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_7435083.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7435083.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7435083.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.97, per 1000 atoms: 0.29 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: 2.676 distance_ideal: 2.720 ideal - model: 0.044 slack: 0.000 delta_slack: 0.044 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: 2.660 distance_ideal: 2.710 ideal - model: 0.050 slack: 0.000 delta_slack: 0.050 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: 0.93 Conformation dependent library (CDL) restraints added in 208.6 milliseconds Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.04: 930 1.04 - 1.27: 2464 1.27 - 1.50: 1541 1.50 - 1.74: 983 1.74 - 1.97: 16 Bond restraints: 5934 Sorted by residual: bond pdb=" N ARG B 100 " pdb=" H ARG B 100 " ideal model delta sigma weight residual 0.860 1.272 -0.412 2.00e-02 2.50e+03 4.24e+02 bond pdb=" N GLU A 66 " pdb=" H GLU A 66 " ideal model delta sigma weight residual 0.860 1.244 -0.384 2.00e-02 2.50e+03 3.69e+02 bond pdb=" C ASP B 68 " pdb=" N VAL B 69 " ideal model delta sigma weight residual 1.333 1.511 -0.179 9.40e-03 1.13e+04 3.61e+02 bond pdb=" N LEU A 53 " pdb=" H LEU A 53 " ideal model delta sigma weight residual 0.860 1.237 -0.377 2.00e-02 2.50e+03 3.56e+02 bond pdb=" CG1 VAL A 173 " pdb="HG11 VAL A 173 " ideal model delta sigma weight residual 0.970 1.347 -0.377 2.00e-02 2.50e+03 3.55e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 5409 3.98 - 7.96: 3519 7.96 - 11.94: 1505 11.94 - 15.92: 332 15.92 - 19.90: 45 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 121.55 137.04 -15.49 7.80e-01 1.64e+00 3.94e+02 angle pdb=" CA ALA B 182 " pdb=" C ALA B 182 " pdb=" O ALA B 182 " ideal model delta sigma weight residual 120.90 138.05 -17.15 1.07e+00 8.73e-01 2.57e+02 angle pdb=" O VAL B 51 " pdb=" C VAL B 51 " pdb=" N LYS B 52 " ideal model delta sigma weight residual 122.67 137.21 -14.54 1.02e+00 9.61e-01 2.03e+02 angle pdb=" CD2 TRP B 146 " pdb=" CE2 TRP B 146 " pdb=" CZ2 TRP B 146 " ideal model delta sigma weight residual 122.40 136.18 -13.78 1.00e+00 1.00e+00 1.90e+02 angle pdb=" O VAL B 144 " pdb=" C VAL B 144 " pdb=" N VAL B 145 " ideal model delta sigma weight residual 123.05 108.27 14.78 1.11e+00 8.12e-01 1.77e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1856 17.40 - 34.80: 122 34.80 - 52.19: 56 52.19 - 69.59: 11 69.59 - 86.99: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA LEU B 172 " pdb=" C LEU B 172 " pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta harmonic sigma weight residual -180.00 -155.25 -24.75 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA VAL A 112 " pdb=" C VAL A 112 " pdb=" N LEU A 113 " pdb=" CA LEU A 113 " ideal model delta harmonic sigma weight residual -180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA ALA A 107 " pdb=" C ALA A 107 " pdb=" N ALA A 108 " pdb=" CA ALA A 108 " ideal model delta harmonic sigma weight residual 180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.267: 235 0.267 - 0.534: 179 0.534 - 0.800: 64 0.800 - 1.067: 11 1.067 - 1.333: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 26 " pdb=" N VAL B 26 " pdb=" C VAL B 26 " pdb=" CB VAL B 26 " both_signs ideal model delta sigma weight residual False 2.44 3.77 -1.33 2.00e-01 2.50e+01 4.44e+01 chirality pdb=" CA TYR B 195 " pdb=" N TYR B 195 " pdb=" C TYR B 195 " pdb=" CB TYR B 195 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA THR B 34 " pdb=" N THR B 34 " pdb=" C THR B 34 " pdb=" CB THR B 34 " both_signs ideal model delta sigma weight residual False 2.53 1.40 1.12 2.00e-01 2.50e+01 3.15e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.102 2.00e-02 2.50e+03 7.32e-02 2.14e+02 pdb=" CG TRP A 146 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.090 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.140 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.126 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.023 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.012 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.083 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.066 2.00e-02 2.50e+03 6.63e-02 1.76e+02 pdb=" CG TRP B 139 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.037 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.067 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.115 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.086 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.126 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.064 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.091 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " 0.069 2.00e-02 2.50e+03 7.35e-02 1.62e+02 pdb=" CG TYR B 67 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " -0.117 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " 0.070 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " 0.087 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " -0.066 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " 0.096 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " 0.067 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " -0.097 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.62: 34 1.62 - 2.36: 2492 2.36 - 3.11: 22245 3.11 - 3.85: 33022 3.85 - 4.60: 52496 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110289 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.874 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.979 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.988 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.018 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.205 2.620 ... (remaining 110284 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_7435083_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2038 r_free= 0.1985 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300194 | | target function (ml) not normalized (work): 805482.269936 | | target function (ml) not normalized (free): 16530.471291 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2160 0.1977 6.6852 6.305| | 2: 2.94 - 2.33 1.00 7339 128 0.1633 0.1564 5.5478 5.5937| | 3: 2.33 - 2.04 0.96 6939 150 0.1607 0.1718 5.1297 5.2318| | 4: 2.04 - 1.85 1.00 7170 155 0.1745 0.1541 4.9621 4.9812| | 5: 1.85 - 1.72 0.99 7113 159 0.1949 0.1707 4.8096 4.8148| | 6: 1.72 - 1.62 0.99 7102 142 0.1954 0.2104 4.6577 4.7555| | 7: 1.62 - 1.54 0.99 7104 148 0.2011 0.1823 4.5612 4.5936| | 8: 1.54 - 1.47 0.96 6798 152 0.2080 0.2367 4.4982 4.557| | 9: 1.47 - 1.41 0.98 6938 155 0.2073 0.2149 4.4002 4.4247| | 10: 1.41 - 1.36 0.99 7022 150 0.2092 0.2191 4.2984 4.3621| | 11: 1.36 - 1.32 0.99 6997 151 0.2103 0.1859 4.229 4.1363| | 12: 1.32 - 1.28 0.98 6976 149 0.2056 0.1767 4.1577 4.1111| | 13: 1.28 - 1.25 0.98 6907 166 0.2022 0.2174 4.1107 4.2| | 14: 1.25 - 1.22 0.98 7015 113 0.2115 0.2170 4.0825 4.1286| | 15: 1.22 - 1.19 0.98 6957 137 0.2146 0.2115 4.0518 4.0369| | 16: 1.19 - 1.17 0.93 6604 132 0.2116 0.2003 3.994 4.0416| | 17: 1.17 - 1.14 0.98 6941 135 0.2184 0.1694 3.9571 3.9043| | 18: 1.14 - 1.12 0.98 6875 142 0.2228 0.2491 3.9276 3.9335| | 19: 1.12 - 1.10 0.97 6949 106 0.2248 0.2412 3.8663 3.9371| | 20: 1.10 - 1.08 0.97 6884 147 0.2305 0.2378 3.8246 3.8837| | 21: 1.08 - 1.07 0.97 