Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8729823.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8729823.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8729823.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.90, per 1000 atoms: 0.28 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: 2.785 distance_ideal: 2.720 ideal - model: -0.065 slack: 0.000 delta_slack: -0.065 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: 2.737 distance_ideal: 2.710 ideal - model: -0.027 slack: 0.000 delta_slack: -0.027 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 138.9 milliseconds Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.03: 864 1.03 - 1.25: 2434 1.25 - 1.47: 1395 1.47 - 1.69: 1200 1.69 - 1.91: 41 Bond restraints: 5934 Sorted by residual: bond pdb=" CA GLU B 17 " pdb=" C GLU B 17 " ideal model delta sigma weight residual 1.524 1.780 -0.256 1.28e-02 6.10e+03 3.99e+02 bond pdb=" C ALA A 189 " pdb=" O ALA A 189 " ideal model delta sigma weight residual 1.234 0.997 0.238 1.20e-02 6.94e+03 3.92e+02 bond pdb=" CA ALA A 148 " pdb=" C ALA A 148 " ideal model delta sigma weight residual 1.523 1.773 -0.250 1.30e-02 5.92e+03 3.70e+02 bond pdb=" CD2 LEU B 185 " pdb="HD22 LEU B 185 " ideal model delta sigma weight residual 0.970 1.352 -0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" CD1 TYR A 194 " pdb=" HD1 TYR A 194 " ideal model delta sigma weight residual 0.930 1.299 -0.369 2.00e-02 2.50e+03 3.41e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.25: 5796 4.25 - 8.50: 3542 8.50 - 12.76: 1217 12.76 - 17.01: 233 17.01 - 21.26: 22 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O GLU B 17 " pdb=" C GLU B 17 " pdb=" N ALA B 18 " ideal model delta sigma weight residual 122.08 141.00 -18.92 1.07e+00 8.73e-01 3.13e+02 angle pdb=" O GLY B 78 " pdb=" C GLY B 78 " pdb=" N ALA B 79 " ideal model delta sigma weight residual 122.18 136.59 -14.41 9.60e-01 1.09e+00 2.25e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" O ALA A 103 " ideal model delta sigma weight residual 120.30 105.52 14.78 1.07e+00 8.73e-01 1.91e+02 angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.51 127.69 -8.18 6.20e-01 2.60e+00 1.74e+02 angle pdb=" O LYS A 52 " pdb=" C LYS A 52 " pdb=" N LEU A 53 " ideal model delta sigma weight residual 123.22 137.84 -14.62 1.14e+00 7.69e-01 1.65e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 1821 16.21 - 32.41: 155 32.41 - 48.62: 48 48.62 - 64.83: 21 64.83 - 81.03: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: 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 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 156.47 23.53 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.219: 201 0.219 - 0.437: 164 0.437 - 0.654: 90 0.654 - 0.871: 28 0.871 - 1.089: 9 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 92 " pdb=" N VAL A 92 " pdb=" C VAL A 92 " pdb=" CB VAL A 92 " both_signs ideal model delta sigma weight residual False 2.44 3.53 -1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA VAL B 89 " pdb=" N VAL B 89 " pdb=" C VAL B 89 " pdb=" CB VAL B 89 " both_signs ideal model delta sigma weight residual False 2.44 3.39 -0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" CA VAL B 69 " pdb=" N VAL B 69 " pdb=" C VAL B 69 " pdb=" CB VAL B 69 " both_signs ideal model delta sigma weight residual False 2.44 3.37 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.044 2.00e-02 2.50e+03 6.59e-02 1.74e+02 pdb=" CG TRP A 146 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.111 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.060 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.048 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.104 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.113 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.048 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.036 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.081 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.021 2.00e-02 2.50e+03 6.33e-02 1.60e+02 pdb=" CG TRP A 139 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.071 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.095 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.046 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " 0.109 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.033 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.092 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.049 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.009 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.013 2.00e-02 2.50e+03 5.92e-02 1.40e+02 pdb=" CG TRP B 139 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.052 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.034 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.092 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.114 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.127 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " -0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.070 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.025 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.055 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 23 1.60 - 2.35: 2251 2.35 - 3.10: 22177 3.10 - 3.85: 32969 3.85 - 4.60: 52876 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110296 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.849 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.898 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.067 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.141 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.166 2.620 ... (remaining 110291 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_8729823_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= 0.2032 r_free= 0.2003 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.300533 | | target function (ml) not normalized (work): 805545.786096 | | target function (ml) not normalized (free): 16570.631177 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2018 6.6673 6.3379| | 2: 2.94 - 2.33 1.00 7339 128 0.1605 0.1699 5.549 5.6003| | 3: 2.33 - 2.04 0.96 6939 150 0.1641 0.1574 5.1408 5.1346| | 4: 2.04 - 1.85 1.00 7170 155 0.1769 0.1551 4.9713 5.0035| | 5: 1.85 - 1.72 0.99 7113 159 0.1907 0.1844 4.7959 4.8556| | 6: 1.72 - 1.62 0.99 7102 142 0.1958 0.2140 4.6657 4.7851| | 7: 1.62 - 1.54 0.99 7104 148 0.2018 0.1712 4.5695 4.5515| | 8: 1.54 - 1.47 0.96 6798 152 0.2060 0.2219 4.4777 4.5815| | 9: 1.47 - 1.41 0.98 6938 155 0.2116 0.2185 4.4021 4.4322| | 10: 1.41 - 1.36 0.99 7022 150 0.2099 0.2108 4.3059 4.2969| | 11: 1.36 - 1.32 0.99 6997 151 0.2091 0.2143 4.2325 4.2921| | 12: 1.32 - 1.28 0.98 6976 149 0.2102 0.2303 4.1956 4.3409| | 13: 1.28 - 1.25 0.98 6907 166 0.2032 0.2117 4.1173 4.1798| | 14: 1.25 - 1.22 0.98 7015 113 0.2055 0.2379 4.0793 4.2445| | 15: 1.22 - 1.19 0.98 6957 137 0.2065 0.2169 4.0388 4.1146| | 16: 1.19 - 1.17 0.93 6604 132 0.2109 0.2174 3.9979 4.0711| | 17: 1.17 - 1.14 0.98 6941 135 0.2150 0.1821 3.9449 3.9303| | 18: 1.14 - 1.12 0.98 6875 142 0.2187 0.2226 3.914 3.8919| | 19: 1.12 - 1.10 0.97 6949 106 0.2265 0.2369 3.869 4.0012| | 20: 1.10 - 1.08 0.97 6884 147 0.2341 0.1995 3.829 3.7507| | 21: 1.08 - 1.07 0.97 6852 152 0.2391 0.2639 3.771 3.8031| | 22: 1.07 - 1.05 0.97 6838 135 0.2607 0.2991 3.7627 3.9054| | 23: 1.05 - 1.03 0.97 6829 159 0.2700 0.2354 