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_3516039.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_3516039.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3516039.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): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.46, per 1000 atoms: 0.37 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: 2.824 distance_ideal: 2.720 ideal - model: -0.104 slack: 0.000 delta_slack: -0.104 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: 2.729 distance_ideal: 2.710 ideal - model: -0.019 slack: 0.000 delta_slack: -0.019 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: 0.99 Conformation dependent library (CDL) restraints added in 208.4 milliseconds Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.03: 811 1.03 - 1.26: 2507 1.26 - 1.48: 1451 1.48 - 1.71: 1144 1.71 - 1.94: 21 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA A 18 " pdb=" CA ALA A 18 " ideal model delta sigma weight residual 1.459 1.708 -0.249 1.19e-02 7.06e+03 4.38e+02 bond pdb=" N ASN A 123 " pdb=" H ASN A 123 " ideal model delta sigma weight residual 0.860 1.246 -0.386 2.00e-02 2.50e+03 3.72e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.462 1.681 -0.219 1.14e-02 7.69e+03 3.68e+02 bond pdb=" N ALA A 35 " pdb=" CA ALA A 35 " ideal model delta sigma weight residual 1.456 1.682 -0.226 1.21e-02 6.83e+03 3.48e+02 bond pdb=" CB GLN B 156 " pdb=" HB3 GLN B 156 " ideal model delta sigma weight residual 0.970 1.341 -0.371 2.00e-02 2.50e+03 3.44e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.11: 5561 4.11 - 8.22: 3517 8.22 - 12.33: 1413 12.33 - 16.44: 286 16.44 - 20.55: 33 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA TRP B 146 " pdb=" C TRP B 146 " pdb=" O TRP B 146 " ideal model delta sigma weight residual 120.46 105.46 15.00 1.07e+00 8.73e-01 1.97e+02 angle pdb=" O PRO B 128 " pdb=" C PRO B 128 " pdb=" N THR B 129 " ideal model delta sigma weight residual 122.23 138.92 -16.69 1.20e+00 6.94e-01 1.93e+02 angle pdb=" O GLY A 65 " pdb=" C GLY A 65 " pdb=" N GLU A 66 " ideal model delta sigma weight residual 122.91 106.05 16.86 1.23e+00 6.61e-01 1.88e+02 angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" O ILE A 134 " ideal model delta sigma weight residual 119.20 109.31 9.89 7.30e-01 1.88e+00 1.84e+02 angle pdb=" C GLY B 29 " pdb=" N ILE B 30 " pdb=" CA ILE B 30 " ideal model delta sigma weight residual 121.66 139.74 -18.08 1.38e+00 5.25e-01 1.72e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 1855 17.33 - 34.65: 134 34.65 - 51.98: 41 51.98 - 69.30: 16 69.30 - 86.63: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual 180.00 -151.29 -28.71 0 5.00e+00 4.00e-02 3.30e+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 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta harmonic sigma weight residual -180.00 -156.64 -23.36 0 5.00e+00 4.00e-02 2.18e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.220: 211 0.220 - 0.440: 160 0.440 - 0.659: 76 0.659 - 0.879: 37 0.879 - 1.099: 8 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE B 121 " pdb=" N ILE B 121 " pdb=" C ILE B 121 " pdb=" CB ILE B 121 " both_signs ideal model delta sigma weight residual False 2.43 3.53 -1.10 2.00e-01 2.50e+01 3.02e+01 chirality pdb=" CA LEU B 43 " pdb=" N LEU B 43 " pdb=" C LEU B 43 " pdb=" CB LEU B 43 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA ILE B 118 " pdb=" N ILE B 118 " pdb=" C ILE B 118 " pdb=" CB ILE B 118 " both_signs ideal model delta sigma weight residual False 2.43 3.42 -0.98 2.00e-01 2.50e+01 2.42e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.152 2.00e-02 2.50e+03 7.49e-02 1.68e+02 pdb=" CG PHE B 164 " -0.093 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.068 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.043 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.103 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.122 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " -0.076 2.00e-02 2.50e+03 6.61e-02 1.31e+02 pdb=" CG TYR A 192 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " -0.096 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " -0.066 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " -0.075 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " 0.122 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.008 2.00e-02 2.50e+03 5.34e-02 1.14e+02 pdb=" CG TRP A 139 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.024 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.057 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.043 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.068 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.059 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.019 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.085 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.098 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.075 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.056 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.52: 17 1.52 - 2.29: 1655 2.29 - 3.06: 21416 3.06 - 3.83: 33312 3.83 - 4.60: 53838 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110238 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.751 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.915 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.032 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.056 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.186 2.620 ... (remaining 110233 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_3516039_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= 0.2038 r_free= 0.2016 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.303059 | | target function (ml) not normalized (work): 806018.880027 | | target function (ml) not normalized (free): 16614.154043 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2129 0.1929 6.6756 6.3096| | 2: 2.94 - 2.33 1.00 7339 128 0.1621 0.1746 5.5446 5.636| | 3: 2.33 - 2.04 0.96 6939 150 0.1640 0.1606 5.1474 5.1703| | 4: 2.04 - 1.85 1.00 7170 155 0.1752 0.1619 4.9609 5.0488| | 5: 1.85 - 1.72 0.99 7113 159 0.1909 0.1823 4.798 4.8412| | 6: 1.72 - 1.62 0.99 7102 142 0.1994 0.1973 4.6808 4.7346| | 7: 1.62 - 1.54 0.99 7104 148 0.2003 0.1823 4.5619 4.607| | 8: 1.54 - 1.47 0.96 6798 152 0.2060 0.2086 4.4761 4.4733| | 9: 1.47 - 1.41 0.98 6938 155 0.2108 0.2180 4.411 4.4725| | 10: 1.41 - 1.36 0.99 7022 150 0.2149 0.2114 4.3082 4.3318| | 11: 1.36 - 1.32 0.99 6997 151 0.2117 0.2205 4.2284 4.3067| | 12: 1.32 - 1.28 0.98 6976 149 0.2126 0.1972 4.1927 4.2209| | 13: 1.28 - 1.25 0.98 6907 166 0.2056 0.2400 4.1321 4.2559| | 14: 1.25 - 1.22 0.98 7015 113 0.2113 0.2457 4.0918 4.3021| | 15: 1.22 - 1.19 0.98 6957 137 0.2102 0.1877 4.0522 4.009| | 16: 1.19 - 1.17 0.93 6604 132 0.2154 0.2215 4.0234 4.0689| | 17: 1.17 - 1.14 0.98 6941 135 0.2164 0.1957 3.9559 3.989| | 18: 1.14 - 1.12 0.98 6875 142 0.2227 0.2273 3.9209 3.9383| | 19: 1.12 - 1.10 0.97 6949 106 0.2255 0.2666 3.8705 4.0678| | 20: 1.10 - 1.08 0.97 6884 147 0.2299 0.2536 3.8253 3.93| | 21: 1.08 - 1.07 0.97 6852 152 0.2448 0.2696 3.7985 3.7887| | 22: 1.07 - 1.05 0.97 6838 135 0.2563 0.2511 3.7498 3.7345| | 23: 1.05 - 1.03 0.97 6829 159 0.2722 0.2682 3.7271 3.783| | 24: 1.03 - 1.02 0.96 6785 133 0.2870 0.2702 3.6974 3.7686| | 25: 1.02 - 