Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2614032.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" 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_2614032.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2614032.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.30, per 1000 atoms: 0.34 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: 2.813 distance_ideal: 2.720 ideal - model: -0.093 slack: 0.000 delta_slack: -0.093 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.708 distance_ideal: 2.710 ideal - model: 0.002 slack: 0.000 delta_slack: 0.002 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 148.0 milliseconds Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.04: 905 1.04 - 1.25: 2402 1.25 - 1.47: 1373 1.47 - 1.69: 1209 1.69 - 1.91: 45 Bond restraints: 5934 Sorted by residual: bond pdb=" C ILE A 45 " pdb=" O ILE A 45 " ideal model delta sigma weight residual 1.237 0.977 0.260 1.11e-02 8.12e+03 5.48e+02 bond pdb=" N ALA B 10 " pdb=" CA ALA B 10 " ideal model delta sigma weight residual 1.453 1.273 0.180 8.30e-03 1.45e+04 4.73e+02 bond pdb=" N VAL A 62 " pdb=" H VAL A 62 " ideal model delta sigma weight residual 0.860 1.279 -0.419 2.00e-02 2.50e+03 4.39e+02 bond pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta sigma weight residual 1.460 1.640 -0.180 8.60e-03 1.35e+04 4.39e+02 bond pdb=" C VAL A 37 " pdb=" N ALA A 38 " ideal model delta sigma weight residual 1.333 1.048 0.286 1.38e-02 5.25e+03 4.28e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 5732 4.28 - 8.56: 3592 8.56 - 12.84: 1234 12.84 - 17.11: 223 17.11 - 21.39: 29 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.38 131.41 -12.03 6.80e-01 2.16e+00 3.13e+02 angle pdb=" O LYS A 131 " pdb=" C LYS A 131 " pdb=" N ASP A 132 " ideal model delta sigma weight residual 122.09 107.76 14.33 1.04e+00 9.25e-01 1.90e+02 angle pdb=" CA ALA A 182 " pdb=" C ALA A 182 " pdb=" O ALA A 182 " ideal model delta sigma weight residual 120.63 106.17 14.46 1.08e+00 8.57e-01 1.79e+02 angle pdb=" CA GLY A 165 " pdb=" C GLY A 165 " pdb=" O GLY A 165 " ideal model delta sigma weight residual 121.05 134.38 -13.33 1.03e+00 9.43e-01 1.67e+02 angle pdb=" O ARG B 49 " pdb=" C ARG B 49 " pdb=" N GLY B 50 " ideal model delta sigma weight residual 122.26 106.40 15.86 1.23e+00 6.61e-01 1.66e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.98: 1852 16.98 - 33.96: 133 33.96 - 50.94: 42 50.94 - 67.91: 19 67.91 - 84.89: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA GLY B 75 " pdb=" C GLY B 75 " pdb=" N ILE B 76 " pdb=" CA ILE B 76 " ideal model delta harmonic sigma weight residual -180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA TRP A 139 " pdb=" C TRP A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.242: 205 0.242 - 0.483: 171 0.483 - 0.725: 87 0.725 - 0.966: 24 0.966 - 1.207: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 173 " pdb=" N VAL B 173 " pdb=" C VAL B 173 " pdb=" CB VAL B 173 " both_signs ideal model delta sigma weight residual False 2.44 3.65 -1.21 2.00e-01 2.50e+01 3.64e+01 chirality pdb=" CB VAL A 114 " pdb=" CA VAL A 114 " pdb=" CG1 VAL A 114 " pdb=" CG2 VAL A 114 " both_signs ideal model delta sigma weight residual False -2.63 -3.72 1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" CB ILE B 105 " pdb=" CA ILE B 105 " pdb=" CG1 ILE B 105 " pdb=" CG2 ILE B 105 " both_signs ideal model delta sigma weight residual False 2.64 1.56 1.09 2.00e-01 2.50e+01 2.95e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.143 2.00e-02 2.50e+03 7.38e-02 2.18e+02 pdb=" CG TRP B 146 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.059 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.130 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.082 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.041 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.113 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.097 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.100 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.027 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.006 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.031 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.031 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 127 " 0.100 2.00e-02 2.50e+03 7.67e-02 1.76e+02 pdb=" CG PHE B 127 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE B 127 " -0.126 2.00e-02 2.50e+03 pdb=" CD2 PHE B 127 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE B 127 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 PHE B 127 " 0.083 2.00e-02 2.50e+03 pdb=" CZ PHE B 127 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 PHE B 127 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 127 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 PHE B 127 " 0.103 2.00e-02 2.50e+03 pdb=" HE2 PHE B 127 " 0.089 2.00e-02 2.50e+03 pdb=" HZ PHE B 127 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.051 2.00e-02 2.50e+03 6.28e-02 1.58e+02 pdb=" CG TRP A 139 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.097 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.078 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.026 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.072 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.093 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.013 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.098 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.008 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.039 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 27 1.61 - 2.35: 2334 2.35 - 3.10: 22093 3.10 - 3.85: 33076 3.85 - 4.60: 52744 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110274 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.857 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.920 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.935 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.045 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.254 2.620 ... (remaining 110269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 12 15.96 2 Mg 2 11.97 3 O 1357 7.97 2 N 488 6.98 3 C 1850 5.99 3 H 2984 1.00 3 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6693 n_use_u_iso = 3419 n_use_u_aniso = 3274 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 6693 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6693 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3419 aniso = 3274) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (1426 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_2614032_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= 0.2037 r_free= 0.1977 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302312 | | target function (ml) not normalized (work): 805879.006940 | | target function (ml) not normalized (free): 16564.333725 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2139 0.1845 6.6964 6.2882| | 2: 2.94 - 2.33 1.00 7339 128 0.1617 0.1759 5.5317 5.5733| | 3: 2.33 - 2.04 0.96 6939 150 0.1630 0.1618 5.1392 5.1546| | 4: 2.04 - 1.85 1.00 7170 155 0.1771 0.1541 4.9749 5.0081| | 5: 1.85 - 1.72 0.99 7113 159 0.1914 0.1637 4.798 4.8049| | 6: 1.72 - 1.62 0.99 7102 142 0.1991 0.2111 4.6683 4.7| | 7: 1.62 - 1.54 0.99 7104 148 0.2000 0.1772 4.5542 4.5567| | 8: 1.54 - 1.47 0.96 6798 152 0.2002 0.2098 4.4664 4.5004| | 9: 1.47 - 1.41 0.98 6938 155 0.2143 0.2202 4.4154 4.4859| | 10: 1.41 - 1.36 0.99 7022 150 0.2140 0.1916 4.3168 4.2343| | 11: 1.36 - 1.32 0.99 6997 151 0.2129 0.2228 4.2389 4.2874| | 12: 1.32 - 1.28 