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_8736011.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8736011.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8736011.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: 1.79, per 1000 atoms: 0.27 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: 2.754 distance_ideal: 2.720 ideal - model: -0.034 slack: 0.000 delta_slack: -0.034 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: 2.780 distance_ideal: 2.710 ideal - model: -0.070 slack: 0.000 delta_slack: -0.070 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 136.3 milliseconds Time building geometry restraints manager: 1.17 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: 995 1.05 - 1.28: 2413 1.28 - 1.51: 1558 1.51 - 1.74: 954 1.74 - 1.97: 14 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.455 1.600 -0.145 7.00e-03 2.04e+04 4.26e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.448 1.621 -0.173 8.80e-03 1.29e+04 3.87e+02 bond pdb=" NH2 ARG B 175 " pdb="HH21 ARG B 175 " ideal model delta sigma weight residual 0.860 1.242 -0.382 2.00e-02 2.50e+03 3.64e+02 bond pdb=" N LEU B 54 " pdb=" CA LEU B 54 " ideal model delta sigma weight residual 1.457 1.692 -0.235 1.23e-02 6.61e+03 3.64e+02 bond pdb=" NH2 ARG A 143 " pdb="HH21 ARG A 143 " ideal model delta sigma weight residual 0.860 1.235 -0.375 2.00e-02 2.50e+03 3.51e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 5735 4.26 - 8.52: 3556 8.52 - 12.77: 1247 12.77 - 17.03: 253 17.03 - 21.29: 19 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY B 174 " pdb=" C GLY B 174 " pdb=" O GLY B 174 " ideal model delta sigma weight residual 122.37 110.15 12.22 7.30e-01 1.88e+00 2.80e+02 angle pdb=" NE ARG A 143 " pdb=" CZ ARG A 143 " pdb=" NH2 ARG A 143 " ideal model delta sigma weight residual 119.20 134.19 -14.99 9.00e-01 1.23e+00 2.77e+02 angle pdb=" O VAL A 19 " pdb=" C VAL A 19 " pdb=" N THR A 20 " ideal model delta sigma weight residual 121.83 137.59 -15.76 1.03e+00 9.43e-01 2.34e+02 angle pdb=" O VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " ideal model delta sigma weight residual 120.07 109.37 10.70 7.10e-01 1.98e+00 2.27e+02 angle pdb=" C ALA B 10 " pdb=" N PRO B 11 " pdb=" CA PRO B 11 " ideal model delta sigma weight residual 119.76 104.52 15.24 1.03e+00 9.43e-01 2.19e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 1851 17.46 - 34.92: 133 34.92 - 52.38: 48 52.38 - 69.84: 13 69.84 - 87.30: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA PHE A 127 " pdb=" C PHE A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual -180.00 -157.58 -22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ALA A 57 " pdb=" C ALA A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 158.96 21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 209 0.214 - 0.427: 147 0.427 - 0.641: 99 0.641 - 0.854: 30 0.854 - 1.068: 7 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA LEU B 153 " pdb=" N LEU B 153 " pdb=" C LEU B 153 " pdb=" CB LEU B 153 " both_signs ideal model delta sigma weight residual False 2.51 3.58 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CB VAL B 144 " pdb=" CA VAL B 144 " pdb=" CG1 VAL B 144 " pdb=" CG2 VAL B 144 " both_signs ideal model delta sigma weight residual False -2.63 -1.63 -1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA LEU B 185 " pdb=" N LEU B 185 " pdb=" C LEU B 185 " pdb=" CB LEU B 185 " both_signs ideal model delta sigma weight residual False 2.51 3.47 -0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.080 2.00e-02 2.50e+03 6.70e-02 1.79e+02 pdb=" CG TRP A 146 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.100 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.041 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.082 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.063 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.021 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.055 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.109 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.014 2.00e-02 2.50e+03 6.38e-02 1.63e+02 pdb=" CG TRP A 139 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.127 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.068 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.080 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.052 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.023 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.105 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.101 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 95 " -0.005 2.00e-02 2.50e+03 6.94e-02 1.45e+02 pdb=" CG PHE B 95 " -0.096 2.00e-02 2.50e+03 pdb=" CD1 PHE B 95 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE B 95 " 0.073 2.00e-02 2.50e+03 pdb=" CE1 PHE B 95 " 0.090 2.00e-02 2.50e+03 pdb=" CE2 PHE B 95 " -0.074 2.00e-02 2.50e+03 pdb=" CZ PHE B 95 " -0.038 2.00e-02 2.50e+03 pdb=" HD1 PHE B 95 " -0.066 2.00e-02 2.50e+03 pdb=" HD2 PHE B 95 " 0.060 2.00e-02 2.50e+03 pdb=" HE1 PHE B 95 " 0.103 2.00e-02 2.50e+03 pdb=" HE2 PHE B 95 " 0.033 2.00e-02 2.50e+03 pdb=" HZ PHE B 95 " -0.093 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.63: 29 1.63 - 2.37: 2561 2.37 - 3.11: 22359 3.11 - 3.86: 32944 3.86 - 4.60: 52314 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110207 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.885 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.934 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.941 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.143 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.228 2.620 ... (remaining 110202 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_8736011_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= 0.2033 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.300144 | | target function (ml) not normalized (work): 805472.950782 | | target function (ml) not normalized (free): 16588.866026 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2131 0.1915 6.6967 6.3025| | 2: 2.94 - 2.33 1.00 7339 128 0.1614 0.1616 5.538 5.5832| | 3: 2.33 - 2.04 0.96 6939 150 0.1651 0.1651 5.1562 5.1848| | 4: 2.04 - 1.85 1.00 7170 155 0.1748 0.1695 4.9677 5.0905| | 5: 1.85 - 1.72 0.99 7113 159 0.1902 0.1804 4.8041 4.8618| | 6: 1.72 - 1.62 0.99 7102 142 0.1997 0.2048 4.6804 4.7498| | 7: 1.62 - 1.54 0.99 7104 148 0.2046 0.1797 4.5642 4.6057| | 8: 1.54 - 1.47 0.96 6798 152 0.2022 0.2226 4.4674 4.5334| | 9: 1.47 - 1.41 0.98 6938 155 0.2104 0.2210 4.399 4.5222| | 10: 1.41 - 1.36 0.99 7022 150 0.2122 0.2206 4.3165 4.3715| | 11: 1.36 - 1.32 0.99 6997 151 0.2113 0.2002 4.2354 4.2255| | 12: 1.32 - 1.28 0.98 6976 149 0.2066 0.1879 4.1677 4.2574| | 13: 1.28 - 1.25 0.98 6907 166 0.2024 0.2183 4.1159 4.1638| | 14: 1.25 - 1.22 0.98 7015 113 0.2076 0.2342 4.077 4.173| | 15: 1.22 - 1.19 0.98 6957 137 0.2135 0.2002 4.0553 4.0559| | 16: 1.19 - 1.17 0.93 6604 132 0.2088 0.2318 3.9825 4.0799| | 17: 1.17 - 1.14 0.98 6941 135 0.2130 0.1791 3.9415 3.9242| | 18: 1.14 - 1.12 0.98 6875 142 0.2216 0.2282 3.9137 3.906| | 19: 1.12 - 1.10 0.97 6949 106 0.2257 0.2392 3.8654 3.9986| | 20: 1.10 - 1.08 0.97 6884 147 0.2302 0.2313 3.8179 3.8612| | 21: 1.08 - 1.07 0.97 6852 152 0.2414 0.2615 3.7904 