1.01 0.93 6552 130 0.3082 0.3150 3.6734 3.7969| | 26: 1.01 - 0.99 0.96 6767 158 0.3195 0.3257 3.6299 3.6185| | 27: 0.99 - 0.98 0.94 6648 131 0.3395 0.3329 3.6362 3.615| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.85 20.69 0.91 0.97 36366.26| | 2: 2.94 - 2.33 7339 128 0.85 21.54 1.08 1.03 15414.39| | 3: 2.33 - 2.04 6939 150 0.93 12.68 1.11 1.06 4209.46| | 4: 2.04 - 1.85 7170 155 0.92 13.88 1.11 1.07 2892.63| | 5: 1.85 - 1.72 7113 159 0.90 16.16 1.11 1.07 2221.80| | 6: 1.72 - 1.62 7102 142 0.89 17.27 1.11 1.08 1754.34| | 7: 1.62 - 1.54 7104 148 0.89 18.06 1.11 1.06 1393.79| | 8: 1.54 - 1.47 6798 152 0.89 18.27 1.10 1.06 1133.89| | 9: 1.47 - 1.41 6938 155 0.88 18.96 1.10 1.04 979.67| | 10: 1.41 - 1.36 7022 150 0.87 20.46 1.10 1.05 876.62| | 11: 1.36 - 1.32 6997 151 0.86 20.86 1.09 1.03 771.99| | 12: 1.32 - 1.28 6976 149 0.86 20.90 1.08 1.03 702.82| | 13: 1.28 - 1.25 6907 166 0.86 21.16 1.08 1.04 670.04| | 14: 1.25 - 1.22 7015 113 0.85 21.99 1.09 1.05 644.99| | 15: 1.22 - 1.19 6957 137 0.86 21.43 1.08 1.04 575.28| | 16: 1.19 - 1.17 6604 132 0.87 20.59 1.08 1.03 498.32| | 17: 1.17 - 1.14 6941 135 0.86 21.01 1.08 1.02 443.02| | 18: 1.14 - 1.12 6875 142 0.86 21.86 1.08 1.01 426.93| | 19: 1.12 - 1.10 6949 106 0.84 23.35 1.07 1.00 417.39| | 20: 1.10 - 1.08 6884 147 0.83 24.09 1.06 0.97 384.51| | 21: 1.08 - 1.07 6852 152 0.83 24.66 1.06 0.96 352.10| | 22: 1.07 - 1.05 6838 135 0.82 25.77 1.05 0.97 328.64| | 23: 1.05 - 1.03 6829 159 0.80 27.64 1.05 0.98 331.92| | 24: 1.03 - 1.02 6785 133 0.78 29.73 1.05 0.98 337.57| | 25: 1.02 - 1.01 6552 130 0.75 31.80 1.03 0.93 327.90| | 26: 1.01 - 0.99 6767 158 0.73 33.77 1.02 0.89 311.47| | 27: 0.99 - 0.98 6648 131 0.72 34.95 1.04 0.85 299.10| |alpha: min = 0.85 max = 1.08 mean = 1.01| |beta: min = 299.10 max = 36366.26 mean = 2910.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.26| |phase err.(test): min = 0.00 max = 89.47 mean = 22.43| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.249 2950 Z= 5.544 Angle : 5.214 18.077 4018 Z= 3.743 Chirality : 0.382 1.099 492 Planarity : 0.030 0.115 512 Dihedral : 12.741 86.630 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.59 % Favored : 96.89 % Rotamer: Outliers : 0.65 % Allowed : 4.84 % Favored : 94.52 % Cbeta Deviations : 29.78 % 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: -2.66 (0.35), residues: 386 helix: -2.98 (0.28), residues: 146 sheet: -0.80 (0.58), residues: 66 loop : -0.80 (0.41), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.017 ARG B 100 TYR 0.128 0.035 TYR A 67 PHE 0.114 0.037 PHE B 164 TRP 0.099 0.030 TRP A 146 HIS 0.060 0.021 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2038 r_free= 0.2016 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.303059 | | target function (ml) not normalized (work): 806018.880027 | | target function (ml) not normalized (free): 16614.154043 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2038 0.2016 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2038 0.2016 n_refl.: 191155 remove outliers: r(all,work,free)=0.2037 0.2038 0.2016 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2036 0.2037 0.2016 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1809 0.1806 0.1953 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1804 0.1952 n_refl.: 191140 ======================== 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 96.04 94 3 0.4205 400.535 295.599 0.436 0.911 0.301 13.296-10.522 100.00 100 1 0.2541 534.497 520.145 0.786 0.912 0.248 10.503-8.327 99.45 178 3 0.2541 565.118 555.582 0.977 0.912 0.220 8.318-6.595 100.00 360 8 0.2429 414.736 403.600 0.976 0.912 0.166 6.588-5.215 100.00 711 7 0.2281 381.101 364.839 0.956 0.912 0.133 5.214-4.128 98.38 1367 28 0.1483 557.435 550.100 1.078 0.912 0.080 4.126-3.266 94.74 2603 46 0.1332 508.132 499.644 1.147 0.913 0.019 3.266-2.585 99.86 5447 97 0.1449 342.774 337.605 1.121 0.912 0.010 2.585-2.046 97.45 10613 204 0.1409 258.603 254.094 1.127 0.911 0.000 2.046-1.619 99.39 21536 464 0.1617 153.054 149.902 1.146 0.910 0.000 1.619-1.281 98.00 42464 925 0.1933 82.395 80.128 1.131 0.908 0.000 1.281-0.980 96.53 101826 2055 0.2324 44.202 41.689 1.116 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0104 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1952 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1804 r_free=0.1952 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.390676 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.197956 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1271 0.1501 0.0230 0.038 1.2 10.7 0.0 0.3 0 11.195 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.01 2.30 1.118 13.107 573.198 0.019 13.00 15.71 2.71 1.245 13.334 573.198 0.017 Individual atomic B min max mean iso aniso Overall: 5.17 73.04 15.01 1.40 435 3274 Protein: 5.17 40.32 11.01 1.40 0 2902 Water: 6.34 73.04 29.41 N/A 435 370 Other: 16.24 30.27 23.26 N/A 0 2 Chain A: 5.36 59.89 13.04 N/A 0 1626 Chain B: 5.17 73.04 12.77 N/A 0 1648 Chain S: 11.65 64.96 30.85 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2162 11.96 - 18.75 644 18.75 - 25.53 314 25.53 - 32.32 264 32.32 - 39.11 159 39.11 - 45.89 100 45.89 - 52.68 43 52.68 - 59.47 17 59.47 - 66.25 5 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1571 r_work=0.1299 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1566 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1285 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1285 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015672 | | target function (ls_wunit_k1) not normalized (work): 2935.377646 | | target function (ls_wunit_k1) not normalized (free): 118.450021 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1285 0.1556 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1474 0.1471 0.1632 n_refl.: 191140 remove outliers: r(all,work,free)=0.1474 0.1471 0.1632 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1497 0.1495 0.1641 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1282 0.1277 0.1547 n_refl.: 191140 remove outliers: r(all,work,free)=0.1282 0.1277 0.1547 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3603 402.814 370.186 0.480 0.962 0.285 13.296-10.522 100.00 100 1 0.2095 534.497 527.055 0.742 0.964 0.240 10.503-8.327 99.45 178 3 0.1772 565.118 562.430 0.888 0.964 0.217 8.318-6.595 100.00 360 8 0.1720 414.736 412.256 0.911 0.964 0.155 6.588-5.215 100.00 711 7 0.1531 381.101 373.731 0.888 0.964 0.150 5.214-4.128 98.38 1367 28 0.0903 557.435 555.113 0.977 0.964 0.049 4.126-3.266 94.74 2603 46 0.0832 508.132 504.233 1.044 0.965 0.019 3.266-2.585 99.86 5447 97 0.0919 342.774 340.374 1.026 0.964 0.005 2.585-2.046 97.45 10613 204 0.0949 258.603 256.356 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1091 153.054 151.389 1.056 0.965 0.000 1.619-1.281 98.00 42464 925 0.1283 82.395 81.404 1.048 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1880 44.202 42.166 1.025 0.964 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0365 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1547 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1547 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1547 | n_water=805 | time (s): 2.960 (total time: 2.960) Filter (dist) r_work=0.1281 r_free=0.1552 | n_water=794 | time (s): 103.060 (total time: 106.020) Filter (q & B) r_work=0.1282 r_free=0.1552 | n_water=790 | time (s): 4.360 (total time: 110.380) Compute maps r_work=0.1282 r_free=0.1552 | n_water=790 | time (s): 1.710 (total time: 112.090) Filter (map) r_work=0.1307 r_free=0.1531 | n_water=650 | time (s): 4.920 (total time: 117.010) Find peaks r_work=0.1307 r_free=0.1531 | n_water=650 | time (s): 0.670 (total time: 117.680) Add new water r_work=0.1330 r_free=0.1564 | n_water=947 | time (s): 4.600 (total time: 122.280) Refine new water occ: r_work=0.1288 r_free=0.1523 adp: r_work=0.1276 r_free=0.1520 occ: r_work=0.1278 r_free=0.1515 adp: r_work=0.1271 r_free=0.1516 occ: r_work=0.1272 r_free=0.1511 adp: r_work=0.1271 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1512 r_work=0.1271 r_free=0.1512 | n_water=947 | time (s): 74.360 (total time: 196.640) Filter (q & B) r_work=0.1274 r_free=0.1514 | n_water=876 | time (s): 4.450 (total time: 201.090) Filter (dist only) r_work=0.1274 r_free=0.1513 | n_water=875 | time (s): 110.150 (total time: 311.