0.98 6976 149 0.2090 0.2040 4.1779 4.2613| | 13: 1.28 - 1.25 0.98 6907 166 0.2023 0.2110 4.1241 4.1528| | 14: 1.25 - 1.22 0.98 7015 113 0.2075 0.2501 4.0832 4.3284| | 15: 1.22 - 1.19 0.98 6957 137 0.2133 0.1957 4.0606 4.0239| | 16: 1.19 - 1.17 0.93 6604 132 0.2128 0.2489 4.0137 4.1546| | 17: 1.17 - 1.14 0.98 6941 135 0.2185 0.1926 3.956 3.9883| | 18: 1.14 - 1.12 0.98 6875 142 0.2236 0.2111 3.9263 3.8424| | 19: 1.12 - 1.10 0.97 6949 106 0.2243 0.2391 3.866 3.9556| | 20: 1.10 - 1.08 0.97 6884 147 0.2324 0.2405 3.8201 3.9623| | 21: 1.08 - 1.07 0.97 6852 152 0.2416 0.2600 3.7885 3.8261| | 22: 1.07 - 1.05 0.97 6838 135 0.2576 0.2644 3.7604 3.792| | 23: 1.05 - 1.03 0.97 6829 159 0.2702 0.2670 3.7306 3.792| | 24: 1.03 - 1.02 0.96 6785 133 0.2902 0.2807 3.7092 3.784| | 25: 1.02 - 1.01 0.93 6552 130 0.3067 0.3083 3.6734 3.7738| | 26: 1.01 - 0.99 0.96 6767 158 0.3202 0.3340 3.6297 3.6337| | 27: 0.99 - 0.98 0.94 6648 131 0.3380 0.3068 3.6286 3.6026| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.17 0.91 0.97 34220.90| | 2: 2.94 - 2.33 7339 128 0.86 20.90 1.08 1.02 14634.24| | 3: 2.33 - 2.04 6939 150 0.93 12.38 1.11 1.05 4083.99| | 4: 2.04 - 1.85 7170 155 0.93 13.19 1.11 1.06 2668.03| | 5: 1.85 - 1.72 7113 159 0.91 15.21 1.11 1.08 2008.77| | 6: 1.72 - 1.62 7102 142 0.90 16.21 1.11 1.08 1574.09| | 7: 1.62 - 1.54 7104 148 0.90 17.04 1.11 1.09 1274.82| | 8: 1.54 - 1.47 6798 152 0.89 17.59 1.10 1.08 1080.99| | 9: 1.47 - 1.41 6938 155 0.89 18.32 1.10 1.08 928.85| | 10: 1.41 - 1.36 7022 150 0.87 19.77 1.09 1.05 824.87| | 11: 1.36 - 1.32 6997 151 0.87 19.92 1.09 1.04 725.68| | 12: 1.32 - 1.28 6976 149 0.87 20.18 1.08 1.03 661.91| | 13: 1.28 - 1.25 6907 166 0.87 20.10 1.07 1.04 622.62| | 14: 1.25 - 1.22 7015 113 0.86 21.61 1.08 1.03 618.99| | 15: 1.22 - 1.19 6957 137 0.85 21.98 1.08 1.04 592.42| | 16: 1.19 - 1.17 6604 132 0.86 21.21 1.08 1.04 529.19| | 17: 1.17 - 1.14 6941 135 0.87 20.84 1.09 1.03 441.40| | 18: 1.14 - 1.12 6875 142 0.87 20.50 1.08 1.02 384.20| | 19: 1.12 - 1.10 6949 106 0.86 21.59 1.07 1.02 376.52| | 20: 1.10 - 1.08 6884 147 0.84 23.43 1.06 1.00 369.54| | 21: 1.08 - 1.07 6852 152 0.83 24.78 1.06 0.98 356.36| | 22: 1.07 - 1.05 6838 135 0.81 26.26 1.05 0.97 343.51| | 23: 1.05 - 1.03 6829 159 0.80 27.83 1.05 0.97 336.95| | 24: 1.03 - 1.02 6785 133 0.77 29.91 1.05 0.98 341.48| | 25: 1.02 - 1.01 6552 130 0.76 31.06 1.03 0.93 315.36| | 26: 1.01 - 0.99 6767 158 0.74 32.72 1.03 0.91 298.47| | 27: 0.99 - 0.98 6648 131 0.74 33.06 1.04 0.90 284.28| |alpha: min = 0.90 max = 1.09 mean = 1.02| |beta: min = 284.28 max = 34220.90 mean = 2748.49| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 21.68| |phase err.(test): min = 0.00 max = 89.56 mean = 21.71| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.286 2950 Z= 5.372 Angle : 5.224 17.135 4018 Z= 3.698 Chirality : 0.389 1.207 492 Planarity : 0.034 0.159 512 Dihedral : 12.746 84.892 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.40 % Favored : 95.08 % Rotamer: Outliers : 0.97 % Allowed : 3.23 % Favored : 95.81 % Cbeta Deviations : 35.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.40), residues: 386 helix: -2.24 (0.35), residues: 148 sheet: -0.46 (0.57), residues: 86 loop : -0.15 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.018 ARG A 97 TYR 0.107 0.039 TYR A 195 PHE 0.103 0.045 PHE A 127 TRP 0.135 0.058 TRP B 146 HIS 0.092 0.035 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= 0.2037 r_free= 0.1977 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302312 | | target function (ml) not normalized (work): 805879.006940 | | target function (ml) not normalized (free): 16564.333725 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2035 0.2037 0.1977 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2035 0.2037 0.1977 n_refl.: 191155 remove outliers: r(all,work,free)=0.2035 0.2037 0.1977 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2032 0.2033 0.1976 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1806 0.1910 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1804 0.1909 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 96.04 94 3 0.4262 400.535 290.755 0.421 0.913 0.291 13.296-10.522 99.01 99 1 0.2543 528.187 517.154 0.776 0.915 0.243 10.503-8.327 98.90 177 3 0.2492 564.205 557.141 0.965 0.915 0.220 8.318-6.595 100.00 360 8 0.2487 414.736 402.970 0.965 0.915 0.160 6.588-5.215 100.00 711 7 0.2242 381.101 364.886 0.953 0.916 0.150 5.214-4.128 98.38 1367 28 0.1522 557.435 548.660 1.062 0.917 0.090 4.126-3.266 94.74 2603 46 0.1340 508.132 498.395 1.132 0.918 0.019 3.266-2.585 99.86 5447 97 0.1454 342.774 337.195 1.106 0.919 0.000 2.585-2.046 97.45 10613 204 0.1394 258.603 254.394 1.107 0.922 0.000 2.046-1.619 99.39 21536 464 0.1631 153.054 150.164 1.122 0.925 0.000 1.619-1.281 98.00 42464 925 0.1925 82.395 80.412 1.101 0.930 0.000 1.281-0.980 96.53 101826 2055 0.2321 44.202 42.040 1.075 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0678 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1909 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1804 r_free=0.1909 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.687573 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.270044 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 0.1267 0.1473 0.0206 0.034 1.2 11.4 0.0 0.6 0 11.344 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.67 14.73 2.06 1.117 13.086 571.270 0.019 13.01 15.45 2.44 1.239 13.327 571.270 0.018 Individual atomic B min max mean iso aniso Overall: 5.25 73.02 15.01 1.39 435 3274 Protein: 5.25 40.59 11.02 1.39 0 2902 Water: 6.24 73.02 29.37 N/A 435 370 Other: 16.00 30.64 23.32 N/A 0 2 Chain A: 5.31 60.42 13.07 N/A 0 1626 Chain B: 5.25 73.02 12.78 N/A 0 1648 Chain S: 11.66 62.30 30.71 N/A 435 0 Histogram: Values Number of atoms 5.25 - 12.03 2172 12.03 - 18.80 631 18.80 - 25.58 322 25.58 - 32.36 260 32.36 - 39.13 158 39.13 - 45.91 104 45.91 - 52.69 40 52.69 - 59.47 15 59.47 - 66.24 6 66.24 - 73.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1301 r_free=0.1545 r_work=0.1300 r_free=0.1541 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1300 r_free = 0.1541 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1285 r_free = 0.1528 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1285 r_free= 0.1528 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015785 | | target function (ls_wunit_k1) not normalized (work): 2956.411071 | | target function (ls_wunit_k1) not normalized (free): 110.810408 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1285 0.1528 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1478 0.1476 0.1602 n_refl.: 191138 remove outliers: r(all,work,free)=0.1478 0.1476 0.1602 n_refl.: 191138 overall B=0.15 to atoms: r(all,work,free)=0.1500 0.1498 0.1613 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1518 n_refl.: 191138 remove outliers: r(all,work,free)=0.1281 0.1276 0.1518 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3674 402.814 367.916 0.475 0.962 0.287 13.296-10.522 99.01 99 1 0.2099 528.187 519.283 0.734 0.963 0.241 10.503-8.327 98.90 177 3 0.1746 564.205 561.523 0.885 0.963 0.217 8.318-6.595 100.00 360 8 0.1767 414.736 411.345 0.909 0.963 0.150 6.588-5.215 100.00 711 7 0.1584 381.101 372.844 0.889 0.963 0.150 5.214-4.128 98.38 1367 28 0.0933 557.435 555.081 0.977 0.964 0.059 4.126-3.266 94.74 2603 46 0.0856 508.132 503.991 1.045 0.964 0.014 3.266-2.585 99.86 5447 97 0.0926 342.774 340.246 1.027 0.964 0.000 2.585-2.046 97.45 10613 204 0.0941 258.603 256.442 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1074 