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_4848787.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4848787.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4848787.pdb" 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" } 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 =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s 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: 1.74, 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: 2.721 distance_ideal: 2.720 ideal - model: -0.001 slack: 0.000 delta_slack: -0.001 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: 2.681 distance_ideal: 2.710 ideal - model: 0.029 slack: 0.000 delta_slack: 0.029 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: 0.85 Conformation dependent library (CDL) restraints added in 111.0 milliseconds Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.02: 740 1.02 - 1.25: 2492 1.25 - 1.48: 1467 1.48 - 1.71: 1209 1.71 - 1.94: 26 Bond restraints: 5934 Sorted by residual: bond pdb=" NE ARG B 149 " pdb=" CZ ARG B 149 " ideal model delta sigma weight residual 1.326 1.083 0.243 1.10e-02 8.26e+03 4.90e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.725 -0.266 1.20e-02 6.94e+03 4.90e+02 bond pdb=" CA GLU B 17 " pdb=" C GLU B 17 " ideal model delta sigma weight residual 1.524 1.784 -0.260 1.26e-02 6.30e+03 4.25e+02 bond pdb=" C GLN A 184 " pdb=" O GLN A 184 " ideal model delta sigma weight residual 1.236 1.491 -0.255 1.29e-02 6.01e+03 3.92e+02 bond pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta sigma weight residual 1.463 1.698 -0.236 1.21e-02 6.83e+03 3.79e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 5282 3.91 - 7.82: 3526 7.82 - 11.73: 1565 11.73 - 15.64: 379 15.64 - 19.55: 58 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA A 57 " pdb=" C ALA A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 121.85 133.32 -11.47 7.00e-01 2.04e+00 2.68e+02 angle pdb=" O GLY B 29 " pdb=" C GLY B 29 " pdb=" N ILE B 30 " ideal model delta sigma weight residual 122.32 141.22 -18.90 1.24e+00 6.50e-01 2.32e+02 angle pdb=" CA VAL A 144 " pdb=" C VAL A 144 " pdb=" O VAL A 144 " ideal model delta sigma weight residual 120.39 105.48 14.91 1.05e+00 9.07e-01 2.02e+02 angle pdb=" O THR A 21 " pdb=" C THR A 21 " pdb=" N ILE A 22 " ideal model delta sigma weight residual 122.15 137.71 -15.56 1.14e+00 7.69e-01 1.86e+02 angle pdb=" O PHE A 164 " pdb=" C PHE A 164 " pdb=" N GLY A 165 " ideal model delta sigma weight residual 122.09 107.49 14.60 1.08e+00 8.57e-01 1.83e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 1832 16.99 - 33.99: 143 33.99 - 50.98: 50 50.98 - 67.97: 19 67.97 - 84.96: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ILE B 45 " pdb=" C ILE B 45 " pdb=" N THR B 46 " pdb=" CA THR B 46 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 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 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 183 0.186 - 0.372: 145 0.372 - 0.559: 102 0.559 - 0.745: 48 0.745 - 0.931: 14 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB VAL A 144 " pdb=" CA VAL A 144 " pdb=" CG1 VAL A 144 " pdb=" CG2 VAL A 144 " both_signs ideal model delta sigma weight residual False -2.63 -1.70 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" CA PHE B 119 " pdb=" N PHE B 119 " pdb=" C PHE B 119 " pdb=" CB PHE B 119 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" CA GLU B 80 " pdb=" N GLU B 80 " pdb=" C GLU B 80 " pdb=" CB GLU B 80 " both_signs ideal model delta sigma weight residual False 2.51 3.39 -0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.122 2.00e-02 2.50e+03 8.50e-02 2.17e+02 pdb=" CG PHE B 164 " 0.059 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.172 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.074 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.058 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.143 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.047 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.022 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.102 2.00e-02 2.50e+03 6.44e-02 1.66e+02 pdb=" CG TRP A 139 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.098 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.076 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.090 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.118 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.076 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.046 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " 0.027 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.076 2.00e-02 2.50e+03 6.00e-02 1.44e+02 pdb=" CG TRP A 146 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.071 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.098 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.120 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.028 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.016 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.039 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.020 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " 0.005 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.039 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.099 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.61: 28 1.61 - 2.36: 2367 2.36 - 3.11: 22378 3.11 - 3.85: 32903 3.85 - 4.60: 52598 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110274 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.868 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.948 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.985 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.078 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.191 2.620 ... (remaining 110269 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_4848787_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= 0.2040 r_free= 0.1981 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.305429 | | target function (ml) not normalized (work): 806462.814102 | | target function (ml) not normalized (free): 16565.198713 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2150 0.1835 6.7154 6.2871| | 2: 2.94 - 2.33 1.00 7339 128 0.1615 0.1614 5.5254 5.5656| | 3: 2.33 - 2.04 0.96 6939 150 0.1624 0.1656 5.1512 5.1752| | 4: 2.04 - 1.85 1.00 7170 155 0.1758 0.1559 4.9776 5.0553| | 5: 1.85 - 1.72 0.99 7113 159 0.1928 0.1872 4.8126 4.8898| | 6: 1.72 - 1.62 0.99 7102 142 0.1999 0.2087 4.6729 4.774| | 7: 1.62 - 1.54 0.99 7104 148 0.2018 0.1682 4.5554 4.5114| | 8: 1.54 - 1.47 0.96 6798 152 0.2057 0.2304 4.4693 4.5782| | 9: 1.47 - 1.41 0.98 6938 155 0.2093 0.2186 4.4037 4.4589| | 10: 1.41 - 1.36 0.99 7022 150 0.2171 0.2123 4.328 4.3574| | 11: 1.36 - 1.32 0.99 6997 151 0.2081 0.2107 4.2386 4.2425| | 12: 1.32 - 1.28 0.98 6976 149 0.2094 0.2034 4.181 4.2622| | 13: 1.28 - 1.25 0.98 6907 166 0.2025 0.2104 4.1379 4.1496| | 14: 1.25 - 1.22 0.98 7015 113 0.2097 0.2399 4.08 4.2406| | 15: 1.22 - 1.19 0.98 6957 137 0.2102 0.1981 4.0413 4.0433| | 16: 1.19 - 1.17 0.93 6604 132 0.2110 0.2246 3.9943 4.061| | 17: 1.17 - 1.14 0.98 6941 135 0.2190 0.1773 3.9583 3.8743| | 18: 1.14 - 1.12 0.98 6875 142 0.2209 0.2127 3.9277 3.8294| | 19: 1.12 - 1.10 0.97 6949 106 0.2276 0.2587 3.8734 4.0076| | 20: 1.10 - 1.08 0.97 6884 147 0.2325 0.2447 3.829 3.8821| | 21: 1.08 - 1.07 0.97 6852 