3.7317 3.7676| | 24: 1.03 - 1.02 0.96 6785 133 0.2888 0.2529 3.7015 3.7205| | 25: 1.02 - 1.01 0.93 6552 130 0.3040 0.3065 3.6746 3.7397| | 26: 1.01 - 0.99 0.96 6767 158 0.3230 0.3034 3.633 3.6017| | 27: 0.99 - 0.98 0.94 6648 131 0.3456 0.2939 3.664 3.569| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 21.03 0.91 0.97 37414.60| | 2: 2.94 - 2.33 7339 128 0.85 21.49 1.08 1.03 15684.10| | 3: 2.33 - 2.04 6939 150 0.93 12.35 1.11 1.06 4070.73| | 4: 2.04 - 1.85 7170 155 0.93 13.34 1.11 1.06 2724.25| | 5: 1.85 - 1.72 7113 159 0.91 15.74 1.11 1.08 2134.17| | 6: 1.72 - 1.62 7102 142 0.90 17.06 1.11 1.08 1739.99| | 7: 1.62 - 1.54 7104 148 0.89 18.04 1.11 1.08 1402.99| | 8: 1.54 - 1.47 6798 152 0.89 18.45 1.10 1.07 1166.39| | 9: 1.47 - 1.41 6938 155 0.88 19.10 1.11 1.07 996.66| | 10: 1.41 - 1.36 7022 150 0.87 20.30 1.09 1.07 886.98| | 11: 1.36 - 1.32 6997 151 0.86 21.05 1.08 1.05 799.37| | 12: 1.32 - 1.28 6976 149 0.86 21.05 1.07 1.03 718.34| | 13: 1.28 - 1.25 6907 166 0.86 21.24 1.07 1.02 668.32| | 14: 1.25 - 1.22 7015 113 0.85 21.97 1.07 1.04 635.27| | 15: 1.22 - 1.19 6957 137 0.86 21.76 1.08 1.04 583.76| | 16: 1.19 - 1.17 6604 132 0.87 20.83 1.07 1.03 502.12| | 17: 1.17 - 1.14 6941 135 0.87 20.36 1.08 1.02 417.13| | 18: 1.14 - 1.12 6875 142 0.87 20.05 1.08 0.99 360.34| | 19: 1.12 - 1.10 6949 106 0.87 20.71 1.07 0.99 338.68| | 20: 1.10 - 1.08 6884 147 0.86 21.62 1.06 0.98 319.56| | 21: 1.08 - 1.07 6852 152 0.84 23.48 1.06 0.99 329.07| | 22: 1.07 - 1.05 6838 135 0.82 25.63 1.06 0.99 332.89| | 23: 1.05 - 1.03 6829 159 0.80 27.28 1.05 0.98 327.67| | 24: 1.03 - 1.02 6785 133 0.79 28.37 1.05 0.98 311.16| | 25: 1.02 - 1.01 6552 130 0.79 28.74 1.03 0.96 286.15| | 26: 1.01 - 0.99 6767 158 0.77 30.15 1.04 0.94 263.12| | 27: 0.99 - 0.98 6648 131 0.78 29.34 1.04 0.93 234.54| |alpha: min = 0.93 max = 1.08 mean = 1.02| |beta: min = 234.54 max = 37414.60 mean = 2935.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.43| |phase err.(test): min = 0.00 max = 89.71 mean = 21.57| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.256 2950 Z= 5.488 Angle : 5.098 18.923 4018 Z= 3.593 Chirality : 0.374 1.089 492 Planarity : 0.033 0.132 512 Dihedral : 12.813 81.034 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 0.32 % Allowed : 5.48 % Favored : 94.19 % Cbeta Deviations : 29.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.38), residues: 386 helix: -2.50 (0.31), residues: 144 sheet: -1.11 (0.53), residues: 86 loop : -0.64 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.022 ARG A 143 TYR 0.100 0.036 TYR A 192 PHE 0.114 0.032 PHE B 127 TRP 0.114 0.036 TRP A 146 HIS 0.052 0.021 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= 0.2032 r_free= 0.2003 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.300533 | | target function (ml) not normalized (work): 805545.786096 | | target function (ml) not normalized (free): 16570.631177 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2030 0.2032 0.2003 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2030 0.2032 0.2003 n_refl.: 191155 remove outliers: r(all,work,free)=0.2030 0.2032 0.2003 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2030 0.2032 0.2003 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1802 0.1799 0.1940 n_refl.: 191145 remove outliers: r(all,work,free)=0.1800 0.1798 0.1940 n_refl.: 191141 ======================== 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 0.4238 400.535 295.642 0.434 0.912 0.301 13.296-10.522 100.00 100 1 0.2549 534.497 521.006 0.789 0.913 0.253 10.503-8.327 99.45 178 3 0.2530 565.118 555.951 0.974 0.913 0.230 8.318-6.595 100.00 360 8 0.2483 414.736 403.774 0.974 0.913 0.175 6.588-5.215 100.00 711 7 0.2314 381.101 365.073 0.960 0.913 0.170 5.214-4.128 98.38 1367 28 0.1519 557.435 549.915 1.077 0.914 0.090 4.126-3.266 94.74 2603 46 0.1341 508.132 499.083 1.144 0.914 0.014 3.266-2.585 99.86 5447 97 0.1431 342.774 337.265 1.119 0.913 0.000 2.585-2.046 97.45 10613 204 0.1395 258.603 254.305 1.126 0.913 0.000 2.046-1.619 99.39 21536 464 0.1613 153.054 149.942 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1925 82.395 80.142 1.128 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2310 44.203 41.669 1.113 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0002 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1798 r_free=0.1940 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 156 GLN Total number of N/Q/H flips: 2 r_work=0.1802 r_free=0.1940 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.396687 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.117435 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 0.1276 0.1508 0.0232 0.039 1.2 10.7 0.0 0.3 0 11.198 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.76 15.08 2.32 1.117 13.111 570.117 0.019 13.03 15.79 2.76 1.240 13.322 570.117 0.018 Individual atomic B min max mean iso aniso Overall: 5.17 73.04 14.98 1.40 435 3274 Protein: 5.17 40.32 10.99 1.40 0 2902 Water: 6.30 73.04 29.36 N/A 435 370 Other: 16.08 30.75 23.42 N/A 0 2 Chain A: 5.41 59.90 13.02 N/A 0 1626 Chain B: 5.17 73.04 12.74 N/A 0 1648 Chain S: 12.29 64.25 30.80 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2166 11.96 - 18.75 644 18.75 - 25.54 306 25.54 - 32.32 273 32.32 - 39.11 151 39.11 - 45.90 107 45.90 - 52.68 39 52.68 - 59.47 19 59.47 - 66.26 3 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1303 r_free=0.1579 r_work=0.1302 r_free=0.1574 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1302 r_free = 0.1574 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1287 r_free = 0.1566 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1287 r_free= 0.1566 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015703 | | target function (ls_wunit_k1) not normalized (work): 2941.148363 | | target function (ls_wunit_k1) not normalized (free): 118.544615 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1287 0.1566 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1477 0.1474 0.1641 n_refl.: 191141 remove outliers: r(all,work,free)=0.1477 0.1474 0.1641 n_refl.: 191141 overall B=0.17 to atoms: r(all,work,free)=0.1501 0.1498 0.1651 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1285 0.1279 0.1557 n_refl.: 191141 remove outliers: r(all,work,free)=0.1284 0.1279 0.1556 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3604 402.814 374.707 0.464 0.997 0.275 13.296-10.522 100.00 100 1 0.2129 534.497 527.003 0.722 0.998 0.250 10.503-8.327 99.45 178 3 0.1755 565.118 561.115 0.857 0.999 0.203 8.318-6.595 100.00 360 8 0.1706 414.736 412.026 0.879 0.998 0.160 6.588-5.215 100.00 711 7 0.1528 381.101 373.496 0.858 0.999 0.160 5.214-4.128 98.38 1367 28 0.0899 557.435 555.312 0.944 0.999 0.054 4.126-3.266 94.74 2603 46 0.0831 508.132 504.265 1.008 1.000 0.014 3.266-2.585 99.86 5447 97 0.0922 342.774 340.300 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.366 1.002 1.000 0.000 2.046-1.619 99.39 21536 464 0.1095 153.054 151.366 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1288 82.395 81.401 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1881 44.202 42.171 0.989 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0378 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1279 r_free=0.1556 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1279 r_free=0.1556 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1556 | n_water=805 | time (s): 2.960 (total time: 2.960) Filter (dist) r_work=0.1284 r_free=0.1562 | n_water=793 | time (s): 94.580 (total time: 97.540) Filter (q & B) r_work=0.1285 r_free=0.1563 | n_water=789 | time (s): 5.360 (total time: 102.900) Compute maps r_work=0.1285 r_free=0.1563 | n_water=789 | time (s): 2.520 (total time: 105.420) Filter (map) r_work=0.1312 r_free=0.1537 | n_water=644 | time (s): 5.010 (total time: 110.430) Find peaks r_work=0.1312 r_free=0.1537 | n_water=644 | time (s): 0.700 (total time: 111.130) Add new water r_work=0.1335 r_free=0.1565 | n_water=955 | time (s): 5.360 (total time: 116.490) Refine new water occ: r_work=0.1291 r_free=0.1527 adp: r_work=0.1278 r_free=0.1523 occ: r_work=0.1280 r_free=0.1523 adp: r_work=0.1274 r_free=0.1521 occ: r_work=0.1275 r_free=0.1522 adp: r_work=0.1272 r_free=0.1521 ADP+occupancy (water only), MIN, final r_work=0.1272 r_free=0.1521 r_work=0.1272 r_free=0.1521 | n_water=955 | time (s): 91.650 (total time: 208.140) Filter (q & B) r_work=0.1276 r_free=0.1524 | n_water=881 | time (s): 5.090 (total time: 213.230) Filter (dist only) r_work=0.1276 r_free=0.1523 | n_water=880 | time (s): 112.820 (total time: 326.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.606843 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 589.858774 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1259 0.1534 0.0276 0.041 1.1 18.2 0.0 0.3 0 11.803 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.59 15.34 2.76 2.037 15.192 589.859 0.015 12.34 15.16 2.82 2.421 15.235 589.859 0.014 Individual atomic B min max mean iso aniso Overall: 5.43 70.26 16.34 1.20 512 3272 Protein: 5.43 40.10 10.96 1.20 0 2902 Water: 6.63 70.26 34.08 N/A 512 368 Other: 16.32 33.39 24.85 N/A 0 2 Chain A: 5.56 56.24 12.98 N/A 0 1624 Chain B: 5.43 68.21 12.79 N/A 0 1648 Chain S: 13.21 70.26 38.44 N/A 512 0 Histogram: Values Number of atoms 5.43 - 11.91 2113 11.91 - 18.40 685 18.40 - 24.88 261 24.88 - 31.36 215 31.36 - 37.84 156 37.84 - 44.33 170 44.33 - 50.81 88 50.81 - 57.29 52 57.29 - 63.77 36 63.77 - 70.26 8 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1516 r_work=0.1235 r_free=0.1517 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1517 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1515 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1515 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013595 | | target function (ls_wunit_k1) not normalized (work): 2546.380197 | | target function (ls_wunit_k1) not normalized (free): 101.444304 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1228 0.1515 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1438 0.1435 0.1616 n_refl.: 191139 remove outliers: r(all,work,free)=0.1438 0.1435 0.1616 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1432 0.1614 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1235 0.1520 n_refl.: 191139 remove outliers: r(all,work,free)=0.1241 0.1235 0.1520 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3252 402.814 378.230 0.488 0.962 0.270 13.296-10.522 100.00 100 1 0.1909 534.497 524.387 0.763 0.963 0.213 10.503-8.327 99.45 178 3 0.1485 565.118 565.950 0.920 0.963 0.174 8.318-6.595 100.00 360 8 0.1567 414.736 414.434 0.939 0.963 0.160 6.588-5.215 100.00 711 7 0.1341 381.101 376.480 0.914 0.963 0.160 5.214-4.128 98.38 1367 28 0.0841 557.435 556.038 0.994 0.963 0.070 4.126-3.266 94.74 2603 46 0.0776 508.132 505.291 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0861 342.774 341.273 1.047 0.962 0.010 2.585-2.046 97.45 10613 204 0.0897 258.603 256.723 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.619 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.362 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.217 1.059 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0474 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1520 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1520 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1520 | n_water=880 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1237 r_free=0.1524 | n_water=874 | time (s): 113.170 (total time: 115.800) Filter (q & B) r_work=0.1237 r_free=0.1524 | n_water=872 | time (s): 4.470 (total time: 120.270) Compute maps r_work=0.1237 r_free=0.1524 | n_water=872 | time (s): 2.580 (total time: 122.850) Filter (map) r_work=0.1275 r_free=0.1528 | n_water=683 | time (s): 5.350 (total time: 128.200) Find peaks r_work=0.1275 r_free=0.1528 | n_water=683 | time (s): 0.690 (total time: 128.890) Add new water r_work=0.1299 r_free=0.1565 | n_water=1009 | time (s): 4.580 (total time: 133.470) Refine new water occ: r_work=0.1246 r_free=0.1508 adp: r_work=0.1240 r_free=0.1504 occ: r_work=0.1236 r_free=0.1500 adp: r_work=0.1236 r_free=0.1500 occ: r_work=0.1233 r_free=0.1498 adp: r_work=0.1233 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1498 r_work=0.1233 r_free=0.1498 | n_water=1009 | time (s): 295.240 (total time: 428.710) Filter (q & B) r_work=0.1238 r_free=0.1507 | n_water=862 | time (s): 4.970 (total time: 433.680) Filter (dist only) r_work=0.1238 r_free=0.1508 | n_water=861 | time (s): 105.770 (total time: 539.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.639018 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.012404 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 0.1225 0.1431 0.0206 0.035 1.1 7.1 0.0 0.0 0 0.820 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.25 14.31 2.06 1.926 14.482 17.012 3.929 12.16 13.92 1.75 2.235 14.389 17.012 3.884 Individual atomic B min max mean iso aniso Overall: 5.55 67.68 15.11 1.06 494 3271 Protein: 5.55 36.27 10.72 1.06 0 2902 Water: 5.68 67.68 29.89 N/A 494 367 Other: 13.88 28.83 21.36 N/A 0 2 Chain A: 5.56 55.17 12.74 N/A 0 1624 Chain B: 5.55 67.68 12.51 N/A 0 1647 Chain S: 5.68 66.27 31.53 N/A 494 0 Histogram: Values Number of atoms 5.55 - 11.77 2132 11.77 - 17.98 692 17.98 - 24.19 299 24.19 - 30.40 246 30.40 - 36.62 163 36.62 - 42.83 136 42.83 - 49.04 60 49.04 - 55.26 24 55.26 - 61.47 10 61.47 - 67.68 3 =========================== Idealize ADP of riding H ========================== r_work=0.1217 r_free=0.1392 r_work=0.1217 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1217 r_free = 0.1392 target_work(ml) = 3.884 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1211 r_free = 0.1378 target_work(ml) = 3.878 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1211 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.877941 | | target function (ml) not normalized (work): 726330.524374 | | target function (ml) not normalized (free): 15187.149374 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1215 0.1211 0.1378 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1428 0.1428 0.1475 n_refl.: 191139 remove outliers: r(all,work,free)=0.1428 0.1428 0.1475 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1423 0.1422 0.1471 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1208 0.1375 n_refl.: 191139 remove outliers: r(all,work,free)=0.1210 0.1206 0.1375 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3717 397.666 346.828 0.420 0.946 0.253 13.296-10.522 99.01 99 1 0.2335 535.265 513.966 0.706 0.947 0.204 10.503-8.327 98.35 176 3 0.2103 555.265 555.967 0.882 0.947 0.149 8.318-6.595 100.00 360 8 0.2101 414.736 409.930 0.895 0.947 0.115 6.588-5.215 100.00 711 7 0.1853 381.101 370.804 0.884 0.947 0.110 5.214-4.128 98.38 1367 28 0.1159 557.435 551.597 0.972 