153.054 151.422 1.056 0.965 0.000 1.619-1.281 98.00 42464 925 0.1275 82.395 81.426 1.047 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1880 44.202 42.135 1.023 0.967 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0334 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1518 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1518 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1518 | n_water=805 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1277 r_free=0.1522 | n_water=800 | time (s): 100.360 (total time: 102.810) Filter (q & B) r_work=0.1278 r_free=0.1520 | n_water=795 | time (s): 4.090 (total time: 106.900) Compute maps r_work=0.1278 r_free=0.1520 | n_water=795 | time (s): 2.390 (total time: 109.290) Filter (map) r_work=0.1301 r_free=0.1519 | n_water=668 | time (s): 5.290 (total time: 114.580) Find peaks r_work=0.1301 r_free=0.1519 | n_water=668 | time (s): 0.640 (total time: 115.220) Add new water r_work=0.1323 r_free=0.1550 | n_water=983 | time (s): 4.300 (total time: 119.520) Refine new water occ: r_work=0.1280 r_free=0.1492 adp: r_work=0.1268 r_free=0.1490 occ: r_work=0.1271 r_free=0.1485 adp: r_work=0.1264 r_free=0.1487 occ: r_work=0.1266 r_free=0.1484 adp: r_work=0.1263 r_free=0.1485 ADP+occupancy (water only), MIN, final r_work=0.1263 r_free=0.1485 r_work=0.1263 r_free=0.1485 | n_water=983 | time (s): 80.220 (total time: 199.740) Filter (q & B) r_work=0.1267 r_free=0.1488 | n_water=907 | time (s): 4.380 (total time: 204.120) Filter (dist only) r_work=0.1267 r_free=0.1489 | n_water=905 | time (s): 118.830 (total time: 322.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.501762 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 581.764244 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 0.1253 0.1511 0.0257 0.038 1.1 19.0 0.0 0.3 0 11.751 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.11 2.57 2.043 15.232 581.764 0.014 12.30 15.00 2.69 2.402 15.277 581.764 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.44 16.40 1.19 536 3273 Protein: 5.38 40.36 11.00 1.19 0 2902 Water: 6.59 68.44 33.66 N/A 536 369 Other: 16.29 33.17 24.73 N/A 0 2 Chain A: 5.56 56.74 13.03 N/A 0 1625 Chain B: 5.38 68.44 12.82 N/A 0 1648 Chain S: 12.42 65.20 37.59 N/A 536 0 Histogram: Values Number of atoms 5.38 - 11.68 2050 11.68 - 17.99 725 17.99 - 24.29 273 24.29 - 30.60 217 30.60 - 36.91 183 36.91 - 43.21 155 43.21 - 49.52 97 49.52 - 55.82 58 55.82 - 62.13 40 62.13 - 68.44 11 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1500 r_work=0.1231 r_free=0.1501 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1501 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1498 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1498 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013295 | | target function (ls_wunit_k1) not normalized (work): 2490.048830 | | target function (ls_wunit_k1) not normalized (free): 102.343962 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1225 0.1498 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1597 n_refl.: 191137 remove outliers: r(all,work,free)=0.1434 0.1431 0.1597 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1428 0.1595 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1232 0.1506 n_refl.: 191137 remove outliers: r(all,work,free)=0.1237 0.1232 0.1506 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3128 402.814 381.973 0.486 0.963 0.265 13.296-10.522 99.01 99 1 0.1911 528.187 518.460 0.752 0.964 0.219 10.503-8.327 98.90 177 3 0.1350 564.205 567.006 0.918 0.964 0.200 8.318-6.595 100.00 360 8 0.1558 414.736 413.074 0.931 0.963 0.139 6.588-5.215 100.00 711 7 0.1352 381.101 376.908 0.910 0.963 0.120 5.214-4.128 98.38 1367 28 0.0837 557.435 555.967 0.995 0.964 0.080 4.126-3.266 94.74 2603 46 0.0757 508.132 505.380 1.059 0.964 0.009 3.266-2.585 99.86 5447 97 0.0856 342.774 341.452 1.046 0.963 0.000 2.585-2.046 97.45 10613 204 0.0892 258.603 256.793 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1039 153.054 151.669 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.351 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.210 1.058 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0580 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1506 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1506 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1506 | n_water=905 | time (s): 3.430 (total time: 3.430) Filter (dist) r_work=0.1233 r_free=0.1507 | n_water=902 | time (s): 117.880 (total time: 121.310) Filter (q & B) r_work=0.1233 r_free=0.1508 | n_water=898 | time (s): 5.080 (total time: 126.390) Compute maps r_work=0.1233 r_free=0.1508 | n_water=898 | time (s): 2.000 (total time: 128.390) Filter (map) r_work=0.1269 r_free=0.1512 | n_water=717 | time (s): 4.990 (total time: 133.380) Find peaks r_work=0.1269 r_free=0.1512 | n_water=717 | time (s): 0.910 (total time: 134.290) Add new water r_work=0.1291 r_free=0.1550 | n_water=1038 | time (s): 4.530 (total time: 138.820) Refine new water occ: r_work=0.1249 r_free=0.1504 adp: r_work=0.1249 r_free=0.1504 occ: r_work=0.1245 r_free=0.1502 adp: r_work=0.1245 r_free=0.1503 occ: r_work=0.1242 r_free=0.1500 adp: r_work=0.1241 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1501 r_work=0.1241 r_free=0.1501 | n_water=1038 | time (s): 312.550 (total time: 451.370) Filter (q & B) r_work=0.1248 r_free=0.1505 | n_water=883 | time (s): 4.290 (total time: 455.660) Filter (dist only) r_work=0.1248 r_free=0.1504 | n_water=882 | time (s): 110.420 (total time: 566.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.665702 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.120975 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1240 0.1439 0.0199 0.034 1.1 6.8 0.0 0.0 0 0.833 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.39 1.99 1.932 14.630 16.121 3.942 12.31 13.96 1.65 2.210 14.538 16.121 3.896 Individual atomic B min max mean iso aniso Overall: 5.52 68.06 15.33 1.07 515 3271 Protein: 5.52 36.89 10.77 1.07 0 2902 Water: 6.66 68.06 30.31 N/A 515 367 Other: 14.22 28.82 21.52 N/A 0 2 Chain A: 5.54 55.89 12.80 N/A 0 1625 Chain B: 5.52 68.06 12.53 N/A 0 1646 Chain S: 14.34 62.89 32.25 N/A 515 0 Histogram: Values Number of atoms 5.52 - 11.78 2130 11.78 - 18.03 682 18.03 - 24.28 311 24.28 - 30.54 234 30.54 - 36.79 175 36.79 - 43.04 146 43.04 - 49.30 70 49.30 - 55.55 26 55.55 - 61.80 10 61.80 - 68.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1396 r_work=0.1232 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1397 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1392 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891008 | | target function (ml) not normalized (work): 728770.322006 | | target function (ml) not normalized (free): 15223.041406 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1391 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1442 0.1442 0.1496 n_refl.: 191137 remove outliers: r(all,work,free)=0.1442 0.1442 0.1496 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1435 0.1492 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1384 n_refl.: 191137 remove outliers: r(all,work,free)=0.1226 0.1223 0.1384 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 92.08 90 3 0.3749 393.895 353.742 0.391 0.946 0.210 13.296-10.522 99.01 99 1 0.2421 528.187 505.934 0.706 0.948 0.210 10.503-8.327 98.35 176 3 0.1977 556.299 559.529 0.885 0.948 0.210 8.318-6.595 100.00 360 8 0.2124 414.736 409.006 0.894 0.947 0.120 6.588-5.215 100.00 711 7 0.1852 381.101 370.661 0.882 0.947 0.100 5.214-4.128 