 - 1.28 0.98 6975 149 0.1034 0.1136 3.4585 3.5816| | 13: 1.28 - 1.25 0.98 6907 166 0.1043 0.1232 3.437 3.5559| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1576 3.4319 3.6785| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1237 3.449 3.4913| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1551 3.465 3.6603| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1224 3.4343 3.44| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1703 3.4397 3.5341| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1740 3.4194 3.5909| | 20: 1.10 - 1.08 0.97 6884 147 0.1586 0.1575 3.4106 3.4305| | 21: 1.08 - 1.07 0.97 6852 152 0.1731 0.2130 3.4189 3.5023| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1957 3.4138 3.4148| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2031 3.434 3.4859| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2252 3.4361 3.5081| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2510 3.4494 3.5246| | 26: 1.01 - 0.99 0.96 6767 158 0.2759 0.2862 3.4165 3.4219| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2808 3.4694 3.3951| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7396 127 0.93 11.71 1.00 0.96 11336.96| | 2: 2.94 - 2.33 7339 128 0.93 12.76 0.99 0.95 5119.91| | 3: 2.33 - 2.04 6939 150 0.96 7.39 1.01 0.96 1636.28| | 4: 2.04 - 1.85 7170 155 0.96 7.43 1.00 0.96 971.91| | 5: 1.85 - 1.72 7113 159 0.96 7.94 1.00 0.96 619.45| | 6: 1.72 - 1.62 7102 142 0.96 7.91 1.00 0.96 436.54| | 7: 1.62 - 1.54 7104 148 0.96 8.07 1.01 0.97 333.19| | 8: 1.54 - 1.47 6798 152 0.96 8.20 1.01 0.97 276.04| | 9: 1.47 - 1.41 6938 155 0.96 8.38 1.00 0.98 227.69| | 10: 1.41 - 1.36 7022 150 0.96 8.82 1.00 0.97 199.54| | 11: 1.36 - 1.32 6997 151 0.96 8.87 0.99 0.96 172.80| | 12: 1.32 - 1.28 6975 149 0.96 8.92 0.98 0.95 159.33| | 13: 1.28 - 1.25 6907 166 0.96 9.47 1.01 0.96 157.02| | 14: 1.25 - 1.22 7015 112 0.95 10.65 1.01 0.97 162.15| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 0.98 165.95| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.96 159.97| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.96 153.71| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.95 147.27| | 19: 1.12 - 1.10 6948 106 0.93 14.09 1.00 0.95 150.32| | 20: 1.10 - 1.08 6884 147 0.92 15.16 1.00 0.94 149.36| | 21: 1.08 - 1.07 6852 152 0.91 16.61 1.00 0.93 152.58| | 22: 1.07 - 1.05 6836 135 0.89 18.27 0.99 0.93 154.54| | 23: 1.05 - 1.03 6827 159 0.87 20.50 0.99 0.92 164.72| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.93 179.05| | 25: 1.02 - 1.01 6552 130 0.83 25.13 0.98 0.90 182.12| | 26: 1.01 - 0.99 6767 158 0.81 26.61 0.98 0.88 176.54| | 27: 0.99 - 0.98 6647 131 0.82 26.30 0.99 0.87 161.08| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.27 max = 11336.96 mean = 925.