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_7723142.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7723142.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7723142.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.50, 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: 2.773 distance_ideal: 2.720 ideal - model: -0.053 slack: 0.000 delta_slack: -0.053 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: 2.706 distance_ideal: 2.710 ideal - model: 0.004 slack: 0.000 delta_slack: 0.004 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: 0.86 Conformation dependent library (CDL) restraints added in 160.6 milliseconds Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.76 - 1.00: 477 1.00 - 1.23: 2658 1.23 - 1.47: 1527 1.47 - 1.70: 1249 1.70 - 1.94: 23 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA B 55 " pdb=" H ALA B 55 " ideal model delta sigma weight residual 0.860 1.250 -0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" C GLU B 61 " pdb=" N VAL B 62 " ideal model delta sigma weight residual 1.331 1.135 0.195 1.01e-02 9.80e+03 3.74e+02 bond pdb=" NE ARG B 27 " pdb=" CZ ARG B 27 " ideal model delta sigma weight residual 1.326 1.533 -0.207 1.10e-02 8.26e+03 3.55e+02 bond pdb=" CD PRO B 109 " pdb=" HD2 PRO B 109 " ideal model delta sigma weight residual 0.970 1.340 -0.370 2.00e-02 2.50e+03 3.41e+02 bond pdb=" N VAL B 114 " pdb=" CA VAL B 114 " ideal model delta sigma weight residual 1.461 1.235 0.226 1.23e-02 6.61e+03 3.38e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 5974 4.41 - 8.83: 3507 8.83 - 13.24: 1143 13.24 - 17.66: 173 17.66 - 22.07: 13 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 83 " pdb=" CZ ARG B 83 " pdb=" NH1 ARG B 83 " ideal model delta sigma weight residual 121.50 138.05 -16.55 1.00e+00 1.00e+00 2.74e+02 angle pdb=" CA GLY A 41 " pdb=" C GLY A 41 " pdb=" O GLY A 41 " ideal model delta sigma weight residual 119.27 136.47 -17.20 1.07e+00 8.73e-01 2.59e+02 angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" N PRO A 135 " ideal model delta sigma weight residual 119.30 131.36 -12.06 8.10e-01 1.52e+00 2.22e+02 angle pdb=" O SER B 98 " pdb=" C SER B 98 " pdb=" N GLY B 99 " ideal model delta sigma weight residual 122.34 139.95 -17.61 1.20e+00 6.94e-01 2.15e+02 angle pdb=" CA CYS A 81 " pdb=" C CYS A 81 " pdb=" O CYS A 81 " ideal model delta sigma weight residual 120.90 135.51 -14.61 1.07e+00 8.73e-01 1.86e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 1830 16.36 - 32.72: 146 32.72 - 49.09: 45 49.09 - 65.45: 24 65.45 - 81.81: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -149.68 -30.32 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 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 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.222: 220 0.222 - 0.442: 150 0.442 - 0.662: 90 0.662 - 0.882: 22 0.882 - 1.102: 10 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 62 " pdb=" N VAL B 62 " pdb=" C VAL B 62 " pdb=" CB VAL B 62 " both_signs ideal model delta sigma weight residual False 2.44 1.34 1.10 2.00e-01 2.50e+01 3.03e+01 chirality pdb=" CA LEU A 53 " pdb=" N LEU A 53 " pdb=" C LEU A 53 " pdb=" CB LEU A 53 " both_signs ideal model delta sigma weight residual False 2.51 3.58 -1.07 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CA ILE B 105 " pdb=" N ILE B 105 " pdb=" C ILE B 105 " pdb=" CB ILE B 105 " both_signs ideal model delta sigma weight residual False 2.43 3.48 -1.05 2.00e-01 2.50e+01 2.75e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " 0.058 2.00e-02 2.50e+03 7.81e-02 1.83e+02 pdb=" CG TYR B 67 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " -0.139 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " 0.140 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " 0.126 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " -0.037 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " 0.004 2.00e-02 2.50e+03 6.38e-02 1.63e+02 pdb=" CG TRP B 139 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.008 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.023 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.097 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.091 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.072 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " 0.037 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " -0.053 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.114 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " 0.113 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.081 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.092 2.00e-02 2.50e+03 6.27e-02 1.57e+02 pdb=" CG TRP A 146 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.017 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.049 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.071 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.118 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.115 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.077 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.017 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.54: 19 1.54 - 2.31: 1802 2.31 - 3.07: 21679 3.07 - 3.84: 33189 3.84 - 4.60: 53564 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110253 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.778 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.899 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.042 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.106 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.176 2.620 ... (remaining 110248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 12 15.96 2 Mg 2 11.97 3 O 1357 7.97 2 N 488 6.98 3 C 1850 5.99 3 H 2984 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6693 n_use_u_iso = 3419 n_use_u_aniso = 3274 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 6693 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6693 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3419 aniso = 3274) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (1426 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_7723142_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= 0.2043 r_free= 0.2014 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.303095 | | target function (ml) not normalized (work): 806025.647003 | | target function (ml) not normalized (free): 16600.845064 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2147 0.1937 6.6803 6.3101| | 2: 2.94 - 2.33 1.00 7339 128 0.1639 0.1659 5.549 5.6205| | 3: 2.33 - 2.04 0.96 6939 150 0.1628 0.1637 5.1494 5.1674| | 4: 2.04 - 1.85 1.00 7170 155 0.1749 0.1675 4.964 5.0743| | 5: 1.85 - 1.72 0.99 7113 159 0.1936 0.1786 4.801 4.8384| | 6: 1.72 - 1.62 0.99 7102 142 0.1948 0.2147 4.6613 4.8235| | 7: 1.62 - 1.54 0.99 7104 148 0.2040 0.1793 4.5629 4.6001| | 8: 1.54 - 1.47 0.96 6798 152 0.2057 0.2172 4.4763 4.5112| | 9: 1.47 - 1.41 0.98 6938 155 0.2120 0.2201 4.3992 4.446| | 10: 1.41 - 1.36 0.99 7022 150 0.2145 0.2348 4.3174 4.4298| | 11: 1.36 - 1.32 0.99 6997 151 0.2165 0.2117 4.2535 4.2312| | 12: 1.32 - 1.28 0.98 6976 149 0.2087 0.1901 4.1736 4.1839| | 13: 1.28 - 1.25 0.98 6907 166 0.2034 0.2134 4.1232 4.1852| | 14: 1.25 - 1.22 0.98 7015 113 0.2099 0.2499 4.0907 4.2883| | 15: 1.22 - 1.19 0.98 6957 137 0.2114 0.2124 4.0506 4.1019| | 16: 1.19 - 1.17 0.93 6604 132 0.2127 0.2423 4.0146 4.1339| | 