152 0.2463 0.2782 3.8034 3.8481| | 22: 1.07 - 1.05 0.97 6838 135 0.2570 0.2830 3.7658 3.7933| | 23: 1.05 - 1.03 0.97 6829 159 0.2686 0.2640 3.7233 3.7821| | 24: 1.03 - 1.02 0.96 6785 133 0.2898 0.2751 3.7062 3.7503| | 25: 1.02 - 1.01 0.93 6552 130 0.3044 0.3007 3.6717 3.7632| | 26: 1.01 - 0.99 0.96 6767 158 0.3255 0.3336 3.6354 3.6533| | 27: 0.99 - 0.98 0.94 6648 131 0.3446 0.2959 3.6527 3.5973| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.94 0.91 0.98 33620.79| | 2: 2.94 - 2.33 7339 128 0.86 20.91 1.09 1.02 14580.24| | 3: 2.33 - 2.04 6939 150 0.93 12.76 1.10 1.05 4297.17| | 4: 2.04 - 1.85 7170 155 0.92 14.06 1.11 1.05 2948.04| | 5: 1.85 - 1.72 7113 159 0.90 16.19 1.11 1.06 2181.19| | 6: 1.72 - 1.62 7102 142 0.90 17.23 1.12 1.06 1698.79| | 7: 1.62 - 1.54 7104 148 0.89 17.43 1.11 1.06 1313.18| | 8: 1.54 - 1.47 6798 152 0.89 18.07 1.10 1.06 1114.44| | 9: 1.47 - 1.41 6938 155 0.88 18.64 1.10 1.08 959.64| | 10: 1.41 - 1.36 7022 150 0.87 20.03 1.10 1.06 860.87| | 11: 1.36 - 1.32 6997 151 0.87 20.10 1.08 1.06 756.06| | 12: 1.32 - 1.28 6976 149 0.87 19.94 1.07 1.04 667.37| | 13: 1.28 - 1.25 6907 166 0.87 20.01 1.06 1.05 621.84| | 14: 1.25 - 1.22 7015 113 0.86 20.87 1.07 1.03 577.98| | 15: 1.22 - 1.19 6957 137 0.86 20.88 1.08 1.03 535.58| | 16: 1.19 - 1.17 6604 132 0.88 19.62 1.08 1.03 453.02| | 17: 1.17 - 1.14 6941 135 0.88 19.51 1.08 1.02 387.35| | 18: 1.14 - 1.12 6875 142 0.88 19.62 1.08 1.00 352.20| | 19: 1.12 - 1.10 6949 106 0.86 21.85 1.07 0.99 368.21| | 20: 1.10 - 1.08 6884 147 0.84 23.72 1.06 0.99 377.98| | 21: 1.08 - 1.07 6852 152 0.82 25.48 1.06 0.97 372.37| | 22: 1.07 - 1.05 6838 135 0.81 26.59 1.05 0.96 351.43| | 23: 1.05 - 1.03 6829 159 0.79 28.11 1.06 0.96 339.56| | 24: 1.03 - 1.02 6785 133 0.77 29.92 1.05 0.97 337.26| | 25: 1.02 - 1.01 6552 130 0.76 31.08 1.03 0.93 319.41| | 26: 1.01 - 0.99 6767 158 0.74 32.60 1.03 0.91 292.64| | 27: 0.99 - 0.98 6648 131 0.76 31.29 1.04 0.90 257.37| |alpha: min = 0.90 max = 1.08 mean = 1.01| |beta: min = 257.37 max = 33620.79 mean = 2749.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.64| |phase err.(test): min = 0.00 max = 88.89 mean = 21.61| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.266 2950 Z= 5.368 Angle : 5.313 18.896 4018 Z= 3.765 Chirality : 0.362 0.931 492 Planarity : 0.035 0.144 512 Dihedral : 13.417 84.963 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 21.43 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.63 % Favored : 95.85 % Rotamer: Outliers : 1.61 % Allowed : 4.19 % Favored : 94.19 % Cbeta Deviations : 32.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.39), residues: 386 helix: -1.85 (0.35), residues: 146 sheet: -1.42 (0.51), residues: 86 loop : -0.40 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.020 ARG B 143 TYR 0.086 0.034 TYR A 195 PHE 0.134 0.039 PHE B 164 TRP 0.143 0.048 TRP A 139 HIS 0.099 0.038 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2040 r_free= 0.1981 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.305429 | | target function (ml) not normalized (work): 806462.814102 | | target function (ml) not normalized (free): 16565.198713 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2038 0.2040 0.1981 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2038 0.2040 0.1981 n_refl.: 191155 remove outliers: r(all,work,free)=0.2038 0.2040 0.1981 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2040 0.2042 0.1982 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1806 0.1905 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1804 0.1905 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.4052 398.008 292.953 0.423 0.934 0.297 13.296-10.522 99.01 99 1 0.2501 528.187 518.458 0.762 0.935 0.246 10.503-8.327 98.90 177 3 0.2473 564.205 559.512 0.945 0.935 0.223 8.318-6.595 100.00 360 8 0.2466 414.736 403.847 0.946 0.935 0.170 6.588-5.215 100.00 711 7 0.2313 381.101 366.490 0.935 0.935 0.160 5.214-4.128 98.38 1367 28 0.1475 557.435 548.664 1.050 0.934 0.080 4.126-3.266 94.74 2603 46 0.1348 508.132 499.156 1.120 0.933 0.023 3.266-2.585 99.86 5447 97 0.1443 342.774 337.377 1.096 0.931 0.000 2.585-2.046 97.45 10613 204 0.1402 258.603 254.246 1.102 0.928 0.000 2.046-1.619 99.39 21536 464 0.1633 153.054 149.758 1.126 0.922 0.000 1.619-1.281 98.00 42464 925 0.1922 82.395 80.196 1.121 0.913 0.000 1.281-0.980 96.53 101826 2056 0.2324 44.203 41.662 1.121 0.896 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0204 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1905 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 r_work=0.1804 r_free=0.1904 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.499812 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 580.310654 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1269 0.1499 0.0229 0.039 1.2 11.0 0.0 0.3 0 11.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.69 14.99 2.29 1.118 13.123 580.311 0.018 12.97 15.65 2.68 1.270 13.394 580.311 0.017 Individual atomic B min max mean iso aniso Overall: 5.23 73.06 15.10 1.42 435 3274 Protein: 5.23 40.94 11.03 1.42 0 2902 Water: 6.40 73.06 29.76 N/A 435 370 Other: 15.91 29.35 22.63 N/A 0 2 Chain A: 5.26 60.51 13.12 N/A 0 1626 Chain B: 5.23 73.06 12.82 N/A 0 1648 Chain S: 11.48 64.93 31.16 N/A 435 0 Histogram: Values Number of atoms 5.23 - 12.02 2176 12.02 - 18.80 627 18.80 - 25.58 312 25.58 - 32.36 257 32.36 - 39.15 160 39.15 - 45.93 106 45.93 - 52.71 47 52.71 - 59.49 18 59.49 - 66.27 5 66.27 - 73.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1565 r_work=0.1296 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1561 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1281 r_free = 0.1548 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015469 | | target function (ls_wunit_k1) not normalized (work): 2897.265002 | | target function (ls_wunit_k1) not normalized (free): 114.530974 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1548 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1468 0.1466 0.1631 n_refl.: 191137 remove outliers: r(all,work,free)=0.1468 0.1466 0.1631 n_refl.: 191137 overall B=0.17 to atoms: r(all,work,free)=0.1492 0.1490 0.1641 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1542 n_refl.: 191137 remove outliers: r(all,work,free)=0.1280 0.1275 0.1541 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3591 398.008 376.652 0.485 0.963 0.276 13.296-10.522 99.01 99 1 0.2090 528.187 521.497 0.739 0.965 0.245 10.503-8.327 98.90 177 3 0.1708 564.205 562.397 0.887 0.965 0.203 8.318-6.595 100.00 360 8 0.1713 414.736 412.536 0.909 0.964 0.160 6.588-5.215 100.00 711 7 0.1524 381.101 373.627 0.887 0.965 0.150 5.214-4.128 98.38 1367 28 0.0901 557.435 555.087 0.976 0.965 0.049 4.126-3.266 94.74 2603 46 0.0829 508.132 504.248 1.043 0.966 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.304 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.342 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.382 1.055 0.966 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.418 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.170 1.023 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0385 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 r_work=0.1276 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1541 | n_water=805 | time (s): 2.920 (total time: 2.920) Filter (dist) r_work=0.1282 r_free=0.1548 | n_water=793 | time (s): 98.350 (total time: 101.270) Filter (q & B) r_work=0.1282 r_free=0.1546 | n_water=789 | time (s): 5.290 (total time: 106.560) Compute maps r_work=0.1282 r_free=0.1546 | n_water=789 | time (s): 1.660 (total time: 108.220) Filter (map) r_work=0.1307 r_free=0.1525 | n_water=653 | time (s): 4.890 (total time: 113.110) Find peaks r_work=0.1307 r_free=0.1525 | n_water=653 | time (s): 0.630 (total time: 113.740) Add new water r_work=0.1330 r_free=0.1557 | n_water=969 | time (s): 4.970 (total time: 118.710) Refine new water occ: r_work=0.1286 r_free=0.1505 adp: r_work=0.1273 r_free=0.1504 occ: r_work=0.1275 r_free=0.1500 adp: r_work=0.1269 r_free=0.1501 occ: r_work=0.1270 r_free=0.1498 adp: r_work=0.1268 r_free=0.1499 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1499 r_work=0.1268 r_free=0.1499 | n_water=969 | time (s): 89.830 (total time: 208.540) Filter (q & B) r_work=0.1271 r_free=0.1500 | n_water=900 | time (s): 4.480 (total time: 213.020) Filter (dist only) r_work=0.1271 r_free=0.1499 | n_water=899 | time (s): 111.270 (total time: 324.