3.7977| | 22: 1.07 - 1.05 0.97 6838 135 0.2594 0.2808 3.7612 3.816| | 23: 1.05 - 1.03 0.97 6829 159 0.2716 0.2549 3.7304 3.7801| | 24: 1.03 - 1.02 0.96 6785 133 0.2848 0.2560 3.6918 3.712| | 25: 1.02 - 1.01 0.93 6552 130 0.3075 0.3029 3.6745 3.7657| | 26: 1.01 - 0.99 0.96 6767 158 0.3221 0.3348 3.631 3.6402| | 27: 0.99 - 0.98 0.94 6648 131 0.3448 0.3201 3.6461 3.6269| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.26 0.91 0.98 34859.30| | 2: 2.94 - 2.33 7339 128 0.85 21.21 1.08 1.02 15070.42| | 3: 2.33 - 2.04 6939 150 0.93 13.04 1.11 1.05 4441.54| | 4: 2.04 - 1.85 7170 155 0.92 14.37 1.11 1.07 3077.57| | 5: 1.85 - 1.72 7113 159 0.90 16.72 1.11 1.07 2327.81| | 6: 1.72 - 1.62 7102 142 0.89 17.70 1.11 1.07 1813.34| | 7: 1.62 - 1.54 7104 148 0.88 18.64 1.11 1.06 1452.01| | 8: 1.54 - 1.47 6798 152 0.88 18.86 1.10 1.05 1200.93| | 9: 1.47 - 1.41 6938 155 0.87 19.71 1.10 1.05 1034.69| | 10: 1.41 - 1.36 7022 150 0.86 20.69 1.09 1.05 899.38| | 11: 1.36 - 1.32 6997 151 0.87 20.68 1.08 1.04 773.69| | 12: 1.32 - 1.28 6976 149 0.87 20.03 1.08 1.03 659.26| | 13: 1.28 - 1.25 6907 166 0.88 19.67 1.08 1.04 597.10| | 14: 1.25 - 1.22 7015 113 0.87 20.36 1.08 1.06 566.83| | 15: 1.22 - 1.19 6957 137 0.87 20.15 1.08 1.06 518.08| | 16: 1.19 - 1.17 6604 132 0.88 19.55 1.07 1.03 453.24| | 17: 1.17 - 1.14 6941 135 0.88 19.64 1.08 1.03 398.73| | 18: 1.14 - 1.12 6875 142 0.87 20.35 1.08 1.01 379.00| | 19: 1.12 - 1.10 6949 106 0.86 21.58 1.07 1.01 369.47| | 20: 1.10 - 1.08 6884 147 0.85 22.78 1.06 0.99 355.56| | 21: 1.08 - 1.07 6852 152 0.84 23.92 1.06 0.98 337.51| | 22: 1.07 - 1.05 6838 135 0.82 25.53 1.06 0.98 329.53| | 23: 1.05 - 1.03 6829 159 0.81 27.09 1.05 0.98 322.64| | 24: 1.03 - 1.02 6785 133 0.78 29.12 1.05 0.98 325.79| | 25: 1.02 - 1.01 6552 130 0.77 30.67 1.03 0.94 312.70| | 26: 1.01 - 0.99 6767 158 0.75 32.43 1.03 0.92 298.56| | 27: 0.99 - 0.98 6648 131 0.75 31.99 1.03 0.91 272.35| |alpha: min = 0.91 max = 1.07 mean = 1.02| |beta: min = 272.35 max = 34859.30 mean = 2846.75| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.65| |phase err.(test): min = 0.00 max = 89.74 mean = 21.74| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.252 2950 Z= 5.397 Angle : 5.186 16.453 4018 Z= 3.709 Chirality : 0.371 1.068 492 Planarity : 0.034 0.141 512 Dihedral : 12.866 87.298 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.40 % Favored : 95.08 % Rotamer: Outliers : 0.97 % Allowed : 5.16 % Favored : 93.87 % Cbeta Deviations : 34.83 % 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: -2.76 (0.38), residues: 386 helix: -2.80 (0.30), residues: 144 sheet: -1.44 (0.54), residues: 86 loop : -0.73 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.136 0.024 ARG A 83 TYR 0.151 0.042 TYR A 194 PHE 0.105 0.044 PHE B 95 TRP 0.122 0.045 TRP A 146 HIS 0.040 0.015 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2033 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.300144 | | target function (ml) not normalized (work): 805472.950782 | | target function (ml) not normalized (free): 16588.866026 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2031 0.2033 0.1995 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2031 0.2033 0.1995 n_refl.: 191155 remove outliers: r(all,work,free)=0.2032 0.2033 0.1995 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2032 0.2033 0.1995 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1803 0.1927 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1801 0.1927 n_refl.: 191140 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4222 400.535 295.233 0.434 0.912 0.301 13.296-10.522 100.00 100 1 0.2533 534.497 521.541 0.790 0.913 0.253 10.503-8.327 98.90 177 3 0.2481 564.205 558.387 0.972 0.913 0.230 8.318-6.595 100.00 360 8 0.2444 414.736 402.679 0.974 0.913 0.170 6.588-5.215 100.00 711 7 0.2274 381.101 365.247 0.963 0.913 0.160 5.214-4.128 98.38 1367 28 0.1485 557.435 550.021 1.070 0.913 0.070 4.126-3.266 94.74 2603 46 0.1347 508.132 499.018 1.148 0.913 0.040 3.266-2.585 99.86 5447 97 0.1434 342.774 337.813 1.120 0.912 0.000 2.585-2.046 97.45 10613 204 0.1408 258.603 254.399 1.126 0.912 0.000 2.046-1.619 99.39 21536 464 0.1625 153.054 149.860 1.144 0.910 0.000 1.619-1.281 98.00 42464 925 0.1924 82.395 80.176 1.130 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2315 44.203 41.689 1.114 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0027 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1801 r_free=0.1927 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1801 r_free=0.1927 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.669195 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 574.968535 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 0.1270 0.1503 0.0233 0.038 1.2 10.5 0.0 0.0 0 11.335 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.03 2.33 1.117 13.112 574.969 0.018 12.96 15.70 2.74 1.250 13.341 574.969 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.04 15.01 1.41 435 3274 Protein: 5.16 40.33 11.00 1.41 0 2902 Water: 6.30 73.04 29.47 N/A 435 370 Other: 16.00 29.87 22.93 N/A 0 2 Chain A: 5.33 59.94 13.05 N/A 0 1626 Chain B: 5.16 73.04 12.77 N/A 0 1648 Chain S: 11.66 62.94 30.87 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2163 11.95 - 18.74 644 18.74 - 25.53 306 25.53 - 32.32 270 32.32 - 39.10 157 39.10 - 45.89 102 45.89 - 52.68 42 52.68 - 59.47 20 59.47 - 66.26 4 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1570 r_work=0.1296 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1566 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 = 0.1281 r_free = 0.1555 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015581 | | target function (ls_wunit_k1) not normalized (work): 2918.257980 | | target function (ls_wunit_k1) not normalized (free): 117.844550 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1555 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1471 0.1468 0.1630 n_refl.: 191140 remove outliers: r(all,work,free)=0.1471 0.1468 0.1630 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1495 0.1493 0.1641 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1547 n_refl.: 191140 remove outliers: r(all,work,free)=0.1279 0.1273 0.1546 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 0.3601 402.814 374.910 0.462 1.001 0.275 13.296-10.522 100.00 100 1 0.2111 534.497 530.050 0.719 1.002 0.239 10.503-8.327 98.90 177 3 0.1739 564.205 562.720 0.855 1.002 0.193 8.318-6.595 100.00 360 8 0.1712 414.736 412.516 0.875 1.002 0.155 6.588-5.215 100.00 711 7 0.1529 381.101 373.875 0.856 1.002 0.150 5.214-4.128 98.38 1367 28 0.0908 557.435 554.688 0.937 1.003 0.050 4.126-3.266 94.74 2603 46 0.0830 508.132 504.393 1.005 1.003 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.300 0.987 1.003 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.352 0.998 1.003 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.371 1.015 1.003 0.000 1.619-1.281 98.00 42464 925 0.1277 82.395 81.410 1.008 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.183 0.986 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0376 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1546 | n_water=805 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1279 r_free=0.1549 | n_water=794 | time (s): 99.600 (total time: 101.880) Filter (q & B) r_work=0.1279 r_free=0.1549 | n_water=791 | time (s): 4.350 (total time: 106.230) Compute maps r_work=0.1279 r_free=0.1549 | n_water=791 | time (s): 2.420 (total time: 108.650) Filter (map) r_work=0.1307 r_free=0.1531 | n_water=650 | time (s): 4.400 (total time: 113.050) Find peaks r_work=0.1307 r_free=0.1531 | n_water=650 | time (s): 0.700 (total time: 113.750) Add new water r_work=0.1329 r_free=0.1560 | n_water=945 | time (s): 4.460 (total time: 118.210) Refine new water occ: r_work=0.1283 r_free=0.1514 adp: r_work=0.1271 r_free=0.1512 occ: r_work=0.1274 r_free=0.1509 adp: r_work=0.1267 r_free=0.1511 occ: r_work=0.1269 r_free=0.1507 adp: r_work=0.1266 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1508 r_work=0.1266 r_free=0.1508 | n_water=945 | time (s): 90.320 (total time: 208.530) Filter (q & B) r_work=0.1269 r_free=0.1510 | n_water=878 | time (s): 4.840 (total time: 213.370) Filter (dist only) r_work=0.1270 r_free=0.1509 | n_water=876 | time (s): 109.540 (total time: 322.