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_7378796.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7378796.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7378796.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.01, per 1000 atoms: 0.30 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: 2.761 distance_ideal: 2.720 ideal - model: -0.041 slack: 0.000 delta_slack: -0.041 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: 2.647 distance_ideal: 2.710 ideal - model: 0.063 slack: 0.000 delta_slack: 0.063 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: 1.03 Conformation dependent library (CDL) restraints added in 115.7 milliseconds Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 1082 1.05 - 1.28: 2335 1.28 - 1.51: 1592 1.51 - 1.74: 909 1.74 - 1.97: 16 Bond restraints: 5934 Sorted by residual: bond pdb=" CA ILE B 134 " pdb=" C ILE B 134 " ideal model delta sigma weight residual 1.523 1.725 -0.202 8.80e-03 1.29e+04 5.27e+02 bond pdb=" C GLU B 176 " pdb=" O GLU B 176 " ideal model delta sigma weight residual 1.237 1.473 -0.236 1.19e-02 7.06e+03 3.94e+02 bond pdb=" N ALA A 57 " pdb=" H ALA A 57 " ideal model delta sigma weight residual 0.860 1.249 -0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" CG2 VAL B 181 " pdb="HG22 VAL B 181 " ideal model delta sigma weight residual 0.970 1.348 -0.378 2.00e-02 2.50e+03 3.57e+02 bond pdb=" CA VAL B 114 " pdb=" C VAL B 114 " ideal model delta sigma weight residual 1.524 1.327 0.197 1.05e-02 9.07e+03 3.53e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.51: 5967 4.51 - 9.02: 3573 9.02 - 13.53: 1104 13.53 - 18.04: 147 18.04 - 22.55: 19 Bond angle restraints: 10810 Sorted by residual: angle pdb=" C ALA A 108 " pdb=" N PRO A 109 " pdb=" CA PRO A 109 " ideal model delta sigma weight residual 119.84 139.97 -20.13 1.25e+00 6.40e-01 2.59e+02 angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 137.30 -15.12 9.60e-01 1.09e+00 2.48e+02 angle pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta sigma weight residual 119.24 135.08 -15.84 1.04e+00 9.25e-01 2.32e+02 angle pdb=" O PHE B 82 " pdb=" C PHE B 82 " pdb=" N ARG B 83 " ideal model delta sigma weight residual 122.12 137.92 -15.80 1.06e+00 8.90e-01 2.22e+02 angle pdb=" CA VAL A 150 " pdb=" C VAL A 150 " pdb=" O VAL A 150 " ideal model delta sigma weight residual 119.91 134.43 -14.52 9.90e-01 1.02e+00 2.15e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1845 17.12 - 34.24: 133 34.24 - 51.36: 50 51.36 - 68.48: 17 68.48 - 85.59: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 151.24 28.76 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 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 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.242: 236 0.242 - 0.482: 149 0.482 - 0.721: 85 0.721 - 0.961: 17 0.961 - 1.201: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ALA B 57 " pdb=" N ALA B 57 " pdb=" C ALA B 57 " pdb=" CB ALA B 57 " both_signs ideal model delta sigma weight residual False 2.48 3.69 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CG LEU A 152 " pdb=" CB LEU A 152 " pdb=" CD1 LEU A 152 " pdb=" CD2 LEU A 152 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.67e+01 chirality pdb=" CB ILE B 121 " pdb=" CA ILE B 121 " pdb=" CG1 ILE B 121 " pdb=" CG2 ILE B 121 " both_signs ideal model delta sigma weight residual False 2.64 1.63 1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 127 " -0.051 2.00e-02 2.50e+03 7.29e-02 1.60e+02 pdb=" CG PHE B 127 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE B 127 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 PHE B 127 " -0.082 2.00e-02 2.50e+03 pdb=" CE1 PHE B 127 " 0.071 2.00e-02 2.50e+03 pdb=" CE2 PHE B 127 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 127 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE B 127 " -0.116 2.00e-02 2.50e+03 pdb=" HD2 PHE B 127 " 0.082 2.00e-02 2.50e+03 pdb=" HE1 PHE B 127 " 0.097 2.00e-02 2.50e+03 pdb=" HE2 PHE B 127 " 0.010 2.00e-02 2.50e+03 pdb=" HZ PHE B 127 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.132 2.00e-02 2.50e+03 7.03e-02 1.48e+02 pdb=" CG PHE B 164 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.040 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.092 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.082 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.052 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.027 2.00e-02 2.50e+03 5.65e-02 1.28e+02 pdb=" CG TRP B 146 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.102 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.076 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.046 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.084 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.111 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.026 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.076 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.045 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.037 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.58: 20 1.58 - 2.33: 2091 2.33 - 3.09: 21975 3.09 - 3.84: 33119 3.84 - 4.60: 53054 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110259 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.821 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.938 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.023 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.145 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.170 2.620 ... (remaining 110254 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_7378796_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2040 r_free= 0.1989 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301363 | | target function (ml) not normalized (work): 805701.287318 | | target function (ml) not normalized (free): 16566.498763 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2141 0.2003 6.6699 6.329| | 2: 2.94 - 2.33 1.00 7339 128 0.1631 0.1634 5.5481 5.5844| | 3: 2.33 - 2.04 0.96 6939 150 0.1625 0.1580 5.1397 5.0975| | 4: 2.04 - 1.85 1.00 7170 155 0.1747 0.1629 4.9487 5.0647| | 5: 1.85 - 1.72 0.99 7113 159 0.1895 0.1651 4.7833 4.7689| | 6: 1.72 - 1.62 0.99 7102 142 0.1999 0.1953 4.6714 4.6406| | 7: 1.62 - 1.54 0.99 7104 148 0.2042 0.1880 4.5691 4.615| | 8: 1.54 - 1.47 0.96 6798 152 0.2046 0.1965 4.4679 4.455| | 9: 1.47 - 1.41 0.98 6938 155 0.2119 0.2283 4.4056 4.5136| | 10: 1.41 - 1.36 0.99 7022 150 0.2145 0.2020 4.3251 4.3096| | 11: 1.36 - 1.32 0.99 6997 151 0.2139 0.2057 4.2474 4.2281| | 12: 1.32 - 1.28 0.98 6976 149 0.2091 0.1993 4.1778 4.268| | 13: 1.28 - 1.25 0.98 6907 166 0.2034 0.2265 4.1179 4.2412| | 14: 1.25 - 1.22 0.98 7015 113 0.2112 0.2192 4.098 4.1865| | 15: 1.22 - 1.19 0.98 6957 137 0.2138 0.1939 4.0535 4.0468| | 16: 1.19 - 1.17 0.93 6604 132 0.2125 0.2117 4.0041 4.0431| | 17: 1.17 - 1.14 0.98 6941 135 0.2149 0.1919 3.9493 3.9628| | 18: 1.14 - 1.12 0.98 6875 142 0.2198 0.2457 3.912 4.0088| | 19: 1.12 - 1.10 0.97 6949 106 0.2268 0.2364 3.8736 3.9725| | 20: 1.10 - 1.08 0.97 6884 147 0.2329 0.2497 3.8278 3.8939| | 21: 1.08 - 1.07 0.97 6852 152 0.2435 0.2681 3.7905 3.8322| | 22: 1.07 - 1.05 0.97 6838 135 0.2575 0.2650 3.7607 3.8059| | 23: 1.05 - 1.03 0.97 6829 159 0.2695 0.2773 3.7321 3.864| | 24: 1.03 - 1.02 0.96 6785 133 0.2853 0.2774 3.6994 3.7897| | 25: 1.02 - 1.01 0.93 6552 130 0.3090 0.3039 3.6758 3.7359| | 26: 1.01 - 0.99 0.96 6767 158 0.3233 0.3244 