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.861390 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 592.518593 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 0.1252 0.1515 0.0263 0.042 1.2 20.4 0.0 0.3 0 11.931 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.15 2.63 2.058 15.304 592.519 0.014 12.31 15.08 2.77 2.452 15.329 592.519 0.014 Individual atomic B min max mean iso aniso Overall: 5.48 69.42 16.45 1.22 531 3272 Protein: 5.48 40.60 11.00 1.22 0 2902 Water: 6.65 69.42 34.05 N/A 531 368 Other: 16.40 32.08 24.24 N/A 0 2 Chain A: 5.57 56.70 13.03 N/A 0 1624 Chain B: 5.48 68.23 12.86 N/A 0 1648 Chain S: 9.53 69.42 38.07 N/A 531 0 Histogram: Values Number of atoms 5.48 - 11.87 2113 11.87 - 18.27 673 18.27 - 24.66 264 24.66 - 31.05 215 31.05 - 37.45 169 37.45 - 43.84 174 43.84 - 50.24 95 50.24 - 56.63 54 56.63 - 63.02 36 63.02 - 69.42 10 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1508 r_work=0.1232 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1509 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1508 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1508 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013239 | | target function (ls_wunit_k1) not normalized (work): 2479.582501 | | target function (ls_wunit_k1) not normalized (free): 99.289661 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1225 0.1508 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1433 0.1430 0.1589 n_refl.: 191136 remove outliers: r(all,work,free)=0.1433 0.1430 0.1589 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1587 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1232 0.1516 n_refl.: 191136 remove outliers: r(all,work,free)=0.1237 0.1232 0.1516 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3187 398.008 372.889 0.486 0.963 0.266 13.296-10.522 99.01 99 1 0.1794 528.187 520.781 0.757 0.965 0.219 10.503-8.327 98.90 177 3 0.1299 564.205 567.770 0.921 0.964 0.200 8.318-6.595 100.00 360 8 0.1533 414.736 414.848 0.933 0.964 0.145 6.588-5.215 100.00 711 7 0.1319 381.101 376.812 0.913 0.964 0.140 5.214-4.128 98.38 1367 28 0.0820 557.435 555.922 0.993 0.964 0.080 4.126-3.266 94.74 2603 46 0.0754 508.132 505.560 1.059 0.964 0.009 3.266-2.585 99.86 5447 97 0.0848 342.774 341.342 1.046 0.963 0.000 2.585-2.046 97.45 10613 204 0.0900 258.603 256.866 1.057 0.962 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.639 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1261 82.395 81.355 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.219 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=-0.0516 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1516 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1516 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1516 | n_water=899 | time (s): 3.350 (total time: 3.350) Filter (dist) r_work=0.1233 r_free=0.1517 | n_water=896 | time (s): 117.680 (total time: 121.030) Filter (q & B) r_work=0.1233 r_free=0.1517 | n_water=895 | time (s): 5.760 (total time: 126.790) Compute maps r_work=0.1233 r_free=0.1517 | n_water=895 | time (s): 1.800 (total time: 128.590) Filter (map) r_work=0.1275 r_free=0.1523 | n_water=696 | time (s): 5.040 (total time: 133.630) Find peaks r_work=0.1275 r_free=0.1523 | n_water=696 | time (s): 0.770 (total time: 134.400) Add new water r_work=0.1298 r_free=0.1549 | n_water=1014 | time (s): 4.700 (total time: 139.100) Refine new water occ: r_work=0.1253 r_free=0.1524 adp: r_work=0.1253 r_free=0.1525 occ: r_work=0.1248 r_free=0.1523 adp: r_work=0.1248 r_free=0.1523 occ: r_work=0.1245 r_free=0.1521 adp: r_work=0.1244 r_free=0.1521 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1521 r_work=0.1244 r_free=0.1521 | n_water=1014 | time (s): 253.350 (total time: 392.450) Filter (q & B) r_work=0.1249 r_free=0.1524 | n_water=885 | time (s): 5.990 (total time: 398.440) Filter (dist only) r_work=0.1249 r_free=0.1524 | n_water=884 | time (s): 124.670 (total time: 523.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.690361 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.492172 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 0.1240 0.1444 0.0204 0.036 1.1 7.7 0.0 0.0 0 0.845 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.44 2.04 1.940 14.669 16.492 3.941 12.34 14.00 1.66 2.276 14.564 16.492 3.897 Individual atomic B min max mean iso aniso Overall: 5.54 67.73 15.38 1.06 517 3271 Protein: 5.54 36.50 10.73 1.06 0 2902 Water: 6.73 67.73 30.62 N/A 517 367 Other: 13.79 27.94 20.87 N/A 0 2 Chain A: 5.57 55.59 12.77 N/A 0 1624 Chain B: 5.54 67.73 12.55 N/A 0 1647 Chain S: 13.29 63.73 32.58 N/A 517 0 Histogram: Values Number of atoms 5.54 - 11.76 2132 11.76 - 17.98 685 17.98 - 24.20 294 24.20 - 30.42 240 30.42 - 36.64 168 36.64 - 42.86 147 42.86 - 49.08 75 49.08 - 55.29 34 55.29 - 61.51 8 61.51 - 67.73 5 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1401 r_work=0.1235 r_free=0.1402 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1402 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1395 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.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891552 | | target function (ml) not normalized (work): 728868.212016 | | target function (ml) not normalized (free): 15224.698439 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1395 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1441 0.1440 0.1502 n_refl.: 191136 remove outliers: r(all,work,free)=0.1441 0.1440 0.1502 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1435 0.1434 0.1498 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1390 n_refl.: 191136 remove outliers: r(all,work,free)=0.1228 0.1225 0.1390 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3817 398.008 360.307 0.421 0.946 0.251 13.296-10.522 99.01 99 1 0.2418 528.187 507.222 0.708 0.948 0.211 10.503-8.327 98.90 177 3 0.1956 564.205 561.778 0.886 0.947 0.195 8.318-6.595 100.00 360 8 0.2063 414.736 410.679 0.898 0.947 0.134 6.588-5.215 100.00 711 7 0.1850 381.101 370.941 0.887 0.947 0.113 5.214-4.128 98.38 1367 28 0.1174 557.435 551.995 0.972 0.947 0.070 4.126-3.266 94.74 2603 46 0.1095 508.132 501.460 1.033 0.948 0.005 3.266-2.585 99.86 5447 97 0.1087 342.774 339.145 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0971 