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.424397 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 599.173600 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 0.1255 0.1528 0.0273 0.042 1.1 18.0 0.0 0.3 0 11.712 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.28 2.73 2.045 15.152 599.174 0.015 12.31 15.16 2.85 2.428 15.208 599.174 0.014 Individual atomic B min max mean iso aniso Overall: 5.34 68.21 16.29 1.21 508 3272 Protein: 5.34 40.65 10.97 1.21 0 2902 Water: 6.56 68.21 33.86 N/A 508 368 Other: 16.56 32.96 24.76 N/A 0 2 Chain A: 5.50 56.03 13.01 N/A 0 1624 Chain B: 5.34 68.21 12.83 N/A 0 1648 Chain S: 13.35 68.04 37.97 N/A 508 0 Histogram: Values Number of atoms 5.34 - 11.62 2043 11.62 - 17.91 722 17.91 - 24.20 267 24.20 - 30.48 206 30.48 - 36.77 175 36.77 - 43.06 160 43.06 - 49.35 109 49.35 - 55.63 48 55.63 - 61.92 37 61.92 - 68.21 13 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1516 r_work=0.1232 r_free=0.1517 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1517 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1515 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1515 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013494 | | target function (ls_wunit_k1) not normalized (work): 2527.467788 | | target function (ls_wunit_k1) not normalized (free): 103.694669 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1515 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1606 n_refl.: 191138 remove outliers: r(all,work,free)=0.1436 0.1433 0.1606 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1430 0.1605 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1232 0.1522 n_refl.: 191138 remove outliers: r(all,work,free)=0.1238 0.1232 0.1522 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 0.3367 402.814 377.398 0.489 0.962 0.273 13.296-10.522 100.00 100 1 0.1902 534.497 529.125 0.764 0.964 0.228 10.503-8.327 98.90 177 3 0.1437 564.205 566.123 0.915 0.963 0.179 8.318-6.595 100.00 360 8 0.1570 414.736 413.803 0.935 0.963 0.160 6.588-5.215 100.00 711 7 0.1335 381.101 376.747 0.915 0.963 0.160 5.214-4.128 98.38 1367 28 0.0831 557.435 555.923 0.992 0.963 0.080 4.126-3.266 94.74 2603 46 0.0763 508.132 505.313 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0857 342.774 341.381 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.756 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.609 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.367 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.223 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=-0.0503 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1523 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1523 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1523 | n_water=876 | time (s): 3.510 (total time: 3.510) Filter (dist) r_work=0.1234 r_free=0.1524 | n_water=869 | time (s): 111.320 (total time: 114.830) Filter (q & B) r_work=0.1235 r_free=0.1524 | n_water=867 | time (s): 4.870 (total time: 119.700) Compute maps r_work=0.1235 r_free=0.1524 | n_water=867 | time (s): 2.410 (total time: 122.110) Filter (map) r_work=0.1274 r_free=0.1509 | n_water=689 | time (s): 5.350 (total time: 127.460) Find peaks r_work=0.1274 r_free=0.1509 | n_water=689 | time (s): 0.750 (total time: 128.210) Add new water r_work=0.1297 r_free=0.1535 | n_water=1001 | time (s): 4.900 (total time: 133.110) Refine new water occ: r_work=0.1252 r_free=0.1507 adp: r_work=0.1252 r_free=0.1507 occ: r_work=0.1248 r_free=0.1505 adp: r_work=0.1247 r_free=0.1505 occ: r_work=0.1245 r_free=0.1505 adp: r_work=0.1244 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1503 r_work=0.1244 r_free=0.1503 | n_water=1001 | time (s): 327.360 (total time: 460.470) Filter (q & B) r_work=0.1248 r_free=0.1510 | n_water=869 | time (s): 4.900 (total time: 465.370) Filter (dist only) r_work=0.1249 r_free=0.1509 | n_water=868 | time (s): 111.830 (total time: 577.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.694053 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.240704 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 0.1237 0.1439 0.0202 0.035 1.1 7.6 0.0 0.0 0 0.847 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.39 2.02 1.934 14.614 15.241 3.938 12.34 13.98 1.64 2.193 14.530 15.241 3.899 Individual atomic B min max mean iso aniso Overall: 5.55 67.89 15.34 1.06 501 3271 Protein: 5.55 37.05 10.76 1.06 0 2902 Water: 6.70 67.89 30.64 N/A 501 367 Other: 14.14 29.42 21.78 N/A 0 2 Chain A: 5.55 55.39 12.81 N/A 0 1624 Chain B: 5.56 67.89 12.57 N/A 0 1647 Chain S: 13.77 60.84 32.66 N/A 501 0 Histogram: Values Number of atoms 5.55 - 11.78 2130 11.78 - 18.02 683 18.02 - 24.25 291 24.25 - 30.48 231 30.48 - 36.72 168 36.72 - 42.95 150 42.95 - 49.18 85 49.18 - 55.42 24 55.42 - 61.65 9 61.65 - 67.89 1 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1399 r_work=0.1235 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1400 target_work(ml) = 3.900 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1397 target_work(ml) = 3.894 | | 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1397 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.894076 | | target function (ml) not normalized (work): 729348.755592 | | target function (ml) not normalized (free): 15233.445986 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1229 0.1396 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1447 0.1446 0.1505 n_refl.: 191138 remove outliers: r(all,work,free)=0.1447 0.1446 0.1505 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1441 0.1440 0.1501 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1226 0.1391 n_refl.: 191138 remove outliers: r(all,work,free)=0.1228 0.1225 0.1391 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 0.3836 398.008 361.215 0.424 0.946 0.241 13.296-10.522 98.02 98 1 0.2354 528.900 509.622 0.715 0.948 0.209 10.503-8.327 97.80 175 3 0.1947 554.286 556.757 0.884 0.948 0.169 8.318-6.595 100.00 360 8 0.2074 414.736 409.036 0.899 0.947 0.130 6.588-5.215 100.00 711 7 0.1799 381.101 371.010 0.888 0.947 0.120 5.214-4.128 98.38 1367 28 0.1161 557.435 552.077 0.971 0.947 0.070 4.126-3.266 94.74 2603 46 0.1090 508.132 501.415 1.034 