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_3580741.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3580741.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3580741.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 2.697 distance_ideal: 2.720 ideal - model: 0.023 slack: 0.000 delta_slack: 0.023 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: 2.753 distance_ideal: 2.710 ideal - model: -0.043 slack: 0.000 delta_slack: -0.043 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 135.7 milliseconds Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.02: 701 1.02 - 1.25: 2555 1.25 - 1.48: 1499 1.48 - 1.71: 1148 1.71 - 1.94: 31 Bond restraints: 5934 Sorted by residual: bond pdb=" C ILE B 121 " pdb=" O ILE B 121 " ideal model delta sigma weight residual 1.236 1.006 0.230 9.90e-03 1.02e+04 5.41e+02 bond pdb=" N ALA A 104 " pdb=" CA ALA A 104 " ideal model delta sigma weight residual 1.455 1.711 -0.256 1.25e-02 6.40e+03 4.19e+02 bond pdb=" NH1 ARG A 83 " pdb="HH11 ARG A 83 " ideal model delta sigma weight residual 0.860 1.255 -0.395 2.00e-02 2.50e+03 3.91e+02 bond pdb=" C GLY A 159 " pdb=" N THR A 160 " ideal model delta sigma weight residual 1.332 1.068 0.263 1.34e-02 5.57e+03 3.86e+02 bond pdb=" NH2 ARG B 149 " pdb="HH22 ARG B 149 " ideal model delta sigma weight residual 0.860 1.249 -0.389 2.00e-02 2.50e+03 3.78e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.98: 6515 4.98 - 9.95: 3422 9.95 - 14.93: 806 14.93 - 19.91: 62 19.91 - 24.88: 5 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" O ILE A 134 " ideal model delta sigma weight residual 119.19 131.72 -12.53 6.50e-01 2.37e+00 3.71e+02 angle pdb=" CG HIS B 116 " pdb=" CD2 HIS B 116 " pdb=" NE2 HIS B 116 " ideal model delta sigma weight residual 107.20 121.88 -14.68 1.00e+00 1.00e+00 2.15e+02 angle pdb=" CD2 TRP B 146 " pdb=" CE2 TRP B 146 " pdb=" CZ2 TRP B 146 " ideal model delta sigma weight residual 122.40 108.15 14.25 1.00e+00 1.00e+00 2.03e+02 angle pdb=" O LYS A 131 " pdb=" C LYS A 131 " pdb=" N ASP A 132 " ideal model delta sigma weight residual 122.11 137.76 -15.65 1.15e+00 7.56e-01 1.85e+02 angle pdb=" CA VAL B 181 " pdb=" C VAL B 181 " pdb=" O VAL B 181 " ideal model delta sigma weight residual 121.27 135.23 -13.96 1.04e+00 9.25e-01 1.80e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 1845 16.91 - 33.82: 137 33.82 - 50.74: 45 50.74 - 67.65: 19 67.65 - 84.56: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta harmonic sigma weight residual -180.00 -155.95 -24.05 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " pdb=" CA PRO A 11 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " pdb=" CA PRO B 11 " ideal model delta harmonic sigma weight residual 180.00 159.63 20.37 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.220: 209 0.220 - 0.441: 164 0.441 - 0.661: 80 0.661 - 0.881: 33 0.881 - 1.101: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ALA A 18 " pdb=" N ALA A 18 " pdb=" C ALA A 18 " pdb=" CB ALA A 18 " both_signs ideal model delta sigma weight residual False 2.48 3.59 -1.10 2.00e-01 2.50e+01 3.03e+01 chirality pdb=" CA ALA A 161 " pdb=" N ALA A 161 " pdb=" C ALA A 161 " pdb=" CB ALA A 161 " both_signs ideal model delta sigma weight residual False 2.48 3.52 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA ILE B 121 " pdb=" N ILE B 121 " pdb=" C ILE B 121 " pdb=" CB ILE B 121 " both_signs ideal model delta sigma weight residual False 2.43 3.47 -1.03 2.00e-01 2.50e+01 2.66e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.034 2.00e-02 2.50e+03 6.78e-02 1.84e+02 pdb=" CG TRP A 139 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.114 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.059 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.070 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.061 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.091 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.040 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.040 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.069 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.024 2.00e-02 2.50e+03 7.46e-02 1.67e+02 pdb=" CG PHE A 119 " -0.086 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.129 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.117 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.132 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.001 2.00e-02 2.50e+03 6.29e-02 1.58e+02 pdb=" CG TRP B 146 " -0.149 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.090 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.096 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.110 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.050 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.006 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.038 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.018 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.051 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.029 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.53: 19 1.53 - 2.30: 1692 2.30 - 3.06: 21516 3.06 - 3.83: 33227 3.83 - 4.60: 53746 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110200 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.761 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.945 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.060 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.172 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.192 2.620 ... (remaining 110195 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_3580741_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= 0.2032 r_free= 0.1959 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.302517 | | target function (ml) not normalized (work): 805917.284022 | | target function (ml) not normalized (free): 16525.051894 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2119 0.1897 6.6914 6.3068| | 2: 2.94 - 2.33 1.00 7339 128 0.1622 0.1435 5.5305 5.5236| | 3: 2.33 - 2.04 0.96 6939 150 0.1628 0.1605 5.1502 5.1417| | 4: 2.04 - 1.85 1.00 7170 155 0.1773 0.1539 4.9706 5.0021| | 5: 1.85 - 1.72 0.99 7113 159 0.1942 0.1842 4.8073 4.836| | 6: 1.72 - 1.62 0.99 7102 142 0.1993 0.1935 4.6642 4.6947| | 7: 1.62 - 1.54 0.99 7104 148 0.2003 0.1882 4.5634 4.5784| | 8: 1.54 - 1.47 0.96 6798 152 0.2016 0.2374 4.4677 4.5951| | 9: 1.47 - 1.41 0.98 6938 155 0.2114 0.1908 4.4004 4.2791| | 10: 1.41 - 1.36 0.99 7022 150 0.2124 0.2065 4.3195 4.3286| | 11: 1.36 - 1.32 0.99 6997 151 0.2097 0.1797 4.2349 4.1102| | 12: 1.32 - 1.28 0.98 6976 149 0.2094 0.2222 4.1818 4.324| | 13: 1.28 - 1.25 0.98 6907 166 0.2004 0.2147 4.1151 4.1759| | 14: 1.25 - 1.22 0.98 7015 113 0.2100 0.2050 4.0818 4.1184| | 15: 1.22 - 1.19 0.98 6957 137 0.2125 0.2013 4.0512 4.0104| | 16: 1.19 - 1.17 0.93 6604 132 0.2110 0.2371 4.0078 4.145| | 17: 1.17 - 1.14 0.98 6941 135 0.2163 0.2075 3.9634 4.0513| | 18: 1.14 - 1.12 0.98 6875 142 0.2184 0.2564 3.9216 4.0199| | 19: 1.12 - 1.10 0.97 6949 106 0.2233 0.2638 3.8704 4.0062| | 20: 1.10 - 1.08 0.97 6884 147 0.2342 0.2338 3.8342 3.8865| | 21: 1.08 - 1.07 0.97 6852 152 0.2421 0.2544 3.7896 3.7811| | 22: 1.07 - 1.05 0.97 6838 135 0.2565 0.2431 3.7562 3.6973| | 23: 1.05 - 1.03 0.97 6829 159 0.2723 0.2733 3.7329 3.8132| | 24: 1.03 - 1.02 0.96 6785 133 0.2859 0.2829 3.6958 3.7804| | 25: 1.02 - 1.01 0.93 6552 130 0.3104 