17: 1.17 - 1.14 0.98 6941 135 0.2200 0.1876 3.9694 3.9929| | 18: 1.14 - 1.12 0.98 6875 142 0.2250 0.2431 3.9328 3.9712| | 19: 1.12 - 1.10 0.97 6949 106 0.2272 0.2434 3.8726 3.9718| | 20: 1.10 - 1.08 0.97 6884 147 0.2293 0.2437 3.8102 3.9275| | 21: 1.08 - 1.07 0.97 6852 152 0.2431 0.2417 3.7869 3.7344| | 22: 1.07 - 1.05 0.97 6838 135 0.2558 0.2597 3.7529 3.7401| | 23: 1.05 - 1.03 0.97 6829 159 0.2733 0.2506 3.7295 3.7647| | 24: 1.03 - 1.02 0.96 6785 133 0.2887 0.2793 3.7021 3.7694| | 25: 1.02 - 1.01 0.93 6552 130 0.3058 0.3047 3.6692 3.7201| | 26: 1.01 - 0.99 0.96 6767 158 0.3207 0.3170 3.6342 3.5957| | 27: 0.99 - 0.98 0.94 6648 131 0.3420 0.2936 3.6435 3.5821| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.59 0.91 0.97 35927.24| | 2: 2.94 - 2.33 7339 128 0.85 21.65 1.09 1.01 15419.34| | 3: 2.33 - 2.04 6939 150 0.93 12.96 1.11 1.05 4347.03| | 4: 2.04 - 1.85 7170 155 0.92 13.84 1.11 1.06 2872.27| | 5: 1.85 - 1.72 7113 159 0.90 16.32 1.12 1.07 2219.50| | 6: 1.72 - 1.62 7102 142 0.89 17.58 1.11 1.06 1784.29| | 7: 1.62 - 1.54 7104 148 0.89 18.27 1.11 1.06 1404.35| | 8: 1.54 - 1.47 6798 152 0.88 18.79 1.10 1.06 1184.27| | 9: 1.47 - 1.41 6938 155 0.88 19.36 1.10 1.05 1001.44| | 10: 1.41 - 1.36 7022 150 0.87 20.49 1.10 1.05 887.33| | 11: 1.36 - 1.32 6997 151 0.87 20.08 1.08 1.03 727.96| | 12: 1.32 - 1.28 6976 149 0.88 19.71 1.08 1.04 647.13| | 13: 1.28 - 1.25 6907 166 0.88 19.68 1.07 1.03 595.71| | 14: 1.25 - 1.22 7015 113 0.86 21.73 1.07 1.04 621.81| | 15: 1.22 - 1.19 6957 137 0.85 22.15 1.07 1.03 590.45| | 16: 1.19 - 1.17 6604 132 0.86 21.97 1.07 1.02 547.95| | 17: 1.17 - 1.14 6941 135 0.86 21.84 1.08 1.02 470.71| | 18: 1.14 - 1.12 6875 142 0.85 22.11 1.08 1.01 436.19| | 19: 1.12 - 1.10 6949 106 0.85 22.46 1.07 1.02 395.64| | 20: 1.10 - 1.08 6884 147 0.85 22.71 1.06 0.99 352.78| | 21: 1.08 - 1.07 6852 152 0.85 22.84 1.06 0.99 314.51| | 22: 1.07 - 1.05 6838 135 0.83 24.39 1.05 0.98 303.93| | 23: 1.05 - 1.03 6829 159 0.81 26.66 1.06 0.99 314.95| | 24: 1.03 - 1.02 6785 133 0.79 28.88 1.05 0.98 317.48| | 25: 1.02 - 1.01 6552 130 0.78 29.91 1.04 0.95 300.62| | 26: 1.01 - 0.99 6767 158 0.77 30.81 1.03 0.92 274.35| | 27: 0.99 - 0.98 6648 131 0.77 30.68 1.02 0.92 253.79| |alpha: min = 0.92 max = 1.07 mean = 1.01| |beta: min = 253.79 max = 35927.24 mean = 2889.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.72| |phase err.(test): min = 0.00 max = 89.35 mean = 21.78| |-----------------------------------------------------------------------------| ----------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 0.258 2950 Z= 5.514 Angle : 5.130 17.607 4018 Z= 3.663 Chirality : 0.371 1.102 492 Planarity : 0.031 0.105 512 Dihedral : 12.707 81.812 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.65 % Allowed : 6.45 % Favored : 92.90 % Cbeta Deviations : 28.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.40), residues: 386 helix: -2.48 (0.31), residues: 144 sheet: -1.16 (0.58), residues: 74 loop : 0.13 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.018 ARG A 175 TYR 0.166 0.038 TYR B 67 PHE 0.139 0.038 PHE A 164 TRP 0.105 0.032 TRP B 139 HIS 0.069 0.025 HIS A 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2043 r_free= 0.2014 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.303095 | | target function (ml) not normalized (work): 806025.647003 | | target function (ml) not normalized (free): 16600.845064 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2042 0.2043 0.2014 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2042 0.2043 0.2014 n_refl.: 191155 remove outliers: r(all,work,free)=0.2042 0.2044 0.2014 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2043 0.2045 0.2015 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1813 0.1811 0.1958 n_refl.: 191145 remove outliers: r(all,work,free)=0.1811 0.1809 0.1958 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 0.4079 402.814 291.807 0.436 0.910 0.301 13.296-10.522 99.01 99 1 0.2510 528.187 519.831 0.789 0.910 0.253 10.503-8.327 99.45 178 3 0.2546 565.118 554.625 0.974 0.911 0.230 8.318-6.595 100.00 360 8 0.2485 414.736 403.613 0.967 0.910 0.159 6.588-5.215 100.00 711 7 0.2257 381.101 366.317 0.952 0.911 0.109 5.214-4.128 98.38 1367 28 0.1495 557.435 550.158 1.077 0.911 0.080 4.126-3.266 94.74 2603 46 0.1364 508.132 498.852 1.144 0.911 0.014 3.266-2.585 99.86 5447 97 0.1472 342.774 337.048 1.121 0.910 0.000 2.585-2.046 97.45 10613 204 0.1396 258.603 254.381 1.129 0.910 0.000 2.046-1.619 99.39 21536 464 0.1610 153.054 149.831 1.146 0.908 0.000 1.619-1.281 98.00 42464 925 0.1939 82.395 80.159 1.132 0.906 0.000 1.281-0.980 96.53 101826 2056 0.2331 44.203 41.637 1.113 0.902 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0102 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1809 r_free=0.1958 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 r_work=0.1809 r_free=0.1957 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.052310 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.984843 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 0.1272 0.1508 0.0236 0.039 1.2 11.6 0.0 0.3 0 11.526 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.08 2.36 1.118 13.117 570.985 0.018 13.00 15.76 2.76 1.269 13.393 570.985 0.017 Individual atomic B min max mean iso aniso Overall: 5.19 73.05 15.11 1.41 435 3274 Protein: 5.19 40.37 11.03 1.41 0 2902 Water: 6.35 73.05 29.77 N/A 435 370 Other: 16.14 30.30 23.22 N/A 0 2 Chain A: 5.32 60.33 13.09 N/A 0 1626 Chain B: 5.19 73.05 12.82 N/A 0 1648 Chain S: 11.94 62.40 31.31 N/A 435 0 Histogram: Values Number of atoms 5.19 - 11.98 2166 11.98 - 18.76 633 18.76 - 25.55 312 25.55 - 32.34 261 32.34 - 39.12 163 39.12 - 45.91 104 45.91 - 52.69 46 52.69 - 59.48 16 59.48 - 66.26 7 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1576 r_work=0.1299 r_free=0.1571 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1571 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 = 0.1284 r_free = 0.1559 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1284 r_free= 0.1559 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015577 | | target function (ls_wunit_k1) not normalized (work): 2917.509663 | | target function (ls_wunit_k1) not normalized (free): 117.063888 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1284 0.1559 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1635 n_refl.: 191139 remove outliers: r(all,work,free)=0.1470 0.1467 0.1635 n_refl.: 191139 overall B=0.16 to atoms: r(all,work,free)=0.1493 0.1491 0.1645 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1547 n_refl.: 191139 remove outliers: r(all,work,free)=0.1281 0.1276 0.1546 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3604 402.814 378.217 0.471 0.997 0.281 13.296-10.522 99.01 99 1 0.2085 528.187 524.540 0.717 0.999 0.244 10.503-8.327 99.45 178 3 0.1759 565.118 564.835 0.859 0.999 0.230 8.318-6.595 100.00 360 8 0.1703 414.736 413.189 0.877 0.999 0.150 6.588-5.215 100.00 711 7 0.1542 381.101 373.451 0.854 0.999 0.140 5.214-4.128 98.38 1367 28 0.0899 557.435 554.350 0.942 0.999 0.070 4.126-3.266 94.74 2603 46 0.0826 508.132 504.302 1.006 1.000 0.014 3.266-2.585 99.86 5447 97 0.0918 342.774 340.374 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.358 1.002 1.000 0.000 2.046-1.619 99.39 21536 464 0.1092 153.054 151.373 1.019 0.999 0.000 1.619-1.281 98.00 42464 925 0.1283 82.395 81.407 1.012 