Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4511945.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" 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" 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_4511945.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4511945.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.01, per 1000 atoms: 0.30 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.812 distance_ideal: 2.720 ideal - model: -0.092 slack: 0.000 delta_slack: -0.092 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: 2.783 distance_ideal: 2.710 ideal - model: -0.073 slack: 0.000 delta_slack: -0.073 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: 0.79 Conformation dependent library (CDL) restraints added in 129.5 milliseconds Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.04: 905 1.04 - 1.27: 2466 1.27 - 1.49: 1455 1.49 - 1.72: 1090 1.72 - 1.95: 18 Bond restraints: 5934 Sorted by residual: bond pdb=" C GLU A 17 " pdb=" O GLU A 17 " ideal model delta sigma weight residual 1.236 1.473 -0.236 1.15e-02 7.56e+03 4.22e+02 bond pdb=" N VAL A 144 " pdb=" CA VAL A 144 " ideal model delta sigma weight residual 1.457 1.681 -0.224 1.14e-02 7.69e+03 3.85e+02 bond pdb=" CD2 PHE B 127 " pdb=" HD2 PHE B 127 " ideal model delta sigma weight residual 0.930 1.305 -0.375 2.00e-02 2.50e+03 3.52e+02 bond pdb=" CG PRO B 128 " pdb=" HG2 PRO B 128 " ideal model delta sigma weight residual 0.970 1.339 -0.369 2.00e-02 2.50e+03 3.40e+02 bond pdb=" CG PRO A 11 " pdb=" HG2 PRO A 11 " ideal model delta sigma weight residual 0.970 1.338 -0.368 2.00e-02 2.50e+03 3.38e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 6149 4.58 - 9.15: 3452 9.15 - 13.73: 1073 13.73 - 18.31: 128 18.31 - 22.89: 8 Bond angle restraints: 10810 Sorted by residual: angle pdb=" OE1 GLN A 184 " pdb=" CD GLN A 184 " pdb=" NE2 GLN A 184 " ideal model delta sigma weight residual 122.60 106.54 16.06 1.00e+00 1.00e+00 2.58e+02 angle pdb=" CA ASP B 163 " pdb=" CB ASP B 163 " pdb=" CG ASP B 163 " ideal model delta sigma weight residual 112.60 128.45 -15.85 1.00e+00 1.00e+00 2.51e+02 angle pdb=" O ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 121.32 134.76 -13.44 8.50e-01 1.38e+00 2.50e+02 angle pdb=" NE ARG B 97 " pdb=" CZ ARG B 97 " pdb=" NH2 ARG B 97 " ideal model delta sigma weight residual 119.20 106.43 12.77 9.00e-01 1.23e+00 2.01e+02 angle pdb=" CA ALA A 10 " pdb=" C ALA A 10 " pdb=" O ALA A 10 " ideal model delta sigma weight residual 120.94 106.71 14.23 1.01e+00 9.80e-01 1.99e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 1843 17.48 - 34.95: 145 34.95 - 52.43: 40 52.43 - 69.90: 18 69.90 - 87.37: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -148.02 -31.98 0 5.00e+00 4.00e-02 4.09e+01 dihedral pdb=" CB TRP A 139 " pdb=" CG TRP A 139 " pdb=" CD1 TRP A 139 " pdb=" HD1 TRP A 139 " ideal model delta harmonic sigma weight residual 0.00 27.37 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ALA A 107 " pdb=" C ALA A 107 " pdb=" N ALA A 108 " pdb=" CA ALA A 108 " ideal model delta harmonic sigma weight residual 180.00 -156.50 -23.50 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.239: 229 0.239 - 0.478: 162 0.478 - 0.717: 67 0.717 - 0.955: 30 0.955 - 1.194: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU A 153 " pdb=" CB LEU A 153 " pdb=" CD1 LEU A 153 " pdb=" CD2 LEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -3.78 1.19 2.00e-01 2.50e+01 3.56e+01 chirality pdb=" CA LEU B 6 " pdb=" N LEU B 6 " pdb=" C LEU B 6 " pdb=" CB LEU B 6 " both_signs ideal model delta sigma weight residual False 2.51 3.49 -0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA LYS A 151 " pdb=" N LYS A 151 " pdb=" C LYS A 151 " pdb=" CB LYS A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.33e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.078 2.00e-02 2.50e+03 6.71e-02 1.80e+02 pdb=" CG TRP A 139 " 0.137 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.026 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.053 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.122 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.092 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " 0.061 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.015 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.019 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.037 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.097 2.00e-02 2.50e+03 6.47e-02 1.68e+02 pdb=" CG TRP B 146 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.104 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.099 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.075 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.093 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.114 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.000 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.003 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.032 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.078 2.00e-02 2.50e+03 7.08e-02 1.50e+02 pdb=" CG PHE A 127 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " 0.110 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " -0.081 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " 0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 127 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 127 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 PHE A 127 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE A 127 " 0.076 2.00e-02 2.50e+03 pdb=" HZ PHE A 127 " -0.079 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.95 - 1.68: 40 1.68 - 2.41: 3217 2.41 - 3.14: 22629 3.14 - 3.87: 32702 3.87 - 4.60: 51668 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110256 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.952 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.969 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.060 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.087 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.142 2.620 ... (remaining 110251 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_4511945_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2029 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.297294 | | target function (ml) not normalized (work): 804939.111263 | | target function (ml) not normalized (free): 16495.235658 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1914 6.6898 6.2904| | 2: 2.94 - 2.33 1.00 7339 128 0.1636 0.1582 5.5306 5.5729| | 3: 2.33 - 2.04 0.96 6939 150 0.1631 0.1513 5.1321 5.1227| | 4: 2.04 - 1.85 1.00 7170 155 0.1736 0.1651 4.9539 5.0462| | 5: 1.85 - 1.72 0.99 7113 159 0.1910 0.1758 4.787 4.8066| | 6: 1.72 - 1.62 0.99 7102 142 0.1974 0.2019 4.673 4.7106| | 7: 1.62 - 1.54 0.99 7104 148 0.2010 0.1734 4.5481 4.5142| | 8: 1.54 - 1.47 0.96 6798 152 0.2032 0.2281 4.465 4.5198| | 9: 1.47 - 1.41 0.98 6938 155 0.2075 0.2170 4.3916 4.434| | 10: 1.41 - 1.36 0.99 7022 150 0.2115 0.2293 4.3098 4.4049| | 11: 1.36 - 1.32 0.99 6997 151 0.2124 0.2028 4.2341 4.2327| | 12: 1.32 - 1.28 0.98 6976 149 0.2068 0.1809 4.1756 4.1249| | 13: 1.28 - 1.25 0.98 6907 166 0.1998 0.2180 4.1075 4.222| | 14: 1.25 - 1.22 0.98 7015 113 0.2096 0.2118 4.0767 4.0681| | 15: 1.22 - 1.19 0.98 6957 137 0.2078 0.2162 4.0434 