98.38 1367 28 0.1170 557.435 552.313 0.974 0.948 0.090 4.126-3.266 94.74 2603 46 0.1102 508.132 500.761 1.033 0.948 0.005 3.266-2.585 99.86 5447 97 0.1083 342.774 339.228 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0957 258.603 255.775 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0966 153.054 151.433 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.492 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.314 1.038 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1085 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1384 | n_water=882 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1224 r_free=0.1387 | n_water=881 | time (s): 110.370 (total time: 112.540) Filter (q & B) r_work=0.1225 r_free=0.1384 | n_water=869 | time (s): 4.890 (total time: 117.430) Compute maps r_work=0.1225 r_free=0.1384 | n_water=869 | time (s): 2.150 (total time: 119.580) Filter (map) r_work=0.1245 r_free=0.1381 | n_water=738 | time (s): 5.060 (total time: 124.640) Find peaks r_work=0.1245 r_free=0.1381 | n_water=738 | time (s): 0.560 (total time: 125.200) Add new water r_work=0.1260 r_free=0.1405 | n_water=974 | time (s): 3.950 (total time: 129.150) Refine new water occ: r_work=0.1214 r_free=0.1365 adp: r_work=0.1206 r_free=0.1359 occ: r_work=0.1203 r_free=0.1360 adp: r_work=0.1203 r_free=0.1359 occ: r_work=0.1201 r_free=0.1359 adp: r_work=0.1201 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1358 r_work=0.1201 r_free=0.1358 | n_water=974 | time (s): 304.130 (total time: 433.280) Filter (q & B) r_work=0.1207 r_free=0.1359 | n_water=877 | time (s): 5.420 (total time: 438.700) Filter (dist only) r_work=0.1207 r_free=0.1359 | n_water=876 | time (s): 113.940 (total time: 552.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.574605 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.513961 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1357 0.0151 0.035 1.1 5.6 0.0 0.0 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.57 1.51 1.840 14.253 15.514 3.874 12.00 13.55 1.55 1.948 14.210 15.514 3.866 Individual atomic B min max mean iso aniso Overall: 5.52 67.66 15.02 1.01 509 3271 Protein: 5.52 33.72 10.68 1.01 0 2902 Water: 5.88 67.66 29.37 N/A 509 367 Other: 13.98 27.84 20.91 N/A 0 2 Chain A: 5.54 54.89 12.67 N/A 0 1625 Chain B: 5.52 67.66 12.43 N/A 0 1646 Chain S: 5.88 60.91 30.91 N/A 509 0 Histogram: Values Number of atoms 5.52 - 11.73 2129 11.73 - 17.95 715 17.95 - 24.16 300 24.16 - 30.38 242 30.38 - 36.59 170 36.59 - 42.80 135 42.80 - 49.02 62 49.02 - 55.23 22 55.23 - 61.45 4 61.45 - 67.66 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1355 r_work=0.1200 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1355 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1355 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= 0.1197 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863914 | | target function (ml) not normalized (work): 723680.251520 | | target function (ml) not normalized (free): 15138.111770 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1355 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1406 0.1405 0.1479 n_refl.: 191133 remove outliers: r(all,work,free)=0.1406 0.1405 0.1479 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1400 0.1399 0.1475 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1344 n_refl.: 191133 remove outliers: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3751 356.585 314.482 0.348 0.973 0.160 13.296-10.522 97.03 97 1 0.2442 481.513 451.667 0.661 0.974 0.156 10.503-8.327 97.80 175 3 0.2091 502.241 497.933 0.843 0.974 0.153 8.318-6.595 100.00 360 8 0.2181 375.794 369.767 0.867 0.973 0.120 6.588-5.215 100.00 711 7 0.1889 345.317 335.449 0.855 0.973 0.085 5.214-4.128 98.38 1367 28 0.1189 505.094 500.256 0.945 0.972 0.080 4.126-3.266 94.74 2603 46 0.1117 460.421 453.290 1.005 0.971 0.000 3.266-2.585 99.86 5447 97 0.1086 310.589 307.300 0.994 0.968 0.000 2.585-2.046 97.45 10613 204 0.0932 234.321 231.955 1.011 0.965 0.000 2.046-1.619 99.39 21536 464 0.0912 138.683 137.370 1.040 0.958 0.000 1.619-1.281 98.00 42464 925 0.0981 74.659 73.963 1.047 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.051 38.386 1.051 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0963 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1344 | n_water=876 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1191 r_free=0.1344 | n_water=876 | time (s): 110.760 (total time: 112.990) Filter (q & B) r_work=0.1192 r_free=0.1344 | n_water=863 | time (s): 4.620 (total time: 117.610) Compute maps r_work=0.1192 r_free=0.1344 | n_water=863 | time (s): 1.920 (total time: 119.530) Filter (map) r_work=0.1213 r_free=0.1350 | n_water=748 | time (s): 4.450 (total time: 123.980) Find peaks r_work=0.1213 r_free=0.1350 | n_water=748 | time (s): 0.590 (total time: 124.570) Add new water r_work=0.1224 r_free=0.1365 | n_water=981 | time (s): 4.110 (total time: 128.680) Refine new water occ: r_work=0.1189 r_free=0.1330 adp: r_work=0.1189 r_free=0.1330 occ: r_work=0.1187 r_free=0.1329 adp: r_work=0.1187 r_free=0.1329 occ: r_work=0.1185 r_free=0.1329 adp: r_work=0.1184 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1328 r_work=0.1184 r_free=0.1328 | n_water=981 | time (s): 272.100 (total time: 400.780) Filter (q & B) r_work=0.1190 r_free=0.1336 | n_water=886 | time (s): 4.760 (total time: 405.540) Filter (dist only) r_work=0.1191 r_free=0.1336 | n_water=884 | time (s): 117.430 (total time: 522.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.536847 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.725583 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 0.1350 0.0156 0.036 1.1 7.0 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.50 1.56 1.799 14.150 15.726 3.765 11.99 13.53 1.54 1.919 14.102 15.726 3.761 Individual atomic B min max mean iso aniso Overall: 5.53 67.12 14.91 0.95 518 3270 Protein: 5.53 31.73 10.59 0.95 0 2902 Water: 5.96 67.12 29.11 N/A 518 366 Other: 13.87 26.05 19.96 N/A 0 2 Chain A: 5.55 53.47 12.52 N/A 0 1624 Chain B: 5.53 67.12 12.31 N/A 0 1646 Chain S: 5.96 60.86 30.71 N/A 518 0 Histogram: Values Number of atoms 5.53 - 11.69 2132 11.69 - 17.85 729 17.85 - 24.00 303 24.00 - 30.16 231 30.16 - 36.32 169 36.32 - 42.48 134 42.48 - 48.64 62 48.64 - 54.80 23 54.80 - 60.96 4 60.96 - 67.12 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1353 r_work=0.1200 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1353 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1353 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760213 | | target function (ml) not normalized (work): 704242.781618 | | target function (ml) not normalized (free): 14747.550310 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1353 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1395 0.1394 0.1488 n_refl.: 191129 remove outliers: r(all,work,free)=0.1395 0.1394 0.1488 n_refl.: 191129 overall B=-0.03 to atoms: r(all,work,free)=0.1389 0.1387 0.1483 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1196 0.1351 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 0.3722 356.351 319.140 0.336 0.976 0.120 13.296-10.522 97.03 97 1 0.2423 481.513 460.943 0.659 0.977 0.119 10.503-8.327 97.80 175 3 0.2198 502.241 495.622 0.834 0.977 0.118 8.318-6.595 100.00 360 8 0.2176 375.794 369.963 0.861 0.976 0.100 6.588-5.215 100.00 711 7 0.1936 345.317 335.073 0.853 0.976 0.090 5.214-4.128 98.38 1367 28 0.1215 505.094 499.901 0.944 0.976 0.080 4.126-3.266 94.74 2603 46 0.1153 460.421 452.885 1.004 0.974 0.000 3.266-2.585 99.86 