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.23| |phase err.(test): min = 0.00 max = 89.92 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1345 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1488 n_refl.: 191128 remove outliers: r(all,work,free)=0.1391 0.1389 0.1488 n_refl.: 191128 overall B=-0.05 to atoms: r(all,work,free)=0.1384 0.1382 0.1483 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1345 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1345 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3742 356.167 325.682 0.313 0.987 0.060 13.296-10.522 97.03 97 1 0.2475 481.265 458.988 0.643 0.989 0.090 10.503-8.327 97.80 175 3 0.2173 501.981 492.398 0.828 0.989 0.089 8.318-6.595 100.00 360 8 0.2167 375.600 370.426 0.855 0.989 0.080 6.588-5.215 100.00 711 7 0.1940 345.139 334.827 0.851 0.990 0.072 5.214-4.128 98.38 1367 28 0.1247 504.833 498.893 0.941 0.991 0.044 4.126-3.266 94.74 2603 46 0.1177 460.183 452.526 1.006 0.992 0.009 3.266-2.585 99.86 5447 97 0.1127 310.428 306.915 0.987 0.993 0.000 2.585-2.046 97.45 10613 204 0.0956 234.200 231.611 0.994 0.996 0.000 2.046-1.619 99.39 21536 464 0.0908 138.611 137.245 1.009 1.000 0.000 1.619-1.281 98.00 42464 925 0.0943 74.620 73.971 0.999 1.007 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.031 38.303 0.967 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0106 ================= 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 : 0.2039 0.2010 0.082 5.196 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1943 0.082 5.196 5.2 78.1 14.6 805 0.000 1_settarget: 0.1800 0.1943 0.082 5.196 5.2 78.1 14.6 805 0.000 1_nqh: 0.1800 0.1943 0.082 5.196 5.2 78.1 14.6 805 0.000 1_weight: 0.1800 0.1943 0.082 5.196 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1267 0.1499 0.039 1.144 5.2 78.1 14.6 805 0.158 1_adp: 0.1295 0.1566 0.039 1.144 5.2 73.1 15.1 805 0.158 1_regHadp: 0.1294 0.1560 0.039 1.144 5.2 73.1 15.1 805 0.158 1_occ: 0.1279 0.1551 0.039 1.144 5.2 73.1 15.1 805 0.158 2_bss: 0.1274 0.1546 0.039 1.144 5.3 73.2 15.2 805 0.158 2_settarget: 0.1274 0.1546 0.039 1.144 5.3 73.2 15.2 805 0.158 2_updatecdl: 0.1274 0.1546 0.039 1.170 5.3 73.2 15.2 805 0.158 2_nqh: 0.1274 0.1546 0.039 1.170 5.3 73.2 15.2 805 0.158 2_sol: 0.1271 0.1501 0.039 1.170 5.3 73.2 16.1 880 n/a 2_weight: 0.1271 0.1501 0.039 1.170 5.3 73.2 16.1 880 n/a 2_xyzrec: 0.1254 0.1515 0.041 1.156 5.3 73.2 16.1 880 n/a 2_adp: 0.1234 0.1499 0.041 1.156 5.5 68.2 16.2 880 n/a 2_regHadp: 0.1235 0.1500 0.041 1.156 5.5 68.2 16.2 880 n/a 2_occ: 0.1229 0.1497 0.041 1.156 5.5 68.2 16.2 880 n/a 3_bss: 0.1236 0.1506 0.041 