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.757211 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 589.557675 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 0.1259 0.1529 0.0270 0.041 1.1 18.2 0.0 0.0 0 11.379 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.59 15.29 2.70 2.042 15.073 589.558 0.015 12.36 15.18 2.83 2.407 15.137 589.558 0.014 Individual atomic B min max mean iso aniso Overall: 5.45 69.16 16.15 1.20 507 3272 Protein: 5.45 39.85 10.99 1.20 0 2902 Water: 6.63 69.16 33.25 N/A 507 368 Other: 16.51 32.79 24.65 N/A 0 2 Chain A: 5.55 56.34 12.99 N/A 0 1624 Chain B: 5.45 68.20 12.82 N/A 0 1648 Chain S: 13.21 69.16 37.13 N/A 507 0 Histogram: Values Number of atoms 5.45 - 11.82 2088 11.82 - 18.19 690 18.19 - 24.56 270 24.56 - 30.93 220 30.93 - 37.30 174 37.30 - 43.67 167 43.67 - 50.04 96 50.04 - 56.41 38 56.41 - 62.78 27 62.78 - 69.16 9 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1519 r_work=0.1236 r_free=0.1520 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1520 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1521 target_work(ls_wunit_k1) = 0.014 | | 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.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1521 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013574 | | target function (ls_wunit_k1) not normalized (work): 2542.475963 | | target function (ls_wunit_k1) not normalized (free): 101.690099 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1230 0.1521 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1444 0.1441 0.1607 n_refl.: 191139 remove outliers: r(all,work,free)=0.1444 0.1441 0.1607 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1440 0.1438 0.1605 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1243 0.1237 0.1528 n_refl.: 191139 remove outliers: r(all,work,free)=0.1243 0.1237 0.1528 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3276 402.814 378.250 0.487 0.962 0.267 13.296-10.522 100.00 100 1 0.1909 534.497 526.664 0.766 0.963 0.228 10.503-8.327 99.45 178 3 0.1450 565.118 567.633 0.921 0.963 0.193 8.318-6.595 100.00 360 8 0.1556 414.736 413.386 0.940 0.962 0.177 6.588-5.215 100.00 711 7 0.1364 381.101 376.212 0.910 0.963 0.133 5.214-4.128 98.38 1367 28 0.0834 557.435 556.323 0.996 0.963 0.080 4.126-3.266 94.74 2603 46 0.0766 508.132 505.660 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0857 342.774 341.316 1.047 0.961 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.785 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.617 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1261 82.395 81.353 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.216 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0533 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1237 r_free=0.1528 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1237 r_free=0.1528 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1237 r_free=0.1528 | n_water=875 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1239 r_free=0.1528 | n_water=870 | time (s): 117.020 (total time: 120.170) Filter (q & B) r_work=0.1239 r_free=0.1529 | n_water=867 | time (s): 4.350 (total time: 124.520) Compute maps r_work=0.1239 r_free=0.1529 | n_water=867 | time (s): 1.740 (total time: 126.260) Filter (map) r_work=0.1276 r_free=0.1523 | n_water=689 | time (s): 5.250 (total time: 131.510) Find peaks r_work=0.1276 r_free=0.1523 | n_water=689 | time (s): 0.690 (total time: 132.200) Add new water r_work=0.1300 r_free=0.1563 | n_water=1022 | time (s): 4.060 (total time: 136.260) Refine new water occ: r_work=0.1252 r_free=0.1512 adp: r_work=0.1252 r_free=0.1512 occ: r_work=0.1249 r_free=0.1510 adp: r_work=0.1249 r_free=0.1510 occ: r_work=0.1246 r_free=0.1508 adp: r_work=0.1246 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1246 r_free=0.1509 r_work=0.1246 r_free=0.1509 | n_water=1022 | time (s): 272.390 (total time: 408.650) Filter (q & B) r_work=0.1251 r_free=0.1514 | n_water=872 | time (s): 5.150 (total time: 413.800) Filter (dist only) r_work=0.1251 r_free=0.1515 | n_water=871 | time (s): 125.510 (total time: 539.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.730510 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.109717 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 0.1438 0.0198 0.035 1.1 9.0 0.0 0.0 0 0.865 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.38 1.98 1.932 14.536 16.110 3.941 12.32 13.98 1.66 2.203 14.446 16.110 3.898 Individual atomic B min max mean iso aniso Overall: 5.52 67.85 15.17 1.07 504 3271 Protein: 5.52 36.53 10.77 1.07 0 2902 Water: 6.68 67.85 29.85 N/A 504 367 Other: 14.32 28.90 21.61 N/A 0 2 Chain A: 5.52 55.55 12.77 N/A 0 1624 Chain B: 5.53 67.85 12.55 N/A 0 1647 Chain S: 13.47 63.32 31.50 N/A 504 0 Histogram: Values Number of atoms 5.52 - 11.75 2129 11.75 - 17.99 682 17.99 - 24.22 309 24.22 - 30.45 248 30.45 - 36.68 172 36.68 - 42.92 137 42.92 - 49.15 69 49.15 - 55.38 19 55.38 - 61.61 8 61.61 - 67.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1398 r_work=0.1232 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1399 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1388 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.