6852 152 0.2433 0.2626 3.7916 3.8397| | 22: 1.07 - 1.05 0.97 6838 135 0.2556 0.2750 3.7561 3.8328| | 23: 1.05 - 1.03 0.97 6829 159 0.2737 0.2618 3.7406 3.8005| | 24: 1.03 - 1.02 0.96 6785 133 0.2860 0.2839 3.7051 3.8106| | 25: 1.02 - 1.01 0.93 6552 130 0.3084 0.3022 3.6772 3.7183| | 26: 1.01 - 0.99 0.96 6767 158 0.3261 0.3300 3.6353 3.6317| | 27: 0.99 - 0.98 0.94 6648 131 0.3411 0.3130 3.6347 3.6089| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.55 0.91 0.97 35668.63| | 2: 2.94 - 2.33 7339 128 0.85 21.33 1.08 1.02 15280.76| | 3: 2.33 - 2.04 6939 150 0.93 12.84 1.11 1.05 4251.49| | 4: 2.04 - 1.85 7170 155 0.93 13.37 1.11 1.05 2699.69| | 5: 1.85 - 1.72 7113 159 0.91 15.86 1.12 1.06 2091.84| | 6: 1.72 - 1.62 7102 142 0.90 16.93 1.11 1.06 1692.76| | 7: 1.62 - 1.54 7104 148 0.88 18.37 1.11 1.08 1435.31| | 8: 1.54 - 1.47 6798 152 0.88 18.64 1.10 1.07 1190.42| | 9: 1.47 - 1.41 6938 155 0.88 18.93 1.10 1.08 1009.55| | 10: 1.41 - 1.36 7022 150 0.88 19.34 1.09 1.06 798.25| | 11: 1.36 - 1.32 6997 151 0.88 18.68 1.08 1.05 651.72| | 12: 1.32 - 1.28 6976 149 0.89 18.03 1.07 1.04 549.66| | 13: 1.28 - 1.25 6907 166 0.88 18.71 1.07 1.04 542.29| | 14: 1.25 - 1.22 7015 113 0.87 20.05 1.08 1.05 539.27| | 15: 1.22 - 1.19 6957 137 0.87 19.85 1.08 1.05 493.68| | 16: 1.19 - 1.17 6604 132 0.88 19.03 1.07 1.04 429.65| | 17: 1.17 - 1.14 6941 135 0.88 19.09 1.08 1.03 372.89| | 18: 1.14 - 1.12 6875 142 0.87 20.15 1.08 1.00 367.04| | 19: 1.12 - 1.10 6949 106 0.86 21.81 1.06 1.00 373.13| | 20: 1.10 - 1.08 6884 147 0.84 23.60 1.06 0.98 374.39| | 21: 1.08 - 1.07 6852 152 0.82 25.20 1.06 0.98 365.15| | 22: 1.07 - 1.05 6838 135 0.81 26.66 1.05 0.97 355.91| | 23: 1.05 - 1.03 6829 159 0.79 28.26 1.05 0.98 350.35| | 24: 1.03 - 1.02 6785 133 0.78 29.76 1.05 0.99 342.70| | 25: 1.02 - 1.01 6552 130 0.76 30.98 1.03 0.94 319.09| | 26: 1.01 - 0.99 6767 158 0.74 32.72 1.03 0.91 299.41| | 27: 0.99 - 0.98 6648 131 0.74 33.06 1.04 0.90 286.54| |alpha: min = 0.90 max = 1.08 mean = 1.02| |beta: min = 286.54 max = 35668.63 mean = 2836.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.46| |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 0.266 2950 Z= 5.583 Angle : 5.179 17.152 4018 Z= 3.711 Chirality : 0.390 1.333 492 Planarity : 0.034 0.145 512 Dihedral : 12.869 86.985 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.97 % Allowed : 3.55 % Favored : 95.48 % Cbeta Deviations : 31.46 % 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: -2.14 (0.37), residues: 386 helix: -2.62 (0.29), residues: 142 sheet: -0.38 (0.60), residues: 62 loop : -0.55 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.016 ARG A 100 TYR 0.135 0.040 TYR B 194 PHE 0.109 0.035 PHE B 119 TRP 0.127 0.045 TRP A 146 HIS 0.079 0.040 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2038 r_free= 0.1985 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300194 | | target function (ml) not normalized (work): 805482.269936 | | target function (ml) not normalized (free): 16530.471291 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2037 0.2038 0.1985 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2037 0.2038 0.1985 n_refl.: 191155 remove outliers: r(all,work,free)=0.2037 0.2039 0.1985 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2034 0.2036 0.1984 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1806 0.1919 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1804 0.1919 n_refl.: 191140 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4089 402.814 291.055 0.434 0.914 0.305 13.296-10.522 100.00 100 1 0.2533 534.497 521.038 0.783 0.915 0.263 10.503-8.327 99.45 178 3 0.2532 565.118 555.747 0.962 0.916 0.243 8.318-6.595 100.00 360 8 0.2473 414.736 402.766 0.958 0.916 0.179 6.588-5.215 100.00 711 7 0.2274 381.101 364.884 0.949 0.916 0.160 5.214-4.128 98.38 1367 28 0.1501 557.435 548.852 1.064 0.917 0.090 4.126-3.266 94.74 2603 46 0.1340 508.132 499.223 1.134 0.918 0.029 3.266-2.585 99.86 5447 97 0.1474 342.774 337.194 1.105 0.919 0.010 2.585-2.046 97.45 10613 204 0.1392 258.603 254.218 1.106 0.921 0.000 2.046-1.619 99.39 21536 464 0.1613 153.054 150.174 1.123 0.924 0.000 1.619-1.281 98.00 42464 925 0.1921 82.395 80.493 1.100 0.929 0.000 1.281-0.980 96.53 101826 2056 0.2332 44.203 41.946 1.074 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0501 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1919 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1804 r_free=0.1919 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.422056 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.325657 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1271 0.1502 0.0231 0.038 1.2 10.5 0.0 0.3 0 11.211 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.02 2.31 1.117 13.092 570.326 0.019 12.98 15.69 2.72 1.235 13.341 570.326 0.017 Individual atomic B min max mean iso aniso Overall: 5.32 73.03 15.03 1.40 435 3274 Protein: 5.32 40.52 11.03 1.40 0 2902 Water: 6.41 73.03 29.45 N/A 435 370 Other: 16.00 30.01 23.01 N/A 0 2 Chain A: 5.32 60.09 13.08 N/A 0 1626 Chain B: 5.32 73.03 12.81 N/A 0 1648 Chain S: 11.60 61.36 30.77 N/A 435 0 Histogram: Values Number of atoms 5.32 - 12.09 2184 12.09 - 18.86 622 18.86 - 25.63 318 25.63 - 32.40 264 32.40 - 39.17 154 39.17 - 45.94 106 45.94 - 52.71 36 52.71 - 59.48 21 59.48 - 66.25 3 66.25 - 73.03 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1569 r_work=0.1297 r_free=0.1564 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1564 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 = 0.1283 r_free = 0.1554 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.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015668 | | target function (ls_wunit_k1) not normalized (work): 2934.565948 | | target function (ls_wunit_k1) not normalized (free): 117.821733 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1554 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1630 n_refl.: 191140 remove outliers: r(all,work,free)=0.1470 0.1467 0.1630 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1492 0.1490 0.1639 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1273 0.1543 n_refl.: 191140 remove outliers: r(all,work,free)=0.1279 0.1273 0.1542 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 0.3608 402.814 376.316 0.472 0.997 0.285 13.296-10.522 100.00 100 1 0.2098 534.497 526.244 0.717 0.998 0.241 10.503-8.327 99.45 178 3 0.1783 565.118 561.660 0.856 0.998 0.220 8.318-6.595 100.00 360 8 0.1701 414.736 413.047 0.878 0.998 0.160 6.588-5.215 100.00 711 7 0.1540 381.101 373.641 0.857 0.999 0.150 5.214-4.128 98.38 1367 28 0.0907 557.435 555.000 0.943 0.999 0.059 4.126-3.266 94.74 2603 46 0.0835 508.132 504.152 1.008 1.000 0.024 3.266-2.585 99.86 5447 97 0.0924 342.774 340.265 0.989 0.999 0.010 2.585-2.046 97.45 10613 204 0.0951 258.603 256.346 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1084 153.054 151.398 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1274 82.395 81.423 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.152 0.988 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0353 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1542 | n_water=805 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1278 r_free=0.1548 | n_water=793 | time (s): 101.580 (total time: 103.940) Filter (q & B) r_work=0.1279 r_free=0.1548 | n_water=789 | time (s): 5.280 (total time: 109.220) Compute maps r_work=0.1279 r_free=0.1548 | n_water=789 | time (s): 2.560 (total time: 111.780) Filter (map) r_work=0.1305 r_free=0.1525 | n_water=648 | time (s): 5.490 (total time: 117.270) Find peaks r_work=0.1305 r_free=0.1525 | n_water=648 | time (s): 0.600 (total time: 117.870) Add new water r_work=0.1329 r_free=0.1559 | n_water=947 | time (s): 4.230 (total time: 122.100) Refine new water occ: r_work=0.1285 r_free=0.1525 adp: r_work=0.1272 r_free=0.1515 occ: r_work=0.1274 r_free=0.1519 adp: r_work=0.1267 r_free=0.1513 occ: r_work=0.1269 r_free=0.1513 adp: r_work=0.1266 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1512 r_work=0.1266 r_free=0.1512 | n_water=947 | time (s): 84.490 (total time: 206.590) Filter (q & B) r_work=0.1270 r_free=0.1517 | n_water=883 | time (s): 4.400 (total time: 210.990) Filter (dist only) r_work=0.1270 r_free=0.1517 | n_water=882 | time (s): 112.400 (total time: 323.