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_5361003.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5361003.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5361003.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.77, per 1000 atoms: 0.26 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: 2.731 distance_ideal: 2.720 ideal - model: -0.011 slack: 0.000 delta_slack: -0.011 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: 2.725 distance_ideal: 2.710 ideal - model: -0.015 slack: 0.000 delta_slack: -0.015 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: 0.71 Conformation dependent library (CDL) restraints added in 195.1 milliseconds Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.02: 799 1.02 - 1.26: 2523 1.26 - 1.49: 1531 1.49 - 1.73: 1062 1.73 - 1.96: 19 Bond restraints: 5934 Sorted by residual: bond pdb=" C CYS A 106 " pdb=" O CYS A 106 " ideal model delta sigma weight residual 1.235 0.965 0.270 1.26e-02 6.30e+03 4.59e+02 bond pdb=" N SER B 155 " pdb=" H SER B 155 " ideal model delta sigma weight residual 0.860 1.257 -0.397 2.00e-02 2.50e+03 3.94e+02 bond pdb=" N THR A 33 " pdb=" H THR A 33 " ideal model delta sigma weight residual 0.860 1.248 -0.388 2.00e-02 2.50e+03 3.77e+02 bond pdb=" CG2 VAL B 144 " pdb="HG22 VAL B 144 " ideal model delta sigma weight residual 0.970 1.338 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" N VAL A 92 " pdb=" H VAL A 92 " ideal model delta sigma weight residual 0.860 1.222 -0.362 2.00e-02 2.50e+03 3.27e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 5467 4.04 - 8.07: 3528 8.07 - 12.11: 1452 12.11 - 16.14: 326 16.14 - 20.18: 37 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 121.71 134.52 -12.81 6.40e-01 2.44e+00 4.00e+02 angle pdb=" NE ARG B 143 " pdb=" CZ ARG B 143 " pdb=" NH1 ARG B 143 " ideal model delta sigma weight residual 121.50 137.49 -15.99 1.00e+00 1.00e+00 2.56e+02 angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" O ILE A 134 " ideal model delta sigma weight residual 119.51 129.21 -9.70 6.20e-01 2.60e+00 2.45e+02 angle pdb=" O ARG B 143 " pdb=" C ARG B 143 " pdb=" N VAL B 144 " ideal model delta sigma weight residual 122.15 139.84 -17.69 1.14e+00 7.69e-01 2.41e+02 angle pdb=" CA ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 117.71 105.03 12.68 9.20e-01 1.18e+00 1.90e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 1866 18.05 - 36.09: 117 36.09 - 54.14: 51 54.14 - 72.18: 13 72.18 - 90.23: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: 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 -152.64 -27.36 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA VAL A 32 " pdb=" C VAL A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta harmonic sigma weight residual 180.00 156.51 23.49 0 5.00e+00 4.00e-02 2.21e+01 dihedral pdb=" CA VAL A 145 " pdb=" C VAL A 145 " pdb=" N TRP A 146 " pdb=" CA TRP A 146 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.247: 227 0.247 - 0.493: 152 0.493 - 0.738: 90 0.738 - 0.984: 18 0.984 - 1.230: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ALA B 57 " pdb=" N ALA B 57 " pdb=" C ALA B 57 " pdb=" CB ALA B 57 " both_signs ideal model delta sigma weight residual False 2.48 3.72 -1.23 2.00e-01 2.50e+01 3.78e+01 chirality pdb=" CA LEU B 171 " pdb=" N LEU B 171 " pdb=" C LEU B 171 " pdb=" CB LEU B 171 " both_signs ideal model delta sigma weight residual False 2.51 1.36 1.15 2.00e-01 2.50e+01 3.28e+01 chirality pdb=" CA GLN A 138 " pdb=" N GLN A 138 " pdb=" C GLN A 138 " pdb=" CB GLN A 138 " both_signs ideal model delta sigma weight residual False 2.51 3.62 -1.11 2.00e-01 2.50e+01 3.06e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.159 2.00e-02 2.50e+03 7.61e-02 1.74e+02 pdb=" CG PHE B 164 " -0.121 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.079 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.084 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 195 " -0.044 