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892368 | | target function (ml) not normalized (work): 729032.809911 | | target function (ml) not normalized (free): 15231.705738 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1227 0.1388 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1444 0.1443 0.1485 n_refl.: 191139 remove outliers: r(all,work,free)=0.1444 0.1443 0.1485 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1438 0.1437 0.1481 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1380 n_refl.: 191139 remove outliers: r(all,work,free)=0.1226 0.1223 0.1380 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3815 398.008 362.632 0.421 0.945 0.246 13.296-10.522 98.02 98 1 0.2403 528.900 507.260 0.712 0.946 0.209 10.503-8.327 98.35 176 3 0.2055 555.265 555.880 0.882 0.946 0.200 8.318-6.595 100.00 360 8 0.2090 414.736 410.565 0.899 0.946 0.125 6.588-5.215 100.00 711 7 0.1845 381.101 370.054 0.885 0.946 0.120 5.214-4.128 98.38 1367 28 0.1171 557.435 552.113 0.972 0.946 0.054 4.126-3.266 94.74 2603 46 0.1087 508.132 501.052 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1082 342.774 339.066 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0958 258.603 255.774 1.034 0.945 0.000 2.046-1.619 99.39 21536 464 0.0968 153.054 151.416 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.487 1.053 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.313 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0973 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1380 | n_water=871 | time (s): 3.210 (total time: 3.210) Filter (dist) r_work=0.1223 r_free=0.1380 | n_water=869 | time (s): 106.690 (total time: 109.900) Filter (q & B) r_work=0.1223 r_free=0.1376 | n_water=858 | time (s): 5.540 (total time: 115.440) Compute maps r_work=0.1223 r_free=0.1376 | n_water=858 | time (s): 2.280 (total time: 117.720) Filter (map) r_work=0.1246 r_free=0.1376 | n_water=720 | time (s): 5.740 (total time: 123.460) Find peaks r_work=0.1246 r_free=0.1376 | n_water=720 | time (s): 0.600 (total time: 124.060) Add new water r_work=0.1261 r_free=0.1391 | n_water=971 | time (s): 4.160 (total time: 128.220) Refine new water occ: r_work=0.1212 r_free=0.1353 adp: r_work=0.1205 r_free=0.1349 occ: r_work=0.1202 r_free=0.1350 adp: r_work=0.1201 r_free=0.1349 occ: r_work=0.1200 r_free=0.1350 adp: r_work=0.1199 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1349 r_work=0.1199 r_free=0.1349 | n_water=971 | time (s): 363.970 (total time: 492.190) Filter (q & B) r_work=0.1203 r_free=0.1348 | n_water=879 | time (s): 5.470 (total time: 497.660) Filter (dist only) r_work=0.1204 r_free=0.1348 | n_water=878 | time (s): 111.690 (total time: 609.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.590160 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.995191 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 0.1352 0.0150 0.036 1.1 6.6 0.0 0.3 0 0.795 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.52 1.50 1.839 14.232 14.995 3.874 11.98 13.49 1.52 1.941 14.194 14.995 3.866 Individual atomic B min max mean iso aniso Overall: 5.50 67.50 14.99 1.00 512 3270 Protein: 5.50 33.51 10.68 1.00 0 2902 Water: 5.96 67.50 29.22 N/A 512 366 Other: 13.96 28.19 21.08 N/A 0 2 Chain A: 5.56 54.68 12.64 N/A 0 1624 Chain B: 5.50 67.50 12.44 N/A 0 1646 Chain S: 5.96 63.34 30.65 N/A 512 0 Histogram: Values Number of atoms 5.50 - 11.70 2115 11.70 - 17.90 724 17.90 - 24.10 311 24.10 - 30.30 247 30.30 - 36.50 164 36.50 - 42.70 133 42.70 - 48.90 66 48.90 - 55.10 15 55.10 - 61.30 5 61.30 - 67.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1349 r_work=0.1198 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1350 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1345 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863684 | | target function (ml) not normalized (work): 723641.048300 | | target function (ml) not normalized (free): 15131.335615 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1345 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1419 0.1418 0.1453 n_refl.: 191134 remove outliers: r(all,work,free)=0.1419 0.1418 0.1453 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1412 0.1411 0.1449 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1347 n_refl.: 191134 remove outliers: r(all,work,free)=0.1196 0.1193 0.1347 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3643 360.786 310.886 0.415 0.946 0.255 13.296-10.522 96.04 96 1 0.2367 480.283 450.591 0.704 0.948 0.204 10.503-8.327 98.35 176 3 0.2113 502.638 495.221 0.868 0.948 0.158 8.318-6.595 100.00 360 8 0.2125 375.429 371.163 0.895 0.948 0.113 6.588-5.215 100.00 711 7 0.1890 344.982 334.948 0.883 0.948 0.087 5.214-4.128 98.38 1367 28 0.1157 504.603 500.198 0.973 0.948 0.060 4.126-3.266 94.74 2603 46 0.1099 459.973 453.622 1.033 0.949 0.009 3.266-2.585 99.86 5447 97 0.1082 310.287 307.181 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0934 234.094 231.780 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0916 138.548 137.292 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0992 74.586 73.882 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.012 38.355 1.038 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1179 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1347 | n_water=878 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1193 r_free=0.1347 | n_water=878 | time (s): 105.760 (total time: 108.310) Filter (q & B) r_work=0.1194 r_free=0.1348 | n_water=870 | time (s): 4.600 (total time: 112.910) Compute maps r_work=0.1194 r_free=0.1348 | n_water=870 | time (s): 2.030 (total time: 114.940) Filter (map) r_work=0.1216 r_free=0.1352 | n_water=749 | time (s): 4.320 (total time: 119.260) Find peaks r_work=0.1216 r_free=0.1352 | n_water=749 | time (s): 0.630 (total time: 119.890) Add new water r_work=0.1227 r_free=0.1363 | n_water=983 | time (s): 4.140 (total time: 124.030) Refine new water occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1191 r_free=0.1337 occ: r_work=0.1188 r_free=0.1339 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1186 r_free=0.1340 adp: r_work=0.1186 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1339 r_work=0.1186 r_free=0.1339 | n_water=983 | time (s): 198.760 (total time: 322.790) Filter (q & B) r_work=0.1190 r_free=0.1346 | n_water=896 | time (s): 5.440 (total time: 328.230) Filter (dist only) r_work=0.1191 r_free=0.1345 | n_water=895 | time (s): 121.430 (total time: 449.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.575535 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.026982 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 0.1351 0.0157 0.036 1.1 7.1 0.0 0.3 0 0.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.51 1.57 1.798 14.165 15.027 3.763 11.97 13.58 1.60 1.880 14.134 15.027 3.761 Individual atomic B min max mean iso aniso Overall: 5.59 67.12 14.98 0.96 529 3270 Protein: 5.59 32.15 10.61 0.96 0 2902 Water: 6.10 67.12 29.13 N/A 529 366 Other: 13.82 26.86 20.34 N/A 0 2 Chain A: 5.59 53.76 12.54 N/A 0 1624 Chain B: 5.59 67.12 12.34 N/A 0 1646 Chain S: 6.10 63.37 30.65 N/A 529 0 Histogram: Values Number of atoms 5.59 - 11.74 2148 11.74 - 17.89 710 17.89 - 24.05 299 24.05 - 30.20 246 30.20 - 36.35 176 36.35 - 42.51 135 42.51 - 48.66 62 48.66 - 54.81 16 54.81 - 60.97 5 60.97 - 67.