4.0654| | 16: 1.19 - 1.17 0.93 6604 132 0.2113 0.2072 3.9978 4.0628| | 17: 1.17 - 1.14 0.98 6941 135 0.2164 0.1976 3.9599 4.0138| | 18: 1.14 - 1.12 0.98 6875 142 0.2192 0.2362 3.912 3.8867| | 19: 1.12 - 1.10 0.97 6949 106 0.2279 0.2444 3.8743 3.9796| | 20: 1.10 - 1.08 0.97 6884 147 0.2307 0.2248 3.817 3.8546| | 21: 1.08 - 1.07 0.97 6852 152 0.2440 0.2442 3.7974 3.7633| | 22: 1.07 - 1.05 0.97 6838 135 0.2558 0.2741 3.7572 3.8143| | 23: 1.05 - 1.03 0.97 6829 159 0.2679 0.2527 3.7262 3.766| | 24: 1.03 - 1.02 0.96 6785 133 0.2839 0.2830 3.6945 3.8137| | 25: 1.02 - 1.01 0.93 6552 130 0.3076 0.2765 3.6751 3.6861| | 26: 1.01 - 0.99 0.96 6767 158 0.3206 0.3128 3.6299 3.5714| | 27: 0.99 - 0.98 0.94 6648 131 0.3445 0.2992 3.6554 3.5875| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.21 0.91 0.96 34037.46| | 2: 2.94 - 2.33 7339 128 0.86 20.83 1.09 1.02 14521.73| | 3: 2.33 - 2.04 6939 150 0.93 12.27 1.11 1.06 4005.03| | 4: 2.04 - 1.85 7170 155 0.93 13.27 1.11 1.07 2691.60| | 5: 1.85 - 1.72 7113 159 0.91 15.39 1.11 1.08 2020.00| | 6: 1.72 - 1.62 7102 142 0.90 16.38 1.11 1.08 1628.11| | 7: 1.62 - 1.54 7104 148 0.89 17.37 1.12 1.09 1318.74| | 8: 1.54 - 1.47 6798 152 0.89 18.49 1.10 1.07 1162.12| | 9: 1.47 - 1.41 6938 155 0.88 19.37 1.10 1.07 1029.40| | 10: 1.41 - 1.36 7022 150 0.87 20.60 1.09 1.05 894.97| | 11: 1.36 - 1.32 6997 151 0.88 19.68 1.08 1.05 724.48| | 12: 1.32 - 1.28 6976 149 0.88 18.86 1.07 1.04 595.71| | 13: 1.28 - 1.25 6907 166 0.88 18.64 1.07 1.04 535.81| | 14: 1.25 - 1.22 7015 113 0.88 19.56 1.08 1.05 516.74| | 15: 1.22 - 1.19 6957 137 0.87 19.84 1.07 1.06 499.78| | 16: 1.19 - 1.17 6604 132 0.88 19.76 1.08 1.05 465.44| | 17: 1.17 - 1.14 6941 135 0.87 20.58 1.08 1.03 427.71| | 18: 1.14 - 1.12 6875 142 0.87 20.81 1.08 1.00 389.73| | 19: 1.12 - 1.10 6949 106 0.86 21.54 1.07 1.00 365.18| | 20: 1.10 - 1.08 6884 147 0.86 22.10 1.07 0.99 335.22| | 21: 1.08 - 1.07 6852 152 0.85 22.83 1.06 1.01 320.34| | 22: 1.07 - 1.05 6838 135 0.83 24.91 1.05 1.00 321.73| | 23: 1.05 - 1.03 6829 159 0.81 26.89 1.04 1.00 325.14| | 24: 1.03 - 1.02 6785 133 0.79 28.88 1.05 0.97 319.15| | 25: 1.02 - 1.01 6552 130 0.78 29.41 1.03 0.94 290.57| | 26: 1.01 - 0.99 6767 158 0.77 30.72 1.04 0.92 268.11| | 27: 0.99 - 0.98 6648 131 0.77 30.84 1.04 0.89 250.79| |alpha: min = 0.89 max = 1.09 mean = 1.02| |beta: min = 250.79 max = 34037.46 mean = 2724.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 21.04| |phase err.(test): min = 0.00 max = 89.86 mean = 21.18| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.250 2950 Z= 5.382 Angle : 5.071 16.749 4018 Z= 3.614 Chirality : 0.383 1.194 492 Planarity : 0.032 0.119 512 Dihedral : 13.082 87.372 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.63 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 30.90 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.38), residues: 386 helix: -2.74 (0.30), residues: 144 sheet: -0.34 (0.62), residues: 66 loop : -0.11 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.129 0.024 ARG A 49 TYR 0.113 0.044 TYR A 194 PHE 0.121 0.040 PHE A 95 TRP 0.149 0.048 TRP A 139 HIS 0.071 0.028 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2029 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.297294 | | target function (ml) not normalized (work): 804939.111263 | | target function (ml) not normalized (free): 16495.235658 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2027 0.2029 0.1961 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2027 0.2029 0.1961 n_refl.: 191155 remove outliers: r(all,work,free)=0.2027 0.2029 0.1961 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2029 0.2031 0.1962 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1798 0.1796 0.1895 n_refl.: 191145 remove outliers: r(all,work,free)=0.1795 0.1794 0.1895 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 0.4113 402.814 290.427 0.423 0.932 0.301 13.296-10.522 99.01 99 1 0.2516 528.187 518.109 0.767 0.933 0.251 10.503-8.327 98.90 177 3 0.2444 564.205 558.628 0.947 0.933 0.227 8.318-6.595 100.00 360 8 0.2494 414.736 402.191 0.947 0.933 0.160 6.588-5.215 100.00 711 7 0.2201 381.101 366.307 0.938 0.932 0.150 5.214-4.128 98.38 1367 28 0.1500 557.435 549.284 1.051 0.932 0.080 4.126-3.266 94.74 2603 46 0.1351 508.132 498.556 1.119 0.931 0.018 3.266-2.585 99.86 5447 97 0.1447 342.774 337.305 1.099 0.928 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 253.925 1.106 0.925 0.000 2.046-1.619 99.39 21536 464 0.1611 153.054 149.742 1.128 0.919 0.000 1.619-1.281 98.00 42464 925 0.1906 82.395 80.216 1.125 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2309 44.203 41.661 1.123 0.893 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0214 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1794 r_free=0.1895 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1794 r_free=0.1895 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.274493 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.084583 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1273 0.1485 0.0212 0.035 1.2 11.7 0.0 0.0 0 11.137 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 14.85 2.12 1.117 13.124 571.085 0.019 13.03 15.53 2.49 1.264 13.375 571.085 0.018 Individual atomic B min max mean iso aniso Overall: 5.17 73.06 15.07 1.41 435 3274 Protein: 5.17 40.93 11.02 1.41 0 2902 Water: 6.37 73.06 29.62 N/A 435 370 Other: 15.98 31.24 23.61 N/A 0 2 Chain A: 5.41 60.53 13.09 N/A 0 1626 Chain B: 5.17 73.06 12.82 N/A 0 1648 Chain S: 11.38 61.39 30.98 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2166 11.96 - 18.75 630 18.75 - 25.54 319 25.54 - 32.33 262 32.33 - 39.11 149 39.11 - 45.90 113 45.90 - 52.69 46 52.69 - 59.48 18 59.48 - 66.27 5 66.27 - 73.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1304 r_free=0.1553 r_work=0.1303 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1303 r_free = 0.1549 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1287 r_free = 0.1536 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1287 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015820 | | target function (ls_wunit_k1) not normalized (work): 2963.055068 | | target function (ls_wunit_k1) not normalized (free): 112.310406 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1287 0.1536 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1477 0.1475 0.1615 n_refl.: 191138 remove outliers: r(all,work,free)=0.1477 0.1475 0.1615 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1501 0.1499 0.1627 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1286 0.1281 0.1529 n_refl.: 191138 remove outliers: r(all,work,free)=0.1286 0.1281 0.1528 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3691 402.814 368.046 0.474 0.963 0.287 13.296-10.522 99.01 99 1 0.2097 528.187 518.956 0.732 0.965 0.243 10.503-8.327 98.90 177 3 0.1737 564.205 566.319 0.890 0.965 0.220 8.318-6.595 100.00 360 8 0.1771 414.736 410.697 0.905 0.964 0.150 6.588-5.215 100.00 711 7 0.1593 381.101 373.543 0.888 0.965 0.140 5.214-4.128 98.38 1367 28 0.0931 557.435 553.998 0.974 0.965 0.054 4.126-3.266 94.74 2603 46 0.0861 508.132 503.982 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0931 342.774 340.438 1.028 0.965 0.000 2.585-2.046 97.45 10613 204 0.0945 258.603 256.362 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.364 