2.00e-02 2.50e+03 6.84e-02 1.40e+02 pdb=" CG TYR B 195 " -0.101 2.00e-02 2.50e+03 pdb=" CD1 TYR B 195 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR B 195 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 TYR B 195 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR B 195 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 195 " -0.124 2.00e-02 2.50e+03 pdb=" OH TYR B 195 " 0.034 2.00e-02 2.50e+03 pdb=" HD1 TYR B 195 " 0.083 2.00e-02 2.50e+03 pdb=" HD2 TYR B 195 " 0.119 2.00e-02 2.50e+03 pdb=" HE1 TYR B 195 " 0.049 2.00e-02 2.50e+03 pdb=" HE2 TYR B 195 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " 0.031 2.00e-02 2.50e+03 5.86e-02 1.38e+02 pdb=" CG TRP B 139 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.051 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.115 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.049 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.117 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.073 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.073 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.022 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.67: 32 1.67 - 2.40: 2994 2.40 - 3.13: 22657 3.13 - 3.87: 32746 3.87 - 4.60: 51838 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110267 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.934 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.000 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.104 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.109 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.165 2.620 ... (remaining 110262 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_5361003_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= 0.2029 r_free= 0.1980 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.297239 | | target function (ml) not normalized (work): 804928.803924 | | target function (ml) not normalized (free): 16553.660523 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2155 0.1895 6.6994 6.3045| | 2: 2.94 - 2.33 1.00 7339 128 0.1597 0.1531 5.5323 5.5658| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1557 5.1601 5.1693| | 4: 2.04 - 1.85 1.00 7170 155 0.1753 0.1691 4.9734 5.0861| | 5: 1.85 - 1.72 0.99 7113 159 0.1910 0.1746 4.793 4.8577| | 6: 1.72 - 1.62 0.99 7102 142 0.1985 0.2017 4.6626 4.755| | 7: 1.62 - 1.54 0.99 7104 148 0.2003 0.1676 4.554 4.4899| | 8: 1.54 - 1.47 0.96 6798 152 0.2036 0.2136 4.4739 4.4701| | 9: 1.47 - 1.41 0.98 6938 155 0.2073 0.2212 4.3891 4.4286| | 10: 1.41 - 1.36 0.99 7022 150 0.2125 0.2181 4.3113 4.3891| | 11: 1.36 - 1.32 0.99 6997 151 0.2104 0.2288 4.2299 4.3013| | 12: 1.32 - 1.28 0.98 6976 149 0.2066 0.2115 4.1736 4.2517| | 13: 1.28 - 1.25 0.98 6907 166 0.2019 0.2061 4.1205 4.1543| | 14: 1.25 - 1.22 0.98 7015 113 0.2054 0.2278 4.0693 4.2155| | 15: 1.22 - 1.19 0.98 6957 137 0.2087 0.2000 4.0389 4.0319| | 16: 1.19 - 1.17 0.93 6604 132 0.2126 0.2330 4.0114 4.0956| | 17: 1.17 - 1.14 0.98 6941 135 0.2139 0.1771 3.949 3.9107| | 18: 1.14 - 1.12 0.98 6875 142 0.2211 0.2338 3.91 3.9123| | 19: 1.12 - 1.10 0.97 6949 106 0.2245 0.2753 3.8613 4.0042| | 20: 1.10 - 1.08 0.97 6884 147 0.2313 0.2192 3.8199 3.8047| | 21: 1.08 - 1.07 0.97 6852 152 0.2410 0.2862 3.7852 3.8591| | 22: 1.07 - 1.05 0.97 6838 135 0.2539 0.2761 3.7487 3.7931| | 23: 1.05 - 1.03 0.97 6829 159 0.2713 0.2457 3.7284 3.7528| | 24: 1.03 - 1.02 0.96 6785 133 0.2853 0.3046 3.6981 3.7595| | 25: 1.02 - 1.01 0.93 6552 130 0.3056 0.3002 3.6691 3.7543| | 26: 1.01 - 0.99 0.96 6767 158 0.3144 0.3326 3.6158 3.6487| | 27: 0.99 - 0.98 0.94 6648 131 0.3387 0.3191 3.6327 3.5984| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.24 0.91 0.97 34687.91| | 2: 2.94 - 2.33 7339 128 0.86 21.07 1.09 1.02 14946.27| | 3: 2.33 - 2.04 6939 150 0.93 12.81 1.10 1.04 4307.13| | 4: 2.04 - 1.85 7170 155 0.92 14.22 1.11 1.05 3022.91| | 5: 1.85 - 1.72 7113 159 0.90 16.14 1.11 1.06 2172.22| | 6: 1.72 - 1.62 