0.2846 3.6818 3.7006| | 26: 1.01 - 0.99 0.96 6767 158 0.3204 0.3326 3.6266 3.672| | 27: 0.99 - 0.98 0.94 6648 131 0.3411 0.3120 3.6447 3.5747| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.25 0.91 0.97 34766.60| | 2: 2.94 - 2.33 7339 128 0.86 20.81 1.08 1.02 14621.54| | 3: 2.33 - 2.04 6939 150 0.93 12.16 1.11 1.04 3895.32| | 4: 2.04 - 1.85 7170 155 0.92 13.40 1.12 1.05 2676.41| | 5: 1.85 - 1.72 7113 159 0.91 15.75 1.12 1.06 2087.59| | 6: 1.72 - 1.62 7102 142 0.89 17.20 1.11 1.07 1704.64| | 7: 1.62 - 1.54 7104 148 0.89 17.69 1.11 1.08 1373.34| | 8: 1.54 - 1.47 6798 152 0.89 17.96 1.10 1.08 1122.31| | 9: 1.47 - 1.41 6938 155 0.90 17.44 1.11 1.07 858.41| | 10: 1.41 - 1.36 7022 150 0.89 18.32 1.09 1.06 729.19| | 11: 1.36 - 1.32 6997 151 0.89 18.02 1.08 1.05 620.02| | 12: 1.32 - 1.28 6976 149 0.88 19.13 1.08 1.05 613.63| | 13: 1.28 - 1.25 6907 166 0.88 19.32 1.07 1.05 583.28| | 14: 1.25 - 1.22 7015 113 0.87 20.69 1.08 1.05 573.44| | 15: 1.22 - 1.19 6957 137 0.87 20.64 1.08 1.04 533.33| | 16: 1.19 - 1.17 6604 132 0.86 21.08 1.07 1.03 517.05| | 17: 1.17 - 1.14 6941 135 0.85 22.61 1.08 1.02 502.17| | 18: 1.14 - 1.12 6875 142 0.84 23.28 1.08 1.00 469.94| | 19: 1.12 - 1.10 6949 106 0.84 23.64 1.07 0.99 425.75| | 20: 1.10 - 1.08 6884 147 0.84 23.36 1.06 0.97 363.47| | 21: 1.08 - 1.07 6852 152 0.84 23.67 1.06 0.97 329.60| | 22: 1.07 - 1.05 6838 135 0.83 25.12 1.06 0.96 314.21| | 23: 1.05 - 1.03 6829 159 0.80 27.31 1.06 0.96 319.08| | 24: 1.03 - 1.02 6785 133 0.78 29.51 1.05 0.96 328.31| | 25: 1.02 - 1.01 6552 130 0.77 30.74 1.02 0.92 310.48| | 26: 1.01 - 0.99 6767 158 0.75 32.20 1.03 0.90 288.72| | 27: 0.99 - 0.98 6648 131 0.76 31.40 1.03 0.89 257.84| |alpha: min = 0.89 max = 1.08 mean = 1.01| |beta: min = 257.84 max = 34766.60 mean = 2760.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.50| |phase err.(test): min = 0.00 max = 89.40 mean = 21.53| |-----------------------------------------------------------------------------| ----------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 0.263 2950 Z= 5.437 Angle : 5.186 16.519 4018 Z= 3.673 Chirality : 0.376 1.101 492 Planarity : 0.032 0.113 512 Dihedral : 12.798 84.559 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.89 % Favored : 95.60 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 30.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.37), residues: 386 helix: -2.47 (0.33), residues: 146 sheet: -1.18 (0.50), residues: 86 loop : -0.78 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.115 0.022 ARG B 175 TYR 0.109 0.039 TYR A 67 PHE 0.119 0.036 PHE A 164 TRP 0.144 0.050 TRP B 146 HIS 0.053 0.021 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= 0.2032 r_free= 0.1959 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.302517 | | target function (ml) not normalized (work): 805917.284022 | | target function (ml) not normalized (free): 16525.051894 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2030 0.2032 0.1959 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2030 0.2032 0.1959 n_refl.: 191155 remove outliers: r(all,work,free)=0.2030 0.2033 0.1959 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2032 0.2034 0.1960 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1798 0.1797 0.1887 n_refl.: 191145 remove outliers: r(all,work,free)=0.1796 0.1794 0.1887 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.4071 398.008 290.975 0.422 0.932 0.299 13.296-10.522 98.02 98 1 0.2467 527.329 513.856 0.768 0.933 0.250 10.503-8.327 98.90 177 3 0.2497 564.205 556.986 0.945 0.934 0.227 8.318-6.595 100.00 360 8 0.2452 414.736 403.611 0.948 0.933 0.180 6.588-5.215 100.00 711 7 0.2227 381.101 366.388 0.934 0.933 0.140 5.214-4.128 98.38 1367 28 0.1496 557.435 549.913 1.048 0.933 0.070 4.126-3.266 94.74 2603 46 0.1322 508.132 499.081 1.116 0.932 0.028 3.266-2.585 99.86 5447 97 0.1435 342.774 338.030 1.095 0.929 0.000 2.585-2.046 97.45 10613 204 0.1398 258.603 254.438 1.104 0.926 0.000 2.046-1.619 99.39 21536 464 0.1621 153.054 149.779 1.131 0.920 0.000 1.619-1.281 98.00 42464 925 0.1915 82.395 80.237 1.122 0.911 0.000 1.281-0.980 96.53 101826 2056 0.2313 44.203 41.700 1.122 0.895 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0183 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1794 r_free=0.1887 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 r_work=0.1801 r_free=0.1897 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.256528 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 567.944381 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 0.1269 0.1504 0.0236 0.039 1.2 11.0 0.0 0.0 0 11.128 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.69 15.04 2.36 1.117 13.122 567.944 0.018 12.96 15.71 2.75 1.238 13.371 567.944 0.017 Individual atomic B min max mean iso aniso Overall: 5.25 73.05 15.06 1.40 435 3274 Protein: 5.25 40.61 11.02 1.40 0 2902 Water: 6.39 73.05 29.60 N/A 435 370 Other: 16.21 29.60 22.90 N/A 0 2 Chain A: 5.29 60.25 13.08 N/A 0 1626 Chain B: 5.25 73.05 12.80 N/A 0 1648 Chain S: 11.98 66.47 31.03 N/A 435 0 Histogram: Values Number of atoms 5.25 - 12.03 2177 12.03 - 18.81 626 18.81 - 25.59 314 25.59 - 32.37 263 32.37 - 39.15 153 39.15 - 45.93 112 45.93 - 52.71 41 52.71 - 59.49 17 59.49 - 66.27 4 66.27 - 73.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1571 r_work=0.1296 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1566 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1280 r_free = 0.1558 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015430 | | target function (ls_wunit_k1) not normalized (work): 2889.952381 | | target function (ls_wunit_k1) not normalized (free): 117.312327 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1285 0.1280 0.1558 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1468 0.1465 0.1637 n_refl.: 191136 remove outliers: r(all,work,free)=0.1468 0.1465 0.1637 n_refl.: 191136 overall B=0.15 to atoms: r(all,work,free)=0.1491 0.1488 0.1647 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1553 n_refl.: 191136 remove outliers: r(all,work,free)=0.1280 0.1275 0.1552 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3588 398.008 377.393 0.464 1.003 0.276 13.296-10.522 98.02 98 1 0.2041 527.329 521.137 0.716 1.004 0.250 10.503-8.327 98.90 177 3 0.1717 564.205 561.874 0.849 1.004 0.203 8.318-6.595 100.00 360 8 0.1715 414.736 412.931 0.872 1.004 0.150 6.588-5.215 100.00 711 7 0.1525 381.101 373.593 0.852 1.004 0.140 5.214-4.128 98.38 1367 28 0.0899 557.435 554.977 0.937 1.005 0.055 4.126-3.266 94.74 2603 46 0.0829 508.132 504.296 1.001 1.005 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.318 0.984 1.005 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.397 0.995 1.005 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.400 1.013 1.006 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.401 1.005 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.159 0.983 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0353 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1552 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1552 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1552 | n_water=805 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1280 r_free=0.1559 | n_water=794 | time (s): 102.820 (total time: 105.710) Filter (q & B) r_work=0.1280 r_free=0.1558 | n_water=790 | time (s): 4.300 (total time: 110.010) Compute maps r_work=0.1280 r_free=0.1558 | n_water=790 | time (s): 2.500 (total time: 112.510) Filter (map) r_work=0.1306 r_free=0.1532 | n_water=651 | time (s): 5.800 (total time: 118.310) Find peaks r_work=0.1306 r_free=0.1532 | n_water=651 | time (s): 0.840 (total time: 119.150) Add new water r_work=0.1329 r_free=0.1562 | n_water=967 | time (s): 4.900 (total time: 124.050) Refine new water occ: r_work=0.1286 r_free=0.1528 adp: r_work=0.1273 r_free=0.1522 occ: r_work=0.1275 r_free=0.1521 adp: r_work=0.1268 r_free=0.1518 occ: r_work=0.1269 r_free=0.1517 adp: r_work=0.1268 r_free=0.1516 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1516 r_work=0.1268 r_free=0.1516 | n_water=967 | time (s): 83.900 (total time: 207.950) Filter (q & B) r_work=0.1272 r_free=0.1517 | n_water=893 | time (s): 4.910 (total time: 212.860) Filter (dist only) r_work=0.1272 r_free=0.1515 | n_water=892 | time (s): 112.770 (total time: 325.