1.056 0.965 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.339 1.048 0.964 0.000 1.281-0.980 96.53 101826 2055 0.1884 44.202 42.171 1.027 0.963 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0365 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1281 r_free=0.1528 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1281 r_free=0.1528 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1281 r_free=0.1528 | n_water=805 | time (s): 2.980 (total time: 2.980) Filter (dist) r_work=0.1282 r_free=0.1530 | n_water=802 | time (s): 97.070 (total time: 100.050) Filter (q & B) r_work=0.1283 r_free=0.1530 | n_water=796 | time (s): 5.280 (total time: 105.330) Compute maps r_work=0.1283 r_free=0.1530 | n_water=796 | time (s): 2.050 (total time: 107.380) Filter (map) r_work=0.1308 r_free=0.1523 | n_water=665 | time (s): 5.110 (total time: 112.490) Find peaks r_work=0.1308 r_free=0.1523 | n_water=665 | time (s): 0.800 (total time: 113.290) Add new water r_work=0.1331 r_free=0.1558 | n_water=982 | time (s): 3.840 (total time: 117.130) Refine new water occ: r_work=0.1285 r_free=0.1514 adp: r_work=0.1273 r_free=0.1507 occ: r_work=0.1276 r_free=0.1503 adp: r_work=0.1269 r_free=0.1502 occ: r_work=0.1271 r_free=0.1497 adp: r_work=0.1268 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1498 r_work=0.1268 r_free=0.1498 | n_water=982 | time (s): 76.400 (total time: 193.530) Filter (q & B) r_work=0.1272 r_free=0.1502 | n_water=905 | time (s): 4.250 (total time: 197.780) Filter (dist only) r_work=0.1272 r_free=0.1502 | n_water=904 | time (s): 113.350 (total time: 311.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.218262 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 576.522860 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 0.1513 0.0258 0.039 1.1 22.8 0.0 0.3 0 11.609 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.13 2.58 2.052 15.292 576.523 0.014 12.31 14.97 2.66 2.433 15.336 576.523 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 70.28 16.48 1.20 535 3273 Protein: 5.38 40.98 11.00 1.20 0 2902 Water: 6.60 70.28 34.05 N/A 535 369 Other: 16.38 33.73 25.06 N/A 0 2 Chain A: 5.52 56.35 13.07 N/A 0 1625 Chain B: 5.38 68.22 12.84 N/A 0 1648 Chain S: 13.33 70.28 38.03 N/A 535 0 Histogram: Values Number of atoms 5.38 - 11.87 2088 11.87 - 18.36 707 18.36 - 24.85 265 24.85 - 31.34 219 31.34 - 37.83 180 37.83 - 44.32 160 44.32 - 50.81 93 50.81 - 57.30 54 57.30 - 63.79 35 63.79 - 70.28 7 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1497 r_work=0.1232 r_free=0.1499 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1499 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1494 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1494 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013357 | | target function (ls_wunit_k1) not normalized (work): 2501.794279 | | target function (ls_wunit_k1) not normalized (free): 98.169044 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1494 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1589 n_refl.: 191137 remove outliers: r(all,work,free)=0.1436 0.1433 0.1589 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1430 0.1588 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1232 0.1500 n_refl.: 191137 remove outliers: r(all,work,free)=0.1237 0.1232 0.1500 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3185 402.814 383.517 0.489 0.963 0.273 13.296-10.522 99.01 99 1 0.1910 528.187 520.858 0.755 0.964 0.233 10.503-8.327 98.90 177 3 0.1387 564.205 567.326 0.922 0.964 0.210 8.318-6.595 100.00 360 8 0.1529 414.736 413.740 0.934 0.963 0.149 6.588-5.215 100.00 711 7 0.1364 381.101 376.803 0.912 0.963 0.141 5.214-4.128 98.38 1367 28 0.0824 557.435 555.568 0.993 0.963 0.070 4.126-3.266 94.74 2603 46 0.0770 508.132 505.127 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0856 342.774 341.279 1.047 0.962 0.010 2.585-2.046 97.45 10613 204 0.0893 258.603 256.730 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1041 153.054 151.635 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.348 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.211 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0573 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1500 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1500 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1500 | n_water=904 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1235 r_free=0.1503 | n_water=896 | time (s): 121.300 (total time: 123.830) Filter (q & B) r_work=0.1235 r_free=0.1503 | n_water=894 | time (s): 4.320 (total time: 128.150) Compute maps r_work=0.1235 r_free=0.1503 | n_water=894 | time (s): 2.560 (total time: 130.710) Filter (map) r_work=0.1274 r_free=0.1509 | n_water=700 | time (s): 4.110 (total time: 134.820) Find peaks r_work=0.1274 r_free=0.1509 | n_water=700 | time (s): 0.690 (total time: 135.510) Add new water r_work=0.1297 r_free=0.1538 | n_water=1005 | time (s): 4.350 (total time: 139.860) Refine new water occ: r_work=0.1253 r_free=0.1491 adp: r_work=0.1254 r_free=0.1493 occ: r_work=0.1249 r_free=0.1490 adp: r_work=0.1249 r_free=0.1492 occ: r_work=0.1246 r_free=0.1491 adp: r_work=0.1245 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1491 r_work=0.1245 r_free=0.1491 | n_water=1005 | time (s): 215.100 (total time: 354.960) Filter (q & B) r_work=0.1250 r_free=0.1501 | n_water=881 | time (s): 4.210 (total time: 359.170) Filter (dist only) r_work=0.1250 r_free=0.1500 | n_water=880 | time (s): 114.490 (total time: 473.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.712530 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.123252 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 0.1239 0.1432 0.0193 0.035 1.1 9.4 0.0 0.0 0 0.856 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.32 1.93 1.936 14.632 17.123 3.940 12.30 13.90 1.60 2.241 14.530 17.123 3.895 Individual atomic B min max mean iso aniso Overall: 5.52 67.73 15.32 1.06 512 3272 Protein: 5.52 36.99 10.76 1.06 0 2902 Water: 6.68 67.73 30.34 N/A 512 368 Other: 14.17 29.11 21.64 N/A 0 2 Chain A: 5.55 55.31 12.82 N/A 0 1625 Chain B: 5.52 67.73 12.55 N/A 0 1647 Chain S: 14.06 62.48 32.12 N/A 512 0 Histogram: Values Number of atoms 5.52 - 11.74 2116 11.74 - 17.96 693 17.96 - 24.18 298 24.18 - 30.40 238 30.40 - 36.63 182 36.63 - 42.85 150 42.85 - 49.07 74 49.07 - 55.29 20 55.29 - 61.51 10 61.51 - 67.73 3 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1390 r_work=0.1231 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1392 target_work(ml) = 3.895 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1387 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890181 | | target function (ml) not normalized (work): 728615.347517 | | target function (ml) not normalized (free): 15218.331616 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1226 0.1386 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1446 0.1445 0.1500 n_refl.: 191137 remove outliers: r(all,work,free)=0.1446 0.1445 0.1500 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1439 0.1438 0.1496 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1380 n_refl.: 191137 remove outliers: r(all,work,free)=0.1225 0.1222 0.1380 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3779 398.895 357.360 0.418 0.947 0.237 