3.6341 3.6016| | 27: 0.99 - 0.98 0.94 6648 131 0.3435 0.3206 3.6414 3.5731| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.82 0.91 0.97 36493.53| | 2: 2.94 - 2.33 7339 128 0.85 21.33 1.08 1.02 15366.36| | 3: 2.33 - 2.04 6939 150 0.93 12.29 1.11 1.06 4020.60| | 4: 2.04 - 1.85 7170 155 0.93 12.81 1.11 1.07 2577.57| | 5: 1.85 - 1.72 7113 159 0.92 14.80 1.11 1.08 1917.02| | 6: 1.72 - 1.62 7102 142 0.91 15.87 1.12 1.08 1502.66| | 7: 1.62 - 1.54 7104 148 0.90 17.10 1.11 1.07 1272.70| | 8: 1.54 - 1.47 6798 152 0.89 17.79 1.11 1.05 1086.51| | 9: 1.47 - 1.41 6938 155 0.88 18.82 1.10 1.05 954.58| | 10: 1.41 - 1.36 7022 150 0.88 19.51 1.09 1.06 830.39| | 11: 1.36 - 1.32 6997 151 0.88 19.57 1.08 1.05 708.53| | 12: 1.32 - 1.28 6976 149 0.87 19.86 1.08 1.04 654.95| | 13: 1.28 - 1.25 6907 166 0.87 20.34 1.07 1.04 628.72| | 14: 1.25 - 1.22 7015 113 0.86 21.36 1.07 1.04 610.20| | 15: 1.22 - 1.19 6957 137 0.86 21.06 1.08 1.03 549.09| | 16: 1.19 - 1.17 6604 132 0.87 20.48 1.07 1.02 487.42| | 17: 1.17 - 1.14 6941 135 0.87 20.73 1.08 1.03 436.86| | 18: 1.14 - 1.12 6875 142 0.86 21.33 1.09 1.01 412.10| | 19: 1.12 - 1.10 6949 106 0.85 22.69 1.07 1.00 399.90| | 20: 1.10 - 1.08 6884 147 0.84 24.00 1.06 0.99 386.43| | 21: 1.08 - 1.07 6852 152 0.82 25.41 1.06 0.98 376.97| | 22: 1.07 - 1.05 6838 135 0.80 27.09 1.05 0.98 366.14| | 23: 1.05 - 1.03 6829 159 0.79 28.90 1.06 0.97 362.42| | 24: 1.03 - 1.02 6785 133 0.77 30.08 1.05 0.97 346.55| | 25: 1.02 - 1.01 6552 130 0.76 31.26 1.03 0.94 321.40| | 26: 1.01 - 0.99 6767 158 0.75 32.21 1.03 0.91 292.58| | 27: 0.99 - 0.98 6648 131 0.75 32.39 1.03 0.89 271.76| |alpha: min = 0.89 max = 1.08 mean = 1.02| |beta: min = 271.76 max = 36493.53 mean = 2856.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.76| |phase err.(test): min = 0.00 max = 89.78 mean = 21.83| |-----------------------------------------------------------------------------| ----------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 0.244 2950 Z= 5.494 Angle : 5.221 20.126 4018 Z= 3.712 Chirality : 0.371 1.201 492 Planarity : 0.034 0.141 512 Dihedral : 12.984 85.594 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.78 % Allowed : 2.59 % Favored : 96.63 % Rotamer: Outliers : 0.65 % Allowed : 3.23 % Favored : 96.13 % Cbeta Deviations : 30.06 % 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: -2.68 (0.37), residues: 386 helix: -2.95 (0.28), residues: 144 sheet: -1.59 (0.46), residues: 86 loop : -0.32 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.027 ARG B 149 TYR 0.119 0.033 TYR B 194 PHE 0.104 0.036 PHE A 119 TRP 0.117 0.036 TRP B 139 HIS 0.075 0.035 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2040 r_free= 0.1989 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301363 | | target function (ml) not normalized (work): 805701.287318 | | target function (ml) not normalized (free): 16566.498763 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2038 0.2040 0.1989 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2038 0.2040 0.1989 n_refl.: 191155 remove outliers: r(all,work,free)=0.2038 0.2040 0.1989 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2039 0.2040 0.1989 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1811 0.1808 0.1923 n_refl.: 191145 remove outliers: r(all,work,free)=0.1808 0.1806 0.1923 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4074 402.814 291.667 0.432 0.913 0.297 13.296-10.522 99.01 99 1 0.2476 528.187 520.086 0.785 0.914 0.243 10.503-8.327 98.90 177 3 0.2479 564.205 558.218 0.972 0.914 0.217 8.318-6.595 100.00 360 8 0.2468 414.736 403.759 0.966 0.914 0.160 6.588-5.215 100.00 711 7 0.2314 381.101 366.014 0.953 0.914 0.160 5.214-4.128 98.38 1367 28 0.1471 557.435 549.927 1.073 0.914 0.070 4.126-3.266 94.74 2603 46 0.1356 508.132 499.453 1.146 0.914 0.025 3.266-2.585 99.86 5447 97 0.1449 342.774 337.659 1.118 0.913 0.020 2.585-2.046 97.45 10613 204 0.1408 258.603 254.016 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1608 153.054 149.966 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1946 82.395 80.218 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2324 44.203 41.676 1.112 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0051 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1806 r_free=0.1923 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 r_work=0.1813 r_free=0.1928 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.791302 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 562.859872 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 0.1273 0.1507 0.0233 0.038 1.2 11.7 0.0 0.0 0 11.396 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.07 2.33 1.117 13.114 562.860 0.018 12.98 15.68 2.70 1.231 13.336 562.860 0.017 Individual atomic B min max mean iso aniso Overall: 5.17 73.05 15.01 1.39 435 3274 Protein: 5.17 40.33 10.98 1.39 0 2902 Water: 6.40 73.05 29.49 N/A 435 370 Other: 15.94 30.39 23.16 N/A 0 2 Chain A: 5.31 59.84 13.03 N/A 0 1626 Chain B: 5.17 73.05 12.76 N/A 0 1648 Chain S: 12.24 64.97 30.92 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2169 11.96 - 18.74 638 18.74 - 25.53 319 25.53 - 32.32 255 32.32 - 39.11 157 39.11 - 45.90 108 45.90 - 52.68 38 52.68 - 59.47 21 59.47 - 66.26 3 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1568 r_work=0.1297 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1563 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 = 0.1282 r_free = 0.1551 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015593 | | target function (ls_wunit_k1) not normalized (work): 2920.549356 | | target function (ls_wunit_k1) not normalized (free): 114.535324 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1551 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1466 0.1463 0.1627 n_refl.: 191138 remove outliers: r(all,work,free)=0.1466 0.1463 0.1627 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1489 0.1487 0.1636 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1540 n_refl.: 191138 remove outliers: r(all,work,free)=0.1279 0.1274 0.1539 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 0.3622 402.814 381.127 0.469 1.001 0.275 13.296-10.522 99.01 99 1 0.2109 528.187 522.621 0.712 1.003 0.239 10.503-8.327 98.90 177 3 0.1742 564.205 563.538 0.855 1.003 0.230 8.318-6.595 100.00 360 8 0.1714 414.736 412.060 0.873 1.003 0.155 6.588-5.215 100.00 711 7 0.1537 381.101 373.593 0.853 1.003 0.150 5.214-4.128 98.38 1367 28 0.0909 557.435 555.080 0.939 1.003 0.049 4.126-3.266 94.74 2603 46 0.0829 508.132 504.193 1.005 1.004 0.014 3.266-2.585 99.86 5447 97 0.0920 342.774 340.216 0.986 1.003 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.329 0.997 1.004 0.000 2.046-1.619 99.39 21536 464 0.1090 153.054 151.352 1.015 1.004 0.000 1.619-1.281 98.00 42464 925 0.1278 82.395 81.414 1.006 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.190 0.985 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0374 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 r_work=0.1277 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1545 | n_water=805 | time (s): 3.300 (total time: 3.300) Filter (dist) r_work=0.1281 r_free=0.1550 | n_water=794 | time (s): 100.580 (total time: 103.880) Filter (q & B) r_work=0.1282 r_free=0.1550 | n_water=789 | time (s): 4.820 (total time: 108.700) Compute maps r_work=0.1282 r_free=0.1550 | n_water=789 | time (s): 2.120 (total time: 110.820) Filter (map) r_work=0.1309 r_free=0.1535 | n_water=653 | time (s): 4.320 (total time: 115.140) Find peaks r_work=0.1309 r_free=0.1535 | n_water=653 | time (s): 0.570 (total time: 115.710) Add new water r_work=0.1331 r_free=0.1566 | n_water=960 | time (s): 4.110 (total time: 119.820) Refine new water occ: r_work=0.1289 r_free=0.1520 adp: r_work=0.1277 r_free=0.1516 occ: r_work=0.1279 r_free=0.1513 adp: r_work=0.1272 r_free=0.1510 occ: r_work=0.1274 r_free=0.1507 adp: r_work=0.1271 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1508 r_work=0.1271 r_free=0.1508 | n_water=960 | time (s): 89.430 (total time: 209.250) Filter (q & B) r_work=0.1275 r_free=0.1510 | n_water=885 | time (s): 4.880 (total time: 214.130) Filter (dist only) r_work=0.1276 r_free=0.1506 | n_water=882 | time (s): 110.640 (total time: 324.