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1358 r_work=0.1198 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1358 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1364 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760000 | | target function (ml) not normalized (work): 704206.661615 | | target function (ml) not normalized (free): 14746.924900 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1364 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1498 n_refl.: 191130 remove outliers: r(all,work,free)=0.1393 0.1391 0.1498 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1385 0.1383 0.1492 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1363 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1194 0.1363 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3561 360.786 334.396 0.440 0.952 0.251 13.296-10.522 96.04 96 1 0.2387 480.283 458.291 0.705 0.953 0.187 10.503-8.327 98.35 176 3 0.2133 502.638 494.808 0.862 0.953 0.157 8.318-6.595 100.00 360 8 0.2169 375.429 370.743 0.888 0.953 0.108 6.588-5.215 100.00 711 7 0.1886 344.982 335.647 0.880 0.953 0.071 5.214-4.128 98.38 1367 28 0.1182 504.603 499.642 0.970 0.954 0.060 4.126-3.266 94.74 2603 46 0.1125 459.973 453.091 1.029 0.954 0.005 3.266-2.585 99.86 5447 97 0.1099 310.287 306.889 1.015 0.954 0.000 2.585-2.046 97.45 10613 204 0.0944 234.094 231.643 1.028 0.954 0.000 2.046-1.619 99.39 21536 464 0.0912 138.548 137.236 1.050 0.954 0.000 1.619-1.281 98.00 42464 925 0.0978 74.586 73.872 1.046 0.954 0.000 1.281-0.980 96.53 101826 2055 0.1655 40.012 38.346 1.032 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1406 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1362 | n_water=895 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1194 r_free=0.1363 | n_water=892 | time (s): 115.980 (total time: 118.320) Filter (q & B) r_work=0.1195 r_free=0.1364 | n_water=882 | time (s): 5.060 (total time: 123.380) Compute maps r_work=0.1195 r_free=0.1364 | n_water=882 | time (s): 2.230 (total time: 125.610) Filter (map) r_work=0.1216 r_free=0.1365 | n_water=764 | time (s): 5.160 (total time: 130.770) Find peaks r_work=0.1216 r_free=0.1365 | n_water=764 | time (s): 0.710 (total time: 131.480) Add new water r_work=0.1226 r_free=0.1378 | n_water=979 | time (s): 5.040 (total time: 136.520) Refine new water occ: r_work=0.1193 r_free=0.1359 adp: r_work=0.1193 r_free=0.1358 occ: r_work=0.1191 r_free=0.1359 adp: r_work=0.1191 r_free=0.1359 occ: r_work=0.1189 r_free=0.1358 adp: r_work=0.1189 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1358 r_work=0.1189 r_free=0.1358 | n_water=979 | time (s): 233.710 (total time: 370.230) Filter (q & B) r_work=0.1194 r_free=0.1363 | n_water=903 | time (s): 4.440 (total time: 374.670) Filter (dist only) r_work=0.1194 r_free=0.1360 | n_water=901 | time (s): 116.300 (total time: 490.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.555202 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.100394 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 0.1198 0.1363 0.0165 0.037 1.1 5.4 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.63 1.65 1.766 14.052 15.100 3.761 12.00 13.65 1.65 1.911 14.002 15.100 3.758 Individual atomic B min max mean iso aniso Overall: 5.58 66.00 14.83 0.91 535 3270 Protein: 5.58 29.47 10.49 0.91 0 2902 Water: 5.73 66.00 28.81 N/A 535 366 Other: 13.86 23.90 18.88 N/A 0 2 Chain A: 5.65 50.96 12.38 N/A 0 1624 Chain B: 5.58 66.00 12.21 N/A 0 1646 Chain S: 5.73 63.53 30.36 N/A 535 0 Histogram: Values Number of atoms 5.58 - 11.62 2119 11.62 - 17.67 772 17.67 - 23.71 272 23.71 - 29.75 234 29.75 - 35.79 175 35.79 - 41.83 141 41.83 - 47.88 66 47.88 - 53.92 19 53.92 - 59.96 5 59.96 - 66.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1365 r_work=0.1201 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1369 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757286 | | target function (ml) not normalized (work): 703698.281559 | | target function (ml) not normalized (free): 14738.115704 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1369 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1497 n_refl.: 191130 remove outliers: r(all,work,free)=0.1395 0.1393 0.1497 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1359 0.1357 0.1472 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1365 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1196 0.1365 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3504 360.786 334.815 0.429 0.953 0.222 13.296-10.522 95.05 95 1 0.2329 479.385 451.314 0.711 0.954 0.154 10.503-8.327 98.35 176 3 0.2185 502.638 493.909 0.882 0.955 0.127 8.318-6.595 100.00 360 8 0.2185 375.429 370.489 0.906 0.955 0.108 6.588-5.215 100.00 711 7 0.1889 344.982 335.603 0.901 0.955 0.085 5.214-4.128 98.38 1367 28 0.1210 504.603 499.309 0.994 0.955 0.080 4.126-3.266 94.74 2603 46 0.1146 459.973 452.915 1.052 0.955 0.000 3.266-2.585 99.86 5447 97 0.1116 310.287 307.003 1.036 0.955 0.000 2.585-2.046 97.45 10613 204 0.0954 234.094 231.611 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0911 138.548 137.261 1.062 0.954 0.000 1.619-1.281 98.00 42464 925 0.0969 74.586 73.894 1.051 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.012 38.354 1.022 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0516 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1365 | n_water=901 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1197 r_free=0.1365 | n_water=901 | time (s): 108.220 (total time: 110.760) Filter (q & B) r_work=0.1197 r_free=0.1366 | n_water=894 | time (s): 5.370 (total time: 116.130) Compute maps r_work=0.1197 r_free=0.1366 | n_water=894 | time (s): 2.340 (total time: 118.470) Filter (map) r_work=0.1218 r_free=0.1364 | n_water=785 | time (s): 5.380 (total time: 123.850) Find peaks r_work=0.1218 r_free=0.1364 | n_water=785 | time (s): 0.660 (total time: 124.510) Add new water r_work=0.1227 r_free=0.1371 | n_water=991 | time (s): 3.960 (total time: 128.470) Refine new water occ: r_work=0.1194 r_free=0.1351 adp: r_work=0.1194 r_free=0.1351 occ: r_work=0.1192 r_free=0.1351 adp: r_work=0.1192 r_free=0.1351 occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1190 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1351 r_work=0.1190 r_free=0.1351 | n_water=991 | time (s): 365.450 (total time: 493.920) Filter (q & B) r_work=0.1195 r_free=0.1359 | n_water=919 | time (s): 4.950 (total time: 498.870) Filter (dist only) r_work=0.1195 r_free=0.1359 | n_water=918 | time (s): 122.660 (total time: 621.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558129 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.894026 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1365 0.0168 0.038 1.1 6.6 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.65 1.68 1.721 13.756 13.894 3.758 12.00 13.68 1.69 1.737 13.746 13.894 3.758 Individual atomic B min max mean iso aniso Overall: 5.36 65.44 14.66 0.88 552 3270 Protein: 5.36 28.87 10.26 0.88 0 2902 Water: 5.57 65.44 28.55 N/A 552 366 Other: 13.64 23.13 18.38 N/A 0 2 Chain A: 5.43 50.58 12.12 N/A 0 1624 Chain B: 5.36 65.44 11.96 N/A 0 1646 Chain S: 5.57 63.34 30.18 N/A 552 0 Histogram: Values Number of atoms 5.36 - 11.37 2118 11.37 - 17.38 772 17.38 - 23.38 288 23.38 - 29.39 226 29.39 - 35.40 176 35.40 - 41.41 139 41.41 - 47.41 73 47.41 - 53.42 23 53.42 - 59.43 4 59.43 - 65.