13.296-10.522 99.01 99 1 0.2374 528.187 507.555 0.709 0.948 0.209 10.503-8.327 98.35 176 3 0.2030 556.299 556.940 0.884 0.948 0.200 8.318-6.595 100.00 360 8 0.2110 414.736 409.150 0.894 0.948 0.115 6.588-5.215 100.00 711 7 0.1840 381.101 370.929 0.881 0.948 0.100 5.214-4.128 98.38 1367 28 0.1173 557.435 552.028 0.971 0.948 0.070 4.126-3.266 94.74 2603 46 0.1101 508.132 501.263 1.032 0.948 0.019 3.266-2.585 99.86 5447 97 0.1085 342.774 339.278 1.020 0.947 0.010 2.585-2.046 97.45 10613 204 0.0955 258.603 255.847 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0963 153.054 151.437 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.496 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.321 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1046 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1380 | n_water=880 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1223 r_free=0.1383 | n_water=879 | time (s): 115.530 (total time: 117.960) Filter (q & B) r_work=0.1224 r_free=0.1380 | n_water=865 | time (s): 4.120 (total time: 122.080) Compute maps r_work=0.1224 r_free=0.1380 | n_water=865 | time (s): 2.150 (total time: 124.230) Filter (map) r_work=0.1243 r_free=0.1380 | n_water=744 | time (s): 4.740 (total time: 128.970) Find peaks r_work=0.1243 r_free=0.1380 | n_water=744 | time (s): 0.530 (total time: 129.500) Add new water r_work=0.1257 r_free=0.1393 | n_water=998 | time (s): 4.810 (total time: 134.310) Refine new water occ: r_work=0.1211 r_free=0.1361 adp: r_work=0.1203 r_free=0.1355 occ: r_work=0.1200 r_free=0.1355 adp: r_work=0.1200 r_free=0.1354 occ: r_work=0.1199 r_free=0.1355 adp: r_work=0.1199 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1355 r_work=0.1199 r_free=0.1355 | n_water=998 | time (s): 246.000 (total time: 380.310) Filter (q & B) r_work=0.1205 r_free=0.1368 | n_water=871 | time (s): 4.300 (total time: 384.610) Filter (dist only) r_work=0.1205 r_free=0.1368 | n_water=870 | time (s): 112.390 (total time: 497.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.612387 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.059407 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1368 0.0163 0.035 1.1 7.0 0.0 0.3 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.68 1.63 1.836 14.205 16.059 3.874 12.00 13.66 1.67 1.920 14.174 16.059 3.866 Individual atomic B min max mean iso aniso Overall: 5.53 67.34 14.97 1.01 502 3272 Protein: 5.53 33.99 10.69 1.01 0 2902 Water: 5.79 67.34 29.24 N/A 502 368 Other: 13.99 28.04 21.01 N/A 0 2 Chain A: 5.53 54.41 12.70 N/A 0 1625 Chain B: 5.53 67.34 12.47 N/A 0 1647 Chain S: 5.79 62.05 30.51 N/A 502 0 Histogram: Values Number of atoms 5.53 - 11.71 2114 11.71 - 17.89 724 17.89 - 24.07 311 24.07 - 30.25 243 30.25 - 36.43 151 36.43 - 42.61 134 42.61 - 48.79 67 48.79 - 54.98 21 54.98 - 61.16 7 61.16 - 67.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1367 r_work=0.1200 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1367 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1364 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864487 | | target function (ml) not normalized (work): 723791.280135 | | target function (ml) not normalized (free): 15145.797523 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1415 0.1413 0.1494 n_refl.: 191134 remove outliers: r(all,work,free)=0.1415 0.1413 0.1494 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1407 0.1406 0.1489 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191134 remove outliers: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191132 ======================== 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 0.3726 361.245 324.658 0.414 0.950 0.241 13.296-10.522 98.02 98 1 0.2361 480.578 455.980 0.702 0.952 0.208 10.503-8.327 97.80 175 3 0.2124 501.969 497.642 0.867 0.952 0.163 8.318-6.595 100.00 360 8 0.2229 375.591 367.819 0.886 0.951 0.125 6.588-5.215 100.00 711 7 0.1945 345.130 334.294 0.874 0.952 0.099 5.214-4.128 98.38 1367 28 0.1218 504.821 499.361 0.966 0.952 0.044 4.126-3.266 94.74 2603 46 0.1126 460.172 453.751 1.030 0.952 0.005 3.266-2.585 99.86 5447 97 0.1086 310.421 307.144 1.017 0.951 0.000 2.585-2.046 97.45 10613 204 0.0929 234.195 231.798 1.030 0.950 0.000 2.046-1.619 99.39 21536 464 0.0910 138.608 137.312 1.054 0.948 0.000 1.619-1.281 98.00 42464 925 0.0986 74.619 73.903 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.030 38.368 1.041 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1199 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1360 | n_water=870 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1196 r_free=0.1360 | n_water=870 | time (s): 113.240 (total time: 116.330) Filter (q & B) r_work=0.1196 r_free=0.1359 | n_water=864 | time (s): 4.280 (total time: 120.610) Compute maps r_work=0.1196 r_free=0.1359 | n_water=864 | time (s): 1.800 (total time: 122.410) Filter (map) r_work=0.1216 r_free=0.1360 | n_water=757 | time (s): 4.650 (total time: 127.060) Find peaks r_work=0.1216 r_free=0.1360 | n_water=757 | time (s): 0.730 (total time: 127.790) Add new water r_work=0.1227 r_free=0.1378 | n_water=978 | time (s): 4.850 (total time: 132.640) Refine new water occ: r_work=0.1192 r_free=0.1351 adp: r_work=0.1192 r_free=0.1350 occ: r_work=0.1190 r_free=0.1350 adp: r_work=0.1190 r_free=0.1349 occ: r_work=0.1188 r_free=0.1350 adp: r_work=0.1188 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1349 r_work=0.1188 r_free=0.1349 | n_water=978 | time (s): 244.990 (total time: 377.630) Filter (q & B) r_work=0.1193 r_free=0.1355 | n_water=888 | time (s): 4.420 (total time: 382.050) Filter (dist only) r_work=0.1193 r_free=0.1354 | n_water=887 | time (s): 109.950 (total time: 492.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544340 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.007102 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 0.1360 0.0163 0.036 1.1 6.6 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.60 1.63 1.801 14.168 15.007 3.765 12.01 13.63 1.62 1.846 14.149 15.007 3.763 Individual atomic B min max mean iso aniso Overall: 5.59 67.10 15.00 0.97 520 3271 Protein: 5.59 33.11 10.63 0.97 0 2902 Water: 5.92 67.10 29.27 N/A 520 367 Other: 13.75 27.34 20.54 N/A 0 2 Chain A: 5.64 53.90 12.61 N/A 0 1624 Chain B: 5.59 67.10 12.40 N/A 0 1647 Chain S: 5.92 60.62 30.69 N/A 520 0 Histogram: Values Number of atoms 5.59 - 11.74 2137 11.74 - 17.89 712 17.89 - 24.04 312 24.04 - 30.19 223 30.19 - 36.34 175 36.34 - 42.50 140 42.50 - 48.65 60 48.65 - 54.80 24 54.80 - 60.95 7 60.95 - 67.10 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1363 r_work=0.1201 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1363 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (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): 3.762275 | | target function (ml) not normalized (work): 704640.227553 | | target function (ml) not normalized (free): 14752.249307 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1410 0.1409 0.1497 n_refl.: 191132 remove outliers: r(all,work,free)=0.1410 0.1409 0.1497 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1402 0.1401 0.1491 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191132 remove outliers: r(all,work,free)=0.1202 0.1199 0.1362 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 