Starting phenix.refine on Sun Jan 12 15:15:38 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4160413.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4160413.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4160413.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.94, per 1000 atoms: 0.29 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: 2.819 distance_ideal: 2.720 ideal - model: -0.099 slack: 0.000 delta_slack: -0.099 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: 2.798 distance_ideal: 2.710 ideal - model: -0.088 slack: 0.000 delta_slack: -0.088 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.26 Conformation dependent library (CDL) restraints added in 229.0 milliseconds Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.02: 764 1.02 - 1.26: 2572 1.26 - 1.50: 1610 1.50 - 1.74: 971 1.74 - 1.98: 17 Bond restraints: 5934 Sorted by residual: bond pdb=" CD2 HIS A 179 " pdb=" NE2 HIS A 179 " ideal model delta sigma weight residual 1.374 1.625 -0.251 1.10e-02 8.26e+03 5.22e+02 bond pdb=" N ILE A 134 " pdb=" CA ILE A 134 " ideal model delta sigma weight residual 1.460 1.647 -0.187 9.30e-03 1.16e+04 4.06e+02 bond pdb=" CE1 PHE A 119 " pdb=" HE1 PHE A 119 " ideal model delta sigma weight residual 0.930 1.317 -0.387 2.00e-02 2.50e+03 3.75e+02 bond pdb=" C LEU B 140 " pdb=" N ASP B 141 " ideal model delta sigma weight residual 1.329 1.110 0.219 1.14e-02 7.69e+03 3.68e+02 bond pdb=" ND1 HIS B 116 " pdb=" CE1 HIS B 116 " ideal model delta sigma weight residual 1.321 1.132 0.189 1.00e-02 1.00e+04 3.59e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 5574 4.07 - 8.14: 3474 8.14 - 12.20: 1431 12.20 - 16.27: 300 16.27 - 20.34: 31 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O LEU A 54 " pdb=" C LEU A 54 " pdb=" N ALA A 55 " ideal model delta sigma weight residual 123.27 141.34 -18.07 1.18e+00 7.18e-01 2.34e+02 angle pdb=" O VAL B 37 " pdb=" C VAL B 37 " pdb=" N ALA B 38 " ideal model delta sigma weight residual 122.05 106.16 15.89 1.05e+00 9.07e-01 2.29e+02 angle pdb=" N GLN B 156 " pdb=" CA GLN B 156 " pdb=" C GLN B 156 " ideal model delta sigma weight residual 113.50 130.14 -16.64 1.23e+00 6.61e-01 1.83e+02 angle pdb=" CA ASP A 84 " pdb=" C ASP A 84 " pdb=" N SER A 85 " ideal model delta sigma weight residual 118.06 135.01 -16.95 1.26e+00 6.30e-01 1.81e+02 angle pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" O GLN A 184 " ideal model delta sigma weight residual 119.12 136.10 -16.98 1.31e+00 5.83e-01 1.68e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1855 17.60 - 35.19: 129 35.19 - 52.78: 45 52.78 - 70.38: 18 70.38 - 87.97: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -154.02 -25.98 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA A 57 " pdb=" C ALA A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 155.43 24.57 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 155.53 24.47 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.240: 225 0.240 - 0.479: 150 0.479 - 0.719: 73 0.719 - 0.958: 40 0.958 - 1.198: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.39 -1.20 2.00e-01 2.50e+01 3.59e+01 chirality pdb=" CA LYS B 177 " pdb=" N LYS B 177 " pdb=" C LYS B 177 " pdb=" CB LYS B 177 " both_signs ideal model delta sigma weight residual False 2.51 3.62 -1.11 2.00e-01 2.50e+01 3.08e+01 chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.61e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.085 2.00e-02 2.50e+03 7.31e-02 2.14e+02 pdb=" CG TRP A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.041 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.132 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.082 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.089 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.044 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.057 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.050 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.085 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.108 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.150 2.00e-02 2.50e+03 7.63e-02 1.75e+02 pdb=" CG PHE B 164 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.075 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.065 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.084 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.094 2.00e-02 2.50e+03 5.77e-02 1.33e+02 pdb=" CG TRP B 139 " 0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " 0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.061 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.077 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " 0.060 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.062 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " -0.023 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.060 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.006 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.042 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.076 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.65: 35 1.65 - 2.39: 2808 2.39 - 3.12: 22476 3.12 - 3.86: 32892 3.86 - 4.60: 51952 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110163 Sorted by model distance: nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.911 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.913 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.031 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.134 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.189 2.620 ... (remaining 110158 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_4160413_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= 0.2028 r_free= 0.1964 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.296156 | | target function (ml) not normalized (work): 804725.801755 | | target function (ml) not normalized (free): 16530.248190 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2136 0.1913 6.6925 6.2979| | 2: 2.94 - 2.33 1.00 7339 128 0.1604 0.1613 5.5329 5.5908| | 3: 2.33 - 2.04 0.96 6939 150 0.1639 0.1713 5.1469 5.2014| | 4: 2.04 - 1.85 1.00 7170 155 0.1748 0.1550 4.9574 5.0075| | 5: 1.85 - 1.72 0.99 7113 159 0.1927 0.1686 4.7926 4.8467| | 6: 1.72 - 1.62 0.99 7102 142 0.1973 0.1857 4.6677 4.6796| | 7: 1.62 - 1.54 0.99 7104 148 0.1995 0.1757 4.5536 4.6168| | 8: 1.54 - 1.47 0.96 6798 152 0.2046 0.2231 4.4742 4.4802| | 9: 1.47 - 1.41 0.98 6938 155 0.2058 0.2137 4.393 4.4856| | 10: 1.41 - 1.36 0.99 7022 150 0.2102 0.2326 4.3108 4.4023| | 11: 1.36 - 1.32 0.99 6997 151 0.2114 0.2157 4.232 4.2415| | 12: 1.32 - 1.28 0.98 6976 149 0.2090 0.1845 4.1787 4.1512| | 13: 1.28 - 1.25 0.98 6907 166 0.2028 0.2038 4.127 4.1355| | 14: 1.25 - 1.22 0.98 7015 113 0.2072 0.2228 4.0678 4.1776| | 15: 1.22 - 1.19 0.98 6957 137 0.2113 0.2017 4.0361 4.0239| | 16: 1.19 - 1.17 0.93 6604 132 0.2091 0.2042 3.9885 3.991| | 17: 1.17 - 1.14 0.98 6941 135 0.2131 0.1861 3.9437 3.9675| | 18: 1.14 - 1.12 0.98 6875 142 0.2233 0.2544 3.9279 4.0245| | 19: 1.12 - 1.10 0.97 6949 106 0.2243 0.2284 3.8613 3.8987| | 20: 1.10 - 1.08 0.97 6884 147 0.2300 0.2259 3.8231 3.8562| | 21: 1.08 - 1.07 0.97 6852 152 0.2416 0.2629 3.7801 3.8201| | 22: 1.07 - 1.05 0.97 6838 135 0.2556 0.2447 3.7527 3.7024| | 23: 1.05 - 1.03 0.97 6829 159 0.2689 0.2702 3.7207 3.8411| | 24: 1.03 - 1.02 0.96 6785 133 0.2899 0.2784 3.698 3.7706| | 25: 1.02 - 1.01 0.93 6552 130 0.3047 0.2643 3.6677 3.6678| | 26: 1.01 - 0.99 0.96 6767 158 0.3206 0.3333 3.626 