0.948 0.009 3.266-2.585 99.86 5447 97 0.1083 342.774 339.109 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0966 258.603 255.773 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0979 153.054 151.388 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1055 82.395 81.480 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.312 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1038 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1391 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1391 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1391 | n_water=868 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1226 r_free=0.1391 | n_water=865 | time (s): 107.150 (total time: 109.820) Filter (q & B) r_work=0.1227 r_free=0.1392 | n_water=853 | time (s): 4.210 (total time: 114.030) Compute maps r_work=0.1227 r_free=0.1392 | n_water=853 | time (s): 2.210 (total time: 116.240) Filter (map) r_work=0.1251 r_free=0.1393 | n_water=705 | time (s): 5.590 (total time: 121.830) Find peaks r_work=0.1251 r_free=0.1393 | n_water=705 | time (s): 0.670 (total time: 122.500) Add new water r_work=0.1266 r_free=0.1411 | n_water=950 | time (s): 3.940 (total time: 126.440) Refine new water occ: r_work=0.1218 r_free=0.1369 adp: r_work=0.1210 r_free=0.1365 occ: r_work=0.1208 r_free=0.1364 adp: r_work=0.1208 r_free=0.1363 occ: r_work=0.1205 r_free=0.1362 adp: r_work=0.1205 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1361 r_work=0.1205 r_free=0.1361 | n_water=950 | time (s): 336.160 (total time: 462.600) Filter (q & B) r_work=0.1211 r_free=0.1368 | n_water=853 | time (s): 4.560 (total time: 467.160) Filter (dist only) r_work=0.1211 r_free=0.1367 | n_water=852 | time (s): 110.240 (total time: 577.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550609 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.127208 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 0.1210 0.1371 0.0161 0.036 1.1 6.0 0.0 0.0 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.71 1.61 1.836 14.207 16.127 3.877 12.03 13.63 1.60 2.028 14.137 16.127 3.866 Individual atomic B min max mean iso aniso Overall: 5.51 67.23 14.90 0.99 485 3271 Protein: 5.51 33.06 10.63 0.99 0 2902 Water: 5.90 67.23 29.46 N/A 485 367 Other: 13.84 27.33 20.58 N/A 0 2 Chain A: 5.61 55.01 12.61 N/A 0 1624 Chain B: 5.51 67.23 12.42 N/A 0 1647 Chain S: 5.90 60.84 31.01 N/A 485 0 Histogram: Values Number of atoms 5.51 - 11.68 2115 11.68 - 17.85 731 17.85 - 24.02 289 24.02 - 30.20 225 30.20 - 36.37 167 36.37 - 42.54 134 42.54 - 48.71 67 48.71 - 54.88 20 54.88 - 61.06 7 61.06 - 67.23 1 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1363 r_work=0.1203 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1363 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863180 | | target function (ml) not normalized (work): 723542.707646 | | target function (ml) not normalized (free): 15133.319573 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1360 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1431 0.1431 0.1468 n_refl.: 191133 remove outliers: r(all,work,free)=0.1431 0.1431 0.1468 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1423 0.1423 0.1463 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1198 0.1360 n_refl.: 191133 remove outliers: r(all,work,free)=0.1201 0.1198 0.1360 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3834 361.353 319.161 0.414 0.945 0.243 13.296-10.522 97.03 97 1 0.2382 481.397 456.698 0.709 0.947 0.198 10.503-8.327 97.80 175 3 0.2141 502.120 496.235 0.864 0.947 0.177 8.318-6.595 100.00 360 8 0.2206 375.703 369.774 0.892 0.947 0.120 6.588-5.215 100.00 711 7 0.1881 345.234 335.462 0.887 0.947 0.100 5.214-4.128 98.38 1367 28 0.1209 504.972 499.784 0.974 0.947 0.090 4.126-3.266 94.74 2603 46 0.1121 460.309 453.884 1.036 0.948 0.009 3.266-2.585 99.86 5447 97 0.1095 310.514 307.315 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0939 234.265 231.816 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0914 138.649 137.344 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0989 74.641 73.927 1.054 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.042 38.385 1.040 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1214 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1360 | n_water=852 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1198 r_free=0.1360 | n_water=852 | time (s): 104.440 (total time: 107.680) Filter (q & B) r_work=0.1198 r_free=0.1360 | n_water=842 | time (s): 4.360 (total time: 112.040) Compute maps r_work=0.1198 r_free=0.1360 | n_water=842 | time (s): 1.710 (total time: 113.750) Filter (map) r_work=0.1219 r_free=0.1356 | n_water=722 | time (s): 4.930 (total time: 118.680) Find peaks r_work=0.1219 r_free=0.1356 | n_water=722 | time (s): 0.680 (total time: 119.360) Add new water r_work=0.1232 r_free=0.1374 | n_water=940 | time (s): 5.520 (total time: 124.880) Refine new water occ: r_work=0.1195 r_free=0.1345 adp: r_work=0.1195 r_free=0.1345 occ: r_work=0.1192 r_free=0.1344 adp: r_work=0.1192 r_free=0.1344 occ: r_work=0.1190 r_free=0.1344 adp: r_work=0.1190 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1343 r_work=0.1190 r_free=0.1343 | n_water=940 | time (s): 280.580 (total time: 405.460) Filter (q & B) r_work=0.1194 r_free=0.1352 | n_water=868 | time (s): 5.430 (total time: 410.890) Filter (dist only) r_work=0.1195 r_free=0.1351 | n_water=866 | time (s): 112.260 (total time: 523.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.512677 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.809277 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 0.1197 0.1356 0.0159 0.037 1.1 8.0 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.56 1.59 1.781 14.051 14.809 3.763 12.01 13.61 1.61 1.807 14.039 14.809 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 67.01 14.87 0.95 499 3271 Protein: 5.57 31.87 10.59 0.95 0 2902 Water: 5.89 67.01 29.24 N/A 499 367 Other: 13.75 26.70 20.23 N/A 0 2 Chain A: 5.60 54.87 12.55 N/A 0 1624 Chain B: 5.57 67.01 12.36 N/A 0 1647 Chain S: 5.89 60.83 30.74 N/A 499 0 Histogram: Values Number of atoms 5.57 - 11.72 2138 11.72 - 17.86 721 17.86 - 24.00 304 24.00 - 30.15 204 30.15 - 36.29 173 36.29 - 42.43 134 42.43 - 48.58 68 48.58 - 54.72 20 54.72 - 60.86 7 60.86 - 67.01 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1362 r_work=0.1201 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1362 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1363 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.