0.3641 361.245 325.487 0.412 0.949 0.239 13.296-10.522 97.03 97 1 0.2345 481.253 457.581 0.702 0.950 0.188 10.503-8.327 97.80 175 3 0.2111 501.969 496.393 0.862 0.951 0.163 8.318-6.595 100.00 360 8 0.2236 375.591 368.328 0.887 0.950 0.105 6.588-5.215 100.00 711 7 0.1938 345.130 334.602 0.880 0.951 0.100 5.214-4.128 98.38 1367 28 0.1222 504.821 499.216 0.969 0.951 0.039 4.126-3.266 94.74 2603 46 0.1140 460.172 453.457 1.033 0.951 0.005 3.266-2.585 99.86 5447 97 0.1095 310.421 307.141 1.018 0.951 0.000 2.585-2.046 97.45 10613 204 0.0939 234.195 231.746 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0914 138.608 137.317 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0983 74.619 73.901 1.049 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1657 40.030 38.362 1.035 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1377 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1362 | n_water=887 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1199 r_free=0.1362 | n_water=887 | time (s): 106.150 (total time: 108.610) Filter (q & B) r_work=0.1199 r_free=0.1362 | n_water=878 | time (s): 4.690 (total time: 113.300) Compute maps r_work=0.1199 r_free=0.1362 | n_water=878 | time (s): 1.950 (total time: 115.250) Filter (map) r_work=0.1219 r_free=0.1364 | n_water=770 | time (s): 5.000 (total time: 120.250) Find peaks r_work=0.1219 r_free=0.1364 | n_water=770 | time (s): 0.610 (total time: 120.860) Add new water r_work=0.1229 r_free=0.1381 | n_water=985 | time (s): 3.860 (total time: 124.720) Refine new water occ: r_work=0.1196 r_free=0.1351 adp: r_work=0.1196 r_free=0.1353 occ: r_work=0.1194 r_free=0.1350 adp: r_work=0.1194 r_free=0.1351 occ: r_work=0.1192 r_free=0.1348 adp: r_work=0.1192 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1350 r_work=0.1192 r_free=0.1350 | n_water=985 | time (s): 290.070 (total time: 414.790) Filter (q & B) r_work=0.1196 r_free=0.1356 | n_water=901 | time (s): 5.380 (total time: 420.170) Filter (dist only) r_work=0.1197 r_free=0.1355 | n_water=899 | time (s): 115.080 (total time: 535.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560709 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.683793 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1362 0.0163 0.036 1.1 8.0 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.62 1.63 1.776 14.124 15.684 3.763 11.99 13.63 1.64 1.855 14.093 15.684 3.759 Individual atomic B min max mean iso aniso Overall: 5.55 66.48 14.97 0.94 532 3271 Protein: 5.55 30.98 10.56 0.94 0 2902 Water: 6.08 66.48 29.18 N/A 532 367 Other: 13.85 25.60 19.73 N/A 0 2 Chain A: 5.61 53.22 12.50 N/A 0 1624 Chain B: 5.55 66.48 12.31 N/A 0 1647 Chain S: 6.08 60.65 30.75 N/A 532 0 Histogram: Values Number of atoms 5.55 - 11.64 2117 11.64 - 17.73 744 17.73 - 23.83 303 23.83 - 29.92 226 29.92 - 36.02 183 36.02 - 42.11 125 42.11 - 48.20 68 48.20 - 54.30 29 54.30 - 60.39 6 60.39 - 66.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1363 r_work=0.1199 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1364 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1361 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758109 | | target function (ml) not normalized (work): 703856.157088 | | target function (ml) not normalized (free): 14739.736929 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1488 n_refl.: 191131 remove outliers: r(all,work,free)=0.1404 0.1403 0.1488 n_refl.: 191131 overall B=-0.23 to atoms: r(all,work,free)=0.1367 0.1366 0.1466 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 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 0.3780 361.245 322.808 0.406 0.951 0.221 13.296-10.522 97.03 97 1 0.2420 481.253 459.331 0.724 0.952 0.195 10.503-8.327 97.80 175 3 0.2129 501.969 495.574 0.884 0.953 0.143 8.318-6.595 100.00 360 8 0.2216 375.591 369.021 0.905 0.952 0.095 6.588-5.215 100.00 711 7 0.1955 345.130 334.352 0.900 0.953 0.090 5.214-4.128 98.38 1367 28 0.1229 504.821 499.034 0.991 0.953 0.029 4.126-3.266 94.74 2603 46 0.1134 460.172 453.390 1.057 0.953 0.000 3.266-2.585 99.86 5447 97 0.1102 310.421 307.136 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0943 234.195 231.717 1.047 0.952 0.000 2.046-1.619 99.39 21536 464 0.0909 138.608 137.315 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0972 74.619 73.907 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.030 38.360 1.023 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0511 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1361 | n_water=899 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1196 r_free=0.1361 | n_water=899 | time (s): 107.580 (total time: 109.990) Filter (q & B) r_work=0.1196 r_free=0.1360 | n_water=894 | time (s): 4.870 (total time: 114.860) Compute maps r_work=0.1196 r_free=0.1360 | n_water=894 | time (s): 2.110 (total time: 116.970) Filter (map) r_work=0.1219 r_free=0.1359 | n_water=781 | time (s): 5.230 (total time: 122.200) Find peaks r_work=0.1219 r_free=0.1359 | n_water=781 | time (s): 0.560 (total time: 122.760) Add new water r_work=0.1227 r_free=0.1371 | n_water=989 | time (s): 4.650 (total time: 127.410) Refine new water occ: r_work=0.1195 r_free=0.1347 adp: r_work=0.1195 r_free=0.1347 occ: r_work=0.1193 r_free=0.1345 adp: r_work=0.1193 r_free=0.1345 occ: r_work=0.1191 r_free=0.1345 adp: r_work=0.1191 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1345 r_work=0.1191 r_free=0.1345 | n_water=989 | time (s): 218.720 (total time: 346.130) Filter (q & B) r_work=0.1196 r_free=0.1357 | n_water=904 | time (s): 5.220 (total time: 351.350) Filter (dist only) r_work=0.1196 r_free=0.1357 | n_water=902 | time (s): 115.770 (total time: 467.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.632240 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.211103 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1364 0.0165 0.037 1.1 7.7 0.0 0.3 0 0.816 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.64 1.65 1.749 13.832 14.211 3.759 12.03 13.68 1.65 1.754 13.830 14.211 3.760 Individual atomic B min max mean iso aniso Overall: 5.41 66.15 14.73 0.92 535 3271 Protein: 5.41 30.48 10.34 0.92 0 2902 Water: 5.79 66.15 28.84 N/A 535 367 Other: 13.62 25.15 19.38 N/A 0 2 Chain A: 5.45 52.97 12.26 N/A 0 1624 Chain B: 5.41 66.15 12.08 N/A 0 1647 Chain S: 5.79 60.43 30.39 N/A 535 0 Histogram: Values Number of atoms 5.41 - 11.48 2142 11.48 - 17.55 737 17.55 - 23.63 288 23.63 - 29.70 224 29.70 - 35.78 189 35.78 - 41.85 123 41.85 - 47.93 69 47.93 - 54.00 27 54.00 - 60.07 5 60.07 - 66.15 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1368 r_work=0.1203 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1368 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1369 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759301 | | target function (ml) not normalized (work): 704079.538103 | | target function (ml) not normalized (free): 14745.481471 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1369 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1378 0.1376 0.1475 n_refl.: 191131 remove outliers: r(all,work,free)=0.1378 0.1376 0.1475 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1386 0.1384 0.1479 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1195 0.1192 0.1357 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 0.3837 