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.513078 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 588.986000 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 0.1256 0.1522 0.0267 0.042 1.1 18.0 0.0 0.0 0 11.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.22 2.67 2.044 15.134 588.986 0.014 12.35 15.17 2.83 2.417 15.217 588.986 0.014 Individual atomic B min max mean iso aniso Overall: 5.41 69.19 16.28 1.20 524 3272 Protein: 5.41 40.56 11.00 1.20 0 2902 Water: 6.71 69.19 33.45 N/A 524 368 Other: 16.46 32.34 24.40 N/A 0 2 Chain A: 5.59 56.73 13.01 N/A 0 1624 Chain B: 5.41 68.23 12.85 N/A 0 1648 Chain S: 13.04 69.19 37.22 N/A 524 0 Histogram: Values Number of atoms 5.41 - 11.79 2080 11.79 - 18.17 706 18.17 - 24.55 268 24.55 - 30.93 212 30.93 - 37.30 182 37.30 - 43.68 168 43.68 - 50.06 95 50.06 - 56.44 51 56.44 - 62.81 22 62.81 - 69.19 12 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1517 r_work=0.1235 r_free=0.1518 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1518 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1518 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.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1518 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013361 | | target function (ls_wunit_k1) not normalized (work): 2502.502792 | | target function (ls_wunit_k1) not normalized (free): 102.616605 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1518 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1601 n_refl.: 191135 remove outliers: r(all,work,free)=0.1434 0.1431 0.1601 n_refl.: 191135 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1428 0.1599 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1526 n_refl.: 191135 remove outliers: r(all,work,free)=0.1241 0.1236 0.1526 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3134 398.008 374.599 0.475 0.963 0.260 13.296-10.522 98.02 98 1 0.1853 527.329 517.010 0.753 0.964 0.213 10.503-8.327 98.90 177 3 0.1393 564.205 567.366 0.917 0.964 0.199 8.318-6.595 100.00 360 8 0.1540 414.736 414.531 0.935 0.964 0.130 6.588-5.215 100.00 711 7 0.1324 381.101 377.042 0.914 0.964 0.130 5.214-4.128 98.38 1367 28 0.0820 557.435 556.059 0.995 0.964 0.080 4.126-3.266 94.74 2603 46 0.0761 508.132 505.530 1.059 0.964 0.019 3.266-2.585 99.86 5447 97 0.0862 342.774 341.352 1.046 0.963 0.010 2.585-2.046 97.45 10613 204 0.0901 258.603 256.769 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1052 153.054 151.618 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1261 82.395 81.342 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.214 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0577 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1526 | n_water=892 | time (s): 3.260 (total time: 3.260) Filter (dist) r_work=0.1238 r_free=0.1527 | n_water=886 | time (s): 119.640 (total time: 122.900) Filter (q & B) r_work=0.1238 r_free=0.1527 | n_water=885 | time (s): 5.960 (total time: 128.860) Compute maps r_work=0.1238 r_free=0.1527 | n_water=885 | time (s): 2.460 (total time: 131.320) Filter (map) r_work=0.1277 r_free=0.1523 | n_water=692 | time (s): 5.070 (total time: 136.390) Find peaks r_work=0.1277 r_free=0.1523 | n_water=692 | time (s): 0.830 (total time: 137.220) Add new water r_work=0.1299 r_free=0.1551 | n_water=1010 | time (s): 4.840 (total time: 142.060) Refine new water occ: r_work=0.1253 r_free=0.1512 adp: r_work=0.1254 r_free=0.1512 occ: r_work=0.1249 r_free=0.1510 adp: r_work=0.1249 r_free=0.1510 occ: r_work=0.1245 r_free=0.1509 adp: r_work=0.1244 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1508 r_work=0.1244 r_free=0.1508 | n_water=1010 | time (s): 214.890 (total time: 356.950) Filter (q & B) r_work=0.1249 r_free=0.1519 | n_water=882 | time (s): 4.150 (total time: 361.100) Filter (dist only) r_work=0.1250 r_free=0.1518 | n_water=881 | time (s): 110.070 (total time: 471.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.720555 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.029289 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1237 0.1442 0.0205 0.036 1.1 6.6 0.0 0.0 0 0.860 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.42 2.05 1.932 14.635 16.029 3.942 12.31 13.99 1.68 2.217 14.543 16.029 3.899 Individual atomic B min max mean iso aniso Overall: 5.53 67.91 15.34 1.06 514 3271 Protein: 5.53 36.99 10.76 1.06 0 2902 Water: 6.69 67.91 30.43 N/A 514 367 Other: 14.06 27.90 20.98 N/A 0 2 Chain A: 5.53 55.93 12.79 N/A 0 1624 Chain B: 5.54 67.91 12.56 N/A 0 1647 Chain S: 15.12 62.72 32.33 N/A 514 0 Histogram: Values Number of atoms 5.53 - 11.77 2134 11.77 - 18.01 680 18.01 - 24.25 294 24.25 - 30.48 237 30.48 - 36.72 179 36.72 - 42.96 154 42.96 - 49.20 70 49.20 - 55.44 26 55.44 - 61.67 9 61.67 - 67.91 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1399 r_work=0.1232 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1400 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1392 target_work(ml) = 3.893 | | 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.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.893075 | | target function (ml) not normalized (work): 729149.500124 | | target function (ml) not normalized (free): 15232.997811 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1226 0.1391 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1436 0.1435 0.1495 n_refl.: 191135 remove outliers: r(all,work,free)=0.1436 0.1435 0.1495 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1430 0.1429 0.1491 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1390 n_refl.: 191135 remove outliers: r(all,work,free)=0.1226 0.1223 0.1390 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3743 398.008 361.349 0.424 0.947 0.256 13.296-10.522 98.02 98 1 0.2491 527.329 506.408 0.716 0.948 0.225 10.503-8.327 98.35 176 3 0.1962 556.299 557.138 0.885 0.948 0.184 8.318-6.595 100.00 360 8 0.2058 414.736 410.725 0.896 0.948 0.124 6.588-5.215 100.00 711 7 0.1782 381.101 371.015 0.885 0.948 0.100 5.214-4.128 98.38 1367 28 0.1147 557.435 552.013 0.972 0.948 0.070 4.126-3.266 94.74 2603 46 0.1079 508.132 501.051 1.032 0.948 0.009 3.266-2.585 99.86 5447 97 0.1078 342.774 339.161 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0966 258.603 255.774 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0976 153.054 151.405 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1055 82.395 81.476 