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.822249 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 569.138722 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1253 0.1531 0.0278 0.040 1.1 14.8 0.0 0.3 0 11.911 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.31 2.78 2.046 15.123 569.139 0.015 12.35 15.23 2.88 2.439 15.179 569.139 0.014 Individual atomic B min max mean iso aniso Overall: 5.45 68.18 16.21 1.19 514 3272 Protein: 5.45 40.18 10.98 1.19 0 2902 Water: 6.57 68.18 33.41 N/A 514 368 Other: 16.33 33.77 25.05 N/A 0 2 Chain A: 5.54 56.26 13.00 N/A 0 1624 Chain B: 5.45 68.18 12.83 N/A 0 1648 Chain S: 12.11 67.98 37.22 N/A 514 0 Histogram: Values Number of atoms 5.45 - 11.72 2071 11.72 - 18.00 703 18.00 - 24.27 265 24.27 - 30.54 213 30.54 - 36.82 179 36.82 - 43.09 162 43.09 - 49.36 106 49.36 - 55.63 42 55.63 - 61.91 33 61.91 - 68.18 12 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1523 r_work=0.1236 r_free=0.1525 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1525 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 = 0.1229 r_free = 0.1523 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.03 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= 0.1229 r_free= 0.1523 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013541 | | target function (ls_wunit_k1) not normalized (work): 2536.267670 | | target function (ls_wunit_k1) not normalized (free): 105.460435 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1523 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1618 n_refl.: 191139 remove outliers: r(all,work,free)=0.1439 0.1436 0.1618 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1436 0.1433 0.1616 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1236 0.1528 n_refl.: 191139 remove outliers: r(all,work,free)=0.1242 0.1236 0.1528 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3278 402.814 377.045 0.491 0.963 0.271 13.296-10.522 100.00 100 1 0.1896 534.497 528.524 0.766 0.964 0.228 10.503-8.327 99.45 178 3 0.1440 565.118 566.204 0.922 0.964 0.191 8.318-6.595 100.00 360 8 0.1539 414.736 414.735 0.936 0.963 0.151 6.588-5.215 100.00 711 7 0.1362 381.101 376.303 0.912 0.963 0.130 5.214-4.128 98.38 1367 28 0.0833 557.435 555.947 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0762 508.132 505.611 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0860 342.774 341.193 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0901 258.603 256.761 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.611 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.345 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.215 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0544 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1528 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1528 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1528 | n_water=882 | time (s): 3.590 (total time: 3.590) Filter (dist) r_work=0.1240 r_free=0.1531 | n_water=874 | time (s): 111.850 (total time: 115.440) Filter (q & B) r_work=0.1240 r_free=0.1530 | n_water=871 | time (s): 4.030 (total time: 119.470) Compute maps r_work=0.1240 r_free=0.1530 | n_water=871 | time (s): 2.020 (total time: 121.490) Filter (map) r_work=0.1279 r_free=0.1522 | n_water=692 | time (s): 5.190 (total time: 126.680) Find peaks r_work=0.1279 r_free=0.1522 | n_water=692 | time (s): 0.850 (total time: 127.530) Add new water r_work=0.1301 r_free=0.1565 | n_water=997 | time (s): 4.740 (total time: 132.270) Refine new water occ: r_work=0.1254 r_free=0.1526 adp: r_work=0.1255 r_free=0.1526 occ: r_work=0.1251 r_free=0.1524 adp: r_work=0.1251 r_free=0.1524 occ: r_work=0.1248 r_free=0.1523 adp: r_work=0.1247 r_free=0.1522 ADP+occupancy (water only), MIN, final r_work=0.1247 r_free=0.1522 r_work=0.1247 r_free=0.1522 | n_water=997 | time (s): 208.650 (total time: 340.920) Filter (q & B) r_work=0.1252 r_free=0.1526 | n_water=876 | time (s): 4.780 (total time: 345.700) Filter (dist only) r_work=0.1254 r_free=0.1526 | n_water=874 | time (s): 126.750 (total time: 472.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.715875 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.101384 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 0.1243 0.1443 0.0200 0.036 1.1 6.8 0.0 0.0 0 0.858 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.43 14.43 2.00 1.927 14.561 16.101 3.943 12.38 14.01 1.63 2.255 14.459 16.101 3.899 Individual atomic B min max mean iso aniso Overall: 5.55 67.78 15.22 1.04 508 3270 Protein: 5.55 36.24 10.72 1.04 0 2902 Water: 6.71 67.78 30.15 N/A 508 366 Other: 14.00 29.32 21.66 N/A 0 2 Chain A: 5.55 55.23 12.74 N/A 0 1624 Chain B: 5.55 67.78 12.50 N/A 0 1646 Chain S: 13.40 63.69 31.93 N/A 508 0 Histogram: Values Number of atoms 5.55 - 11.77 2140 11.77 - 17.99 687 17.99 - 24.22 286 24.22 - 30.44 240 30.44 - 36.66 187 36.66 - 42.89 129 42.89 - 49.11 76 49.11 - 55.34 22 55.34 - 61.56 8 61.56 - 67.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1401 r_work=0.1239 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1401 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1393 target_work(ml) = 3.893 | | 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= 0.1232 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892594 | | target function (ml) not normalized (work): 729075.082034 | | target function (ml) not normalized (free): 15232.608613 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1232 0.1392 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1446 0.1446 0.1485 n_refl.: 191139 remove outliers: r(all,work,free)=0.1446 0.1446 0.1485 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1440 0.1482 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1232 0.1229 0.1386 n_refl.: 191139 remove outliers: r(all,work,free)=0.1231 0.1228 0.1386 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3835 398.895 353.235 0.418 0.946 0.248 13.296-10.522 98.02 98 1 0.2338 528.900 510.474 0.718 0.947 0.229 10.503-8.327 98.35 176 3 0.1979 555.265 555.592 0.883 0.947 0.178 8.318-6.595 100.00 360 8 0.2099 414.736 409.378 0.901 0.947 0.140 6.588-5.215 100.00 711 7 0.1878 381.101 370.590 0.885 0.947 0.114 5.214-4.128 98.38 1367 28 0.1172 557.435 551.772 0.973 0.947 0.090 4.126-3.266 94.74 2603 46 0.1097 508.132 501.124 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1091 342.774 339.065 