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.175 0.990 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0366 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1546 | n_water=805 | time (s): 2.740 (total time: 2.740) Filter (dist) r_work=0.1281 r_free=0.1555 | n_water=793 | time (s): 98.600 (total time: 101.340) Filter (q & B) r_work=0.1282 r_free=0.1555 | n_water=789 | time (s): 5.520 (total time: 106.860) Compute maps r_work=0.1282 r_free=0.1555 | n_water=789 | time (s): 2.570 (total time: 109.430) Filter (map) r_work=0.1306 r_free=0.1535 | n_water=654 | time (s): 4.290 (total time: 113.720) Find peaks r_work=0.1306 r_free=0.1535 | n_water=654 | time (s): 0.790 (total time: 114.510) Add new water r_work=0.1329 r_free=0.1564 | n_water=961 | time (s): 3.810 (total time: 118.320) Refine new water occ: r_work=0.1287 r_free=0.1526 adp: r_work=0.1275 r_free=0.1522 occ: r_work=0.1277 r_free=0.1521 adp: r_work=0.1270 r_free=0.1519 occ: r_work=0.1272 r_free=0.1516 adp: r_work=0.1269 r_free=0.1518 ADP+occupancy (water only), MIN, final r_work=0.1269 r_free=0.1518 r_work=0.1269 r_free=0.1518 | n_water=961 | time (s): 95.310 (total time: 213.630) Filter (q & B) r_work=0.1273 r_free=0.1517 | n_water=890 | time (s): 4.660 (total time: 218.290) Filter (dist only) r_work=0.1273 r_free=0.1516 | n_water=889 | time (s): 108.990 (total time: 327.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.607307 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 594.111592 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 0.1258 0.1530 0.0272 0.040 1.1 18.4 0.0 0.3 0 11.304 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.58 15.30 2.72 2.052 15.291 594.112 0.014 12.31 15.16 2.85 2.417 15.364 594.112 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 70.43 16.53 1.22 521 3272 Protein: 5.38 41.09 11.01 1.22 0 2902 Water: 6.62 70.43 34.50 N/A 521 368 Other: 16.21 33.92 25.06 N/A 0 2 Chain A: 5.50 55.87 13.06 N/A 0 1624 Chain B: 5.38 68.21 12.89 N/A 0 1648 Chain S: 10.02 70.43 38.83 N/A 521 0 Histogram: Values Number of atoms 5.38 - 11.89 2111 11.89 - 18.39 687 18.39 - 24.89 250 24.89 - 31.40 213 31.40 - 37.90 167 37.90 - 44.41 159 44.41 - 50.91 101 50.91 - 57.42 62 57.42 - 63.92 32 63.92 - 70.43 11 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1516 r_work=0.1232 r_free=0.1517 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1517 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1519 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1519 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013394 | | target function (ls_wunit_k1) not normalized (work): 2508.628735 | | target function (ls_wunit_k1) not normalized (free): 103.942537 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1519 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1437 0.1611 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1437 0.1611 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1437 0.1434 0.1609 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1232 0.1526 n_refl.: 191138 remove outliers: r(all,work,free)=0.1238 0.1232 0.1526 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3218 402.814 378.648 0.498 0.962 0.277 13.296-10.522 99.01 99 1 0.1836 528.187 521.154 0.762 0.963 0.228 10.503-8.327 99.45 178 3 0.1413 565.118 566.771 0.922 0.963 0.179 8.318-6.595 100.00 360 8 0.1518 414.736 415.130 0.936 0.963 0.155 6.588-5.215 100.00 711 7 0.1350 381.101 376.355 0.912 0.963 0.150 5.214-4.128 98.38 1367 28 0.0815 557.435 556.414 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0759 508.132 505.515 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0864 342.774 341.270 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0904 258.603 256.743 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1048 153.054 151.631 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.358 1.076 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.221 1.062 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0613 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1526 | n_water=889 | time (s): 3.570 (total time: 3.570) Filter (dist) r_work=0.1235 r_free=0.1527 | n_water=881 | time (s): 110.690 (total time: 114.260) Filter (q & B) r_work=0.1235 r_free=0.1527 | n_water=878 | time (s): 5.050 (total time: 119.310) Compute maps r_work=0.1235 r_free=0.1527 | n_water=878 | time (s): 1.750 (total time: 121.060) Filter (map) r_work=0.1274 r_free=0.1528 | n_water=682 | time (s): 4.670 (total time: 125.730) Find peaks r_work=0.1274 r_free=0.1528 | n_water=682 | time (s): 0.700 (total time: 126.430) Add new water r_work=0.1297 r_free=0.1573 | n_water=1009 | time (s): 4.010 (total time: 130.440) Refine new water occ: r_work=0.1252 r_free=0.1527 adp: r_work=0.1253 r_free=0.1528 occ: r_work=0.1248 r_free=0.1521 adp: r_work=0.1249 r_free=0.1523 occ: r_work=0.1245 r_free=0.1517 adp: r_work=0.1245 r_free=0.1519 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1519 r_work=0.1245 r_free=0.1519 | n_water=1009 | time (s): 342.390 (total time: 472.830) Filter (q & B) r_work=0.1250 r_free=0.1531 | n_water=862 | time (s): 4.200 (total time: 477.030) Filter (dist only) r_work=0.1251 r_free=0.1531 | n_water=861 | time (s): 109.780 (total time: 586.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.635092 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.020998 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 0.1241 0.1446 0.0205 0.034 1.1 8.3 0.0 0.0 0 0.818 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.46 2.05 1.945 14.605 16.021 3.939 12.37 14.09 1.72 2.231 14.514 16.021 3.899 Individual atomic B min max mean iso aniso Overall: 5.57 67.85 15.27 1.06 494 3271 Protein: 5.57 37.29 10.78 1.06 0 2902 Water: 6.72 67.85 30.38 N/A 494 367 Other: 14.08 30.16 22.12 N/A 0 2 Chain A: 5.58 55.09 12.83 N/A 0 1624 Chain B: 5.57 67.85 12.62 N/A 0 1647 Chain S: 12.83 60.91 32.13 N/A 494 0 Histogram: Values Number of atoms 5.57 - 11.80 2132 11.80 - 18.03 687 18.03 - 24.25 287 24.25 - 30.48 227 30.48 - 36.71 188 36.71 - 42.94 136 42.94 - 49.17 69 49.17 - 55.40 30 55.40 - 61.63 8 61.63 - 67.85 1 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1410 r_work=0.1238 r_free=0.1411 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1411 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1399 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1399 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892923 | | target function (ml) not normalized (work): 729132.756107 | | target function (ml) not normalized (free): 15226.177597 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1399 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1452 0.1452 0.1481 n_refl.: 191138 remove outliers: r(all,work,free)=0.1452 0.1452 0.1481 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1445 0.1444 0.1476 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1389 n_refl.: 191138 remove outliers: r(all,work,free)=0.1229 0.1226 0.1389 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3870 393.525 358.465 0.417 0.946 0.241 13.296-10.522 98.02 98 1 0.2357 528.900 508.246 0.708 0.947 0.215 10.503-8.327 98.35 176 3 0.2049 555.265 557.552 0.886 0.947 0.174 8.318-6.595 100.00 360 8 0.2088 414.736 409.203 0.898 0.946 0.135 6.588-5.215 100.00 711 7 0.1848 381.101 369.606 0.887 0.947 0.130 5.214-4.128 98.38 1367 28 0.1172 557.435 552.184 