258.603 255.776 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.427 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.498 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.326 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=-0.1042 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1390 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1390 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1390 | n_water=884 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1226 r_free=0.1394 | n_water=882 | time (s): 108.170 (total time: 110.530) Filter (q & B) r_work=0.1227 r_free=0.1393 | n_water=870 | time (s): 5.260 (total time: 115.790) Compute maps r_work=0.1227 r_free=0.1393 | n_water=870 | time (s): 2.040 (total time: 117.830) Filter (map) r_work=0.1251 r_free=0.1386 | n_water=716 | time (s): 3.850 (total time: 121.680) Find peaks r_work=0.1251 r_free=0.1386 | n_water=716 | time (s): 0.540 (total time: 122.220) Add new water r_work=0.1266 r_free=0.1414 | n_water=971 | time (s): 4.380 (total time: 126.600) Refine new water occ: r_work=0.1217 r_free=0.1370 adp: r_work=0.1210 r_free=0.1366 occ: r_work=0.1207 r_free=0.1367 adp: r_work=0.1207 r_free=0.1367 occ: r_work=0.1207 r_free=0.1367 adp: r_work=0.1207 r_free=0.1367 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1367 r_work=0.1207 r_free=0.1367 | n_water=971 | time (s): 214.740 (total time: 341.340) Filter (q & B) r_work=0.1213 r_free=0.1376 | n_water=838 | time (s): 5.970 (total time: 347.310) Filter (dist only) r_work=0.1213 r_free=0.1378 | n_water=836 | time (s): 111.060 (total time: 458.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.606852 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.822586 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 0.1211 0.1379 0.0167 0.033 1.1 6.0 0.0 0.3 0 0.803 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 13.79 1.67 1.829 14.085 15.823 3.875 12.04 13.76 1.72 1.934 14.051 15.823 3.866 Individual atomic B min max mean iso aniso Overall: 5.50 67.24 14.78 1.00 469 3271 Protein: 5.50 33.24 10.66 1.00 0 2902 Water: 5.81 67.24 29.08 N/A 469 367 Other: 13.98 26.81 20.39 N/A 0 2 Chain A: 5.52 54.37 12.65 N/A 0 1624 Chain B: 5.50 67.24 12.46 N/A 0 1647 Chain S: 5.81 61.25 30.36 N/A 469 0 Histogram: Values Number of atoms 5.50 - 11.67 2104 11.67 - 17.85 739 17.85 - 24.02 332 24.02 - 30.19 193 30.19 - 36.37 146 36.37 - 42.54 127 42.54 - 48.72 63 48.72 - 54.89 29 54.89 - 61.07 5 61.07 - 67.24 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1376 r_work=0.1204 r_free=0.1376 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1376 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1374 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864839 | | target function (ml) not normalized (work): 723864.950010 | | target function (ml) not normalized (free): 15142.349678 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1202 0.1375 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1434 0.1433 0.1499 n_refl.: 191136 remove outliers: r(all,work,free)=0.1434 0.1433 0.1499 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1427 0.1426 0.1495 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1201 0.1373 n_refl.: 191136 remove outliers: r(all,work,free)=0.1204 0.1201 0.1373 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3813 360.391 324.406 0.422 0.945 0.254 13.296-10.522 99.01 99 1 0.2538 478.267 457.269 0.699 0.946 0.200 10.503-8.327 97.80 175 3 0.2093 501.899 503.229 0.879 0.946 0.177 8.318-6.595 100.00 360 8 0.2184 375.538 369.762 0.892 0.946 0.119 6.588-5.215 100.00 711 7 0.1922 345.082 335.187 0.884 0.946 0.100 5.214-4.128 98.38 1367 28 0.1221 504.750 499.095 0.973 0.946 0.070 4.126-3.266 94.74 2603 46 0.1138 460.107 453.242 1.036 0.946 0.000 3.266-2.585 99.86 5447 97 0.1089 310.377 307.087 1.023 0.946 0.000 2.585-2.046 97.45 10613 204 0.0943 234.162 231.623 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0915 138.588 137.242 1.058 0.945 0.000 1.619-1.281 98.00 42464 925 0.0987 74.608 73.861 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.024 38.342 1.039 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1149 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1373 | n_water=836 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1201 r_free=0.1373 | n_water=836 | time (s): 99.160 (total time: 101.630) Filter (q & B) r_work=0.1201 r_free=0.1372 | n_water=830 | time (s): 5.340 (total time: 106.970) Compute maps r_work=0.1201 r_free=0.1372 | n_water=830 | time (s): 1.580 (total time: 108.550) Filter (map) r_work=0.1222 r_free=0.1360 | n_water=719 | time (s): 4.820 (total time: 113.370) Find peaks r_work=0.1222 r_free=0.1360 | n_water=719 | time (s): 0.680 (total time: 114.050) Add new water r_work=0.1234 r_free=0.1386 | n_water=958 | time (s): 4.670 (total time: 118.720) Refine new water occ: r_work=0.1197 r_free=0.1354 adp: r_work=0.1197 r_free=0.1354 occ: r_work=0.1195 r_free=0.1354 adp: r_work=0.1195 r_free=0.1353 occ: r_work=0.1193 r_free=0.1353 adp: r_work=0.1193 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1353 r_work=0.1193 r_free=0.1353 | n_water=958 | time (s): 260.140 (total time: 378.860) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=874 | time (s): 5.050 (total time: 383.910) Filter (dist only) r_work=0.1197 r_free=0.1362 | n_water=873 | time (s): 113.090 (total time: 497.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.583567 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.704998 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1369 0.0169 0.036 1.1 6.6 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.69 1.69 1.791 14.046 15.705 3.764 12.03 13.72 1.68 1.853 14.019 15.705 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 66.88 14.80 0.96 507 3270 Protein: 5.58 32.31 10.59 0.96 0 2902 Water: 5.95 66.88 28.78 N/A 507 366 Other: 13.79 25.74 19.77 N/A 0 2 Chain A: 5.58 53.55 12.55 N/A 0 1624 Chain B: 5.58 66.88 12.35 N/A 0 1646 Chain S: 5.95 61.10 29.97 N/A 507 0 Histogram: Values Number of atoms 5.58 - 11.71 2138 11.71 - 17.84 722 17.84 - 23.97 315 23.97 - 30.10 225 30.10 - 36.23 159 36.23 - 42.36 124 42.36 - 48.49 61 48.49 - 54.62 27 54.62 - 60.75 4 60.75 - 66.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1372 r_work=0.1203 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1372 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1374 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760981 | | target function (ml) not normalized (work): 704405.390353 | | target function (ml) not normalized (free): 14749.754280 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1374 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1430 0.1429 0.1489 n_refl.: 191134 remove outliers: r(all,work,free)=0.1430 0.1429 0.1489 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1422 0.1421 0.1483 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1200 0.1373 n_refl.: 191134 remove outliers: r(all,work,free)=0.1204 0.1200 0.1373 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3860 360.391 322.001 0.402 0.947 0.242 13.296-10.522 99.01 99 1 0.2594 478.267 457.192 0.687 0.949 0.185 10.503-8.327 97.80 175 3 0.2115 501.899 495.506 0.860 0.949 0.160 8.318-6.595 100.00 360 8 0.2198 375.538 370.116 0.887 0.949 0.110 6.588-5.215 100.00 711 7 0.1926 345.082 335.352 