7102 142 0.90 16.84 1.12 1.08 1657.67| | 7: 1.62 - 1.54 7104 148 0.90 16.64 1.11 1.07 1211.37| | 8: 1.54 - 1.47 6798 152 0.89 17.49 1.10 1.07 1060.18| | 9: 1.47 - 1.41 6938 155 0.89 18.33 1.10 1.07 929.97| | 10: 1.41 - 1.36 7022 150 0.87 20.19 1.10 1.06 870.08| | 11: 1.36 - 1.32 6997 151 0.87 20.41 1.09 1.04 754.62| | 12: 1.32 - 1.28 6976 149 0.87 20.66 1.07 1.02 688.56| | 13: 1.28 - 1.25 6907 166 0.87 20.11 1.07 1.03 618.87| | 14: 1.25 - 1.22 7015 113 0.87 20.71 1.07 1.05 580.16| | 15: 1.22 - 1.19 6957 137 0.87 20.10 1.08 1.06 516.27| | 16: 1.19 - 1.17 6604 132 0.88 19.54 1.08 1.05 462.21| | 17: 1.17 - 1.14 6941 135 0.87 19.90 1.08 1.05 408.67| | 18: 1.14 - 1.12 6875 142 0.87 20.18 1.09 1.03 377.28| | 19: 1.12 - 1.10 6949 106 0.86 21.29 1.07 1.01 361.29| | 20: 1.10 - 1.08 6884 147 0.85 22.47 1.06 0.99 344.83| | 21: 1.08 - 1.07 6852 152 0.84 23.81 1.06 0.98 335.32| | 22: 1.07 - 1.05 6838 135 0.82 25.40 1.06 0.98 324.36| | 23: 1.05 - 1.03 6829 159 0.81 27.02 1.06 0.98 319.65| | 24: 1.03 - 1.02 6785 133 0.79 28.98 1.05 0.99 327.57| | 25: 1.02 - 1.01 6552 130 0.76 31.00 1.03 0.95 319.06| | 26: 1.01 - 0.99 6767 158 0.74 32.98 1.03 0.92 308.59| | 27: 0.99 - 0.98 6648 131 0.74 32.83 1.03 0.90 284.28| |alpha: min = 0.90 max = 1.08 mean = 1.02| |beta: min = 284.28 max = 34687.91 mean = 2799.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 21.45| |phase err.(test): min = 0.00 max = 89.78 mean = 21.72| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.285 2950 Z= 5.429 Angle : 5.217 17.689 4018 Z= 3.692 Chirality : 0.390 1.230 492 Planarity : 0.034 0.123 512 Dihedral : 12.862 90.227 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.18 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 31.74 % 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: -2.34 (0.38), residues: 386 helix: -2.39 (0.32), residues: 144 sheet: -0.76 (0.52), residues: 86 loop : -0.89 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.024 ARG B 97 TYR 0.099 0.036 TYR B 192 PHE 0.150 0.040 PHE A 164 TRP 0.130 0.042 TRP B 139 HIS 0.063 0.034 HIS B 116 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= 0.2029 r_free= 0.1980 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.297239 | | target function (ml) not normalized (work): 804928.803924 | | target function (ml) not normalized (free): 16553.660523 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2027 0.2029 0.1980 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2027 0.2029 0.1980 n_refl.: 191155 remove outliers: r(all,work,free)=0.2027 0.2029 0.1980 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2028 0.2030 0.1981 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1796 0.1794 0.1919 n_refl.: 191145 remove outliers: r(all,work,free)=0.1794 0.1792 0.1919 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 0.4063 402.814 291.785 0.422 0.935 0.299 13.296-10.522 99.01 99 1 0.2493 528.187 520.559 0.770 0.936 0.259 10.503-8.327 99.45 178 3 0.2475 565.118 557.175 0.941 0.936 0.243 8.318-6.595 100.00 360 8 0.2481 414.736 402.025 0.947 0.935 0.230 6.588-5.215 100.00 711 7 0.2258 381.101 366.642 0.933 0.935 0.160 5.214-4.128 98.38 1367 28 0.1515 557.435 549.829 1.050 0.935 0.090 4.126-3.266 94.74 2603 46 0.1348 508.132 498.889 1.120 0.934 0.018 3.266-2.585 99.86 5447 97 0.1429 342.774 338.116 1.095 0.931 0.000 2.585-2.046 97.45 10613 204 0.1402 258.603 254.276 1.102 0.928 0.000 2.046-1.619 99.39 21536 464 0.1616 153.054 149.733 1.127 0.922 0.000 1.619-1.281 98.00 42464 925 0.1909 82.395 80.221 1.121 0.913 0.000 1.281-0.980 96.53 101826 2056 0.2298 44.203 41.697 1.122 0.896 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0123 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1792 r_free=0.1919 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1793 r_free=0.1921 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.334147 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.490073 