Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6548452.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6548452.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6548452.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } 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: 1.77, per 1000 atoms: 0.26 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: 2.636 distance_ideal: 2.720 ideal - model: 0.084 slack: 0.000 delta_slack: 0.084 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: 2.708 distance_ideal: 2.710 ideal - model: 0.002 slack: 0.000 delta_slack: 0.002 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 147.0 milliseconds Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.01: 672 1.01 - 1.25: 2560 1.25 - 1.48: 1478 1.48 - 1.71: 1195 1.71 - 1.94: 29 Bond restraints: 5934 Sorted by residual: bond pdb=" NE ARG A 149 " pdb=" CZ ARG A 149 " ideal model delta sigma weight residual 1.326 1.565 -0.239 1.10e-02 8.26e+03 4.72e+02 bond pdb=" N GLU B 137 " pdb=" H GLU B 137 " ideal model delta sigma weight residual 0.860 1.284 -0.424 2.00e-02 2.50e+03 4.49e+02 bond pdb=" CA ILE B 134 " pdb=" C ILE B 134 " ideal model delta sigma weight residual 1.525 1.700 -0.176 8.40e-03 1.42e+04 4.37e+02 bond pdb=" C LEU B 140 " pdb=" N ASP B 141 " ideal model delta sigma weight residual 1.329 1.560 -0.231 1.14e-02 7.69e+03 4.10e+02 bond pdb=" C CYS A 81 " pdb=" O CYS A 81 " ideal model delta sigma weight residual 1.236 1.468 -0.231 1.15e-02 7.56e+03 4.05e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.81: 6291 4.81 - 9.62: 3436 9.62 - 14.42: 981 14.42 - 19.23: 99 19.23 - 24.04: 3 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA B 3 " pdb=" C ALA B 3 " pdb=" N SER B 4 " ideal model delta sigma weight residual 122.87 144.03 -21.16 1.23e+00 6.61e-01 2.96e+02 angle pdb=" CA HIS A 96 " pdb=" CB HIS A 96 " pdb=" CG HIS A 96 " ideal model delta sigma weight residual 113.80 99.39 14.41 1.00e+00 1.00e+00 2.08e+02 angle pdb=" O ILE B 169 " pdb=" C ILE B 169 " pdb=" N ASP B 170 " ideal model delta sigma weight residual 121.87 108.04 13.83 9.70e-01 1.06e+00 2.03e+02 angle pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " pdb=" NH1 ARG A 49 " ideal model delta sigma weight residual 121.50 135.67 -14.17 1.00e+00 1.00e+00 2.01e+02 angle pdb=" CA HIS A 179 " pdb=" C HIS A 179 " pdb=" O HIS A 179 " ideal model delta sigma weight residual 120.24 104.88 15.36 1.11e+00 8.12e-01 1.91e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 1841 16.89 - 33.77: 142 33.77 - 50.66: 39 50.66 - 67.54: 25 67.54 - 84.42: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA LEU B 72 " pdb=" C LEU B 72 " pdb=" N PRO B 73 " pdb=" CA PRO B 73 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA VAL A 32 " pdb=" C VAL A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta harmonic sigma weight residual 180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA GLU B 61 " pdb=" C GLU B 61 " pdb=" N VAL B 62 " pdb=" CA VAL B 62 " ideal model delta harmonic sigma weight residual 180.00 -158.68 -21.32 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.214: 223 0.214 - 0.427: 132 0.427 - 0.640: 78 0.640 - 0.853: 49 0.853 - 1.065: 10 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB ILE A 162 " pdb=" CA ILE A 162 " pdb=" CG1 ILE A 162 " pdb=" CG2 ILE A 162 " both_signs ideal model delta sigma weight residual False 2.64 3.71 -1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" CB ILE B 70 " pdb=" CA ILE B 70 " pdb=" CG1 ILE B 70 " pdb=" CG2 ILE B 70 " both_signs ideal model delta sigma weight residual False 2.64 1.62 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.44 -1.00 2.00e-01 2.50e+01 2.49e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.081 2.00e-02 2.50e+03 7.87e-02 2.48e+02 pdb=" CG TRP A 146 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.086 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.079 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.103 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.133 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.139 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.046 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.053 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.102 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.086 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " 0.036 2.00e-02 2.50e+03 6.07e-02 1.47e+02 pdb=" CG TRP B 139 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.098 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.130 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.091 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.071 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " -0.043 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.098 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 82 " -0.124 2.00e-02 2.50e+03 6.90e-02 1.43e+02 pdb=" CG PHE A 82 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 82 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 82 " 0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE A 82 " -0.076 2.00e-02 2.50e+03 pdb=" CE2 PHE A 82 " -0.082 2.00e-02 2.50e+03 pdb=" CZ PHE A 82 " -0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 82 " 0.119 2.00e-02 2.50e+03 pdb=" HD2 PHE A 82 " 0.073 2.00e-02 2.50e+03 pdb=" HE1 PHE A 82 " 0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 82 " 0.043 2.00e-02 2.50e+03 pdb=" HZ PHE A 82 " 0.013 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.57: 20 1.57 - 2.33: 2003 2.33 - 3.09: 21966 3.09 - 3.84: 33031 3.84 - 4.60: 53233 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110253 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.814 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.990 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.068 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.077 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.192 2.620 ... (remaining 110248 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_6548452_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2029 r_free= 0.2019 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298664 | | target function (ml) not normalized (work): 805195.615169 | | target function (ml) not normalized (free): 16609.685714 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1920 6.6912 6.2922| | 2: 2.94 - 2.33 1.00 7339 128 0.1626 0.1705 5.5346 5.5972| | 3: 2.33 - 2.04 0.96 6939 150 0.1631 0.1617 5.1451 5.1539| | 4: 2.04 - 1.85 1.00 7170 155 0.1739 0.1670 4.9665 5.0695| | 5: 1.85 - 1.72 0.99 7113 159 0.1913 0.1804 4.812 4.8213| | 6: 1.72 - 1.62 0.99 7102 142 0.1965 0.2323 4.6744 4.8849| | 7: 1.62 - 1.54 0.99 7104 148 0.1996 0.1839 4.5604 4.6005| | 8: 1.54 - 1.47 0.96 6798 152 0.2039 0.2044 4.4752 4.4884| | 9: 1.47 - 1.41 0.98 6938 155 0.2127 0.2344 4.4126 4.56| | 10: 1.41 - 1.36 0.99 7022 150 0.2107 0.2286 4.3121 4.3798| | 11: 1.36 - 1.32 0.99 6997 151 0.2057 0.2125 4.2194 4.2639| | 12: 1.32 - 1.28 0.98 6976 149 0.2087 0.1883 4.1761 4.1936| | 13: 1.28 - 1.25 0.98 6907 166 0.2014 0.2322 4.1124 4.2921| | 14: 1.25 - 1.22 0.98 7015 113 0.2097 0.2395 4.0853 4.2901| | 15: 1.22 - 1.19 0.98 6957 137 0.2117 0.2100 4.0445 4.0478| | 16: 1.19 - 1.17 0.93 6604 132 0.2084 0.2036 3.9899 3.9963| | 17: 1.17 - 1.14 0.98 6941 135 0.2172 0.1973 3.9609 4.0248| | 18: 1.14 - 1.12 0.98 6875 