0.884 0.949 0.090 5.214-4.128 98.38 1367 28 0.1229 504.750 499.180 0.973 0.949 0.080 4.126-3.266 94.74 2603 46 0.1148 460.107 453.277 1.035 0.949 0.000 3.266-2.585 99.86 5447 97 0.1108 310.377 307.114 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0952 234.162 231.636 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0914 138.588 137.267 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0975 74.608 73.892 1.055 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.024 38.351 1.043 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1280 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1373 | n_water=873 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1201 r_free=0.1371 | n_water=868 | time (s): 104.360 (total time: 106.630) Filter (q & B) r_work=0.1202 r_free=0.1370 | n_water=856 | time (s): 4.320 (total time: 110.950) Compute maps r_work=0.1202 r_free=0.1370 | n_water=856 | time (s): 1.700 (total time: 112.650) Filter (map) r_work=0.1227 r_free=0.1363 | n_water=727 | time (s): 4.490 (total time: 117.140) Find peaks r_work=0.1227 r_free=0.1363 | n_water=727 | time (s): 0.740 (total time: 117.880) Add new water r_work=0.1238 r_free=0.1389 | n_water=949 | time (s): 4.740 (total time: 122.620) Refine new water occ: r_work=0.1199 r_free=0.1356 adp: r_work=0.1199 r_free=0.1354 occ: r_work=0.1196 r_free=0.1355 adp: r_work=0.1196 r_free=0.1354 occ: r_work=0.1195 r_free=0.1355 adp: r_work=0.1195 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1354 r_work=0.1195 r_free=0.1354 | n_water=949 | time (s): 223.270 (total time: 345.890) Filter (q & B) r_work=0.1199 r_free=0.1360 | n_water=877 | time (s): 4.250 (total time: 350.140) Filter (dist only) r_work=0.1199 r_free=0.1361 | n_water=876 | time (s): 112.210 (total time: 462.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544168 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.667672 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 0.1202 0.1362 0.0159 0.037 1.1 6.1 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.62 1.59 1.763 13.965 14.668 3.761 12.05 13.65 1.59 1.891 13.920 14.668 3.760 Individual atomic B min max mean iso aniso Overall: 5.57 65.78 14.71 0.90 510 3270 Protein: 5.57 29.87 10.49 0.90 0 2902 Water: 5.98 65.78 28.68 N/A 510 366 Other: 13.83 23.25 18.54 N/A 0 2 Chain A: 5.65 51.88 12.40 N/A 0 1624 Chain B: 5.57 65.78 12.22 N/A 0 1646 Chain S: 5.98 60.74 30.07 N/A 510 0 Histogram: Values Number of atoms 5.57 - 11.59 2111 11.59 - 17.61 776 17.61 - 23.63 288 23.63 - 29.65 207 29.65 - 35.67 171 35.67 - 41.69 123 41.69 - 47.72 69 47.72 - 53.74 28 53.74 - 59.76 5 59.76 - 65.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1365 r_work=0.1206 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1365 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1368 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759464 | | target function (ml) not normalized (work): 704121.369921 | | target function (ml) not normalized (free): 14739.373129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1368 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1432 0.1431 0.1494 n_refl.: 191134 remove outliers: r(all,work,free)=0.1432 0.1431 0.1494 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1424 0.1423 0.1488 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1366 n_refl.: 191134 remove outliers: r(all,work,free)=0.1205 0.1202 0.1366 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3604 352.360 305.721 0.389 0.946 0.221 13.296-10.522 97.03 97 1 0.2414 481.185 453.624 0.684 0.948 0.170 10.503-8.327 97.80 175 3 0.2161 501.899 495.937 0.861 0.948 0.150 8.318-6.595 100.00 360 8 0.2169 375.538 370.860 0.888 0.948 0.115 6.588-5.215 100.00 711 7 0.1934 345.082 335.813 0.887 0.948 0.100 5.214-4.128 98.38 1367 28 0.1238 504.750 499.357 0.975 0.948 0.080 4.126-3.266 94.74 2603 46 0.1159 460.107 453.411 1.037 0.949 0.000 3.266-2.585 99.86 5447 97 0.1120 310.377 307.270 1.022 0.948 0.000 2.585-2.046 97.45 10613 204 0.0958 234.162 231.694 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0913 138.588 137.326 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0971 74.608 73.920 1.054 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.024 38.359 1.041 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1329 ============================ 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=876 | time (s): 2.950 (total time: 2.950) Filter (dist) r_work=0.1202 r_free=0.1366 | n_water=876 | time (s): 100.290 (total time: 103.240) Filter (q & B) r_work=0.1202 r_free=0.1367 | n_water=870 | time (s): 4.130 (total time: 107.370) Compute maps r_work=0.1202 r_free=0.1367 | n_water=870 | time (s): 1.980 (total time: 109.350) Filter (map) r_work=0.1224 r_free=0.1355 | n_water=756 | time (s): 5.180 (total time: 114.530) Find peaks r_work=0.1224 r_free=0.1355 | n_water=756 | time (s): 0.880 (total time: 115.410) Add new water r_work=0.1232 r_free=0.1371 | n_water=970 | time (s): 4.520 (total time: 119.930) Refine new water occ: r_work=0.1199 r_free=0.1347 adp: r_work=0.1199 r_free=0.1347 occ: r_work=0.1197 r_free=0.1345 adp: r_work=0.1197 r_free=0.1345 occ: r_work=0.1195 r_free=0.1344 adp: r_work=0.1195 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1344 r_work=0.1195 r_free=0.1344 | n_water=970 | time (s): 281.950 (total time: 401.880) Filter (q & B) r_work=0.1200 r_free=0.1351 | n_water=886 | time (s): 5.370 (total time: 407.250) Filter (dist only) r_work=0.1201 r_free=0.1351 | n_water=884 | time (s): 113.680 (total time: 520.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560973 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.551035 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1360 0.0157 0.037 1.1 5.6 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.60 1.57 1.720 13.847 14.551 3.759 12.04 13.61 1.57 1.770 13.827 14.551 3.757 Individual atomic B min max mean iso aniso Overall: 5.57 64.64 14.66 0.89 519 3269 Protein: 5.57 29.07 10.43 0.89 0 2902 Water: 5.95 64.64 28.55 N/A 519 365 Other: 13.84 22.25 18.05 N/A 0 2 Chain A: 5.62 51.44 12.31 N/A 0 1624 Chain B: 5.57 64.64 12.12 N/A 0 1645 Chain S: 5.95 60.32 30.07 N/A 519 0 Histogram: Values Number of atoms 5.57 - 11.48 2088 11.48 - 17.39 800 17.39 - 23.29 279 23.29 - 29.20 211 29.20 - 35.11 175 35.11 - 41.01 118 41.01 - 46.92 78 46.92 - 52.83 31 52.83 - 58.73 5 58.73 - 64.