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.314 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1023 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1390 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1390 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1390 | n_water=881 | time (s): 3.370 (total time: 3.370) Filter (dist) r_work=0.1223 r_free=0.1389 | n_water=878 | time (s): 117.540 (total time: 120.910) Filter (q & B) r_work=0.1224 r_free=0.1387 | n_water=862 | time (s): 4.580 (total time: 125.490) Compute maps r_work=0.1224 r_free=0.1387 | n_water=862 | time (s): 2.000 (total time: 127.490) Filter (map) r_work=0.1247 r_free=0.1387 | n_water=728 | time (s): 4.130 (total time: 131.620) Find peaks r_work=0.1247 r_free=0.1387 | n_water=728 | time (s): 0.580 (total time: 132.200) Add new water r_work=0.1260 r_free=0.1402 | n_water=963 | time (s): 3.950 (total time: 136.150) Refine new water occ: r_work=0.1213 r_free=0.1368 adp: r_work=0.1205 r_free=0.1363 occ: r_work=0.1203 r_free=0.1365 adp: r_work=0.1203 r_free=0.1364 occ: r_work=0.1201 r_free=0.1366 adp: r_work=0.1200 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1364 r_work=0.1200 r_free=0.1364 | n_water=963 | time (s): 362.670 (total time: 498.820) Filter (q & B) r_work=0.1205 r_free=0.1370 | n_water=881 | time (s): 4.300 (total time: 503.120) Filter (dist only) r_work=0.1206 r_free=0.1370 | n_water=879 | time (s): 112.730 (total time: 615.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568803 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.205281 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1368 0.0161 0.036 1.1 6.3 0.0 0.0 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.68 1.61 1.837 14.269 16.205 3.875 11.99 13.66 1.66 2.013 14.205 16.205 3.865 Individual atomic B min max mean iso aniso Overall: 5.49 67.28 15.02 0.99 512 3271 Protein: 5.49 33.26 10.64 0.99 0 2902 Water: 5.72 67.28 29.49 N/A 512 367 Other: 13.90 26.28 20.09 N/A 0 2 Chain A: 5.59 54.27 12.60 N/A 0 1624 Chain B: 5.49 67.28 12.42 N/A 0 1647 Chain S: 5.72 62.77 31.06 N/A 512 0 Histogram: Values Number of atoms 5.49 - 11.67 2115 11.67 - 17.85 733 17.85 - 24.03 280 24.03 - 30.21 251 30.21 - 36.38 173 36.38 - 42.56 140 42.56 - 48.74 61 48.74 - 54.92 23 54.92 - 61.10 5 61.10 - 67.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1366 r_work=0.1199 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1366 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1365 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863272 | | target function (ml) not normalized (work): 723563.860803 | | target function (ml) not normalized (free): 15136.561821 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1364 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1420 0.1419 0.1485 n_refl.: 191134 remove outliers: r(all,work,free)=0.1420 0.1419 0.1485 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1413 0.1412 0.1480 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1363 n_refl.: 191134 remove outliers: r(all,work,free)=0.1198 0.1195 0.1363 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 0.3769 361.337 321.239 0.408 0.947 0.241 13.296-10.522 97.03 97 1 0.2498 478.322 456.126 0.708 0.948 0.209 10.503-8.327 97.80 175 3 0.2054 502.097 499.161 0.866 0.949 0.200 8.318-6.595 100.00 360 8 0.2177 375.686 370.827 0.889 0.948 0.113 6.588-5.215 100.00 711 7 0.1876 345.218 335.555 0.885 0.948 0.093 5.214-4.128 98.38 1367 28 0.1196 504.949 500.122 0.974 0.948 0.080 4.126-3.266 94.74 2603 46 0.1115 460.288 453.905 1.033 0.949 0.005 3.266-2.585 99.86 5447 97 0.1085 310.499 307.385 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0936 234.254 231.809 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0912 138.643 137.333 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0987 74.637 73.922 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.040 38.379 1.037 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1186 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1363 | n_water=879 | time (s): 2.740 (total time: 2.740) Filter (dist) r_work=0.1195 r_free=0.1363 | n_water=878 | time (s): 123.030 (total time: 125.770) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=866 | time (s): 4.650 (total time: 130.420) Compute maps r_work=0.1196 r_free=0.1362 | n_water=866 | time (s): 1.740 (total time: 132.160) Filter (map) r_work=0.1216 r_free=0.1369 | n_water=744 | time (s): 4.450 (total time: 136.610) Find peaks r_work=0.1216 r_free=0.1369 | n_water=744 | time (s): 0.550 (total time: 137.160) Add new water r_work=0.1229 r_free=0.1383 | n_water=958 | time (s): 3.980 (total time: 141.140) Refine new water occ: r_work=0.1195 r_free=0.1348 adp: r_work=0.1195 r_free=0.1349 occ: r_work=0.1192 r_free=0.1347 adp: r_work=0.1192 r_free=0.1347 occ: r_work=0.1191 r_free=0.1346 adp: r_work=0.1190 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1347 r_work=0.1190 r_free=0.1347 | n_water=958 | time (s): 222.110 (total time: 363.250) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=889 | time (s): 5.600 (total time: 368.850) Filter (dist only) r_work=0.1194 r_free=0.1355 | n_water=888 | time (s): 111.170 (total time: 480.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.537276 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.965797 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 0.1362 0.0165 0.037 1.1 7.5 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.62 1.65 1.784 14.119 14.966 3.764 12.01 13.65 1.65 1.824 14.100 14.966 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 67.03 14.97 0.95 522 3270 Protein: 5.58 31.93 10.58 0.95 0 2902 Water: 5.78 67.03 29.30 N/A 522 366 Other: 13.77 25.68 19.72 N/A 0 2 Chain A: 5.58 53.64 12.53 N/A 0 1624 Chain B: 5.58 67.03 12.33 N/A 0 1646 Chain S: 5.78 62.72 30.88 N/A 522 0 Histogram: Values Number of atoms 5.58 - 11.72 2143 11.72 - 17.87 723 17.87 - 24.01 290 24.01 - 30.16 233 30.16 - 36.30 173 36.30 - 42.45 132 42.45 - 48.59 66 48.59 - 54.74 25 54.74 - 60.88 5 60.88 - 67.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1365 r_work=0.1201 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1366 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1365 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761189 | | target function (ml) not normalized (work): 704433.039619 | | target function (ml) not normalized (free): 14747.309993 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1365 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1405 0.1404 0.1486 n_refl.: 191131 remove outliers: r(all,work,free)=0.1405 0.1404 0.1486 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1398 0.1396 0.1481 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1364 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 0.3816 361.337 325.888 0.405 0.950 0.225 13.296-10.522 97.03 97 1 0.2529 478.322 459.562 0.710 0.951 0.200 10.503-8.327 97.80 175 3 0.2047 502.097 498.182 0.860 0.952 0.200 8.318-6.595 100.00 360 8 0.2133 375.686 371.389 0.885 0.951 0.104 6.588-5.215 100.00 711 7 0.1907 345.218 335.340 0.881 0.952 0.083 5.214-4.128 98.38 1367 28 0.1206 504.949 500.045 0.972 0.952 0.070 4.126-3.266 94.74 2603 46 0.1142 460.288 453.789 1.031 0.952 0.005 3.266-2.585 99.86 5447 97 0.1105 310.499 307.213 1.018 0.952 0.000 2.585-2.046 97.45 10613 204 0.0947 234.254 231.790 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0913 