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1369 r_work=0.1200 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1369 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1372 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757366 | | target function (ml) not normalized (work): 703709.510928 | | target function (ml) not normalized (free): 14742.617083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1372 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1362 0.1360 0.1488 n_refl.: 191129 remove outliers: r(all,work,free)=0.1362 0.1360 0.1488 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1369 0.1366 0.1493 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1362 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1362 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3587 360.786 332.942 0.416 0.975 0.213 13.296-10.522 95.05 95 1 0.2320 479.385 460.411 0.714 0.977 0.149 10.503-8.327 98.35 176 3 0.2170 502.638 494.151 0.871 0.977 0.123 8.318-6.595 100.00 360 8 0.2185 375.429 369.855 0.893 0.977 0.103 6.588-5.215 100.00 711 7 0.1909 344.982 335.227 0.890 0.977 0.083 5.214-4.128 98.38 1367 28 0.1209 504.603 499.083 0.980 0.978 0.034 4.126-3.266 94.74 2603 46 0.1148 459.973 452.433 1.040 0.979 0.005 3.266-2.585 99.86 5447 97 0.1117 310.287 306.642 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0956 234.094 231.484 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0910 138.548 137.166 1.046 0.985 0.000 1.619-1.281 98.00 42464 925 0.0951 74.586 73.925 1.034 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.012 38.328 1.000 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0613 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1362 | n_water=918 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1189 r_free=0.1363 | n_water=915 | time (s): 113.150 (total time: 115.460) Filter (q & B) r_work=0.1189 r_free=0.1363 | n_water=904 | time (s): 4.170 (total time: 119.630) Compute maps r_work=0.1189 r_free=0.1363 | n_water=904 | time (s): 1.720 (total time: 121.350) Filter (map) r_work=0.1212 r_free=0.1359 | n_water=789 | time (s): 4.470 (total time: 125.820) Find peaks r_work=0.1212 r_free=0.1359 | n_water=789 | time (s): 0.760 (total time: 126.580) Add new water r_work=0.1220 r_free=0.1366 | n_water=1003 | time (s): 4.190 (total time: 130.770) Refine new water occ: r_work=0.1188 r_free=0.1344 adp: r_work=0.1188 r_free=0.1344 occ: r_work=0.1186 r_free=0.1342 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=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1341 r_work=0.1184 r_free=0.1341 | n_water=1003 | time (s): 223.760 (total time: 354.530) Filter (q & B) r_work=0.1188 r_free=0.1350 | n_water=916 | time (s): 5.150 (total time: 359.680) Filter (dist only) r_work=0.1189 r_free=0.1349 | n_water=915 | time (s): 120.150 (total time: 479.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.484707 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.954634 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 0.1355 0.0163 0.038 1.1 5.5 0.0 0.3 0 0.742 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.55 1.63 1.681 13.761 13.955 3.756 11.92 13.56 1.64 1.696 13.754 13.955 3.754 Individual atomic B min max mean iso aniso Overall: 5.47 65.02 14.67 0.87 549 3270 Protein: 5.47 28.54 10.33 0.87 0 2902 Water: 5.69 65.02 28.44 N/A 549 366 Other: 13.72 22.60 18.16 N/A 0 2 Chain A: 5.56 50.42 12.15 N/A 0 1624 Chain B: 5.47 65.02 12.00 N/A 0 1646 Chain S: 5.69 63.48 30.13 N/A 549 0 Histogram: Values Number of atoms 5.47 - 11.43 2108 11.43 - 17.38 788 17.38 - 23.34 284 23.34 - 29.29 220 29.29 - 35.25 179 35.25 - 41.20 131 41.20 - 47.15 78 47.15 - 53.11 23 53.11 - 59.06 5 59.06 - 65.02 3 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1356 r_work=0.1192 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1356 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1357 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753586 | | target function (ml) not normalized (work): 703001.673737 | | target function (ml) not normalized (free): 14728.876144 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1190 0.1357 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1377 0.1375 0.1493 n_refl.: 191129 remove outliers: r(all,work,free)=0.1377 0.1375 0.1493 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1379 0.1377 0.1494 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1357 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1357 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3571 360.786 332.991 0.433 0.913 0.198 13.296-10.522 95.05 95 1 0.2311 479.385 461.469 0.761 0.914 0.140 10.503-8.327 98.35 176 3 0.2163 502.638 494.502 0.930 0.915 0.110 8.318-6.595 100.00 360 8 0.2160 375.429 370.159 0.948 0.915 0.086 6.588-5.215 100.00 711 7 0.1933 344.982 335.308 0.947 0.915 0.077 5.214-4.128 98.38 1367 28 0.1224 504.603 498.858 1.046 0.916 0.050 4.126-3.266 94.74 2603 46 0.1152 459.973 452.418 1.110 0.917 0.000 3.266-2.585 99.86 5447 97 0.1120 310.287 306.654 1.092 0.918 0.000 2.585-2.046 97.45 10613 204 0.0959 234.094 231.496 1.102 0.920 0.000 2.046-1.619 99.39 21536 464 0.0912 138.548 137.181 1.119 0.923 0.000 1.619-1.281 98.00 42464 925 0.0947 74.586 73.933 1.108 0.928 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.012 38.313 1.074 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0200 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1357 | n_water=915 | time (s): 2.790 (total time: 2.790) Filter (dist) r_work=0.1189 r_free=0.1357 | n_water=915 | time (s): 115.060 (total time: 117.850) Filter (q & B) r_work=0.1189 r_free=0.1358 | n_water=910 | time (s): 5.460 (total time: 123.310) Compute maps r_work=0.1189 r_free=0.1358 | n_water=910 | time (s): 1.740 (total time: 125.050) Filter (map) r_work=0.1210 r_free=0.1357 | n_water=804 | time (s): 5.380 (total time: 130.430) Find peaks r_work=0.1210 r_free=0.1357 | n_water=804 | time (s): 0.590 (total time: 131.020) Add new water r_work=0.1217 r_free=0.1365 | n_water=1024 | time (s): 4.120 (total time: 135.140) Refine new water occ: r_work=0.1186 r_free=0.1343 adp: r_work=0.1186 r_free=0.1344 occ: r_work=0.1184 r_free=0.1341 adp: r_work=0.1184 r_free=0.1342 occ: r_work=0.1183 r_free=0.1340 adp: r_work=0.1182 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1341 r_work=0.1182 r_free=0.1341 | n_water=1024 | time (s): 286.930 (total time: 422.070) Filter (q & B) r_work=0.1187 r_free=0.1353 | n_water=931 | time (s): 4.540 (total time: 426.610) Filter (dist only) r_work=0.1188 r_free=0.1353 | n_water=929 | time (s): 120.170 (total time: 546.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.623338 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.137057 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 0.1189 0.1356 0.0167 0.038 1.1 6.1 0.0 0.3 0 0.812 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.56 1.67 1.683 13.799 14.137 3.754 11.89 13.56 1.67 1.707 13.795 14.137 3.752 Individual atomic B min max mean iso aniso Overall: 5.54 64.00 14.72 0.86 563 3270 Protein: 5.54 28.14 10.34 0.86 0 2902 Water: 5.78 64.00 28.40 N/A 563 366 Other: 13.80 22.10 17.95 N/A 0 2 Chain A: 5.59 49.97 12.14 N/A 0 1624 Chain B: 5.54 64.00 11.99 N/A 0 1646 Chain S: 5.78 63.65 30.14 N/A 563 0 Histogram: Values Number of atoms 5.54 - 11.39 2080 11.39 - 17.24 814 17.24 - 23.08 277 23.08 - 28.93 222 28.93 - 34.77 191 34.77 - 40.62 129 40.62 - 46.46 83 46.46 - 52.31 29 52.31 - 58.16 3 58.16 - 64.00 5 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1356 r_work=0.1189 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1356 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1354 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751487 | | target function (ml) not normalized (work): 702608.487612 | | target function (ml) not normalized (free): 14722.610073 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1354 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1385 0.1383 0.1506 n_refl.: 191129 remove outliers: r(all,work,free)=0.1385 0.1383 0.1506 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1385 0.1383 0.1506 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1190 0.1187 0.1351 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3620 360.786 331.806 0.390 0.994 0.188 13.296-10.522 95.05 95 1 0.2329 479.385 460.899 0.692 0.996 