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0977 258.603 255.730 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0980 153.054 151.395 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.483 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.315 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1021 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1228 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1386 | n_water=874 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1228 r_free=0.1387 | n_water=872 | time (s): 107.610 (total time: 110.240) Filter (q & B) r_work=0.1229 r_free=0.1386 | n_water=860 | time (s): 4.910 (total time: 115.150) Compute maps r_work=0.1229 r_free=0.1386 | n_water=860 | time (s): 2.030 (total time: 117.180) Filter (map) r_work=0.1249 r_free=0.1382 | n_water=727 | time (s): 4.040 (total time: 121.220) Find peaks r_work=0.1249 r_free=0.1382 | n_water=727 | time (s): 0.580 (total time: 121.800) Add new water r_work=0.1264 r_free=0.1402 | n_water=960 | time (s): 5.250 (total time: 127.050) Refine new water occ: r_work=0.1217 r_free=0.1374 adp: r_work=0.1210 r_free=0.1369 occ: r_work=0.1207 r_free=0.1371 adp: r_work=0.1207 r_free=0.1371 occ: r_work=0.1207 r_free=0.1371 adp: r_work=0.1207 r_free=0.1371 ADP+occupancy (water only), MIN, final r_work=0.1207 r_free=0.1371 r_work=0.1207 r_free=0.1371 | n_water=960 | time (s): 149.670 (total time: 276.720) Filter (q & B) r_work=0.1213 r_free=0.1380 | n_water=842 | time (s): 4.210 (total time: 280.930) Filter (dist only) r_work=0.1213 r_free=0.1379 | n_water=841 | time (s): 106.610 (total time: 387.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.534650 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.487162 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 0.1213 0.1385 0.0171 0.034 1.1 5.6 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 13.85 1.71 1.821 14.048 15.487 3.876 12.05 13.83 1.79 1.902 14.017 15.487 3.868 Individual atomic B min max mean iso aniso Overall: 5.52 67.39 14.74 1.00 476 3269 Protein: 5.52 33.25 10.66 1.00 0 2902 Water: 5.71 67.39 28.83 N/A 476 365 Other: 14.00 28.25 21.13 N/A 0 2 Chain A: 5.52 54.24 12.61 N/A 0 1623 Chain B: 5.53 67.39 12.42 N/A 0 1646 Chain S: 5.71 63.71 30.02 N/A 476 0 Histogram: Values Number of atoms 5.52 - 11.70 2122 11.70 - 17.89 725 17.89 - 24.08 336 24.08 - 30.27 202 30.27 - 36.45 151 36.45 - 42.64 111 42.64 - 48.83 71 48.83 - 55.02 20 55.02 - 61.20 5 61.20 - 67.39 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1383 r_work=0.1205 r_free=0.1384 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1384 target_work(ml) = 3.868 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1377 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.866044 | | target function (ml) not normalized (work): 724079.118242 | | target function (ml) not normalized (free): 15153.583975 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1378 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1417 0.1416 0.1483 n_refl.: 191133 remove outliers: r(all,work,free)=0.1417 0.1416 0.1483 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1410 0.1409 0.1479 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1373 n_refl.: 191133 remove outliers: r(all,work,free)=0.1204 0.1201 0.1373 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3829 361.382 323.847 0.409 0.949 0.231 13.296-10.522 98.02 98 1 0.2460 479.160 459.777 0.701 0.951 0.199 10.503-8.327 98.35 176 3 0.2180 503.046 494.527 0.858 0.951 0.159 8.318-6.595 100.00 360 8 0.2247 375.733 368.987 0.890 0.951 0.120 6.588-5.215 100.00 711 7 0.1954 345.261 335.122 0.880 0.951 0.110 5.214-4.128 98.38 1367 28 0.1216 505.012 499.154 0.969 0.951 0.070 4.126-3.266 94.74 2603 46 0.1125 460.346 453.913 1.031 0.951 0.005 3.266-2.585 99.86 5447 97 0.1097 310.538 307.172 1.018 0.950 0.000 2.585-2.046 97.45 10613 204 0.0940 234.283 231.799 1.030 0.950 0.000 2.046-1.619 99.39 21536 464 0.0914 138.660 137.335 1.054 0.948 0.000 1.619-1.281 98.00 42464 925 0.0989 74.647 73.923 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.045 38.381 1.040 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1144 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1373 | n_water=841 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1201 r_free=0.1373 | n_water=841 | time (s): 96.810 (total time: 99.480) Filter (q & B) r_work=0.1201 r_free=0.1372 | n_water=833 | time (s): 4.290 (total time: 103.770) Compute maps r_work=0.1201 r_free=0.1372 | n_water=833 | time (s): 1.850 (total time: 105.620) Filter (map) r_work=0.1222 r_free=0.1367 | n_water=724 | time (s): 4.330 (total time: 109.950) Find peaks r_work=0.1222 r_free=0.1367 | n_water=724 | time (s): 0.700 (total time: 110.650) Add new water r_work=0.1235 r_free=0.1385 | n_water=965 | time (s): 4.430 (total time: 115.080) Refine new water occ: r_work=0.1196 r_free=0.1359 adp: r_work=0.1196 r_free=0.1358 occ: r_work=0.1194 r_free=0.1357 adp: r_work=0.1194 r_free=0.1357 occ: r_work=0.1192 r_free=0.1356 adp: r_work=0.1192 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1356 r_work=0.1192 r_free=0.1356 | n_water=965 | time (s): 188.090 (total time: 303.170) Filter (q & B) r_work=0.1195 r_free=0.1363 | n_water=885 | time (s): 4.460 (total time: 307.630) Filter (dist only) r_work=0.1195 r_free=0.1362 | n_water=884 | time (s): 115.940 (total time: 423.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533866 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.757124 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1371 0.0173 0.036 1.1 8.9 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.71 1.73 1.789 14.097 14.757 3.766 12.02 13.75 1.73 1.840 14.076 14.757 3.763 Individual atomic B min max mean iso aniso Overall: 5.57 67.14 14.90 0.96 520 3268 Protein: 5.57 32.23 10.60 0.96 0 2902 Water: 5.79 67.14 29.02 N/A 520 364 Other: 13.83 27.47 20.65 N/A 0 2 Chain A: 5.59 53.61 12.53 N/A 0 1623 Chain B: 5.57 67.14 12.33 N/A 0 1645 Chain S: 5.79 63.70 30.44 N/A 520 0 Histogram: Values Number of atoms 5.57 - 11.73 2144 11.73 - 17.88 720 17.88 - 24.04 308 24.04 - 30.20 222 30.20 - 36.36 177 36.36 - 42.51 124 42.51 - 48.67 67 48.67 - 54.83 19 54.83 - 60.98 5 60.98 - 67.