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1361 r_work=0.1204 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1362 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** 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= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756742 | | target function (ml) not normalized (work): 703592.664920 | | target function (ml) not normalized (free): 14732.331081 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1402 0.1400 0.1495 n_refl.: 191129 remove outliers: r(all,work,free)=0.1402 0.1400 0.1495 n_refl.: 191129 overall B=-0.01 to atoms: r(all,work,free)=0.1400 0.1399 0.1493 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1352 n_refl.: 191129 remove outliers: r(all,work,free)=0.1195 0.1192 0.1352 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3581 352.360 322.454 0.411 0.972 0.225 13.296-10.522 97.03 97 1 0.2471 481.185 460.337 0.691 0.973 0.168 10.503-8.327 97.80 175 3 0.2182 501.899 494.272 0.855 0.974 0.147 8.315-6.595 100.00 359 8 0.2164 374.592 370.223 0.881 0.974 0.109 6.588-5.215 100.00 711 7 0.1938 345.082 335.198 0.881 0.974 0.090 5.214-4.128 98.38 1367 28 0.1247 504.750 498.637 0.972 0.975 0.090 4.126-3.266 94.74 2603 46 0.1163 460.107 452.577 1.031 0.976 0.000 3.266-2.585 99.86 5447 97 0.1120 310.377 306.801 1.015 0.977 0.000 2.585-2.046 97.45 10613 204 0.0964 234.162 231.436 1.025 0.979 0.000 2.046-1.619 99.39 21536 464 0.0907 138.588 137.180 1.044 0.982 0.000 1.619-1.281 98.00 42464 925 0.0946 74.608 73.946 1.037 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.024 38.320 1.010 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0205 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1352 | n_water=884 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1192 r_free=0.1352 | n_water=884 | time (s): 110.340 (total time: 112.560) Filter (q & B) r_work=0.1192 r_free=0.1354 | n_water=876 | time (s): 4.130 (total time: 116.690) Compute maps r_work=0.1192 r_free=0.1354 | n_water=876 | time (s): 1.650 (total time: 118.340) Filter (map) r_work=0.1214 r_free=0.1348 | n_water=763 | time (s): 5.360 (total time: 123.700) Find peaks r_work=0.1214 r_free=0.1348 | n_water=763 | time (s): 0.650 (total time: 124.350) Add new water r_work=0.1223 r_free=0.1365 | n_water=974 | time (s): 4.340 (total time: 128.690) Refine new water occ: r_work=0.1189 r_free=0.1343 adp: r_work=0.1189 r_free=0.1343 occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1187 r_free=0.1341 occ: r_work=0.1185 r_free=0.1339 adp: r_work=0.1185 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1339 r_work=0.1185 r_free=0.1339 | n_water=974 | time (s): 186.920 (total time: 315.610) Filter (q & B) r_work=0.1189 r_free=0.1349 | n_water=893 | time (s): 4.510 (total time: 320.120) Filter (dist only) r_work=0.1190 r_free=0.1349 | n_water=891 | time (s): 116.100 (total time: 436.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.564038 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.484509 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1354 0.0162 0.038 1.1 6.1 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.54 1.62 1.701 13.811 14.485 3.756 11.93 13.57 1.64 1.725 13.801 14.485 3.754 Individual atomic B min max mean iso aniso Overall: 5.61 63.65 14.66 0.87 526 3269 Protein: 5.61 28.54 10.42 0.87 0 2902 Water: 6.03 63.65 28.43 N/A 526 365 Other: 13.86 22.20 18.03 N/A 0 2 Chain A: 5.66 51.00 12.27 N/A 0 1624 Chain B: 5.61 63.65 12.09 N/A 0 1645 Chain S: 6.03 59.96 30.05 N/A 526 0 Histogram: Values Number of atoms 5.61 - 11.41 2067 11.41 - 17.22 818 17.22 - 23.02 270 23.02 - 28.83 218 28.83 - 34.63 180 34.63 - 40.43 120 40.43 - 46.24 79 46.24 - 52.04 35 52.04 - 57.85 5 57.85 - 63.65 3 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1357 r_work=0.1193 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1358 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1357 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753333 | | target function (ml) not normalized (work): 702950.402491 | | target function (ml) not normalized (free): 14723.836306 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1357 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1498 n_refl.: 191128 remove outliers: r(all,work,free)=0.1406 0.1404 0.1498 n_refl.: 191128 overall B=-0.02 to atoms: r(all,work,free)=0.1403 0.1401 0.1495 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1355 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1190 0.1355 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3574 352.360 322.901 0.397 0.994 0.217 13.296-10.522 97.03 97 1 0.2406 481.185 462.346 0.673 0.996 0.158 10.503-8.327 97.80 175 3 0.2186 501.899 493.681 0.836 0.996 0.116 8.315-6.595 100.00 359 8 0.2144 374.592 369.404 0.859 0.996 0.100 6.588-5.215 100.00 711 7 0.1943 345.082 334.783 0.862 0.997 0.100 5.214-4.128 98.38 1367 28 0.1250 504.750 498.609 0.947 0.997 0.039 4.126-3.266 94.74 2603 46 0.1172 460.107 452.303 1.009 0.999 0.005 3.266-2.585 99.86 5447 97 0.1122 310.377 306.792 0.993 1.000 0.000 2.585-2.046 97.45 10613 204 0.0965 234.162 231.460 1.003 1.002 0.000 2.046-1.619 99.39 21536 464 0.0906 138.588 137.220 1.021 1.005 0.000 1.619-1.281 98.00 42464 925 0.0942 74.608 73.960 1.015 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.024 38.314 0.990 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0457 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1355 | n_water=891 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1191 r_free=0.1355 | n_water=890 | time (s): 122.830 (total time: 125.220) Filter (q & B) r_work=0.1191 r_free=0.1356 | n_water=882 | time (s): 5.170 (total time: 130.390) Compute maps r_work=0.1191 r_free=0.1356 | n_water=882 | time (s): 2.250 (total time: 132.640) Filter (map) r_work=0.1213 r_free=0.1357 | n_water=771 | time (s): 5.010 (total time: 137.650) Find peaks r_work=0.1213 r_free=0.1357 | n_water=771 | time (s): 0.630 (total time: 138.280) Add new water r_work=0.1221 r_free=0.1373 | n_water=989 | time (s): 4.060 (total time: 142.340) Refine new water occ: r_work=0.1187 r_free=0.1344 adp: r_work=0.1187 r_free=0.1344 occ: r_work=0.1185 r_free=0.1341 adp: r_work=0.1185 r_free=0.1342 occ: r_work=0.1184 r_free=0.1340 adp: r_work=0.1184 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1340 r_work=0.1184 r_free=0.1340 | n_water=989 | time (s): 214.620 (total time: 356.960) Filter (q & B) r_work=0.1188 r_free=0.1353 | n_water=899 | time (s): 4.340 (total time: 361.300) Filter (dist only) r_work=0.1189 r_free=0.1352 | n_water=896 | time (s): 112.200 (total time: 473.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.579996 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.820662 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1359 0.0167 0.038 1.1 5.1 0.0 0.3 0 0.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.59 1.67 1.693 13.770 13.821 3.754 11.94 13.63 1.70 1.698 13.765 13.821 3.754 Individual atomic B min max mean iso aniso Overall: 5.58 63.15 14.61 0.86 531 3269 Protein: 5.58 28.33 10.42 0.86 0 2902 Water: 6.02 63.15 28.18 N/A 531 365 Other: 13.86 22.13 18.00 N/A 0 2 Chain A: 5.71 50.84 12.23 N/A 0 1624 Chain B: 5.58 63.15 12.06 N/A 0 1645 Chain S: 6.02 59.99 29.77 N/A 531 0 Histogram: Values Number of atoms 5.58 - 11.34 2052 11.34 - 17.09 835 17.09 - 22.85 274 22.85 - 28.61 220 28.61 - 34.37 176 34.37 - 40.12 119 40.12 - 45.88 77 45.88 - 51.64 36 51.64 - 57.39 8 57.39 - 63.15 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1363 r_work=0.1194 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1363 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1364 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753714 | | target function (ml) not normalized (work): 703021.844368 | | target function (ml) not normalized (free): 14730.927163 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1192 0.1364 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1515 n_refl.: 191128 remove outliers: r(all,work,free)=0.1411 0.1410 0.1515 n_refl.: 191128 overall B=-0.11 to atoms: r(all,work,free)=0.1393 0.1391 0.1500 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1363 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1363 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3589 352.360 321.608 0.392 0.972 0.207 