142 0.2223 0.2303 3.9296 3.8884| | 19: 1.12 - 1.10 0.97 6949 106 0.2272 0.2289 3.8642 3.949| | 20: 1.10 - 1.08 0.97 6884 147 0.2326 0.2284 3.8192 3.9265| | 21: 1.08 - 1.07 0.97 6852 152 0.2386 0.2536 3.7774 3.7543| | 22: 1.07 - 1.05 0.97 6838 135 0.2542 0.2347 3.748 3.7129| | 23: 1.05 - 1.03 0.97 6829 159 0.2676 0.2783 3.7159 3.8415| | 24: 1.03 - 1.02 0.96 6785 133 0.2869 0.2704 3.6938 3.7459| | 25: 1.02 - 1.01 0.93 6552 130 0.3046 0.2990 3.6683 3.7138| | 26: 1.01 - 0.99 0.96 6767 158 0.3189 0.3082 3.6217 3.6092| | 27: 0.99 - 0.98 0.94 6648 131 0.3441 0.3395 3.6373 3.6252| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.26 0.91 0.97 34605.66| | 2: 2.94 - 2.33 7339 128 0.86 21.12 1.09 1.02 14823.83| | 3: 2.33 - 2.04 6939 150 0.93 12.64 1.11 1.05 4182.75| | 4: 2.04 - 1.85 7170 155 0.92 14.09 1.11 1.05 2930.01| | 5: 1.85 - 1.72 7113 159 0.90 16.85 1.11 1.06 2325.63| | 6: 1.72 - 1.62 7102 142 0.89 18.15 1.11 1.05 1887.62| | 7: 1.62 - 1.54 7104 148 0.88 18.93 1.11 1.05 1485.77| | 8: 1.54 - 1.47 6798 152 0.88 18.72 1.10 1.05 1187.14| | 9: 1.47 - 1.41 6938 155 0.87 19.75 1.10 1.05 1046.39| | 10: 1.41 - 1.36 7022 150 0.87 20.48 1.09 1.04 892.45| | 11: 1.36 - 1.32 6997 151 0.87 20.60 1.08 1.04 775.69| | 12: 1.32 - 1.28 6976 149 0.87 20.41 1.08 1.03 673.84| | 13: 1.28 - 1.25 6907 166 0.86 20.84 1.07 1.03 651.87| | 14: 1.25 - 1.22 7015 113 0.85 21.97 1.08 1.02 625.14| | 15: 1.22 - 1.19 6957 137 0.86 21.73 1.08 1.03 576.49| | 16: 1.19 - 1.17 6604 132 0.87 20.60 1.08 1.03 493.69| | 17: 1.17 - 1.14 6941 135 0.87 20.56 1.08 1.02 426.04| | 18: 1.14 - 1.12 6875 142 0.87 20.56 1.08 1.00 380.55| | 19: 1.12 - 1.10 6949 106 0.86 21.71 1.07 1.00 364.50| | 20: 1.10 - 1.08 6884 147 0.85 22.40 1.06 0.99 340.76| | 21: 1.08 - 1.07 6852 152 0.85 22.91 1.06 0.99 318.25| | 22: 1.07 - 1.05 6838 135 0.84 24.27 1.06 1.00 309.17| | 23: 1.05 - 1.03 6829 159 0.81 26.46 1.06 0.99 314.26| | 24: 1.03 - 1.02 6785 133 0.78 29.00 1.06 0.98 319.91| | 25: 1.02 - 1.01 6552 130 0.77 30.61 1.03 0.93 309.03| | 26: 1.01 - 0.99 6767 158 0.74 33.00 1.03 0.91 301.83| | 27: 0.99 - 0.98 6648 131 0.73 34.36 1.03 0.89 304.35| |alpha: min = 0.89 max = 1.06 mean = 1.01| |beta: min = 301.83 max = 34605.66 mean = 2823.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.88| |phase err.(test): min = 0.00 max = 89.10 mean = 21.91| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.255 2950 Z= 5.529 Angle : 5.244 21.164 4018 Z= 3.726 Chirality : 0.382 1.065 492 Planarity : 0.034 0.121 512 Dihedral : 12.556 84.424 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.78 % Allowed : 2.59 % Favored : 96.63 % Rotamer: Outliers : 1.29 % Allowed : 4.52 % Favored : 94.19 % Cbeta Deviations : 31.46 % 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: -1.95 (0.40), residues: 386 helix: -2.32 (0.35), residues: 144 sheet: -0.96 (0.52), residues: 86 loop : -0.10 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.020 ARG A 143 TYR 0.076 0.032 TYR B 192 PHE 0.108 0.041 PHE A 95 TRP 0.124 0.045 TRP A 146 HIS 0.092 0.037 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2029 r_free= 0.2019 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298664 | | target function (ml) not normalized (work): 805195.615169 | | target function (ml) not normalized (free): 16609.685714 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2028 0.2029 0.2019 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2028 0.2029 0.2019 n_refl.: 191155 remove outliers: r(all,work,free)=0.2028 0.2029 0.2019 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2028 0.2029 0.2019 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1801 0.1798 0.1954 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1796 0.1954 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 0.4080 402.814 292.435 0.435 0.912 0.297 13.296-10.522 99.01 99 1 0.2526 528.187 519.297 0.789 0.913 0.248 10.503-8.327 99.45 178 3 0.2484 565.118 557.210 0.980 0.913 0.227 8.318-6.595 100.00 360 8 0.2511 414.736 402.890 0.977 0.913 0.190 6.588-5.215 100.00 711 7 0.2310 381.101 366.329 0.962 0.913 0.150 5.214-4.128 98.38 1367 28 0.1478 557.435 549.887 1.081 0.913 0.090 4.126-3.266 94.74 2603 46 0.1347 508.132 498.643 1.143 0.913 0.019 3.266-2.585 99.86 5447 97 0.1443 342.774 337.552 1.121 0.913 0.005 2.585-2.046 97.45 10613 204 0.1399 258.603 254.239 1.127 0.912 0.000 2.046-1.619 99.39 21536 464 0.1610 153.054 149.886 1.145 0.911 0.000 1.619-1.281 98.00 42464 925 0.1917 82.395 80.212 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2311 44.203 41.697 1.114 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0114 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1796 r_free=0.1954 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1796 r_free=0.1954 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.388823 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 572.166900 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 0.1501 0.0230 0.039 1.2 11.0 0.0 0.3 0 11.194 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.01 2.30 1.117 13.107 572.167 0.018 13.01 15.73 2.72 1.257 13.343 572.167 0.017 Individual atomic B min max mean iso aniso Overall: 5.14 73.04 15.02 1.40 435 3274 Protein: 5.14 40.31 11.01 1.40 0 2902 Water: 6.38 73.04 29.48 N/A 435 370 Other: 15.99 30.61 23.30 N/A 0 2 Chain A: 5.38 59.49 13.06 N/A 0 1626 Chain B: 5.14 73.04 12.77 N/A 0 1648 Chain S: 11.63 63.44 30.88 N/A 435 0 Histogram: Values Number of atoms 5.14 - 11.93 2162 11.93 - 18.72 636 18.72 - 25.51 322 25.51 - 32.30 261 32.30 - 39.09 159 39.09 - 45.88 103 45.88 - 52.67 42 52.67 - 59.46 19 59.46 - 66.25 4 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1302 r_free=0.1573 r_work=0.1301 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1301 r_free = 0.1568 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 = 0.1286 r_free = 0.1557 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1286 r_free= 0.1557 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015663 | | target function (ls_wunit_k1) not normalized (work): 2933.692432 | | target function (ls_wunit_k1) not normalized (free): 116.268544 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1286 0.1557 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1469 0.1467 0.1637 n_refl.: 191139 remove outliers: r(all,work,free)=0.1469 0.1467 0.1637 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1493 0.1491 0.1647 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1278 0.1546 n_refl.: 191139 remove outliers: r(all,work,free)=0.1283 0.1278 0.1545 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 0.3613 402.814 378.420 0.489 0.963 0.283 13.296-10.522 99.01 99 1 0.2072 528.187 517.952 0.731 0.965 0.236 10.503-8.327 99.45 178 3 0.1761 565.118 562.614 0.888 0.965 0.213 8.318-6.595 100.00 360 8 0.1720 414.736 411.599 0.910 0.965 0.160 6.588-5.215 100.00 711 7 0.1536 381.101 373.534 0.888 0.965 0.150 5.214-4.128 98.38 1367 28 0.0904 557.435 554.384 0.978 0.965 0.080 4.126-3.266 94.74 2603 46 0.0833 508.132 504.384 1.042 0.966 0.014 3.266-2.585 99.86 5447 97 0.0923 342.774 340.403 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.408 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1094 153.054 151.382 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1284 82.395 81.394 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.146 