0.947 0.060 4.126-3.266 94.74 2603 46 0.1085 508.132 501.438 1.033 0.947 0.009 3.266-2.585 99.86 5447 97 0.1073 342.774 339.200 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0947 258.603 255.713 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0944 153.054 151.520 1.056 0.944 0.000 1.619-1.281 98.00 42464 925 0.1024 82.395 81.524 1.053 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1674 44.202 42.328 1.038 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0911 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1206 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1206 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1206 r_free=0.1375 | n_water=861 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1207 r_free=0.1375 | n_water=860 | time (s): 107.270 (total time: 110.400) Filter (q & B) r_work=0.1207 r_free=0.1376 | n_water=851 | time (s): 5.120 (total time: 115.520) Compute maps r_work=0.1207 r_free=0.1376 | n_water=851 | time (s): 2.480 (total time: 118.000) Filter (map) r_work=0.1228 r_free=0.1374 | n_water=721 | time (s): 5.410 (total time: 123.410) Find peaks r_work=0.1228 r_free=0.1374 | n_water=721 | time (s): 0.620 (total time: 124.030) Add new water r_work=0.1239 r_free=0.1379 | n_water=961 | time (s): 4.030 (total time: 128.060) Refine new water occ: r_work=0.1204 r_free=0.1359 adp: r_work=0.1204 r_free=0.1358 occ: r_work=0.1202 r_free=0.1360 adp: r_work=0.1201 r_free=0.1359 occ: r_work=0.1200 r_free=0.1361 adp: r_work=0.1199 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1360 r_work=0.1199 r_free=0.1360 | n_water=961 | time (s): 217.970 (total time: 346.030) Filter (q & B) r_work=0.1204 r_free=0.1368 | n_water=881 | time (s): 5.490 (total time: 351.520) Filter (dist only) r_work=0.1204 r_free=0.1368 | n_water=880 | time (s): 114.180 (total time: 465.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.602107 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.267410 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1372 0.0170 0.036 1.1 7.8 0.0 0.0 0 0.801 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.72 1.70 1.826 14.244 16.267 3.871 11.96 13.70 1.74 1.914 14.210 16.267 3.864 Individual atomic B min max mean iso aniso Overall: 5.51 67.26 15.07 1.00 514 3270 Protein: 5.51 33.35 10.65 1.00 0 2902 Water: 5.64 67.26 29.65 N/A 514 366 Other: 13.98 27.85 20.92 N/A 0 2 Chain A: 5.54 54.15 12.60 N/A 0 1623 Chain B: 5.51 67.26 12.43 N/A 0 1647 Chain S: 5.64 61.46 31.35 N/A 514 0 Histogram: Values Number of atoms 5.51 - 11.68 2114 11.68 - 17.86 731 17.86 - 24.03 296 24.03 - 30.21 234 30.21 - 36.38 171 36.38 - 42.56 138 42.56 - 48.74 66 48.74 - 54.91 23 54.91 - 61.09 9 61.09 - 67.26 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1370 r_work=0.1196 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1370 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1370 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862426 | | target function (ml) not normalized (work): 723405.339595 | | target function (ml) not normalized (free): 15139.996112 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1193 0.1370 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1486 n_refl.: 191134 remove outliers: r(all,work,free)=0.1411 0.1410 0.1486 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1405 0.1403 0.1482 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1369 n_refl.: 191134 remove outliers: r(all,work,free)=0.1195 0.1191 0.1369 n_refl.: 191131 ======================== 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 0.3545 352.015 324.498 0.437 0.947 0.251 13.296-10.522 98.02 98 1 0.2394 478.444 463.236 0.710 0.949 0.198 10.503-8.327 98.35 176 3 0.2131 502.294 496.319 0.864 0.949 0.170 8.318-6.595 100.00 360 8 0.2112 375.171 370.691 0.892 0.949 0.118 6.588-5.215 100.00 711 7 0.1887 344.745 335.395 0.883 0.949 0.097 5.214-4.128 98.38 1367 28 0.1184 504.257 498.591 0.973 0.949 0.080 4.126-3.266 94.74 2603 46 0.1108 459.657 453.158 1.033 0.949 0.009 3.266-2.585 99.86 5447 97 0.1076 310.074 306.814 1.019 0.949 0.000 2.585-2.046 97.45 10613 204 0.0933 233.933 231.416 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0911 138.453 137.128 1.054 0.948 0.000 1.619-1.281 98.00 42464 925 0.0987 74.535 73.811 1.050 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1660 39.985 38.321 1.035 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1105 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1369 | n_water=880 | time (s): 3.110 (total time: 3.110) Filter (dist) r_work=0.1192 r_free=0.1369 | n_water=879 | time (s): 111.820 (total time: 114.930) Filter (q & B) r_work=0.1192 r_free=0.1368 | n_water=871 | time (s): 4.540 (total time: 119.470) Compute maps r_work=0.1192 r_free=0.1368 | n_water=871 | time (s): 2.140 (total time: 121.610) Filter (map) r_work=0.1212 r_free=0.1357 | n_water=751 | time (s): 4.260 (total time: 125.870) Find peaks r_work=0.1212 r_free=0.1357 | n_water=751 | time (s): 0.590 (total time: 126.460) Add new water r_work=0.1224 r_free=0.1371 | n_water=973 | time (s): 3.990 (total time: 130.450) Refine new water occ: r_work=0.1189 r_free=0.1345 adp: r_work=0.1189 r_free=0.1345 occ: r_work=0.1186 r_free=0.1346 adp: r_work=0.1186 r_free=0.1346 occ: r_work=0.1185 r_free=0.1348 adp: r_work=0.1185 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1347 r_work=0.1185 r_free=0.1347 | n_water=973 | time (s): 256.100 (total time: 386.550) Filter (q & B) r_work=0.1188 r_free=0.1355 | n_water=894 | time (s): 4.410 (total time: 390.960) Filter (dist only) r_work=0.1189 r_free=0.1355 | n_water=893 | time (s): 115.570 (total time: 506.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.536521 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.154757 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1359 0.0166 0.036 1.1 7.3 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.59 1.66 1.790 14.165 16.155 3.762 11.97 13.62 1.65 1.880 14.129 16.155 3.759 Individual atomic B min max mean iso aniso Overall: 5.57 66.77 15.00 0.96 527 3270 Protein: 5.57 31.65 10.57 0.96 0 2902 Water: 5.81 66.77 29.40 N/A 527 366 Other: 13.85 26.15 20.00 N/A 0 2 Chain A: 5.58 53.63 12.49 N/A 0 1623 Chain B: 5.57 66.77 12.32 N/A 0 1647 Chain S: 5.81 61.43 31.12 N/A 527 0 Histogram: Values Number of atoms 5.57 - 11.69 2131 11.69 - 17.81 734 17.81 - 23.93 287 23.93 - 30.05 238 30.05 - 36.17 167 36.17 - 42.29 138 42.29 - 48.41 67 48.41 - 54.53 23 54.53 - 60.65 10 60.65 - 66.