3.6333| | 27: 0.99 - 0.98 0.94 6648 131 0.3395 0.3270 3.6286 3.6406| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.23 0.91 0.97 34672.37| | 2: 2.94 - 2.33 7339 128 0.86 20.94 1.08 1.02 14816.40| | 3: 2.33 - 2.04 6939 150 0.93 12.56 1.11 1.05 4152.28| | 4: 2.04 - 1.85 7170 155 0.93 13.31 1.11 1.07 2744.07| | 5: 1.85 - 1.72 7113 159 0.91 15.66 1.12 1.06 2052.01| | 6: 1.72 - 1.62 7102 142 0.90 16.30 1.11 1.06 1587.15| | 7: 1.62 - 1.54 7104 148 0.89 18.09 1.10 1.07 1374.30| | 8: 1.54 - 1.47 6798 152 0.88 18.88 1.11 1.05 1195.41| | 9: 1.47 - 1.41 6938 155 0.87 19.82 1.10 1.06 1058.95| | 10: 1.41 - 1.36 7022 150 0.87 20.31 1.09 1.04 867.81| | 11: 1.36 - 1.32 6997 151 0.88 19.31 1.09 1.06 692.75| | 12: 1.32 - 1.28 6976 149 0.89 18.33 1.08 1.05 575.75| | 13: 1.28 - 1.25 6907 166 0.89 18.17 1.07 1.07 534.75| | 14: 1.25 - 1.22 7015 113 0.88 19.50 1.08 1.05 517.69| | 15: 1.22 - 1.19 6957 137 0.88 19.67 1.08 1.05 489.80| | 16: 1.19 - 1.17 6604 132 0.88 19.37 1.07 1.03 446.90| | 17: 1.17 - 1.14 6941 135 0.87 20.15 1.08 1.03 416.18| | 18: 1.14 - 1.12 6875 142 0.86 20.99 1.08 1.01 397.95| | 19: 1.12 - 1.10 6949 106 0.85 22.32 1.07 0.99 386.28| | 20: 1.10 - 1.08 6884 147 0.84 23.15 1.06 0.98 360.84| | 21: 1.08 - 1.07 6852 152 0.83 24.25 1.06 0.98 343.96| | 22: 1.07 - 1.05 6838 135 0.82 25.53 1.05 0.97 326.87| | 23: 1.05 - 1.03 6829 159 0.80 27.39 1.06 0.97 325.75| | 24: 1.03 - 1.02 6785 133 0.78 29.07 1.05 0.97 314.86| | 25: 1.02 - 1.01 6552 130 0.77 30.10 1.03 0.94 298.63| | 26: 1.01 - 0.99 6767 158 0.75 32.43 1.04 0.92 296.20| | 27: 0.99 - 0.98 6648 131 0.72 34.45 1.04 0.90 311.75| |alpha: min = 0.90 max = 1.07 mean = 1.02| |beta: min = 296.20 max = 34672.37 mean = 2774.72| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.41| |phase err.(test): min = 0.00 max = 89.46 mean = 21.63| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.251 2950 Z= 5.594 Angle : 5.201 18.066 4018 Z= 3.682 Chirality : 0.396 1.198 492 Planarity : 0.033 0.189 512 Dihedral : 12.938 87.972 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.29 % Allowed : 4.52 % Favored : 94.19 % Cbeta Deviations : 28.65 % 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: -2.10 (0.41), residues: 386 helix: -2.89 (0.31), residues: 146 sheet: -0.07 (0.55), residues: 86 loop : -0.29 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.103 0.022 ARG A 149 TYR 0.100 0.037 TYR A 194 PHE 0.122 0.035 PHE B 164 TRP 0.132 0.045 TRP A 139 HIS 0.054 0.025 HIS B 96 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= 0.2028 r_free= 0.1964 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.296156 | | target function (ml) not normalized (work): 804725.801755 | | target function (ml) not normalized (free): 16530.248190 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2026 0.2028 0.1964 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2026 0.2028 0.1964 n_refl.: 191155 remove outliers: r(all,work,free)=0.2026 0.2028 0.1964 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2026 0.2028 0.1964 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1796 0.1794 0.1899 n_refl.: 191145 remove outliers: r(all,work,free)=0.1794 0.1792 0.1899 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4052 402.814 293.276 0.436 0.913 0.299 13.296-10.522 99.01 99 1 0.2525 528.187 519.402 0.789 0.914 0.253 10.503-8.327 99.45 178 3 0.2553 565.118 554.730 0.973 0.914 0.233 8.318-6.595 100.00 360 8 0.2480 414.736 404.502 0.977 0.914 0.200 6.588-5.215 100.00 711 7 0.2285 381.101 364.961 0.960 0.914 0.170 5.214-4.128 98.38 1367 28 0.1456 557.435 549.873 1.072 0.914 0.080 4.126-3.266 94.74 2603 46 0.1348 508.132 499.314 1.146 0.914 0.014 3.266-2.585 99.86 5447 97 0.1429 342.774 338.239 1.120 0.913 0.000 2.585-2.046 97.45 10613 204 0.1396 258.603 254.180 1.125 0.913 0.000 2.046-1.619 99.39 21536 464 0.1615 153.054 149.947 1.143 0.912 0.000 1.619-1.281 98.00 42464 925 0.1910 82.395 80.150 1.128 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2307 44.203 41.683 1.112 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0031 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1792 r_free=0.1899 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1792 r_free=0.1899 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.208663 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.525497 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 0.1271 0.1500 0.0228 0.039 1.2 10.7 0.0 0.3 0 11.104 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.00 2.28 1.117 13.109 573.525 0.018 13.00 15.72 2.71 1.270 13.363 573.525 0.017 Individual atomic B min max mean iso aniso Overall: 5.15 73.04 15.06 1.41 435 3274 Protein: 5.15 40.32 11.02 1.41 0 2902 Water: 6.34 73.04 29.60 N/A 435 370 Other: 16.05 30.31 23.18 N/A 0 2 Chain A: 5.33 59.48 13.08 N/A 0 1626 Chain B: 5.15 73.04 12.80 N/A 0 1648 Chain S: 12.06 63.94 30.98 N/A 435 0 Histogram: Values Number of atoms 5.15 - 11.94 2161 11.94 - 18.73 637 18.73 - 25.52 318 25.52 - 32.31 254 32.31 - 39.10 163 39.10 - 45.89 108 45.89 - 52.67 43 52.67 - 59.46 20 59.46 - 66.25 4 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1301 r_free=0.1572 r_work=0.1300 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1300 r_free = 0.1567 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 = 0.1285 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1285 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015632 | | target function (ls_wunit_k1) not normalized (work): 2927.860660 | | target function (ls_wunit_k1) not normalized (free): 115.701891 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1285 0.1556 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1472 0.1469 0.1632 n_refl.: 191139 remove outliers: r(all,work,free)=0.1472 0.1469 0.1632 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1495 0.1493 0.1642 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1282 0.1277 0.1548 n_refl.: 191139 remove outliers: r(all,work,free)=0.1282 0.1277 0.1547 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3591 402.814 378.891 0.471 1.002 0.281 13.296-10.522 99.01 99 1 0.2090 528.187 522.737 0.716 1.004 0.255 10.503-8.327 99.45 178 3 0.1752 565.118 561.447 0.853 1.004 0.208 8.318-6.595 100.00 360 8 0.1703 414.736 411.943 0.875 1.004 0.165 6.588-5.215 100.00 711 7 0.1523 381.101 373.751 0.854 1.004 0.160 5.214-4.128 98.38 1367 28 0.0904 557.435 555.199 0.937 1.004 0.054 4.126-3.266 94.74 2603 46 0.0834 508.132 504.260 1.003 1.005 0.014 3.266-2.585 99.86 5447 97 0.0923 342.774 340.214 0.985 1.004 0.000 2.585-2.046 97.45 10613 204 0.0955 258.603 256.334 0.996 1.005 0.000 2.046-1.619 99.39 21536 464 0.1093 153.054 151.348 1.013 1.005 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.409 1.006 1.005 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.177 0.984 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0376 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1547 | n_water=805 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1282 r_free=0.1550 | n_water=794 | time (s): 97.880 (total time: 101.080) Filter (q & B) r_work=0.1282 r_free=0.1550 | n_water=790 | time (s): 5.090 (total time: 106.170) Compute maps r_work=0.1282 r_free=0.1550 | n_water=790 | time (s): 1.940 (total time: 108.110) Filter (map) r_work=0.1307 r_free=0.1529 | n_water=656 | time (s): 4.820 (total time: 112.930) Find peaks r_work=0.1307 r_free=0.1529 | n_water=656 | time (s): 0.900 (total time: 113.830) Add new water r_work=0.1330 r_free=0.1559 | n_water=966 | time (s): 5.030 (total time: 118.860) Refine new water occ: r_work=0.1287 r_free=0.1504 adp: r_work=0.1275 r_free=0.1505 occ: r_work=0.1277 r_free=0.1502 adp: r_work=0.1271 r_free=0.1502 occ: r_work=0.1272 r_free=0.1501 adp: r_work=0.1269 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1269 r_free=0.1502 r_work=0.1269 r_free=0.1502 | n_water=966 | time (s): 89.990 (total time: 208.850) Filter (q & B) r_work=0.1273 r_free=0.1505 | n_water=891 | time (s): 5.530 (total time: 214.380) Filter (dist only) r_work=0.1273 r_free=0.1504 | n_water=890 | time (s): 112.080 (total time: 326.