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.457100 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.553998 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 0.1258 0.1515 0.0257 0.041 1.1 19.5 0.0 0.0 0 12.229 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.58 15.15 2.57 2.036 15.155 573.554 0.015 12.35 15.01 2.66 2.398 15.200 573.554 0.014 Individual atomic B min max mean iso aniso Overall: 5.33 69.23 16.29 1.19 514 3272 Protein: 5.33 40.54 10.98 1.19 0 2902 Water: 6.54 69.23 33.73 N/A 514 368 Other: 16.39 32.97 24.68 N/A 0 2 Chain A: 5.52 56.25 12.99 N/A 0 1624 Chain B: 5.33 68.21 12.81 N/A 0 1648 Chain S: 12.51 69.23 37.87 N/A 514 0 Histogram: Values Number of atoms 5.33 - 11.72 2070 11.72 - 18.11 711 18.11 - 24.50 270 24.50 - 30.89 211 30.89 - 37.28 168 37.28 - 43.67 162 43.67 - 50.06 103 50.06 - 56.45 47 56.45 - 62.84 31 62.84 - 69.23 13 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1502 r_work=0.1236 r_free=0.1503 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1503 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 = 0.1498 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 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= 0.1498 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013486 | | target function (ls_wunit_k1) not normalized (work): 2525.836282 | | target function (ls_wunit_k1) not normalized (free): 101.733855 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1498 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1441 0.1438 0.1590 n_refl.: 191137 remove outliers: r(all,work,free)=0.1441 0.1438 0.1590 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1438 0.1435 0.1588 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1505 n_refl.: 191137 remove outliers: r(all,work,free)=0.1241 0.1236 0.1505 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3226 402.814 382.011 0.492 0.962 0.274 13.296-10.522 99.01 99 1 0.1864 528.187 521.912 0.760 0.964 0.236 10.503-8.327 98.90 177 3 0.1422 564.205 567.393 0.919 0.963 0.197 8.318-6.595 100.00 360 8 0.1553 414.736 413.494 0.935 0.963 0.153 6.588-5.215 100.00 711 7 0.1352 381.101 377.037 0.912 0.963 0.130 5.214-4.128 98.38 1367 28 0.0833 557.435 556.202 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0766 508.132 505.269 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0864 342.774 341.390 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0904 258.603 256.753 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.609 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1258 82.395 81.342 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.215 1.060 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0481 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1505 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1505 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1505 | n_water=882 | time (s): 3.160 (total time: 3.160) Filter (dist) r_work=0.1237 r_free=0.1509 | n_water=878 | time (s): 117.860 (total time: 121.020) Filter (q & B) r_work=0.1237 r_free=0.1509 | n_water=875 | time (s): 5.690 (total time: 126.710) Compute maps r_work=0.1237 r_free=0.1509 | n_water=875 | time (s): 2.270 (total time: 128.980) Filter (map) r_work=0.1276 r_free=0.1519 | n_water=686 | time (s): 4.770 (total time: 133.750) Find peaks r_work=0.1276 r_free=0.1519 | n_water=686 | time (s): 0.650 (total time: 134.400) Add new water r_work=0.1299 r_free=0.1555 | n_water=1014 | time (s): 5.090 (total time: 139.490) Refine new water occ: r_work=0.1254 r_free=0.1511 adp: r_work=0.1255 r_free=0.1511 occ: r_work=0.1251 r_free=0.1507 adp: r_work=0.1251 r_free=0.1507 occ: r_work=0.1248 r_free=0.1502 adp: r_work=0.1247 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1247 r_free=0.1503 r_work=0.1247 r_free=0.1503 | n_water=1014 | time (s): 319.860 (total time: 459.350) Filter (q & B) r_work=0.1253 r_free=0.1504 | n_water=863 | time (s): 4.380 (total time: 463.730) Filter (dist only) r_work=0.1253 r_free=0.1504 | n_water=862 | time (s): 105.450 (total time: 569.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.672291 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.844968 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 0.1242 0.1433 0.0190 0.036 1.1 6.8 0.0 0.0 0 0.836 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.42 14.33 1.90 1.926 14.535 15.845 3.941 12.36 13.96 1.59 2.206 14.443 15.845 3.899 Individual atomic B min max mean iso aniso Overall: 5.51 67.84 15.19 1.06 495 3271 Protein: 5.51 36.91 10.75 1.06 0 2902 Water: 6.68 67.84 30.13 N/A 495 367 Other: 14.09 28.61 21.35 N/A 0 2 Chain A: 5.51 55.43 12.76 N/A 0 1624 Chain B: 5.54 67.84 12.54 N/A 0 1647 Chain S: 12.82 64.48 31.99 N/A 495 0 Histogram: Values Number of atoms 5.51 - 11.74 2133 11.74 - 17.98 679 17.98 - 24.21 299 24.21 - 30.44 231 30.44 - 36.68 176 36.68 - 42.91 145 42.91 - 49.14 68 49.14 - 55.37 24 55.37 - 61.61 7 61.61 - 67.84 4 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1396 r_work=0.1237 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1397 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1381 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1381 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892337 | | target function (ml) not normalized (work): 729019.062120 | | target function (ml) not normalized (free): 15223.995188 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1381 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1446 0.1445 0.1475 n_refl.: 191137 remove outliers: r(all,work,free)=0.1446 0.1445 0.1475 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1439 0.1472 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1228 0.1375 n_refl.: 191137 remove outliers: r(all,work,free)=0.1230 0.1227 0.1375 n_refl.: 191133 ======================== 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 0.3823 398.008 362.126 0.423 0.947 0.247 13.296-10.522 98.02 98 1 0.2376 528.900 506.620 0.709 0.948 0.222 10.503-8.327 97.80 175 3 0.1978 554.286 558.295 0.882 0.948 0.187 8.318-6.595 100.00 360 8 0.2105 414.736 410.305 0.898 0.948 0.137 6.588-5.215 100.00 711 7 0.1838 381.101 370.899 0.885 0.948 0.113 5.214-4.128 98.38 1367 28 0.1174 557.435 551.973 0.971 0.948 0.070 4.126-3.266 94.74 2603 46 0.1097 508.132 501.293 1.033 0.948 0.009 3.266-2.585 99.86 5447 97 0.1087 342.774 339.039 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0968 258.603 255.768 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0978 153.054 151.400 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1055 82.395 81.490 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.317 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0982 