5447 97 0.1107 310.589 307.296 0.993 0.972 0.000 2.585-2.046 97.45 10613 204 0.0946 234.321 231.863 1.008 0.968 0.000 2.046-1.619 99.39 21536 464 0.0914 138.683 137.352 1.037 0.962 0.000 1.619-1.281 98.00 42464 925 0.0972 74.659 73.956 1.044 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1643 40.051 38.375 1.048 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1138 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1351 | n_water=884 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1197 r_free=0.1351 | n_water=882 | time (s): 127.660 (total time: 130.270) Filter (q & B) r_work=0.1197 r_free=0.1349 | n_water=870 | time (s): 4.370 (total time: 134.640) Compute maps r_work=0.1197 r_free=0.1349 | n_water=870 | time (s): 1.990 (total time: 136.630) Filter (map) r_work=0.1218 r_free=0.1354 | n_water=750 | time (s): 5.480 (total time: 142.110) Find peaks r_work=0.1218 r_free=0.1354 | n_water=750 | time (s): 0.870 (total time: 142.980) Add new water r_work=0.1228 r_free=0.1366 | n_water=967 | time (s): 4.410 (total time: 147.390) Refine new water occ: r_work=0.1195 r_free=0.1338 adp: r_work=0.1195 r_free=0.1338 occ: r_work=0.1193 r_free=0.1337 adp: r_work=0.1193 r_free=0.1337 occ: r_work=0.1191 r_free=0.1337 adp: r_work=0.1191 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1337 r_work=0.1191 r_free=0.1337 | n_water=967 | time (s): 201.680 (total time: 349.070) Filter (q & B) r_work=0.1195 r_free=0.1343 | n_water=892 | time (s): 4.730 (total time: 353.800) Filter (dist only) r_work=0.1196 r_free=0.1342 | n_water=891 | time (s): 112.040 (total time: 465.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.559479 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.829059 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 0.1344 0.0145 0.036 1.1 6.8 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.44 1.45 1.758 14.018 13.829 3.760 11.99 13.46 1.46 1.777 14.009 13.829 3.760 Individual atomic B min max mean iso aniso Overall: 5.57 66.88 14.87 0.92 525 3270 Protein: 5.57 30.81 10.55 0.92 0 2902 Water: 5.99 66.88 28.92 N/A 525 366 Other: 13.80 25.51 19.66 N/A 0 2 Chain A: 5.60 52.88 12.46 N/A 0 1624 Chain B: 5.57 66.88 12.26 N/A 0 1646 Chain S: 5.99 60.82 30.49 N/A 525 0 Histogram: Values Number of atoms 5.57 - 11.70 2139 11.70 - 17.83 740 17.83 - 23.96 296 23.96 - 30.09 228 30.09 - 36.22 172 36.22 - 42.35 132 42.35 - 48.48 59 48.48 - 54.61 23 54.61 - 60.74 4 60.74 - 66.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1346 r_work=0.1199 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1346 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1345 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759131 | | target function (ml) not normalized (work): 704036.386636 | | target function (ml) not normalized (free): 14732.859734 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1344 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1388 0.1387 0.1483 n_refl.: 191128 remove outliers: r(all,work,free)=0.1388 0.1387 0.1483 n_refl.: 191128 overall B=-0.01 to atoms: r(all,work,free)=0.1387 0.1386 0.1483 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1337 n_refl.: 191128 remove outliers: r(all,work,free)=0.1193 0.1190 0.1337 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 0.3718 356.351 325.062 0.361 0.935 0.110 13.296-10.522 97.03 97 1 0.2427 481.513 459.845 0.700 0.936 0.109 10.503-8.327 97.80 175 3 0.2249 502.241 494.194 0.887 0.936 0.106 8.318-6.595 100.00 360 8 0.2194 375.794 369.480 0.915 0.936 0.090 6.588-5.215 100.00 711 7 0.1930 345.317 334.504 0.912 0.936 0.090 5.214-4.128 98.38 1367 28 0.1214 505.094 499.140 1.008 0.936 0.060 4.126-3.266 94.74 2603 46 0.1157 460.421 452.281 1.071 0.936 0.000 3.266-2.585 99.86 5447 97 0.1106 310.589 306.908 1.058 0.935 0.000 2.585-2.046 97.45 10613 204 0.0952 234.321 231.723 1.072 0.935 0.000 2.046-1.619 99.39 21536 464 0.0913 138.683 137.252 1.096 0.934 0.000 1.619-1.281 98.00 42464 925 0.0953 74.659 73.991 1.097 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.051 38.341 1.081 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0143 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1337 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1337 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1337 | n_water=891 | time (s): 3.300 (total time: 3.300) Filter (dist) r_work=0.1190 r_free=0.1337 | n_water=891 | time (s): 120.860 (total time: 124.160) Filter (q & B) r_work=0.1191 r_free=0.1337 | n_water=878 | time (s): 4.850 (total time: 129.010) Compute maps r_work=0.1191 r_free=0.1337 | n_water=878 | time (s): 2.350 (total time: 131.360) Filter (map) r_work=0.1213 r_free=0.1344 | n_water=765 | time (s): 5.030 (total time: 136.390) Find peaks r_work=0.1213 r_free=0.1344 | n_water=765 | time (s): 0.610 (total time: 137.000) Add new water r_work=0.1221 r_free=0.1353 | n_water=980 | time (s): 4.670 (total time: 141.670) Refine new water occ: r_work=0.1188 r_free=0.1328 adp: r_work=0.1188 r_free=0.1327 occ: r_work=0.1186 r_free=0.1326 adp: r_work=0.1186 r_free=0.1326 occ: r_work=0.1184 r_free=0.1324 adp: r_work=0.1184 r_free=0.1324 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1324 r_work=0.1184 r_free=0.1324 | n_water=980 | time (s): 228.940 (total time: 370.610) Filter (q & B) r_work=0.1188 r_free=0.1333 | n_water=903 | time (s): 4.610 (total time: 375.220) Filter (dist only) r_work=0.1188 r_free=0.1332 | n_water=902 | time (s): 114.340 (total time: 489.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.509522 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.000089 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 0.1190 0.1340 0.0150 0.037 1.1 7.5 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.40 1.50 1.740 14.014 14.000 3.758 11.92 13.41 1.49 1.834 13.978 14.000 3.756 Individual atomic B min max mean iso aniso Overall: 5.61 65.94 14.83 0.89 536 3270 Protein: 5.61 28.92 10.50 0.89 0 2902 Water: 6.00 65.94 28.75 N/A 536 366 Other: 13.90 23.24 18.57 N/A 0 2 Chain A: 5.68 51.02 12.38 N/A 0 1624 Chain B: 5.61 65.94 12.19 N/A 0 1646 Chain S: 6.00 60.74 30.36 N/A 536 0 Histogram: Values Number of atoms 5.61 - 11.65 2116 11.65 - 17.68 780 17.68 - 23.71 282 23.71 - 29.74 220 29.74 - 35.77 178 35.77 - 41.81 136 41.81 - 47.84 60 47.84 - 53.87 28 53.87 - 59.90 4 59.90 - 65.94 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1341 r_work=0.1192 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1342 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1340 target_work(ml) = 3.755 | | 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= 0.1190 r_free= 0.1340 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755141 | | target function (ml) not normalized (work): 703289.020630 | | target function (ml) not normalized (free): 14722.180344 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1340 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1487 n_refl.: 191128 remove outliers: r(all,work,free)=0.1391 0.1390 0.1487 n_refl.: 191128 overall B=-0.01 to atoms: r(all,work,free)=0.1389 0.1387 0.1485 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1340 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1340 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 0.3733 356.351 324.895 0.329 1.011 0.100 13.296-10.522 97.03 97 1 0.2430 481.513 461.089 0.648 1.012 0.115 10.503-8.327 97.80 175 3 0.2211 502.241 494.686 0.819 1.013 0.122 8.318-6.595 100.00 360 8 0.2181 375.794 369.889 0.845 1.012 0.096 6.588-5.215 100.00 711 7 0.1937 345.317 334.684 0.844 1.012 0.077 