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1362 r_work=0.1197 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1362 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758231 | | target function (ml) not normalized (work): 703879.121284 | | target function (ml) not normalized (free): 14742.571296 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1366 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1394 0.1392 0.1494 n_refl.: 191131 remove outliers: r(all,work,free)=0.1394 0.1392 0.1494 n_refl.: 191131 overall B=-0.03 to atoms: r(all,work,free)=0.1387 0.1385 0.1489 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1362 n_refl.: 191131 remove outliers: r(all,work,free)=0.1198 0.1194 0.1362 n_refl.: 191131 ======================== 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 0.3605 352.015 321.864 0.412 0.953 0.227 13.296-10.522 98.02 98 1 0.2459 478.444 458.937 0.690 0.955 0.183 10.503-8.327 98.35 176 3 0.2151 502.294 495.899 0.857 0.955 0.160 8.318-6.595 100.00 360 8 0.2145 375.171 370.535 0.883 0.954 0.119 6.588-5.215 100.00 711 7 0.1919 344.745 335.353 0.879 0.954 0.100 5.214-4.128 98.38 1367 28 0.1188 504.257 498.856 0.969 0.955 0.080 4.126-3.266 94.74 2603 46 0.1129 459.657 452.898 1.028 0.955 0.005 3.266-2.585 99.86 5447 97 0.1101 310.074 306.807 1.014 0.954 0.000 2.585-2.046 97.45 10613 204 0.0944 233.933 231.382 1.026 0.953 0.000 2.046-1.619 99.39 21536 464 0.0915 138.453 137.137 1.050 0.952 0.000 1.619-1.281 98.00 42464 925 0.0976 74.535 73.820 1.048 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1650 39.985 38.317 1.036 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1214 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1362 | n_water=893 | time (s): 2.810 (total time: 2.810) Filter (dist) r_work=0.1194 r_free=0.1362 | n_water=893 | time (s): 103.680 (total time: 106.490) Filter (q & B) r_work=0.1195 r_free=0.1362 | n_water=883 | time (s): 5.740 (total time: 112.230) Compute maps r_work=0.1195 r_free=0.1362 | n_water=883 | time (s): 2.090 (total time: 114.320) Filter (map) r_work=0.1217 r_free=0.1356 | n_water=759 | time (s): 4.390 (total time: 118.710) Find peaks r_work=0.1217 r_free=0.1356 | n_water=759 | time (s): 0.570 (total time: 119.280) Add new water r_work=0.1229 r_free=0.1377 | n_water=977 | time (s): 4.150 (total time: 123.430) Refine new water occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1348 occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1191 r_free=0.1347 occ: r_work=0.1189 r_free=0.1347 adp: r_work=0.1189 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1347 r_work=0.1189 r_free=0.1347 | n_water=977 | time (s): 204.550 (total time: 327.980) Filter (q & B) r_work=0.1193 r_free=0.1354 | n_water=911 | time (s): 5.320 (total time: 333.300) Filter (dist only) r_work=0.1194 r_free=0.1354 | n_water=910 | time (s): 116.560 (total time: 449.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565393 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.626590 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1363 0.0166 0.037 1.1 7.7 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.63 1.66 1.756 14.078 14.627 3.759 12.00 13.68 1.68 1.849 14.044 14.627 3.758 Individual atomic B min max mean iso aniso Overall: 5.58 65.89 14.95 0.91 545 3269 Protein: 5.58 29.40 10.48 0.91 0 2902 Water: 5.97 65.89 29.17 N/A 545 365 Other: 13.85 24.02 18.94 N/A 0 2 Chain A: 5.66 53.19 12.37 N/A 0 1623 Chain B: 5.58 65.89 12.20 N/A 0 1646 Chain S: 5.97 61.38 30.91 N/A 545 0 Histogram: Values Number of atoms 5.58 - 11.61 2115 11.61 - 17.64 769 17.64 - 23.67 282 23.67 - 29.70 229 29.70 - 35.73 170 35.73 - 41.77 135 41.77 - 47.80 75 47.80 - 53.83 27 53.83 - 59.86 10 59.86 - 65.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1368 r_work=0.1200 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1368 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1369 target_work(ml) = 3.757 | | 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.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757424 | | target function (ml) not normalized (work): 703727.889246 | | target function (ml) not normalized (free): 14742.849649 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1369 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1500 n_refl.: 191131 remove outliers: r(all,work,free)=0.1395 0.1393 0.1500 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1360 0.1358 0.1476 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1366 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1366 n_refl.: 191131 ======================== 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 0.3583 352.015 322.136 0.418 0.953 0.219 13.296-10.522 98.02 98 1 0.2426 478.444 460.244 0.698 0.955 0.158 10.503-8.327 98.35 176 3 0.2224 502.294 494.656 0.877 0.955 0.130 8.318-6.595 100.00 360 8 0.2151 375.171 371.074 0.903 0.955 0.103 6.588-5.215 100.00 711 7 0.1938 344.745 335.340 0.900 0.955 0.087 5.214-4.128 98.38 1367 28 0.1204 504.257 498.768 0.992 0.955 0.044 4.126-3.266 94.74 2603 46 0.1147 459.657 452.863 1.053 0.955 0.005 3.266-2.585 99.86 5447 97 0.1114 310.074 306.763 1.037 0.955 0.000 2.585-2.046 97.45 10613 204 0.0948 233.933 231.353 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0914 138.453 137.156 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0970 74.535 73.826 1.052 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1649 39.985 38.317 1.024 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0485 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1367 | n_water=910 | time (s): 2.830 (total time: 2.830) Filter (dist) r_work=0.1197 r_free=0.1367 | n_water=910 | time (s): 104.260 (total time: 107.090) Filter (q & B) r_work=0.1198 r_free=0.1365 | n_water=899 | time (s): 4.160 (total time: 111.250) Compute maps r_work=0.1198 r_free=0.1365 | n_water=899 | time (s): 2.000 (total time: 113.250) Filter (map) r_work=0.1219 r_free=0.1357 | n_water=773 | time (s): 4.780 (total time: 118.030) Find peaks r_work=0.1219 r_free=0.1357 | n_water=773 | time (s): 0.850 (total time: 118.880) Add new water r_work=0.1228 r_free=0.1371 | n_water=989 | time (s): 4.380 (total time: 123.260) Refine new water occ: r_work=0.1194 r_free=0.1347 adp: r_work=0.1195 r_free=0.1347 occ: r_work=0.1192 r_free=0.1347 adp: r_work=0.1192 r_free=0.1347 occ: r_work=0.1191 r_free=0.1348 adp: r_work=0.1191 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1348 r_work=0.1191 r_free=0.1348 | n_water=989 | time (s): 215.090 (total time: 338.350) Filter (q & B) r_work=0.1196 r_free=0.1352 | n_water=914 | time (s): 4.340 (total time: 342.690) Filter (dist only) r_work=0.1196 r_free=0.1352 | n_water=912 | time (s): 115.420 (total time: 458.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.501348 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.514566 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1359 0.0160 0.037 1.1 6.3 0.0 0.3 0 0.751 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.59 1.60 1.720 13.767 14.515 3.759 12.01 13.62 1.62 1.777 13.748 14.515 3.757 Individual atomic B min max mean iso aniso Overall: 5.41 64.47 14.66 0.88 547 3269 Protein: 5.41 28.37 10.24 0.88 0 2902 Water: 5.78 64.47 28.72 N/A 547 365 Other: 13.68 22.11 17.89 N/A 0 2 Chain A: 5.46 52.47 12.09 N/A 0 1623 Chain B: 5.41 64.47 11.94 N/A 0 1646 Chain S: 5.78 61.20 30.50 N/A 547 0 Histogram: Values Number of atoms 5.41 - 11.32 2094 11.32 - 17.22 790 17.22 - 23.13 278 23.13 - 29.03 223 29.03 - 34.94 176 34.94 - 40.85 134 40.85 - 46.75 79 46.75 - 52.66 28 52.66 - 58.56 9 58.56 - 64.47 5 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1363 r_work=0.1201 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1363 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756112 | | target function (ml) not normalized (work): 703482.266044 | | target function (ml) not normalized (free): 14736.924142 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1367 0.1366 0.1468 n_refl.: 191131 remove outliers: r(all,work,free)=0.1367 0.1366 0.1468 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1375 0.1374 0.1473 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1351 n_refl.: 191131 remove outliers: r(all,work,free)=0.1193 0.1190 0.1351 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3614 