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1375 | n_water=862 | time (s): 2.900 (total time: 2.900) Filter (dist) r_work=0.1227 r_free=0.1375 | n_water=861 | time (s): 110.110 (total time: 113.010) Filter (q & B) r_work=0.1228 r_free=0.1375 | n_water=852 | time (s): 4.380 (total time: 117.390) Compute maps r_work=0.1228 r_free=0.1375 | n_water=852 | time (s): 1.930 (total time: 119.320) Filter (map) r_work=0.1249 r_free=0.1381 | n_water=713 | time (s): 4.700 (total time: 124.020) Find peaks r_work=0.1249 r_free=0.1381 | n_water=713 | time (s): 0.810 (total time: 124.830) Add new water r_work=0.1264 r_free=0.1397 | n_water=948 | time (s): 5.440 (total time: 130.270) Refine new water occ: r_work=0.1217 r_free=0.1367 adp: r_work=0.1209 r_free=0.1363 occ: r_work=0.1206 r_free=0.1362 adp: r_work=0.1206 r_free=0.1362 occ: r_work=0.1204 r_free=0.1362 adp: r_work=0.1204 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1361 r_work=0.1204 r_free=0.1361 | n_water=948 | time (s): 301.080 (total time: 431.350) Filter (q & B) r_work=0.1208 r_free=0.1360 | n_water=858 | time (s): 4.190 (total time: 435.540) Filter (dist only) r_work=0.1208 r_free=0.1359 | n_water=856 | time (s): 110.750 (total time: 546.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.603295 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.483751 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1361 0.0154 0.036 1.1 6.5 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.61 1.54 1.833 14.185 15.484 3.875 12.00 13.57 1.57 1.944 14.141 15.484 3.866 Individual atomic B min max mean iso aniso Overall: 5.52 67.42 14.93 1.00 489 3271 Protein: 5.52 33.66 10.66 1.00 0 2902 Water: 5.89 67.42 29.37 N/A 489 367 Other: 13.95 27.71 20.83 N/A 0 2 Chain A: 5.54 54.33 12.62 N/A 0 1624 Chain B: 5.52 67.42 12.44 N/A 0 1647 Chain S: 5.89 64.31 30.95 N/A 489 0 Histogram: Values Number of atoms 5.52 - 11.71 2125 11.71 - 17.90 716 17.90 - 24.09 296 24.09 - 30.28 225 30.28 - 36.47 177 36.47 - 42.66 135 42.66 - 48.85 62 48.85 - 55.04 18 55.04 - 61.23 1 61.23 - 67.42 5 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1357 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1355 target_work(ml) = 3.864 | | 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.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864257 | | target function (ml) not normalized (work): 723744.367482 | | target function (ml) not normalized (free): 15133.314301 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1355 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1424 0.1424 0.1470 n_refl.: 191133 remove outliers: r(all,work,free)=0.1424 0.1424 0.1470 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1417 0.1465 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1353 n_refl.: 191133 remove outliers: r(all,work,free)=0.1198 0.1195 0.1353 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 92.08 90 3 0.3676 361.072 310.990 0.418 0.947 0.251 13.296-10.522 96.04 96 1 0.2340 480.664 453.894 0.708 0.948 0.211 10.503-8.327 97.80 175 3 0.2063 502.151 496.931 0.866 0.948 0.190 8.318-6.595 100.00 360 8 0.2175 375.727 370.286 0.896 0.948 0.130 6.588-5.215 100.00 711 7 0.1886 345.256 335.566 0.883 0.948 0.090 5.214-4.128 98.38 1367 28 0.1193 505.004 500.290 0.971 0.948 0.044 4.126-3.266 94.74 2603 46 0.1118 460.338 454.001 1.034 0.949 0.005 3.266-2.585 99.86 5447 97 0.1087 310.533 307.426 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0933 234.280 231.878 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0911 138.658 137.392 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0991 74.646 73.950 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.044 38.391 1.038 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1141 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1353 | n_water=856 | time (s): 2.740 (total time: 2.740) Filter (dist) r_work=0.1195 r_free=0.1353 | n_water=856 | time (s): 105.100 (total time: 107.840) Filter (q & B) r_work=0.1195 r_free=0.1353 | n_water=847 | time (s): 4.710 (total time: 112.550) Compute maps r_work=0.1195 r_free=0.1353 | n_water=847 | time (s): 2.370 (total time: 114.920) Filter (map) r_work=0.1218 r_free=0.1353 | n_water=728 | time (s): 5.520 (total time: 120.440) Find peaks r_work=0.1218 r_free=0.1353 | n_water=728 | time (s): 0.870 (total time: 121.310) Add new water r_work=0.1230 r_free=0.1365 | n_water=954 | time (s): 5.140 (total time: 126.450) Refine new water occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1344 occ: r_work=0.1191 r_free=0.1344 adp: r_work=0.1191 r_free=0.1343 occ: r_work=0.1189 r_free=0.1344 adp: r_work=0.1189 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1344 r_work=0.1189 r_free=0.1344 | n_water=954 | time (s): 272.340 (total time: 398.790) Filter (q & B) r_work=0.1193 r_free=0.1346 | n_water=874 | time (s): 4.580 (total time: 403.370) Filter (dist only) r_work=0.1193 r_free=0.1345 | n_water=873 | time (s): 117.010 (total time: 520.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.603826 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.842345 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 0.1347 0.0152 0.037 1.1 5.6 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.47 1.52 1.793 14.110 14.842 3.764 12.00 13.52 1.52 1.866 14.080 14.842 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 67.07 14.91 0.95 507 3270 Protein: 5.57 32.12 10.59 0.95 0 2902 Water: 6.04 67.07 29.26 N/A 507 366 Other: 13.79 26.43 20.11 N/A 0 2 Chain A: 5.57 53.90 12.51 N/A 0 1623 Chain B: 5.57 67.07 12.34 N/A 0 1647 Chain S: 6.04 64.15 30.91 N/A 507 0 Histogram: Values Number of atoms 5.57 - 11.72 2148 11.72 - 17.87 710 17.87 - 24.02 300 24.02 - 30.17 220 30.17 - 36.32 166 36.32 - 42.47 145 42.47 - 48.62 64 48.62 - 54.77 18 54.77 - 60.92 1 60.92 - 67.07 5 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1352 r_work=0.1200 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1352 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1354 target_work(ml) = 3.761 | | 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.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761388 | | target function (ml) not normalized (work): 704462.841142 | | target function (ml) not normalized (free): 14743.251877 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1492 n_refl.: 191129 remove outliers: r(all,work,free)=0.1398 0.1396 0.1492 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1391 0.1389 0.1487 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1352 n_refl.: 191129 remove outliers: r(all,work,free)=0.1200 0.1197 0.1352 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 92.08 90 3 0.3708 361.072 331.746 0.435 0.954 0.247 13.296-10.522 96.04 96 1 0.2388 480.664 462.449 0.707 0.955 0.204 10.503-8.327 97.80 175 3 0.2041 502.151 497.167 0.857 0.955 0.183 8.315-6.595 100.00 359 8 0.2160 374.781 370.967 0.887 0.955 0.130 6.588-5.215 100.00 711 7 0.1893 345.256 335.419 0.878 0.955 0.090 5.214-4.128 98.38 1367 28 0.1201 505.004 500.170 0.965 0.955 0.039 4.126-3.266 94.74 2603 46 0.1138 460.338 453.601 1.028 0.955 0.005 3.266-2.585 99.86 5447 97 0.1103 310.533 307.285 1.014 0.954 0.000 2.585-2.046 97.45 10613 204 0.0945 234.280 231.720 1.026 0.954 0.000 2.046-1.619 99.39 21536 464 0.0917 138.658 137.310 1.050 0.952 0.000 1.619-1.281 98.00 42464 925 0.0980 74.646 73.921 1.048 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.044 