5.214-4.128 98.38 1367 28 0.1220 505.094 499.159 0.933 1.013 0.060 4.126-3.266 94.74 2603 46 0.1160 460.421 452.207 0.991 1.013 0.000 3.266-2.585 99.86 5447 97 0.1108 310.589 306.911 0.979 1.012 0.000 2.585-2.046 97.45 10613 204 0.0954 234.321 231.739 0.991 1.012 0.000 2.046-1.619 99.39 21536 464 0.0913 138.683 137.282 1.014 1.011 0.000 1.619-1.281 98.00 42464 925 0.0948 74.659 73.999 1.015 1.010 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.051 38.334 1.002 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0393 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1340 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1340 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1340 | n_water=902 | time (s): 3.290 (total time: 3.290) Filter (dist) r_work=0.1189 r_free=0.1340 | n_water=901 | time (s): 126.900 (total time: 130.190) Filter (q & B) r_work=0.1190 r_free=0.1339 | n_water=890 | time (s): 4.290 (total time: 134.480) Compute maps r_work=0.1190 r_free=0.1339 | n_water=890 | time (s): 2.240 (total time: 136.720) Filter (map) r_work=0.1212 r_free=0.1347 | n_water=776 | time (s): 5.430 (total time: 142.150) Find peaks r_work=0.1212 r_free=0.1347 | n_water=776 | time (s): 0.660 (total time: 142.810) Add new water r_work=0.1220 r_free=0.1356 | n_water=984 | time (s): 4.050 (total time: 146.860) Refine new water occ: r_work=0.1188 r_free=0.1326 adp: r_work=0.1188 r_free=0.1327 occ: r_work=0.1186 r_free=0.1325 adp: r_work=0.1186 r_free=0.1326 occ: r_work=0.1185 r_free=0.1325 adp: r_work=0.1184 r_free=0.1326 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1326 r_work=0.1184 r_free=0.1326 | n_water=984 | time (s): 315.230 (total time: 462.090) Filter (q & B) r_work=0.1188 r_free=0.1330 | n_water=913 | time (s): 4.680 (total time: 466.770) Filter (dist only) r_work=0.1189 r_free=0.1329 | n_water=911 | time (s): 116.480 (total time: 583.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.476887 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.425419 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1337 0.0145 0.037 1.1 5.8 0.0 0.3 0 0.738 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.37 1.45 1.714 13.961 14.425 3.756 11.91 13.38 1.48 1.745 13.947 14.425 3.753 Individual atomic B min max mean iso aniso Overall: 5.66 64.85 14.84 0.88 545 3270 Protein: 5.66 28.63 10.49 0.88 0 2902 Water: 6.05 64.85 28.71 N/A 545 366 Other: 13.92 22.26 18.09 N/A 0 2 Chain A: 5.71 50.68 12.33 N/A 0 1624 Chain B: 5.66 64.85 12.15 N/A 0 1646 Chain S: 6.05 60.61 30.45 N/A 545 0 Histogram: Values Number of atoms 5.66 - 11.58 2098 11.58 - 17.50 798 17.50 - 23.42 274 23.42 - 29.34 218 29.34 - 35.26 186 35.26 - 41.17 129 41.17 - 47.09 73 47.09 - 53.01 32 53.01 - 58.93 5 58.93 - 64.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1339 r_work=0.1191 r_free=0.1339 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1339 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1337 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1337 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752621 | | target function (ml) not normalized (work): 702817.175812 | | target function (ml) not normalized (free): 14715.255835 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1337 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1398 0.1397 0.1493 n_refl.: 191128 remove outliers: r(all,work,free)=0.1398 0.1397 0.1493 n_refl.: 191128 overall B=-0.02 to atoms: r(all,work,free)=0.1394 0.1393 0.1490 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1336 n_refl.: 191128 remove outliers: r(all,work,free)=0.1191 0.1188 0.1336 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3719 356.351 326.447 0.320 1.011 0.080 13.296-10.522 97.03 97 1 0.2426 481.513 461.849 0.642 1.012 0.100 10.503-8.327 97.80 175 3 0.2229 502.241 493.865 0.818 1.013 0.102 8.318-6.595 100.00 360 8 0.2166 375.794 370.238 0.844 1.012 0.090 6.588-5.215 100.00 711 7 0.1970 345.317 334.602 0.843 1.012 0.080 5.214-4.128 98.38 1367 28 0.1229 505.094 499.257 0.933 1.013 0.070 4.126-3.266 94.74 2603 46 0.1162 460.421 452.056 0.991 1.013 0.000 3.266-2.585 99.86 5447 97 0.1116 310.589 306.883 0.979 1.012 0.000 2.585-2.046 97.45 10613 204 0.0954 234.321 231.769 0.991 1.012 0.000 2.046-1.619 99.39 21536 464 0.0909 138.683 137.278 1.014 1.012 0.000 1.619-1.281 98.00 42464 925 0.0940 74.659 74.008 1.016 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.051 38.326 1.003 1.010 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0559 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1336 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1336 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1336 | n_water=911 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1188 r_free=0.1336 | n_water=911 | time (s): 111.540 (total time: 114.130) Filter (q & B) r_work=0.1189 r_free=0.1335 | n_water=897 | time (s): 5.590 (total time: 119.720) Compute maps r_work=0.1189 r_free=0.1335 | n_water=897 | time (s): 2.240 (total time: 121.960) Filter (map) r_work=0.1211 r_free=0.1348 | n_water=785 | time (s): 5.870 (total time: 127.830) Find peaks r_work=0.1211 r_free=0.1348 | n_water=785 | time (s): 0.630 (total time: 128.460) Add new water r_work=0.1218 r_free=0.1356 | n_water=990 | time (s): 4.920 (total time: 133.380) Refine new water occ: r_work=0.1186 r_free=0.1321 adp: r_work=0.1186 r_free=0.1321 occ: r_work=0.1184 r_free=0.1320 adp: r_work=0.1184 r_free=0.1320 occ: r_work=0.1182 r_free=0.1318 adp: r_work=0.1182 r_free=0.1320 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1320 r_work=0.1182 r_free=0.1320 | n_water=990 | time (s): 206.630 (total time: 340.010) Filter (q & B) r_work=0.1186 r_free=0.1327 | n_water=920 | time (s): 4.480 (total time: 344.490) Filter (dist only) r_work=0.1187 r_free=0.1327 | n_water=918 | time (s): 118.270 (total time: 462.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.526621 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.049719 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1336 0.0148 0.038 1.1 6.3 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.36 1.48 1.705 13.930 14.050 3.754 11.90 13.38 1.49 1.723 13.924 14.050 3.753 Individual atomic B min max mean iso aniso Overall: 5.67 63.95 14.83 0.86 552 3270 Protein: 5.67 28.19 10.47 0.86 0 2902 Water: 6.18 63.95 28.58 N/A 552 366 Other: 13.92 22.45 18.19 N/A 0 2 Chain A: 5.72 50.46 12.28 N/A 0 1624 Chain B: 5.67 63.95 12.12 N/A 0 1646 Chain S: 6.18 60.45 30.38 N/A 552 0 Histogram: Values Number of atoms 5.67 - 11.50 2071 11.50 - 17.33 821 17.33 - 23.15 274 23.15 - 28.98 218 28.98 - 34.81 187 34.81 - 40.64 133 40.64 - 46.46 78 46.46 - 52.29 29 52.29 - 58.12 9 58.12 - 63.