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1375 r_work=0.1202 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1375 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1377 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762429 | | target function (ml) not normalized (work): 704672.810210 | | target function (ml) not normalized (free): 14756.389312 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1377 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1410 0.1409 0.1482 n_refl.: 191133 remove outliers: r(all,work,free)=0.1410 0.1409 0.1482 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1402 0.1401 0.1477 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1377 n_refl.: 191133 remove outliers: r(all,work,free)=0.1204 0.1200 0.1377 n_refl.: 191132 ======================== 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 0.3913 361.382 321.740 0.394 0.948 0.218 13.296-10.522 97.03 97 1 0.2390 481.435 458.677 0.696 0.950 0.186 10.503-8.327 98.35 176 3 0.2179 503.046 495.514 0.858 0.951 0.151 8.318-6.595 100.00 360 8 0.2195 375.733 370.019 0.891 0.950 0.114 6.588-5.215 100.00 711 7 0.1939 345.261 334.682 0.882 0.951 0.093 5.214-4.128 98.38 1367 28 0.1212 505.012 499.438 0.970 0.951 0.039 4.126-3.266 94.74 2603 46 0.1141 460.346 453.737 1.034 0.951 0.005 3.266-2.585 99.86 5447 97 0.1105 310.538 307.200 1.019 0.951 0.000 2.585-2.046 97.45 10613 204 0.0946 234.283 231.806 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0915 138.660 137.349 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0980 74.647 73.934 1.048 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1656 40.045 38.374 1.033 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1352 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1377 | n_water=884 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1201 r_free=0.1376 | n_water=882 | time (s): 116.710 (total time: 119.260) Filter (q & B) r_work=0.1201 r_free=0.1376 | n_water=871 | time (s): 4.060 (total time: 123.320) Compute maps r_work=0.1201 r_free=0.1376 | n_water=871 | time (s): 1.950 (total time: 125.270) Filter (map) r_work=0.1222 r_free=0.1369 | n_water=761 | time (s): 5.320 (total time: 130.590) Find peaks r_work=0.1222 r_free=0.1369 | n_water=761 | time (s): 0.880 (total time: 131.470) Add new water r_work=0.1230 r_free=0.1375 | n_water=966 | time (s): 4.270 (total time: 135.740) Refine new water occ: r_work=0.1198 r_free=0.1348 adp: r_work=0.1198 r_free=0.1347 occ: r_work=0.1197 r_free=0.1349 adp: r_work=0.1197 r_free=0.1349 occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1351 r_work=0.1195 r_free=0.1351 | n_water=966 | time (s): 172.690 (total time: 308.430) Filter (q & B) r_work=0.1199 r_free=0.1363 | n_water=892 | time (s): 4.660 (total time: 313.090) Filter (dist only) r_work=0.1199 r_free=0.1363 | n_water=891 | time (s): 114.880 (total time: 427.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.491202 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.132849 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 0.1365 0.0163 0.036 1.1 5.6 0.0 0.3 0 0.746 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.65 1.63 1.764 14.017 14.133 3.763 12.06 13.69 1.64 1.919 13.967 14.133 3.761 Individual atomic B min max mean iso aniso Overall: 5.57 66.06 14.78 0.89 527 3268 Protein: 5.57 29.22 10.48 0.89 0 2902 Water: 5.84 66.06 28.80 N/A 527 364 Other: 13.90 24.25 19.07 N/A 0 2 Chain A: 5.62 52.70 12.37 N/A 0 1623 Chain B: 5.57 66.06 12.19 N/A 0 1645 Chain S: 5.84 63.82 30.30 N/A 527 0 Histogram: Values Number of atoms 5.57 - 11.62 2116 11.62 - 17.67 772 17.67 - 23.72 288 23.72 - 29.77 216 29.77 - 35.81 173 35.81 - 41.86 121 41.86 - 47.91 78 47.91 - 53.96 24 53.96 - 60.01 4 60.01 - 66.06 3 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1370 r_work=0.1206 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1370 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1373 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760491 | | target function (ml) not normalized (work): 704306.028084 | | target function (ml) not normalized (free): 14743.860177 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1373 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1492 n_refl.: 191132 remove outliers: r(all,work,free)=0.1409 0.1408 0.1492 n_refl.: 191132 overall B=-0.23 to atoms: r(all,work,free)=0.1373 0.1372 0.1470 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1371 n_refl.: 191132 remove outliers: r(all,work,free)=0.1205 0.1202 0.1371 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 92.08 90 3 0.3796 361.078 310.326 0.392 0.950 0.205 13.296-10.522 97.03 97 1 0.2390 481.435 462.158 0.712 0.952 0.170 10.503-8.327 98.35 176 3 0.2206 503.046 495.795 0.878 0.952 0.150 8.318-6.595 100.00 360 8 0.2206 375.733 370.558 0.907 0.952 0.090 6.588-5.215 100.00 711 7 0.1936 345.261 334.948 0.903 0.952 0.090 5.214-4.128 98.38 1367 28 0.1222 505.012 499.667 0.994 0.952 0.034 4.126-3.266 94.74 2603 46 0.1156 460.346 453.489 1.058 0.952 0.000 3.266-2.585 99.86 5447 97 0.1114 310.538 307.154 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0956 234.283 231.782 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0915 138.660 137.368 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0973 74.647 73.955 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.045 38.382 1.025 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0497 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1371 | n_water=891 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1202 r_free=0.1372 | n_water=890 | time (s): 121.580 (total time: 124.600) Filter (q & B) r_work=0.1203 r_free=0.1371 | n_water=882 | time (s): 4.430 (total time: 129.030) Compute maps r_work=0.1203 r_free=0.1371 | n_water=882 | time (s): 2.240 (total time: 131.270) Filter (map) r_work=0.1224 r_free=0.1368 | n_water=767 | time (s): 5.340 (total time: 136.610) Find peaks r_work=0.1224 r_free=0.1368 | n_water=767 | time (s): 0.910 (total time: 137.520) Add new water r_work=0.1232 r_free=0.1375 | n_water=973 | time (s): 4.220 (total time: 141.740) Refine new water occ: r_work=0.1200 r_free=0.1350 adp: r_work=0.1200 r_free=0.1351 occ: r_work=0.1198 r_free=0.1349 adp: r_work=0.1198 r_free=0.1350 occ: r_work=0.1197 r_free=0.1349 adp: r_work=0.1197 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1350 r_work=0.1197 r_free=0.1350 | n_water=973 | time (s): 155.130 (total time: 296.870) Filter (q & B) r_work=0.1201 r_free=0.1363 | n_water=899 | time (s): 5.050 (total time: 301.920) Filter (dist only) r_work=0.1201 r_free=0.1362 | n_water=897 | time (s): 115.970 (total time: 417.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.519060 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.178005 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1366 0.0162 0.038 1.1 6.6 0.0 0.3 0 0.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.66 1.62 1.715 13.695 14.178 3.761 12.03 13.68 1.64 1.763 13.677 14.178 3.758 Individual atomic B min max mean iso aniso Overall: 5.42 64.78 14.55 0.88 533 3268 Protein: 5.42 28.45 10.24 0.88 0 2902 Water: 5.71 64.78 28.49 N/A 533 364 Other: 13.74 22.13 17.93 N/A 0 2 Chain A: 5.45 52.07 12.09 N/A 0 1623 Chain B: 5.42 64.78 11.93 N/A 0 1645 Chain S: 5.71 63.83 30.13 N/A 533 0 Histogram: Values Number of atoms 5.42 - 11.36 2112 11.36 - 17.29 775 17.29 - 23.23 283 23.23 - 29.16 215 29.16 - 35.10 179 35.10 - 41.04 121 41.04 - 46.97 79 46.97 - 52.91 27 52.91 - 58.84 7 58.84 - 64.