38.374 1.037 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1238 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1352 | n_water=873 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1197 r_free=0.1352 | n_water=873 | time (s): 108.880 (total time: 111.440) Filter (q & B) r_work=0.1197 r_free=0.1352 | n_water=865 | time (s): 5.070 (total time: 116.510) Compute maps r_work=0.1197 r_free=0.1352 | n_water=865 | time (s): 1.870 (total time: 118.380) Filter (map) r_work=0.1217 r_free=0.1368 | n_water=751 | time (s): 4.520 (total time: 122.900) Find peaks r_work=0.1217 r_free=0.1368 | n_water=751 | time (s): 0.750 (total time: 123.650) Add new water r_work=0.1227 r_free=0.1379 | n_water=960 | time (s): 4.670 (total time: 128.320) Refine new water occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1195 r_free=0.1341 occ: r_work=0.1193 r_free=0.1340 adp: r_work=0.1193 r_free=0.1340 occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1191 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1340 r_work=0.1191 r_free=0.1340 | n_water=960 | time (s): 210.660 (total time: 338.980) Filter (q & B) r_work=0.1195 r_free=0.1347 | n_water=886 | time (s): 4.310 (total time: 343.290) Filter (dist only) r_work=0.1196 r_free=0.1346 | n_water=885 | time (s): 114.010 (total time: 457.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.542635 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.682105 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 0.1200 0.1350 0.0150 0.037 1.1 5.8 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.50 1.50 1.761 14.020 14.682 3.763 12.02 13.53 1.50 1.904 13.970 14.682 3.760 Individual atomic B min max mean iso aniso Overall: 5.57 66.00 14.80 0.90 519 3270 Protein: 5.57 29.38 10.48 0.90 0 2902 Water: 6.01 66.00 28.96 N/A 519 366 Other: 13.84 23.47 18.65 N/A 0 2 Chain A: 5.64 53.33 12.36 N/A 0 1623 Chain B: 5.57 66.00 12.21 N/A 0 1647 Chain S: 6.01 63.71 30.63 N/A 519 0 Histogram: Values Number of atoms 5.57 - 11.62 2121 11.62 - 17.66 767 17.66 - 23.70 285 23.70 - 29.74 207 29.74 - 35.79 176 35.79 - 41.83 132 41.83 - 47.87 74 47.87 - 53.91 21 53.91 - 59.96 1 59.96 - 66.00 5 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1353 r_work=0.1203 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1353 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1354 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759133 | | target function (ml) not normalized (work): 704036.835785 | | target function (ml) not normalized (free): 14740.155579 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1354 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1399 0.1398 0.1490 n_refl.: 191128 remove outliers: r(all,work,free)=0.1399 0.1398 0.1490 n_refl.: 191128 overall B=-0.22 to atoms: r(all,work,free)=0.1364 0.1363 0.1466 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1200 0.1352 n_refl.: 191128 remove outliers: r(all,work,free)=0.1202 0.1200 0.1352 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 92.08 90 3 0.3693 361.072 331.571 0.433 0.953 0.227 13.296-10.522 96.04 96 1 0.2374 480.664 463.001 0.716 0.954 0.176 10.503-8.327 97.80 175 3 0.2141 502.151 496.555 0.878 0.955 0.153 8.315-6.595 100.00 359 8 0.2165 374.781 370.071 0.907 0.954 0.110 6.588-5.215 100.00 711 7 0.1926 345.256 335.760 0.903 0.955 0.110 5.214-4.128 98.38 1367 28 0.1221 505.004 500.104 0.993 0.955 0.070 4.126-3.266 94.74 2603 46 0.1163 460.338 453.278 1.054 0.955 0.005 3.266-2.585 99.86 5447 97 0.1109 310.533 307.257 1.037 0.954 0.000 2.585-2.046 97.45 10613 204 0.0953 234.280 231.760 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0915 138.658 137.324 1.063 0.953 0.000 1.619-1.281 98.00 42464 925 0.0973 74.646 73.935 1.051 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.044 38.380 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=0.0491 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1352 | n_water=885 | time (s): 2.620 (total time: 2.620) Filter (dist) r_work=0.1200 r_free=0.1352 | n_water=885 | time (s): 107.400 (total time: 110.020) Filter (q & B) r_work=0.1200 r_free=0.1351 | n_water=879 | time (s): 4.400 (total time: 114.420) Compute maps r_work=0.1200 r_free=0.1351 | n_water=879 | time (s): 1.770 (total time: 116.190) Filter (map) r_work=0.1221 r_free=0.1363 | n_water=761 | time (s): 5.330 (total time: 121.520) Find peaks r_work=0.1221 r_free=0.1363 | n_water=761 | time (s): 0.840 (total time: 122.360) Add new water r_work=0.1231 r_free=0.1371 | n_water=965 | time (s): 5.550 (total time: 127.910) Refine new water occ: r_work=0.1198 r_free=0.1338 adp: r_work=0.1198 r_free=0.1338 occ: r_work=0.1196 r_free=0.1339 adp: r_work=0.1196 r_free=0.1339 occ: r_work=0.1195 r_free=0.1340 adp: r_work=0.1195 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1340 r_work=0.1195 r_free=0.1340 | n_water=965 | time (s): 239.830 (total time: 367.740) Filter (q & B) r_work=0.1199 r_free=0.1345 | n_water=888 | time (s): 4.210 (total time: 371.950) Filter (dist only) r_work=0.1199 r_free=0.1345 | n_water=887 | time (s): 114.350 (total time: 486.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.592980 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.488790 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1347 0.0145 0.038 1.1 5.1 0.0 0.3 0 0.796 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.47 1.45 1.717 13.693 14.489 3.760 12.02 13.48 1.47 1.757 13.676 14.489 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 64.77 14.55 0.88 521 3270 Protein: 5.39 28.61 10.25 0.88 0 2902 Water: 5.82 64.77 28.61 N/A 521 366 Other: 13.66 22.18 17.92 N/A 0 2 Chain A: 5.43 52.70 12.09 N/A 0 1623 Chain B: 5.39 64.77 11.96 N/A 0 1647 Chain S: 5.82 63.00 30.40 N/A 521 0 Histogram: Values Number of atoms 5.39 - 11.32 2095 11.32 - 17.26 786 17.26 - 23.20 285 23.20 - 29.14 208 29.14 - 35.08 179 35.08 - 41.02 127 41.02 - 46.95 75 46.95 - 52.89 30 52.89 - 58.83 1 58.83 - 64.77 5 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1349 r_work=0.1202 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1349 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1352 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757078 | | target function (ml) not normalized (work): 703651.914242 | | target function (ml) not normalized (free): 14731.433617 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1352 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1371 0.1369 0.1476 n_refl.: 191128 remove outliers: r(all,work,free)=0.1371 0.1369 0.1476 n_refl.: 191128 overall B=0.06 to atoms: r(all,work,free)=0.1379 0.1377 0.1481 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1342 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 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 92.08 90 3 0.3690 361.072 331.334 0.423 0.973 0.221 13.296-10.522 96.04 96 1 0.2374 480.664 462.611 0.704 0.975 0.164 10.503-8.327 97.80 175 3 0.2161 502.151 496.175 0.866 0.975 0.140 8.315-6.595 100.00 359 8 0.2195 374.781 369.131 0.893 0.975 0.100 6.588-5.215 100.00 711 7 0.1943 345.256 335.035 0.891 0.975 0.100 5.214-4.128 98.38 1367 28 0.1230 505.004 499.748 0.981 0.976 0.049 4.126-3.266 94.74 2603 46 0.1175 460.338 452.712 1.042 0.977 0.005 3.266-2.585 99.86 5447 97 0.1112 310.533 307.031 1.026 0.978 0.000 2.585-2.046 97.45 10613 204 0.0957 234.280 231.658 1.033 0.979 0.000 2.046-1.619 99.39 21536 464 0.0908 138.658 137.250 1.049 