13.296-10.522 97.03 97 1 0.2409 481.185 461.562 0.674 0.974 0.146 10.503-8.327 97.80 175 3 0.2209 501.899 493.679 0.841 0.974 0.113 8.315-6.595 100.00 359 8 0.2152 374.592 369.605 0.865 0.974 0.093 6.588-5.215 100.00 711 7 0.1954 345.082 334.721 0.866 0.975 0.080 5.214-4.128 98.38 1367 28 0.1256 504.750 498.471 0.955 0.976 0.039 4.126-3.266 94.74 2603 46 0.1185 460.107 452.263 1.016 0.977 0.005 3.266-2.585 99.86 5447 97 0.1123 310.377 306.749 1.000 0.978 0.000 2.585-2.046 97.45 10613 204 0.0964 234.162 231.428 1.007 0.981 0.000 2.046-1.619 99.39 21536 464 0.0906 138.588 137.220 1.023 0.985 0.000 1.619-1.281 98.00 42464 925 0.0940 74.608 73.964 1.013 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.024 38.310 0.981 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0233 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1363 After: r_work=0.1193 r_free=0.1363 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1363 | n_water=896 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1193 r_free=0.1364 | n_water=894 | time (s): 120.080 (total time: 123.020) Filter (q & B) r_work=0.1194 r_free=0.1364 | n_water=882 | time (s): 4.150 (total time: 127.170) Compute maps r_work=0.1194 r_free=0.1364 | n_water=882 | time (s): 1.640 (total time: 128.810) Filter (map) r_work=0.1218 r_free=0.1358 | n_water=768 | time (s): 4.610 (total time: 133.420) Find peaks r_work=0.1218 r_free=0.1358 | n_water=768 | time (s): 0.710 (total time: 134.130) Add new water r_work=0.1225 r_free=0.1370 | n_water=982 | time (s): 3.690 (total time: 137.820) Refine new water occ: r_work=0.1192 r_free=0.1346 adp: r_work=0.1193 r_free=0.1346 occ: r_work=0.1190 r_free=0.1346 adp: r_work=0.1190 r_free=0.1346 occ: r_work=0.1189 r_free=0.1346 adp: r_work=0.1189 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1346 r_work=0.1189 r_free=0.1346 | n_water=982 | time (s): 316.530 (total time: 454.350) Filter (q & B) r_work=0.1193 r_free=0.1357 | n_water=900 | time (s): 5.150 (total time: 459.500) Filter (dist only) r_work=0.1194 r_free=0.1357 | n_water=898 | time (s): 117.500 (total time: 577.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560174 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.535656 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1359 0.0164 0.038 1.1 7.3 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.59 1.64 1.686 13.658 13.536 3.754 11.96 13.61 1.65 1.691 13.653 13.536 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 62.22 14.49 0.85 533 3269 Protein: 5.56 27.94 10.32 0.85 0 2902 Water: 6.02 62.22 27.96 N/A 533 365 Other: 13.82 21.98 17.90 N/A 0 2 Chain A: 5.63 50.49 12.11 N/A 0 1624 Chain B: 5.56 62.22 11.95 N/A 0 1645 Chain S: 6.02 59.94 29.58 N/A 533 0 Histogram: Values Number of atoms 5.56 - 11.22 2038 11.22 - 16.89 840 16.89 - 22.56 280 22.56 - 28.22 213 28.22 - 33.89 191 33.89 - 39.55 110 39.55 - 45.22 82 45.22 - 50.89 37 50.89 - 56.55 7 56.55 - 62.22 4 =========================== 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) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753915 | | target function (ml) not normalized (work): 703059.463994 | | target function (ml) not normalized (free): 14724.882535 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1373 0.1545 5.7022 5.8059| | 2: 2.94 - 2.33 1.00 7339 128 0.1077 0.1322 5.0932 5.1726| | 3: 2.33 - 2.04 0.96 6939 150 0.0906 0.1173 4.6587 4.7423| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1042 4.391 4.5557| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0997 4.1496 4.248| | 6: 1.72 - 1.62 0.99 7102 142 0.0893 0.1071 3.9427 4.0696| | 7: 1.62 - 1.54 0.99 7104 148 0.0886 0.0965 3.7958 3.9316| | 8: 1.54 - 1.47 0.96 6798 152 0.0885 0.1287 3.6931 3.8957| | 9: 1.47 - 1.41 0.98 6938 155 0.0924 0.1110 3.6158 3.7374| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1179 3.5511 3.671| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1134 3.4821 3.5846| | 12: 1.32 - 1.28 0.98 6975 149 0.1028 0.1123 3.4561 3.5779| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1229 3.4342 3.5545| | 14: 1.25 - 1.22 0.98 7015 112 0.1102 0.1575 3.4299 3.6762| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1238 3.4469 3.4899| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1559 3.4649 3.6649| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1230 3.4345 3.4442| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1717 3.4387 3.5368| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1749 3.4199 3.5978| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1570 3.4103 3.4324| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2137 3.4175 3.5056| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1957 3.4129 3.4165| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2031 3.4329 3.487| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2246 3.4357 3.5066| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2532 3.449 3.5278| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2860 3.4158 3.4253| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2805 3.4687 3.3953| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 12.24 1.00 0.98 12067.61| | 2: 2.94 - 2.33 7339 128 0.92 13.20 0.99 0.98 5396.45| | 3: 2.33 - 2.04 6939 150 0.96 7.60 1.01 0.98 1678.51| | 4: 2.04 - 1.85 7170 155 0.96 7.59 1.00 0.98 993.35| | 5: 1.85 - 1.72 7113 159 0.96 8.02 1.00 0.98 631.18| | 6: 1.72 - 1.62 7102 142 0.96 7.96 1.00 0.99 438.50| | 7: 1.62 - 1.54 7104 148 0.96 8.04 1.01 1.00 332.33| | 8: 1.54 - 1.47 6798 152 0.96 8.14 1.01 1.00 273.72| | 9: 1.47 - 1.41 6938 155 0.96 8.33 1.00 1.00 225.77| | 10: 1.41 - 1.36 7022 150 0.96 8.80 1.00 1.00 199.00| | 11: 1.36 - 1.32 6997 151 0.96 8.86 0.99 0.98 172.69| | 12: 1.32 - 1.28 6975 149 0.96 8.93 0.98 0.97 159.24| | 13: 1.28 - 1.25 6907 166 0.96 9.46 1.01 0.98 156.80| | 14: 1.25 - 1.22 7015 112 0.95 10.64 1.01 0.99 162.02| | 15: 1.22 - 1.19 6956 137 0.95 11.22 1.01 1.00 166.24| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.00 0.98 160.72| | 17: 1.17 - 1.14 6940 135 0.94 12.29 1.01 0.99 154.84| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.97 148.45| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.97 151.73| | 20: 1.10 - 1.08 6884 147 0.92 15.24 1.00 0.96 150.59| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.96 153.67| | 22: 1.07 - 1.05 6836 135 0.89 18.31 1.00 0.95 155.12| | 23: 1.05 - 1.03 6827 159 0.87 20.51 1.00 0.95 164.99| | 24: 1.03 - 1.02 6784 133 0.85 23.18 1.00 0.95 179.37| | 25: 1.02 - 1.01 6552 130 0.83 25.21 0.98 0.92 182.64| | 26: 1.01 - 0.99 6767 158 0.81 26.68 0.98 0.91 177.03| | 27: 0.99 - 0.98 6647 131 0.82 26.30 0.99 0.90 160.98| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 148.45 max = 12067.61 mean = 967.92| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.31| |phase err.