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760588 | | target function (ml) not normalized (work): 704320.506323 | | target function (ml) not normalized (free): 14740.293520 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1412 0.1411 0.1469 n_refl.: 191131 remove outliers: r(all,work,free)=0.1412 0.1411 0.1469 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1404 0.1403 0.1464 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3888 361.353 323.262 0.404 0.951 0.227 13.296-10.522 97.03 97 1 0.2381 481.397 461.315 0.704 0.953 0.188 10.503-8.327 97.80 175 3 0.2129 502.120 495.656 0.856 0.953 0.170 8.318-6.595 100.00 360 8 0.2152 375.703 370.228 0.886 0.953 0.115 6.588-5.215 100.00 711 7 0.1903 345.234 335.165 0.880 0.953 0.090 5.214-4.128 98.38 1367 28 0.1219 504.972 499.711 0.969 0.953 0.080 4.126-3.266 94.74 2603 46 0.1130 460.309 453.860 1.031 0.953 0.005 3.266-2.585 99.86 5447 97 0.1104 310.514 307.207 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0946 234.265 231.766 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0915 138.649 137.342 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0977 74.641 73.929 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.042 38.370 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1300 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1361 | n_water=866 | time (s): 3.270 (total time: 3.270) Filter (dist) r_work=0.1197 r_free=0.1361 | n_water=866 | time (s): 106.200 (total time: 109.470) Filter (q & B) r_work=0.1198 r_free=0.1361 | n_water=856 | time (s): 5.000 (total time: 114.470) Compute maps r_work=0.1198 r_free=0.1361 | n_water=856 | time (s): 2.000 (total time: 116.470) Filter (map) r_work=0.1217 r_free=0.1355 | n_water=755 | time (s): 4.660 (total time: 121.130) Find peaks r_work=0.1217 r_free=0.1355 | n_water=755 | time (s): 0.620 (total time: 121.750) Add new water r_work=0.1228 r_free=0.1372 | n_water=961 | time (s): 4.850 (total time: 126.600) Refine new water occ: r_work=0.1194 r_free=0.1340 adp: r_work=0.1194 r_free=0.1341 occ: r_work=0.1192 r_free=0.1338 adp: r_work=0.1192 r_free=0.1339 occ: r_work=0.1191 r_free=0.1337 adp: r_work=0.1190 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1337 r_work=0.1190 r_free=0.1337 | n_water=961 | time (s): 228.140 (total time: 354.740) Filter (q & B) r_work=0.1194 r_free=0.1345 | n_water=884 | time (s): 5.500 (total time: 360.240) Filter (dist only) r_work=0.1195 r_free=0.1345 | n_water=883 | time (s): 114.190 (total time: 474.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.527729 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.040194 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 0.1197 0.1352 0.0154 0.038 1.1 6.1 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.52 1.54 1.759 14.025 15.040 3.761 12.00 13.55 1.55 1.878 13.983 15.040 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 65.96 14.82 0.91 516 3271 Protein: 5.57 29.75 10.49 0.91 0 2902 Water: 5.97 65.96 29.05 N/A 516 367 Other: 13.80 23.76 18.78 N/A 0 2 Chain A: 5.64 54.39 12.41 N/A 0 1624 Chain B: 5.57 65.96 12.24 N/A 0 1647 Chain S: 5.97 60.91 30.66 N/A 516 0 Histogram: Values Number of atoms 5.57 - 11.61 2108 11.61 - 17.65 776 17.65 - 23.69 286 23.69 - 29.72 205 29.72 - 35.76 172 35.76 - 41.80 134 41.80 - 47.84 74 47.84 - 53.88 23 53.88 - 59.92 7 59.92 - 65.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1355 r_work=0.1200 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1355 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757680 | | target function (ml) not normalized (work): 703775.802529 | | target function (ml) not normalized (free): 14731.559622 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1462 n_refl.: 191131 remove outliers: r(all,work,free)=0.1407 0.1406 0.1462 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1370 0.1369 0.1440 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1353 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 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 0.3716 361.049 314.029 0.407 0.951 0.225 13.296-10.522 96.04 96 1 0.2364 480.634 457.209 0.716 0.952 0.181 10.503-8.327 97.80 175 3 0.2173 502.120 495.803 0.878 0.953 0.160 8.318-6.595 100.00 360 8 0.2158 375.703 370.509 0.908 0.952 0.110 6.588-5.215 100.00 711 7 0.1913 345.234 335.286 0.904 0.953 0.100 5.214-4.128 98.38 1367 28 0.1224 504.972 499.793 0.995 0.953 0.080 4.126-3.266 94.74 2603 46 0.1142 460.309 453.891 1.056 0.953 0.005 3.266-2.585 99.86 5447 97 0.1110 310.514 307.169 1.039 0.952 0.000 2.585-2.046 97.45 10613 204 0.0949 234.265 231.831 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0911 138.649 137.387 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0970 74.641 73.952 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.042 38.378 1.026 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0487 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1353 | n_water=883 | time (s): 2.800 (total time: 2.800) Filter (dist) r_work=0.1197 r_free=0.1353 | n_water=883 | time (s): 110.100 (total time: 112.900) Filter (q & B) r_work=0.1197 r_free=0.1352 | n_water=874 | time (s): 4.860 (total time: 117.760) Compute maps r_work=0.1197 r_free=0.1352 | n_water=874 | time (s): 2.420 (total time: 120.180) Filter (map) r_work=0.1218 r_free=0.1346 | n_water=763 | time (s): 4.760 (total time: 124.940) Find peaks r_work=0.1218 r_free=0.1346 | n_water=763 | time (s): 0.550 (total time: 125.490) Add new water r_work=0.1229 r_free=0.1361 | n_water=961 | time (s): 3.960 (total time: 129.450) Refine new water occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1196 r_free=0.1342 occ: r_work=0.1193 r_free=0.1340 adp: r_work=0.1193 r_free=0.1340 occ: r_work=0.1191 r_free=0.1340 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=961 | time (s): 180.580 (total time: 310.030) Filter (q & B) r_work=0.1194 r_free=0.1345 | n_water=903 | time (s): 5.520 (total time: 315.550) Filter (dist only) r_work=0.1195 r_free=0.1345 | n_water=901 | time (s): 123.660 (total time: 439.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.498081 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.405694 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1351 0.0153 0.038 1.1 7.0 0.0 0.3 0 0.749 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.51 1.53 1.722 13.767 14.406 3.759 12.00 13.56 1.56 1.774 13.743 14.406 3.758 Individual atomic B min max mean iso aniso Overall: 5.41 64.81 14.65 0.88 534 3271 Protein: 5.41 28.65 10.25 0.88 0 2902 Water: 5.78 64.81 28.80 N/A 534 367 Other: 13.69 22.17 17.93 N/A 0 2 Chain A: 5.47 53.74 12.13 N/A 0 1624 Chain B: 5.41 64.81 11.97 N/A 0 1647 Chain S: 5.78 60.81 30.52 N/A 534 0 Histogram: Values Number of atoms 5.41 - 11.35 2105 11.35 - 17.29 774 17.29 - 23.23 283 23.23 - 29.17 210 29.17 - 35.11 187 35.11 - 41.05 132 41.05 - 46.99 75 46.99 - 52.93 29 52.93 - 58.87 7 58.87 - 64.81 3 =========================== 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) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1359 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757447 | | target function (ml) not normalized (work): 703724.722779 | | target function (ml) not normalized (free): 14735.721417 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1366 0.1365 0.1451 n_refl.: 191129 remove outliers: r(all,work,free)=0.1366 0.1365 0.1451 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1374 0.1373 0.1455 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1348 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1348 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 0.3738 361.049 331.539 0.419 0.974 0.221 13.296-10.522 96.04 96 1 0.2384 480.634 461.787 0.709 0.976 0.171 10.503-8.327 97.80 175 3 0.2188 502.120 494.563 0.864 0.976 0.147 8.318-6.595 100.00 360 8 0.2129 375.703 370.380 0.891 0.976 0.090 6.588-5.215 100.00 711 7 0.1898 345.234 334.926 0.891 0.977 0.085 5.214-4.128 98.38 