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0380 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1278 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1545 | n_water=805 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1283 r_free=0.1550 | n_water=794 | time (s): 109.930 (total time: 112.590) Filter (q & B) r_work=0.1283 r_free=0.1549 | n_water=789 | time (s): 5.140 (total time: 117.730) Compute maps r_work=0.1283 r_free=0.1549 | n_water=789 | time (s): 2.480 (total time: 120.210) Filter (map) r_work=0.1307 r_free=0.1532 | n_water=657 | time (s): 4.870 (total time: 125.080) Find peaks r_work=0.1307 r_free=0.1532 | n_water=657 | time (s): 0.790 (total time: 125.870) Add new water r_work=0.1331 r_free=0.1558 | n_water=969 | time (s): 4.470 (total time: 130.340) Refine new water occ: r_work=0.1288 r_free=0.1515 adp: r_work=0.1275 r_free=0.1513 occ: r_work=0.1278 r_free=0.1510 adp: r_work=0.1271 r_free=0.1511 occ: r_work=0.1272 r_free=0.1510 adp: r_work=0.1271 r_free=0.1511 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1511 r_work=0.1271 r_free=0.1511 | n_water=969 | time (s): 84.690 (total time: 215.030) Filter (q & B) r_work=0.1275 r_free=0.1514 | n_water=896 | time (s): 4.230 (total time: 219.260) Filter (dist only) r_work=0.1275 r_free=0.1514 | n_water=895 | time (s): 112.940 (total time: 332.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.878047 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 591.263715 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1256 0.1533 0.0277 0.040 1.1 18.2 0.0 0.3 0 11.939 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.33 2.77 2.045 15.153 591.264 0.014 12.30 15.22 2.92 2.435 15.250 591.264 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.21 16.34 1.21 527 3272 Protein: 5.38 40.22 10.98 1.21 0 2902 Water: 6.62 68.21 33.73 N/A 527 368 Other: 16.31 33.00 24.66 N/A 0 2 Chain A: 5.50 55.44 13.00 N/A 0 1624 Chain B: 5.38 68.21 12.82 N/A 0 1648 Chain S: 12.87 67.93 37.67 N/A 527 0 Histogram: Values Number of atoms 5.38 - 11.66 2060 11.66 - 17.94 709 17.94 - 24.23 263 24.23 - 30.51 209 30.51 - 36.79 177 36.79 - 43.07 187 43.07 - 49.36 105 49.36 - 55.64 51 55.64 - 61.92 27 61.92 - 68.21 11 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1522 r_work=0.1230 r_free=0.1522 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1522 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 = 0.1224 r_free = 0.1521 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 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= 0.1224 r_free= 0.1521 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013380 | | target function (ls_wunit_k1) not normalized (work): 2506.018762 | | target function (ls_wunit_k1) not normalized (free): 104.549468 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1224 0.1520 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1433 0.1430 0.1618 n_refl.: 191138 remove outliers: r(all,work,free)=0.1433 0.1430 0.1618 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1616 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1527 n_refl.: 191138 remove outliers: r(all,work,free)=0.1237 0.1231 0.1527 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 0.3281 402.814 378.505 0.492 0.962 0.271 13.296-10.522 99.01 99 1 0.1898 528.187 519.821 0.757 0.964 0.223 10.503-8.327 99.45 178 3 0.1401 565.118 567.909 0.921 0.963 0.183 8.318-6.595 100.00 360 8 0.1551 414.736 414.096 0.938 0.963 0.167 6.588-5.215 100.00 711 7 0.1367 381.101 376.364 0.911 0.963 0.127 5.214-4.128 98.38 1367 28 0.0816 557.435 556.221 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0750 508.132 505.456 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0858 342.774 341.398 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.752 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.632 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.358 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.220 1.058 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0514 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1527 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1527 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1527 | n_water=895 | time (s): 3.270 (total time: 3.270) Filter (dist) r_work=0.1233 r_free=0.1528 | n_water=891 | time (s): 124.210 (total time: 127.480) Filter (q & B) r_work=0.1233 r_free=0.1528 | n_water=887 | time (s): 4.860 (total time: 132.340) Compute maps r_work=0.1233 r_free=0.1528 | n_water=887 | time (s): 1.820 (total time: 134.160) Filter (map) r_work=0.1271 r_free=0.1520 | n_water=697 | time (s): 5.290 (total time: 139.450) Find peaks r_work=0.1271 r_free=0.1520 | n_water=697 | time (s): 0.620 (total time: 140.070) Add new water r_work=0.1293 r_free=0.1556 | n_water=1012 | time (s): 4.410 (total time: 144.480) Refine new water occ: r_work=0.1250 r_free=0.1516 adp: r_work=0.1251 r_free=0.1516 occ: r_work=0.1247 r_free=0.1513 adp: r_work=0.1247 r_free=0.1514 occ: r_work=0.1244 r_free=0.1510 adp: r_work=0.1243 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1512 r_work=0.1243 r_free=0.1512 | n_water=1012 | time (s): 305.950 (total time: 450.430) Filter (q & B) r_work=0.1247 r_free=0.1522 | n_water=874 | time (s): 6.030 (total time: 456.460) Filter (dist only) r_work=0.1247 r_free=0.1522 | n_water=873 | time (s): 115.590 (total time: 572.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.648390 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.015228 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 0.1238 0.1436 0.0198 0.035 1.1 8.2 0.0 0.0 0 0.824 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.36 1.98 1.932 14.591 16.015 3.939 12.35 13.96 1.61 2.209 14.503 16.015 3.898 Individual atomic B min max mean iso aniso Overall: 5.53 67.84 15.29 1.06 506 3271 Protein: 5.53 36.70 10.75 1.06 0 2902 Water: 6.67 67.84 30.38 N/A 506 367 Other: 14.01 28.61 21.31 N/A 0 2 Chain A: 5.53 54.65 12.78 N/A 0 1624 Chain B: 5.56 67.84 12.55 N/A 0 1647 Chain S: 13.06 64.71 32.26 N/A 506 0 Histogram: Values Number of atoms 5.53 - 11.76 2134 11.76 - 17.99 685 17.99 - 24.22 293 24.22 - 30.46 229 30.46 - 36.69 180 36.69 - 42.92 150 42.92 - 49.15 75 49.15 - 55.38 21 55.38 - 61.61 8 61.61 - 67.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1396 r_work=0.1235 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1397 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1379 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1379 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891728 | | target function (ml) not normalized (work): 728908.963756 | | target function (ml) not normalized (free): 15219.838034 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1230 0.1378 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1445 0.1444 0.1473 n_refl.: 191138 remove outliers: r(all,work,free)=0.1445 0.1444 0.1473 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1439 0.1438 0.1469 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1226 0.1373 n_refl.: 191138 remove outliers: r(all,work,free)=0.1229 0.1226 0.1373 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 0.3879 398.008 361.056 0.430 0.946 0.259 13.296-10.522 99.01 99 1 0.2426 528.187 511.652 0.713 0.947 0.229 10.503-8.327 98.35 176 3 0.2009 555.265 559.040 0.889 0.947 0.179 8.318-6.595 100.00 360 8 0.2101 414.736 408.984 0.896 0.946 0.135 