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 0.1270 0.1497 0.0227 0.037 1.2 11.6 0.0 0.3 0 11.167 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 14.97 2.27 1.117 13.118 575.490 0.019 12.96 15.66 2.70 1.220 13.299 575.490 0.017 Individual atomic B min max mean iso aniso Overall: 5.11 73.05 14.93 1.40 435 3274 Protein: 5.11 40.32 10.99 1.40 0 2902 Water: 6.36 73.05 29.15 N/A 435 370 Other: 16.01 30.49 23.25 N/A 0 2 Chain A: 5.36 60.32 13.01 N/A 0 1626 Chain B: 5.11 73.05 12.74 N/A 0 1648 Chain S: 11.79 62.20 30.47 N/A 435 0 Histogram: Values Number of atoms 5.11 - 11.91 2148 11.91 - 18.70 659 18.70 - 25.49 321 25.49 - 32.29 264 32.29 - 39.08 153 39.08 - 45.88 103 45.88 - 52.67 41 52.67 - 59.46 15 59.46 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1566 r_work=0.1295 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1561 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 = 0.1281 r_free = 0.1551 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015677 | | target function (ls_wunit_k1) not normalized (work): 2936.174681 | | target function (ls_wunit_k1) not normalized (free): 116.692620 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1551 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1469 0.1467 0.1629 n_refl.: 191139 remove outliers: r(all,work,free)=0.1469 0.1467 0.1629 n_refl.: 191139 overall B=0.16 to atoms: r(all,work,free)=0.1492 0.1490 0.1638 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1545 n_refl.: 191139 remove outliers: r(all,work,free)=0.1280 0.1275 0.1545 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 0.3602 402.814 376.608 0.471 1.001 0.287 13.296-10.522 99.01 99 1 0.2114 528.187 524.150 0.720 1.003 0.259 10.503-8.327 99.45 178 3 0.1754 565.118 562.111 0.853 1.003 0.213 8.318-6.595 100.00 360 8 0.1739 414.736 410.691 0.874 1.002 0.180 6.588-5.215 100.00 711 7 0.1544 381.101 373.502 0.853 1.003 0.150 5.214-4.128 98.38 1367 28 0.0912 557.435 555.260 0.940 1.003 0.054 4.126-3.266 94.74 2603 46 0.0838 508.132 504.119 1.004 1.004 0.014 3.266-2.585 99.86 5447 97 0.0927 342.774 340.224 0.986 1.003 0.000 2.585-2.046 97.45 10613 204 0.0950 258.603 256.348 0.997 1.004 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.375 1.015 1.004 0.000 1.619-1.281 98.00 42464 925 0.1276 82.395 81.408 1.007 1.004 0.000 1.281-0.980 96.53 101826 2056 0.1873 44.203 42.171 0.984 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0366 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1545 | n_water=805 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1278 r_free=0.1548 | n_water=797 | time (s): 99.990 (total time: 102.540) Filter (q & B) r_work=0.1279 r_free=0.1548 | n_water=792 | time (s): 5.300 (total time: 107.840) Compute maps r_work=0.1279 r_free=0.1548 | n_water=792 | time (s): 1.920 (total time: 109.760) Filter (map) r_work=0.1305 r_free=0.1529 | n_water=657 | time (s): 4.530 (total time: 114.290) Find peaks r_work=0.1305 r_free=0.1529 | n_water=657 | time (s): 0.590 (total time: 114.880) Add new water r_work=0.1329 r_free=0.1563 | n_water=954 | time (s): 4.220 (total time: 119.100) Refine new water occ: r_work=0.1285 r_free=0.1511 adp: r_work=0.1271 r_free=0.1507 occ: r_work=0.1274 r_free=0.1506 adp: r_work=0.1267 r_free=0.1504 occ: r_work=0.1268 r_free=0.1506 adp: r_work=0.1265 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1265 r_free=0.1504 r_work=0.1265 r_free=0.1504 | n_water=954 | time (s): 79.440 (total time: 198.540) Filter (q & B) r_work=0.1269 r_free=0.1509 | n_water=887 | time (s): 5.310 (total time: 203.850) Filter (dist only) r_work=0.1269 r_free=0.1508 | n_water=886 | time (s): 113.430 (total time: 317.