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1368 r_work=0.1204 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1368 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757757 | | target function (ml) not normalized (work): 703790.224532 | | target function (ml) not normalized (free): 14734.069219 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1367 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1371 0.1370 0.1464 n_refl.: 191131 remove outliers: r(all,work,free)=0.1371 0.1370 0.1464 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1379 0.1378 0.1468 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1358 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 92.08 90 3 0.3749 361.078 330.618 0.446 0.909 0.215 13.296-10.522 97.03 97 1 0.2407 481.435 460.892 0.746 0.911 0.159 10.503-8.327 98.35 176 3 0.2264 503.046 494.322 0.924 0.911 0.125 8.318-6.595 100.00 360 8 0.2194 375.733 369.873 0.958 0.911 0.098 6.588-5.215 100.00 711 7 0.1939 345.261 334.653 0.951 0.911 0.080 5.214-4.128 98.38 1367 28 0.1234 505.012 499.150 1.049 0.912 0.029 4.126-3.266 94.74 2603 46 0.1162 460.346 452.866 1.116 0.913 0.000 3.266-2.585 99.86 5447 97 0.1113 310.538 306.848 1.098 0.914 0.000 2.585-2.046 97.45 10613 204 0.0960 234.283 231.646 1.106 0.915 0.000 2.046-1.619 99.39 21536 464 0.0909 138.660 137.272 1.123 0.918 0.000 1.619-1.281 98.00 42464 925 0.0950 74.647 73.991 1.110 0.922 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.045 38.359 1.074 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0585 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1358 | n_water=897 | time (s): 2.640 (total time: 2.640) Filter (dist) r_work=0.1193 r_free=0.1358 | n_water=897 | time (s): 117.920 (total time: 120.560) Filter (q & B) r_work=0.1193 r_free=0.1357 | n_water=892 | time (s): 4.300 (total time: 124.860) Compute maps r_work=0.1193 r_free=0.1357 | n_water=892 | time (s): 1.550 (total time: 126.410) Filter (map) r_work=0.1215 r_free=0.1356 | n_water=774 | time (s): 4.360 (total time: 130.770) Find peaks r_work=0.1215 r_free=0.1356 | n_water=774 | time (s): 0.880 (total time: 131.650) Add new water r_work=0.1222 r_free=0.1363 | n_water=975 | time (s): 4.820 (total time: 136.470) Refine new water occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1190 r_free=0.1342 occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1188 r_free=0.1342 occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1188 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1342 r_work=0.1188 r_free=0.1342 | n_water=975 | time (s): 125.270 (total time: 261.740) Filter (q & B) r_work=0.1193 r_free=0.1352 | n_water=886 | time (s): 4.800 (total time: 266.540) Filter (dist only) r_work=0.1193 r_free=0.1352 | n_water=884 | time (s): 113.860 (total time: 380.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.512234 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.228517 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 0.1196 0.1355 0.0159 0.038 1.1 5.3 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.55 1.59 1.675 13.607 14.229 3.757 11.96 13.57 1.61 1.691 13.604 14.229 3.754 Individual atomic B min max mean iso aniso Overall: 5.49 64.02 14.43 0.87 520 3268 Protein: 5.49 28.20 10.31 0.87 0 2902 Water: 5.87 64.02 27.96 N/A 520 364 Other: 13.81 22.21 18.01 N/A 0 2 Chain A: 5.59 51.75 12.12 N/A 0 1623 Chain B: 5.49 63.97 11.97 N/A 0 1645 Chain S: 5.87 64.02 29.45 N/A 520 0 Histogram: Values Number of atoms 5.49 - 11.34 2070 11.34 - 17.20 816 17.20 - 23.05 300 23.05 - 28.90 216 28.90 - 34.76 162 34.76 - 40.61 102 40.61 - 46.46 86 46.46 - 52.32 23 52.32 - 58.17 10 58.17 - 64.02 3 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1357 r_work=0.1196 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1357 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1357 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754136 | | target function (ml) not normalized (work): 703112.131436 | | target function (ml) not normalized (free): 14720.580389 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1357 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1478 n_refl.: 191131 remove outliers: r(all,work,free)=0.1391 0.1389 0.1478 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1393 0.1391 0.1480 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1193 0.1355 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1355 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3671 361.078 331.445 0.418 0.973 0.220 13.296-10.522 96.04 96 1 0.2331 480.672 456.591 0.692 0.974 0.160 10.503-8.327 98.35 176 3 0.2290 503.046 494.206 0.858 0.975 0.135 8.318-6.595 100.00 360 8 0.2241 375.733 369.784 0.891 0.975 0.099 6.588-5.215 100.00 711 7 0.1964 345.261 334.503 0.886 0.975 0.083 5.214-4.128 98.38 1367 28 0.1240 505.012 498.913 0.978 0.976 0.034 4.126-3.266 94.74 2603 46 0.1175 460.346 452.792 1.043 0.977 0.000 3.266-2.585 99.86 5447 97 0.1119 310.538 306.867 1.026 0.978 0.000 2.585-2.046 97.45 10613 204 0.0962 234.283 231.647 1.034 0.980 0.000 2.046-1.619 99.39 21536 464 0.0908 138.660 137.304 1.050 0.984 0.000 1.619-1.281 98.00 42464 925 0.0945 74.647 74.007 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.045 38.348 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1355 | n_water=884 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1193 r_free=0.1355 | n_water=884 | time (s): 118.320 (total time: 120.750) Filter (q & B) r_work=0.1194 r_free=0.1351 | n_water=872 | time (s): 5.050 (total time: 125.800) Compute maps r_work=0.1194 r_free=0.1351 | n_water=872 | time (s): 1.890 (total time: 127.690) Filter (map) r_work=0.1214 r_free=0.1358 | n_water=777 | time (s): 4.440 (total time: 132.130) Find peaks r_work=0.1214 r_free=0.1358 | n_water=777 | time (s): 0.890 (total time: 133.020) Add new water r_work=0.1221 r_free=0.1367 | n_water=988 | time (s): 4.990 (total time: 138.010) Refine new water occ: r_work=0.1188 r_free=0.1337 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1186 r_free=0.1336 adp: r_work=0.1186 r_free=0.1337 occ: r_work=0.1184 r_free=0.1336 adp: r_work=0.1184 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1337 r_work=0.1184 r_free=0.1337 | n_water=988 | time (s): 261.870 (total time: 399.880) Filter (q & B) r_work=0.1189 r_free=0.1346 | n_water=908 | time (s): 4.550 (total time: 404.430) Filter (dist only) r_work=0.1190 r_free=0.1345 | n_water=906 | time (s): 113.520 (total time: 517.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.479033 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.515685 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 0.039 1.1 8.5 0.0 0.3 0 0.740 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.52 1.59 1.678 13.730 13.516 3.755 11.94 13.56 1.62 1.682 13.726 13.516 3.755 Individual atomic B min max mean iso aniso Overall: 5.50 64.08 14.62 0.86 542 3268 Protein: 5.50 28.05 10.33 0.86 0 2902 Water: 5.95 64.08 28.36 N/A 542 364 Other: 13.86 22.17 18.02 N/A 0 2 Chain A: 5.62 51.65 12.12 N/A 0 1623 Chain B: 5.50 63.61 11.97 N/A 0 1645 Chain S: 5.95 64.08 30.18 N/A 542 0 Histogram: Values Number of atoms 5.50 - 11.36 2075 11.36 - 17.21 817 17.21 - 23.07 287 23.07 - 28.93 211 28.93 - 34.79 183 34.79 - 40.65 112 40.65 - 46.51 88 46.51 - 52.36 24 52.36 - 58.22 10 58.22 - 64.08 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1356 r_work=0.1194 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1356 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1358 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754451 | | target function (ml) not normalized (work): 703167.465252 | | target function (ml) not normalized (free): 14727.380779 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1489 n_refl.: 191130 remove outliers: r(all,work,free)=0.1393 0.1391 0.1489 n_refl.: 191130 overall B=-0.00 to atoms: r(all,work,free)=0.1392 0.1390 0.1488 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1192 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1196 0.1192 0.1358 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3661 361.078 330.859 0.403 0.974 0.198 13.296-10.522 96.04 96 1 0.2382 480.672 460.469 0.698 0.976 0.155 10.503-8.327 98.35 176 3 0.2261 503.046 494.360 0.859 0.976 0.124 