(test): min = 0.00 max = 89.12 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1362 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1494 n_refl.: 191128 remove outliers: r(all,work,free)=0.1403 0.1401 0.1494 n_refl.: 191128 overall B=-0.04 to atoms: r(all,work,free)=0.1397 0.1395 0.1490 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1360 n_refl.: 191128 remove outliers: r(all,work,free)=0.1198 0.1194 0.1360 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3599 352.360 320.637 0.416 0.914 0.207 13.296-10.522 97.03 97 1 0.2419 481.185 461.147 0.716 0.916 0.146 10.503-8.327 97.80 175 3 0.2209 501.899 492.878 0.894 0.916 0.111 8.315-6.595 100.00 359 8 0.2136 374.592 369.516 0.922 0.916 0.090 6.588-5.215 100.00 711 7 0.1970 345.082 334.308 0.922 0.916 0.077 5.214-4.128 98.38 1367 28 0.1264 504.750 498.459 1.016 0.917 0.034 4.126-3.266 94.74 2603 46 0.1188 460.107 452.388 1.085 0.919 0.005 3.266-2.585 99.86 5447 97 0.1126 310.377 306.846 1.066 0.920 0.000 2.585-2.046 97.45 10613 204 0.0967 234.162 231.465 1.073 0.922 0.000 2.046-1.619 99.39 21536 464 0.0909 138.588 137.232 1.090 0.926 0.000 1.619-1.281 98.00 42464 925 0.0943 74.608 73.963 1.079 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.024 38.309 1.045 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0080 ================= 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 : 0.2040 0.1981 0.081 5.313 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1905 0.081 5.313 5.2 78.1 14.6 805 0.000 1_settarget: 0.1804 0.1905 0.081 5.313 5.2 78.1 14.6 805 0.000 1_nqh: 0.1804 0.1904 0.081 5.313 5.2 78.1 14.6 805 0.002 1_weight: 0.1804 0.1904 0.081 5.313 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1269 0.1499 0.039 1.160 5.2 78.1 14.6 805 0.158 1_adp: 0.1297 0.1565 0.039 1.160 5.2 73.1 15.1 805 0.158 1_regHadp: 0.1296 0.1561 0.039 1.160 5.2 73.1 15.1 805 0.158 1_occ: 0.1281 0.1548 0.039 1.160 5.2 73.1 15.1 805 0.158 2_bss: 0.1275 0.1541 0.039 1.160 5.4 73.2 15.3 805 0.158 2_settarget: 0.1275 0.1541 0.039 1.160 5.4 73.2 15.3 805 0.158 2_updatecdl: 0.1275 0.1541 0.039 1.174 5.4 73.2 15.3 805 0.158 2_nqh: 0.1276 0.1541 0.039 1.174 5.4 73.2 15.3 805 0.156 2_sol: 0.1271 0.1499 0.039 1.174 5.4 73.2 16.4 899 n/a 2_weight: 0.1271 0.1499 0.039 1.174 5.4 73.2 16.4 899 n/a 2_xyzrec: 0.1252 0.1515 0.042 1.161 5.4 73.2 16.4 899 n/a 2_adp: 0.1232 0.1508 0.042 1.161 5.5 69.4 16.5 899 n/a 2_regHadp: 0.1232 0.1509 0.042 1.161 5.5 69.4 16.5 899 n/a 2_occ: 0.1225 0.1508 0.042 1.161 5.5 69.4 16.5 899 n/a 3_bss: 0.1232 0.1516 0.042 1.161 5.5 69.4 16.4 899 n/a 3_settarget: 0.1232 0.1516 0.042 1.161 5.5 69.4 16.4 899 n/a 3_updatecdl: 0.1232 0.1516 0.042 1.167 5.5 69.4 16.4 899 n/a 3_nqh: 0.1232 0.1516 0.042 1.167 5.5 69.4 16.4 899 n/a 3_sol: 0.1249 0.1524 0.042 1.167 5.5 68.2 15.6 884 n/a 3_weight: 0.1249 0.1524 0.042 1.167 5.5 68.2 15.6 884 n/a 3_xyzrec: 0.1240 0.1444 0.036 1.101 5.5 68.2 15.6 884 n/a 3_adp: 0.1234 0.1401 0.036 1.101 5.5 67.7 15.4 884 n/a 3_regHadp: 0.1235 0.1402 0.036 1.101 5.5 67.7 15.4 884 n/a 3_occ: 0.1229 0.1395 0.036 1.101 5.5 67.7 15.4 884 n/a 4_bss: 0.1225 0.1390 0.036 1.101 5.5 67.7 15.3 884 n/a 4_settarget: 0.1225 0.1390 0.036 1.101 5.5 67.7 15.3 884 n/a 4_updatecdl: 0.1225 0.1390 0.036 1.103 5.5 67.7 15.3 884 n/a 4_nqh: 0.1225 0.1390 0.036 1.103 5.5 67.7 15.3 884 n/a 4_sol: 0.1213 0.1378 0.036 1.103 5.5 67.7 14.8 836 n/a 4_weight: 0.1213 0.1378 0.036 1.103 5.5 67.7 14.8 836 n/a 4_xyzrec: 0.1211 0.1379 0.033 1.122 5.5 67.7 14.8 836 n/a 4_adp: 0.1204 0.1376 0.033 1.122 5.5 67.2 14.8 836 n/a 4_regHadp: 0.1204 0.1376 0.033 1.122 5.5 67.2 14.8 836 n/a 4_occ: 0.1202 0.1374 0.033 1.122 5.5 67.2 14.8 836 n/a 5_bss: 0.1201 0.1373 0.033 1.122 5.5 67.2 14.7 836 n/a 5_settarget: 0.1201 0.1373 0.033 1.122 5.5 67.2 14.7 836 n/a 5_updatecdl: 0.1201 0.1373 0.033 1.123 5.5 67.2 14.7 836 n/a 5_nqh: 0.1201 0.1373 0.033 1.123 5.5 67.2 14.7 836 n/a 5_sol: 0.1197 0.1362 0.033 1.123 5.5 67.2 14.8 873 n/a 5_weight: 0.1197 0.1362 0.033 1.123 5.5 67.2 14.8 873 n/a 5_xyzrec: 0.1200 0.1369 0.036 1.124 5.5 67.2 14.8 873 n/a 5_adp: 0.1203 0.1372 0.036 1.124 5.6 66.9 14.8 873 n/a 5_regHadp: 0.1203 0.1372 0.036 1.124 5.6 66.9 14.8 873 n/a 5_occ: 0.1202 0.1374 0.036 1.124 5.6 66.9 14.8 873 n/a 6_bss: 0.1201 0.1373 0.036 1.124 5.5 66.8 14.8 873 n/a 6_settarget: 0.1201 0.1373 0.036 1.124 5.5 66.8 14.8 873 n/a 6_updatecdl: 0.1201 0.1373 0.036 1.124 5.5 66.8 14.8 873 n/a 6_nqh: 0.1201 0.1373 0.036 1.124 5.5 66.8 14.8 873 n/a 6_sol: 0.1199 0.1361 0.036 1.124 5.5 66.8 14.8 876 n/a 6_weight: 0.1199 0.1361 0.036 1.124 5.5 66.8 14.8 876 n/a 6_xyzrec: 0.1202 0.1362 0.037 1.122 5.5 66.8 14.8 876 n/a 6_adp: 0.1206 0.1365 0.037 1.122 5.6 65.8 14.7 876 n/a 6_regHadp: 0.1206 0.1365 0.037 1.122 5.6 65.8 14.7 876 n/a 6_occ: 0.1204 0.1368 0.037 1.122 5.6 65.8 14.7 876 n/a 7_bss: 0.1202 0.1366 0.037 1.122 5.5 65.7 14.7 876 n/a 7_settarget: 0.1202 0.1366 0.037 1.122 5.5 65.7 14.7 876 n/a 7_updatecdl: 0.1202 0.1366 0.037 1.122 5.5 65.7 14.7 876 n/a 7_nqh: 0.1202 0.1366 0.037 1.122 5.5 65.7 14.7 876 n/a 7_sol: 0.1201 0.1351 0.037 1.122 5.5 65.7 14.7 884 n/a 7_weight: 0.1201 0.1351 0.037 1.122 5.5 65.7 14.7 884 n/a 7_xyzrec: 0.1203 0.1360 0.037 1.118 5.5 65.7 14.7 884 n/a 7_adp: 0.1204 0.1361 0.037 1.118 5.6 64.6 14.7 884 n/a 7_regHadp: 0.1204 0.1362 0.037 1.118 5.6 64.6 14.7 884 n/a 7_occ: 0.1202 0.1361 0.037 1.118 5.6 64.6 14.7 884 n/a 8_bss: 0.1192 0.1352 0.037 1.118 5.6 64.6 14.7 884 n/a 8_settarget: 0.1192 0.1352 0.037 1.118 5.6 64.6 14.7 884 n/a 8_updatecdl: 0.1192 0.1352 0.037 1.117 5.6 64.6 14.7 884 n/a 8_nqh: 0.1192 0.1352 0.037 1.117 5.6 64.6 14.7 884 n/a 8_sol: 0.1190 0.1349 0.037 1.117 5.6 64.6 14.7 891 n/a 8_weight: 0.1190 0.1349 0.037 1.117 5.6 64.6 14.7 891 n/a 8_xyzrec: 0.1192 0.1354 0.038 1.119 5.6 64.6 14.7 891 n/a 8_adp: 0.1193 0.1357 0.038 1.119 5.6 63.6 14.7 891 n/a 8_regHadp: 0.1193 0.1358 0.038 1.119 5.6 63.6 14.7 891 n/a 8_occ: 0.1191 0.1357 0.038 1.119 5.6 63.6 14.7 891 n/a 9_bss: 0.1190 0.1355 0.038 1.119 5.6 63.6 14.6 891 n/a 9_settarget: 0.1190 0.1355 0.038 1.119 5.6 63.6 14.6 891 n/a 9_updatecdl: 0.1190 0.1355 0.038 1.119 5.6 63.6 14.6 891 n/a 9_nqh: 0.1190 0.1355 0.038 1.119 5.6 63.6 14.6 891 n/a 9_sol: 0.1189 0.1352 0.038 1.119 5.6 63.6 14.6 896 n/a 9_weight: 0.1189 0.1352 0.038 1.119 5.6 63.6 14.6 896 n/a 9_xyzrec: 0.1192 0.1359 0.038 1.118 5.6 63.6 14.6 896 n/a 9_adp: 0.1194 0.1363 0.038 1.118 5.6 63.2 14.6 896 n/a 9_regHadp: 0.1194 0.1363 0.038 1.118 5.6 63.2 14.6 896 n/a 9_occ: 0.1192 0.1364 0.038 1.118 5.6 63.2 14.6 896 n/a 10_bss: 0.1192 0.1363 0.038 1.118 5.5 63.0 14.5 896 n/a 10_settarget: 0.1192 0.1363 0.038 1.118 5.5 63.0 14.5 896 n/a 10_updatecdl: 0.1192 0.1363 0.038 1.118 5.5 63.0 14.5 896 n/a 10_setrh: 0.1193 0.1363 0.038 1.118 5.5 63.0 14.5 896 n/a 10_nqh: 0.1193 0.1363 0.038 1.118 5.5 63.0 14.5 896 n/a 10_sol: 0.1194 0.1357 0.038 1.118 5.5 63.0 14.5 898 n/a 10_weight: 0.1194 0.1357 0.038 1.118 5.5 63.0 14.5 898 n/a 10_xyzrec: 0.1194 0.1359 0.038 1.134 5.5 63.0 14.5 898 n/a 10_adp: 0.1196 0.1361 0.038 1.134 5.6 62.2 14.5 898 n/a 10_regHadp: 0.1196 0.1361 0.038 1.134 5.6 62.2 14.5 898 n/a 10_occ: 0.1195 0.1362 0.038 1.134 5.6 62.2 14.5 898 n/a end: 0.1194 0.1360 0.038 1.134 5.5 62.2 14.5 898 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4848787_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4848787_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1800 Refinement macro-cycles (run) : 12040.7100 Write final files (write_after_run_outputs) : 170.4500 Total : 12218.3400 Total CPU time: 3.40 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:51 PST -0800 (1736736051.19 s) Start R-work = 0.1804, R-free = 0.1905 Final R-work = 0.1194, R-free = 0.1360 =============================================================================== Job complete usr+sys time: 12507.85 seconds wall clock time: 209 minutes 30.36 seconds (12570.36 seconds total)