1367 28 0.1229 504.972 499.259 0.978 0.977 0.039 4.126-3.266 94.74 2603 46 0.1147 460.309 452.960 1.040 0.978 0.000 3.266-2.585 99.86 5447 97 0.1114 310.514 306.901 1.024 0.979 0.000 2.585-2.046 97.45 10613 204 0.0957 234.265 231.628 1.032 0.980 0.000 2.046-1.619 99.39 21536 464 0.0908 138.649 137.260 1.048 0.983 0.000 1.619-1.281 98.00 42464 925 0.0951 74.641 73.976 1.037 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.042 38.350 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=0.0618 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1348 | n_water=901 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1190 r_free=0.1346 | n_water=899 | time (s): 112.630 (total time: 115.110) Filter (q & B) r_work=0.1190 r_free=0.1344 | n_water=889 | time (s): 5.130 (total time: 120.240) Compute maps r_work=0.1190 r_free=0.1344 | n_water=889 | time (s): 1.690 (total time: 121.930) Filter (map) r_work=0.1211 r_free=0.1341 | n_water=781 | time (s): 4.190 (total time: 126.120) Find peaks r_work=0.1211 r_free=0.1341 | n_water=781 | time (s): 0.550 (total time: 126.670) Add new water r_work=0.1219 r_free=0.1357 | n_water=982 | time (s): 4.290 (total time: 130.960) Refine new water occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1187 r_free=0.1339 occ: r_work=0.1185 r_free=0.1340 adp: r_work=0.1185 r_free=0.1340 occ: r_work=0.1183 r_free=0.1340 adp: r_work=0.1183 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1340 r_work=0.1183 r_free=0.1340 | n_water=982 | time (s): 161.780 (total time: 292.740) Filter (q & B) r_work=0.1187 r_free=0.1342 | n_water=918 | time (s): 4.720 (total time: 297.460) Filter (dist only) r_work=0.1187 r_free=0.1343 | n_water=916 | time (s): 119.750 (total time: 417.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.571835 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.736339 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1347 0.0157 0.038 1.1 6.1 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.47 1.57 1.678 13.791 14.736 3.755 11.90 13.48 1.59 1.693 13.785 14.736 3.752 Individual atomic B min max mean iso aniso Overall: 5.49 63.87 14.74 0.88 549 3271 Protein: 5.49 28.42 10.32 0.88 0 2902 Water: 5.96 63.87 28.76 N/A 549 367 Other: 13.76 22.01 17.89 N/A 0 2 Chain A: 5.56 53.30 12.16 N/A 0 1624 Chain B: 5.49 63.87 12.01 N/A 0 1647 Chain S: 5.96 60.94 30.56 N/A 549 0 Histogram: Values Number of atoms 5.49 - 11.33 2069 11.33 - 17.17 816 17.17 - 23.01 274 23.01 - 28.85 216 28.85 - 34.68 183 34.68 - 40.52 134 40.52 - 46.36 84 46.36 - 52.20 34 52.20 - 58.04 7 58.04 - 63.87 3 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1348 r_work=0.1190 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1349 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1350 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751610 | | target function (ml) not normalized (work): 702631.603740 | | target function (ml) not normalized (free): 14713.881632 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1378 0.1377 0.1470 n_refl.: 191129 remove outliers: r(all,work,free)=0.1378 0.1377 0.1470 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1380 0.1379 0.1471 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1348 n_refl.: 191129 remove outliers: r(all,work,free)=0.1190 0.1187 0.1348 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 0.3687 361.049 331.092 0.411 0.974 0.213 13.296-10.522 96.04 96 1 0.2399 480.634 461.519 0.701 0.976 0.156 10.503-8.327 97.80 175 3 0.2191 502.120 494.002 0.861 0.976 0.130 8.318-6.595 100.00 360 8 0.2143 375.703 369.712 0.892 0.976 0.101 6.588-5.215 100.00 711 7 0.1913 345.234 335.207 0.887 0.976 0.083 5.214-4.128 98.38 1367 28 0.1249 504.972 499.021 0.978 0.977 0.039 4.126-3.266 94.74 2603 46 0.1155 460.309 452.715 1.040 0.978 0.000 3.266-2.585 99.86 5447 97 0.1117 310.514 306.829 1.024 0.979 0.000 2.585-2.046 97.45 10613 204 0.0955 234.265 231.642 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0902 138.649 137.295 1.050 0.984 0.000 1.619-1.281 98.00 42464 925 0.0942 74.641 73.993 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.042 38.340 1.009 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1348 | n_water=916 | time (s): 2.810 (total time: 2.810) Filter (dist) r_work=0.1187 r_free=0.1347 | n_water=914 | time (s): 114.720 (total time: 117.530) Filter (q & B) r_work=0.1188 r_free=0.1345 | n_water=903 | time (s): 4.770 (total time: 122.300) Compute maps r_work=0.1188 r_free=0.1345 | n_water=903 | time (s): 2.520 (total time: 124.820) Filter (map) r_work=0.1208 r_free=0.1339 | n_water=785 | time (s): 4.440 (total time: 129.260) Find peaks r_work=0.1208 r_free=0.1339 | n_water=785 | time (s): 0.780 (total time: 130.040) Add new water r_work=0.1216 r_free=0.1353 | n_water=985 | time (s): 5.510 (total time: 135.550) Refine new water occ: r_work=0.1185 r_free=0.1332 adp: r_work=0.1186 r_free=0.1333 occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1184 r_free=0.1332 occ: r_work=0.1182 r_free=0.1332 adp: r_work=0.1182 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1332 r_work=0.1182 r_free=0.1332 | n_water=985 | time (s): 212.990 (total time: 348.540) Filter (q & B) r_work=0.1187 r_free=0.1337 | n_water=907 | time (s): 5.250 (total time: 353.790) Filter (dist only) r_work=0.1187 r_free=0.1336 | n_water=906 | time (s): 122.390 (total time: 476.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507171 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.572530 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1341 0.0151 0.039 1.1 4.9 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.41 1.51 1.682 13.774 14.573 3.753 11.91 13.45 1.54 1.679 13.773 14.573 3.751 Individual atomic B min max mean iso aniso Overall: 5.51 63.49 14.70 0.87 539 3271 Protein: 5.51 28.32 10.35 0.87 0 2902 Water: 5.94 63.49 28.62 N/A 539 367 Other: 13.83 22.09 17.96 N/A 0 2 Chain A: 5.62 53.18 12.17 N/A 0 1624 Chain B: 5.51 63.49 12.02 N/A 0 1647 Chain S: 5.94 60.98 30.50 N/A 539 0 Histogram: Values Number of atoms 5.51 - 11.31 2057 11.31 - 17.11 831 17.11 - 22.91 272 22.91 - 28.70 210 28.70 - 34.50 179 34.50 - 40.30 131 40.30 - 46.10 84 46.10 - 51.90 35 51.90 - 57.70 8 57.70 - 63.49 3 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1345 r_work=0.1191 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1345 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1346 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751124 | | target function (ml) not normalized (work): 702540.567544 | | target function (ml) not normalized (free): 14711.464798 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1189 0.1346 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1392 0.1390 0.1476 n_refl.: 191129 remove outliers: r(all,work,free)=0.1392 0.1390 0.1476 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1391 0.1390 0.1476 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1345 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 0.3661 361.049 330.857 0.412 0.973 0.215 13.296-10.522 96.04 96 1 0.2397 480.634 461.450 0.697 0.975 0.149 10.503-8.327 97.80 175 3 0.2236 502.120 492.994 0.859 0.976 0.120 8.318-6.595 100.00 360 8 0.2153 375.703 369.900 0.889 0.975 0.096 6.588-5.215 100.00 711 7 