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1338 r_work=0.1190 r_free=0.1339 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1339 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1336 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1336 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752379 | | target function (ml) not normalized (work): 702771.743034 | | target function (ml) not normalized (free): 14716.347572 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1336 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1402 0.1400 0.1505 n_refl.: 191128 remove outliers: r(all,work,free)=0.1402 0.1400 0.1505 n_refl.: 191128 overall B=-0.03 to atoms: r(all,work,free)=0.1397 0.1395 0.1501 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1188 0.1335 n_refl.: 191128 remove outliers: r(all,work,free)=0.1190 0.1188 0.1335 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 0.3744 356.351 325.406 0.319 1.010 0.080 13.296-10.522 97.03 97 1 0.2424 481.513 461.768 0.646 1.012 0.110 10.503-8.327 97.80 175 3 0.2205 502.241 494.819 0.819 1.012 0.110 8.318-6.595 100.00 360 8 0.2171 375.794 370.512 0.844 1.012 0.094 6.588-5.215 100.00 711 7 0.1952 345.317 334.608 0.843 1.012 0.079 5.214-4.128 98.38 1367 28 0.1220 505.094 499.250 0.933 1.012 0.070 4.126-3.266 94.74 2603 46 0.1162 460.421 452.031 0.992 1.013 0.000 3.266-2.585 99.86 5447 97 0.1115 310.589 306.978 0.980 1.012 0.000 2.585-2.046 97.45 10613 204 0.0957 234.321 231.765 0.991 1.013 0.000 2.046-1.619 99.39 21536 464 0.0909 138.683 137.278 1.014 1.013 0.000 1.619-1.281 98.00 42464 925 0.0940 74.659 74.007 1.016 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.051 38.318 1.004 1.014 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0699 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1188 r_free=0.1335 After: r_work=0.1188 r_free=0.1336 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1336 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1336 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1336 | n_water=918 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1188 r_free=0.1336 | n_water=918 | time (s): 119.110 (total time: 122.240) Filter (q & B) r_work=0.1189 r_free=0.1336 | n_water=908 | time (s): 5.540 (total time: 127.780) Compute maps r_work=0.1189 r_free=0.1336 | n_water=908 | time (s): 1.790 (total time: 129.570) Filter (map) r_work=0.1207 r_free=0.1345 | n_water=813 | time (s): 4.530 (total time: 134.100) Find peaks r_work=0.1207 r_free=0.1345 | n_water=813 | time (s): 0.530 (total time: 134.630) Add new water r_work=0.1214 r_free=0.1352 | n_water=999 | time (s): 4.170 (total time: 138.800) Refine new water occ: r_work=0.1186 r_free=0.1326 adp: r_work=0.1186 r_free=0.1327 occ: r_work=0.1184 r_free=0.1326 adp: r_work=0.1184 r_free=0.1327 occ: r_work=0.1182 r_free=0.1326 adp: r_work=0.1182 r_free=0.1326 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1326 r_work=0.1182 r_free=0.1326 | n_water=999 | time (s): 272.950 (total time: 411.750) Filter (q & B) r_work=0.1186 r_free=0.1333 | n_water=926 | time (s): 4.390 (total time: 416.140) Filter (dist only) r_work=0.1187 r_free=0.1333 | n_water=924 | time (s): 122.960 (total time: 539.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507260 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.014328 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1336 0.0147 0.038 1.2 7.3 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.36 1.47 1.695 13.872 14.014 3.754 11.90 13.38 1.49 1.702 13.878 14.014 3.753 Individual atomic B min max mean iso aniso Overall: 5.67 62.86 14.77 0.86 558 3270 Protein: 5.67 28.05 10.46 0.86 0 2902 Water: 6.11 62.86 28.30 N/A 558 366 Other: 13.94 22.42 18.18 N/A 0 2 Chain A: 5.74 50.33 12.25 N/A 0 1624 Chain B: 5.67 62.86 12.08 N/A 0 1646 Chain S: 6.11 60.27 30.03 N/A 558 0 Histogram: Values Number of atoms 5.67 - 11.39 2053 11.39 - 17.11 829 17.11 - 22.83 279 22.83 - 28.55 222 28.55 - 34.27 191 34.27 - 39.98 123 39.98 - 45.70 86 45.70 - 51.42 33 51.42 - 57.14 9 57.14 - 62.86 3 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1338 r_work=0.1190 r_free=0.1338 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1338 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1338 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1338 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753447 | | target function (ml) not normalized (work): 702971.845017 | | target function (ml) not normalized (free): 14721.957036 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1353 0.1408 5.6832 5.7513| | 2: 2.94 - 2.33 1.00 7339 128 0.1062 0.1351 5.0654 5.1695| | 3: 2.33 - 2.04 0.96 6939 150 0.0903 0.1127 4.6524 4.7129| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1057 4.39 4.5683| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.0976 4.1498 4.2395| | 6: 1.72 - 1.62 0.99 7102 142 0.0899 0.1092 3.9485 4.0846| | 7: 1.62 - 1.54 0.99 7104 148 0.0883 0.0950 3.7986 3.9289| | 8: 1.54 - 1.47 0.96 6798 152 0.0889 0.1292 3.6997 3.8973| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1120 3.6199 3.7582| | 10: 1.41 - 1.36 0.99 7022 150 0.0977 0.1190 3.5566 3.6791| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1135 3.4857 3.5881| | 12: 1.32 - 1.28 0.98 6975 149 0.1027 0.1124 3.4581 3.5761| | 13: 1.28 - 1.25 0.98 6907 166 0.1033 0.1239 3.4332 3.5612| | 14: 1.25 - 1.22 0.98 7015 112 0.1099 0.1572 3.4325 3.6845| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1239 3.4492 3.4926| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1559 3.4671 3.6662| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1228 3.4349 3.4433| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1715 3.4397 3.537| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1750 3.4203 3.5967| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1582 3.4116 3.4368| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2133 3.4184 3.5035| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1950 3.4136 3.4141| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2017 3.4332 3.4849| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2239 3.4362 3.5064| | 25: 1.02 - 1.01 0.93 6552 130 0.2608 0.2526 3.4498 3.5242| | 26: 1.01 - 0.99 0.96 6767 158 0.2753 0.2846 3.4165 3.4244| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2797 3.4696 3.3966| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.36 1.00 0.97 10752.91| | 2: 2.94 - 2.33 7339 128 0.93 12.47 0.99 0.97 4935.36| | 3: 2.33 - 2.04 6939 150 0.96 7.46 1.01 0.97 1651.25| | 4: 2.04 - 1.85 7170 155 0.96 7.57 1.00 0.97 994.56| | 5: 1.85 - 1.72 7113 159 0.96 8.04 1.00 0.97 631.61| | 6: 1.72 - 1.62 7102 142 0.96 8.01 1.00 0.98 444.13| | 7: 1.62 - 1.54 7104 148 0.96 8.09 1.01 0.99 336.45| | 8: 1.54 - 1.47 6798 152 0.96 8.25 1.00 0.98 278.29| | 9: 1.47 - 1.41 6938 155 0.96 8.48 1.00 0.99 231.17| | 10: 1.41 - 1.36 7022 150 0.96 8.92 1.00 0.99 202.62| | 11: 1.36 - 1.32 6997 151 0.96 8.94 0.99 0.98 174.96| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.99 0.97 160.13| | 13: 1.28 - 1.25 6907 166 0.96 9.42 1.00 0.97 157.51| | 14: 1.25 - 1.22 7015 112 0.95 10.69 1.00 0.98 163.41| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.00 0.98 167.54| | 16: 1.19 - 1.17 6604 132 0.95 11.51 1.00 0.97 161.90| | 17: 1.17 - 1.14 6940 135 0.94 12.30 1.01 0.97 155.03| | 18: 1.14 - 1.12 6875 142 0.94 12.80 1.01 0.96 148.67| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.96 151.83| | 20: 1.10 - 1.08 6884 147 0.92 15.24 1.00 0.96 150.83| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.95 153.49| | 22: 1.07 - 1.05 6836 135 0.89 18.26 1.00 0.95 154.73| | 23: 1.05 - 1.03 6827 159 0.87 20.43 1.00 0.94 164.13| | 24: 1.03 - 1.02 6784 133 0.85 23.09 1.00 0.95 178.44| | 25: 1.02 - 1.01 6552 130 0.83 25.10 0.99 0.92 181.70| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.99 0.91 176.75| | 27: 0.99 - 0.98 6647 131 0.82 26.34 1.00 0.90 161.66| |alpha: min = 0.90 max = 0.99 mean = 0.96| |beta: min = 148.67 max = 10752.91 mean = 898.07| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.25| |phase err.