6.588-5.215 100.00 711 7 0.1820 381.101 370.718 0.888 0.947 0.120 5.214-4.128 98.38 1367 28 0.1175 557.435 551.877 0.974 0.947 0.080 4.126-3.266 94.74 2603 46 0.1092 508.132 501.042 1.033 0.947 0.005 3.266-2.585 99.86 5447 97 0.1083 342.774 339.010 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0967 258.603 255.734 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0980 153.054 151.389 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.476 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.314 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1016 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1373 | n_water=873 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1226 r_free=0.1372 | n_water=872 | time (s): 119.470 (total time: 122.080) Filter (q & B) r_work=0.1227 r_free=0.1372 | n_water=859 | time (s): 4.270 (total time: 126.350) Compute maps r_work=0.1227 r_free=0.1372 | n_water=859 | time (s): 1.830 (total time: 128.180) Filter (map) r_work=0.1251 r_free=0.1388 | n_water=711 | time (s): 5.230 (total time: 133.410) Find peaks r_work=0.1251 r_free=0.1388 | n_water=711 | time (s): 0.540 (total time: 133.950) Add new water r_work=0.1267 r_free=0.1405 | n_water=962 | time (s): 4.690 (total time: 138.640) Refine new water occ: r_work=0.1218 r_free=0.1359 adp: r_work=0.1211 r_free=0.1356 occ: r_work=0.1209 r_free=0.1355 adp: r_work=0.1209 r_free=0.1355 occ: r_work=0.1209 r_free=0.1355 adp: r_work=0.1209 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1209 r_free=0.1355 r_work=0.1209 r_free=0.1355 | n_water=962 | time (s): 181.610 (total time: 320.250) Filter (q & B) r_work=0.1215 r_free=0.1363 | n_water=829 | time (s): 4.790 (total time: 325.040) Filter (dist only) r_work=0.1215 r_free=0.1362 | n_water=828 | time (s): 107.730 (total time: 432.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.591444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.500808 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 0.1212 0.1365 0.0153 0.036 1.1 5.8 0.0 0.3 0 0.796 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 13.65 1.53 1.833 14.084 15.501 3.875 12.06 13.62 1.55 2.012 14.018 15.501 3.867 Individual atomic B min max mean iso aniso Overall: 5.51 67.24 14.71 0.98 462 3270 Protein: 5.51 32.92 10.62 0.98 0 2902 Water: 5.98 67.24 29.02 N/A 462 366 Other: 13.89 26.93 20.41 N/A 0 2 Chain A: 5.60 53.04 12.59 N/A 0 1624 Chain B: 5.51 67.24 12.39 N/A 0 1646 Chain S: 5.98 64.69 30.40 N/A 462 0 Histogram: Values Number of atoms 5.51 - 11.68 2117 11.68 - 17.85 737 17.85 - 24.03 330 24.03 - 30.20 187 30.20 - 36.37 135 36.37 - 42.55 129 42.55 - 48.72 64 48.72 - 54.89 24 54.89 - 61.07 6 61.07 - 67.24 3 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1362 r_work=0.1207 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1362 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1359 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865059 | | target function (ml) not normalized (work): 723902.439288 | | target function (ml) not normalized (free): 15134.595529 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1358 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1439 0.1439 0.1478 n_refl.: 191135 remove outliers: r(all,work,free)=0.1439 0.1439 0.1478 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1431 0.1431 0.1473 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1354 n_refl.: 191135 remove outliers: r(all,work,free)=0.1205 0.1202 0.1354 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3563 361.137 312.896 0.416 0.943 0.243 13.296-10.522 97.03 97 1 0.2455 478.461 451.197 0.699 0.945 0.196 10.503-8.327 98.35 176 3 0.2185 503.129 496.479 0.867 0.945 0.173 8.315-6.595 100.00 359 8 0.2214 374.848 370.207 0.895 0.945 0.129 6.588-5.215 100.00 711 7 0.1921 345.318 335.425 0.885 0.945 0.100 5.214-4.128 98.38 1367 28 0.1226 505.095 499.925 0.977 0.945 0.090 4.126-3.266 94.74 2603 46 0.1137 460.422 453.992 1.037 0.946 0.000 3.266-2.585 99.86 5447 97 0.1092 310.589 307.501 1.024 0.945 0.000 2.585-2.046 97.45 10613 204 0.0941 234.322 231.928 1.036 0.945 0.000 2.046-1.619 99.39 21536 464 0.0918 138.683 137.417 1.059 0.945 0.000 1.619-1.281 98.00 42464 925 0.0988 74.659 73.967 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.051 38.402 1.040 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1202 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1354 | n_water=828 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1202 r_free=0.1354 | n_water=828 | time (s): 100.550 (total time: 103.010) Filter (q & B) r_work=0.1202 r_free=0.1355 | n_water=817 | time (s): 5.320 (total time: 108.330) Compute maps r_work=0.1202 r_free=0.1355 | n_water=817 | time (s): 1.640 (total time: 109.970) Filter (map) r_work=0.1223 r_free=0.1363 | n_water=711 | time (s): 4.140 (total time: 114.110) Find peaks r_work=0.1223 r_free=0.1363 | n_water=711 | time (s): 0.720 (total time: 114.830) Add new water r_work=0.1237 r_free=0.1380 | n_water=944 | time (s): 4.370 (total time: 119.200) Refine new water occ: r_work=0.1198 r_free=0.1348 adp: r_work=0.1198 r_free=0.1348 occ: r_work=0.1196 r_free=0.1348 adp: r_work=0.1195 r_free=0.1347 occ: r_work=0.1194 r_free=0.1348 adp: r_work=0.1193 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1347 r_work=0.1193 r_free=0.1347 | n_water=944 | time (s): 266.380 (total time: 385.580) Filter (q & B) r_work=0.1197 r_free=0.1352 | n_water=870 | time (s): 4.310 (total time: 389.890) Filter (dist only) r_work=0.1197 r_free=0.1350 | n_water=869 | time (s): 112.840 (total time: 502.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.549156 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.944300 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1357 0.0156 0.036 1.1 7.8 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.57 1.56 1.777 14.029 14.944 3.766 12.05 13.63 1.58 1.851 13.996 14.944 3.764 Individual atomic B min max mean iso aniso Overall: 5.55 66.76 14.80 0.94 505 3268 Protein: 5.55 31.12 10.55 0.94 0 2902 Water: 6.01 66.76 29.01 N/A 505 364 Other: 13.83 25.55 19.69 N/A 0 2 Chain A: 5.58 52.08 12.47 N/A 0 1623 Chain B: 5.55 66.76 12.27 N/A 0 1645 Chain S: 6.01 64.67 30.54 N/A 505 0 Histogram: Values Number of atoms 5.55 - 11.67 2130 11.67 - 17.79 739 17.79 - 23.91 309 23.91 - 30.03 205 30.03 - 36.16 168 36.16 - 42.28 127 42.28 - 48.40 63 48.40 - 54.52 23 54.52 - 60.64 5 60.64 - 66.76 4 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1363 r_work=0.1205 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1363 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1368 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.763235 | | target function (ml) not normalized (work): 704812.519022 | | target function (ml) not normalized (free): 14758.477696 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1368 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1502 n_refl.: 191130 remove outliers: r(all,work,free)=0.1404 0.1402 0.1502 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1396 0.1395 0.1496 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1365 n_refl.: 191130 remove outliers: r(all,work,free)=0.1206 0.1202 0.1365 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3762 361.137 331.073 0.421 0.950 0.224 13.296-10.522 97.03 97 1 0.2457 478.461 460.521 0.707 0.952 0.195 10.503-8.327 97.80 175 3 0.2126 502.242 