0.130 10.503-8.327 98.35 176 3 0.2162 502.638 495.234 0.852 0.996 0.113 8.318-6.595 100.00 360 8 0.2164 375.429 370.156 0.869 0.996 0.085 6.588-5.215 100.00 711 7 0.1933 344.982 335.158 0.869 0.997 0.080 5.214-4.128 98.38 1367 28 0.1226 504.603 498.994 0.959 0.998 0.034 4.126-3.266 94.74 2603 46 0.1157 459.973 452.382 1.019 0.999 0.000 3.266-2.585 99.86 5447 97 0.1120 310.287 306.642 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0956 234.094 231.517 1.012 1.003 0.000 2.046-1.619 99.39 21536 464 0.0909 138.548 137.181 1.027 1.007 0.000 1.619-1.281 98.00 42464 925 0.0941 74.586 73.941 1.018 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.012 38.306 0.988 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0082 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1351 After: r_work=0.1188 r_free=0.1352 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1352 | n_water=929 | time (s): 2.790 (total time: 2.790) Filter (dist) r_work=0.1188 r_free=0.1352 | n_water=929 | time (s): 117.420 (total time: 120.210) Filter (q & B) r_work=0.1188 r_free=0.1351 | n_water=922 | time (s): 4.440 (total time: 124.650) Compute maps r_work=0.1188 r_free=0.1351 | n_water=922 | time (s): 2.470 (total time: 127.120) Filter (map) r_work=0.1206 r_free=0.1351 | n_water=822 | time (s): 4.670 (total time: 131.790) Find peaks r_work=0.1206 r_free=0.1351 | n_water=822 | time (s): 0.880 (total time: 132.670) Add new water r_work=0.1211 r_free=0.1356 | n_water=1027 | time (s): 5.660 (total time: 138.330) Refine new water occ: r_work=0.1185 r_free=0.1332 adp: r_work=0.1185 r_free=0.1332 occ: r_work=0.1183 r_free=0.1331 adp: r_work=0.1183 r_free=0.1332 occ: r_work=0.1183 r_free=0.1332 adp: r_work=0.1183 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1332 r_work=0.1183 r_free=0.1332 | n_water=1027 | time (s): 211.280 (total time: 349.610) Filter (q & B) r_work=0.1189 r_free=0.1348 | n_water=916 | time (s): 4.980 (total time: 354.590) Filter (dist only) r_work=0.1189 r_free=0.1348 | n_water=914 | time (s): 122.380 (total time: 476.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.478374 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.605275 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 0.1191 0.1351 0.0160 0.038 1.1 6.5 0.0 0.3 0 0.739 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.51 1.60 1.679 13.717 13.605 3.754 11.93 13.53 1.61 1.678 13.716 13.605 3.754 Individual atomic B min max mean iso aniso Overall: 5.54 63.71 14.59 0.85 548 3270 Protein: 5.54 28.03 10.35 0.85 0 2902 Water: 5.86 63.71 28.04 N/A 548 366 Other: 13.81 22.14 17.98 N/A 0 2 Chain A: 5.63 49.84 12.13 N/A 0 1624 Chain B: 5.54 63.63 11.99 N/A 0 1646 Chain S: 5.86 63.71 29.70 N/A 548 0 Histogram: Values Number of atoms 5.54 - 11.36 2068 11.36 - 17.18 827 17.18 - 22.99 282 22.99 - 28.81 221 28.81 - 34.62 192 34.62 - 40.44 115 40.44 - 46.26 77 46.26 - 52.07 28 52.07 - 57.89 3 57.89 - 63.71 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1353 r_work=0.1193 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1353 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753367 | | target function (ml) not normalized (work): 702960.689664 | | target function (ml) not normalized (free): 14724.957363 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1356 0.1438 5.6835 5.7424| | 2: 2.94 - 2.33 1.00 7339 128 0.1067 0.1353 5.0697 5.1746| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1212 4.6576 4.7661| | 4: 2.04 - 1.85 1.00 7170 155 0.0903 0.1078 4.3985 4.5888| | 5: 1.85 - 1.72 0.99 7113 159 0.0934 0.0988 4.1558 4.2508| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1095 3.9495 4.0841| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0952 3.801 3.9384| | 8: 1.54 - 1.47 0.96 6798 152 0.0889 0.1308 3.6981 3.8913| | 9: 1.47 - 1.41 0.98 6938 155 0.0926 0.1108 3.6204 3.7464| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1176 3.5527 3.6707| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1118 3.481 3.5811| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1127 3.455 3.5712| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1221 3.4335 3.5524| | 14: 1.25 - 1.22 0.98 7015 112 0.1108 0.1590 3.4308 3.68| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1240 3.4477 3.4928| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1562 3.4654 3.6629| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1238 3.4349 3.4479| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1709 3.4383 3.5336| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1734 3.4189 3.5885| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1576 3.4087 3.431| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2135 3.4179 3.5034| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1950 3.4121 3.4117| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2018 3.4327 3.4829| | 24: 1.03 - 1.02 0.96 6784 133 0.2329 0.2250 3.4346 3.5074| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2504 3.4482 3.5235| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2850 3.4152 3.4224| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2805 3.4684 3.3954| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.29 1.00 0.96 10728.86| | 2: 2.94 - 2.33 7339 128 0.93 12.63 0.99 0.95 5004.94| | 3: 2.33 - 2.04 6939 150 0.96 7.76 1.01 0.95 1741.11| | 4: 2.04 - 1.85 7170 155 0.96 7.82 1.00 0.95 1034.10| | 5: 1.85 - 1.72 7113 159 0.96 8.21 1.00 0.96 647.37| | 6: 1.72 - 1.62 7102 142 0.96 8.09 1.00 0.96 448.86| | 7: 1.62 - 1.54 7104 148 0.96 8.18 1.01 0.97 339.23| | 8: 1.54 - 1.47 6798 152 0.96 8.27 1.01 0.97 279.10| | 9: 1.47 - 1.41 6938 155 0.96 8.42 1.00 0.98 229.36| | 10: 1.41 - 1.36 7022 150 0.96 8.82 1.00 0.97 199.78| | 11: 1.36 - 1.32 6997 151 0.96 8.81 0.99 0.96 171.79| | 12: 1.32 - 1.28 6975 149 0.96 8.85 0.98 0.95 157.64| | 13: 1.28 - 1.25 6907 166 0.96 9.43 1.01 0.96 155.55| | 14: 1.25 - 1.22 7015 112 0.95 10.61 1.01 0.96 161.28| | 15: 1.22 - 1.19 6956 137 0.95 11.22 1.01 0.97 166.31| | 16: 1.19 - 1.17 6604 132 0.95 11.48 1.01 0.96 160.85| | 17: 1.17 - 1.14 6940 135 0.94 12.30 1.01 0.96 154.82| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.94 147.54| | 19: 1.12 - 1.10 6948 106 0.93 14.11 1.00 0.94 150.41| | 20: 1.10 - 1.08 6884 147 0.92 15.14 1.00 0.94 149.16| | 21: 1.08 - 1.07 6852 152 0.91 16.60 1.00 0.93 152.36| | 22: 1.07 - 1.05 6836 135 0.89 18.23 0.99 0.93 153.96| | 23: 1.05 - 1.03 6827 159 0.87 20.43 0.99 0.92 163.74| | 24: 1.03 - 1.02 6784 133 0.85 23.09 0.99 0.93 178.08| | 25: 1.02 - 1.01 6552 130 0.83 25.09 0.98 0.90 181.35| | 26: 1.01 - 0.99 6767 158 0.81 26.58 0.98 0.88 176.12| | 27: 0.99 - 0.98 6647 131 0.82 26.28 0.99 0.87 160.76| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.54 max = 10728.86 mean = 904.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.96 mean = 13.25| |phase err.