0.1934 345.234 334.985 0.886 0.976 0.080 5.214-4.128 98.38 1367 28 0.1254 504.972 499.076 0.978 0.977 0.044 4.126-3.266 94.74 2603 46 0.1168 460.309 452.763 1.042 0.978 0.005 3.266-2.585 99.86 5447 97 0.1121 310.514 306.927 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0957 234.265 231.651 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0903 138.649 137.293 1.051 0.985 0.000 1.619-1.281 98.00 42464 925 0.0939 74.641 74.000 1.042 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.042 38.337 1.013 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0100 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1345 After: r_work=0.1189 r_free=0.1346 ================================== NQH flips ================================== r_work=0.1189 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1346 | n_water=906 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1190 r_free=0.1346 | n_water=904 | time (s): 120.000 (total time: 122.580) Filter (q & B) r_work=0.1190 r_free=0.1346 | n_water=898 | time (s): 4.840 (total time: 127.420) Compute maps r_work=0.1190 r_free=0.1346 | n_water=898 | time (s): 2.170 (total time: 129.590) Filter (map) r_work=0.1212 r_free=0.1348 | n_water=781 | time (s): 5.110 (total time: 134.700) Find peaks r_work=0.1212 r_free=0.1348 | n_water=781 | time (s): 0.560 (total time: 135.260) Add new water r_work=0.1219 r_free=0.1360 | n_water=984 | time (s): 4.030 (total time: 139.290) Refine new water occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1187 r_free=0.1339 occ: r_work=0.1185 r_free=0.1339 adp: r_work=0.1185 r_free=0.1339 occ: r_work=0.1184 r_free=0.1338 adp: r_work=0.1183 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1338 r_work=0.1183 r_free=0.1338 | n_water=984 | time (s): 309.970 (total time: 449.260) Filter (q & B) r_work=0.1187 r_free=0.1342 | n_water=915 | time (s): 5.250 (total time: 454.510) Filter (dist only) r_work=0.1188 r_free=0.1342 | n_water=913 | time (s): 123.290 (total time: 577.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.528532 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.380547 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1347 0.0156 0.039 1.2 8.3 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.47 1.56 1.682 13.784 14.381 3.753 11.92 13.50 1.58 1.682 13.783 14.381 3.753 Individual atomic B min max mean iso aniso Overall: 5.56 62.73 14.70 0.87 546 3271 Protein: 5.56 28.13 10.36 0.87 0 2902 Water: 6.00 62.73 28.49 N/A 546 367 Other: 13.85 22.12 17.98 N/A 0 2 Chain A: 5.67 52.94 12.16 N/A 0 1624 Chain B: 5.56 62.73 12.02 N/A 0 1647 Chain S: 6.00 61.02 30.36 N/A 546 0 Histogram: Values Number of atoms 5.56 - 11.28 2046 11.28 - 17.00 839 17.00 - 22.71 273 22.71 - 28.43 209 28.43 - 34.15 187 34.15 - 39.86 125 39.86 - 45.58 91 45.58 - 51.30 35 51.30 - 57.02 9 57.02 - 62.73 3 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1350 r_work=0.1192 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752808 | | target function (ml) not normalized (work): 702855.994198 | | target function (ml) not normalized (free): 14716.610213 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1363 0.1480 5.6905 5.7654| | 2: 2.94 - 2.33 1.00 7339 128 0.1064 0.1303 5.0741 5.1564| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1185 4.6509 4.7433| | 4: 2.04 - 1.85 1.00 7170 155 0.0892 0.1023 4.3845 4.5436| | 5: 1.85 - 1.72 0.99 7113 159 0.0929 0.0985 4.1479 4.2483| | 6: 1.72 - 1.62 0.99 7102 142 0.0895 0.1084 3.9433 4.0668| | 7: 1.62 - 1.54 0.99 7104 148 0.0887 0.0951 3.7946 3.9182| | 8: 1.54 - 1.47 0.96 6798 152 0.0889 0.1328 3.6967 3.9049| | 9: 1.47 - 1.41 0.98 6938 155 0.0925 0.1114 3.6205 3.7448| | 10: 1.41 - 1.36 0.99 7022 150 0.0974 0.1207 3.5547 3.6764| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1127 3.4839 3.5823| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1111 3.4576 3.5752| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1252 3.4356 3.5727| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1587 3.432 3.6837| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1235 3.4485 3.4834| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1543 3.4649 3.6542| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1240 3.4335 3.4477| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1700 3.4382 3.5267| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1756 3.4195 3.5969| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1585 3.41 3.4356| | 21: 1.08 - 1.07 0.97 6852 152 0.1725 0.2135 3.4175 3.5039| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1954 3.413 3.414| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2019 3.4331 3.4866| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2254 3.4358 3.5127| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2517 3.4498 3.5238| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2854 3.4158 3.4221| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2804 3.4692 3.3974| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.72 1.00 0.95 11174.71| | 2: 2.94 - 2.33 7339 128 0.93 12.69 0.99 0.95 5071.06| | 3: 2.33 - 2.04 6939 150 0.96 7.45 1.01 0.96 1649.00| | 4: 2.04 - 1.85 7170 155 0.96 7.50 1.00 0.96 984.58| | 5: 1.85 - 1.72 7113 159 0.96 8.00 1.00 0.96 628.57| | 6: 1.72 - 1.62 7102 142 0.96 7.95 1.00 0.96 437.33| | 7: 1.62 - 1.54 7104 148 0.96 8.01 1.01 0.97 330.98| | 8: 1.54 - 1.47 6798 152 0.96 8.18 1.01 0.97 275.72| | 9: 1.47 - 1.41 6938 155 0.96 8.39 1.00 0.98 228.89| | 10: 1.41 - 1.36 7022 150 0.96 8.87 1.00 0.97 201.44| | 11: 1.36 - 1.32 6997 151 0.96 8.88 0.99 0.96 173.61| | 12: 1.32 - 1.28 6975 149 0.96 8.93 0.98 0.95 159.70| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.01 0.96 157.89| | 14: 1.25 - 1.22 7015 112 0.95 10.68 1.01 0.97 163.15| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 0.98 166.69| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.96 160.00| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.96 153.73| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.95 147.49| | 19: 1.12 - 1.10 6948 106 0.93 14.13 1.00 0.95 151.20| | 20: 1.10 - 1.08 6884 147 0.92 15.23 1.00 0.94 150.39| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.93 153.49| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.93 155.08| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.92 164.94| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.93 179.29| | 25: 1.02 - 1.01 6552 130 0.83 25.15 0.98 0.90 182.25| | 26: 1.01 - 0.99 6767 158 0.81 26.61 0.98 0.89 176.73| | 27: 0.99 - 0.98 6647 131 0.82 26.30 0.99 0.87 161.23| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.49 max = 11174.71 mean = 918.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.25| |phase err.