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.308241 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 594.793476 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 0.1255 0.1525 0.0270 0.039 1.1 20.1 0.0 0.3 0 11.654 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.25 2.70 2.036 15.178 594.793 0.015 12.30 15.08 2.78 2.366 15.259 594.793 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 71.56 16.39 1.21 518 3272 Protein: 5.39 40.13 10.98 1.21 0 2902 Water: 6.56 71.56 34.09 N/A 518 368 Other: 16.22 33.08 24.65 N/A 0 2 Chain A: 5.47 56.36 13.00 N/A 0 1624 Chain B: 5.39 68.21 12.81 N/A 0 1648 Chain S: 13.70 71.56 38.42 N/A 518 0 Histogram: Values Number of atoms 5.39 - 12.01 2129 12.01 - 18.62 683 18.62 - 25.24 262 25.24 - 31.86 205 31.86 - 38.47 168 38.47 - 45.09 172 45.09 - 51.71 87 51.71 - 58.32 54 58.32 - 64.94 23 64.94 - 71.56 7 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1509 r_work=0.1231 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1510 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 = 0.1224 r_free = 0.1510 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013411 | | target function (ls_wunit_k1) not normalized (work): 2511.883946 | | target function (ls_wunit_k1) not normalized (free): 105.406444 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1224 0.1510 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1603 n_refl.: 191139 remove outliers: r(all,work,free)=0.1435 0.1432 0.1603 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1601 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1516 n_refl.: 191139 remove outliers: r(all,work,free)=0.1237 0.1231 0.1515 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3273 402.814 379.893 0.499 0.962 0.281 13.296-10.522 99.01 99 1 0.1900 528.187 520.947 0.763 0.963 0.236 10.503-8.327 99.45 178 3 0.1441 565.118 568.555 0.923 0.963 0.184 8.318-6.595 100.00 360 8 0.1531 414.736 413.715 0.937 0.963 0.160 6.588-5.215 100.00 711 7 0.1329 381.101 376.557 0.913 0.963 0.160 5.214-4.128 98.38 1367 28 0.0818 557.435 556.267 0.995 0.963 0.070 4.126-3.266 94.74 2603 46 0.0765 508.132 505.368 1.059 0.963 0.015 3.266-2.585 99.86 5447 97 0.0865 342.774 341.240 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0899 258.603 256.704 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.593 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1251 82.395 81.353 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1868 44.202 42.217 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0524 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1515 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1515 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1515 | n_water=886 | time (s): 3.320 (total time: 3.320) Filter (dist) r_work=0.1234 r_free=0.1514 | n_water=879 | time (s): 114.070 (total time: 117.390) Filter (q & B) r_work=0.1234 r_free=0.1514 | n_water=877 | time (s): 4.350 (total time: 121.740) Compute maps r_work=0.1234 r_free=0.1514 | n_water=877 | time (s): 1.930 (total time: 123.670) Filter (map) r_work=0.1271 r_free=0.1502 | n_water=693 | time (s): 5.540 (total time: 129.210) Find peaks r_work=0.1271 r_free=0.1502 | n_water=693 | time (s): 0.910 (total time: 130.120) Add new water r_work=0.1295 r_free=0.1536 | n_water=1001 | time (s): 5.390 (total time: 135.510) Refine new water occ: r_work=0.1250 r_free=0.1501 adp: r_work=0.1251 r_free=0.1502 occ: r_work=0.1246 r_free=0.1500 adp: r_work=0.1246 r_free=0.1501 occ: r_work=0.1243 r_free=0.1499 adp: r_work=0.1242 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1500 r_work=0.1242 r_free=0.1500 | n_water=1001 | time (s): 232.600 (total time: 368.110) Filter (q & B) r_work=0.1247 r_free=0.1501 | n_water=879 | time (s): 6.090 (total time: 374.200) Filter (dist only) r_work=0.1247 r_free=0.1501 | n_water=878 | time (s): 122.570 (total time: 496.