(test): min = 0.00 max = 89.29 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1504 n_refl.: 191129 remove outliers: r(all,work,free)=0.1398 0.1396 0.1504 n_refl.: 191129 overall B=-0.05 to atoms: r(all,work,free)=0.1390 0.1388 0.1499 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1354 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1354 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3605 360.786 331.912 0.415 0.915 0.193 13.296-10.522 95.05 95 1 0.2263 479.385 460.880 0.735 0.916 0.131 10.503-8.327 98.35 176 3 0.2213 502.638 494.268 0.900 0.917 0.105 8.318-6.595 100.00 360 8 0.2184 375.429 370.217 0.922 0.917 0.092 6.588-5.215 100.00 711 7 0.1943 344.982 335.032 0.919 0.917 0.081 5.214-4.128 98.38 1367 28 0.1243 504.603 498.533 1.018 0.918 0.060 4.126-3.266 94.74 2603 46 0.1160 459.973 452.307 1.082 0.920 0.000 3.266-2.585 99.86 5447 97 0.1119 310.287 306.692 1.064 0.921 0.000 2.585-2.046 97.45 10613 204 0.0961 234.094 231.507 1.071 0.924 0.000 2.046-1.619 99.39 21536 464 0.0912 138.548 137.167 1.087 0.928 0.000 1.619-1.281 98.00 42464 925 0.0945 74.586 73.939 1.075 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.012 38.303 1.040 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0118 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2038 0.2016 0.083 5.214 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1952 0.083 5.214 5.2 78.0 14.6 805 0.000 1_settarget: 0.1804 0.1952 0.083 5.214 5.2 78.0 14.6 805 0.000 1_nqh: 0.1804 0.1952 0.083 5.214 5.2 78.0 14.6 805 0.000 1_weight: 0.1804 0.1952 0.083 5.214 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1501 0.038 1.153 5.2 78.0 14.6 805 0.154 1_adp: 0.1300 0.1571 0.038 1.153 5.2 73.0 15.0 805 0.154 1_regHadp: 0.1299 0.1566 0.038 1.153 5.2 73.0 15.0 805 0.154 1_occ: 0.1285 0.1556 0.038 1.153 5.2 73.0 15.0 805 0.154 2_bss: 0.1277 0.1547 0.038 1.153 5.3 73.2 15.2 805 0.154 2_settarget: 0.1277 0.1547 0.038 1.153 5.3 73.2 15.2 805 0.154 2_updatecdl: 0.1277 0.1547 0.038 1.163 5.3 73.2 15.2 805 0.154 2_nqh: 0.1277 0.1547 0.038 1.163 5.3 73.2 15.2 805 0.154 2_sol: 0.1274 0.1513 0.038 1.163 5.3 73.2 16.0 875 n/a 2_weight: 0.1274 0.1513 0.038 1.163 5.3 73.2 16.0 875 n/a 2_xyzrec: 0.1259 0.1529 0.041 1.128 5.3 73.2 16.0 875 n/a 2_adp: 0.1236 0.1519 0.041 1.128 5.4 69.2 16.2 875 n/a 2_regHadp: 0.1236 0.1520 0.041 1.128 5.4 69.2 16.2 875 n/a 2_occ: 0.1230 0.1521 0.041 1.128 5.4 69.2 16.2 875 n/a 3_bss: 0.1237 0.1528 0.041 1.128 5.4 69.1 16.1 875 n/a 3_settarget: 0.1237 0.1528 0.041 1.128 5.4 69.1 16.1 875 n/a 3_updatecdl: 0.1237 0.1528 0.041 1.128 5.4 69.1 16.1 875 n/a 3_nqh: 0.1237 0.1528 0.041 1.128 5.4 69.1 16.1 875 n/a 3_sol: 0.1251 0.1515 0.041 1.128 5.4 68.2 15.3 871 n/a 3_weight: 0.1251 0.1515 0.041 1.128 5.4 68.2 15.3 871 n/a 3_xyzrec: 0.1240 0.1438 0.035 1.104 5.4 68.2 15.3 871 n/a 3_adp: 0.1232 0.1398 0.035 1.104 5.5 67.8 15.2 871 n/a 3_regHadp: 0.1232 0.1399 0.035 1.104 5.5 67.8 15.2 871 n/a 3_occ: 0.1227 0.1388 0.035 1.104 5.5 67.8 15.2 871 n/a 4_bss: 0.1223 0.1380 0.035 1.104 5.5 67.8 15.1 871 n/a 4_settarget: 0.1223 0.1380 0.035 1.104 5.5 67.8 15.1 871 n/a 4_updatecdl: 0.1223 0.1380 0.035 1.110 5.5 67.8 15.1 871 n/a 4_nqh: 0.1223 0.1380 0.035 1.110 5.5 67.8 15.1 871 n/a 4_sol: 0.1204 0.1348 0.035 1.110 5.5 67.8 15.1 878 n/a 4_weight: 0.1204 0.1348 0.035 1.110 5.5 67.8 15.1 878 n/a 4_xyzrec: 0.1202 0.1352 0.036 1.122 5.5 67.8 15.1 878 n/a 4_adp: 0.1198 0.1349 0.036 1.122 5.5 67.5 15.0 878 n/a 4_regHadp: 0.1198 0.1350 0.036 1.122 5.5 67.5 15.0 878 n/a 4_occ: 0.1195 0.1345 0.036 1.122 5.5 67.5 15.0 878 n/a 5_bss: 0.1193 0.1347 0.036 1.122 5.5 67.5 15.0 878 n/a 5_settarget: 0.1193 0.1347 0.036 1.122 5.5 67.5 15.0 878 n/a 5_updatecdl: 0.1193 0.1347 0.036 1.122 5.5 67.5 15.0 878 n/a 5_nqh: 0.1193 0.1347 0.036 1.122 5.5 67.5 15.0 878 n/a 5_sol: 0.1191 0.1345 0.036 1.122 5.5 67.5 15.0 895 n/a 5_weight: 0.1191 0.1345 0.036 1.122 5.5 67.5 15.0 895 n/a 5_xyzrec: 0.1194 0.1351 0.036 1.133 5.5 67.5 15.0 895 n/a 5_adp: 0.1197 0.1358 0.036 1.133 5.6 67.1 15.0 895 n/a 5_regHadp: 0.1198 0.1358 0.036 1.133 5.6 67.1 15.0 895 n/a 5_occ: 0.1196 0.1364 0.036 1.133 5.6 67.1 15.0 895 n/a 6_bss: 0.1194 0.1362 0.036 1.133 5.5 67.1 14.9 895 n/a 6_settarget: 0.1194 0.1362 0.036 1.133 5.5 67.1 14.9 895 n/a 6_updatecdl: 0.1194 0.1362 0.036 1.132 5.5 67.1 14.9 895 n/a 6_nqh: 0.1194 0.1362 0.036 1.132 5.5 67.1 14.9 895 n/a 6_sol: 0.1194 0.1360 0.036 1.132 5.5 67.1 14.9 901 n/a 6_weight: 0.1194 0.1360 0.036 1.132 5.5 67.1 14.9 901 n/a 6_xyzrec: 0.1198 0.1363 0.037 1.123 5.5 67.1 14.9 901 n/a 6_adp: 0.1200 0.1365 0.037 1.123 5.6 66.0 14.8 901 n/a 6_regHadp: 0.1201 0.1366 0.037 1.123 5.6 66.0 14.8 901 n/a 6_occ: 0.1199 0.1369 0.037 1.123 5.6 66.0 14.8 901 n/a 7_bss: 0.1197 0.1365 0.037 1.123 5.3 65.8 14.6 901 n/a 7_settarget: 0.1197 0.1365 0.037 1.123 5.3 65.8 14.6 901 n/a 7_updatecdl: 0.1197 0.1365 0.037 1.124 5.3 65.8 14.6 901 n/a 7_nqh: 0.1197 0.1365 0.037 1.124 5.3 65.8 14.6 901 n/a 7_sol: 0.1195 0.1359 0.037 1.124 5.3 65.8 14.7 918 n/a 7_weight: 0.1195 0.1359 0.037 1.124 5.3 65.8 14.7 918 n/a 7_xyzrec: 0.1197 0.1365 0.038 1.126 5.3 65.8 14.7 918 n/a 7_adp: 0.1200 0.1369 0.038 1.126 5.4 65.4 14.7 918 n/a 7_regHadp: 0.1200 0.1369 0.038 1.126 5.4 65.4 14.7 918 n/a 7_occ: 0.1198 0.1372 0.038 1.126 5.4 65.4 14.7 918 n/a 8_bss: 0.1189 0.1362 0.038 1.126 5.4 65.5 14.7 918 n/a 8_settarget: 0.1189 0.1362 0.038 1.126 5.4 65.5 14.7 918 n/a 8_updatecdl: 0.1189 0.1362 0.038 1.126 5.4 65.5 14.7 918 n/a 8_nqh: 0.1189 0.1362 0.038 1.126 5.4 65.5 14.7 918 n/a 8_sol: 0.1189 0.1349 0.038 1.126 5.4 65.5 14.7 915 n/a 8_weight: 0.1189 0.1349 0.038 1.126 5.4 65.5 14.7 915 n/a 8_xyzrec: 0.1192 0.1355 0.038 1.113 5.4 65.5 14.7 915 n/a 8_adp: 0.1192 0.1356 0.038 1.113 5.5 65.0 14.7 915 n/a 8_regHadp: 0.1192 0.1356 0.038 1.113 5.5 65.0 14.7 915 n/a 8_occ: 0.1190 0.1357 0.038 1.113 5.5 65.0 14.7 915 n/a 9_bss: 0.1189 0.1357 0.038 1.113 5.5 65.0 14.7 915 n/a 9_settarget: 0.1189 0.1357 0.038 1.113 5.5 65.0 14.7 915 n/a 9_updatecdl: 0.1189 0.1357 0.038 1.114 5.5 65.0 14.7 915 n/a 9_nqh: 0.1189 0.1357 0.038 1.114 5.5 65.0 14.7 915 n/a 9_sol: 0.1188 0.1353 0.038 1.114 5.5 65.0 14.7 929 n/a 9_weight: 0.1188 0.1353 0.038 1.114 5.5 65.0 14.7 929 n/a 9_xyzrec: 0.1189 0.1356 0.038 1.138 5.5 65.0 14.7 929 n/a 9_adp: 0.1189 0.1356 0.038 1.138 5.5 64.0 14.7 929 n/a 9_regHadp: 0.1189 0.1356 0.038 1.138 5.5 64.0 14.7 929 n/a 9_occ: 0.1188 0.1354 0.038 1.138 5.5 64.0 14.7 929 n/a 10_bss: 0.1187 0.1351 0.038 1.138 5.5 64.0 14.7 929 n/a 10_settarget: 0.1187 0.1351 0.038 1.138 5.5 64.0 14.7 929 n/a 10_updatecdl: 0.1187 0.1351 0.038 1.138 5.5 64.0 14.7 929 n/a 10_setrh: 0.1188 0.1352 0.038 1.138 5.5 64.0 14.7 929 n/a 10_nqh: 0.1188 0.1352 0.038 1.138 5.5 64.0 14.7 929 n/a 10_sol: 0.1189 0.1348 0.038 1.138 5.5 64.0 14.6 914 n/a 10_weight: 0.1189 0.1348 0.038 1.138 5.5 64.0 14.6 914 n/a 10_xyzrec: 0.1191 0.1351 0.038 1.149 5.5 64.0 14.6 914 n/a 10_adp: 0.1193 0.1353 0.038 1.149 5.5 63.7 14.6 914 n/a 10_regHadp: 0.1193 0.1353 0.038 1.149 5.5 63.7 14.6 914 n/a 10_occ: 0.1192 0.1353 0.038 1.149 5.5 63.7 14.6 914 n/a end: 0.1191 0.1354 0.038 1.149 5.5 63.7 14.5 914 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3516039_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3516039_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2000 Refinement macro-cycles (run) : 12286.2500 Write final files (write_after_run_outputs) : 135.8600 Total : 12428.3100 Total CPU time: 3.46 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:19 PST -0800 (1736736259.73 s) Start R-work = 0.1804, R-free = 0.1952 Final R-work = 0.1191, R-free = 0.1354 =============================================================================== Job complete usr+sys time: 12680.14 seconds wall clock time: 212 minutes 17.56 seconds (12737.56 seconds total)