499.223 0.858 0.952 0.180 8.315-6.595 100.00 359 8 0.2171 374.848 370.897 0.886 0.952 0.125 6.588-5.215 100.00 711 7 0.1934 345.318 335.487 0.884 0.952 0.110 5.214-4.128 98.38 1367 28 0.1220 505.095 499.732 0.971 0.952 0.080 4.126-3.266 94.74 2603 46 0.1159 460.422 453.529 1.032 0.953 0.005 3.266-2.585 99.86 5447 97 0.1107 310.589 307.312 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0951 234.322 231.802 1.028 0.953 0.000 2.046-1.619 99.39 21536 464 0.0922 138.683 137.357 1.050 0.953 0.000 1.619-1.281 98.00 42464 925 0.0978 74.659 73.944 1.046 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.051 38.388 1.031 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1316 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1366 | n_water=869 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1203 r_free=0.1365 | n_water=868 | time (s): 108.740 (total time: 111.310) Filter (q & B) r_work=0.1203 r_free=0.1365 | n_water=857 | time (s): 4.590 (total time: 115.900) Compute maps r_work=0.1203 r_free=0.1365 | n_water=857 | time (s): 2.120 (total time: 118.020) Filter (map) r_work=0.1225 r_free=0.1365 | n_water=733 | time (s): 4.660 (total time: 122.680) Find peaks r_work=0.1225 r_free=0.1365 | n_water=733 | time (s): 0.860 (total time: 123.540) Add new water r_work=0.1237 r_free=0.1378 | n_water=951 | time (s): 5.040 (total time: 128.580) Refine new water occ: r_work=0.1200 r_free=0.1345 adp: r_work=0.1201 r_free=0.1345 occ: r_work=0.1199 r_free=0.1345 adp: r_work=0.1198 r_free=0.1345 occ: r_work=0.1197 r_free=0.1344 adp: r_work=0.1197 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1345 r_work=0.1197 r_free=0.1345 | n_water=951 | time (s): 210.810 (total time: 339.390) Filter (q & B) r_work=0.1200 r_free=0.1354 | n_water=887 | time (s): 5.270 (total time: 344.660) Filter (dist only) r_work=0.1200 r_free=0.1352 | n_water=886 | time (s): 113.370 (total time: 458.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.484385 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.184885 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1358 0.0153 0.037 1.1 7.5 0.0 0.3 0 0.742 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.58 1.53 1.745 13.958 14.185 3.764 12.08 13.61 1.53 1.861 13.911 14.185 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 65.55 14.74 0.89 522 3268 Protein: 5.58 29.00 10.45 0.89 0 2902 Water: 5.95 65.55 28.80 N/A 522 364 Other: 13.88 22.91 18.39 N/A 0 2 Chain A: 5.61 51.73 12.33 N/A 0 1623 Chain B: 5.58 65.55 12.15 N/A 0 1645 Chain S: 5.95 64.71 30.41 N/A 522 0 Histogram: Values Number of atoms 5.58 - 11.58 2112 11.58 - 17.57 774 17.57 - 23.57 288 23.57 - 29.57 213 29.57 - 35.56 174 35.56 - 41.56 126 41.56 - 47.56 63 47.56 - 53.55 31 53.55 - 59.55 4 59.55 - 65.55 5 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1361 r_work=0.1208 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1361 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1363 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761831 | | target function (ml) not normalized (work): 704545.876567 | | target function (ml) not normalized (free): 14752.951974 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1206 0.1363 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1515 n_refl.: 191129 remove outliers: r(all,work,free)=0.1403 0.1401 0.1515 n_refl.: 191129 overall B=-0.22 to atoms: r(all,work,free)=0.1369 0.1366 0.1489 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1204 0.1362 n_refl.: 191129 remove outliers: r(all,work,free)=0.1207 0.1204 0.1362 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3733 361.137 330.711 0.418 0.953 0.205 13.296-10.522 97.03 97 1 0.2462 478.461 461.210 0.712 0.955 0.161 10.503-8.327 97.80 175 3 0.2164 502.242 498.092 0.876 0.955 0.138 8.315-6.595 100.00 359 8 0.2185 374.848 371.193 0.901 0.955 0.108 6.588-5.215 100.00 711 7 0.1946 345.318 335.608 0.903 0.955 0.090 5.214-4.128 98.38 1367 28 0.1231 505.095 499.849 0.994 0.955 0.090 4.126-3.266 94.74 2603 46 0.1162 460.422 453.571 1.055 0.955 0.005 3.266-2.585 99.86 5447 97 0.1124 310.589 307.254 1.037 0.955 0.000 2.585-2.046 97.45 10613 204 0.0958 234.322 231.794 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0921 138.683 137.356 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0972 74.659 73.958 1.051 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.051 38.393 1.023 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0487 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1205 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1362 | n_water=886 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1205 r_free=0.1362 | n_water=886 | time (s): 108.090 (total time: 110.570) Filter (q & B) r_work=0.1205 r_free=0.1361 | n_water=875 | time (s): 4.970 (total time: 115.540) Compute maps r_work=0.1205 r_free=0.1361 | n_water=875 | time (s): 2.150 (total time: 117.690) Filter (map) r_work=0.1228 r_free=0.1361 | n_water=747 | time (s): 4.110 (total time: 121.800) Find peaks r_work=0.1228 r_free=0.1361 | n_water=747 | time (s): 0.780 (total time: 122.580) Add new water r_work=0.1238 r_free=0.1377 | n_water=962 | time (s): 4.610 (total time: 127.190) Refine new water occ: r_work=0.1201 r_free=0.1347 adp: r_work=0.1202 r_free=0.1347 occ: r_work=0.1199 r_free=0.1347 adp: r_work=0.1199 r_free=0.1346 occ: r_work=0.1198 r_free=0.1347 adp: r_work=0.1198 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1347 r_work=0.1198 r_free=0.1347 | n_water=962 | time (s): 188.050 (total time: 315.240) Filter (q & B) r_work=0.1202 r_free=0.1350 | n_water=892 | time (s): 4.390 (total time: 319.630) Filter (dist only) r_work=0.1202 r_free=0.1348 | n_water=891 | time (s): 116.840 (total time: 436.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.511454 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.700144 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1359 0.0154 0.038 1.1 8.0 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.59 1.54 1.707 13.649 14.700 3.763 12.04 13.60 1.56 1.732 13.631 14.700 3.759 Individual atomic B min max mean iso aniso Overall: 5.38 64.54 14.50 0.88 527 3268 Protein: 5.38 28.55 10.23 0.88 0 2902 Water: 5.79 64.54 28.40 N/A 527 364 Other: 13.66 22.03 17.85 N/A 0 2 Chain A: 5.44 51.23 12.07 N/A 0 1623 Chain B: 5.38 64.36 11.91 N/A 0 1645 Chain S: 5.79 64.54 30.08 N/A 527 0 Histogram: Values Number of atoms 5.38 - 11.30 2092 11.30 - 17.21 794 17.21 - 23.13 283 23.13 - 29.05 216 29.05 - 34.96 179 34.96 - 40.88 116 40.88 - 46.79 77 46.79 - 52.71 29 52.71 - 58.62 4 58.62 - 64.54 5 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1360 r_work=0.1204 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1360 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 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 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758327 | | target function (ml) not normalized (work): 703889.583028 | | target function (ml) not normalized (free): 14746.488807 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1362 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1372 0.1370 0.1497 n_refl.: 191129 remove outliers: r(all,work,free)=0.1372 0.1370 0.1497 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1372 0.1370 0.1497 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1352 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1193 