0.973 0.947 0.090 4.126-3.266 94.74 2603 46 0.1095 508.132 501.185 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1084 342.774 339.087 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0967 258.603 255.720 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0979 153.054 151.393 1.058 0.944 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.490 1.055 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.320 1.043 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1149 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1389 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1389 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1389 | n_water=861 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1226 r_free=0.1389 | n_water=861 | time (s): 100.320 (total time: 102.740) Filter (q & B) r_work=0.1227 r_free=0.1386 | n_water=852 | time (s): 5.230 (total time: 107.970) Compute maps r_work=0.1227 r_free=0.1386 | n_water=852 | time (s): 1.880 (total time: 109.850) Filter (map) r_work=0.1253 r_free=0.1397 | n_water=699 | time (s): 5.210 (total time: 115.060) Find peaks r_work=0.1253 r_free=0.1397 | n_water=699 | time (s): 0.660 (total time: 115.720) Add new water r_work=0.1269 r_free=0.1408 | n_water=951 | time (s): 4.680 (total time: 120.400) Refine new water occ: r_work=0.1216 r_free=0.1373 adp: r_work=0.1209 r_free=0.1369 occ: r_work=0.1207 r_free=0.1370 adp: r_work=0.1207 r_free=0.1369 occ: r_work=0.1205 r_free=0.1370 adp: r_work=0.1204 r_free=0.1369 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1369 r_work=0.1204 r_free=0.1369 | n_water=951 | time (s): 346.930 (total time: 467.330) Filter (q & B) r_work=0.1210 r_free=0.1369 | n_water=857 | time (s): 6.000 (total time: 473.330) Filter (dist only) r_work=0.1210 r_free=0.1367 | n_water=856 | time (s): 108.280 (total time: 581.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.596980 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.784677 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1368 0.0161 0.035 1.1 6.8 0.0 0.3 0 0.798 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.68 1.61 1.841 14.230 15.785 3.874 12.00 13.61 1.62 1.952 14.186 15.785 3.865 Individual atomic B min max mean iso aniso Overall: 5.53 67.42 14.97 1.01 491 3269 Protein: 5.53 34.03 10.69 1.01 0 2902 Water: 5.91 67.42 29.47 N/A 491 365 Other: 14.02 28.80 21.41 N/A 0 2 Chain A: 5.55 54.05 12.68 N/A 0 1623 Chain B: 5.53 67.42 12.49 N/A 0 1646 Chain S: 5.91 60.98 30.88 N/A 491 0 Histogram: Values Number of atoms 5.53 - 11.72 2122 11.72 - 17.91 717 17.91 - 24.10 293 24.10 - 30.29 233 30.29 - 36.47 175 36.47 - 42.66 123 42.66 - 48.85 65 48.85 - 55.04 24 55.04 - 61.23 7 61.23 - 67.42 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1362 r_work=0.1200 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1362 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1359 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.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863570 | | target function (ml) not normalized (work): 723615.701954 | | target function (ml) not normalized (free): 15134.259701 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1427 0.1426 0.1472 n_refl.: 191133 remove outliers: r(all,work,free)=0.1427 0.1426 0.1472 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1419 0.1418 0.1467 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1359 n_refl.: 191133 remove outliers: r(all,work,free)=0.1199 0.1196 0.1359 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 91.09 89 3 0.3774 348.471 310.758 0.398 0.945 0.231 13.296-10.522 97.03 97 1 0.2424 481.106 458.143 0.712 0.947 0.210 10.503-8.327 98.35 176 3 0.2071 502.702 494.470 0.866 0.947 0.174 8.318-6.595 100.00 360 8 0.2148 375.476 370.221 0.895 0.946 0.114 6.588-5.215 100.00 711 7 0.1918 345.025 334.360 0.881 0.947 0.074 5.214-4.128 98.38 1367 28 0.1181 504.666 499.793 0.975 0.947 0.060 4.126-3.266 94.74 2603 46 0.1113 460.031 453.689 1.035 0.947 0.000 3.266-2.585 99.86 5447 97 0.1094 310.326 307.148 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0937 234.123 231.668 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0915 138.566 137.258 1.058 0.946 0.000 1.619-1.281 98.00 42464 925 0.0988 74.596 73.880 1.054 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.017 38.355 1.041 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1261 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1359 | n_water=856 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1196 r_free=0.1360 | n_water=855 | time (s): 114.000 (total time: 116.430) Filter (q & B) r_work=0.1197 r_free=0.1360 | n_water=847 | time (s): 4.290 (total time: 120.720) Compute maps r_work=0.1197 r_free=0.1360 | n_water=847 | time (s): 1.630 (total time: 122.350) Filter (map) r_work=0.1222 r_free=0.1372 | n_water=720 | time (s): 5.260 (total time: 127.610) Find peaks r_work=0.1222 r_free=0.1372 | n_water=720 | time (s): 0.660 (total time: 128.270) Add new water r_work=0.1232 r_free=0.1384 | n_water=952 | time (s): 3.870 (total time: 132.140) Refine new water occ: r_work=0.1195 r_free=0.1350 adp: r_work=0.1195 r_free=0.1350 occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1191 r_free=0.1345 adp: r_work=0.1191 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1345 r_work=0.1191 r_free=0.1345 | n_water=952 | time (s): 228.460 (total time: 360.600) Filter (q & B) r_work=0.1194 r_free=0.1353 | n_water=874 | time (s): 4.740 (total time: 365.340) Filter (dist only) r_work=0.1195 r_free=0.1351 | n_water=872 | time (s): 113.040 (total time: 478.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.532366 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.098047 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 0.1355 0.0157 0.035 1.1 7.7 0.0 0.3 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.55 1.57 1.801 14.122 15.098 3.764 12.04 13.60 1.56 2.014 14.050 15.098 3.761 Individual atomic B min max mean iso aniso Overall: 5.57 66.25 14.82 0.93 507 3269 Protein: 5.57 30.35 10.53 0.93 0 2902 Water: 6.04 66.25 29.08 N/A 507 365 Other: 13.83 24.90 19.37 N/A 0 2 Chain A: 5.63 52.57 12.48 N/A 0 1623 Chain B: 5.57 66.25 12.31 N/A 0 1646 Chain S: 6.04 61.21 30.49 N/A 507 0 Histogram: Values Number of atoms 5.57 - 11.64 2114 11.64 - 17.71 759 17.71 - 23.78 297 23.78 - 29.84 198 29.84 - 35.91 177 35.91 - 41.98 128 41.98 - 48.05 70 48.05 - 54.11 25 54.11 - 60.18 6 60.18 - 66.