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.333930 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 595.541996 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 0.1257 0.1521 0.0264 0.042 1.1 15.5 0.0 0.0 0 11.667 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.21 2.64 2.052 15.215 595.542 0.015 12.33 15.09 2.76 2.442 15.264 595.542 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 68.73 16.36 1.21 522 3272 Protein: 5.40 40.52 10.99 1.21 0 2902 Water: 6.69 68.73 33.84 N/A 522 368 Other: 16.36 32.57 24.47 N/A 0 2 Chain A: 5.54 56.03 13.01 N/A 0 1624 Chain B: 5.40 68.21 12.85 N/A 0 1648 Chain S: 13.09 68.73 37.83 N/A 522 0 Histogram: Values Number of atoms 5.40 - 11.73 2072 11.73 - 18.07 702 18.07 - 24.40 262 24.40 - 30.73 210 30.73 - 37.06 170 37.06 - 43.40 180 43.40 - 49.73 111 49.73 - 56.06 51 56.06 - 62.39 24 62.39 - 68.73 12 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1509 r_work=0.1233 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1509 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1505 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013446 | | target function (ls_wunit_k1) not normalized (work): 2518.331049 | | target function (ls_wunit_k1) not normalized (free): 98.989273 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1505 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1437 0.1434 0.1601 n_refl.: 191138 remove outliers: r(all,work,free)=0.1437 0.1434 0.1601 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1431 0.1599 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1512 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1233 0.1512 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3328 402.814 385.985 0.513 0.961 0.277 13.296-10.522 99.01 99 1 0.1873 528.187 527.804 0.773 0.962 0.222 10.503-8.327 99.45 178 3 0.1458 565.118 566.137 0.925 0.962 0.174 8.318-6.595 100.00 360 8 0.1512 414.736 414.439 0.942 0.961 0.160 6.588-5.215 100.00 711 7 0.1340 381.101 376.309 0.915 0.961 0.160 5.214-4.128 98.38 1367 28 0.0831 557.435 555.873 0.995 0.962 0.080 4.126-3.266 94.74 2603 46 0.0764 508.132 505.535 1.061 0.962 0.014 3.266-2.585 99.86 5447 97 0.0854 342.774 341.071 1.047 0.961 0.000 2.585-2.046 97.45 10613 204 0.0898 258.603 256.750 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.578 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.418 1.072 0.958 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.222 1.054 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0563 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1512 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1512 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1512 | n_water=890 | time (s): 2.990 (total time: 2.990) Filter (dist) r_work=0.1235 r_free=0.1514 | n_water=885 | time (s): 119.350 (total time: 122.340) Filter (q & B) r_work=0.1236 r_free=0.1514 | n_water=883 | time (s): 5.170 (total time: 127.510) Compute maps r_work=0.1236 r_free=0.1514 | n_water=883 | time (s): 1.660 (total time: 129.170) Filter (map) r_work=0.1273 r_free=0.1524 | n_water=693 | time (s): 4.960 (total time: 134.130) Find peaks r_work=0.1273 r_free=0.1524 | n_water=693 | time (s): 0.770 (total time: 134.900) Add new water r_work=0.1298 r_free=0.1566 | n_water=1015 | time (s): 4.880 (total time: 139.780) Refine new water occ: r_work=0.1253 r_free=0.1514 adp: r_work=0.1253 r_free=0.1515 occ: r_work=0.1249 r_free=0.1510 adp: r_work=0.1249 r_free=0.1511 occ: r_work=0.1246 r_free=0.1506 adp: r_work=0.1246 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1246 r_free=0.1507 r_work=0.1246 r_free=0.1507 | n_water=1015 | time (s): 271.800 (total time: 411.580) Filter (q & B) r_work=0.1251 r_free=0.1508 | n_water=877 | time (s): 6.310 (total time: 417.890) Filter (dist only) r_work=0.1251 r_free=0.1508 | n_water=876 | time (s): 114.200 (total time: 532.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.649246 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.209367 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1239 0.1431 0.0193 0.036 1.1 7.0 0.0 0.0 0 0.825 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.31 1.93 1.936 14.586 16.209 3.939 12.34 13.95 1.61 2.245 14.487 16.209 3.898 Individual atomic B min max mean iso aniso Overall: 5.52 67.77 15.25 1.05 509 3271 Protein: 5.52 36.52 10.74 1.05 0 2902 Water: 6.72 67.77 30.19 N/A 509 367 Other: 14.15 28.45 21.30 N/A 0 2 Chain A: 5.55 54.98 12.77 N/A 0 1624 Chain B: 5.52 67.77 12.55 N/A 0 1647 Chain S: 12.13 61.94 31.92 N/A 509 0 Histogram: Values Number of atoms 5.52 - 11.74 2129 11.74 - 17.97 691 17.97 - 24.19 303 24.19 - 30.42 231 30.42 - 36.64 179 36.64 - 42.87 140 42.87 - 49.09 73 49.09 - 55.32 23 55.32 - 61.54 9 61.54 - 67.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1395 r_work=0.1235 r_free=0.1396 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1396 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1390 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892045 | | target function (ml) not normalized (work): 728968.289925 | | target function (ml) not normalized (free): 15217.963450 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1390 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1441 0.1481 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1441 0.1481 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1435 0.1477 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1381 n_refl.: 191138 remove outliers: r(all,work,free)=0.1227 0.1224 0.1381 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 0.3722 398.008 363.987 0.422 0.947 0.240 13.296-10.522 99.01 99 1 0.2511 528.187 505.922 0.704 0.948 0.205 10.503-8.327 98.35 176 3 0.2010 555.265 559.947 0.887 0.948 0.176 8.318-6.595 100.00 360 8 0.2064 414.736 409.718 0.897 0.948 0.131 6.588-5.215 100.00 711 7 0.1834 381.101 370.645 0.885 0.948 0.110 5.214-4.128 98.38 1367 28 0.1174 557.435 551.434 0.969 0.948 0.070 4.126-3.266 94.74 2603 46 0.1078 508.132 501.343 1.033 0.948 0.014 3.266-2.585 99.86 5447 97 0.1081 342.774 339.143 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0964 258.603 255.747 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0974 153.054 151.401 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1054 82.395 81.492 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1690 44.202 42.322 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1032 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1381 | n_water=876 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1224 r_free=0.1382 | n_water=875 | time (s): 119.690 (total time: 122.040) Filter (q & B) r_work=0.1225 r_free=0.1380 | n_water=864 | time (s): 4.900 (total time: 126.940) Compute maps r_work=0.1225 r_free=0.1380 | n_water=864 | time (s): 2.560 (total time: 129.500) Filter (map) r_work=0.1248 r_free=0.1386 | n_water=719 | time (s): 5.130 (total time: 134.630) Find peaks r_work=0.1248 r_free=0.1386 | n_water=719 | time (s): 0.870 (total time: 135.500) Add new water r_work=0.1262 r_free=0.1398 | n_water=964 | time (s): 4.500 (total time: 140.000) Refine new water occ: r_work=0.1213 r_free=0.1367 adp: r_work=0.1205 r_free=0.1363 occ: r_work=0.1202 r_free=0.1365 adp: r_work=0.1202 r_free=0.1363 occ: r_work=0.1200 r_free=0.1367 adp: r_work=0.1200 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1365 r_work=0.1200 r_free=0.1365 | n_water=964 | time (s): 302.460 (total time: 442.460) Filter (q & B) r_work=0.1205 r_free=0.1371 | n_water=878 | time (s): 4.890 (total time: 447.350) Filter (dist only) r_work=0.1205 r_free=0.1371 | n_water=876 | time (s): 109.700 (total time: 557.