361.245 320.794 0.384 0.995 0.211 13.296-10.522 97.03 97 1 0.2393 481.253 460.214 0.688 0.997 0.165 10.503-8.327 97.80 175 3 0.2199 501.969 493.050 0.850 0.997 0.143 8.318-6.595 100.00 360 8 0.2210 375.591 368.060 0.872 0.997 0.090 6.588-5.215 100.00 711 7 0.1976 345.130 334.160 0.868 0.997 0.080 5.214-4.128 98.38 1367 28 0.1230 504.821 498.516 0.957 0.998 0.024 4.126-3.266 94.74 2603 46 0.1154 460.172 452.765 1.019 0.999 0.000 3.266-2.585 99.86 5447 97 0.1112 310.421 306.832 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0947 234.195 231.600 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.608 137.244 1.026 1.005 0.000 1.619-1.281 98.00 42464 925 0.0956 74.619 73.942 1.014 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.030 38.329 0.981 1.018 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0570 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1357 | n_water=902 | time (s): 2.990 (total time: 2.990) Filter (dist) r_work=0.1192 r_free=0.1356 | n_water=901 | time (s): 111.000 (total time: 113.990) Filter (q & B) r_work=0.1192 r_free=0.1357 | n_water=892 | time (s): 4.430 (total time: 118.420) Compute maps r_work=0.1192 r_free=0.1357 | n_water=892 | time (s): 1.740 (total time: 120.160) Filter (map) r_work=0.1215 r_free=0.1355 | n_water=782 | time (s): 4.310 (total time: 124.470) Find peaks r_work=0.1215 r_free=0.1355 | n_water=782 | time (s): 0.660 (total time: 125.130) Add new water r_work=0.1222 r_free=0.1366 | n_water=997 | time (s): 4.880 (total time: 130.010) Refine new water occ: r_work=0.1189 r_free=0.1343 adp: r_work=0.1189 r_free=0.1344 occ: r_work=0.1187 r_free=0.1342 adp: r_work=0.1187 r_free=0.1342 occ: r_work=0.1186 r_free=0.1340 adp: r_work=0.1185 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1341 r_work=0.1185 r_free=0.1341 | n_water=997 | time (s): 205.050 (total time: 335.060) Filter (q & B) r_work=0.1191 r_free=0.1349 | n_water=907 | time (s): 4.330 (total time: 339.390) Filter (dist only) r_work=0.1191 r_free=0.1348 | n_water=905 | time (s): 117.650 (total time: 457.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.571154 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.563417 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 0.1194 0.1357 0.0162 0.037 1.1 6.6 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.57 1.62 1.711 13.875 14.563 3.758 11.96 13.59 1.63 1.803 13.845 14.563 3.756 Individual atomic B min max mean iso aniso Overall: 5.50 65.06 14.74 0.89 538 3271 Protein: 5.50 28.73 10.36 0.89 0 2902 Water: 5.81 65.06 28.79 N/A 538 367 Other: 13.74 22.68 18.21 N/A 0 2 Chain A: 5.54 52.86 12.25 N/A 0 1624 Chain B: 5.50 65.06 12.08 N/A 0 1647 Chain S: 5.81 60.59 30.44 N/A 538 0 Histogram: Values Number of atoms 5.50 - 11.46 2108 11.46 - 17.41 777 17.41 - 23.37 278 23.37 - 29.32 214 29.32 - 35.28 190 35.28 - 41.23 125 41.23 - 47.19 82 47.19 - 53.15 27 53.15 - 59.10 5 59.10 - 65.06 3 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1359 r_work=0.1196 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1358 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755785 | | target function (ml) not normalized (work): 703420.896840 | | target function (ml) not normalized (free): 14735.866443 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1194 0.1358 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1394 0.1392 0.1488 n_refl.: 191131 remove outliers: r(all,work,free)=0.1394 0.1392 0.1488 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1396 0.1394 0.1489 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1355 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1355 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 0.3902 361.245 319.229 0.411 0.911 0.205 13.296-10.522 97.03 97 1 0.2429 481.253 459.763 0.746 0.912 0.161 10.503-8.327 97.80 175 3 0.2182 501.969 493.863 0.925 0.913 0.140 8.318-6.595 100.00 360 8 0.2215 375.591 368.402 0.949 0.913 0.090 6.588-5.215 100.00 711 7 0.1974 345.130 334.411 0.947 0.913 0.090 5.214-4.128 98.38 1367 28 0.1243 504.821 498.605 1.044 0.914 0.030 4.126-3.266 94.74 2603 46 0.1161 460.172 452.811 1.113 0.915 0.005 3.266-2.585 99.86 5447 97 0.1123 310.421 306.703 1.094 0.916 0.000 2.585-2.046 97.45 10613 204 0.0954 234.195 231.577 1.104 0.918 0.000 2.046-1.619 99.39 21536 464 0.0909 138.608 137.241 1.122 0.921 0.000 1.619-1.281 98.00 42464 925 0.0951 74.619 73.950 1.111 0.926 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.030 38.318 1.077 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1355 | n_water=905 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1193 r_free=0.1355 | n_water=904 | time (s): 112.320 (total time: 114.650) Filter (q & B) r_work=0.1194 r_free=0.1354 | n_water=896 | time (s): 4.650 (total time: 119.300) Compute maps r_work=0.1194 r_free=0.1354 | n_water=896 | time (s): 1.740 (total time: 121.040) Filter (map) r_work=0.1216 r_free=0.1358 | n_water=784 | time (s): 5.390 (total time: 126.430) Find peaks r_work=0.1216 r_free=0.1358 | n_water=784 | time (s): 0.650 (total time: 127.080) Add new water r_work=0.1223 r_free=0.1367 | n_water=994 | time (s): 4.770 (total time: 131.850) Refine new water occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1192 r_free=0.1344 occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1342 r_work=0.1189 r_free=0.1342 | n_water=994 | time (s): 123.480 (total time: 255.330) Filter (q & B) r_work=0.1195 r_free=0.1353 | n_water=894 | time (s): 4.280 (total time: 259.610) Filter (dist only) r_work=0.1196 r_free=0.1352 | n_water=891 | time (s): 113.240 (total time: 372.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568373 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.230776 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 0.1357 0.0160 0.037 1.1 5.6 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.57 1.60 1.695 13.732 14.231 3.757 11.98 13.58 1.60 1.732 13.721 14.231 3.755 Individual atomic B min max mean iso aniso Overall: 5.55 63.86 14.56 0.87 524 3271 Protein: 5.55 28.28 10.36 0.87 0 2902 Water: 5.92 63.86 28.21 N/A 524 367 Other: 13.82 22.25 18.03 N/A 0 2 Chain A: 5.60 52.69 12.21 N/A 0 1624 Chain B: 5.55 63.86 12.06 N/A 0 1647 Chain S: 5.92 60.71 29.68 N/A 524 0 Histogram: Values Number of atoms 5.55 - 11.38 2080 11.38 - 17.22 801 17.22 - 23.05 296 23.05 - 28.88 214 28.88 - 34.71 172 34.71 - 40.54 112 40.54 - 46.37 82 46.37 - 52.20 29 52.20 - 58.03 5 58.03 - 63.86 4 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1358 r_work=0.1198 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1358 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1358 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755087 | | target function (ml) not normalized (work): 703290.185791 | | target function (ml) not normalized (free): 14730.525170 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1358 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1411 0.1409 0.1493 n_refl.: 191131 remove outliers: r(all,work,free)=0.1411 0.1409 0.1493 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1410 0.1409 0.1493 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1358 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 0.3898 361.245 318.412 0.387 0.972 0.211 13.296-10.522 97.03 97 1 0.2415 481.253 459.364 0.699 0.974 0.164 10.503-8.327 