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1360 r_work=0.1204 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1361 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1359 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760124 | | target function (ml) not normalized (work): 704229.934395 | | target function (ml) not normalized (free): 14739.836895 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1360 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1483 n_refl.: 191130 remove outliers: r(all,work,free)=0.1411 0.1410 0.1483 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1403 0.1402 0.1477 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1356 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1356 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3780 343.705 308.039 0.376 0.951 0.215 13.296-10.522 97.03 97 1 0.2399 481.106 462.752 0.693 0.953 0.169 10.503-8.327 98.35 176 3 0.2171 502.702 493.836 0.856 0.953 0.147 8.315-6.595 100.00 359 8 0.2128 374.530 370.727 0.886 0.953 0.106 6.588-5.215 100.00 711 7 0.1938 345.025 334.840 0.877 0.953 0.083 5.214-4.128 98.38 1367 28 0.1226 504.666 499.000 0.969 0.953 0.060 4.126-3.266 94.74 2603 46 0.1139 460.031 453.309 1.030 0.953 0.000 3.266-2.585 99.86 5447 97 0.1109 310.326 307.029 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0950 234.123 231.594 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0913 138.566 137.251 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0977 74.596 73.880 1.052 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.017 38.348 1.041 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1366 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1356 | n_water=872 | time (s): 3.070 (total time: 3.070) Filter (dist) r_work=0.1200 r_free=0.1356 | n_water=871 | time (s): 116.430 (total time: 119.500) Filter (q & B) r_work=0.1200 r_free=0.1355 | n_water=863 | time (s): 4.000 (total time: 123.500) Compute maps r_work=0.1200 r_free=0.1355 | n_water=863 | time (s): 2.260 (total time: 125.760) Filter (map) r_work=0.1224 r_free=0.1366 | n_water=737 | time (s): 4.630 (total time: 130.390) Find peaks r_work=0.1224 r_free=0.1366 | n_water=737 | time (s): 0.530 (total time: 130.920) Add new water r_work=0.1234 r_free=0.1377 | n_water=956 | time (s): 5.040 (total time: 135.960) Refine new water occ: r_work=0.1197 r_free=0.1342 adp: r_work=0.1197 r_free=0.1341 occ: r_work=0.1194 r_free=0.1343 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1193 r_free=0.1345 adp: r_work=0.1192 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1343 r_work=0.1192 r_free=0.1343 | n_water=956 | time (s): 253.070 (total time: 389.030) Filter (q & B) r_work=0.1195 r_free=0.1348 | n_water=894 | time (s): 4.640 (total time: 393.670) Filter (dist only) r_work=0.1196 r_free=0.1347 | n_water=893 | time (s): 111.080 (total time: 504.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.529663 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.020907 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 0.1199 0.1357 0.0158 0.037 1.1 8.4 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.57 1.58 1.737 13.979 15.021 3.760 11.99 13.57 1.58 1.794 13.950 15.021 3.757 Individual atomic B min max mean iso aniso Overall: 5.58 65.11 14.82 0.90 528 3269 Protein: 5.58 29.17 10.48 0.90 0 2902 Water: 5.98 65.11 28.95 N/A 528 365 Other: 13.91 22.50 18.20 N/A 0 2 Chain A: 5.65 52.25 12.37 N/A 0 1623 Chain B: 5.58 65.11 12.22 N/A 0 1646 Chain S: 5.98 61.35 30.49 N/A 528 0 Histogram: Values Number of atoms 5.58 - 11.53 2092 11.53 - 17.48 787 17.48 - 23.44 293 23.44 - 29.39 201 29.39 - 35.34 179 35.34 - 41.30 129 41.30 - 47.25 78 47.25 - 53.20 27 53.20 - 59.16 6 59.16 - 65.11 5 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1357 r_work=0.1199 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1361 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756350 | | target function (ml) not normalized (work): 703515.604705 | | target function (ml) not normalized (free): 14734.083545 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1405 0.1404 0.1479 n_refl.: 191128 remove outliers: r(all,work,free)=0.1405 0.1404 0.1479 n_refl.: 191128 overall B=-0.24 to atoms: r(all,work,free)=0.1366 0.1365 0.1456 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1356 n_refl.: 191128 remove outliers: r(all,work,free)=0.1200 0.1197 0.1356 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3925 343.705 305.487 0.342 0.952 0.149 13.296-10.522 97.03 97 1 0.2432 481.106 463.012 0.700 0.953 0.144 10.503-8.327 98.35 176 3 0.2187 502.702 494.926 0.879 0.954 0.140 8.315-6.595 100.00 359 8 0.2125 374.530 370.399 0.907 0.953 0.111 6.588-5.215 100.00 711 7 0.1948 345.025 334.713 0.902 0.953 0.094 5.214-4.128 98.38 1367 28 0.1222 504.666 499.447 0.992 0.954 0.034 4.126-3.266 94.74 2603 46 0.1141 460.031 453.460 1.056 0.954 0.000 3.266-2.585 99.86 5447 97 0.1114 310.326 307.072 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0951 234.123 231.607 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0908 138.566 137.281 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0967 74.596 73.902 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.017 38.349 1.025 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0521 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1356 | n_water=893 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1197 r_free=0.1355 | n_water=892 | time (s): 123.690 (total time: 126.210) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=881 | time (s): 5.320 (total time: 131.530) Compute maps r_work=0.1198 r_free=0.1356 | n_water=881 | time (s): 2.280 (total time: 133.810) Filter (map) r_work=0.1222 r_free=0.1360 | n_water=753 | time (s): 5.450 (total time: 139.260) Find peaks r_work=0.1222 r_free=0.1360 | n_water=753 | time (s): 0.890 (total time: 140.150) Add new water r_work=0.1230 r_free=0.1370 | n_water=956 | time (s): 4.320 (total time: 144.470) Refine new water occ: r_work=0.1198 r_free=0.1348 adp: r_work=0.1198 r_free=0.1348 occ: r_work=0.1198 r_free=0.1348 adp: r_work=0.1198 r_free=0.1348 occ: r_work=0.1198 r_free=0.1348 adp: r_work=0.1198 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1348 r_work=0.1198 r_free=0.1348 | n_water=956 | time (s): 212.150 (total time: 356.620) Filter (q & B) r_work=0.1203 r_free=0.1352 | n_water=848 | time (s): 4.700 (total time: 361.320) Filter (dist only) r_work=0.1203 r_free=0.1351 | n_water=847 | time (s): 103.860 (total time: 465.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.513163 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.683996 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1355 0.0149 0.037 1.1 5.1 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.55 1.49 1.715 13.510 14.684 3.759 12.09 13.59 1.50 1.750 13.495 14.684 3.758 Individual atomic B min max mean iso aniso Overall: 5.39 63.82 14.25 0.88 482 3269 Protein: 5.39 28.40 10.23 0.88 0 2902 Water: 5.81 63.82 27.99 N/A 482 365 Other: 13.71 21.99 17.85 N/A 0 2 Chain A: 5.45 51.76 12.09 N/A 0 1623 Chain B: 5.39 63.82 11.94 N/A 0 1646 Chain S: 5.81 61.17 29.38 N/A 482 0 Histogram: Values Number of atoms 5.39 - 11.24 2069 11.24 - 17.08 806 17.08 - 22.92 318 22.92 - 28.76 165 28.76 - 34.61 163 34.61 - 40.45 116 40.45 - 46.29 76 46.29 - 52.14 24 52.14 - 57.98 9 57.98 - 63.82 5 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1359 r_work=0.1210 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1210 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1208 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1208 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757511 | | target function (ml) not normalized (work): 703733.023556 | | target function (ml) not normalized (free): 14731.143030 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1208 0.1360 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1469 n_refl.: 191128 remove outliers: r(all,work,free)=0.1391 0.1390 0.1469 n_refl.: 191128 overall B=0.06 to atoms: r(all,work,free)=0.1400 0.1399 0.1474 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1354 n_refl.: 191128 remove outliers: r(all,work,free)=0.1201 0.1198 0.1354 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3761 343.705 304.879 0.358 0.995 0.197 13.296-10.522 97.03 97 1 0.2452 481.106 