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.615103 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.666609 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 0.1203 0.1371 0.0168 0.036 1.1 7.7 0.0 0.3 0 0.808 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.71 1.68 1.829 14.247 15.667 3.874 11.96 13.67 1.71 1.920 14.212 15.667 3.865 Individual atomic B min max mean iso aniso Overall: 5.52 67.38 15.06 1.00 509 3271 Protein: 5.52 33.52 10.67 1.00 0 2902 Water: 5.97 67.38 29.57 N/A 509 367 Other: 14.07 27.41 20.74 N/A 0 2 Chain A: 5.52 53.96 12.65 N/A 0 1624 Chain B: 5.52 67.38 12.46 N/A 0 1647 Chain S: 5.97 61.89 31.11 N/A 509 0 Histogram: Values Number of atoms 5.52 - 11.71 2118 11.71 - 17.89 722 17.89 - 24.08 296 24.08 - 30.27 245 30.27 - 36.45 169 36.45 - 42.64 130 42.64 - 48.82 70 48.82 - 55.01 22 55.01 - 61.19 6 61.19 - 67.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1368 r_work=0.1196 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1368 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1368 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862921 | | target function (ml) not normalized (work): 723501.904830 | | target function (ml) not normalized (free): 15132.914412 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1368 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1421 0.1421 0.1473 n_refl.: 191135 remove outliers: r(all,work,free)=0.1421 0.1421 0.1473 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1414 0.1413 0.1469 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1367 n_refl.: 191135 remove outliers: r(all,work,free)=0.1196 0.1193 0.1367 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3753 361.218 317.841 0.402 0.946 0.225 13.296-10.522 97.03 97 1 0.2387 481.217 450.738 0.697 0.947 0.197 10.503-8.327 98.35 176 3 0.2052 502.818 497.102 0.871 0.948 0.167 8.318-6.595 100.00 360 8 0.2135 375.563 369.612 0.894 0.947 0.117 6.588-5.215 100.00 711 7 0.1884 345.105 335.099 0.887 0.947 0.093 5.214-4.128 98.38 1367 28 0.1185 504.784 499.562 0.971 0.948 0.050 4.126-3.266 94.74 2603 46 0.1106 460.137 453.719 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1078 310.398 307.277 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0936 234.177 231.713 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0914 138.598 137.326 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0988 74.613 73.908 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.027 38.375 1.039 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1174 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1367 | n_water=876 | time (s): 3.000 (total time: 3.000) Filter (dist) r_work=0.1193 r_free=0.1367 | n_water=876 | time (s): 105.800 (total time: 108.800) Filter (q & B) r_work=0.1193 r_free=0.1366 | n_water=866 | time (s): 5.500 (total time: 114.300) Compute maps r_work=0.1193 r_free=0.1366 | n_water=866 | time (s): 2.570 (total time: 116.870) Filter (map) r_work=0.1216 r_free=0.1369 | n_water=749 | time (s): 4.620 (total time: 121.490) Find peaks r_work=0.1216 r_free=0.1369 | n_water=749 | time (s): 0.610 (total time: 122.100) Add new water r_work=0.1227 r_free=0.1377 | n_water=972 | time (s): 4.090 (total time: 126.190) Refine new water occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1192 r_free=0.1345 occ: r_work=0.1189 r_free=0.1344 adp: r_work=0.1189 r_free=0.1344 occ: r_work=0.1188 r_free=0.1344 adp: r_work=0.1187 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1345 r_work=0.1187 r_free=0.1345 | n_water=972 | time (s): 196.530 (total time: 322.720) Filter (q & B) r_work=0.1191 r_free=0.1350 | n_water=892 | time (s): 4.790 (total time: 327.510) Filter (dist only) r_work=0.1192 r_free=0.1349 | n_water=891 | time (s): 111.910 (total time: 439.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566464 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.122692 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1357 0.0164 0.037 1.1 6.3 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.57 1.64 1.795 14.183 16.123 3.763 11.96 13.59 1.63 1.891 14.144 16.123 3.759 Individual atomic B min max mean iso aniso Overall: 5.53 66.87 15.01 0.96 524 3271 Protein: 5.53 31.66 10.58 0.96 0 2902 Water: 6.04 66.87 29.41 N/A 524 367 Other: 13.92 25.65 19.78 N/A 0 2 Chain A: 5.56 52.84 12.53 N/A 0 1624 Chain B: 5.53 66.87 12.35 N/A 0 1647 Chain S: 6.04 61.89 31.05 N/A 524 0 Histogram: Values Number of atoms 5.53 - 11.66 2119 11.66 - 17.80 741 17.80 - 23.93 300 23.93 - 30.06 230 30.06 - 36.20 162 36.20 - 42.33 134 42.33 - 48.47 79 48.47 - 54.60 23 54.60 - 60.74 5 60.74 - 66.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1359 r_work=0.1197 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1360 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1362 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758209 | | target function (ml) not normalized (work): 703878.732562 | | target function (ml) not normalized (free): 14735.391747 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1194 0.1362 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1398 0.1397 0.1468 n_refl.: 191132 remove outliers: r(all,work,free)=0.1398 0.1397 0.1468 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1391 0.1390 0.1463 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191132 remove outliers: r(all,work,free)=0.1196 0.1193 0.1360 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3774 361.218 322.645 0.394 0.952 0.215 13.296-10.522 97.03 97 1 0.2388 481.217 460.969 0.689 0.954 0.163 10.503-8.327 98.35 176 3 0.2132 502.818 496.136 0.861 0.954 0.140 8.318-6.595 100.00 360 8 0.2134 375.563 370.185 0.886 0.954 0.111 6.588-5.215 100.00 711 7 0.1872 345.105 335.319 0.882 0.954 0.093 5.214-4.128 98.38 1367 28 0.1198 504.784 499.487 0.966 0.954 0.044 4.126-3.266 94.74 2603 46 0.1134 460.137 453.318 1.028 0.954 0.009 3.266-2.585 99.86 5447 97 0.1095 310.398 307.103 1.015 0.953 0.000 2.585-2.046 97.45 10613 204 0.0944 234.177 231.670 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0909 138.598 137.308 1.051 0.951 0.000 1.619-1.281 98.00 42464 925 0.0975 74.613 73.904 1.050 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.027 38.360 1.039 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1257 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1360 | n_water=891 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1193 r_free=0.1361 | n_water=890 | time (s): 110.250 (total time: 112.600) Filter (q & B) r_work=0.1194 r_free=0.1362 | n_water=881 | time (s): 4.930 (total time: 117.530) Compute maps r_work=0.1194 r_free=0.1362 | n_water=881 | time (s): 1.590 (total time: 119.120) Filter (map) r_work=0.1216 r_free=0.1358 | n_water=766 | time (s): 5.000 (total time: 124.120) Find peaks r_work=0.1216 r_free=0.1358 | n_water=766 | time (s): 0.560 (total time: 124.680) Add new water r_work=0.1227 r_free=0.1364 | n_water=984 | time (s): 4.290 (total time: 128.970) Refine new water occ: r_work=0.1192 r_free=0.1340 adp: r_work=0.1192 r_free=0.1340 occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1341 occ: r_work=0.1187 r_free=0.1343 adp: r_work=0.1187 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1342 r_work=0.1187 r_free=0.1342 | n_water=984 | time (s): 230.070 (total time: 359.040) Filter (q & B) r_work=0.1191 r_free=0.1343 | n_water=909 | time (s): 5.730 (total time: 364.770) Filter (dist only) r_work=0.1191 r_free=0.1342 | n_water=907 | time (s): 124.580 (total time: 489.