0.982 0.000 1.619-1.281 98.00 42464 925 0.0950 74.646 73.980 1.038 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.044 38.356 1.004 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0632 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1342 | n_water=887 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1191 r_free=0.1342 | n_water=887 | time (s): 105.830 (total time: 108.480) Filter (q & B) r_work=0.1192 r_free=0.1345 | n_water=878 | time (s): 5.580 (total time: 114.060) Compute maps r_work=0.1192 r_free=0.1345 | n_water=878 | time (s): 2.530 (total time: 116.590) Filter (map) r_work=0.1212 r_free=0.1355 | n_water=770 | time (s): 4.620 (total time: 121.210) Find peaks r_work=0.1212 r_free=0.1355 | n_water=770 | time (s): 0.870 (total time: 122.080) Add new water r_work=0.1222 r_free=0.1362 | n_water=979 | time (s): 4.920 (total time: 127.000) Refine new water occ: r_work=0.1188 r_free=0.1325 adp: r_work=0.1188 r_free=0.1326 occ: r_work=0.1186 r_free=0.1325 adp: r_work=0.1186 r_free=0.1325 occ: r_work=0.1184 r_free=0.1324 adp: r_work=0.1184 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1325 r_work=0.1184 r_free=0.1325 | n_water=979 | time (s): 234.570 (total time: 361.570) Filter (q & B) r_work=0.1188 r_free=0.1334 | n_water=909 | time (s): 5.060 (total time: 366.630) Filter (dist only) r_work=0.1188 r_free=0.1333 | n_water=907 | time (s): 117.040 (total time: 483.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.564588 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.037771 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 0.0148 0.038 1.1 6.5 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.40 1.48 1.678 13.749 14.038 3.755 11.93 13.43 1.50 1.689 13.741 14.038 3.754 Individual atomic B min max mean iso aniso Overall: 5.43 64.38 14.67 0.87 541 3270 Protein: 5.43 28.35 10.31 0.87 0 2902 Water: 5.92 64.38 28.58 N/A 541 366 Other: 13.72 22.17 17.94 N/A 0 2 Chain A: 5.56 52.54 12.12 N/A 0 1623 Chain B: 5.43 64.38 12.00 N/A 0 1647 Chain S: 5.92 62.84 30.41 N/A 541 0 Histogram: Values Number of atoms 5.43 - 11.32 2075 11.32 - 17.22 811 17.22 - 23.11 284 23.11 - 29.01 211 29.01 - 34.90 186 34.90 - 40.80 125 40.80 - 46.69 79 46.69 - 52.59 33 52.59 - 58.49 2 58.49 - 64.38 5 =========================== 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) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1346 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** 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= 0.1346 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753690 | | target function (ml) not normalized (work): 703017.287522 | | target function (ml) not normalized (free): 14723.935826 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1346 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1382 0.1380 0.1490 n_refl.: 191128 remove outliers: r(all,work,free)=0.1382 0.1380 0.1490 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1384 0.1382 0.1492 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1342 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1342 n_refl.: 191126 ======================== 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 0.3661 356.157 321.130 0.361 0.996 0.150 13.296-10.522 96.04 96 1 0.2380 480.664 462.026 0.680 0.997 0.139 10.503-8.327 97.80 175 3 0.2166 502.151 495.829 0.845 0.997 0.126 8.315-6.595 100.00 359 8 0.2149 374.781 369.447 0.873 0.997 0.104 6.588-5.215 100.00 711 7 0.1947 345.256 335.300 0.870 0.998 0.087 5.214-4.128 98.38 1367 28 0.1233 505.004 499.777 0.959 0.998 0.039 4.126-3.266 94.74 2603 46 0.1170 460.338 452.631 1.019 1.000 0.005 3.266-2.585 99.86 5447 97 0.1120 310.533 306.989 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0958 234.280 231.694 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0906 138.658 137.289 1.027 1.005 0.000 1.619-1.281 98.00 42464 925 0.0945 74.646 73.998 1.018 1.010 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.044 38.344 0.988 1.019 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0204 ============================ 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): 2.550 (total time: 2.550) Filter (dist) r_work=0.1190 r_free=0.1341 | n_water=906 | time (s): 123.940 (total time: 126.490) Filter (q & B) r_work=0.1190 r_free=0.1343 | n_water=897 | time (s): 4.550 (total time: 131.040) Compute maps r_work=0.1190 r_free=0.1343 | n_water=897 | time (s): 2.280 (total time: 133.320) Filter (map) r_work=0.1212 r_free=0.1351 | n_water=781 | time (s): 4.440 (total time: 137.760) Find peaks r_work=0.1212 r_free=0.1351 | n_water=781 | time (s): 0.620 (total time: 138.380) Add new water r_work=0.1219 r_free=0.1357 | n_water=983 | time (s): 4.350 (total time: 142.730) Refine new water occ: r_work=0.1188 r_free=0.1329 adp: r_work=0.1188 r_free=0.1329 occ: r_work=0.1186 r_free=0.1330 adp: r_work=0.1186 r_free=0.1330 occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1184 r_free=0.1330 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1330 r_work=0.1184 r_free=0.1330 | n_water=983 | time (s): 204.380 (total time: 347.110) Filter (q & B) r_work=0.1188 r_free=0.1337 | n_water=912 | time (s): 4.670 (total time: 351.780) Filter (dist only) r_work=0.1188 r_free=0.1337 | n_water=910 | time (s): 118.310 (total time: 470.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.572741 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.719793 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 0.1341 0.0150 0.039 1.1 6.0 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.41 1.50 1.680 13.754 14.720 3.754 11.90 13.42 1.52 1.684 13.752 14.720 3.751 Individual atomic B min max mean iso aniso Overall: 5.54 63.58 14.66 0.87 544 3270 Protein: 5.54 28.33 10.34 0.87 0 2902 Water: 5.97 63.58 28.43 N/A 544 366 Other: 13.80 22.20 18.00 N/A 0 2 Chain A: 5.60 52.22 12.12 N/A 0 1623 Chain B: 5.54 63.58 12.01 N/A 0 1647 Chain S: 5.97 62.52 30.27 N/A 544 0 Histogram: Values Number of atoms 5.54 - 11.34 2067 11.34 - 17.15 824 17.15 - 22.95 273 22.95 - 28.76 217 28.76 - 34.56 185 34.56 - 40.37 121 40.37 - 46.17 80 46.17 - 51.98 37 51.98 - 57.78 5 57.78 - 63.58 5 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1342 r_work=0.1190 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1342 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1342 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1342 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751075 | | target function (ml) not normalized (work): 702520.166461 | | target function (ml) not normalized (free): 14720.154289 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1380 0.1377 0.1495 n_refl.: 191126 remove outliers: r(all,work,free)=0.1380 0.1377 0.1495 n_refl.: 191126 overall B=-0.00 to atoms: r(all,work,free)=0.1379 0.1377 0.1495 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1340 n_refl.: 191126 remove outliers: r(all,work,free)=0.1190 0.1187 0.1340 n_refl.: 191125 ======================== 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 89.11 87 3 0.3524 355.917 325.537 0.338 0.995 0.090 13.296-10.522 96.04 96 1 0.2378 480.664 461.308 0.667 0.997 0.109 10.503-8.327 97.80 175 3 0.2178 502.151 495.447 0.842 0.997 0.112 8.315-6.595 100.00 359 8 0.2146 374.781 369.228 0.870 0.997 0.098 6.588-5.215 100.00 711 7 0.1962 345.256 335.233 0.870 0.997 0.083 5.214-4.128 98.38 1367 28 0.1239 505.004 499.548 0.959 0.998 0.070 4.126-3.266 94.74 2603 46 