462.642 0.677 0.997 0.152 10.503-8.327 98.35 176 3 0.2266 502.702 493.626 0.841 0.998 0.133 8.315-6.595 100.00 359 8 0.2239 374.530 368.687 0.872 0.997 0.110 6.588-5.215 100.00 711 7 0.1975 345.025 334.061 0.869 0.998 0.110 5.214-4.128 98.38 1367 28 0.1275 504.666 498.196 0.958 0.999 0.070 4.126-3.266 94.74 2603 46 0.1181 460.031 452.601 1.020 1.000 0.000 3.266-2.585 99.86 5447 97 0.1129 310.326 306.750 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0963 234.123 231.460 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0911 138.566 137.191 1.026 1.005 0.000 1.619-1.281 98.00 42464 925 0.0949 74.596 73.940 1.015 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.017 38.324 0.982 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0576 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1354 | n_water=847 | time (s): 2.700 (total time: 2.700) Filter (dist) r_work=0.1198 r_free=0.1354 | n_water=847 | time (s): 100.750 (total time: 103.450) Filter (q & B) r_work=0.1199 r_free=0.1352 | n_water=837 | time (s): 5.580 (total time: 109.030) Compute maps r_work=0.1199 r_free=0.1352 | n_water=837 | time (s): 1.690 (total time: 110.720) Filter (map) r_work=0.1219 r_free=0.1356 | n_water=734 | time (s): 5.150 (total time: 115.870) Find peaks r_work=0.1219 r_free=0.1356 | n_water=734 | time (s): 0.740 (total time: 116.610) Add new water r_work=0.1229 r_free=0.1370 | n_water=949 | time (s): 4.170 (total time: 120.780) Refine new water occ: r_work=0.1192 r_free=0.1338 adp: r_work=0.1192 r_free=0.1338 occ: r_work=0.1190 r_free=0.1339 adp: r_work=0.1190 r_free=0.1339 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1340 r_work=0.1188 r_free=0.1340 | n_water=949 | time (s): 207.040 (total time: 327.820) Filter (q & B) r_work=0.1191 r_free=0.1346 | n_water=881 | time (s): 5.130 (total time: 332.950) Filter (dist only) r_work=0.1192 r_free=0.1346 | n_water=879 | time (s): 113.880 (total time: 446.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.618899 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.747211 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 0.0158 0.037 1.1 6.5 0.0 0.3 0 0.809 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.51 1.58 1.673 13.639 14.747 3.754 11.93 13.53 1.60 1.681 13.628 14.747 3.752 Individual atomic B min max mean iso aniso Overall: 5.50 62.88 14.48 0.88 514 3269 Protein: 5.50 28.21 10.31 0.88 0 2902 Water: 5.89 62.88 28.26 N/A 514 365 Other: 13.77 22.08 17.93 N/A 0 2 Chain A: 5.56 51.46 12.12 N/A 0 1623 Chain B: 5.50 62.88 11.98 N/A 0 1646 Chain S: 5.89 61.34 29.95 N/A 514 0 Histogram: Values Number of atoms 5.50 - 11.24 2051 11.24 - 16.98 821 16.98 - 22.71 286 22.71 - 28.45 202 28.45 - 34.19 177 34.19 - 39.93 116 39.93 - 45.67 85 45.67 - 51.41 27 51.41 - 57.14 13 57.14 - 62.88 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1354 r_work=0.1194 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1354 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1355 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751585 | | target function (ml) not normalized (work): 702623.130817 | | target function (ml) not normalized (free): 14719.566553 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1355 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1393 0.1392 0.1473 n_refl.: 191128 remove outliers: r(all,work,free)=0.1393 0.1392 0.1473 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1395 0.1394 0.1474 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1356 n_refl.: 191128 remove outliers: r(all,work,free)=0.1193 0.1190 0.1356 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3573 343.198 294.688 0.357 0.995 0.203 13.296-10.522 97.03 97 1 0.2431 481.106 463.096 0.673 0.997 0.144 10.503-8.327 98.35 176 3 0.2305 502.702 492.452 0.841 0.997 0.117 8.315-6.595 100.00 359 8 0.2173 374.530 369.691 0.870 0.997 0.093 6.588-5.215 100.00 711 7 0.1969 345.025 334.532 0.867 0.998 0.077 5.214-4.128 98.38 1367 28 0.1251 504.666 498.516 0.958 0.999 0.070 4.126-3.266 94.74 2603 46 0.1169 460.031 452.786 1.019 1.000 0.000 3.266-2.585 99.86 5447 97 0.1118 310.326 306.864 1.003 1.001 0.000 2.585-2.046 97.45 10613 204 0.0960 234.123 231.527 1.010 1.003 0.000 2.046-1.619 99.39 21536 464 0.0904 138.566 137.245 1.027 1.006 0.000 1.619-1.281 98.00 42464 925 0.0940 74.596 73.963 1.018 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.017 38.317 0.987 1.019 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1356 | n_water=879 | time (s): 3.100 (total time: 3.100) Filter (dist) r_work=0.1190 r_free=0.1356 | n_water=879 | time (s): 107.350 (total time: 110.450) Filter (q & B) r_work=0.1191 r_free=0.1355 | n_water=873 | time (s): 5.410 (total time: 115.860) Compute maps r_work=0.1191 r_free=0.1355 | n_water=873 | time (s): 2.340 (total time: 118.200) Filter (map) r_work=0.1214 r_free=0.1354 | n_water=755 | time (s): 4.120 (total time: 122.320) Find peaks r_work=0.1214 r_free=0.1354 | n_water=755 | time (s): 0.690 (total time: 123.010) Add new water r_work=0.1221 r_free=0.1365 | n_water=955 | time (s): 4.070 (total time: 127.080) Refine new water occ: r_work=0.1187 r_free=0.1338 adp: r_work=0.1188 r_free=0.1337 occ: r_work=0.1186 r_free=0.1339 adp: r_work=0.1186 r_free=0.1338 occ: r_work=0.1184 r_free=0.1341 adp: r_work=0.1184 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1340 r_work=0.1184 r_free=0.1340 | n_water=955 | time (s): 221.940 (total time: 349.020) Filter (q & B) r_work=0.1188 r_free=0.1348 | n_water=888 | time (s): 5.510 (total time: 354.530) Filter (dist only) r_work=0.1188 r_free=0.1347 | n_water=887 | time (s): 118.540 (total time: 473.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524531 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.868680 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 5.8 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.55 1.63 1.679 13.664 13.869 3.753 11.93 13.58 1.65 1.675 13.665 13.869 3.753 Individual atomic B min max mean iso aniso Overall: 5.54 62.73 14.52 0.86 522 3269 Protein: 5.54 28.16 10.34 0.86 0 2902 Water: 5.99 62.73 28.19 N/A 522 365 Other: 13.80 22.09 17.94 N/A 0 2 Chain A: 5.60 51.41 12.13 N/A 0 1623 Chain B: 5.54 62.73 12.00 N/A 0 1646 Chain S: 5.99 61.37 29.89 N/A 522 0 Histogram: Values Number of atoms 5.54 - 11.26 2049 11.26 - 16.98 828 16.98 - 22.70 280 22.70 - 28.42 209 28.42 - 34.14 181 34.14 - 39.86 117 39.86 - 45.58 83 45.58 - 51.30 25 51.30 - 57.02 14 57.02 - 62.73 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1358 r_work=0.1194 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1358 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1361 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752710 | | target function (ml) not normalized (work): 702830.112443 | | target function (ml) not normalized (free): 14722.322407 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1361 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1491 n_refl.: 191127 remove outliers: r(all,work,free)=0.1397 0.1395 0.1491 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1396 0.1394 0.1491 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1191 0.1359 n_refl.: 191127 remove outliers: r(all,work,free)=0.1195 0.1191 0.1359 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3488 343.198 315.018 0.383 0.994 0.207 13.296-10.522 97.03 97 1 0.2428 481.106 463.701 0.673 0.996 