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.505451 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.983153 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1347 0.0153 0.037 1.1 6.6 0.0 0.3 0 0.753 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.47 1.53 1.760 14.082 14.983 3.758 11.95 13.48 1.53 1.849 14.051 14.983 3.756 Individual atomic B min max mean iso aniso Overall: 5.56 66.04 14.94 0.91 540 3271 Protein: 5.56 29.77 10.51 0.91 0 2902 Water: 5.97 66.04 29.13 N/A 540 367 Other: 13.87 23.58 18.73 N/A 0 2 Chain A: 5.65 52.39 12.41 N/A 0 1624 Chain B: 5.56 66.04 12.25 N/A 0 1647 Chain S: 5.97 61.91 30.75 N/A 540 0 Histogram: Values Number of atoms 5.56 - 11.61 2116 11.61 - 17.66 769 17.66 - 23.71 288 23.71 - 29.75 218 29.75 - 35.80 176 35.80 - 41.85 132 41.85 - 47.90 78 47.90 - 53.94 24 53.94 - 59.99 8 59.99 - 66.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1349 r_work=0.1196 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1349 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1350 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755428 | | target function (ml) not normalized (work): 703357.947327 | | target function (ml) not normalized (free): 14721.965462 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1350 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1397 0.1396 0.1465 n_refl.: 191132 remove outliers: r(all,work,free)=0.1397 0.1396 0.1465 n_refl.: 191132 overall B=-0.23 to atoms: r(all,work,free)=0.1360 0.1359 0.1444 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1349 n_refl.: 191132 remove outliers: r(all,work,free)=0.1196 0.1193 0.1349 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3811 361.218 321.439 0.392 0.951 0.201 13.296-10.522 97.03 97 1 0.2368 481.217 461.652 0.709 0.953 0.156 10.503-8.327 98.35 176 3 0.2138 502.818 496.347 0.884 0.954 0.137 8.318-6.595 100.00 360 8 0.2136 375.563 370.772 0.909 0.953 0.108 6.588-5.215 100.00 711 7 0.1871 345.105 336.119 0.906 0.953 0.090 5.214-4.128 98.38 1367 28 0.1204 504.784 499.598 0.992 0.954 0.039 4.126-3.266 94.74 2603 46 0.1136 460.137 453.194 1.054 0.954 0.005 3.266-2.585 99.86 5447 97 0.1099 310.398 307.064 1.038 0.953 0.000 2.585-2.046 97.45 10613 204 0.0947 234.177 231.654 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0908 138.598 137.334 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0969 74.613 73.912 1.054 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.027 38.357 1.025 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0496 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1349 | n_water=907 | time (s): 3.030 (total time: 3.030) Filter (dist) r_work=0.1193 r_free=0.1349 | n_water=906 | time (s): 113.110 (total time: 116.140) Filter (q & B) r_work=0.1194 r_free=0.1349 | n_water=896 | time (s): 5.210 (total time: 121.350) Compute maps r_work=0.1194 r_free=0.1349 | n_water=896 | time (s): 2.460 (total time: 123.810) Filter (map) r_work=0.1214 r_free=0.1345 | n_water=786 | time (s): 5.030 (total time: 128.840) Find peaks r_work=0.1214 r_free=0.1345 | n_water=786 | time (s): 0.580 (total time: 129.420) Add new water r_work=0.1223 r_free=0.1346 | n_water=1010 | time (s): 3.900 (total time: 133.320) Refine new water occ: r_work=0.1191 r_free=0.1325 adp: r_work=0.1191 r_free=0.1326 occ: r_work=0.1189 r_free=0.1326 adp: r_work=0.1188 r_free=0.1327 occ: r_work=0.1187 r_free=0.1327 adp: r_work=0.1186 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1329 r_work=0.1186 r_free=0.1329 | n_water=1010 | time (s): 199.500 (total time: 332.820) Filter (q & B) r_work=0.1191 r_free=0.1331 | n_water=924 | time (s): 6.240 (total time: 339.060) Filter (dist only) r_work=0.1191 r_free=0.1330 | n_water=922 | time (s): 117.010 (total time: 456.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568423 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.357992 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 0.1337 0.0145 0.038 1.1 6.6 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.37 1.45 1.727 13.842 14.358 3.756 11.95 13.40 1.45 1.794 13.821 14.358 3.754 Individual atomic B min max mean iso aniso Overall: 5.42 64.59 14.77 0.88 555 3271 Protein: 5.42 28.46 10.25 0.88 0 2902 Water: 5.83 64.59 28.98 N/A 555 367 Other: 13.70 22.00 17.85 N/A 0 2 Chain A: 5.46 51.62 12.12 N/A 0 1624 Chain B: 5.42 64.59 11.97 N/A 0 1647 Chain S: 5.83 61.80 30.80 N/A 555 0 Histogram: Values Number of atoms 5.42 - 11.33 2100 11.33 - 17.25 782 17.25 - 23.17 275 23.17 - 29.09 222 29.09 - 35.00 179 35.00 - 40.92 142 40.92 - 46.84 83 46.84 - 52.76 30 52.76 - 58.67 9 58.67 - 64.59 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1340 r_work=0.1195 r_free=0.1340 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1340 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 = 0.1339 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1339 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.753906 | | target function (ml) not normalized (work): 703072.788231 | | target function (ml) not normalized (free): 14714.017102 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1339 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1365 0.1364 0.1448 n_refl.: 191132 remove outliers: r(all,work,free)=0.1365 0.1364 0.1448 n_refl.: 191132 overall B=0.06 to atoms: r(all,work,free)=0.1372 0.1371 0.1452 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1184 0.1329 n_refl.: 191132 remove outliers: r(all,work,free)=0.1186 0.1184 0.1329 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3583 356.334 312.889 0.408 0.909 0.193 13.296-10.522 96.04 96 1 0.2294 480.337 456.194 0.745 0.910 0.146 10.503-8.327 98.35 176 3 0.2121 502.818 495.958 0.936 0.911 0.123 8.318-6.595 100.00 360 8 0.2108 375.563 371.060 0.956 0.911 0.100 6.588-5.215 100.00 711 7 0.1895 345.105 335.523 0.958 0.911 0.083 5.214-4.128 98.38 1367 28 0.1205 504.784 499.325 1.049 0.912 0.039 4.126-3.266 94.74 2603 46 0.1138 460.137 452.857 1.115 0.913 0.005 3.266-2.585 99.86 5447 97 0.1100 310.398 306.950 1.098 0.913 0.000 2.585-2.046 97.45 10613 204 0.0951 234.177 231.593 1.106 0.915 0.000 2.046-1.619 99.39 21536 464 0.0905 138.598 137.279 1.124 0.917 0.000 1.619-1.281 98.00 42464 925 0.0950 74.613 73.970 1.112 0.920 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.027 38.341 1.075 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0625 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1329 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1184 r_free=0.1329 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1329 | n_water=922 | time (s): 2.830 (total time: 2.830) Filter (dist) r_work=0.1184 r_free=0.1329 | n_water=922 | time (s): 109.900 (total time: 112.730) Filter (q & B) r_work=0.1184 r_free=0.1329 | n_water=913 | time (s): 4.970 (total time: 117.700) Compute maps r_work=0.1184 r_free=0.1329 | n_water=913 | time (s): 1.640 (total time: 119.340) Filter (map) r_work=0.1204 r_free=0.1337 | n_water=808 | time (s): 4.190 (total time: 123.530) Find peaks r_work=0.1204 r_free=0.1337 | n_water=808 | time (s): 0.600 (total time: 124.130) Add new water r_work=0.1210 r_free=0.1334 | n_water=1011 | time (s): 4.760 (total time: 128.890) Refine new water occ: r_work=0.1181 r_free=0.1317 adp: r_work=0.1181 r_free=0.1317 occ: r_work=0.1179 r_free=0.1319 adp: r_work=0.1179 r_free=0.1319 occ: r_work=0.1177 r_free=0.1320 adp: r_work=0.1177 r_free=0.1321 ADP+occupancy (water only), MIN, final r_work=0.1177 r_free=0.1321 r_work=0.1177 r_free=0.1321 | n_water=1011 | time (s): 260.360 (total time: 389.250) Filter (q & B) r_work=0.1180 r_free=0.1322 | n_water=938 | time (s): 5.140 (total time: 394.390) Filter (dist only) r_work=0.1181 r_free=0.1322 | n_water=936 | time (s): 121.480 (total time: 515.