8.318-6.595 100.00 360 8 0.2191 375.733 370.299 0.890 0.976 0.086 6.588-5.215 100.00 711 7 0.1960 345.261 334.715 0.886 0.977 0.073 5.214-4.128 98.38 1367 28 0.1233 505.012 499.182 0.978 0.978 0.039 4.126-3.266 94.74 2603 46 0.1164 460.346 452.836 1.042 0.979 0.005 3.266-2.585 99.86 5447 97 0.1123 310.538 306.872 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0965 234.283 231.607 1.032 0.983 0.000 2.046-1.619 99.39 21536 464 0.0908 138.660 137.292 1.049 0.987 0.000 1.619-1.281 98.00 42464 925 0.0945 74.647 74.000 1.040 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.045 38.336 1.009 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0094 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1358 After: r_work=0.1193 r_free=0.1359 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1359 | n_water=906 | time (s): 2.780 (total time: 2.780) Filter (dist) r_work=0.1193 r_free=0.1359 | n_water=906 | time (s): 122.030 (total time: 124.810) Filter (q & B) r_work=0.1193 r_free=0.1358 | n_water=897 | time (s): 5.380 (total time: 130.190) Compute maps r_work=0.1193 r_free=0.1358 | n_water=897 | time (s): 2.350 (total time: 132.540) Filter (map) r_work=0.1214 r_free=0.1356 | n_water=788 | time (s): 5.430 (total time: 137.970) Find peaks r_work=0.1214 r_free=0.1356 | n_water=788 | time (s): 0.760 (total time: 138.730) Add new water r_work=0.1220 r_free=0.1364 | n_water=983 | time (s): 4.210 (total time: 142.940) Refine new water occ: r_work=0.1192 r_free=0.1348 adp: r_work=0.1192 r_free=0.1348 occ: r_work=0.1190 r_free=0.1348 adp: r_work=0.1190 r_free=0.1348 occ: r_work=0.1189 r_free=0.1348 adp: r_work=0.1189 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1349 r_work=0.1189 r_free=0.1349 | n_water=983 | time (s): 180.860 (total time: 323.800) Filter (q & B) r_work=0.1192 r_free=0.1357 | n_water=910 | time (s): 4.250 (total time: 328.050) Filter (dist only) r_work=0.1193 r_free=0.1356 | n_water=908 | time (s): 113.840 (total time: 441.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.577261 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.204806 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 0.1358 0.0165 0.039 1.1 7.5 0.0 0.3 0 0.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.58 1.65 1.675 13.720 14.205 3.755 11.92 13.57 1.65 1.675 13.719 14.205 3.752 Individual atomic B min max mean iso aniso Overall: 5.56 64.11 14.61 0.86 544 3268 Protein: 5.56 28.05 10.35 0.86 0 2902 Water: 6.00 64.11 28.21 N/A 544 364 Other: 13.86 22.13 17.99 N/A 0 2 Chain A: 5.67 51.34 12.11 N/A 0 1623 Chain B: 5.56 62.61 11.96 N/A 0 1645 Chain S: 6.00 64.11 30.05 N/A 544 0 Histogram: Values Number of atoms 5.56 - 11.42 2083 11.42 - 17.27 825 17.27 - 23.12 265 23.12 - 28.98 225 28.98 - 34.83 177 34.83 - 40.69 119 40.69 - 46.54 81 46.54 - 52.40 22 52.40 - 58.25 12 58.25 - 64.11 3 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1357 r_work=0.1193 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1357 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1359 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752288 | | target function (ml) not normalized (work): 702762.234678 | | target function (ml) not normalized (free): 14719.705299 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1365 0.1530 5.695 5.7799| | 2: 2.94 - 2.33 1.00 7339 128 0.1069 0.1322 5.0817 5.177| | 3: 2.33 - 2.04 0.96 6939 150 0.0908 0.1192 4.6581 4.7562| | 4: 2.04 - 1.85 1.00 7170 155 0.0895 0.1039 4.3876 4.5539| | 5: 1.85 - 1.72 0.99 7113 159 0.0925 0.0989 4.1429 4.242| | 6: 1.72 - 1.62 0.99 7102 142 0.0890 0.1049 3.9379 4.0553| | 7: 1.62 - 1.54 0.99 7104 148 0.0883 0.0962 3.7885 3.921| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1286 3.6919 3.8933| | 9: 1.47 - 1.41 0.98 6938 155 0.0922 0.1104 3.6156 3.7394| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1184 3.5521 3.6713| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1116 3.4819 3.5854| | 12: 1.32 - 1.28 0.98 6975 149 0.1032 0.1119 3.4573 3.5743| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1242 3.4346 3.5667| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1581 3.4306 3.6771| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1239 3.4466 3.4932| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1551 3.464 3.6536| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1229 3.433 3.4419| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1706 3.438 3.5315| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1765 3.4197 3.603| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1582 3.4105 3.4346| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2142 3.418 3.5062| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1962 3.4132 3.4155| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2011 3.433 3.4849| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2251 3.4355 3.5099| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2522 3.4494 3.5267| | 26: 1.01 - 0.99 0.96 6767 158 0.2753 0.2863 3.4153 3.4246| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2805 3.4687 3.3956| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7398 127 0.93 11.85 1.00 0.95 11446.82| | 2: 2.94 - 2.33 7339 128 0.92 12.92 0.99 0.95 5213.63| | 3: 2.33 - 2.04 6939 150 0.96 7.67 1.01 0.95 1699.99| | 4: 2.04 - 1.85 7170 155 0.96 7.53 1.00 0.95 988.18| | 5: 1.85 - 1.72 7113 159 0.96 7.93 1.00 0.96 621.97| | 6: 1.72 - 1.62 7102 142 0.96 7.83 1.00 0.96 430.14| | 7: 1.62 - 1.54 7104 148 0.96 7.94 1.01 0.97 326.98| | 8: 1.54 - 1.47 6798 152 0.96 8.09 1.01 0.97 271.65| | 9: 1.47 - 1.41 6938 155 0.96 8.30 1.00 0.98 225.82| | 10: 1.41 - 1.36 7022 150 0.96 8.81 1.00 0.97 199.66| | 11: 1.36 - 1.32 6997 151 0.96 8.86 0.99 0.96 172.99| | 12: 1.32 - 1.28 6975 149 0.96 8.93 0.98 0.95 159.13| | 13: 1.28 - 1.25 6907 166 0.96 9.48 1.01 0.96 156.98| | 14: 1.25 - 1.22 7015 112 0.95 10.65 1.01 0.97 162.32| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 0.98 166.11| | 16: 1.19 - 1.17 6604 132 0.95 11.38 1.01 0.96 159.57| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.96 153.44| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.95 147.64| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.95 151.79| | 20: 1.10 - 1.08 6884 147 0.92 15.26 1.00 0.94 150.97| | 21: 1.08 - 1.07 6852 152 0.91 16.69 1.00 0.93 153.96| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.93 155.09| | 23: 1.05 - 1.03 6827 159 0.87 20.50 0.99 0.92 164.84| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.93 179.16| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.90 182.44| | 26: 1.01 - 0.99 6767 158 0.81 26.64 0.98 0.88 176.98| | 27: 0.99 - 0.98 6647 131 0.82 26.29 0.99 0.87 161.21| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.64 max = 11446.82 mean = 935.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.26| |phase err.