0.146 10.503-8.327 98.35 176 3 0.2286 502.702 492.803 0.841 0.996 0.120 8.315-6.595 100.00 359 8 0.2183 374.530 369.594 0.870 0.996 0.096 6.588-5.215 100.00 711 7 0.1967 345.025 334.562 0.869 0.997 0.080 5.214-4.128 98.38 1367 28 0.1247 504.666 498.645 0.956 0.998 0.034 4.126-3.266 94.74 2603 46 0.1174 460.031 452.644 1.020 0.999 0.000 3.266-2.585 99.86 5447 97 0.1124 310.326 306.771 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0963 234.123 231.473 1.012 1.003 0.000 2.046-1.619 99.39 21536 464 0.0907 138.566 137.207 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0940 74.596 73.948 1.020 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.017 38.305 0.990 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0139 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1359 After: r_work=0.1192 r_free=0.1360 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1360 | n_water=887 | time (s): 2.760 (total time: 2.760) Filter (dist) r_work=0.1192 r_free=0.1360 | n_water=887 | time (s): 111.090 (total time: 113.850) Filter (q & B) r_work=0.1193 r_free=0.1359 | n_water=878 | time (s): 4.430 (total time: 118.280) Compute maps r_work=0.1193 r_free=0.1359 | n_water=878 | time (s): 1.880 (total time: 120.160) Filter (map) r_work=0.1215 r_free=0.1357 | n_water=768 | time (s): 5.630 (total time: 125.790) Find peaks r_work=0.1215 r_free=0.1357 | n_water=768 | time (s): 0.650 (total time: 126.440) Add new water r_work=0.1222 r_free=0.1371 | n_water=983 | time (s): 4.900 (total time: 131.340) Refine new water occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1187 r_free=0.1342 adp: r_work=0.1187 r_free=0.1342 occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1186 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1342 r_work=0.1186 r_free=0.1342 | n_water=983 | time (s): 264.510 (total time: 395.850) Filter (q & B) r_work=0.1190 r_free=0.1352 | n_water=895 | time (s): 4.670 (total time: 400.520) Filter (dist only) r_work=0.1190 r_free=0.1352 | n_water=893 | time (s): 116.510 (total time: 517.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.574130 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.568688 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 0.1353 0.0162 0.038 1.2 10.4 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.53 1.62 1.676 13.691 13.569 3.753 11.93 13.56 1.63 1.673 13.691 13.569 3.753 Individual atomic B min max mean iso aniso Overall: 5.55 62.32 14.55 0.85 528 3269 Protein: 5.55 27.98 10.35 0.85 0 2902 Water: 6.01 62.32 28.20 N/A 528 365 Other: 13.82 22.10 17.96 N/A 0 2 Chain A: 5.65 51.27 12.12 N/A 0 1623 Chain B: 5.55 62.32 11.99 N/A 0 1646 Chain S: 6.01 61.39 30.02 N/A 528 0 Histogram: Values Number of atoms 5.55 - 11.23 2035 11.23 - 16.91 844 16.91 - 22.58 275 22.58 - 28.26 211 28.26 - 33.94 180 33.94 - 39.62 117 39.62 - 45.29 87 45.29 - 50.97 27 50.97 - 56.65 16 56.65 - 62.32 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1356 r_work=0.1193 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1356 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1356 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752701 | | target function (ml) not normalized (work): 702828.365028 | | target function (ml) not normalized (free): 14715.398430 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1362 0.1505 5.6899 5.7567| | 2: 2.94 - 2.33 1.00 7339 128 0.1064 0.1330 5.0692 5.1672| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1154 4.6559 4.7356| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1070 4.3903 4.5729| | 5: 1.85 - 1.72 0.99 7113 159 0.0934 0.0975 4.1514 4.2406| | 6: 1.72 - 1.62 0.99 7102 142 0.0895 0.1087 3.945 4.0705| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0966 3.797 3.9245| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1322 3.6975 3.9039| | 9: 1.47 - 1.41 0.98 6938 155 0.0924 0.1119 3.6191 3.7433| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1181 3.5539 3.6678| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1114 3.4816 3.5814| | 12: 1.32 - 1.28 0.98 6975 149 0.1032 0.1128 3.4567 3.5817| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1235 3.4355 3.5593| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1583 3.4311 3.6785| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1238 3.4464 3.4893| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1541 3.4634 3.6529| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1235 3.432 3.4425| | 18: 1.14 - 1.12 0.98 6875 142 0.1381 0.1700 3.437 3.5291| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1745 3.419 3.5941| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1574 3.4092 3.4314| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2129 3.4185 3.5053| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1950 3.4132 3.4157| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2020 3.4328 3.485| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2253 3.435 3.5087| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2516 3.4487 3.5253| | 26: 1.01 - 0.99 0.96 6767 158 0.2754 0.2851 3.4151 3.4208| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2808 3.4684 3.3947| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7395 127 0.93 11.41 1.00 0.96 10904.12| | 2: 2.94 - 2.33 7339 128 0.93 12.59 0.99 0.95 5000.29| | 3: 2.33 - 2.04 6939 150 0.96 7.51 1.01 0.95 1667.89| | 4: 2.04 - 1.85 7170 155 0.96 7.60 1.00 0.96 999.38| | 5: 1.85 - 1.72 7113 159 0.96 8.01 1.00 0.96 629.97| | 6: 1.72 - 1.62 7102 142 0.96 7.99 1.00 0.96 440.44| | 7: 1.62 - 1.54 7104 148 0.96 8.08 1.01 0.97 333.21| | 8: 1.54 - 1.47 6798 152 0.96 8.22 1.01 0.97 276.82| | 9: 1.47 - 1.41 6938 155 0.96 8.39 1.00 0.98 228.10| | 10: 1.41 - 1.36 7022 150 0.96 8.82 1.00 0.97 199.81| | 11: 1.36 - 1.32 6997 151 0.96 8.81 0.99 0.96 172.21| | 12: 1.32 - 1.28 6975 149 0.96 8.90 0.98 0.95 158.83| | 13: 1.28 - 1.25 6907 166 0.96 9.51 1.01 0.96 157.47| | 14: 1.25 - 1.22 7015 112 0.95 10.67 1.01 0.97 162.42| | 15: 1.22 - 1.19 6956 137 0.95 11.21 1.01 0.98 165.82| | 16: 1.19 - 1.17 6604 132 0.95 11.36 1.01 0.96 158.86| | 17: 1.17 - 1.14 6940 135 0.94 12.19 1.01 0.96 152.75| | 18: 1.14 - 1.12 6875 142 0.94 12.68 1.01 0.95 146.58| | 19: 1.12 - 1.10 6948 106 0.93 14.11 1.00 0.95 150.45| | 20: 1.10 - 1.08 6884 147 0.92 15.19 1.00 0.94 149.83| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.93 153.22| | 22: 1.07 - 1.05 6836 135 0.89 18.28 0.99 0.93 154.87| | 23: 1.05 - 1.03 6827 159 0.87 20.50 0.99 0.92 164.62| | 24: 1.03 - 1.02 6784 133 0.85 23.13 0.99 0.93 178.68| | 25: 1.02 - 1.01 6552 130 0.83 25.11 0.98 0.90 181.55| | 26: 1.01 - 0.99 6767 158 0.81 26.58 0.98 0.89 176.17| | 27: 0.99 - 0.98 6647 131 0.82 26.30 0.99 0.87 160.98| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.58 max = 10904.12 mean = 906.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.23| |phase err.