0.1352 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3729 361.137 330.510 0.434 0.909 0.209 13.296-10.522 97.03 97 1 0.2489 478.461 461.433 0.739 0.910 0.159 10.503-8.327 97.80 175 3 0.2172 502.242 496.528 0.908 0.911 0.137 8.315-6.595 100.00 359 8 0.2209 374.848 370.358 0.936 0.911 0.106 6.588-5.215 100.00 711 7 0.1950 345.318 335.223 0.939 0.911 0.090 5.214-4.128 98.38 1367 28 0.1242 505.095 499.380 1.032 0.912 0.067 4.126-3.266 94.74 2603 46 0.1167 460.422 452.828 1.096 0.913 0.005 3.266-2.585 99.86 5447 97 0.1125 310.589 306.985 1.078 0.913 0.000 2.585-2.046 97.45 10613 204 0.0957 234.322 231.663 1.084 0.915 0.000 2.046-1.619 99.39 21536 464 0.0912 138.683 137.289 1.099 0.917 0.000 1.619-1.281 98.00 42464 925 0.0947 74.659 74.001 1.084 0.921 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.051 38.363 1.044 0.928 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1352 | n_water=891 | time (s): 3.040 (total time: 3.040) Filter (dist) r_work=0.1193 r_free=0.1352 | n_water=891 | time (s): 110.760 (total time: 113.800) Filter (q & B) r_work=0.1193 r_free=0.1352 | n_water=883 | time (s): 4.540 (total time: 118.340) Compute maps r_work=0.1193 r_free=0.1352 | n_water=883 | time (s): 1.690 (total time: 120.030) Filter (map) r_work=0.1215 r_free=0.1360 | n_water=757 | time (s): 4.160 (total time: 124.190) Find peaks r_work=0.1215 r_free=0.1360 | n_water=757 | time (s): 0.540 (total time: 124.730) Add new water r_work=0.1224 r_free=0.1374 | n_water=969 | time (s): 3.870 (total time: 128.600) Refine new water occ: r_work=0.1192 r_free=0.1343 adp: r_work=0.1192 r_free=0.1343 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1342 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1341 r_work=0.1188 r_free=0.1341 | n_water=969 | time (s): 294.310 (total time: 422.910) Filter (q & B) r_work=0.1192 r_free=0.1352 | n_water=896 | time (s): 4.630 (total time: 427.540) Filter (dist only) r_work=0.1192 r_free=0.1350 | n_water=895 | time (s): 116.560 (total time: 544.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554960 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.867589 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1356 0.0161 0.039 1.1 8.7 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.56 1.61 1.674 13.631 14.868 3.757 11.96 13.61 1.65 1.687 13.621 14.868 3.755 Individual atomic B min max mean iso aniso Overall: 5.42 64.58 14.52 0.88 531 3268 Protein: 5.42 28.15 10.24 0.88 0 2902 Water: 5.84 64.58 28.38 N/A 531 364 Other: 13.69 21.94 17.81 N/A 0 2 Chain A: 5.51 50.91 12.04 N/A 0 1623 Chain B: 5.42 63.43 11.89 N/A 0 1645 Chain S: 5.84 64.58 30.23 N/A 531 0 Histogram: Values Number of atoms 5.42 - 11.34 2090 11.34 - 17.25 804 17.25 - 23.17 284 23.17 - 29.08 208 29.08 - 35.00 180 35.00 - 40.92 116 40.92 - 46.83 77 46.83 - 52.75 30 52.75 - 58.67 5 58.67 - 64.58 5 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1361 r_work=0.1196 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1361 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1360 target_work(ml) = 3.755 | | 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= 0.1194 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754849 | | target function (ml) not normalized (work): 703238.111992 | | target function (ml) not normalized (free): 14736.670089 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1380 0.1377 0.1512 n_refl.: 191129 remove outliers: r(all,work,free)=0.1380 0.1377 0.1512 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1380 0.1377 0.1512 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3738 361.137 329.849 0.397 0.974 0.197 13.296-10.522 97.03 97 1 0.2479 478.461 462.122 0.684 0.976 0.148 10.503-8.327 97.80 175 3 0.2192 502.242 496.209 0.846 0.976 0.127 8.315-6.595 100.00 359 8 0.2205 374.848 370.920 0.870 0.976 0.090 6.588-5.215 100.00 711 7 0.1959 345.318 335.104 0.874 0.977 0.090 5.214-4.128 98.38 1367 28 0.1252 505.095 499.159 0.963 0.978 0.063 4.126-3.266 94.74 2603 46 0.1173 460.422 452.700 1.023 0.979 0.000 3.266-2.585 99.86 5447 97 0.1131 310.589 306.953 1.006 0.980 0.000 2.585-2.046 97.45 10613 204 0.0959 234.322 231.642 1.012 0.981 0.000 2.046-1.619 99.39 21536 464 0.0910 138.683 137.313 1.027 0.985 0.000 1.619-1.281 98.00 42464 925 0.0942 74.659 74.008 1.014 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.051 38.354 0.978 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0790 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1358 | n_water=895 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1193 r_free=0.1358 | n_water=895 | time (s): 105.580 (total time: 108.070) Filter (q & B) r_work=0.1194 r_free=0.1359 | n_water=882 | time (s): 4.760 (total time: 112.830) Compute maps r_work=0.1194 r_free=0.1359 | n_water=882 | time (s): 2.350 (total time: 115.180) Filter (map) r_work=0.1217 r_free=0.1368 | n_water=754 | time (s): 5.360 (total time: 120.540) Find peaks r_work=0.1217 r_free=0.1368 | n_water=754 | time (s): 0.690 (total time: 121.230) Add new water r_work=0.1226 r_free=0.1391 | n_water=978 | time (s): 3.910 (total time: 125.140) Refine new water occ: r_work=0.1191 r_free=0.1353 adp: r_work=0.1191 r_free=0.1353 occ: r_work=0.1189 r_free=0.1353 adp: r_work=0.1189 r_free=0.1353 occ: r_work=0.1188 r_free=0.1352 adp: r_work=0.1188 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1352 r_work=0.1188 r_free=0.1352 | n_water=978 | time (s): 187.450 (total time: 312.590) Filter (q & B) r_work=0.1191 r_free=0.1359 | n_water=902 | time (s): 3.990 (total time: 316.580) Filter (dist only) r_work=0.1192 r_free=0.1358 | n_water=901 | time (s): 117.740 (total time: 434.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.477312 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.102661 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1362 0.0166 0.039 1.1 6.5 0.0 0.3 0 0.739 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.62 1.66 1.670 13.611 14.103 3.757 11.97 13.65 1.67 1.672 13.607 14.103 3.756 Individual atomic B min max mean iso aniso Overall: 5.43 63.06 14.49 0.86 537 3268 Protein: 5.43 27.99 10.25 0.86 0 2902 Water: 5.91 63.06 28.11 N/A 537 364 Other: 13.72 21.98 17.85 N/A 0 2 Chain A: 5.54 50.78 12.03 N/A 0 1623 Chain B: 5.43 63.06 11.88 N/A 0 1645 Chain S: 5.91 60.95 29.89 N/A 537 0 Histogram: Values Number of atoms 5.43 - 11.20 2054 11.20 - 16.96 832 16.96 - 22.72 286 22.72 - 28.48 213 28.48 - 34.25 174 34.25 - 40.01 118 40.01 - 45.77 82 45.77 - 51.53 34 51.53 - 57.30 8 57.30 - 63.06 4 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1365 r_work=0.1198 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1366 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755970 | | target function (ml) not normalized (work): 703448.038891 | | target function (ml) not normalized (free): 14739.759816 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1366 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1389 0.1387 0.1520 n_refl.: 191129 remove outliers: r(all,work,free)=0.1389 0.1387 0.1520 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1389 0.1387 0.1520 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1364 n_refl.: 191129 remove outliers: r(all,work,free)=0.1198 0.1195 0.1364 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3758 361.137 328.429 0.386 0.994 0.203 13.296-10.522 97.03 97 1 0.2485 478.461 