(test): min = 0.00 max = 89.83 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1359 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1496 n_refl.: 191130 remove outliers: r(all,work,free)=0.1400 0.1398 0.1496 n_refl.: 191130 overall B=-0.06 to atoms: r(all,work,free)=0.1392 0.1390 0.1491 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1194 0.1191 0.1358 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3684 361.078 328.695 0.395 0.974 0.209 13.296-10.522 96.04 96 1 0.2388 480.672 462.037 0.675 0.976 0.145 10.503-8.327 98.35 176 3 0.2290 503.046 493.906 0.836 0.976 0.117 8.318-6.595 100.00 360 8 0.2194 375.733 370.306 0.866 0.976 0.086 6.588-5.215 100.00 711 7 0.1985 345.261 334.556 0.862 0.977 0.073 5.214-4.128 98.38 1367 28 0.1247 505.012 498.880 0.954 0.978 0.034 4.126-3.266 94.74 2603 46 0.1164 460.346 452.777 1.017 0.979 0.000 3.266-2.585 99.86 5447 97 0.1116 310.538 306.883 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0966 234.283 231.617 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0904 138.660 137.302 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0942 74.647 74.005 1.011 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.045 38.331 0.979 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0121 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2038 0.1985 0.082 5.179 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1919 0.082 5.179 5.2 78.0 14.6 805 0.000 1_settarget: 0.1804 0.1919 0.082 5.179 5.2 78.0 14.6 805 0.000 1_nqh: 0.1804 0.1919 0.082 5.179 5.2 78.0 14.6 805 0.000 1_weight: 0.1804 0.1919 0.082 5.179 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1502 0.038 1.157 5.2 78.0 14.6 805 0.154 1_adp: 0.1298 0.1569 0.038 1.157 5.3 73.0 15.0 805 0.154 1_regHadp: 0.1297 0.1564 0.038 1.157 5.3 73.0 15.0 805 0.154 1_occ: 0.1283 0.1554 0.038 1.157 5.3 73.0 15.0 805 0.154 2_bss: 0.1273 0.1542 0.038 1.157 5.5 73.2 15.2 805 0.154 2_settarget: 0.1273 0.1542 0.038 1.157 5.5 73.2 15.2 805 0.154 2_updatecdl: 0.1273 0.1542 0.038 1.162 5.5 73.2 15.2 805 0.154 2_nqh: 0.1273 0.1542 0.038 1.162 5.5 73.2 15.2 805 0.154 2_sol: 0.1270 0.1517 0.038 1.162 5.5 73.2 16.1 882 n/a 2_weight: 0.1270 0.1517 0.038 1.162 5.5 73.2 16.1 882 n/a 2_xyzrec: 0.1253 0.1531 0.040 1.132 5.5 73.2 16.1 882 n/a 2_adp: 0.1235 0.1523 0.040 1.132 5.5 68.2 16.2 882 n/a 2_regHadp: 0.1236 0.1525 0.040 1.132 5.5 68.2 16.2 882 n/a 2_occ: 0.1229 0.1523 0.040 1.132 5.5 68.2 16.2 882 n/a 3_bss: 0.1236 0.1528 0.040 1.132 5.4 68.2 16.2 882 n/a 3_settarget: 0.1236 0.1528 0.040 1.132 5.4 68.2 16.2 882 n/a 3_updatecdl: 0.1236 0.1528 0.040 1.136 5.4 68.2 16.2 882 n/a 3_nqh: 0.1236 0.1528 0.040 1.136 5.4 68.2 16.2 882 n/a 3_sol: 0.1254 0.1526 0.040 1.136 5.4 68.2 15.4 874 n/a 3_weight: 0.1254 0.1526 0.040 1.136 5.4 68.2 15.4 874 n/a 3_xyzrec: 0.1243 0.1443 0.036 1.102 5.4 68.2 15.4 874 n/a 3_adp: 0.1238 0.1401 0.036 1.102 5.5 67.8 15.2 874 n/a 3_regHadp: 0.1239 0.1401 0.036 1.102 5.5 67.8 15.2 874 n/a 3_occ: 0.1232 0.1393 0.036 1.102 5.5 67.8 15.2 874 n/a 4_bss: 0.1228 0.1386 0.036 1.102 5.5 67.8 15.2 874 n/a 4_settarget: 0.1228 0.1386 0.036 1.102 5.5 67.8 15.2 874 n/a 4_updatecdl: 0.1228 0.1386 0.036 1.106 5.5 67.8 15.2 874 n/a 4_nqh: 0.1228 0.1386 0.036 1.106 5.5 67.8 15.2 874 n/a 4_sol: 0.1213 0.1379 0.036 1.106 5.5 67.8 14.8 841 n/a 4_weight: 0.1213 0.1379 0.036 1.106 5.5 67.8 14.8 841 n/a 4_xyzrec: 0.1213 0.1385 0.034 1.109 5.5 67.8 14.8 841 n/a 4_adp: 0.1205 0.1383 0.034 1.109 5.5 67.4 14.7 841 n/a 4_regHadp: 0.1205 0.1384 0.034 1.109 5.5 67.4 14.7 841 n/a 4_occ: 0.1203 0.1377 0.034 1.109 5.5 67.4 14.7 841 n/a 5_bss: 0.1201 0.1373 0.034 1.109 5.5 67.4 14.7 841 n/a 5_settarget: 0.1201 0.1373 0.034 1.109 5.5 67.4 14.7 841 n/a 5_updatecdl: 0.1201 0.1373 0.034 1.110 5.5 67.4 14.7 841 n/a 5_nqh: 0.1201 0.1373 0.034 1.110 5.5 67.4 14.7 841 n/a 5_sol: 0.1195 0.1362 0.034 1.110 5.5 67.4 14.9 884 n/a 5_weight: 0.1195 0.1362 0.034 1.110 5.5 67.4 14.9 884 n/a 5_xyzrec: 0.1198 0.1371 0.036 1.119 5.5 67.4 14.9 884 n/a 5_adp: 0.1202 0.1375 0.036 1.119 5.6 67.1 14.9 884 n/a 5_regHadp: 0.1202 0.1375 0.036 1.119 5.6 67.1 14.9 884 n/a 5_occ: 0.1200 0.1377 0.036 1.119 5.6 67.1 14.9 884 n/a 6_bss: 0.1200 0.1377 0.036 1.119 5.5 67.1 14.9 884 n/a 6_settarget: 0.1200 0.1377 0.036 1.119 5.5 67.1 14.9 884 n/a 6_updatecdl: 0.1200 0.1377 0.036 1.119 5.5 67.1 14.9 884 n/a 6_nqh: 0.1200 0.1377 0.036 1.119 5.5 67.1 14.9 884 n/a 6_sol: 0.1199 0.1363 0.036 1.119 5.5 67.1 14.9 891 n/a 6_weight: 0.1199 0.1363 0.036 1.119 5.5 67.1 14.9 891 n/a 6_xyzrec: 0.1202 0.1365 0.036 1.121 5.5 67.1 14.9 891 n/a 6_adp: 0.1206 0.1370 0.036 1.121 5.6 66.1 14.8 891 n/a 6_regHadp: 0.1206 0.1370 0.036 1.121 5.6 66.1 14.8 891 n/a 6_occ: 0.1204 0.1373 0.036 1.121 5.6 66.1 14.8 891 n/a 7_bss: 0.1203 0.1371 0.036 1.121 5.3 65.8 14.6 891 n/a 7_settarget: 0.1203 0.1371 0.036 1.121 5.3 65.8 14.6 891 n/a 7_updatecdl: 0.1203 0.1371 0.036 1.122 5.3 65.8 14.6 891 n/a 7_nqh: 0.1203 0.1371 0.036 1.122 5.3 65.8 14.6 891 n/a 7_sol: 0.1201 0.1362 0.036 1.122 5.3 65.8 14.6 897 n/a 7_weight: 0.1201 0.1362 0.036 1.122 5.3 65.8 14.6 897 n/a 7_xyzrec: 0.1203 0.1366 0.038 1.122 5.3 65.8 14.6 897 n/a 7_adp: 0.1204 0.1368 0.038 1.122 5.4 64.8 14.5 897 n/a 7_regHadp: 0.1204 0.1368 0.038 1.122 5.4 64.8 14.5 897 n/a 7_occ: 0.1202 0.1367 0.038 1.122 5.4 64.8 14.5 897 n/a 8_bss: 0.1193 0.1358 0.038 1.122 5.5 64.8 14.6 897 n/a 8_settarget: 0.1193 0.1358 0.038 1.122 5.5 64.8 14.6 897 n/a 8_updatecdl: 0.1193 0.1358 0.038 1.122 5.5 64.8 14.6 897 n/a 8_nqh: 0.1193 0.1358 0.038 1.122 5.5 64.8 14.6 897 n/a 8_sol: 0.1193 0.1352 0.038 1.122 5.5 64.8 14.4 884 n/a 8_weight: 0.1193 0.1352 0.038 1.122 5.5 64.8 14.4 884 n/a 8_xyzrec: 0.1196 0.1355 0.038 1.117 5.5 64.8 14.4 884 n/a 8_adp: 0.1196 0.1357 0.038 1.117 5.5 64.0 14.4 884 n/a 8_regHadp: 0.1196 0.1357 0.038 1.117 5.5 64.0 14.4 884 n/a 8_occ: 0.1195 0.1357 0.038 1.117 5.5 64.0 14.4 884 n/a 9_bss: 0.1193 0.1355 0.038 1.117 5.5 64.0 14.4 884 n/a 9_settarget: 0.1193 0.1355 0.038 1.117 5.5 64.0 14.4 884 n/a 9_updatecdl: 0.1193 0.1355 0.038 1.117 5.5 64.0 14.4 884 n/a 9_nqh: 0.1193 0.1355 0.038 1.117 5.5 64.0 14.4 884 n/a 9_sol: 0.1190 0.1345 0.038 1.117 5.5 64.0 14.6 906 n/a 9_weight: 0.1190 0.1345 0.038 1.117 5.5 64.0 14.6 906 n/a 9_xyzrec: 0.1193 0.1352 0.039 1.112 5.5 64.0 14.6 906 n/a 9_adp: 0.1194 0.1356 0.039 1.112 5.5 64.1 14.6 906 n/a 9_regHadp: 0.1194 0.1356 0.039 1.112 5.5 64.1 14.6 906 n/a 9_occ: 0.1193 0.1358 0.039 1.112 5.5 64.1 14.6 906 n/a 10_bss: 0.1192 0.1358 0.039 1.112 5.5 64.1 14.6 906 n/a 10_settarget: 0.1192 0.1358 0.039 1.112 5.5 64.1 14.6 906 n/a 10_updatecdl: 0.1192 0.1358 0.039 1.112 5.5 64.1 14.6 906 n/a 10_setrh: 0.1193 0.1359 0.039 1.112 5.5 64.1 14.6 906 n/a 10_nqh: 0.1193 0.1359 0.039 1.112 5.5 64.1 14.6 906 n/a 10_sol: 0.1193 0.1356 0.039 1.112 5.5 64.1 14.6 908 n/a 10_weight: 0.1193 0.1356 0.039 1.112 5.5 64.1 14.6 908 n/a 10_xyzrec: 0.1193 0.1358 0.039 1.149 5.5 64.1 14.6 908 n/a 10_adp: 0.1193 0.1357 0.039 1.149 5.6 64.1 14.6 908 n/a 10_regHadp: 0.1193 0.1357 0.039 1.149 5.6 64.1 14.6 908 n/a 10_occ: 0.1192 0.1359 0.039 1.149 5.6 64.1 14.6 908 n/a end: 0.1191 0.1358 0.039 1.149 5.5 64.1 14.6 908 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7435083_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7435083_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.8400 Refinement macro-cycles (run) : 11471.5200 Write final files (write_after_run_outputs) : 177.7900 Total : 11655.1500 Total CPU time: 3.25 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:31:27 PST -0800 (1736735487.61 s) Start R-work = 0.1804, R-free = 0.1919 Final R-work = 0.1191, R-free = 0.1358 =============================================================================== Job complete usr+sys time: 11981.43 seconds wall clock time: 200 minutes 43.57 seconds (12043.57 seconds total)