0.1169 460.338 452.681 1.019 1.000 0.000 3.266-2.585 99.86 5447 97 0.1118 310.533 307.004 1.003 1.001 0.000 2.585-2.046 97.45 10613 204 0.0956 234.280 231.724 1.012 1.003 0.000 2.046-1.619 99.39 21536 464 0.0904 138.658 137.294 1.028 1.006 0.000 1.619-1.281 98.00 42464 925 0.0939 74.646 74.003 1.020 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.044 38.332 0.990 1.023 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0071 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1340 After: r_work=0.1188 r_free=0.1341 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1341 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1341 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1341 | n_water=910 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1188 r_free=0.1341 | n_water=909 | time (s): 126.150 (total time: 128.660) Filter (q & B) r_work=0.1189 r_free=0.1343 | n_water=899 | time (s): 4.530 (total time: 133.190) Compute maps r_work=0.1189 r_free=0.1343 | n_water=899 | time (s): 1.940 (total time: 135.130) Filter (map) r_work=0.1209 r_free=0.1351 | n_water=793 | time (s): 5.050 (total time: 140.180) Find peaks r_work=0.1209 r_free=0.1351 | n_water=793 | time (s): 0.570 (total time: 140.750) Add new water r_work=0.1217 r_free=0.1360 | n_water=999 | time (s): 4.050 (total time: 144.800) Refine new water occ: r_work=0.1185 r_free=0.1326 adp: r_work=0.1185 r_free=0.1326 occ: r_work=0.1183 r_free=0.1325 adp: r_work=0.1183 r_free=0.1325 occ: r_work=0.1181 r_free=0.1324 adp: r_work=0.1181 r_free=0.1324 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1324 r_work=0.1181 r_free=0.1324 | n_water=999 | time (s): 260.750 (total time: 405.550) Filter (q & B) r_work=0.1185 r_free=0.1331 | n_water=928 | time (s): 4.430 (total time: 409.980) Filter (dist only) r_work=0.1186 r_free=0.1331 | n_water=926 | time (s): 120.620 (total time: 530.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.528104 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.895604 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 0.1187 0.1333 0.0146 0.039 1.1 7.7 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 13.33 1.46 1.681 13.793 14.896 3.752 11.88 13.35 1.47 1.679 13.794 14.896 3.751 Individual atomic B min max mean iso aniso Overall: 5.56 62.69 14.72 0.87 560 3270 Protein: 5.56 28.24 10.36 0.87 0 2902 Water: 6.05 62.69 28.37 N/A 560 366 Other: 13.84 22.23 18.04 N/A 0 2 Chain A: 5.66 51.86 12.12 N/A 0 1623 Chain B: 5.56 62.69 12.01 N/A 0 1647 Chain S: 6.05 62.44 30.25 N/A 560 0 Histogram: Values Number of atoms 5.56 - 11.27 2043 11.27 - 16.98 841 16.98 - 22.70 274 22.70 - 28.41 218 28.41 - 34.13 202 34.13 - 39.84 117 39.84 - 45.55 79 45.55 - 51.27 46 51.27 - 56.98 4 56.98 - 62.69 6 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1335 r_work=0.1188 r_free=0.1335 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1335 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1334 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191125 (all), 2.01 % free)-----------| | | | r_work= 0.1186 r_free= 0.1334 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750578 | | target function (ml) not normalized (work): 702423.221449 | | target function (ml) not normalized (free): 14714.397522 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7393 127 0.1348 0.1406 5.6782 5.7573| | 2: 2.94 - 2.33 1.00 7339 128 0.1064 0.1313 5.0708 5.1617| | 3: 2.33 - 2.04 0.96 6939 150 0.0897 0.1144 4.6443 4.7351| | 4: 2.04 - 1.85 1.00 7170 155 0.0892 0.1027 4.3843 4.5502| | 5: 1.85 - 1.72 0.99 7113 159 0.0925 0.0998 4.1428 4.2373| | 6: 1.72 - 1.62 0.99 7102 142 0.0889 0.1093 3.9404 4.0787| | 7: 1.62 - 1.54 0.99 7104 148 0.0884 0.0947 3.795 3.9292| | 8: 1.54 - 1.47 0.96 6798 152 0.0887 0.1305 3.6963 3.8983| | 9: 1.47 - 1.41 0.98 6938 155 0.0920 0.1104 3.6163 3.7443| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1194 3.5523 3.6883| | 11: 1.36 - 1.32 0.99 6997 151 0.0987 0.1114 3.4797 3.5714| | 12: 1.32 - 1.28 0.98 6975 149 0.1028 0.1120 3.4549 3.5755| | 13: 1.28 - 1.25 0.98 6907 166 0.1035 0.1226 3.4309 3.5535| | 14: 1.25 - 1.22 0.98 7015 112 0.1102 0.1584 3.428 3.6751| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1243 3.4456 3.492| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1552 3.4632 3.6611| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1223 3.4322 3.4385| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1697 3.4374 3.5319| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1742 3.419 3.5967| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1582 3.4102 3.4357| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2131 3.4182 3.5033| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1967 3.4134 3.4184| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2023 3.4333 3.4868| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2252 3.4358 3.51| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2503 3.4492 3.5232| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2876 3.4161 3.4255| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2798 3.4698 3.395| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7393 127 0.93 11.50 1.00 0.95 10984.16| | 2: 2.94 - 2.33 7339 128 0.93 12.58 0.99 0.95 5009.61| | 3: 2.33 - 2.04 6939 150 0.96 7.45 1.01 0.96 1646.88| | 4: 2.04 - 1.85 7170 155 0.96 7.51 1.00 0.96 983.59| | 5: 1.85 - 1.72 7113 159 0.96 7.97 1.00 0.96 626.13| | 6: 1.72 - 1.62 7102 142 0.96 7.99 1.00 0.96 440.38| | 7: 1.62 - 1.54 7104 148 0.96 8.08 1.01 0.97 335.22| | 8: 1.54 - 1.47 6798 152 0.96 8.22 1.01 0.97 277.92| | 9: 1.47 - 1.41 6938 155 0.96 8.40 1.00 0.98 229.27| | 10: 1.41 - 1.36 7022 150 0.96 8.88 1.00 0.97 201.11| | 11: 1.36 - 1.32 6997 151 0.96 8.84 0.99 0.96 172.63| | 12: 1.32 - 1.28 6975 149 0.96 8.89 0.98 0.95 158.57| | 13: 1.28 - 1.25 6907 166 0.96 9.38 1.01 0.96 155.41| | 14: 1.25 - 1.22 7015 112 0.95 10.60 1.01 0.97 161.19| | 15: 1.22 - 1.19 6956 137 0.95 11.16 1.01 0.98 165.25| | 16: 1.19 - 1.17 6604 132 0.95 11.40 1.01 0.96 159.78| | 17: 1.17 - 1.14 6940 135 0.94 12.22 1.01 0.96 153.39| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.95 147.43| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.95 151.05| | 20: 1.10 - 1.08 6884 147 0.92 15.24 1.00 0.94 150.67| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.86| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.93 155.60| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 165.18| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.99 0.93 179.36| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.98 0.90 182.11| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.89 176.46| | 27: 0.99 - 0.98 6647 131 0.82 26.23 0.99 0.87 160.54| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.43 max = 10984.16 mean = 908.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.94 mean = 13.23| |phase err.(test): min = 0.00 max = 86.99 mean = 13.