97.80 175 3 0.2243 501.969 493.413 0.861 0.975 0.142 8.318-6.595 100.00 360 8 0.2263 375.591 367.857 0.886 0.975 0.095 6.588-5.215 100.00 711 7 0.2000 345.130 334.070 0.885 0.975 0.090 5.214-4.128 98.38 1367 28 0.1259 504.821 498.439 0.978 0.976 0.050 4.126-3.266 94.74 2603 46 0.1172 460.172 452.794 1.044 0.977 0.005 3.266-2.585 99.86 5447 97 0.1128 310.421 306.662 1.026 0.979 0.000 2.585-2.046 97.45 10613 204 0.0960 234.195 231.584 1.034 0.981 0.000 2.046-1.619 99.39 21536 464 0.0910 138.608 137.245 1.051 0.985 0.000 1.619-1.281 98.00 42464 925 0.0947 74.619 73.959 1.042 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.030 38.311 1.011 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1196 r_free=0.1358 After: r_work=0.1197 r_free=0.1358 ================================== NQH flips ================================== r_work=0.1197 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1358 | n_water=891 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1197 r_free=0.1358 | n_water=890 | time (s): 120.630 (total time: 123.180) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=883 | time (s): 4.190 (total time: 127.370) Compute maps r_work=0.1198 r_free=0.1356 | n_water=883 | time (s): 1.820 (total time: 129.190) Filter (map) r_work=0.1216 r_free=0.1355 | n_water=786 | time (s): 4.250 (total time: 133.440) Find peaks r_work=0.1216 r_free=0.1355 | n_water=786 | time (s): 0.670 (total time: 134.110) Add new water r_work=0.1225 r_free=0.1368 | n_water=990 | time (s): 4.690 (total time: 138.800) Refine new water occ: r_work=0.1193 r_free=0.1342 adp: r_work=0.1193 r_free=0.1343 occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1341 occ: r_work=0.1190 r_free=0.1340 adp: r_work=0.1190 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1340 r_work=0.1190 r_free=0.1340 | n_water=990 | time (s): 190.270 (total time: 329.070) Filter (q & B) r_work=0.1194 r_free=0.1347 | n_water=908 | time (s): 5.420 (total time: 334.490) Filter (dist only) r_work=0.1194 r_free=0.1348 | n_water=906 | time (s): 118.770 (total time: 453.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.541055 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.159867 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1351 0.0155 0.038 1.2 8.0 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.51 1.55 1.686 13.777 14.160 3.756 11.96 13.52 1.56 1.681 13.778 14.160 3.755 Individual atomic B min max mean iso aniso Overall: 5.54 63.47 14.67 0.87 539 3271 Protein: 5.54 28.24 10.38 0.87 0 2902 Water: 6.03 63.47 28.41 N/A 539 367 Other: 13.84 22.30 18.07 N/A 0 2 Chain A: 5.65 52.60 12.21 N/A 0 1624 Chain B: 5.54 63.47 12.06 N/A 0 1647 Chain S: 6.03 60.74 30.10 N/A 539 0 Histogram: Values Number of atoms 5.54 - 11.34 2059 11.34 - 17.13 827 17.13 - 22.92 280 22.92 - 28.71 216 28.71 - 34.51 185 34.51 - 40.30 119 40.30 - 46.09 86 46.09 - 51.88 27 51.88 - 57.67 7 57.67 - 63.47 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1352 r_work=0.1197 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1352 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1352 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755007 | | target function (ml) not normalized (work): 703275.270798 | | target function (ml) not normalized (free): 14728.510815 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1369 0.1459 5.6956 5.7573| | 2: 2.94 - 2.33 1.00 7339 128 0.1074 0.1336 5.0766 5.1817| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1147 4.6524 4.7232| | 4: 2.04 - 1.85 1.00 7170 155 0.0903 0.1073 4.3954 4.5826| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0993 4.1501 4.2413| | 6: 1.72 - 1.62 0.99 7102 142 0.0897 0.1098 3.9472 4.0895| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0948 3.7983 3.9115| | 8: 1.54 - 1.47 0.96 6798 152 0.0895 0.1309 3.7015 3.9089| | 9: 1.47 - 1.41 0.98 6938 155 0.0927 0.1135 3.6243 3.7606| | 10: 1.41 - 1.36 0.99 7022 150 0.0977 0.1199 3.5602 3.6856| | 11: 1.36 - 1.32 0.99 6997 151 0.0994 0.1142 3.4885 3.5977| | 12: 1.32 - 1.28 0.98 6975 149 0.1033 0.1126 3.4609 3.5814| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1230 3.4367 3.5585| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1582 3.4328 3.6756| | 15: 1.22 - 1.19 0.98 6956 137 0.1172 0.1255 3.4491 3.5006| | 16: 1.19 - 1.17 0.93 6604 132 0.1252 0.1558 3.4666 3.6592| | 17: 1.17 - 1.14 0.98 6940 135 0.1304 0.1234 3.4354 3.4456| | 18: 1.14 - 1.12 0.98 6875 142 0.1388 0.1711 3.4397 3.5339| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1743 3.4195 3.5919| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1586 3.4101 3.4339| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2132 3.4177 3.5004| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1938 3.4119 3.4129| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2017 3.433 3.484| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2248 3.4352 3.5093| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2505 3.4495 3.5219| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2856 3.4162 3.422| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2805 3.4687 3.3972| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7399 127 0.93 11.50 1.00 0.96 10990.05| | 2: 2.94 - 2.33 7339 128 0.93 12.65 0.99 0.96 5045.25| | 3: 2.33 - 2.04 6939 150 0.96 7.60 1.01 0.95 1687.14| | 4: 2.04 - 1.85 7170 155 0.96 7.66 1.00 0.96 1010.55| | 5: 1.85 - 1.72 7113 159 0.96 8.07 1.00 0.96 636.29| | 6: 1.72 - 1.62 7102 142 0.96 8.03 1.00 0.96 443.94| | 7: 1.62 - 1.54 7104 148 0.96 8.11 1.01 0.97 334.72| | 8: 1.54 - 1.47 6798 152 0.96 8.31 1.01 0.97 280.44| | 9: 1.47 - 1.41 6938 155 0.96 8.55 1.00 0.98 233.89| | 10: 1.41 - 1.36 7022 150 0.96 9.03 1.00 0.97 206.30| | 11: 1.36 - 1.32 6997 151 0.96 9.02 0.99 0.96 177.20| | 12: 1.32 - 1.28 6975 149 0.96 9.01 0.98 0.95 161.75| | 13: 1.28 - 1.25 6907 166 0.96 9.51 1.01 0.96 157.95| | 14: 1.25 - 1.22 7015 112 0.95 10.68 1.01 0.97 162.77| | 15: 1.22 - 1.19 6956 137 0.95 11.25 1.01 0.98 167.00| | 16: 1.19 - 1.17 6604 132 0.95 11.50 1.01 0.96 161.58| | 17: 1.17 - 1.14 6940 135 0.94 12.32 1.01 0.96 155.30| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.95 148.38| | 19: 1.12 - 1.10 6948 106 0.93 14.13 1.00 0.95 150.88| | 20: 1.10 - 1.08 6884 147 0.92 15.18 1.00 0.94 149.67| | 21: 1.08 - 1.07 6852 152 0.91 16.59 1.00 0.93 152.44| | 22: 1.07 - 1.05 6836 135 0.89 18.24 0.99 0.93 154.25| | 23: 1.05 - 1.03 6827 159 0.87 20.44 0.99 0.92 163.91| | 24: 1.03 - 1.02 6784 133 0.85 23.12 0.99 0.93 178.48| | 25: 1.02 - 1.01 6552 130 0.83 25.12 0.98 0.90 181.57| | 26: 1.01 - 0.99 6767 158 0.81 26.64 0.98 0.89 176.68| | 27: 0.99 - 0.98 6647 131 0.82 26.40 0.99 0.87 161.89| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.38 max = 10990.05 mean = 914.23| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.29| |phase err.