138.643 137.349 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0979 74.637 73.923 1.047 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1656 40.040 38.369 1.032 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1314 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1364 | n_water=888 | time (s): 3.100 (total time: 3.100) Filter (dist) r_work=0.1199 r_free=0.1364 | n_water=888 | time (s): 117.440 (total time: 120.540) Filter (q & B) r_work=0.1199 r_free=0.1364 | n_water=876 | time (s): 5.380 (total time: 125.920) Compute maps r_work=0.1199 r_free=0.1364 | n_water=876 | time (s): 2.100 (total time: 128.020) Filter (map) r_work=0.1219 r_free=0.1363 | n_water=758 | time (s): 5.610 (total time: 133.630) Find peaks r_work=0.1219 r_free=0.1363 | n_water=758 | time (s): 0.750 (total time: 134.380) Add new water r_work=0.1231 r_free=0.1381 | n_water=980 | time (s): 4.050 (total time: 138.430) Refine new water occ: r_work=0.1196 r_free=0.1355 adp: r_work=0.1196 r_free=0.1355 occ: r_work=0.1194 r_free=0.1354 adp: r_work=0.1193 r_free=0.1354 occ: r_work=0.1192 r_free=0.1355 adp: r_work=0.1191 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1354 r_work=0.1191 r_free=0.1354 | n_water=980 | time (s): 260.740 (total time: 399.170) Filter (q & B) r_work=0.1196 r_free=0.1360 | n_water=903 | time (s): 4.360 (total time: 403.530) Filter (dist only) r_work=0.1196 r_free=0.1358 | n_water=902 | time (s): 114.970 (total time: 518.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.503972 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.779459 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1361 0.0161 0.038 1.1 6.8 0.0 0.3 0 0.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.61 1.61 1.759 14.065 14.779 3.762 12.02 13.64 1.62 1.872 14.025 14.779 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 66.06 14.90 0.91 536 3270 Protein: 5.58 29.66 10.49 0.91 0 2902 Water: 5.80 66.06 29.09 N/A 536 366 Other: 13.84 23.32 18.58 N/A 0 2 Chain A: 5.63 52.84 12.40 N/A 0 1624 Chain B: 5.58 66.06 12.21 N/A 0 1646 Chain S: 5.80 62.67 30.75 N/A 536 0 Histogram: Values Number of atoms 5.58 - 11.63 2122 11.63 - 17.67 766 17.67 - 23.72 276 23.72 - 29.77 220 29.77 - 35.82 184 35.82 - 41.87 133 41.87 - 47.92 70 47.92 - 53.97 27 53.97 - 60.01 6 60.01 - 66.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1364 r_work=0.1202 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1364 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1365 target_work(ml) = 3.759 | | 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= 0.1200 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758545 | | target function (ml) not normalized (work): 703937.889261 | | target function (ml) not normalized (free): 14732.883196 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1365 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1496 n_refl.: 191131 remove outliers: r(all,work,free)=0.1403 0.1402 0.1496 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1368 0.1367 0.1473 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1362 n_refl.: 191131 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 0.3875 361.337 323.765 0.400 0.950 0.209 13.296-10.522 97.03 97 1 0.2506 478.322 459.715 0.710 0.952 0.158 10.503-8.327 97.80 175 3 0.2148 502.097 496.760 0.885 0.952 0.133 8.318-6.595 100.00 360 8 0.2146 375.686 371.468 0.908 0.952 0.103 6.588-5.215 100.00 711 7 0.1910 345.218 335.104 0.904 0.952 0.083 5.214-4.128 98.38 1367 28 0.1221 504.949 499.711 0.994 0.952 0.039 4.126-3.266 94.74 2603 46 0.1151 460.288 453.286 1.056 0.953 0.005 3.266-2.585 99.86 5447 97 0.1111 310.499 307.175 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0954 234.254 231.765 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0909 138.643 137.340 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0970 74.637 73.930 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.040 38.366 1.026 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0481 ============================ 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=902 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1199 r_free=0.1362 | n_water=902 | time (s): 109.500 (total time: 111.840) Filter (q & B) r_work=0.1200 r_free=0.1360 | n_water=893 | time (s): 5.100 (total time: 116.940) Compute maps r_work=0.1200 r_free=0.1360 | n_water=893 | time (s): 1.620 (total time: 118.560) Filter (map) r_work=0.1220 r_free=0.1356 | n_water=774 | time (s): 4.830 (total time: 123.390) Find peaks r_work=0.1220 r_free=0.1356 | n_water=774 | time (s): 0.710 (total time: 124.100) Add new water r_work=0.1229 r_free=0.1371 | n_water=990 | time (s): 4.480 (total time: 128.580) Refine new water occ: r_work=0.1197 r_free=0.1347 adp: r_work=0.1197 r_free=0.1347 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=0.1348 adp: r_work=0.1193 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1348 r_work=0.1193 r_free=0.1348 | n_water=990 | time (s): 243.990 (total time: 372.570) Filter (q & B) r_work=0.1198 r_free=0.1354 | n_water=906 | time (s): 5.810 (total time: 378.380) Filter (dist only) r_work=0.1198 r_free=0.1354 | n_water=904 | time (s): 112.320 (total time: 490.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.509194 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.757688 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1357 0.0156 0.038 1.1 6.0 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.57 1.56 1.722 13.750 14.758 3.759 12.01 13.59 1.57 1.775 13.730 14.758 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 64.75 14.62 0.89 538 3270 Protein: 5.39 28.72 10.25 0.89 0 2902 Water: 5.69 64.75 28.66 N/A 538 366 Other: 13.70 22.05 17.87 N/A 0 2 Chain A: 5.44 52.19 12.12 N/A 0 1624 Chain B: 5.39 64.75 11.95 N/A 0 1646 Chain S: 5.69 58.53 30.38 N/A 538 0 Histogram: Values Number of atoms 5.39 - 11.32 2096 11.32 - 17.26 791 17.26 - 23.20 275 23.20 - 29.13 217 29.13 - 35.07 187 35.07 - 41.01 132 41.01 - 46.94 71 46.94 - 52.88 32 52.88 - 58.82 6 58.82 - 64.75 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1359 r_work=0.1202 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1359 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1359 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756190 | | target function (ml) not normalized (work): 703496.741892 | | target function (ml) not normalized (free): 14723.712391 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1359 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1375 0.1373 0.1476 n_refl.: 191131 remove outliers: r(all,work,free)=0.1375 0.1373 0.1476 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1383 0.1382 0.1481 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1348 n_refl.: 191131 remove outliers: r(all,work,free)=0.1194 0.1191 0.1348 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 93.07 91 3 0.3927 361.337 321.927 0.375 0.995 0.195 13.296-10.522 96.04 96 1 0.2472 480.612 456.321 0.677 0.997 0.143 10.503-8.327 97.80 175 3 0.2181 502.097 495.505 0.849 0.998 0.120 8.318-6.595 100.00 360 8 0.2200 375.686 370.221 0.872 0.997 0.098 6.588-5.215 100.00 711 7 0.1915 345.218 334.640 0.869 0.998 0.080 5.214-4.128 98.38 1367 28 0.1229 504.949 499.234 0.958 0.999 0.029 4.126-3.266 94.74 2603 46 0.1162 460.288 452.681 1.018 1.000 0.000 3.266-2.585 99.86 5447 97 