461.265 0.663 0.996 0.148 10.503-8.327 97.80 175 3 0.2204 502.242 495.585 0.822 0.997 0.123 8.315-6.595 100.00 359 8 0.2227 374.848 370.297 0.848 0.996 0.103 6.588-5.215 100.00 711 7 0.1973 345.318 334.605 0.851 0.997 0.090 5.214-4.128 98.38 1367 28 0.1253 505.095 499.070 0.936 0.998 0.044 4.126-3.266 94.74 2603 46 0.1178 460.422 452.588 0.997 0.999 0.000 3.266-2.585 99.86 5447 97 0.1135 310.589 306.921 0.980 1.000 0.000 2.585-2.046 97.45 10613 204 0.0960 234.322 231.613 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0912 138.683 137.311 1.000 1.007 0.000 1.619-1.281 98.00 42464 925 0.0943 74.659 74.008 0.989 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.051 38.345 0.956 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0424 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1364 After: r_work=0.1196 r_free=0.1365 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1365 | n_water=901 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1196 r_free=0.1365 | n_water=901 | time (s): 115.650 (total time: 118.220) Filter (q & B) r_work=0.1197 r_free=0.1362 | n_water=890 | time (s): 3.980 (total time: 122.200) Compute maps r_work=0.1197 r_free=0.1362 | n_water=890 | time (s): 1.990 (total time: 124.190) Filter (map) r_work=0.1221 r_free=0.1367 | n_water=761 | time (s): 4.610 (total time: 128.800) Find peaks r_work=0.1221 r_free=0.1367 | n_water=761 | time (s): 0.520 (total time: 129.320) Add new water r_work=0.1229 r_free=0.1389 | n_water=976 | time (s): 3.940 (total time: 133.260) Refine new water occ: r_work=0.1195 r_free=0.1356 adp: r_work=0.1195 r_free=0.1356 occ: r_work=0.1193 r_free=0.1356 adp: r_work=0.1193 r_free=0.1356 occ: r_work=0.1191 r_free=0.1356 adp: r_work=0.1191 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1356 r_work=0.1191 r_free=0.1356 | n_water=976 | time (s): 238.850 (total time: 372.110) Filter (q & B) r_work=0.1195 r_free=0.1363 | n_water=901 | time (s): 4.750 (total time: 376.860) Filter (dist only) r_work=0.1196 r_free=0.1362 | n_water=900 | time (s): 118.340 (total time: 495.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.625595 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.724998 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1362 0.0167 0.039 1.1 7.7 0.0 0.3 0 0.813 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.62 1.67 1.665 13.609 14.725 3.756 11.95 13.62 1.67 1.657 13.613 14.725 3.753 Individual atomic B min max mean iso aniso Overall: 5.50 62.07 14.49 0.87 536 3268 Protein: 5.50 28.02 10.28 0.87 0 2902 Water: 5.82 62.07 28.06 N/A 536 364 Other: 13.77 21.99 17.88 N/A 0 2 Chain A: 5.61 50.43 12.03 N/A 0 1623 Chain B: 5.50 62.07 11.89 N/A 0 1645 Chain S: 5.82 61.09 29.91 N/A 536 0 Histogram: Values Number of atoms 5.50 - 11.16 2033 11.16 - 16.82 844 16.82 - 22.47 287 22.47 - 28.13 205 28.13 - 33.79 183 33.79 - 39.45 117 39.45 - 45.10 85 45.10 - 50.76 36 50.76 - 56.42 7 56.42 - 62.07 7 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1362 r_work=0.1195 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1362 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1363 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753423 | | target function (ml) not normalized (work): 702971.167218 | | target function (ml) not normalized (free): 14727.673704 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1373 0.1524 5.7045 5.807| | 2: 2.94 - 2.33 1.00 7339 128 0.1076 0.1334 5.0946 5.1849| | 3: 2.33 - 2.04 0.96 6939 150 0.0900 0.1171 4.6515 4.7396| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1057 4.3912 4.5746| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0994 4.1505 4.2475| | 6: 1.72 - 1.62 0.99 7102 142 0.0895 0.1084 3.9461 4.0725| | 7: 1.62 - 1.54 0.99 7104 148 0.0888 0.1000 3.7968 3.9386| | 8: 1.54 - 1.47 0.96 6798 152 0.0883 0.1294 3.692 3.8917| | 9: 1.47 - 1.41 0.98 6938 155 0.0921 0.1124 3.6139 3.7407| | 10: 1.41 - 1.36 0.99 7022 150 0.0968 0.1163 3.5475 3.6561| | 11: 1.36 - 1.32 0.99 6997 151 0.0987 0.1107 3.4768 3.5689| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1133 3.4544 3.588| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1239 3.4346 3.5585| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1585 3.4312 3.6733| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1254 3.4479 3.4968| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1559 3.4638 3.6654| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1234 3.4338 3.4427| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1710 3.4382 3.5353| | 19: 1.12 - 1.10 0.97 6948 106 0.1465 0.1731 3.418 3.5941| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1573 3.4093 3.4285| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2126 3.4179 3.5042| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1955 3.4133 3.4167| | 23: 1.05 - 1.03 0.97 6827 159 0.2116 0.2036 3.4329 3.487| | 24: 1.03 - 1.02 0.96 6784 133 0.2329 0.2251 3.4355 3.5076| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2525 3.4492 3.5294| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2862 3.416 3.4267| | 27: 0.99 - 0.98 0.94 6647 131 0.3038 0.2811 3.4681 3.396| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 12.31 1.00 0.97 12207.96| | 2: 2.94 - 2.33 7339 128 0.92 13.30 0.99 0.97 5444.84| | 3: 2.33 - 2.04 6939 150 0.96 7.59 1.01 0.98 1682.20| | 4: 2.04 - 1.85 7170 155 0.96 7.64 1.00 0.98 1006.39| | 5: 1.85 - 1.72 7113 159 0.96 8.10 1.00 0.98 638.26| | 6: 1.72 - 1.62 7102 142 0.96 8.04 1.00 0.98 445.04| | 7: 1.62 - 1.54 7104 148 0.96 8.17 1.01 0.99 336.96| | 8: 1.54 - 1.47 6798 152 0.96 8.21 1.01 1.00 276.25| | 9: 1.47 - 1.41 6938 155 0.96 8.31 1.00 1.00 225.43| | 10: 1.41 - 1.36 7022 150 0.96 8.69 1.00 0.99 195.88| | 11: 1.36 - 1.32 6997 151 0.96 8.72 0.99 0.98 169.52| | 12: 1.32 - 1.28 6975 149 0.96 8.84 0.98 0.97 157.57| | 13: 1.28 - 1.25 6907 166 0.96 9.49 1.01 0.98 156.95| | 14: 1.25 - 1.22 7015 112 0.95 10.68 1.01 0.99 162.69| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 1.00 166.78| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.98 160.60| | 17: 1.17 - 1.14 6940 135 0.94 12.26 1.01 0.98 154.39| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.97 147.56| | 19: 1.12 - 1.10 6948 106 0.93 14.10 1.00 0.97 150.48| | 20: 1.10 - 1.08 6884 147 0.92 15.15 1.00 0.96 149.47| | 21: 1.08 - 1.07 6852 152 0.91 16.61 1.00 0.95 152.93| | 22: 1.07 - 1.05 6836 135 0.89 18.27 0.99 0.95 154.84| | 23: 1.05 - 1.03 6827 159 0.87 20.49 0.99 0.94 164.98| | 24: 1.03 - 1.02 6784 133 0.85 23.16 0.99 0.95 179.41| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.97 0.92 182.76| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.90 177.19| | 27: 0.99 - 0.98 6647 131 0.82 26.27 0.98 0.89 161.28| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 147.56 max = 12207.96 mean = 976.42| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.30| |phase err.