1.156 5.4 68.2 16.1 880 n/a 3_settarget: 0.1236 0.1506 0.041 1.156 5.4 68.2 16.1 880 n/a 3_updatecdl: 0.1236 0.1506 0.041 1.159 5.4 68.2 16.1 880 n/a 3_nqh: 0.1236 0.1506 0.041 1.159 5.4 68.2 16.1 880 n/a 3_sol: 0.1240 0.1490 0.041 1.159 5.4 68.2 15.2 854 n/a 3_weight: 0.1240 0.1490 0.041 1.159 5.4 68.2 15.2 854 n/a 3_xyzrec: 0.1227 0.1423 0.035 1.112 5.4 68.2 15.2 854 n/a 3_adp: 0.1219 0.1385 0.035 1.112 5.6 67.5 15.0 854 n/a 3_regHadp: 0.1220 0.1386 0.035 1.112 5.6 67.5 15.0 854 n/a 3_occ: 0.1213 0.1373 0.035 1.112 5.6 67.5 15.0 854 n/a 4_bss: 0.1209 0.1368 0.035 1.112 5.5 67.4 15.0 854 n/a 4_settarget: 0.1209 0.1368 0.035 1.112 5.5 67.4 15.0 854 n/a 4_updatecdl: 0.1209 0.1368 0.035 1.112 5.5 67.4 15.0 854 n/a 4_nqh: 0.1209 0.1368 0.035 1.112 5.5 67.4 15.0 854 n/a 4_sol: 0.1206 0.1357 0.035 1.112 5.5 67.4 15.1 882 n/a 4_weight: 0.1206 0.1357 0.035 1.112 5.5 67.4 15.1 882 n/a 4_xyzrec: 0.1204 0.1362 0.036 1.125 5.5 67.4 15.1 882 n/a 4_adp: 0.1198 0.1360 0.036 1.125 5.5 67.0 15.0 882 n/a 4_regHadp: 0.1198 0.1361 0.036 1.125 5.5 67.0 15.0 882 n/a 4_occ: 0.1196 0.1360 0.036 1.125 5.5 67.0 15.0 882 n/a 5_bss: 0.1194 0.1359 0.036 1.125 5.5 67.0 15.0 882 n/a 5_settarget: 0.1194 0.1359 0.036 1.125 5.5 67.0 15.0 882 n/a 5_updatecdl: 0.1194 0.1359 0.036 1.125 5.5 67.0 15.0 882 n/a 5_nqh: 0.1194 0.1359 0.036 1.125 5.5 67.0 15.0 882 n/a 5_sol: 0.1192 0.1352 0.036 1.125 5.5 67.0 15.0 888 n/a 5_weight: 0.1192 0.1352 0.036 1.125 5.5 67.0 15.0 888 n/a 5_xyzrec: 0.1195 0.1362 0.037 1.127 5.5 67.0 15.0 888 n/a 5_adp: 0.1200 0.1363 0.037 1.127 5.6 66.7 14.9 888 n/a 5_regHadp: 0.1200 0.1363 0.037 1.127 5.6 66.7 14.9 888 n/a 5_occ: 0.1198 0.1364 0.037 1.127 5.6 66.7 14.9 888 n/a 6_bss: 0.1197 0.1361 0.037 1.127 5.6 66.7 14.9 888 n/a 6_settarget: 0.1197 0.1361 0.037 1.127 5.6 66.7 14.9 888 n/a 6_updatecdl: 0.1197 0.1361 0.037 1.127 5.6 66.7 14.9 888 n/a 6_nqh: 0.1197 0.1361 0.037 1.127 5.6 66.7 14.9 888 n/a 6_sol: 0.1195 0.1345 0.037 1.127 5.6 66.7 14.9 894 n/a 6_weight: 0.1195 0.1345 0.037 1.127 5.6 66.7 14.9 894 n/a 6_xyzrec: 0.1198 0.1357 0.038 1.128 5.6 66.7 14.9 894 n/a 6_adp: 0.1204 0.1360 0.038 1.128 5.6 65.8 14.8 894 n/a 6_regHadp: 0.1204 0.1361 0.038 1.128 5.6 65.8 14.8 894 n/a 6_occ: 0.1202 0.1364 0.038 1.128 5.6 65.8 14.8 894 n/a 7_bss: 0.1201 0.1360 0.038 1.128 5.3 65.5 14.6 894 n/a 7_settarget: 0.1201 0.1360 0.038 1.128 5.3 65.5 14.6 894 n/a 7_updatecdl: 0.1201 0.1360 0.038 1.128 5.3 65.5 14.6 894 n/a 7_nqh: 0.1201 0.1360 0.038 1.128 5.3 65.5 14.6 894 n/a 7_sol: 0.1200 0.1348 0.038 1.128 5.3 65.5 14.6 899 n/a 7_weight: 0.1200 0.1348 0.038 1.128 5.3 65.5 14.6 899 n/a 7_xyzrec: 0.1204 0.1348 0.038 1.126 5.3 65.5 14.6 899 n/a 7_adp: 