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.557063 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.480982 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 0.1184 0.1328 0.0144 0.038 1.1 6.8 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 13.28 1.44 1.678 13.846 14.481 3.752 11.84 13.30 1.46 1.696 13.838 14.481 3.750 Individual atomic B min max mean iso aniso Overall: 5.50 63.54 14.83 0.88 569 3271 Protein: 5.50 28.28 10.32 0.88 0 2902 Water: 5.86 63.54 28.81 N/A 569 367 Other: 13.80 22.20 18.00 N/A 0 2 Chain A: 5.58 51.25 12.15 N/A 0 1624 Chain B: 5.50 63.54 12.01 N/A 0 1647 Chain S: 5.86 61.99 30.65 N/A 569 0 Histogram: Values Number of atoms 5.50 - 11.31 2063 11.31 - 17.11 820 17.11 - 22.91 270 22.91 - 28.72 225 28.72 - 34.52 189 34.52 - 40.32 133 40.32 - 46.13 93 46.13 - 51.93 35 51.93 - 57.73 8 57.73 - 63.54 4 =========================== Idealize ADP of riding H ========================== r_work=0.1184 r_free=0.1330 r_work=0.1185 r_free=0.1330 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1185 r_free = 0.1330 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1183 r_free = 0.1333 target_work(ml) = 3.750 | | 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.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1183 r_free= 0.1333 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.749928 | | target function (ml) not normalized (work): 702316.462443 | | target function (ml) not normalized (free): 14709.074393 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1186 0.1183 0.1333 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1370 0.1368 0.1459 n_refl.: 191129 remove outliers: r(all,work,free)=0.1370 0.1368 0.1459 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1372 0.1370 0.1460 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1184 0.1181 0.1332 n_refl.: 191129 remove outliers: r(all,work,free)=0.1184 0.1181 0.1332 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 0.3502 356.334 327.041 0.396 0.976 0.194 13.296-10.522 95.05 95 1 0.2253 479.557 458.344 0.704 0.978 0.140 10.503-8.327 98.35 176 3 0.2106 502.818 495.780 0.868 0.978 0.111 8.318-6.595 100.00 360 8 0.2109 375.563 370.795 0.886 0.978 0.089 6.588-5.215 100.00 711 7 0.1894 345.105 335.904 0.889 0.979 0.080 5.214-4.128 98.38 1367 28 0.1209 504.784 499.219 0.975 0.979 0.029 4.126-3.266 94.74 2603 46 0.1139 460.137 452.700 1.038 0.981 0.000 3.266-2.585 99.86 5447 97 0.1102 310.398 306.954 1.022 0.981 0.000 2.585-2.046 97.45 10613 204 0.0952 234.177 231.531 1.030 0.983 0.000 2.046-1.619 99.39 21536 464 0.0902 138.598 137.264 1.047 0.986 0.000 1.619-1.281 98.00 42464 925 0.0942 74.613 73.975 1.038 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.027 38.332 1.007 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0174 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1181 r_free=0.1332 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1181 r_free=0.1332 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1181 r_free=0.1332 | n_water=936 | time (s): 2.820 (total time: 2.820) Filter (dist) r_work=0.1181 r_free=0.1332 | n_water=936 | time (s): 115.720 (total time: 118.540) Filter (q & B) r_work=0.1181 r_free=0.1334 | n_water=924 | time (s): 4.290 (total time: 122.830) Compute maps r_work=0.1181 r_free=0.1334 | n_water=924 | time (s): 1.910 (total time: 124.740) Filter (map) r_work=0.1200 r_free=0.1336 | n_water=825 | time (s): 4.690 (total time: 129.430) Find peaks r_work=0.1200 r_free=0.1336 | n_water=825 | time (s): 0.690 (total time: 130.120) Add new water r_work=0.1206 r_free=0.1340 | n_water=1021 | time (s): 5.100 (total time: 135.220) Refine new water occ: r_work=0.1179 r_free=0.1319 adp: r_work=0.1179 r_free=0.1319 occ: r_work=0.1177 r_free=0.1320 adp: r_work=0.1177 r_free=0.1321 occ: r_work=0.1176 r_free=0.1321 adp: r_work=0.1175 r_free=0.1322 ADP+occupancy (water only), MIN, final r_work=0.1175 r_free=0.1322 r_work=0.1175 r_free=0.1322 | n_water=1021 | time (s): 301.370 (total time: 436.590) Filter (q & B) r_work=0.1180 r_free=0.1327 | n_water=940 | time (s): 4.980 (total time: 441.570) Filter (dist only) r_work=0.1180 r_free=0.1327 | n_water=938 | time (s): 122.100 (total time: 563.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.508428 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.627452 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 0.1184 0.1332 0.0148 0.039 1.1 5.6 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 13.32 1.48 1.680 13.848 13.627 3.751 11.85 13.34 1.49 1.680 13.847 13.627 3.751 Individual atomic B min max mean iso aniso Overall: 5.53 63.28 14.82 0.86 571 3271 Protein: 5.53 28.13 10.34 0.86 0 2902 Water: 5.98 63.28 28.68 N/A 571 367 Other: 13.84 22.16 18.00 N/A 0 2 Chain A: 5.60 51.19 12.15 N/A 0 1624 Chain B: 5.53 63.28 12.02 N/A 0 1647 Chain S: 5.98 62.03 30.53 N/A 571 0 Histogram: Values Number of atoms 5.53 - 11.31 2059 11.31 - 17.08 827 17.08 - 22.86 268 22.86 - 28.63 226 28.63 - 34.41 193 34.41 - 40.18 130 40.18 - 45.96 93 45.96 - 51.73 34 51.73 - 57.51 8 57.51 - 63.28 4 =========================== Idealize ADP of riding H ========================== r_work=0.1185 r_free=0.1334 r_work=0.1186 r_free=0.1334 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1186 r_free = 0.1334 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1184 r_free = 0.1336 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1184 r_free= 0.1336 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750971 | | target function (ml) not normalized (work): 702508.102680 | | target function (ml) not normalized (free): 14715.427677 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1184 0.1336 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1381 0.1379 0.1471 n_refl.: 191128 remove outliers: r(all,work,free)=0.1381 0.1379 0.1471 n_refl.: 191128 overall B=-0.01 to atoms: r(all,work,free)=0.1380 0.1378 0.1470 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1187 0.1184 0.1336 n_refl.: 191128 remove outliers: r(all,work,free)=0.1187 0.1184 0.1336 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 0.3562 356.334 325.348 0.378 0.994 0.179 13.296-10.522 95.05 95 1 0.2269 479.557 462.576 0.695 0.996 0.131 10.503-8.327 98.35 176 3 0.2145 502.818 495.562 0.850 0.996 0.102 8.318-6.595 100.00 360 8 0.2112 375.563 370.342 0.868 0.996 0.079 6.588-5.215 100.00 711 7 0.1920 345.105 335.866 0.871 