(test): min = 0.00 max = 89.07 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1338 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1513 n_refl.: 191128 remove outliers: r(all,work,free)=0.1406 0.1404 0.1513 n_refl.: 191128 overall B=-0.17 to atoms: r(all,work,free)=0.1379 0.1377 0.1491 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1337 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1337 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 0.3754 356.351 325.954 0.319 0.986 0.070 13.296-10.522 97.03 97 1 0.2455 481.513 460.496 0.651 0.987 0.104 10.503-8.327 97.80 175 3 0.2202 502.241 495.450 0.827 0.988 0.104 8.318-6.595 100.00 360 8 0.2163 375.794 370.953 0.852 0.988 0.086 6.588-5.215 100.00 711 7 0.1967 345.317 334.702 0.852 0.988 0.070 5.214-4.128 98.38 1367 28 0.1225 505.094 499.307 0.942 0.989 0.050 4.126-3.266 94.74 2603 46 0.1158 460.421 452.201 1.002 0.991 0.000 3.266-2.585 99.86 5447 97 0.1112 310.589 307.047 0.986 0.992 0.000 2.585-2.046 97.45 10613 204 0.0957 234.321 231.805 0.992 0.995 0.000 2.046-1.619 99.39 21536 464 0.0911 138.683 137.305 1.007 0.999 0.000 1.619-1.281 98.00 42464 925 0.0943 74.659 74.008 0.996 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.051 38.315 0.963 1.019 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0363 ================= 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 : 0.2037 0.1977 0.080 5.224 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1909 0.080 5.224 5.2 78.0 14.6 805 0.000 1_settarget: 0.1804 0.1909 0.080 5.224 5.2 78.0 14.6 805 0.000 1_nqh: 0.1804 0.1909 0.080 5.224 5.2 78.0 14.6 805 0.000 1_weight: 0.1804 0.1909 0.080 5.224 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1267 0.1473 0.034 1.152 5.2 78.0 14.6 805 0.140 1_adp: 0.1301 0.1545 0.034 1.152 5.2 73.0 15.0 805 0.140 1_regHadp: 0.1300 0.1541 0.034 1.152 5.2 73.0 15.0 805 0.140 1_occ: 0.1285 0.1528 0.034 1.152 5.2 73.0 15.0 805 0.140 2_bss: 0.1276 0.1518 0.034 1.152 5.4 73.2 15.2 805 0.140 2_settarget: 0.1276 0.1518 0.034 1.152 5.4 73.2 15.2 805 0.140 2_updatecdl: 0.1276 0.1518 0.034 1.174 5.4 73.2 15.2 805 0.140 2_nqh: 0.1276 0.1518 0.034 1.174 5.4 73.2 15.2 805 0.140 2_sol: 0.1267 0.1489 0.034 1.174 5.4 73.2 16.3 905 n/a 2_weight: 0.1267 0.1489 0.034 1.174 5.4 73.2 16.3 905 n/a 2_xyzrec: 0.1253 0.1511 0.038 1.143 5.4 73.2 16.3 905 n/a 2_adp: 0.1231 0.1500 0.038 1.143 5.4 68.4 16.4 905 n/a 2_regHadp: 0.1231 0.1501 0.038 1.143 5.4 68.4 16.4 905 n/a 2_occ: 0.1225 0.1498 0.038 1.143 5.4 68.4 16.4 905 n/a 3_bss: 0.1232 0.1506 0.038 1.143 5.4 68.4 16.4 905 n/a 3_settarget: 0.1232 0.1506 0.038 1.143 5.4 68.4 16.4 905 n/a 3_updatecdl: 0.1232 0.1506 0.038 1.150 5.4 68.4 16.4 905 n/a 3_nqh: 0.1232 0.1506 0.038 1.150 5.4 68.4 16.4 905 n/a 3_sol: 0.1248 0.1504 0.038 1.150 5.4 68.4 15.5 882 n/a 3_weight: 0.1248 0.1504 0.038 1.150 5.4 68.4 15.5 882 n/a 3_xyzrec: 0.1240 0.1439 0.034 1.094 5.4 68.4 15.5 882 n/a 3_adp: 0.1231 0.1396 0.034 1.094 5.5 68.1 15.3 882 n/a 3_regHadp: 0.1232 0.1397 0.034 1.094 5.5 68.1 15.3 882 n/a 3_occ: 0.1227 0.1392 0.034 1.094 5.5 68.1 15.3 882 n/a 4_bss: 0.1223 0.1384 0.034 1.094 5.5 68.0 15.3 882 n/a 4_settarget: 0.1223 0.1384 0.034 1.094 5.5 68.0 15.3 882 n/a 4_updatecdl: 0.1223 0.1384 0.034 1.091 5.5 68.0 15.3 882 n/a 4_nqh: 0.1223 0.1384 0.034 1.091 5.5 68.0 15.3 882 n/a 4_sol: 0.1207 0.1359 0.034 1.091 5.5 68.0 15.1 876 n/a 4_weight: 0.1207 0.1359 0.034 1.091 5.5 68.0 15.1 876 n/a 4_xyzrec: 0.1205 0.1357 0.035 1.115 5.5 68.0 15.1 876 n/a 4_adp: 0.1200 0.1355 0.035 1.115 5.5 67.7 15.0 876 n/a 4_regHadp: 0.1200 0.1355 0.035 1.115 5.5 67.7 15.0 876 n/a 4_occ: 0.1197 0.1355 0.035 1.115 5.5 67.7 15.0 876 n/a 5_bss: 0.1191 0.1344 0.035 1.115 5.5 67.6 15.0 876 n/a 5_settarget: 0.1191 0.1344 0.035 1.115 5.5 67.6 15.0 876 n/a 5_updatecdl: 0.1191 0.1344 0.035 1.115 5.5 67.6 15.0 876 n/a 5_nqh: 0.1191 0.1344 0.035 1.115 5.5 67.6 15.0 876 n/a 5_sol: 0.1191 0.1336 0.035 1.115 5.5 67.6 15.0 884 n/a 5_weight: 0.1191 0.1336 0.035 1.115 5.5 67.6 15.0 884 n/a 5_xyzrec: 0.1194 0.1350 0.036 1.120 5.5 67.6 15.0 884 n/a 5_adp: 0.1199 0.1353 0.036 1.120 5.5 67.1 14.9 884 n/a 5_regHadp: 0.1200 0.1353 0.036 1.120 5.5 67.1 14.9 884 n/a 5_occ: 0.1197 0.1353 0.036 1.120 5.5 67.1 14.9 884 n/a 6_bss: 0.1197 0.1351 0.036 1.120 5.5 67.1 14.9 884 n/a 6_settarget: 0.1197 0.1351 0.036 1.120 5.5 67.1 14.9 884 n/a 6_updatecdl: 0.1197 0.1351 0.036 1.120 5.5 67.1 14.9 884 n/a 6_nqh: 0.1197 0.1351 0.036 1.120 5.5 67.1 14.9 884 n/a 6_sol: 0.1196 0.1342 0.036 1.120 5.5 67.1 14.9 891 n/a 6_weight: 0.1196 0.1342 0.036 1.120 5.5 67.1 14.9 891 n/a 6_xyzrec: 0.1198 0.1344 0.036 1.124 5.5 67.1 14.9 891 n/a 6_adp: 0.1199 0.1346 0.036 1.124 5.6 66.9 14.9 891 n/a 6_regHadp: 0.1199 0.1346 0.036 1.124 5.6 66.9 14.9 891 n/a 6_occ: 0.1197 0.1345 0.036 1.124 5.6 66.9 14.9 891 n/a 7_bss: 0.1190 0.1337 0.036 1.124 5.6 66.9 14.9 891 n/a 7_settarget: 0.1190 0.1337 0.036 1.124 5.6 66.9 14.9 891 n/a 7_updatecdl: 0.1190 0.1337 0.036 1.125 5.6 66.9 14.9 891 n/a 7_nqh: 0.1190 0.1337 0.036 1.125 5.6 66.9 14.9 891 n/a 7_sol: 0.1188 0.1332 0.036 1.125 5.6 66.9 14.9 902 n/a 7_weight: 0.1188 0.1332 0.036 1.125 5.6 66.9 14.9 902 n/a 7_xyzrec: 0.1190 0.1340 0.037 1.116 5.6 66.9 14.9 902 n/a 7_adp: 0.1192 0.1341 0.037 1.116 5.6 65.9 14.8 902 n/a 7_regHadp: 0.1192 0.1342 0.037 1.116 5.6 65.9 14.8 902 n/a 7_occ: 0.1190 0.1340 0.037 1.116 5.6 65.9 14.8 902 n/a 8_bss: 0.1189 0.1340 0.037 1.116 5.6 65.9 14.8 902 n/a 8_settarget: 0.1189 0.1340 0.037 1.116 5.6 65.9 14.8 902 n/a 8_updatecdl: 0.1189 0.1340 0.037 1.116 5.6 65.9 14.8 902 n/a 8_nqh: 0.1189 0.1340 0.037 1.116 5.6 65.9 14.8 902 n/a 8_sol: 0.1189 0.1329 0.037 1.116 5.6 65.9 14.9 911 n/a 8_weight: 0.1189 0.1329 0.037 1.116 5.6 65.9 14.9 911 n/a 8_xyzrec: 0.1192 0.1337 0.037 1.114 5.6 65.9 14.9 911 n/a 8_adp: 0.1191 0.1339 0.037 1.114 5.7 64.9 14.8 911 n/a 8_regHadp: 0.1191 0.1339 0.037 1.114 5.7 64.9 14.8 911 n/a 8_occ: 0.1189 0.1337 0.037 1.114 5.7 64.9 14.8 911 n/a 9_bss: 0.1188 0.1336 0.037 1.114 5.6 64.8 14.8 911 n/a 9_settarget: 0.1188 0.1336 0.037 1.114 5.6 64.8 14.8 911 n/a 9_updatecdl: 0.1188 0.1336 0.037 1.114 5.6 64.8 14.8 911 n/a 9_nqh: 0.1188 0.1336 0.037 1.114 5.6 64.8 14.8 911 n/a 9_sol: 0.1187 0.1327 0.037 1.114 5.6 64.8 14.8 918 n/a 9_weight: 0.1187 0.1327 0.037 1.114 5.6 64.8 14.8 918 n/a 9_xyzrec: 0.1189 0.1336 0.038 1.122 5.6 64.8 14.8 918 n/a 9_adp: 0.1190 0.1338 0.038 1.122 5.7 63.9 14.8 918 n/a 9_regHadp: 0.1190 0.1339 0.038 1.122 5.7 63.9 14.8 918 n/a 9_occ: 0.1188 0.1336 0.038 1.122 5.7 63.9 14.8 918 n/a 10_bss: 0.1188 0.1335 0.038 1.122 5.6 63.9 14.8 918 n/a 10_settarget: 0.1188 0.1335 0.038 1.122 5.6 63.9 14.8 918 n/a 10_updatecdl: 0.1188 0.1335 0.038 1.121 5.6 63.9 14.8 918 n/a 10_setrh: 0.1188 0.1336 0.038 1.121 5.6 63.9 14.8 918 n/a 10_nqh: 0.1188 0.1336 0.038 1.121 5.6 63.9 14.8 918 n/a 10_sol: 0.1187 0.1333 0.038 1.121 5.6 63.9 14.8 924 n/a 10_weight: 0.1187 0.1333 0.038 1.121 5.6 63.9 14.8 924 n/a 10_xyzrec: 0.1189 0.1336 0.038 1.152 5.6 63.9 14.8 924 n/a 10_adp: 0.1190 0.1338 0.038 1.152 5.7 62.9 14.8 924 n/a 10_regHadp: 0.1190 0.1338 0.038 1.152 5.7 62.9 14.8 924 n/a 10_occ: 0.1189 0.1338 0.038 1.152 5.7 62.9 14.8 924 n/a end: 0.1189 0.1338 0.038 1.152 5.5 62.7 14.6 924 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2614032_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2614032_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0000 Refinement macro-cycles (run) : 12189.8400 Write final files (write_after_run_outputs) : 150.3200 Total : 12347.1600 Total CPU time: 3.44 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:06 PST -0800 (1736736186.57 s) Start R-work = 0.1804, R-free = 0.1909 Final R-work = 0.1189, R-free = 0.1338 =============================================================================== Job complete usr+sys time: 12615.52 seconds wall clock time: 211 minutes 20.61 seconds (12680.61 seconds total)