0.1115 310.499 306.995 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0956 234.254 231.677 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0904 138.643 137.276 1.026 1.004 0.000 1.619-1.281 98.00 42464 925 0.0949 74.637 73.980 1.015 1.008 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.040 38.345 0.982 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0587 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1348 | n_water=904 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1191 r_free=0.1348 | n_water=903 | time (s): 115.340 (total time: 118.020) Filter (q & B) r_work=0.1192 r_free=0.1345 | n_water=895 | time (s): 4.580 (total time: 122.600) Compute maps r_work=0.1192 r_free=0.1345 | n_water=895 | time (s): 2.510 (total time: 125.110) Filter (map) r_work=0.1212 r_free=0.1351 | n_water=781 | time (s): 5.290 (total time: 130.400) Find peaks r_work=0.1212 r_free=0.1351 | n_water=781 | time (s): 0.760 (total time: 131.160) Add new water r_work=0.1220 r_free=0.1361 | n_water=992 | time (s): 4.340 (total time: 135.500) Refine new water occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1188 r_free=0.1339 occ: r_work=0.1186 r_free=0.1337 adp: r_work=0.1186 r_free=0.1338 occ: r_work=0.1185 r_free=0.1337 adp: r_work=0.1185 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1337 r_work=0.1185 r_free=0.1337 | n_water=992 | time (s): 243.580 (total time: 379.080) Filter (q & B) r_work=0.1190 r_free=0.1345 | n_water=913 | time (s): 5.500 (total time: 384.580) Filter (dist only) r_work=0.1190 r_free=0.1344 | n_water=912 | time (s): 119.770 (total time: 504.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566535 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.639984 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 0.1192 0.1346 0.0154 0.038 1.1 5.1 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.46 1.54 1.681 13.772 13.640 3.755 11.94 13.48 1.54 1.689 13.765 13.640 3.754 Individual atomic B min max mean iso aniso Overall: 5.44 64.50 14.70 0.87 546 3270 Protein: 5.44 28.50 10.32 0.87 0 2902 Water: 5.93 64.50 28.62 N/A 546 366 Other: 13.75 22.10 17.93 N/A 0 2 Chain A: 5.54 52.12 12.16 N/A 0 1624 Chain B: 5.44 64.50 12.00 N/A 0 1646 Chain S: 5.93 58.63 30.39 N/A 546 0 Histogram: Values Number of atoms 5.44 - 11.35 2082 11.35 - 17.25 807 17.25 - 23.16 273 23.16 - 29.07 227 29.07 - 34.97 180 34.97 - 40.88 132 40.88 - 46.78 75 46.78 - 52.69 33 52.69 - 58.60 5 58.60 - 64.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1348 r_work=0.1194 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1348 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1349 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754084 | | target function (ml) not normalized (work): 703098.581634 | | target function (ml) not normalized (free): 14720.145167 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1349 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1390 0.1388 0.1478 n_refl.: 191130 remove outliers: r(all,work,free)=0.1390 0.1388 0.1478 n_refl.: 191130 overall B=0.01 to atoms: r(all,work,free)=0.1392 0.1390 0.1479 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1345 n_refl.: 191130 remove outliers: r(all,work,free)=0.1194 0.1191 0.1345 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3829 356.482 316.462 0.336 0.995 0.130 13.296-10.522 96.04 96 1 0.2451 480.612 459.697 0.674 0.997 0.125 10.503-8.327 97.80 175 3 0.2196 502.097 494.264 0.845 0.997 0.121 8.318-6.595 100.00 360 8 0.2200 375.686 369.884 0.871 0.997 0.092 6.588-5.215 100.00 711 7 0.1946 345.218 334.525 0.867 0.998 0.080 5.214-4.128 98.38 1367 28 0.1238 504.949 499.248 0.958 0.998 0.029 4.126-3.266 94.74 2603 46 0.1164 460.288 452.567 1.019 1.000 0.000 3.266-2.585 99.86 5447 97 0.1117 310.499 307.029 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0959 234.254 231.616 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0905 138.643 137.293 1.028 1.005 0.000 1.619-1.281 98.00 42464 925 0.0946 74.637 73.991 1.018 1.010 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.040 38.333 0.988 1.019 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0202 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1345 | n_water=912 | time (s): 3.430 (total time: 3.430) Filter (dist) r_work=0.1191 r_free=0.1345 | n_water=911 | time (s): 112.070 (total time: 115.500) Filter (q & B) r_work=0.1192 r_free=0.1344 | n_water=903 | time (s): 5.010 (total time: 120.510) Compute maps r_work=0.1192 r_free=0.1344 | n_water=903 | time (s): 1.740 (total time: 122.250) Filter (map) r_work=0.1212 r_free=0.1348 | n_water=792 | time (s): 5.010 (total time: 127.260) Find peaks r_work=0.1212 r_free=0.1348 | n_water=792 | time (s): 0.790 (total time: 128.050) Add new water r_work=0.1219 r_free=0.1361 | n_water=997 | time (s): 4.180 (total time: 132.230) Refine new water occ: r_work=0.1188 r_free=0.1334 adp: r_work=0.1188 r_free=0.1334 occ: r_work=0.1186 r_free=0.1333 adp: r_work=0.1186 r_free=0.1334 occ: r_work=0.1185 r_free=0.1333 adp: r_work=0.1185 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1334 r_work=0.1185 r_free=0.1334 | n_water=997 | time (s): 284.280 (total time: 416.510) Filter (q & B) r_work=0.1189 r_free=0.1339 | n_water=924 | time (s): 5.540 (total time: 422.050) Filter (dist only) r_work=0.1189 r_free=0.1338 | n_water=921 | time (s): 118.900 (total time: 540.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.514590 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.548038 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1343 0.0150 0.039 1.1 5.3 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.43 1.50 1.681 13.793 14.548 3.755 11.92 13.45 1.54 1.689 13.787 14.548 3.752 Individual atomic B min max mean iso aniso Overall: 5.54 63.72 14.72 0.87 555 3270 Protein: 5.54 28.36 10.35 0.87 0 2902 Water: 5.97 63.72 28.48 N/A 555 366 Other: 13.81 22.17 17.99 N/A 0 2 Chain A: 5.61 51.78 12.15 N/A 0 1624 Chain B: 5.54 63.72 12.00 N/A 0 1646 Chain S: 5.97 58.74 30.26 N/A 555 0 Histogram: Values Number of atoms 5.54 - 11.36 2074 11.36 - 17.17 819 17.17 - 22.99 268 22.99 - 28.81 222 28.81 - 34.63 192 34.63 - 40.44 128 40.44 - 46.26 80 46.26 - 52.08 33 52.08 - 57.90 6 57.90 - 63.72 3 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1346 r_work=0.1192 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1346 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1345 target_work(ml) = 3.752 | | 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.