352.015 319.454 0.431 0.909 0.206 13.296-10.522 97.03 97 1 0.2422 480.715 458.113 0.734 0.910 0.154 10.503-8.327 98.35 176 3 0.2201 502.294 494.425 0.927 0.911 0.137 8.318-6.595 100.00 360 8 0.2150 375.171 370.178 0.950 0.911 0.096 6.588-5.215 100.00 711 7 0.1960 344.745 335.084 0.952 0.911 0.085 5.214-4.128 98.38 1367 28 0.1221 504.257 498.357 1.051 0.912 0.034 4.126-3.266 94.74 2603 46 0.1158 459.657 452.380 1.117 0.913 0.005 3.266-2.585 99.86 5447 97 0.1117 310.074 306.586 1.098 0.913 0.000 2.585-2.046 97.45 10613 204 0.0951 233.933 231.271 1.107 0.915 0.000 2.046-1.619 99.39 21536 464 0.0911 138.453 137.080 1.124 0.917 0.000 1.619-1.281 98.00 42464 925 0.0951 74.535 73.871 1.112 0.921 0.000 1.281-0.980 96.53 101826 2055 0.1628 39.985 38.296 1.076 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0580 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1351 | n_water=912 | time (s): 2.870 (total time: 2.870) Filter (dist) r_work=0.1190 r_free=0.1352 | n_water=911 | time (s): 115.230 (total time: 118.100) Filter (q & B) r_work=0.1191 r_free=0.1353 | n_water=899 | time (s): 4.160 (total time: 122.260) Compute maps r_work=0.1191 r_free=0.1353 | n_water=899 | time (s): 1.670 (total time: 123.930) Filter (map) r_work=0.1214 r_free=0.1351 | n_water=775 | time (s): 4.140 (total time: 128.070) Find peaks r_work=0.1214 r_free=0.1351 | n_water=775 | time (s): 0.610 (total time: 128.680) Add new water r_work=0.1221 r_free=0.1358 | n_water=983 | time (s): 4.970 (total time: 133.650) Refine new water occ: r_work=0.1187 r_free=0.1338 adp: r_work=0.1187 r_free=0.1338 occ: r_work=0.1186 r_free=0.1338 adp: r_work=0.1185 r_free=0.1338 occ: r_work=0.1184 r_free=0.1339 adp: r_work=0.1184 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1339 r_work=0.1184 r_free=0.1339 | n_water=983 | time (s): 317.900 (total time: 451.550) Filter (q & B) r_work=0.1189 r_free=0.1342 | n_water=915 | time (s): 4.350 (total time: 455.900) Filter (dist only) r_work=0.1189 r_free=0.1341 | n_water=914 | time (s): 117.760 (total time: 573.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.519568 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.254178 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 0.1350 0.0158 0.038 1.1 7.3 0.0 0.3 0 0.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.50 1.58 1.676 13.735 14.254 3.755 11.93 13.51 1.59 1.682 13.733 14.254 3.753 Individual atomic B min max mean iso aniso Overall: 5.46 64.07 14.65 0.87 549 3269 Protein: 5.46 28.25 10.32 0.87 0 2902 Water: 5.87 64.07 28.41 N/A 549 365 Other: 13.75 22.20 17.97 N/A 0 2 Chain A: 5.57 52.36 12.13 N/A 0 1623 Chain B: 5.46 64.07 11.99 N/A 0 1646 Chain S: 5.87 61.30 30.08 N/A 549 0 Histogram: Values Number of atoms 5.46 - 11.32 2070 11.32 - 17.18 814 17.18 - 23.04 284 23.04 - 28.90 229 28.90 - 34.77 181 34.77 - 40.63 121 40.63 - 46.49 75 46.49 - 52.35 27 52.35 - 58.21 12 58.21 - 64.07 5 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1351 r_work=0.1193 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1352 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1352 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753124 | | target function (ml) not normalized (work): 702918.856042 | | target function (ml) not normalized (free): 14726.567265 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1352 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1383 0.1381 0.1486 n_refl.: 191130 remove outliers: r(all,work,free)=0.1383 0.1381 0.1486 n_refl.: 191130 overall B=0.01 to atoms: r(all,work,free)=0.1385 0.1383 0.1488 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1351 n_refl.: 191130 remove outliers: r(all,work,free)=0.1193 0.1190 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 0.3625 347.739 318.552 0.399 0.975 0.207 13.296-10.522 96.04 96 1 0.2328 479.835 454.405 0.685 0.976 0.148 10.503-8.327 98.35 176 3 0.2246 502.294 493.486 0.860 0.977 0.123 8.318-6.595 100.00 360 8 0.2164 375.171 370.224 0.883 0.977 0.090 6.588-5.215 100.00 711 7 0.1968 344.745 335.082 0.886 0.977 0.090 5.214-4.128 98.38 1367 28 0.1238 504.257 498.329 0.978 0.978 0.039 4.126-3.266 94.74 2603 46 0.1166 459.657 452.393 1.041 0.979 0.005 3.266-2.585 99.86 5447 97 0.1119 310.074 306.555 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0953 233.933 231.283 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0910 138.453 137.102 1.049 0.985 0.000 1.619-1.281 98.00 42464 925 0.0947 74.535 73.885 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1625 39.985 38.285 1.009 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0208 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1191 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1353 | n_water=914 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1192 r_free=0.1351 | n_water=912 | time (s): 111.530 (total time: 113.800) Filter (q & B) r_work=0.1193 r_free=0.1351 | n_water=898 | time (s): 4.620 (total time: 118.420) Compute maps r_work=0.1193 r_free=0.1351 | n_water=898 | time (s): 2.270 (total time: 120.690) Filter (map) r_work=0.1213 r_free=0.1352 | n_water=778 | time (s): 5.740 (total time: 126.430) Find peaks r_work=0.1213 r_free=0.1352 | n_water=778 | time (s): 0.790 (total time: 127.220) Add new water r_work=0.1221 r_free=0.1362 | n_water=986 | time (s): 4.850 (total time: 132.070) Refine new water occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1188 r_free=0.1342 occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1186 r_free=0.1342 occ: r_work=0.1185 r_free=0.1343 adp: r_work=0.1185 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1343 r_work=0.1185 r_free=0.1343 | n_water=986 | time (s): 188.520 (total time: 320.590) Filter (q & B) r_work=0.1189 r_free=0.1347 | n_water=913 | time (s): 5.710 (total time: 326.300) Filter (dist only) r_work=0.1189 r_free=0.1346 | n_water=912 | time (s): 115.610 (total time: 441.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.549795 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.498722 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 0.1193 0.1352 0.0159 0.038 1.1 7.5 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.52 1.59 1.680 13.765 14.499 3.754 11.92 13.53 1.61 1.688 13.765 14.499 3.752 Individual atomic B min max mean iso aniso Overall: 5.53 63.08 14.68 0.87 547 3269 Protein: 5.53 28.11 10.34 0.87 0 2902 Water: 5.96 63.08 28.50 N/A 547 365 Other: 13.80 22.21 18.01 N/A 0 2 Chain A: 5.62 52.02 12.13 N/A 0 1623 Chain B: 5.53 63.08 11.99 N/A 0 1646 Chain S: 5.96 60.04 30.37 N/A 547 0 Histogram: Values Number of atoms 5.53 - 11.29 2062 11.29 - 17.04 822 17.04 - 22.80 277 22.80 - 28.55 218 28.55 - 34.31 173 34.31 - 40.06 136 40.06 - 45.82 78 45.82 - 51.57 30 51.57 - 57.32 15 57.32 - 63.08 5 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1353 r_work=0.1192 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1353 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1356 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751645 | | target function (ml) not normalized (work): 702634.255618 | | target function (ml) not normalized (free): 14724.259101 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1356 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1491 n_refl.: 191128 remove outliers: r(all,work,free)=0.1391 0.1389 0.1491 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1391 0.1389 0.1490 