(test): min = 0.00 max = 89.48 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1363 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1518 n_refl.: 191129 remove outliers: r(all,work,free)=0.1395 0.1393 0.1518 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1395 0.1393 0.1518 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1361 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1193 0.1361 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3786 361.137 326.991 0.390 0.974 0.197 13.296-10.522 97.03 97 1 0.2492 478.461 461.668 0.674 0.976 0.144 10.503-8.327 97.80 175 3 0.2214 502.242 495.314 0.838 0.976 0.113 8.315-6.595 100.00 359 8 0.2214 374.848 370.901 0.865 0.976 0.093 6.588-5.215 100.00 711 7 0.1960 345.318 334.862 0.867 0.977 0.080 5.214-4.128 98.38 1367 28 0.1253 505.095 499.143 0.954 0.978 0.039 4.126-3.266 94.74 2603 46 0.1175 460.422 452.638 1.018 0.979 0.000 3.266-2.585 99.86 5447 97 0.1132 310.589 306.941 1.001 0.980 0.000 2.585-2.046 97.45 10613 204 0.0959 234.322 231.640 1.007 0.983 0.000 2.046-1.619 99.39 21536 464 0.0908 138.683 137.325 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0940 74.659 74.013 1.012 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.051 38.340 0.979 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0096 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2029 0.2019 0.082 5.244 5.2 78.0 14.6 805 0.000 1_bss: 0.1796 0.1954 0.082 5.244 5.2 78.0 14.6 805 0.000 1_settarget: 0.1796 0.1954 0.082 5.244 5.2 78.0 14.6 805 0.000 1_nqh: 0.1796 0.1954 0.082 5.244 5.2 78.0 14.6 805 0.000 1_weight: 0.1796 0.1954 0.082 5.244 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1501 0.039 1.156 5.2 78.0 14.6 805 0.156 1_adp: 0.1302 0.1573 0.039 1.156 5.1 73.0 15.0 805 0.156 1_regHadp: 0.1301 0.1568 0.039 1.156 5.1 73.0 15.0 805 0.156 1_occ: 0.1286 0.1557 0.039 1.156 5.1 73.0 15.0 805 0.156 2_bss: 0.1278 0.1545 0.039 1.156 5.3 73.2 15.2 805 0.156 2_settarget: 0.1278 0.1545 0.039 1.156 5.3 73.2 15.2 805 0.156 2_updatecdl: 0.1278 0.1545 0.039 1.159 5.3 73.2 15.2 805 0.156 2_nqh: 0.1278 0.1545 0.039 1.159 5.3 73.2 15.2 805 0.156 2_sol: 0.1275 0.1514 0.039 1.159 5.3 73.2 16.2 895 n/a 2_weight: 0.1275 0.1514 0.039 1.159 5.3 73.2 16.2 895 n/a 2_xyzrec: 0.1256 0.1533 0.040 1.144 5.3 73.2 16.2 895 n/a 2_adp: 0.1230 0.1522 0.040 1.144 5.4 68.2 16.3 895 n/a 2_regHadp: 0.1230 0.1522 0.040 1.144 5.4 68.2 16.3 895 n/a 2_occ: 0.1224 0.1521 0.040 1.144 5.4 68.2 16.3 895 n/a 3_bss: 0.1231 0.1527 0.040 1.144 5.4 68.2 16.3 895 n/a 3_settarget: 0.1231 0.1527 0.040 1.144 5.4 68.2 16.3 895 n/a 3_updatecdl: 0.1231 0.1527 0.040 1.147 5.4 68.2 16.3 895 n/a 3_nqh: 0.1231 0.1527 0.040 1.147 5.4 68.2 16.3 895 n/a 3_sol: 0.1247 0.1522 0.040 1.147 5.4 68.2 15.5 873 n/a 3_weight: 0.1247 0.1522 0.040 1.147 5.4 68.2 15.5 873 n/a 3_xyzrec: 0.1238 0.1436 0.035 1.100 5.4 68.2 15.5 873 n/a 3_adp: 0.1235 0.1396 0.035 1.100 5.5 67.8 15.3 873 n/a 3_regHadp: 0.1235 0.1397 0.035 1.100 5.5 67.8 15.3 873 n/a 3_occ: 0.1230 0.1379 0.035 1.100 5.5 67.8 15.3 873 n/a 4_bss: 0.1226 0.1373 0.035 1.100 5.5 67.8 15.3 873 n/a 4_settarget: 0.1226 0.1373 0.035 1.100 5.5 67.8 15.3 873 n/a 4_updatecdl: 0.1226 0.1373 0.035 1.105 5.5 67.8 15.3 873 n/a 4_nqh: 0.1226 0.1373 0.035 1.105 5.5 67.8 15.3 873 n/a 4_sol: 0.1215 0.1362 0.035 1.105 5.5 67.8 14.8 828 n/a 4_weight: 0.1215 0.1362 0.035 1.105 5.5 67.8 14.8 828 n/a 4_xyzrec: 0.1212 0.1365 0.036 1.120 5.5 67.8 14.8 828 n/a 4_adp: 0.1207 0.1362 0.036 1.120 5.5 67.2 14.7 828 n/a 4_regHadp: 0.1207 0.1362 0.036 1.120 5.5 67.2 14.7 828 n/a 4_occ: 0.1204 0.1359 0.036 1.120 5.5 67.2 14.7 828 n/a 5_bss: 0.1202 0.1354 0.036 1.120 5.5 67.2 14.7 828 n/a 5_settarget: 0.1202 0.1354 0.036 1.120 5.5 67.2 14.7 828 n/a 5_updatecdl: 0.1202 0.1354 0.036 1.120 5.5 67.2 14.7 828 n/a 5_nqh: 0.1202 0.1354 0.036 1.120 5.5 67.2 14.7 828 n/a 5_sol: 0.1197 0.1350 0.036 1.120 5.5 67.2 14.9 869 n/a 5_weight: 0.1197 0.1350 0.036 1.120 5.5 67.2 14.9 869 n/a 5_xyzrec: 0.1201 0.1357 0.036 1.127 5.5 67.2 14.9 869 n/a 5_adp: 0.1205 0.1363 0.036 1.127 5.5 66.8 14.8 869 n/a 5_regHadp: 0.1205 0.1363 0.036 1.127 5.5 66.8 14.8 869 n/a 5_occ: 0.1203 0.1368 0.036 1.127 5.5 66.8 14.8 869 n/a 6_bss: 0.1202 0.1366 0.036 1.127 5.5 66.7 14.8 869 n/a 6_settarget: 0.1202 0.1366 0.036 1.127 5.5 66.7 14.8 869 n/a 6_updatecdl: 0.1202 0.1366 0.036 1.127 5.5 66.7 14.8 869 n/a 6_nqh: 0.1202 0.1366 0.036 1.127 5.5 66.7 14.8 869 n/a 6_sol: 0.1200 0.1352 0.036 1.127 5.5 66.7 14.8 886 n/a 6_weight: 0.1200 0.1352 0.036 1.127 5.5 66.7 14.8 886 n/a 6_xyzrec: 0.1205 0.1358 0.037 1.119 5.5 66.7 14.8 886 n/a 6_adp: 0.1208 0.1361 0.037 1.119 5.6 65.5 14.7 886 n/a 6_regHadp: 0.1208 0.1361 0.037 1.119 5.6 65.5 14.7 886 n/a 6_occ: 0.1206 0.1363 0.037 1.119 5.6 65.5 14.7 886 n/a 7_bss: 0.1205 0.1362 0.037 1.119 5.4 65.3 14.5 886 n/a 7_settarget: 0.1205 0.1362 0.037 1.119 5.4 65.3 14.5 886 n/a 7_updatecdl: 0.1205 0.1362 0.037 1.119 5.4 65.3 14.5 886 n/a 7_nqh: 0.1205 0.1362 0.037 1.119 5.4 65.3 14.5 886 n/a 7_sol: 0.1202 0.1348 0.037 1.119 5.4 65.3 14.5 891 n/a 7_weight: 0.1202 0.1348 0.037 1.119 5.4 65.3 14.5 891 n/a 7_xyzrec: 0.1205 0.1359 0.038 1.120 5.4 65.3 14.5 891 n/a 7_adp: 0.1204 0.1360 0.038 1.120 5.4 64.5 14.5 891 n/a 7_regHadp: 0.1204 0.1360 0.038 1.120 5.4 64.5 14.5 891 n/a 7_occ: 0.1202 0.1362 0.038 1.120 5.4 64.5 14.5 891 n/a 8_bss: 0.1193 0.1352 0.038 1.120 5.4 64.5 14.5 891 n/a 8_settarget: 0.1193 0.1352 0.038 1.120 5.4 64.5 14.5 891 n/a 8_updatecdl: 0.1193 0.1352 0.038 1.120 5.4 64.5 14.5 891 n/a 8_nqh: 0.1193 0.1352 0.038 1.120 5.4 64.5 14.5 891 n/a 8_sol: 0.1192 0.1350 0.038 1.120 5.4 64.5 14.5 895 n/a 8_weight: 0.1192 0.1350 0.038 1.120 5.4 64.5 14.5 895 n/a 8_xyzrec: 0.1195 0.1356 0.039 1.118 5.4 64.5 14.5 895 n/a 8_adp: 0.1196 0.1361 0.039 1.118 5.4 64.6 14.5 895 n/a 8_regHadp: 0.1196 0.1361 0.039 1.118 5.4 64.6 14.5 895 n/a 8_occ: 0.1194 0.1360 0.039 1.118 5.4 64.6 14.5 895 n/a 9_bss: 0.1193 0.1358 0.039 1.118 5.4 64.6 14.5 895 n/a 9_settarget: 0.1193 0.1358 0.039 1.118 5.4 64.6 14.5 895 n/a 9_updatecdl: 0.1193 0.1358 0.039 1.118 5.4 64.6 14.5 895 n/a 9_nqh: 0.1193 0.1358 0.039 1.118 5.4 64.6 14.5 895 n/a 9_sol: 0.1192 0.1358 0.039 1.118 5.4 63.4 14.5 901 n/a 9_weight: 0.1192 0.1358 0.039 1.118 5.4 63.4 14.5 901 n/a 9_xyzrec: 0.1196 0.1362 0.039 1.107 5.4 63.4 14.5 901 n/a 9_adp: 0.1198 0.1365 0.039 1.107 5.4 63.1 14.5 901 n/a 9_regHadp: 0.1198 0.1365 0.039 1.107 5.4 63.1 14.5 901 n/a 9_occ: 0.1196 0.1366 0.039 1.107 5.4 63.1 14.5 901 n/a 10_bss: 0.1195 0.1364 0.039 1.107 5.4 63.1 14.5 901 n/a 10_settarget: 0.1195 0.1364 0.039 1.107 5.4 63.1 14.5 901 n/a 10_updatecdl: 0.1195 0.1364 0.039 1.107 5.4 63.1 14.5 901 n/a 10_setrh: 0.1196 0.1365 0.039 1.107 5.4 63.1 14.5 901 n/a 10_nqh: 0.1196 0.1365 0.039 1.107 5.4 63.1 14.5 901 n/a 10_sol: 0.1196 0.1362 0.039 1.107 5.4 63.1 14.5 900 n/a 10_weight: 0.1196 0.1362 0.039 1.107 5.4 63.1 14.5 900 n/a 10_xyzrec: 0.1196 0.1362 0.039 1.111 5.4 63.1 14.5 900 n/a 10_adp: 0.1195 0.1362 0.039 1.111 5.5 62.1 14.5 900 n/a 10_regHadp: 0.1195 0.1362 0.039 1.111 5.5 62.1 14.5 900 n/a 10_occ: 0.1194 0.1363 0.039 1.111 5.5 62.1 14.5 900 n/a end: 0.1193 0.1361 0.039 1.111 5.5 62.1 14.5 900 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6548452_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6548452_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.9700 Refinement macro-cycles (run) : 11927.4500 Write final files (write_after_run_outputs) : 154.9700 Total : 12088.3900 Total CPU time: 3.37 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:38:36 PST -0800 (1736735917.00 s) Start R-work = 0.1796, R-free = 0.1954 Final R-work = 0.1193, R-free = 0.1361 =============================================================================== Job complete usr+sys time: 12385.30 seconds wall clock time: 207 minutes 22.83 seconds (12442.83 seconds total)