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1186 0.1334 n_refl.: 191125 re-set all scales: r(all,work,free)=0.1378 0.1376 0.1492 n_refl.: 191125 remove outliers: r(all,work,free)=0.1378 0.1376 0.1492 n_refl.: 191125 overall B=-0.06 to atoms: r(all,work,free)=0.1370 0.1368 0.1486 n_refl.: 191125 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1185 0.1329 n_refl.: 191125 remove outliers: r(all,work,free)=0.1188 0.1185 0.1329 n_refl.: 191125 ======================== 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 89.11 87 3 0.3505 355.917 333.377 0.336 0.986 0.080 13.296-10.522 96.04 96 1 0.2385 480.664 461.085 0.650 0.988 0.091 10.503-8.327 97.80 175 3 0.2174 502.151 494.497 0.829 0.988 0.093 8.315-6.595 100.00 359 8 0.2131 374.781 369.602 0.855 0.988 0.083 6.588-5.215 100.00 711 7 0.1959 345.256 335.182 0.853 0.989 0.073 5.214-4.128 98.38 1367 28 0.1220 505.004 499.642 0.942 0.990 0.024 4.126-3.266 94.74 2603 46 0.1162 460.338 452.670 1.004 0.991 0.000 3.266-2.585 99.86 5447 97 0.1115 310.533 307.073 0.988 0.992 0.000 2.585-2.046 97.45 10613 204 0.0955 234.280 231.713 0.994 0.995 0.000 2.046-1.619 99.39 21536 464 0.0902 138.658 137.282 1.010 0.999 0.000 1.619-1.281 98.00 42464 925 0.0940 74.646 74.002 0.999 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.044 38.325 0.967 1.019 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0123 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2040 0.1989 0.082 5.221 5.2 78.0 14.6 805 0.000 1_bss: 0.1806 0.1923 0.082 5.221 5.2 78.0 14.6 805 0.000 1_settarget: 0.1806 0.1923 0.082 5.221 5.2 78.0 14.6 805 0.000 1_nqh: 0.1813 0.1928 0.082 5.221 5.2 78.0 14.6 805 0.002 1_weight: 0.1813 0.1928 0.082 5.221 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1273 0.1507 0.038 1.159 5.2 78.0 14.6 805 0.157 1_adp: 0.1298 0.1568 0.038 1.159 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1297 0.1563 0.038 1.159 5.2 73.0 15.0 805 0.157 1_occ: 0.1282 0.1551 0.038 1.159 5.2 73.0 15.0 805 0.157 2_bss: 0.1274 0.1539 0.038 1.159 5.3 73.2 15.2 805 0.157 2_settarget: 0.1274 0.1539 0.038 1.159 5.3 73.2 15.2 805 0.157 2_updatecdl: 0.1274 0.1539 0.038 1.170 5.3 73.2 15.2 805 0.157 2_nqh: 0.1277 0.1545 0.038 1.170 5.3 73.2 15.2 805 0.155 2_sol: 0.1276 0.1506 0.038 1.170 5.3 73.2 16.2 882 n/a 2_weight: 0.1276 0.1506 0.038 1.170 5.3 73.2 16.2 882 n/a 2_xyzrec: 0.1258 0.1515 0.041 1.145 5.3 73.2 16.2 882 n/a 2_adp: 0.1235 0.1502 0.041 1.145 5.3 69.2 16.3 882 n/a 2_regHadp: 0.1236 0.1503 0.041 1.145 5.3 69.2 16.3 882 n/a 2_occ: 0.1229 0.1498 0.041 1.145 5.3 69.2 16.3 882 n/a 3_bss: 0.1236 0.1505 0.041 1.145 5.3 69.2 16.3 882 n/a 3_settarget: 0.1236 0.1505 0.041 1.145 5.3 69.2 16.3 882 n/a 3_updatecdl: 0.1236 0.1505 0.041 1.148 5.3 69.2 16.3 882 n/a 3_nqh: 0.1236 0.1505 0.041 1.148 5.3 69.2 16.3 882 n/a 3_sol: 0.1253 0.1504 0.041 1.148 5.3 68.2 15.4 862 n/a 3_weight: 0.1253 0.1504 0.041 1.148 5.3 68.2 15.4 862 n/a 3_xyzrec: 0.1242 0.1433 0.036 1.100 5.3 68.2 15.4 862 n/a 3_adp: 0.1236 0.1396 0.036 1.100 5.5 67.8 15.2 862 n/a 3_regHadp: 0.1237 0.1397 0.036 1.100 5.5 67.8 15.2 862 n/a 3_occ: 0.1231 0.1381 0.036 1.100 5.5 67.8 15.2 862 n/a 4_bss: 0.1227 0.1375 0.036 1.100 5.5 67.8 15.2 862 n/a 4_settarget: 0.1227 0.1375 0.036 1.100 5.5 67.8 15.2 862 n/a 4_updatecdl: 0.1227 0.1375 0.036 1.101 5.5 67.8 15.2 862 n/a 4_nqh: 0.1227 0.1375 0.036 1.101 5.5 67.8 15.2 862 n/a 4_sol: 0.1208 0.1359 0.036 1.101 5.5 67.8 15.0 856 n/a 4_weight: 0.1208 0.1359 0.036 1.101 5.5 67.8 15.0 856 n/a 4_xyzrec: 0.1207 0.1361 0.036 1.119 5.5 67.8 15.0 856 n/a 4_adp: 0.1200 0.1357 0.036 1.119 5.5 67.4 14.9 856 n/a 4_regHadp: 0.1200 0.1357 0.036 1.119 5.5 67.4 14.9 856 n/a 4_occ: 0.1197 0.1355 0.036 1.119 5.5 67.4 14.9 856 n/a 5_bss: 0.1195 0.1353 0.036 1.119 5.5 67.4 14.9 856 n/a 5_settarget: 0.1195 0.1353 0.036 1.119 5.5 67.4 14.9 856 n/a 5_updatecdl: 0.1195 0.1353 0.036 1.119 5.5 67.4 14.9 856 n/a 5_nqh: 0.1195 0.1353 0.036 1.119 5.5 67.4 14.9 856 n/a 5_sol: 0.1193 0.1345 0.036 1.119 5.5 67.4 15.0 873 n/a 5_weight: 0.1193 0.1345 0.036 1.119 5.5 67.4 15.0 873 n/a 5_xyzrec: 0.1195 0.1347 0.037 1.133 5.5 67.4 15.0 873 n/a 5_adp: 0.1200 0.1352 0.037 1.133 5.6 67.1 14.9 873 n/a 5_regHadp: 0.1200 0.1352 0.037 1.133 5.6 67.1 14.9 873 n/a 5_occ: 0.1199 0.1354 0.037 1.133 5.6 67.1 14.9 873 n/a 6_bss: 0.1197 0.1352 0.037 1.133 5.5 67.0 14.9 873 n/a 6_settarget: 0.1197 0.1352 0.037 1.133 5.5 67.0 14.9 873 n/a 6_updatecdl: 0.1197 0.1352 0.037 1.134 5.5 67.0 14.9 873 n/a 6_nqh: 0.1197 0.1352 0.037 1.134 5.5 67.0 14.9 873 n/a 6_sol: 0.1196 0.1346 0.037 1.134 5.5 67.0 14.9 885 n/a 6_weight: 0.1196 0.1346 0.037 1.134 5.5 67.0 14.9 885 n/a 6_xyzrec: 0.1200 0.1350 0.037 1.119 5.5 67.0 14.9 885 n/a 6_adp: 0.1202 0.1353 0.037 1.119 5.6 66.0 14.8 885 n/a 6_regHadp: 0.1203 0.1353 0.037 1.119 5.6 66.0 14.8 885 n/a 6_occ: 0.1200 0.1354 0.037 1.119 5.6 66.0 14.8 885 n/a 7_bss: 0.1200 0.1352 0.037 1.119 5.3 65.8 14.6 885 n/a 7_settarget: 0.1200 0.1352 0.037 1.119 5.3 65.8 14.6 885 n/a 7_updatecdl: 0.1200 0.1352 0.037 1.119 5.3 65.8 14.6 885 n/a 7_nqh: 0.1200 0.1352 0.037 1.119 5.3 65.8 14.6 885 n/a 7_sol: 0.1199 0.1345 0.037 1.119 5.3 65.8 14.6 887 n/a 7_weight: 0.1199 0.1345 0.037 1.119 5.3 65.8 14.6 887 n/a 7_xyzrec: 0.1201 0.1347 0.038 1.130 5.3 65.8 14.6 887 n/a 7_adp: 0.1202 0.1349 0.038 1.130 5.4 64.8 14.5 887 n/a 7_regHadp: 0.1202 0.1349 0.038 1.130 5.4 64.8 14.5 887 n/a 7_occ: 0.1201 0.1352 0.038 1.130 5.4 64.8 14.5 887 n/a 8_bss: 0.1191 0.1342 0.038 1.130 5.4 64.8 14.6 887 n/a 8_settarget: 0.1191 0.1342 0.038 1.130 5.4 64.8 14.6 887 n/a 8_updatecdl: 0.1191 0.1342 0.038 1.130 5.4 64.8 14.6 887 n/a 8_nqh: 0.1191 0.1342 0.038 1.130 5.4 64.8 14.6 887 n/a 8_sol: 0.1188 0.1333 0.038 1.130 5.4 64.8 14.7 907 n/a 8_weight: 0.1188 0.1333 0.038 1.130 5.4 64.8 14.7 907 n/a 8_xyzrec: 0.1191 0.1340 0.038 1.119 5.4 64.8 14.7 907 n/a 8_adp: 0.1193 0.1343 0.038 1.119 5.4 64.4 14.7 907 n/a 8_regHadp: 0.1193 0.1343 0.038 1.119 5.4 64.4 14.7 907 n/a 8_occ: 0.1191 0.1346 0.038 1.119 5.4 64.4 14.7 907 n/a 9_bss: 0.1189 0.1342 0.038 1.119 5.4 64.4 14.7 907 n/a 9_settarget: 0.1189 0.1342 0.038 1.119 5.4 64.4 14.7 907 n/a 9_updatecdl: 0.1189 0.1342 0.038 1.119 5.4 64.4 14.7 907 n/a 9_nqh: 0.1189 0.1342 0.038 1.119 5.4 64.4 14.7 907 n/a 9_sol: 0.1188 0.1337 0.038 1.119 5.4 64.4 14.7 910 n/a 9_weight: 0.1188 0.1337 0.038 1.119 5.4 64.4 14.7 910 n/a 9_xyzrec: 0.1191 0.1341 0.039 1.119 5.4 64.4 14.7 910 n/a 9_adp: 0.1190 0.1342 0.039 1.119 5.5 63.6 14.7 910 n/a 9_regHadp: 0.1190 0.1342 0.039 1.119 5.5 63.6 14.7 910 n/a 9_occ: 0.1188 0.1342 0.039 1.119 5.5 63.6 14.7 910 n/a 10_bss: 0.1187 0.1340 0.039 1.119 5.5 63.6 14.7 910 n/a 10_settarget: 0.1187 0.1340 0.039 1.119 5.5 63.6 14.7 910 n/a 10_updatecdl: 0.1187 0.1340 0.039 1.119 5.5 63.6 14.7 910 n/a 10_setrh: 0.1188 0.1341 0.039 1.119 5.5 63.6 14.7 910 n/a 10_nqh: 0.1188 0.1341 0.039 1.119 5.5 63.6 14.7 910 n/a 10_sol: 0.1186 0.1331 0.039 1.119 5.5 63.6 14.7 926 n/a 10_weight: 0.1186 0.1331 0.039 1.119 5.5 63.6 14.7 926 n/a 10_xyzrec: 0.1187 0.1333 0.039 1.144 5.5 63.6 14.7 926 n/a 10_adp: 0.1188 0.1335 0.039 1.144 5.6 62.7 14.7 926 n/a 10_regHadp: 0.1188 0.1335 0.039 1.144 5.6 62.7 14.7 926 n/a 10_occ: 0.1186 0.1334 0.039 1.144 5.6 62.7 14.7 926 n/a end: 0.1185 0.1329 0.039 1.144 5.5 62.6 14.7 926 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7378796_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7378796_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.3800 Refinement macro-cycles (run) : 12181.6600 Write final files (write_after_run_outputs) : 161.0000 Total : 12350.0400 Total CPU time: 3.44 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:07 PST -0800 (1736736187.14 s) Start R-work = 0.1806, R-free = 0.1923 Final R-work = 0.1185, R-free = 0.1329 =============================================================================== Job complete usr+sys time: 12619.44 seconds wall clock time: 211 minutes 21.63 seconds (12681.63 seconds total)