(test): min = 0.00 max = 89.56 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1352 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1416 0.1414 0.1487 n_refl.: 191131 remove outliers: r(all,work,free)=0.1416 0.1414 0.1487 n_refl.: 191131 overall B=-0.06 to atoms: r(all,work,free)=0.1406 0.1405 0.1481 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3883 356.717 317.737 0.398 0.913 0.205 13.296-10.522 97.03 97 1 0.2371 481.253 460.383 0.724 0.915 0.161 10.503-8.327 97.80 175 3 0.2193 501.969 493.441 0.897 0.916 0.114 8.318-6.595 100.00 360 8 0.2212 375.591 368.430 0.921 0.915 0.090 6.588-5.215 100.00 711 7 0.1968 345.130 334.605 0.919 0.916 0.080 5.214-4.128 98.38 1367 28 0.1247 504.821 498.642 1.015 0.917 0.030 4.126-3.266 94.74 2603 46 0.1171 460.172 452.758 1.084 0.918 0.005 3.266-2.585 99.86 5447 97 0.1124 310.421 306.792 1.065 0.920 0.000 2.585-2.046 97.45 10613 204 0.0961 234.195 231.568 1.073 0.922 0.000 2.046-1.619 99.39 21536 464 0.0911 138.608 137.241 1.089 0.926 0.000 1.619-1.281 98.00 42464 925 0.0947 74.619 73.958 1.078 0.933 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.030 38.299 1.043 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0132 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2029 0.1961 0.080 5.071 5.2 78.0 14.6 805 0.000 1_bss: 0.1794 0.1895 0.080 5.071 5.2 78.1 14.6 805 0.000 1_settarget: 0.1794 0.1895 0.080 5.071 5.2 78.1 14.6 805 0.000 1_nqh: 0.1794 0.1895 0.080 5.071 5.2 78.1 14.6 805 0.000 1_weight: 0.1794 0.1895 0.080 5.071 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1273 0.1485 0.035 1.167 5.2 78.1 14.6 805 0.139 1_adp: 0.1304 0.1553 0.035 1.167 5.2 73.1 15.1 805 0.139 1_regHadp: 0.1303 0.1549 0.035 1.167 5.2 73.1 15.1 805 0.139 1_occ: 0.1287 0.1536 0.035 1.167 5.2 73.1 15.1 805 0.139 2_bss: 0.1281 0.1528 0.035 1.167 5.3 73.2 15.2 805 0.139 2_settarget: 0.1281 0.1528 0.035 1.167 5.3 73.2 15.2 805 0.139 2_updatecdl: 0.1281 0.1528 0.035 1.183 5.3 73.2 15.2 805 0.139 2_nqh: 0.1281 0.1528 0.035 1.183 5.3 73.2 15.2 805 0.139 2_sol: 0.1272 0.1502 0.035 1.183 5.3 73.2 16.4 904 n/a 2_weight: 0.1272 0.1502 0.035 1.183 5.3 73.2 16.4 904 n/a 2_xyzrec: 0.1255 0.1513 0.039 1.132 5.3 73.2 16.4 904 n/a 2_adp: 0.1231 0.1497 0.039 1.132 5.4 70.3 16.5 904 n/a 2_regHadp: 0.1232 0.1499 0.039 1.132 5.4 70.3 16.5 904 n/a 2_occ: 0.1226 0.1494 0.039 1.132 5.4 70.3 16.5 904 n/a 3_bss: 0.1232 0.1500 0.039 1.132 5.4 70.3 16.5 904 n/a 3_settarget: 0.1232 0.1500 0.039 1.132 5.4 70.3 16.5 904 n/a 3_updatecdl: 0.1232 0.1500 0.039 1.134 5.4 70.3 16.5 904 n/a 3_nqh: 0.1232 0.1500 0.039 1.134 5.4 70.3 16.5 904 n/a 3_sol: 0.1250 0.1500 0.039 1.134 5.4 68.2 15.5 880 n/a 3_weight: 0.1250 0.1500 0.039 1.134 5.4 68.2 15.5 880 n/a 3_xyzrec: 0.1239 0.1432 0.035 1.100 5.4 68.2 15.5 880 n/a 3_adp: 0.1230 0.1390 0.035 1.100 5.5 67.7 15.3 880 n/a 3_regHadp: 0.1231 0.1392 0.035 1.100 5.5 67.7 15.3 880 n/a 3_occ: 0.1226 0.1387 0.035 1.100 5.5 67.7 15.3 880 n/a 4_bss: 0.1222 0.1380 0.035 1.100 5.5 67.7 15.3 880 n/a 4_settarget: 0.1222 0.1380 0.035 1.100 5.5 67.7 15.3 880 n/a 4_updatecdl: 0.1222 0.1380 0.035 1.105 5.5 67.7 15.3 880 n/a 4_nqh: 0.1222 0.1380 0.035 1.105 5.5 67.7 15.3 880 n/a 4_sol: 0.1205 0.1368 0.035 1.105 5.5 67.7 15.0 870 n/a 4_weight: 0.1205 0.1368 0.035 1.105 5.5 67.7 15.0 870 n/a 4_xyzrec: 0.1205 0.1368 0.035 1.124 5.5 67.7 15.0 870 n/a 4_adp: 0.1200 0.1367 0.035 1.124 5.5 67.3 15.0 870 n/a 4_regHadp: 0.1200 0.1367 0.035 1.124 5.5 67.3 15.0 870 n/a 4_occ: 0.1198 0.1364 0.035 1.124 5.5 67.3 15.0 870 n/a 5_bss: 0.1196 0.1360 0.035 1.124 5.5 67.3 14.9 870 n/a 5_settarget: 0.1196 0.1360 0.035 1.124 5.5 67.3 14.9 870 n/a 5_updatecdl: 0.1196 0.1360 0.035 1.124 5.5 67.3 14.9 870 n/a 5_nqh: 0.1196 0.1360 0.035 1.124 5.5 67.3 14.9 870 n/a 5_sol: 0.1193 0.1354 0.035 1.124 5.5 67.3 15.0 887 n/a 5_weight: 0.1193 0.1354 0.035 1.124 5.5 67.3 15.0 887 n/a 5_xyzrec: 0.1197 0.1360 0.036 1.128 5.5 67.3 15.0 887 n/a 5_adp: 0.1201 0.1363 0.036 1.128 5.6 67.1 15.0 887 n/a 5_regHadp: 0.1201 0.1363 0.036 1.128 5.6 67.1 15.0 887 n/a 5_occ: 0.1199 0.1363 0.036 1.128 5.6 67.1 15.0 887 n/a 6_bss: 0.1199 0.1362 0.036 1.128 5.5 67.1 15.0 887 n/a 6_settarget: 0.1199 0.1362 0.036 1.128 5.5 67.1 15.0 887 n/a 6_updatecdl: 0.1199 0.1362 0.036 1.128 5.5 67.1 15.0 887 n/a 6_nqh: 0.1199 0.1362 0.036 1.128 5.5 67.1 15.0 887 n/a 6_sol: 0.1197 0.1355 0.036 1.128 5.5 67.1 15.0 899 n/a 6_weight: 0.1197 0.1355 0.036 1.128 5.5 67.1 15.0 899 n/a 6_xyzrec: 0.1199 0.1362 0.036 1.131 5.5 67.1 15.0 899 n/a 6_adp: 0.1199 0.1363 0.036 1.131 5.5 66.5 15.0 899 n/a 6_regHadp: 0.1199 0.1364 0.036 1.131 5.5 66.5 15.0 899 n/a 6_occ: 0.1197 0.1361 0.036 1.131 5.5 66.5 15.0 899 n/a 7_bss: 0.1196 0.1361 0.036 1.131 5.3 66.3 14.7 899 n/a 7_settarget: 0.1196 0.1361 0.036 1.131 5.3 66.3 14.7 899 n/a 7_updatecdl: 0.1196 0.1361 0.036 1.132 5.3 66.3 14.7 899 n/a 7_nqh: 0.1196 0.1361 0.036 1.132 5.3 66.3 14.7 899 n/a 7_sol: 0.1196 0.1357 0.036 1.132 5.3 66.3 14.7 902 n/a 7_weight: 0.1196 0.1357 0.036 1.132 5.3 66.3 14.7 902 n/a 7_xyzrec: 0.1199 0.1364 0.037 1.133 5.3 66.3 14.7 902 n/a 7_adp: 0.1203 0.1368 0.037 1.133 5.4 66.1 14.7 902 n/a 7_regHadp: 0.1203 0.1368 0.037 1.133 5.4 66.1 14.7 902 n/a 7_occ: 0.1201 0.1369 0.037 1.133 5.4 66.1 14.7 902 n/a 8_bss: 0.1192 0.1357 0.037 1.133 5.5 66.2 14.8 902 n/a 8_settarget: 0.1192 0.1357 0.037 1.133 5.5 66.2 14.8 902 n/a 8_updatecdl: 0.1192 0.1357 0.037 1.132 5.5 66.2 14.8 902 n/a 8_nqh: 0.1192 0.1357 0.037 1.132 5.5 66.2 14.8 902 n/a 8_sol: 0.1191 0.1348 0.037 1.132 5.5 66.2 14.8 905 n/a 8_weight: 0.1191 0.1348 0.037 1.132 5.5 66.2 14.8 905 n/a 8_xyzrec: 0.1194 0.1357 0.037 1.128 5.5 66.2 14.8 905 n/a 8_adp: 0.1196 0.1359 0.037 1.128 5.5 65.1 14.7 905 n/a 8_regHadp: 0.1196 0.1359 0.037 1.128 5.5 65.1 14.7 905 n/a 8_occ: 0.1194 0.1358 0.037 1.128 5.5 65.1 14.7 905 n/a 9_bss: 0.1193 0.1355 0.037 1.128 5.5 65.1 14.8 905 n/a 9_settarget: 0.1193 0.1355 0.037 1.128 5.5 65.1 14.8 905 n/a 9_updatecdl: 0.1193 0.1355 0.037 1.128 5.5 65.1 14.8 905 n/a 9_nqh: 0.1193 0.1355 0.037 1.128 5.5 65.1 14.8 905 n/a 9_sol: 0.1196 0.1352 0.037 1.128 5.5 65.1 14.6 891 n/a 9_weight: 0.1196 0.1352 0.037 1.128 5.5 65.1 14.6 891 n/a 9_xyzrec: 0.1197 0.1357 0.037 1.125 5.5 65.1 14.6 891 n/a 9_adp: 0.1198 0.1358 0.037 1.125 5.6 63.9 14.6 891 n/a 9_regHadp: 0.1198 0.1358 0.037 1.125 5.6 63.9 14.6 891 n/a 9_occ: 0.1197 0.1358 0.037 1.125 5.6 63.9 14.6 891 n/a 10_bss: 0.1196 0.1358 0.037 1.125 5.6 63.9 14.6 891 n/a 10_settarget: 0.1196 0.1358 0.037 1.125 5.6 63.9 14.6 891 n/a 10_updatecdl: 0.1196 0.1358 0.037 1.125 5.6 63.9 14.6 891 n/a 10_setrh: 0.1197 0.1358 0.037 1.125 5.6 63.9 14.6 891 n/a 10_nqh: 0.1197 0.1358 0.037 1.125 5.6 63.9 14.6 891 n/a 10_sol: 0.1194 0.1348 0.037 1.125 5.6 63.9 14.7 906 n/a 10_weight: 0.1194 0.1348 0.037 1.125 5.6 63.9 14.7 906 n/a 10_xyzrec: 0.1196 0.1351 0.038 1.155 5.6 63.9 14.7 906 n/a 10_adp: 0.1196 0.1352 0.038 1.155 5.5 63.5 14.7 906 n/a 10_regHadp: 0.1197 0.1352 0.038 1.155 5.5 63.5 14.7 906 n/a 10_occ: 0.1195 0.1352 0.038 1.155 5.5 63.5 14.7 906 n/a end: 0.1194 0.1351 0.038 1.155 5.5 63.4 14.6 906 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4511945_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4511945_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.7400 Refinement macro-cycles (run) : 11714.8100 Write final files (write_after_run_outputs) : 181.4300 Total : 11901.9800 Total CPU time: 3.32 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:35:35 PST -0800 (1736735735.90 s) Start R-work = 0.1794, R-free = 0.1895 Final R-work = 0.1194, R-free = 0.1351 =============================================================================== Job complete usr+sys time: 12248.40 seconds wall clock time: 205 minutes 8.37 seconds (12308.37 seconds total)