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1355 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1190 0.1355 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3573 347.739 317.186 0.393 0.975 0.201 13.296-10.522 96.04 96 1 0.2369 479.835 464.474 0.698 0.976 0.147 10.503-8.327 98.35 176 3 0.2234 502.294 493.889 0.859 0.977 0.118 8.318-6.595 100.00 360 8 0.2183 375.171 370.378 0.885 0.976 0.097 6.588-5.215 100.00 711 7 0.1980 344.745 334.774 0.884 0.977 0.090 5.214-4.128 98.38 1367 28 0.1241 504.257 498.439 0.978 0.978 0.044 4.126-3.266 94.74 2603 46 0.1170 459.657 452.189 1.042 0.979 0.005 3.266-2.585 99.86 5447 97 0.1128 310.074 306.481 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0954 233.933 231.266 1.032 0.982 0.000 2.046-1.619 99.39 21536 464 0.0907 138.453 137.093 1.050 0.986 0.000 1.619-1.281 98.00 42464 925 0.0944 74.535 73.883 1.041 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1622 39.985 38.279 1.011 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1355 After: r_work=0.1191 r_free=0.1356 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1356 | n_water=912 | time (s): 2.320 (total time: 2.320) Filter (dist) r_work=0.1191 r_free=0.1356 | n_water=912 | time (s): 116.450 (total time: 118.770) Filter (q & B) r_work=0.1192 r_free=0.1357 | n_water=892 | time (s): 4.800 (total time: 123.570) Compute maps r_work=0.1192 r_free=0.1357 | n_water=892 | time (s): 1.990 (total time: 125.560) Filter (map) r_work=0.1214 r_free=0.1351 | n_water=774 | time (s): 5.170 (total time: 130.730) Find peaks r_work=0.1214 r_free=0.1351 | n_water=774 | time (s): 0.870 (total time: 131.600) Add new water r_work=0.1222 r_free=0.1362 | n_water=992 | time (s): 4.860 (total time: 136.460) Refine new water occ: r_work=0.1188 r_free=0.1339 adp: r_work=0.1188 r_free=0.1339 occ: r_work=0.1186 r_free=0.1339 adp: r_work=0.1186 r_free=0.1339 occ: r_work=0.1185 r_free=0.1340 adp: r_work=0.1185 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1340 r_work=0.1185 r_free=0.1340 | n_water=992 | time (s): 300.440 (total time: 436.900) Filter (q & B) r_work=0.1189 r_free=0.1347 | n_water=918 | time (s): 5.980 (total time: 442.880) Filter (dist only) r_work=0.1189 r_free=0.1348 | n_water=916 | time (s): 115.700 (total time: 558.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.490195 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.904913 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 0.1193 0.1354 0.0161 0.038 1.2 10.9 0.0 0.3 0 0.745 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.54 1.61 1.679 13.733 13.905 3.755 11.95 13.56 1.62 1.677 13.733 13.905 3.755 Individual atomic B min max mean iso aniso Overall: 5.56 62.70 14.62 0.86 551 3269 Protein: 5.56 28.00 10.35 0.86 0 2902 Water: 6.00 62.70 28.13 N/A 551 365 Other: 13.84 22.21 18.02 N/A 0 2 Chain A: 5.65 51.90 12.12 N/A 0 1623 Chain B: 5.56 62.70 11.99 N/A 0 1646 Chain S: 6.00 60.07 29.85 N/A 551 0 Histogram: Values Number of atoms 5.56 - 11.27 2052 11.27 - 16.99 831 16.99 - 22.70 285 22.70 - 28.41 227 28.41 - 34.13 176 34.13 - 39.84 120 39.84 - 45.56 80 45.56 - 51.27 28 51.27 - 56.98 15 56.98 - 62.70 6 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1356 r_work=0.1195 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1356 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1356 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755192 | | target function (ml) not normalized (work): 703298.664743 | | target function (ml) not normalized (free): 14733.765281 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1363 0.1465 5.6871 5.7445| | 2: 2.94 - 2.33 1.00 7339 128 0.1066 0.1332 5.0684 5.1645| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1191 4.6564 4.7633| | 4: 2.04 - 1.85 1.00 7170 155 0.0903 0.1047 4.3952 4.5687| | 5: 1.85 - 1.72 0.99 7113 159 0.0940 0.1013 4.1583 4.2508| | 6: 1.72 - 1.62 0.99 7102 142 0.0900 0.1088 3.9518 4.0887| | 7: 1.62 - 1.54 0.99 7104 148 0.0895 0.0976 3.8044 3.9363| | 8: 1.54 - 1.47 0.96 6798 152 0.0896 0.1310 3.7052 3.8954| | 9: 1.47 - 1.41 0.98 6938 155 0.0930 0.1137 3.6272 3.7669| | 10: 1.41 - 1.36 0.99 7022 150 0.0981 0.1206 3.5622 3.6885| | 11: 1.36 - 1.32 0.99 6997 151 0.1000 0.1135 3.4923 3.5985| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1129 3.4636 3.5927| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1249 3.4391 3.5679| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1583 3.4339 3.677| | 15: 1.22 - 1.19 0.98 6956 137 0.1170 0.1250 3.4485 3.4934| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1548 3.4639 3.6551| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1230 3.432 3.4404| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1694 3.4373 3.5268| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1756 3.4174 3.5928| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1571 3.4091 3.4319| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2139 3.4177 3.5044| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1959 3.4121 3.4154| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2013 3.4323 3.4848| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2259 3.4344 3.5099| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2505 3.4484 3.5211| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2841 3.4148 3.4185| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2816 3.4664 3.3989| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.26 1.00 0.96 10655.74| | 2: 2.94 - 2.33 7339 128 0.93 12.53 0.99 0.95 4952.79| | 3: 2.33 - 2.04 6939 150 0.96 7.68 1.01 0.95 1709.91| | 4: 2.04 - 1.85 7170 155 0.96 7.71 1.00 0.95 1012.81| | 5: 1.85 - 1.72 7113 159 0.96 8.17 1.00 0.96 645.87| | 6: 1.72 - 1.62 7102 142 0.96 8.12 1.00 0.96 451.18| | 7: 1.62 - 1.54 7104 148 0.96 8.24 1.01 0.97 342.46| | 8: 1.54 - 1.47 6798 152 0.96 8.36 1.01 0.97 283.07| | 9: 1.47 - 1.41 6938 155 0.96 8.63 1.00 0.98 236.26| | 10: 1.41 - 1.36 7022 150 0.96 9.12 1.00 0.97 208.22| | 11: 1.36 - 1.32 6997 151 0.96 9.17 0.99 0.96 180.36| | 12: 1.32 - 1.28 6975 149 0.96 9.15 0.98 0.95 164.42| | 13: 1.28 - 1.25 6907 166 0.96 9.63 1.01 0.96 160.12| | 14: 1.25 - 1.22 7015 112 0.95 10.77 1.01 0.96 164.21| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.01 0.98 166.92| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.01 0.96 160.11| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.96 152.87| | 18: 1.14 - 1.12 6875 142 0.94 12.70 1.01 0.94 146.51| | 19: 1.12 - 1.10 6948 106 0.93 14.10 1.00 0.94 150.14| | 20: 1.10 - 1.08 6884 147 0.92 15.22 1.00 0.94 149.85| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.27| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.93 155.05| | 23: 1.05 - 1.03 6827 159 0.87 20.50 0.99 0.92 164.49| | 24: 1.03 - 1.02 6784 133 0.85 23.12 0.99 0.93 178.35| | 25: 1.02 - 1.01 6552 130 0.83 25.08 0.98 0.90 181.08| | 26: 1.01 - 0.99 6767 158 0.81 26.64 0.98 0.89 176.52| | 27: 0.99 - 0.98 6647 131 0.82 26.48 0.99 0.87 162.69| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.51 max = 10655.74 mean = 899.56| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.94 mean = 13.32| |phase err.