0.997 0.070 5.214-4.128 98.38 1367 28 0.1204 504.784 499.038 0.957 0.998 0.020 4.126-3.266 94.74 2603 46 0.1147 460.137 452.626 1.019 0.999 0.000 3.266-2.585 99.86 5447 97 0.1110 310.398 306.981 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0958 234.177 231.492 1.012 1.002 0.000 2.046-1.619 99.39 21536 464 0.0905 138.598 137.256 1.029 1.006 0.000 1.619-1.281 98.00 42464 925 0.0942 74.613 73.973 1.020 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.027 38.320 0.991 1.023 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0153 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1184 r_free=0.1336 After: r_work=0.1185 r_free=0.1336 ================================== NQH flips ================================== r_work=0.1185 r_free=0.1336 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1336 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1336 | n_water=938 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1185 r_free=0.1336 | n_water=938 | time (s): 115.800 (total time: 118.950) Filter (q & B) r_work=0.1185 r_free=0.1337 | n_water=929 | time (s): 5.250 (total time: 124.200) Compute maps r_work=0.1185 r_free=0.1337 | n_water=929 | time (s): 1.940 (total time: 126.140) Filter (map) r_work=0.1204 r_free=0.1337 | n_water=823 | time (s): 5.070 (total time: 131.210) Find peaks r_work=0.1204 r_free=0.1337 | n_water=823 | time (s): 0.620 (total time: 131.830) Add new water r_work=0.1209 r_free=0.1341 | n_water=1021 | time (s): 4.240 (total time: 136.070) Refine new water occ: r_work=0.1182 r_free=0.1320 adp: r_work=0.1182 r_free=0.1320 occ: r_work=0.1181 r_free=0.1321 adp: r_work=0.1181 r_free=0.1321 occ: r_work=0.1179 r_free=0.1323 adp: r_work=0.1179 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1323 r_work=0.1179 r_free=0.1323 | n_water=1021 | time (s): 289.650 (total time: 425.720) Filter (q & B) r_work=0.1183 r_free=0.1329 | n_water=938 | time (s): 5.600 (total time: 431.320) Filter (dist only) r_work=0.1184 r_free=0.1329 | n_water=936 | time (s): 121.100 (total time: 552.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.572416 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.809445 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 0.1184 0.1330 0.0146 0.039 1.1 8.2 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.84 13.30 1.46 1.677 13.837 14.809 3.751 11.82 13.30 1.47 1.668 13.843 14.809 3.748 Individual atomic B min max mean iso aniso Overall: 5.58 62.33 14.81 0.87 569 3271 Protein: 5.58 28.26 10.37 0.87 0 2902 Water: 6.02 62.33 28.58 N/A 569 367 Other: 13.87 22.07 17.97 N/A 0 2 Chain A: 5.67 50.89 12.15 N/A 0 1624 Chain B: 5.58 62.33 12.02 N/A 0 1647 Chain S: 6.02 62.16 30.49 N/A 569 0 Histogram: Values Number of atoms 5.58 - 11.25 2035 11.25 - 16.93 843 16.93 - 22.60 271 22.60 - 28.28 220 28.28 - 33.95 199 33.95 - 39.63 124 39.63 - 45.30 93 45.30 - 50.98 42 50.98 - 56.65 7 56.65 - 62.33 6 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1330 r_work=0.1183 r_free=0.1330 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1183 r_free = 0.1330 target_work(ml) = 3.748 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1182 r_free = 0.1330 target_work(ml) = 3.748 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1182 r_free= 0.1330 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.748202 | | target function (ml) not normalized (work): 701989.598802 | | target function (ml) not normalized (free): 14705.309895 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1330 0.1364 5.6645 5.6977| | 2: 2.94 - 2.33 1.00 7339 128 0.1057 0.1326 5.0505 5.1571| | 3: 2.33 - 2.04 0.96 6939 150 0.0900 0.1183 4.6486 4.7489| | 4: 2.04 - 1.85 1.00 7170 155 0.0890 0.1049 4.3829 4.5632| | 5: 1.85 - 1.72 0.99 7113 159 0.0925 0.0975 4.1436 4.2458| | 6: 1.72 - 1.62 0.99 7102 142 0.0890 0.1079 3.939 4.0697| | 7: 1.62 - 1.54 0.99 7104 148 0.0881 0.0943 3.7889 3.9244| | 8: 1.54 - 1.47 0.96 6798 152 0.0881 0.1283 3.6873 3.8814| | 9: 1.47 - 1.41 0.98 6938 155 0.0920 0.1105 3.6119 3.7342| | 10: 1.41 - 1.36 0.99 7022 150 0.0970 0.1182 3.5483 3.6651| | 11: 1.36 - 1.32 0.99 6997 151 0.0987 0.1118 3.4788 3.5872| | 12: 1.32 - 1.28 0.98 6975 149 0.1028 0.1122 3.4541 3.5756| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1226 3.4334 3.5593| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1580 3.4303 3.6794| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1241 3.4459 3.4922| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1554 3.463 3.6614| | 17: 1.17 - 1.14 0.98 6940 135 0.1296 0.1230 3.4317 3.4452| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1702 3.4367 3.5302| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1763 3.4182 3.6031| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1570 3.4088 3.4297| | 21: 1.08 - 1.07 0.97 6852 152 0.1725 0.2138 3.417 3.5042| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1962 3.4119 3.4148| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2019 3.432 3.4825| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2244 3.4349 3.5071| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2525 3.4487 3.5273| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2855 3.4154 3.4232| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2809 3.4683 3.3958| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.94 10.65 1.00 0.96 9750.64| | 2: 2.94 - 2.33 7339 128 0.93 12.00 0.99 0.96 4638.86| | 3: 2.33 - 2.04 6939 150 0.96 7.62 1.01 0.96 1691.79| | 4: 2.04 - 1.85 7170 155 0.96 7.60 1.00 0.96 1000.62| | 5: 1.85 - 1.72 7113 159 0.96 8.02 1.00 0.96 628.88| | 6: 1.72 - 1.62 7102 142 0.96 7.92 1.00 0.96 436.23| | 7: 1.62 - 1.54 7104 148 0.96 7.98 1.01 0.97 329.08| | 8: 1.54 - 1.47 6798 152 0.96 8.07 1.01 0.97 270.49| | 9: 1.47 - 1.41 6938 155 0.96 8.25 1.00 0.98 223.44| | 10: 1.41 - 1.36 7022 150 0.96 8.73 1.00 0.97 197.25| | 11: 1.36 - 1.32 6997 151 0.96 8.82 0.99 0.96 171.90| | 12: 1.32 - 1.28 6975 149 0.96 8.92 0.98 0.95 159.12| | 13: 1.28 - 1.25 6907 166 0.96 9.49 1.01 0.96 157.38| | 14: 1.25 - 1.22 7015 112 0.95 10.70 1.01 0.97 162.51| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 0.98 166.42| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.96 160.08| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.96 154.07| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.95 147.53| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.95 150.94| | 20: 1.10 - 1.08 6884 147 0.92 15.20 1.00 0.94 149.75| | 21: 1.08 - 1.07 6852 152 0.91 16.61 1.00 0.93 152.86| | 22: 1.07 - 1.05 6836 135 0.89 18.25 0.99 0.93 154.29| | 23: 1.05 - 1.03 6827 159 0.87 20.45 0.99 0.92 164.14| | 24: 1.03 - 1.02 6784 133 0.85 23.13 0.99 0.93 178.62| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.98 0.90 182.07| | 26: 1.01 - 0.99 6767 158 0.81 26.64 0.98 0.88 176.78| | 27: 0.99 - 0.98 6647 131 0.82 26.30 0.99 0.87 161.07| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.53 max = 9750.64 mean = 846.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.17| |phase err.