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751848 | | target function (ml) not normalized (work): 702672.374119 | | target function (ml) not normalized (free): 14720.441243 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1345 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1387 0.1386 0.1482 n_refl.: 191128 remove outliers: r(all,work,free)=0.1387 0.1386 0.1482 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1387 0.1385 0.1482 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1190 0.1341 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1341 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3697 356.249 322.233 0.316 0.987 0.060 13.296-10.522 96.04 96 1 0.2447 480.612 459.028 0.667 0.988 0.093 10.503-8.327 97.80 175 3 0.2209 502.097 493.828 0.852 0.988 0.108 8.318-6.595 100.00 360 8 0.2200 375.686 369.750 0.877 0.988 0.089 6.588-5.215 100.00 711 7 0.1952 345.218 334.368 0.873 0.989 0.077 5.214-4.128 98.38 1367 28 0.1238 504.949 499.337 0.966 0.990 0.029 4.126-3.266 94.74 2603 46 0.1166 460.288 452.592 1.029 0.991 0.000 3.266-2.585 99.86 5447 97 0.1123 310.499 306.998 1.013 0.992 0.000 2.585-2.046 97.45 10613 204 0.0959 234.254 231.598 1.020 0.994 0.000 2.046-1.619 99.39 21536 464 0.0901 138.643 137.303 1.038 0.998 0.000 1.619-1.281 98.00 42464 925 0.0942 74.637 73.990 1.029 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.040 38.323 0.999 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0091 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1341 After: r_work=0.1190 r_free=0.1341 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1341 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1341 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1341 | n_water=921 | time (s): 3.380 (total time: 3.380) Filter (dist) r_work=0.1190 r_free=0.1341 | n_water=921 | time (s): 127.260 (total time: 130.640) Filter (q & B) r_work=0.1191 r_free=0.1342 | n_water=907 | time (s): 5.650 (total time: 136.290) Compute maps r_work=0.1191 r_free=0.1342 | n_water=907 | time (s): 2.450 (total time: 138.740) Filter (map) r_work=0.1213 r_free=0.1345 | n_water=791 | time (s): 5.160 (total time: 143.900) Find peaks r_work=0.1213 r_free=0.1345 | n_water=791 | time (s): 0.580 (total time: 144.480) Add new water r_work=0.1219 r_free=0.1353 | n_water=994 | time (s): 4.140 (total time: 148.620) Refine new water occ: r_work=0.1188 r_free=0.1328 adp: r_work=0.1188 r_free=0.1327 occ: r_work=0.1186 r_free=0.1328 adp: r_work=0.1186 r_free=0.1328 occ: r_work=0.1185 r_free=0.1329 adp: r_work=0.1185 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1329 r_work=0.1185 r_free=0.1329 | n_water=994 | time (s): 246.590 (total time: 395.210) Filter (q & B) r_work=0.1189 r_free=0.1339 | n_water=921 | time (s): 5.450 (total time: 400.660) Filter (dist only) r_work=0.1190 r_free=0.1338 | n_water=919 | time (s): 118.760 (total time: 519.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.511212 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.711206 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 0.1192 0.1339 0.0147 0.039 1.2 9.5 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.39 1.47 1.682 13.782 13.711 3.754 11.94 13.42 1.48 1.677 13.783 13.711 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 63.50 14.70 0.86 554 3269 Protein: 5.56 28.25 10.36 0.86 0 2902 Water: 5.99 63.50 28.40 N/A 554 365 Other: 13.84 22.17 18.01 N/A 0 2 Chain A: 5.62 51.70 12.14 N/A 0 1623 Chain B: 5.56 63.50 12.01 N/A 0 1646 Chain S: 5.99 58.77 30.22 N/A 554 0 Histogram: Values Number of atoms 5.56 - 11.35 2065 11.35 - 17.15 832 17.15 - 22.94 265 22.94 - 28.74 223 28.74 - 34.53 192 34.53 - 40.33 122 40.33 - 46.12 82 46.12 - 51.92 33 51.92 - 57.71 6 57.71 - 63.50 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1342 r_work=0.1194 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1342 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1344 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754089 | | target function (ml) not normalized (work): 703088.253113 | | target function (ml) not normalized (free): 14720.511727 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1365 0.1412 5.6898 5.768| | 2: 2.94 - 2.33 1.00 7339 128 0.1070 0.1369 5.0811 5.1872| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1192 4.6581 4.754| | 4: 2.04 - 1.85 1.00 7170 155 0.0896 0.1032 4.3882 4.5526| | 5: 1.85 - 1.72 0.99 7113 159 0.0929 0.0972 4.1452 4.2251| | 6: 1.72 - 1.62 0.99 7102 142 0.0892 0.1073 3.9383 4.0543| | 7: 1.62 - 1.54 0.99 7104 148 0.0888 0.0949 3.795 3.9269| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1321 3.7003 3.9053| | 9: 1.47 - 1.41 0.98 6938 155 0.0927 0.1122 3.6241 3.7518| | 10: 1.41 - 1.36 0.99 7022 150 0.0979 0.1183 3.5596 3.6761| | 11: 1.36 - 1.32 0.99 6997 151 0.0997 0.1134 3.4883 3.5919| | 12: 1.32 - 1.28 0.98 6975 149 0.1033 0.1128 3.4605 3.5812| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1238 3.4369 3.5609| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1571 3.4319 3.6749| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1240 3.4473 3.4925| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1542 3.4644 3.655| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1228 3.4329 3.4437| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1697 3.438 3.5281| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1737 3.42 3.5869| | 20: 1.10 - 1.08 0.97 6884 147 0.1586 0.1585 3.4113 3.4364| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2127 3.4193 3.5053| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1957 3.4139 3.4153| | 23: 1.05 - 1.03 0.97 6827 159 0.2122 0.2025 3.4342 3.4888| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2257 3.4361 3.5115| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2502 3.4499 3.5225| | 26: 1.01 - 0.99 0.96 6767 158 0.2759 0.2852 3.4167 3.4216| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2810 3.4688 3.3971| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7395 127 0.93 11.70 1.00 0.96 11288.05| | 2: 2.94 - 2.33 7339 128 0.93 12.82 0.99 0.95 5168.54| | 3: 2.33 - 2.04 6939 150 0.96 7.66 1.01 0.95 1704.81| | 4: 2.04 - 1.85 7170 155 0.96 7.54 1.00 0.95 988.53| | 5: 1.85 - 1.72 7113 159 0.96 7.88 1.00 0.96 616.31| | 6: 1.72 - 1.62 7102 142 0.96 7.81 1.00 0.96 428.50| | 7: 1.62 - 1.54 7104 148 0.96 8.01 1.01 0.97 330.70| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 0.97 278.26| | 9: 1.47 - 1.41 6938 155 0.96 8.53 1.00 0.98 233.10| | 10: 1.41 - 1.36 7022 150 0.96 8.98 1.00 0.97 204.76| | 11: 1.36 - 1.32 6997 151 0.96 9.01 0.99 0.96 176.53| | 12: 1.32 - 1.28 6975 149 0.96 9.01 0.98 0.95 161.28| | 13: 1.28 - 1.25 6907 166 0.96 9.50 1.01 0.96 157.61| | 14: 1.25 - 1.22 7015 112 0.95 10.66 1.01 0.96 162.19| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 0.98 165.95| | 16: 1.19 - 1.17 6604 132 0.95 11.41 1.01 0.96 160.02| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.96 153.51| | 18: 1.14 - 1.12 6875 142 0.94 12.70 1.01 0.95 147.09| | 19: 1.12 - 1.10 6948 106 0.93 14.11 1.00 0.95 150.71| | 20: 1.10 - 1.08 6884 147 0.92 15.23 1.00 0.94 150.36| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.71| | 22: 1.07 - 1.05 6836 135 0.89 18.34 0.99 0.93 155.50| | 23: 1.05 - 1.03 6827 159 0.87 20.54 0.99 0.92 165.27| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.93 179.36| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.98 0.90 182.11| | 26: 1.01 - 0.99 6767 158 0.81 26.64 0.98 0.89 176.86| | 27: 0.99 - 0.98 6647 131 0.82 26.40 0.99 0.87 162.21| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.09 max = 11288.05 mean = 928.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.28| |phase err.