(test): min = 0.00 max = 87.70 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1486 n_refl.: 191129 remove outliers: r(all,work,free)=0.1401 0.1399 0.1486 n_refl.: 191129 overall B=-0.06 to atoms: r(all,work,free)=0.1391 0.1389 0.1479 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1348 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 0.3637 361.049 330.968 0.424 0.916 0.213 13.296-10.522 96.04 96 1 0.2425 480.634 460.361 0.720 0.918 0.149 10.503-8.327 97.80 175 3 0.2211 502.120 492.903 0.891 0.918 0.106 8.318-6.595 100.00 360 8 0.2136 375.703 369.944 0.919 0.918 0.088 6.588-5.215 100.00 711 7 0.1918 345.234 334.815 0.918 0.919 0.087 5.214-4.128 98.38 1367 28 0.1267 504.972 498.782 1.014 0.920 0.057 4.126-3.266 94.74 2603 46 0.1164 460.309 452.609 1.080 0.921 0.000 3.266-2.585 99.86 5447 97 0.1119 310.514 306.998 1.062 0.922 0.000 2.585-2.046 97.45 10613 204 0.0962 234.265 231.656 1.069 0.924 0.000 2.046-1.619 99.39 21536 464 0.0906 138.649 137.290 1.086 0.928 0.000 1.619-1.281 98.00 42464 925 0.0943 74.641 73.994 1.076 0.934 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.042 38.329 1.042 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0130 ================= 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 : 0.2033 0.1995 0.081 5.186 5.2 78.0 14.6 805 0.000 1_bss: 0.1801 0.1927 0.081 5.186 5.2 78.0 14.6 805 0.000 1_settarget: 0.1801 0.1927 0.081 5.186 5.2 78.0 14.6 805 0.000 1_nqh: 0.1801 0.1927 0.081 5.186 5.2 78.0 14.6 805 0.000 1_weight: 0.1801 0.1927 0.081 5.186 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1503 0.038 1.163 5.2 78.0 14.6 805 0.154 1_adp: 0.1297 0.1570 0.038 1.163 5.2 73.0 15.0 805 0.154 1_regHadp: 0.1296 0.1566 0.038 1.163 5.2 73.0 15.0 805 0.154 1_occ: 0.1281 0.1555 0.038 1.163 5.2 73.0 15.0 805 0.154 2_bss: 0.1273 0.1546 0.038 1.163 5.3 73.2 15.2 805 0.154 2_settarget: 0.1273 0.1546 0.038 1.163 5.3 73.2 15.2 805 0.154 2_updatecdl: 0.1273 0.1546 0.038 1.172 5.3 73.2 15.2 805 0.154 2_nqh: 0.1273 0.1546 0.038 1.172 5.3 73.2 15.2 805 0.154 2_sol: 0.1270 0.1509 0.038 1.172 5.3 73.2 16.2 876 n/a 2_weight: 0.1270 0.1509 0.038 1.172 5.3 73.2 16.2 876 n/a 2_xyzrec: 0.1255 0.1528 0.042 1.141 5.3 73.2 16.2 876 n/a 2_adp: 0.1232 0.1516 0.042 1.141 5.3 68.2 16.3 876 n/a 2_regHadp: 0.1232 0.1517 0.042 1.141 5.3 68.2 16.3 876 n/a 2_occ: 0.1226 0.1515 0.042 1.141 5.3 68.2 16.3 876 n/a 3_bss: 0.1232 0.1523 0.042 1.141 5.3 68.2 16.3 876 n/a 3_settarget: 0.1232 0.1523 0.042 1.141 5.3 68.2 16.3 876 n/a 3_updatecdl: 0.1232 0.1523 0.042 1.148 5.3 68.2 16.3 876 n/a 3_nqh: 0.1232 0.1523 0.042 1.148 5.3 68.2 16.3 876 n/a 3_sol: 0.1249 0.1509 0.042 1.148 5.3 68.2 15.5 868 n/a 3_weight: 0.1249 0.1509 0.042 1.148 5.3 68.2 15.5 868 n/a 3_xyzrec: 0.1237 0.1439 0.035 1.093 5.3 68.2 15.5 868 n/a 3_adp: 0.1234 0.1399 0.035 1.093 5.5 67.9 15.3 868 n/a 3_regHadp: 0.1235 0.1400 0.035 1.093 5.5 67.9 15.3 868 n/a 3_occ: 0.1229 0.1397 0.035 1.093 5.5 67.9 15.3 868 n/a 4_bss: 0.1225 0.1391 0.035 1.093 5.5 67.9 15.3 868 n/a 4_settarget: 0.1225 0.1391 0.035 1.093 5.5 67.9 15.3 868 n/a 4_updatecdl: 0.1225 0.1391 0.035 1.099 5.5 67.9 15.3 868 n/a 4_nqh: 0.1225 0.1391 0.035 1.099 5.5 67.9 15.3 868 n/a 4_sol: 0.1211 0.1367 0.035 1.099 5.5 67.9 15.0 852 n/a 4_weight: 0.1211 0.1367 0.035 1.099 5.5 67.9 15.0 852 n/a 4_xyzrec: 0.1210 0.1371 0.036 1.114 5.5 67.9 15.0 852 n/a 4_adp: 0.1203 0.1363 0.036 1.114 5.5 67.2 14.9 852 n/a 4_regHadp: 0.1203 0.1363 0.036 1.114 5.5 67.2 14.9 852 n/a 4_occ: 0.1200 0.1360 0.036 1.114 5.5 67.2 14.9 852 n/a 5_bss: 0.1198 0.1360 0.036 1.114 5.5 67.2 14.9 852 n/a 5_settarget: 0.1198 0.1360 0.036 1.114 5.5 67.2 14.9 852 n/a 5_updatecdl: 0.1198 0.1360 0.036 1.114 5.5 67.2 14.9 852 n/a 5_nqh: 0.1198 0.1360 0.036 1.114 5.5 67.2 14.9 852 n/a 5_sol: 0.1195 0.1351 0.036 1.114 5.5 67.2 14.9 866 n/a 5_weight: 0.1195 0.1351 0.036 1.114 5.5 67.2 14.9 866 n/a 5_xyzrec: 0.1197 0.1356 0.037 1.125 5.5 67.2 14.9 866 n/a 5_adp: 0.1201 0.1362 0.037 1.125 5.6 67.0 14.9 866 n/a 5_regHadp: 0.1201 0.1362 0.037 1.125 5.6 67.0 14.9 866 n/a 5_occ: 0.1199 0.1363 0.037 1.125 5.6 67.0 14.9 866 n/a 6_bss: 0.1197 0.1361 0.037 1.125 5.5 67.0 14.8 866 n/a 6_settarget: 0.1197 0.1361 0.037 1.125 5.5 67.0 14.8 866 n/a 6_updatecdl: 0.1197 0.1361 0.037 1.126 5.5 67.0 14.8 866 n/a 6_nqh: 0.1197 0.1361 0.037 1.126 5.5 67.0 14.8 866 n/a 6_sol: 0.1195 0.1345 0.037 1.126 5.5 67.0 14.9 883 n/a 6_weight: 0.1195 0.1345 0.037 1.126 5.5 67.0 14.9 883 n/a 6_xyzrec: 0.1197 0.1352 0.038 1.115 5.5 67.0 14.9 883 n/a 6_adp: 0.1200 0.1355 0.038 1.115 5.6 66.0 14.8 883 n/a 6_regHadp: 0.1200 0.1355 0.038 1.115 5.6 66.0 14.8 883 n/a 6_occ: 0.1198 0.1355 0.038 1.115 5.6 66.0 14.8 883 n/a 7_bss: 0.1197 0.1353 0.038 1.115 5.3 65.7 14.6 883 n/a 7_settarget: 0.1197 0.1353 0.038 1.115 5.3 65.7 14.6 883 n/a 7_updatecdl: 0.1197 0.1353 0.038 1.115 5.3 65.7 14.6 883 n/a 7_nqh: 0.1197 0.1353 0.038 1.115 5.3 65.7 14.6 883 n/a 7_sol: 0.1195 0.1345 0.038 1.115 5.3 65.7 14.7 901 n/a 7_weight: 0.1195 0.1345 0.038 1.115 5.3 65.7 14.7 901 n/a 7_xyzrec: 0.1198 0.1351 0.038 1.115 5.3 65.7 14.7 901 n/a 7_adp: 0.1200 0.1357 0.038 1.115 5.4 64.8 14.6 901 n/a 7_regHadp: 0.1200 0.1357 0.038 1.115 5.4 64.8 14.6 901 n/a 7_occ: 0.1198 0.1359 0.038 1.115 5.4 64.8 14.6 901 n/a 8_bss: 0.1189 0.1348 0.038 1.115 5.5 64.9 14.7 901 n/a 8_settarget: 0.1189 0.1348 0.038 1.115 5.5 64.9 14.7 901 n/a 8_updatecdl: 0.1189 0.1348 0.038 1.116 5.5 64.9 14.7 901 n/a 8_nqh: 0.1189 0.1348 0.038 1.116 5.5 64.9 14.7 901 n/a 8_sol: 0.1187 0.1343 0.038 1.116 5.5 64.9 14.8 916 n/a 8_weight: 0.1187 0.1343 0.038 1.116 5.5 64.9 14.8 916 n/a 8_xyzrec: 0.1190 0.1347 0.038 1.121 5.5 64.9 14.8 916 n/a 8_adp: 0.1190 0.1348 0.038 1.121 5.5 63.9 14.7 916 n/a 8_regHadp: 0.1190 0.1349 0.038 1.121 5.5 63.9 14.7 916 n/a 8_occ: 0.1188 0.1350 0.038 1.121 5.5 63.9 14.7 916 n/a 9_bss: 0.1187 0.1348 0.038 1.121 5.5 63.9 14.8 916 n/a 9_settarget: 0.1187 0.1348 0.038 1.121 5.5 63.9 14.8 916 n/a 9_updatecdl: 0.1187 0.1348 0.038 1.121 5.5 63.9 14.8 916 n/a 9_nqh: 0.1187 0.1348 0.038 1.121 5.5 63.9 14.8 916 n/a 9_sol: 0.1187 0.1336 0.038 1.121 5.5 63.9 14.7 906 n/a 9_weight: 0.1187 0.1336 0.038 1.121 5.5 63.9 14.7 906 n/a 9_xyzrec: 0.1190 0.1341 0.039 1.108 5.5 63.9 14.7 906 n/a 9_adp: 0.1191 0.1345 0.039 1.108 5.5 63.5 14.7 906 n/a 9_regHadp: 0.1191 0.1345 0.039 1.108 5.5 63.5 14.7 906 n/a 9_occ: 0.1189 0.1346 0.039 1.108 5.5 63.5 14.7 906 n/a 10_bss: 0.1189 0.1345 0.039 1.108 5.5 63.5 14.7 906 n/a 10_settarget: 0.1189 0.1345 0.039 1.108 5.5 63.5 14.7 906 n/a 10_updatecdl: 0.1189 0.1345 0.039 1.108 5.5 63.5 14.7 906 n/a 10_setrh: 0.1189 0.1346 0.039 1.108 5.5 63.5 14.7 906 n/a 10_nqh: 0.1189 0.1346 0.039 1.108 5.5 63.5 14.7 906 n/a 10_sol: 0.1188 0.1342 0.039 1.108 5.5 63.5 14.7 913 n/a 10_weight: 0.1188 0.1342 0.039 1.108 5.5 63.5 14.7 913 n/a 10_xyzrec: 0.1190 0.1347 0.039 1.153 5.5 63.5 14.7 913 n/a 10_adp: 0.1192 0.1350 0.039 1.153 5.6 62.7 14.7 913 n/a 10_regHadp: 0.1192 0.1350 0.039 1.153 5.6 62.7 14.7 913 n/a 10_occ: 0.1191 0.1350 0.039 1.153 5.6 62.7 14.7 913 n/a end: 0.1190 0.1348 0.039 1.153 5.5 62.7 14.6 913 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8736011_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8736011_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.7900 Refinement macro-cycles (run) : 12161.1800 Write final files (write_after_run_outputs) : 161.9200 Total : 12329.8900 Total CPU time: 3.44 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:45 PST -0800 (1736736165.62 s) Start R-work = 0.1801, R-free = 0.1927 Final R-work = 0.1190, R-free = 0.1348 =============================================================================== Job complete usr+sys time: 12609.32 seconds wall clock time: 211 minutes 13.03 seconds (12673.03 seconds total)