(test): min = 0.00 max = 89.42 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1356 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1490 n_refl.: 191127 remove outliers: r(all,work,free)=0.1402 0.1401 0.1490 n_refl.: 191127 overall B=-0.06 to atoms: r(all,work,free)=0.1393 0.1391 0.1483 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1191 0.1356 n_refl.: 191127 remove outliers: r(all,work,free)=0.1195 0.1191 0.1356 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3443 343.198 315.153 0.386 0.973 0.213 13.296-10.522 97.03 97 1 0.2425 481.106 463.926 0.672 0.975 0.147 10.503-8.327 98.35 176 3 0.2242 502.702 493.262 0.839 0.975 0.120 8.315-6.595 100.00 359 8 0.2153 374.530 369.740 0.867 0.975 0.094 6.588-5.215 100.00 711 7 0.1964 345.025 334.600 0.865 0.976 0.075 5.214-4.128 98.38 1367 28 0.1243 504.666 498.550 0.952 0.977 0.024 4.126-3.266 94.74 2603 46 0.1176 460.031 452.595 1.017 0.978 0.000 3.266-2.585 99.86 5447 97 0.1119 310.326 306.791 1.001 0.980 0.000 2.585-2.046 97.45 10613 204 0.0962 234.123 231.481 1.007 0.982 0.000 2.046-1.619 99.39 21536 464 0.0910 138.566 137.210 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0944 74.596 73.947 1.012 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.017 38.300 0.979 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0135 ================= 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 : 0.2043 0.2014 0.083 5.130 5.2 78.0 14.6 805 0.000 1_bss: 0.1809 0.1958 0.083 5.130 5.2 78.0 14.6 805 0.000 1_settarget: 0.1809 0.1958 0.083 5.130 5.2 78.0 14.6 805 0.000 1_nqh: 0.1809 0.1957 0.083 5.130 5.2 78.0 14.6 805 0.002 1_weight: 0.1809 0.1957 0.083 5.130 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1272 0.1508 0.039 1.169 5.2 78.0 14.6 805 0.160 1_adp: 0.1300 0.1576 0.039 1.169 5.2 73.0 15.1 805 0.160 1_regHadp: 0.1299 0.1571 0.039 1.169 5.2 73.0 15.1 805 0.160 1_occ: 0.1284 0.1559 0.039 1.169 5.2 73.0 15.1 805 0.160 2_bss: 0.1276 0.1546 0.039 1.169 5.4 73.2 15.3 805 0.160 2_settarget: 0.1276 0.1546 0.039 1.169 5.4 73.2 15.3 805 0.160 2_updatecdl: 0.1276 0.1546 0.039 1.180 5.4 73.2 15.3 805 0.160 2_nqh: 0.1276 0.1546 0.039 1.180 5.4 73.2 15.3 805 0.160 2_sol: 0.1273 0.1516 0.039 1.180 5.4 73.2 16.4 889 n/a 2_weight: 0.1273 0.1516 0.039 1.180 5.4 73.2 16.4 889 n/a 2_xyzrec: 0.1258 0.1530 0.040 1.142 5.4 73.2 16.4 889 n/a 2_adp: 0.1231 0.1516 0.040 1.142 5.4 70.4 16.5 889 n/a 2_regHadp: 0.1232 0.1517 0.040 1.142 5.4 70.4 16.5 889 n/a 2_occ: 0.1226 0.1519 0.040 1.142 5.4 70.4 16.5 889 n/a 3_bss: 0.1232 0.1526 0.040 1.142 5.4 70.4 16.5 889 n/a 3_settarget: 0.1232 0.1526 0.040 1.142 5.4 70.4 16.5 889 n/a 3_updatecdl: 0.1232 0.1526 0.040 1.141 5.4 70.4 16.5 889 n/a 3_nqh: 0.1232 0.1526 0.040 1.141 5.4 70.4 16.5 889 n/a 3_sol: 0.1251 0.1531 0.040 1.141 5.4 68.2 15.4 861 n/a 3_weight: 0.1251 0.1531 0.040 1.141 5.4 68.2 15.4 861 n/a 3_xyzrec: 0.1241 0.1446 0.034 1.099 5.4 68.2 15.4 861 n/a 3_adp: 0.1237 0.1410 0.034 1.099 5.6 67.9 15.3 861 n/a 3_regHadp: 0.1238 0.1411 0.034 1.099 5.6 67.9 15.3 861 n/a 3_occ: 0.1231 0.1399 0.034 1.099 5.6 67.9 15.3 861 n/a 4_bss: 0.1226 0.1389 0.034 1.099 5.5 67.8 15.2 861 n/a 4_settarget: 0.1226 0.1389 0.034 1.099 5.5 67.8 15.2 861 n/a 4_updatecdl: 0.1226 0.1389 0.034 1.104 5.5 67.8 15.2 861 n/a 4_nqh: 0.1226 0.1389 0.034 1.104 5.5 67.8 15.2 861 n/a 4_sol: 0.1210 0.1367 0.034 1.104 5.5 67.8 15.1 856 n/a 4_weight: 0.1210 0.1367 0.034 1.104 5.5 67.8 15.1 856 n/a 4_xyzrec: 0.1207 0.1368 0.035 1.124 5.5 67.8 15.1 856 n/a 4_adp: 0.1200 0.1362 0.035 1.124 5.5 67.4 15.0 856 n/a 4_regHadp: 0.1200 0.1362 0.035 1.124 5.5 67.4 15.0 856 n/a 4_occ: 0.1198 0.1359 0.035 1.124 5.5 67.4 15.0 856 n/a 5_bss: 0.1196 0.1359 0.035 1.124 5.5 67.4 14.9 856 n/a 5_settarget: 0.1196 0.1359 0.035 1.124 5.5 67.4 14.9 856 n/a 5_updatecdl: 0.1196 0.1359 0.035 1.124 5.5 67.4 14.9 856 n/a 5_nqh: 0.1196 0.1359 0.035 1.124 5.5 67.4 14.9 856 n/a 5_sol: 0.1195 0.1351 0.035 1.124 5.5 67.4 15.0 872 n/a 5_weight: 0.1195 0.1351 0.035 1.124 5.5 67.4 15.0 872 n/a 5_xyzrec: 0.1198 0.1355 0.035 1.122 5.5 67.4 15.0 872 n/a 5_adp: 0.1204 0.1360 0.035 1.122 5.6 66.2 14.8 872 n/a 5_regHadp: 0.1204 0.1361 0.035 1.122 5.6 66.2 14.8 872 n/a 5_occ: 0.1201 0.1359 0.035 1.122 5.6 66.2 14.8 872 n/a 6_bss: 0.1199 0.1356 0.035 1.122 5.5 66.2 14.8 872 n/a 6_settarget: 0.1199 0.1356 0.035 1.122 5.5 66.2 14.8 872 n/a 6_updatecdl: 0.1199 0.1356 0.035 1.123 5.5 66.2 14.8 872 n/a 6_nqh: 0.1199 0.1356 0.035 1.123 5.5 66.2 14.8 872 n/a 6_sol: 0.1196 0.1347 0.035 1.123 5.5 66.2 14.9 893 n/a 6_weight: 0.1196 0.1347 0.035 1.123 5.5 66.2 14.9 893 n/a 6_xyzrec: 0.1199 0.1357 0.037 1.125 5.5 66.2 14.9 893 n/a 6_adp: 0.1199 0.1357 0.037 1.125 5.6 65.1 14.8 893 n/a 6_regHadp: 0.1199 0.1358 0.037 1.125 5.6 65.1 14.8 893 n/a 6_occ: 0.1197 0.1361 0.037 1.125 5.6 65.1 14.8 893 n/a 7_bss: 0.1197 0.1356 0.037 1.125 5.3 64.9 14.6 893 n/a 7_settarget: 0.1197 0.1356 0.037 1.125 5.3 64.9 14.6 893 n/a 7_updatecdl: 0.1197 0.1356 0.037 1.125 5.3 64.9 14.6 893 n/a 7_nqh: 0.1197 0.1356 0.037 1.125 5.3 64.9 14.6 893 n/a 7_sol: 0.1203 0.1351 0.037 1.125 5.3 64.9 14.3 847 n/a 7_weight: 0.1203 0.1351 0.037 1.125 5.3 64.9 14.3 847 n/a 7_xyzrec: 0.1207 0.1355 0.037 1.123 5.3 64.9 14.3 847 n/a 7_adp: 0.1209 0.1359 0.037 1.123 5.4 63.8 14.2 847 n/a 7_regHadp: 0.1210 0.1360 0.037 1.123 5.4 63.8 14.2 847 n/a 7_occ: 0.1208 0.1360 0.037 1.123 5.4 63.8 14.2 847 n/a 8_bss: 0.1198 0.1354 0.037 1.123 5.5 63.9 14.3 847 n/a 8_settarget: 0.1198 0.1354 0.037 1.123 5.5 63.9 14.3 847 n/a 8_updatecdl: 0.1198 0.1354 0.037 1.123 5.5 63.9 14.3 847 n/a 8_nqh: 0.1198 0.1354 0.037 1.123 5.5 63.9 14.3 847 n/a 8_sol: 0.1192 0.1346 0.037 1.123 5.5 63.9 14.5 879 n/a 8_weight: 0.1192 0.1346 0.037 1.123 5.5 63.9 14.5 879 n/a 8_xyzrec: 0.1194 0.1351 0.037 1.127 5.5 63.9 14.5 879 n/a 8_adp: 0.1194 0.1354 0.037 1.127 5.5 62.9 14.5 879 n/a 8_regHadp: 0.1194 0.1354 0.037 1.127 5.5 62.9 14.5 879 n/a 8_occ: 0.1192 0.1355 0.037 1.127 5.5 62.9 14.5 879 n/a 9_bss: 0.1190 0.1356 0.037 1.127 5.5 62.9 14.5 879 n/a 9_settarget: 0.1190 0.1356 0.037 1.127 5.5 62.9 14.5 879 n/a 9_updatecdl: 0.1190 0.1356 0.037 1.127 5.5 62.9 14.5 879 n/a 9_nqh: 0.1190 0.1356 0.037 1.127 5.5 62.9 14.5 879 n/a 9_sol: 0.1188 0.1347 0.037 1.127 5.5 62.9 14.5 887 n/a 9_weight: 0.1188 0.1347 0.037 1.127 5.5 62.9 14.5 887 n/a 9_xyzrec: 0.1192 0.1355 0.038 1.121 5.5 62.9 14.5 887 n/a 9_adp: 0.1194 0.1358 0.038 1.121 5.5 62.7 14.5 887 n/a 9_regHadp: 0.1194 0.1358 0.038 1.121 5.5 62.7 14.5 887 n/a 9_occ: 0.1193 0.1361 0.038 1.121 5.5 62.7 14.5 887 n/a 10_bss: 0.1191 0.1359 0.038 1.121 5.5 62.7 14.5 887 n/a 10_settarget: 0.1191 0.1359 0.038 1.121 5.5 62.7 14.5 887 n/a 10_updatecdl: 0.1191 0.1359 0.038 1.122 5.5 62.7 14.5 887 n/a 10_setrh: 0.1192 0.1360 0.038 1.122 5.5 62.7 14.5 887 n/a 10_nqh: 0.1192 0.1360 0.038 1.122 5.5 62.7 14.5 887 n/a 10_sol: 0.1190 0.1352 0.038 1.122 5.5 62.7 14.6 893 n/a 10_weight: 0.1190 0.1352 0.038 1.122 5.5 62.7 14.6 893 n/a 10_xyzrec: 0.1191 0.1353 0.038 1.155 5.5 62.7 14.6 893 n/a 10_adp: 0.1193 0.1356 0.038 1.155 5.6 62.3 14.6 893 n/a 10_regHadp: 0.1193 0.1356 0.038 1.155 5.6 62.3 14.6 893 n/a 10_occ: 0.1192 0.1356 0.038 1.155 5.6 62.3 14.6 893 n/a end: 0.1191 0.1356 0.038 1.155 5.5 62.3 14.5 893 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7723142_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7723142_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3200 Refinement macro-cycles (run) : 12132.6800 Write final files (write_after_run_outputs) : 156.6700 Total : 12295.6700 Total CPU time: 3.43 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:12 PST -0800 (1736736132.16 s) Start R-work = 0.1809, R-free = 0.1958 Final R-work = 0.1191, R-free = 0.1356 =============================================================================== Job complete usr+sys time: 12571.79 seconds wall clock time: 210 minutes 33.54 seconds (12633.54 seconds total)