(test): min = 0.00 max = 86.96 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1344 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1392 0.1391 0.1493 n_refl.: 191127 remove outliers: r(all,work,free)=0.1392 0.1391 0.1493 n_refl.: 191127 overall B=-0.05 to atoms: r(all,work,free)=0.1384 0.1382 0.1487 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1343 n_refl.: 191127 remove outliers: r(all,work,free)=0.1195 0.1192 0.1343 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3730 356.249 327.268 0.306 0.994 0.050 13.296-10.522 96.04 96 1 0.2434 480.612 460.323 0.645 0.996 0.096 10.503-8.327 97.80 175 3 0.2241 502.097 492.826 0.821 0.996 0.096 8.318-6.595 100.00 360 8 0.2187 375.686 370.403 0.847 0.996 0.082 6.588-5.215 100.00 711 7 0.1960 345.218 334.504 0.843 0.997 0.070 5.214-4.128 98.38 1367 28 0.1242 504.949 499.119 0.936 0.998 0.029 4.126-3.266 94.74 2603 46 0.1169 460.288 452.381 0.997 0.999 0.000 3.266-2.585 99.86 5447 97 0.1123 310.499 307.027 0.981 1.000 0.000 2.585-2.046 97.45 10613 204 0.0962 234.254 231.628 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0906 138.643 137.290 1.002 1.007 0.000 1.619-1.281 98.00 42464 925 0.0946 74.637 73.987 0.992 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.040 38.312 0.961 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0118 ================= 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 : 0.2032 0.1959 0.080 5.186 5.2 78.0 14.6 805 0.000 1_bss: 0.1794 0.1887 0.080 5.186 5.2 78.1 14.6 805 0.000 1_settarget: 0.1794 0.1887 0.080 5.186 5.2 78.1 14.6 805 0.000 1_nqh: 0.1801 0.1897 0.080 5.186 5.2 78.1 14.6 805 0.002 1_weight: 0.1801 0.1897 0.080 5.186 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1269 0.1504 0.039 1.152 5.2 78.1 14.6 805 0.159 1_adp: 0.1297 0.1571 0.039 1.152 5.3 73.1 15.1 805 0.159 1_regHadp: 0.1296 0.1566 0.039 1.152 5.3 73.1 15.1 805 0.159 1_occ: 0.1280 0.1558 0.039 1.152 5.3 73.1 15.1 805 0.159 2_bss: 0.1275 0.1552 0.039 1.152 5.4 73.2 15.2 805 0.159 2_settarget: 0.1275 0.1552 0.039 1.152 5.4 73.2 15.2 805 0.159 2_updatecdl: 0.1275 0.1552 0.039 1.163 5.4 73.2 15.2 805 0.159 2_nqh: 0.1275 0.1552 0.039 1.163 5.4 73.2 15.2 805 0.159 2_sol: 0.1272 0.1515 0.039 1.163 5.4 73.2 16.1 892 n/a 2_weight: 0.1272 0.1515 0.039 1.163 5.4 73.2 16.1 892 n/a 2_xyzrec: 0.1256 0.1522 0.042 1.132 5.4 73.2 16.1 892 n/a 2_adp: 0.1235 0.1517 0.042 1.132 5.4 69.2 16.3 892 n/a 2_regHadp: 0.1235 0.1518 0.042 1.132 5.4 69.2 16.3 892 n/a 2_occ: 0.1229 0.1518 0.042 1.132 5.4 69.2 16.3 892 n/a 3_bss: 0.1236 0.1526 0.042 1.132 5.4 69.2 16.3 892 n/a 3_settarget: 0.1236 0.1526 0.042 1.132 5.4 69.2 16.3 892 n/a 3_updatecdl: 0.1236 0.1526 0.042 1.141 5.4 69.2 16.3 892 n/a 3_nqh: 0.1236 0.1526 0.042 1.141 5.4 69.2 16.3 892 n/a 3_sol: 0.1250 0.1518 0.042 1.141 5.4 68.2 15.5 881 n/a 3_weight: 0.1250 0.1518 0.042 1.141 5.4 68.2 15.5 881 n/a 3_xyzrec: 0.1237 0.1442 0.036 1.106 5.4 68.2 15.5 881 n/a 3_adp: 0.1231 0.1399 0.036 1.106 5.5 67.9 15.3 881 n/a 3_regHadp: 0.1232 0.1400 0.036 1.106 5.5 67.9 15.3 881 n/a 3_occ: 0.1226 0.1392 0.036 1.106 5.5 67.9 15.3 881 n/a 4_bss: 0.1223 0.1390 0.036 1.106 5.5 67.9 15.3 881 n/a 4_settarget: 0.1223 0.1390 0.036 1.106 5.5 67.9 15.3 881 n/a 4_updatecdl: 0.1223 0.1390 0.036 1.106 5.5 67.9 15.3 881 n/a 4_nqh: 0.1223 0.1390 0.036 1.106 5.5 67.9 15.3 881 n/a 4_sol: 0.1206 0.1370 0.036 1.106 5.5 67.9 15.1 879 n/a 4_weight: 0.1206 0.1370 0.036 1.106 5.5 67.9 15.1 879 n/a 4_xyzrec: 0.1207 0.1368 0.036 1.118 5.5 67.9 15.1 879 n/a 4_adp: 0.1199 0.1366 0.036 1.118 5.5 67.3 15.0 879 n/a 4_regHadp: 0.1199 0.1366 0.036 1.118 5.5 67.3 15.0 879 n/a 4_occ: 0.1197 0.1365 0.036 1.118 5.5 67.3 15.0 879 n/a 5_bss: 0.1195 0.1363 0.036 1.118 5.5 67.2 15.0 879 n/a 5_settarget: 0.1195 0.1363 0.036 1.118 5.5 67.2 15.0 879 n/a 5_updatecdl: 0.1195 0.1363 0.036 1.118 5.5 67.2 15.0 879 n/a 5_nqh: 0.1195 0.1363 0.036 1.118 5.5 67.2 15.0 879 n/a 5_sol: 0.1194 0.1355 0.036 1.118 5.5 67.2 15.0 888 n/a 5_weight: 0.1194 0.1355 0.036 1.118 5.5 67.2 15.0 888 n/a 5_xyzrec: 0.1197 0.1362 0.037 1.125 5.5 67.2 15.0 888 n/a 5_adp: 0.1201 0.1365 0.037 1.125 5.6 67.0 15.0 888 n/a 5_regHadp: 0.1201 0.1366 0.037 1.125 5.6 67.0 15.0 888 n/a 5_occ: 0.1199 0.1365 0.037 1.125 5.6 67.0 15.0 888 n/a 6_bss: 0.1199 0.1364 0.037 1.125 5.5 67.0 14.9 888 n/a 6_settarget: 0.1199 0.1364 0.037 1.125 5.5 67.0 14.9 888 n/a 6_updatecdl: 0.1199 0.1364 0.037 1.125 5.5 67.0 14.9 888 n/a 6_nqh: 0.1199 0.1364 0.037 1.125 5.5 67.0 14.9 888 n/a 6_sol: 0.1196 0.1358 0.037 1.125 5.5 67.0 15.0 902 n/a 6_weight: 0.1196 0.1358 0.037 1.125 5.5 67.0 15.0 902 n/a 6_xyzrec: 0.1200 0.1361 0.038 1.123 5.5 67.0 15.0 902 n/a 6_adp: 0.1202 0.1364 0.038 1.123 5.6 66.1 14.9 902 n/a 6_regHadp: 0.1202 0.1364 0.038 1.123 5.6 66.1 14.9 902 n/a 6_occ: 0.1200 0.1365 0.038 1.123 5.6 66.1 14.9 902 n/a 7_bss: 0.1199 0.1362 0.038 1.123 5.4 65.8 14.7 902 n/a 7_settarget: 0.1199 0.1362 0.038 1.123 5.4 65.8 14.7 902 n/a 7_updatecdl: 0.1199 0.1362 0.038 1.123 5.4 65.8 14.7 902 n/a 7_nqh: 0.1199 0.1362 0.038 1.123 5.4 65.8 14.7 902 n/a 7_sol: 0.1198 0.1354 0.038 1.123 5.4 65.8 14.7 904 n/a 7_weight: 0.1198 0.1354 0.038 1.123 5.4 65.8 14.7 904 n/a 7_xyzrec: 0.1201 0.1357 0.038 1.125 5.4 65.8 14.7 904 n/a 7_adp: 0.1201 0.1359 0.038 1.125 5.4 64.8 14.6 904 n/a 7_regHadp: 0.1202 0.1359 0.038 1.125 5.4 64.8 14.6 904 n/a 7_occ: 0.1200 0.1359 0.038 1.125 5.4 64.8 14.6 904 n/a 8_bss: 0.1191 0.1348 0.038 1.125 5.4 64.8 14.7 904 n/a 8_settarget: 0.1191 0.1348 0.038 1.125 5.4 64.8 14.7 904 n/a 8_updatecdl: 0.1191 0.1348 0.038 1.124 5.4 64.8 14.7 904 n/a 8_nqh: 0.1191 0.1348 0.038 1.124 5.4 64.8 14.7 904 n/a 8_sol: 0.1190 0.1344 0.038 1.124 5.4 64.8 14.7 912 n/a 8_weight: 0.1190 0.1344 0.038 1.124 5.4 64.8 14.7 912 n/a 8_xyzrec: 0.1192 0.1346 0.038 1.125 5.4 64.8 14.7 912 n/a 8_adp: 0.1194 0.1348 0.038 1.125 5.4 64.5 14.7 912 n/a 8_regHadp: 0.1194 0.1348 0.038 1.125 5.4 64.5 14.7 912 n/a 8_occ: 0.1193 0.1349 0.038 1.125 5.4 64.5 14.7 912 n/a 9_bss: 0.1191 0.1345 0.038 1.125 5.5 64.5 14.7 912 n/a 9_settarget: 0.1191 0.1345 0.038 1.125 5.5 64.5 14.7 912 n/a 9_updatecdl: 0.1191 0.1345 0.038 1.125 5.5 64.5 14.7 912 n/a 9_nqh: 0.1191 0.1345 0.038 1.125 5.5 64.5 14.7 912 n/a 9_sol: 0.1189 0.1338 0.038 1.125 5.5 64.5 14.7 921 n/a 9_weight: 0.1189 0.1338 0.038 1.125 5.5 64.5 14.7 921 n/a 9_xyzrec: 0.1193 0.1343 0.039 1.117 5.5 64.5 14.7 921 n/a 9_adp: 0.1192 0.1346 0.039 1.117 5.5 63.7 14.7 921 n/a 9_regHadp: 0.1192 0.1346 0.039 1.117 5.5 63.7 14.7 921 n/a 9_occ: 0.1190 0.1345 0.039 1.117 5.5 63.7 14.7 921 n/a 10_bss: 0.1189 0.1341 0.039 1.117 5.5 63.7 14.7 921 n/a 10_settarget: 0.1189 0.1341 0.039 1.117 5.5 63.7 14.7 921 n/a 10_updatecdl: 0.1189 0.1341 0.039 1.118 5.5 63.7 14.7 921 n/a 10_setrh: 0.1190 0.1341 0.039 1.118 5.5 63.7 14.7 921 n/a 10_nqh: 0.1190 0.1341 0.039 1.118 5.5 63.7 14.7 921 n/a 10_sol: 0.1190 0.1338 0.039 1.118 5.5 63.7 14.7 919 n/a 10_weight: 0.1190 0.1338 0.039 1.118 5.5 63.7 14.7 919 n/a 10_xyzrec: 0.1192 0.1339 0.039 1.153 5.5 63.7 14.7 919 n/a 10_adp: 0.1194 0.1342 0.039 1.153 5.6 63.5 14.7 919 n/a 10_regHadp: 0.1194 0.1342 0.039 1.153 5.6 63.5 14.7 919 n/a 10_occ: 0.1193 0.1344 0.039 1.153 5.6 63.5 14.7 919 n/a end: 0.1193 0.1343 0.039 1.153 5.5 63.5 14.6 919 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3580741_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3580741_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0700 Refinement macro-cycles (run) : 12330.0800 Write final files (write_after_run_outputs) : 149.2100 Total : 12486.3600 Total CPU time: 3.48 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:45:21 PST -0800 (1736736321.48 s) Start R-work = 0.1794, R-free = 0.1887 Final R-work = 0.1193, R-free = 0.1343 =============================================================================== Job complete usr+sys time: 12764.59 seconds wall clock time: 213 minutes 47.65 seconds (12827.65 seconds total)