(test): min = 0.00 max = 87.91 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1496 n_refl.: 191128 remove outliers: r(all,work,free)=0.1400 0.1398 0.1496 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1391 0.1390 0.1490 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3591 347.739 317.144 0.411 0.916 0.213 13.296-10.522 96.04 96 1 0.2357 479.835 463.861 0.722 0.917 0.146 10.503-8.327 98.35 176 3 0.2259 502.294 493.530 0.890 0.918 0.116 8.318-6.595 100.00 360 8 0.2196 375.171 370.233 0.918 0.918 0.097 6.588-5.215 100.00 711 7 0.1974 344.745 335.066 0.917 0.918 0.079 5.214-4.128 98.38 1367 28 0.1243 504.257 498.330 1.016 0.919 0.039 4.126-3.266 94.74 2603 46 0.1167 459.657 452.160 1.083 0.920 0.005 3.266-2.585 99.86 5447 97 0.1123 310.074 306.625 1.063 0.922 0.000 2.585-2.046 97.45 10613 204 0.0960 233.933 231.258 1.070 0.924 0.000 2.046-1.619 99.39 21536 464 0.0915 138.453 137.079 1.087 0.928 0.000 1.619-1.281 98.00 42464 925 0.0950 74.535 73.879 1.076 0.934 0.000 1.281-0.980 96.53 101826 2055 0.1625 39.985 38.269 1.042 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0124 ================= 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 : 0.2032 0.2003 0.082 5.098 5.2 78.0 14.6 805 0.000 1_bss: 0.1798 0.1940 0.082 5.098 5.2 78.0 14.6 805 0.000 1_settarget: 0.1798 0.1940 0.082 5.098 5.2 78.0 14.6 805 0.000 1_nqh: 0.1802 0.1940 0.082 5.098 5.2 78.0 14.6 805 0.003 1_weight: 0.1802 0.1940 0.082 5.098 5.2 78.0 14.6 805 0.003 1_xyzrec: 0.1276 0.1508 0.039 1.172 5.2 78.0 14.6 805 0.160 1_adp: 0.1303 0.1579 0.039 1.172 5.2 73.0 15.0 805 0.160 1_regHadp: 0.1302 0.1574 0.039 1.172 5.2 73.0 15.0 805 0.160 1_occ: 0.1287 0.1566 0.039 1.172 5.2 73.0 15.0 805 0.160 2_bss: 0.1279 0.1556 0.039 1.172 5.3 73.2 15.1 805 0.160 2_settarget: 0.1279 0.1556 0.039 1.172 5.3 73.2 15.1 805 0.160 2_updatecdl: 0.1279 0.1556 0.039 1.178 5.3 73.2 15.1 805 0.160 2_nqh: 0.1279 0.1556 0.039 1.178 5.3 73.2 15.1 805 0.160 2_sol: 0.1276 0.1523 0.039 1.178 5.3 73.2 16.3 880 n/a 2_weight: 0.1276 0.1523 0.039 1.178 5.3 73.2 16.3 880 n/a 2_xyzrec: 0.1259 0.1534 0.041 1.131 5.3 73.2 16.3 880 n/a 2_adp: 0.1234 0.1516 0.041 1.131 5.4 70.3 16.3 880 n/a 2_regHadp: 0.1235 0.1517 0.041 1.131 5.4 70.3 16.3 880 n/a 2_occ: 0.1228 0.1515 0.041 1.131 5.4 70.3 16.3 880 n/a 3_bss: 0.1235 0.1520 0.041 1.131 5.4 70.2 16.3 880 n/a 3_settarget: 0.1235 0.1520 0.041 1.131 5.4 70.2 16.3 880 n/a 3_updatecdl: 0.1235 0.1520 0.041 1.136 5.4 70.2 16.3 880 n/a 3_nqh: 0.1235 0.1520 0.041 1.136 5.4 70.2 16.3 880 n/a 3_sol: 0.1238 0.1508 0.041 1.136 5.4 68.2 15.3 861 n/a 3_weight: 0.1238 0.1508 0.041 1.136 5.4 68.2 15.3 861 n/a 3_xyzrec: 0.1225 0.1431 0.035 1.092 5.4 68.2 15.3 861 n/a 3_adp: 0.1217 0.1392 0.035 1.092 5.6 67.7 15.1 861 n/a 3_regHadp: 0.1217 0.1392 0.035 1.092 5.6 67.7 15.1 861 n/a 3_occ: 0.1211 0.1378 0.035 1.092 5.6 67.7 15.1 861 n/a 4_bss: 0.1206 0.1375 0.035 1.092 5.5 67.7 15.1 861 n/a 4_settarget: 0.1206 0.1375 0.035 1.092 5.5 67.7 15.1 861 n/a 4_updatecdl: 0.1206 0.1375 0.035 1.097 5.5 67.7 15.1 861 n/a 4_nqh: 0.1206 0.1375 0.035 1.097 5.5 67.7 15.1 861 n/a 4_sol: 0.1204 0.1368 0.035 1.097 5.5 67.7 15.1 880 n/a 4_weight: 0.1204 0.1368 0.035 1.097 5.5 67.7 15.1 880 n/a 4_xyzrec: 0.1202 0.1372 0.036 1.131 5.5 67.7 15.1 880 n/a 4_adp: 0.1196 0.1370 0.036 1.131 5.5 67.3 15.1 880 n/a 4_regHadp: 0.1196 0.1370 0.036 1.131 5.5 67.3 15.1 880 n/a 4_occ: 0.1193 0.1370 0.036 1.131 5.5 67.3 15.1 880 n/a 5_bss: 0.1191 0.1369 0.036 1.131 5.5 67.2 15.0 880 n/a 5_settarget: 0.1191 0.1369 0.036 1.131 5.5 67.2 15.0 880 n/a 5_updatecdl: 0.1191 0.1369 0.036 1.131 5.5 67.2 15.0 880 n/a 5_nqh: 0.1191 0.1369 0.036 1.131 5.5 67.2 15.0 880 n/a 5_sol: 0.1189 0.1355 0.036 1.131 5.5 67.2 15.1 893 n/a 5_weight: 0.1189 0.1355 0.036 1.131 5.5 67.2 15.1 893 n/a 5_xyzrec: 0.1192 0.1359 0.036 1.125 5.5 67.2 15.1 893 n/a 5_adp: 0.1197 0.1362 0.036 1.125 5.6 66.8 15.0 893 n/a 5_regHadp: 0.1197 0.1362 0.036 1.125 5.6 66.8 15.0 893 n/a 5_occ: 0.1196 0.1366 0.036 1.125 5.6 66.8 15.0 893 n/a 6_bss: 0.1194 0.1362 0.036 1.125 5.5 66.7 15.0 893 n/a 6_settarget: 0.1194 0.1362 0.036 1.125 5.5 66.7 15.0 893 n/a 6_updatecdl: 0.1194 0.1362 0.036 1.125 5.5 66.7 15.0 893 n/a 6_nqh: 0.1194 0.1362 0.036 1.125 5.5 66.7 15.0 893 n/a 6_sol: 0.1194 0.1354 0.036 1.125 5.5 66.7 15.0 910 n/a 6_weight: 0.1194 0.1354 0.036 1.125 5.5 66.7 15.0 910 n/a 6_xyzrec: 0.1197 0.1363 0.037 1.123 5.5 66.7 15.0 910 n/a 6_adp: 0.1200 0.1368 0.037 1.123 5.6 65.9 14.9 910 n/a 6_regHadp: 0.1200 0.1368 0.037 1.123 5.6 65.9 14.9 910 n/a 6_occ: 0.1198 0.1369 0.037 1.123 5.6 65.9 14.9 910 n/a 7_bss: 0.1197 0.1367 0.037 1.123 5.4 65.7 14.7 910 n/a 7_settarget: 0.1197 0.1367 0.037 1.123 5.4 65.7 14.7 910 n/a 7_updatecdl: 0.1197 0.1367 0.037 1.122 5.4 65.7 14.7 910 n/a 7_nqh: 0.1197 0.1367 0.037 1.122 5.4 65.7 14.7 910 n/a 7_sol: 0.1196 0.1352 0.037 1.122 5.4 65.7 14.7 912 n/a 7_weight: 0.1196 0.1352 0.037 1.122 5.4 65.7 14.7 912 n/a 7_xyzrec: 0.1199 0.1359 0.037 1.120 5.4 65.7 14.7 912 n/a 7_adp: 0.1201 0.1363 0.037 1.120 5.4 64.5 14.7 912 n/a 7_regHadp: 0.1201 0.1363 0.037 1.120 5.4 64.5 14.7 912 n/a 7_occ: 0.1199 0.1363 0.037 1.120 5.4 64.5 14.7 912 n/a 8_bss: 0.1190 0.1351 0.037 1.120 5.5 64.5 14.7 912 n/a 8_settarget: 0.1190 0.1351 0.037 1.120 5.5 64.5 14.7 912 n/a 8_updatecdl: 0.1190 0.1351 0.037 1.120 5.5 64.5 14.7 912 n/a 8_nqh: 0.1190 0.1351 0.037 1.120 5.5 64.5 14.7 912 n/a 8_sol: 0.1189 0.1341 0.037 1.120 5.5 64.5 14.7 914 n/a 8_weight: 0.1189 0.1341 0.037 1.120 5.5 64.5 14.7 914 n/a 8_xyzrec: 0.1192 0.1350 0.038 1.113 5.5 64.5 14.7 914 n/a 8_adp: 0.1193 0.1351 0.038 1.113 5.5 64.1 14.7 914 n/a 8_regHadp: 0.1193 0.1352 0.038 1.113 5.5 64.1 14.7 914 n/a 8_occ: 0.1192 0.1352 0.038 1.113 5.5 64.1 14.7 914 n/a 9_bss: 0.1190 0.1351 0.038 1.113 5.5 64.1 14.7 914 n/a 9_settarget: 0.1190 0.1351 0.038 1.113 5.5 64.1 14.7 914 n/a 9_updatecdl: 0.1190 0.1351 0.038 1.113 5.5 64.1 14.7 914 n/a 9_nqh: 0.1191 0.1353 0.038 1.113 5.5 64.1 14.7 914 n/a 9_sol: 0.1189 0.1346 0.038 1.113 5.5 64.1 14.7 912 n/a 9_weight: 0.1189 0.1346 0.038 1.113 5.5 64.1 14.7 912 n/a 9_xyzrec: 0.1193 0.1352 0.038 1.121 5.5 64.1 14.7 912 n/a 9_adp: 0.1192 0.1353 0.038 1.121 5.5 63.1 14.7 912 n/a 9_regHadp: 0.1192 0.1353 0.038 1.121 5.5 63.1 14.7 912 n/a 9_occ: 0.1191 0.1356 0.038 1.121 5.5 63.1 14.7 912 n/a 10_bss: 0.1190 0.1355 0.038 1.121 5.5 63.1 14.7 912 n/a 10_settarget: 0.1190 0.1355 0.038 1.121 5.5 63.1 14.7 912 n/a 10_updatecdl: 0.1190 0.1355 0.038 1.121 5.5 63.1 14.7 912 n/a 10_setrh: 0.1191 0.1356 0.038 1.121 5.5 63.1 14.7 912 n/a 10_nqh: 0.1191 0.1356 0.038 1.121 5.5 63.1 14.7 912 n/a 10_sol: 0.1189 0.1348 0.038 1.121 5.5 63.1 14.6 916 n/a 10_weight: 0.1189 0.1348 0.038 1.121 5.5 63.1 14.6 916 n/a 10_xyzrec: 0.1193 0.1354 0.038 1.157 5.5 63.1 14.6 916 n/a 10_adp: 0.1195 0.1356 0.038 1.157 5.6 62.7 14.6 916 n/a 10_regHadp: 0.1195 0.1356 0.038 1.157 5.6 62.7 14.6 916 n/a 10_occ: 0.1195 0.1356 0.038 1.157 5.6 62.7 14.6 916 n/a end: 0.1194 0.1357 0.038 1.157 5.5 62.6 14.6 916 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8729823_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8729823_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.5600 Refinement macro-cycles (run) : 12254.6500 Write final files (write_after_run_outputs) : 144.6300 Total : 12406.8400 Total CPU time: 3.46 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:03 PST -0800 (1736736243.32 s) Start R-work = 0.1798, R-free = 0.1940 Final R-work = 0.1194, R-free = 0.1357 =============================================================================== Job complete usr+sys time: 12670.55 seconds wall clock time: 212 minutes 13.31 seconds (12733.31 seconds total)