(test): min = 0.00 max = 89.85 mean = 13.34| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1185 0.1182 0.1330 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1386 0.1385 0.1468 n_refl.: 191128 remove outliers: r(all,work,free)=0.1386 0.1385 0.1468 n_refl.: 191128 overall B=-0.04 to atoms: r(all,work,free)=0.1381 0.1379 0.1464 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1183 0.1180 0.1329 n_refl.: 191128 remove outliers: r(all,work,free)=0.1183 0.1180 0.1329 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 0.3517 356.334 325.284 0.379 0.992 0.198 13.296-10.522 95.05 95 1 0.2265 479.557 462.512 0.676 0.994 0.123 10.503-8.327 98.35 176 3 0.2127 502.818 495.402 0.828 0.994 0.093 8.318-6.595 100.00 360 8 0.2118 375.563 370.411 0.846 0.994 0.081 6.588-5.215 100.00 711 7 0.1914 345.105 335.920 0.848 0.994 0.070 5.214-4.128 98.38 1367 28 0.1213 504.784 498.781 0.934 0.994 0.024 4.126-3.266 94.74 2603 46 0.1145 460.137 452.680 0.997 0.995 0.000 3.266-2.585 99.86 5447 97 0.1102 310.398 306.946 0.983 0.994 0.000 2.585-2.046 97.45 10613 204 0.0957 234.177 231.471 0.993 0.995 0.000 2.046-1.619 99.39 21536 464 0.0902 138.598 137.232 1.012 0.995 0.000 1.619-1.281 98.00 42464 925 0.0937 74.613 73.973 1.010 0.996 0.000 1.281-0.980 96.53 101826 2055 0.1620 40.027 38.316 0.990 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0079 ================= 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 : 0.2028 0.1964 0.083 5.201 5.2 78.0 14.6 805 0.000 1_bss: 0.1792 0.1899 0.083 5.201 5.2 78.0 14.6 805 0.000 1_settarget: 0.1792 0.1899 0.083 5.201 5.2 78.0 14.6 805 0.000 1_nqh: 0.1792 0.1899 0.083 5.201 5.2 78.0 14.6 805 0.000 1_weight: 0.1792 0.1899 0.083 5.201 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1500 0.039 1.160 5.2 78.0 14.6 805 0.155 1_adp: 0.1301 0.1572 0.039 1.160 5.1 73.0 15.1 805 0.155 1_regHadp: 0.1300 0.1567 0.039 1.160 5.1 73.0 15.1 805 0.155 1_occ: 0.1285 0.1556 0.039 1.160 5.1 73.0 15.1 805 0.155 2_bss: 0.1277 0.1547 0.039 1.160 5.3 73.2 15.2 805 0.155 2_settarget: 0.1277 0.1547 0.039 1.160 5.3 73.2 15.2 805 0.155 2_updatecdl: 0.1277 0.1547 0.039 1.164 5.3 73.2 15.2 805 0.155 2_nqh: 0.1277 0.1547 0.039 1.164 5.3 73.2 15.2 805 0.155 2_sol: 0.1273 0.1504 0.039 1.164 5.3 73.2 16.3 890 n/a 2_weight: 0.1273 0.1504 0.039 1.164 5.3 73.2 16.3 890 n/a 2_xyzrec: 0.1257 0.1521 0.042 1.147 5.3 73.2 16.3 890 n/a 2_adp: 0.1233 0.1509 0.042 1.147 5.4 68.7 16.4 890 n/a 2_regHadp: 0.1233 0.1509 0.042 1.147 5.4 68.7 16.4 890 n/a 2_occ: 0.1226 0.1505 0.042 1.147 5.4 68.7 16.4 890 n/a 3_bss: 0.1233 0.1512 0.042 1.147 5.4 68.7 16.3 890 n/a 3_settarget: 0.1233 0.1512 0.042 1.147 5.4 68.7 16.3 890 n/a 3_updatecdl: 0.1233 0.1512 0.042 1.154 5.4 68.7 16.3 890 n/a 3_nqh: 0.1233 0.1512 0.042 1.154 5.4 68.7 16.3 890 n/a 3_sol: 0.1251 0.1508 0.042 1.154 5.4 68.2 15.4 876 n/a 3_weight: 0.1251 0.1508 0.042 1.154 5.4 68.2 15.4 876 n/a 3_xyzrec: 0.1239 0.1431 0.036 1.104 5.4 68.2 15.4 876 n/a 3_adp: 0.1234 0.1395 0.036 1.104 5.5 67.8 15.3 876 n/a 3_regHadp: 0.1235 0.1396 0.036 1.104 5.5 67.8 15.3 876 n/a 3_occ: 0.1229 0.1390 0.036 1.104 5.5 67.8 15.3 876 n/a 4_bss: 0.1224 0.1381 0.036 1.104 5.5 67.7 15.2 876 n/a 4_settarget: 0.1224 0.1381 0.036 1.104 5.5 67.7 15.2 876 n/a 4_updatecdl: 0.1224 0.1381 0.036 1.104 5.5 67.7 15.2 876 n/a 4_nqh: 0.1224 0.1381 0.036 1.104 5.5 67.7 15.2 876 n/a 4_sol: 0.1205 0.1371 0.036 1.104 5.5 67.7 15.1 876 n/a 4_weight: 0.1205 0.1371 0.036 1.104 5.5 67.7 15.1 876 n/a 4_xyzrec: 0.1203 0.1371 0.036 1.127 5.5 67.7 15.1 876 n/a 4_adp: 0.1196 0.1368 0.036 1.127 5.5 67.4 15.1 876 n/a 4_regHadp: 0.1196 0.1368 0.036 1.127 5.5 67.4 15.1 876 n/a 4_occ: 0.1195 0.1368 0.036 1.127 5.5 67.4 15.1 876 n/a 5_bss: 0.1193 0.1367 0.036 1.127 5.5 67.3 15.0 876 n/a 5_settarget: 0.1193 0.1367 0.036 1.127 5.5 67.3 15.0 876 n/a 5_updatecdl: 0.1193 0.1367 0.036 1.128 5.5 67.3 15.0 876 n/a 5_nqh: 0.1193 0.1367 0.036 1.128 5.5 67.3 15.0 876 n/a 5_sol: 0.1192 0.1349 0.036 1.128 5.5 67.3 15.1 891 n/a 5_weight: 0.1192 0.1349 0.036 1.128 5.5 67.3 15.1 891 n/a 5_xyzrec: 0.1194 0.1357 0.037 1.129 5.5 67.3 15.1 891 n/a 5_adp: 0.1196 0.1359 0.037 1.129 5.5 66.9 15.0 891 n/a 5_regHadp: 0.1197 0.1360 0.037 1.129 5.5 66.9 15.0 891 n/a 5_occ: 0.1194 0.1362 0.037 1.129 5.5 66.9 15.0 891 n/a 6_bss: 0.1193 0.1360 0.037 1.129 5.5 66.8 15.0 891 n/a 6_settarget: 0.1193 0.1360 0.037 1.129 5.5 66.8 15.0 891 n/a 6_updatecdl: 0.1193 0.1360 0.037 1.129 5.5 66.8 15.0 891 n/a 6_nqh: 0.1193 0.1360 0.037 1.129 5.5 66.8 15.0 891 n/a 6_sol: 0.1191 0.1342 0.037 1.129 5.5 66.8 15.0 907 n/a 6_weight: 0.1191 0.1342 0.037 1.129 5.5 66.8 15.0 907 n/a 6_xyzrec: 0.1194 0.1347 0.037 1.125 5.5 66.8 15.0 907 n/a 6_adp: 0.1195 0.1349 0.037 1.125 5.6 66.0 14.9 907 n/a 6_regHadp: 0.1196 0.1349 0.037 1.125 5.6 66.0 14.9 907 n/a 6_occ: 0.1193 0.1350 0.037 1.125 5.6 66.0 14.9 907 n/a 7_bss: 0.1193 0.1349 0.037 1.125 5.3 65.8 14.7 907 n/a 7_settarget: 0.1193 0.1349 0.037 1.125 5.3 65.8 14.7 907 n/a 7_updatecdl: 0.1193 0.1349 0.037 1.126 5.3 65.8 14.7 907 n/a 7_nqh: 0.1193 0.1349 0.037 1.126 5.3 65.8 14.7 907 n/a 7_sol: 0.1191 0.1330 0.037 1.126 5.3 65.8 14.8 922 n/a 7_weight: 0.1191 0.1330 0.037 1.126 5.3 65.8 14.8 922 n/a 7_xyzrec: 0.1192 0.1337 0.038 1.130 5.3 65.8 14.8 922 n/a 7_adp: 0.1195 0.1340 0.038 1.130 5.4 64.6 14.8 922 n/a 7_regHadp: 0.1195 0.1340 0.038 1.130 5.4 64.6 14.8 922 n/a 7_occ: 0.1193 0.1339 0.038 1.130 5.4 64.6 14.8 922 n/a 8_bss: 0.1184 0.1329 0.038 1.130 5.5 64.6 14.8 922 n/a 8_settarget: 0.1184 0.1329 0.038 1.130 5.5 64.6 14.8 922 n/a 8_updatecdl: 0.1184 0.1329 0.038 1.130 5.5 64.6 14.8 922 n/a 8_nqh: 0.1184 0.1329 0.038 1.130 5.5 64.6 14.8 922 n/a 8_sol: 0.1181 0.1322 0.038 1.130 5.5 64.6 14.8 936 n/a 8_weight: 0.1181 0.1322 0.038 1.130 5.5 64.6 14.8 936 n/a 8_xyzrec: 0.1184 0.1328 0.038 1.123 5.5 64.6 14.8 936 n/a 8_adp: 0.1184 0.1330 0.038 1.123 5.5 63.5 14.8 936 n/a 8_regHadp: 0.1185 0.1330 0.038 1.123 5.5 63.5 14.8 936 n/a 8_occ: 0.1183 0.1333 0.038 1.123 5.5 63.5 14.8 936 n/a 9_bss: 0.1181 0.1332 0.038 1.123 5.5 63.5 14.8 936 n/a 9_settarget: 0.1181 0.1332 0.038 1.123 5.5 63.5 14.8 936 n/a 9_updatecdl: 0.1181 0.1332 0.038 1.123 5.5 63.5 14.8 936 n/a 9_nqh: 0.1181 0.1332 0.038 1.123 5.5 63.5 14.8 936 n/a 9_sol: 0.1180 0.1327 0.038 1.123 5.5 63.5 14.8 938 n/a 9_weight: 0.1180 0.1327 0.038 1.123 5.5 63.5 14.8 938 n/a 9_xyzrec: 0.1184 0.1332 0.039 1.113 5.5 63.5 14.8 938 n/a 9_adp: 0.1185 0.1334 0.039 1.113 5.5 63.3 14.8 938 n/a 9_regHadp: 0.1186 0.1334 0.039 1.113 5.5 63.3 14.8 938 n/a 9_occ: 0.1184 0.1336 0.039 1.113 5.5 63.3 14.8 938 n/a 10_bss: 0.1184 0.1336 0.039 1.113 5.5 63.3 14.8 938 n/a 10_settarget: 0.1184 0.1336 0.039 1.113 5.5 63.3 14.8 938 n/a 10_updatecdl: 0.1184 0.1336 0.039 1.113 5.5 63.3 14.8 938 n/a 10_setrh: 0.1185 0.1336 0.039 1.113 5.5 63.3 14.8 938 n/a 10_nqh: 0.1185 0.1336 0.039 1.113 5.5 63.3 14.8 938 n/a 10_sol: 0.1184 0.1329 0.039 1.113 5.5 63.3 14.8 936 n/a 10_weight: 0.1184 0.1329 0.039 1.113 5.5 63.3 14.8 936 n/a 10_xyzrec: 0.1184 0.1330 0.039 1.137 5.5 63.3 14.8 936 n/a 10_adp: 0.1183 0.1330 0.039 1.137 5.6 62.3 14.8 936 n/a 10_regHadp: 0.1183 0.1330 0.039 1.137 5.6 62.3 14.8 936 n/a 10_occ: 0.1182 0.1330 0.039 1.137 5.6 62.3 14.8 936 n/a end: 0.1180 0.1329 0.039 1.137 5.5 62.3 14.8 936 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4160413_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4160413_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.8400 Refinement macro-cycles (run) : 12212.4800 Write final files (write_after_run_outputs) : 141.6100 Total : 12360.9300 Total CPU time: 3.44 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:12 PST -0800 (1736736192.63 s) Start R-work = 0.1792, R-free = 0.1899 Final R-work = 0.1180, R-free = 0.1329 =============================================================================== Job complete usr+sys time: 12613.60 seconds wall clock time: 211 minutes 14.31 seconds (12674.31 seconds total)