0.1202 0.1348 0.038 1.126 5.4 64.5 14.6 899 n/a 7_regHadp: 0.1202 0.1348 0.038 1.126 5.4 64.5 14.6 899 n/a 7_occ: 0.1200 0.1348 0.038 1.126 5.4 64.5 14.6 899 n/a 8_bss: 0.1191 0.1337 0.038 1.126 5.5 64.6 14.6 899 n/a 8_settarget: 0.1191 0.1337 0.038 1.126 5.5 64.6 14.6 899 n/a 8_updatecdl: 0.1191 0.1337 0.038 1.127 5.5 64.6 14.6 899 n/a 8_nqh: 0.1191 0.1337 0.038 1.127 5.5 64.6 14.6 899 n/a 8_sol: 0.1188 0.1337 0.038 1.127 5.5 64.6 14.6 907 n/a 8_weight: 0.1188 0.1337 0.038 1.127 5.5 64.6 14.6 907 n/a 8_xyzrec: 0.1191 0.1343 0.039 1.122 5.5 64.6 14.6 907 n/a 8_adp: 0.1192 0.1345 0.039 1.122 5.5 63.7 14.6 907 n/a 8_regHadp: 0.1192 0.1345 0.039 1.122 5.5 63.7 14.6 907 n/a 8_occ: 0.1191 0.1344 0.039 1.122 5.5 63.7 14.6 907 n/a 9_bss: 0.1189 0.1342 0.039 1.122 5.5 63.7 14.6 907 n/a 9_settarget: 0.1189 0.1342 0.039 1.122 5.5 63.7 14.6 907 n/a 9_updatecdl: 0.1189 0.1342 0.039 1.122 5.5 63.7 14.6 907 n/a 9_nqh: 0.1189 0.1342 0.039 1.122 5.5 63.7 14.6 907 n/a 9_sol: 0.1188 0.1334 0.039 1.122 5.5 63.7 14.6 911 n/a 9_weight: 0.1188 0.1334 0.039 1.122 5.5 63.7 14.6 911 n/a 9_xyzrec: 0.1190 0.1338 0.039 1.133 5.5 63.7 14.6 911 n/a 9_adp: 0.1191 0.1341 0.039 1.133 5.5 62.8 14.6 911 n/a 9_regHadp: 0.1192 0.1341 0.039 1.133 5.5 62.8 14.6 911 n/a 9_occ: 0.1190 0.1340 0.039 1.133 5.5 62.8 14.6 911 n/a 10_bss: 0.1190 0.1338 0.039 1.133 5.5 62.8 14.6 911 n/a 10_settarget: 0.1190 0.1338 0.039 1.133 5.5 62.8 14.6 911 n/a 10_updatecdl: 0.1190 0.1338 0.039 1.134 5.5 62.8 14.6 911 n/a 10_setrh: 0.1190 0.1339 0.039 1.134 5.5 62.8 14.6 911 n/a 10_nqh: 0.1190 0.1339 0.039 1.134 5.5 62.8 14.6 911 n/a 10_sol: 0.1190 0.1338 0.039 1.134 5.5 62.8 14.6 905 n/a 10_weight: 0.1190 0.1338 0.039 1.134 5.5 62.8 14.6 905 n/a 10_xyzrec: 0.1191 0.1340 0.039 1.151 5.5 62.8 14.6 905 n/a 10_adp: 0.1193 0.1343 0.039 1.151 5.6 62.6 14.6 905 n/a 10_regHadp: 0.1193 0.1343 0.039 1.151 5.6 62.6 14.6 905 n/a 10_occ: 0.1193 0.1345 0.039 1.151 5.6 62.6 14.6 905 n/a end: 0.1192 0.1345 0.039 1.151 5.5 62.5 14.5 905 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4016894_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4016894_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1200 Refinement macro-cycles (run) : 12268.0300 Write final files (write_after_run_outputs) : 150.1900 Total : 12425.3400 Total CPU time: 3.46 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:21 PST -0800 (1736736261.47 s) Start R-work = 0.1800, R-free = 0.1943 Final R-work = 0.1192, R-free = 0.1345 =============================================================================== Job complete usr+sys time: 12695.83 seconds wall clock time: 212 minutes 37.49 seconds (12757.49 seconds total)