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.711278 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.573420 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 0.1235 0.1431 0.0196 0.034 1.1 6.8 0.0 0.0 0 0.856 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.31 1.96 1.935 14.613 15.573 3.935 12.34 13.99 1.65 2.246 14.515 15.573 3.897 Individual atomic B min max mean iso aniso Overall: 5.54 69.39 15.30 1.04 512 3270 Protein: 5.54 36.39 10.74 1.04 0 2902 Water: 6.69 69.39 30.37 N/A 512 366 Other: 13.98 28.91 21.45 N/A 0 2 Chain A: 5.54 55.52 12.76 N/A 0 1624 Chain B: 5.55 67.81 12.50 N/A 0 1646 Chain S: 13.29 69.39 32.34 N/A 512 0 Histogram: Values Number of atoms 5.54 - 11.93 2172 11.93 - 18.31 668 18.31 - 24.70 305 24.70 - 31.08 233 31.08 - 37.47 163 37.47 - 43.85 139 43.85 - 50.23 66 50.23 - 56.62 25 56.62 - 63.00 7 63.00 - 69.39 4 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1399 r_work=0.1235 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1401 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1394 target_work(ml) = 3.891 | | 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1394 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891176 | | target function (ml) not normalized (work): 728805.608574 | | target function (ml) not normalized (free): 15227.016762 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1394 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1444 0.1443 0.1491 n_refl.: 191138 remove outliers: r(all,work,free)=0.1444 0.1443 0.1491 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1437 0.1487 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1384 n_refl.: 191138 remove outliers: r(all,work,free)=0.1228 0.1225 0.1384 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3798 398.008 363.862 0.422 0.947 0.241 13.296-10.522 99.01 99 1 0.2457 528.187 509.156 0.706 0.948 0.204 10.503-8.327 98.35 176 3 0.2030 555.265 557.810 0.888 0.948 0.173 8.318-6.595 100.00 360 8 0.2098 414.736 408.689 0.898 0.948 0.140 6.588-5.215 100.00 711 7 0.1807 381.101 371.148 0.885 0.948 0.123 5.214-4.128 98.38 1367 28 0.1156 557.435 552.339 0.973 0.948 0.090 4.126-3.266 94.74 2603 46 0.1099 508.132 501.035 1.031 0.948 0.005 3.266-2.585 99.86 5447 97 0.1095 342.774 339.009 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0965 258.603 255.757 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0976 153.054 151.394 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.484 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.316 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1041 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1385 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1385 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1385 | n_water=878 | time (s): 3.050 (total time: 3.050) Filter (dist) r_work=0.1225 r_free=0.1385 | n_water=878 | time (s): 105.530 (total time: 108.580) Filter (q & B) r_work=0.1226 r_free=0.1382 | n_water=862 | time (s): 4.830 (total time: 113.410) Compute maps r_work=0.1226 r_free=0.1382 | n_water=862 | time (s): 2.240 (total time: 115.650) Filter (map) r_work=0.1248 r_free=0.1384 | n_water=734 | time (s): 4.440 (total time: 120.090) Find peaks r_work=0.1248 r_free=0.1384 | n_water=734 | time (s): 0.550 (total time: 120.640) Add new water r_work=0.1262 r_free=0.1404 | n_water=978 | time (s): 4.420 (total time: 125.060) Refine new water occ: r_work=0.1215 r_free=0.1368 adp: r_work=0.1207 r_free=0.1364 occ: r_work=0.1205 r_free=0.1363 adp: r_work=0.1205 r_free=0.1363 occ: r_work=0.1203 r_free=0.1363 adp: r_work=0.1203 r_free=0.1362 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1362 r_work=0.1203 r_free=0.1362 | n_water=978 | time (s): 313.230 (total time: 438.290) Filter (q & B) r_work=0.1208 r_free=0.1370 | n_water=877 | time (s): 5.220 (total time: 443.510) Filter (dist only) r_work=0.1209 r_free=0.1369 | n_water=875 | time (s): 109.900 (total time: 553.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566955 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.922666 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1372 0.0165 0.036 1.1 6.0 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.72 1.65 1.825 14.235 15.923 3.875 11.98 13.67 1.69 1.971 14.182 15.923 3.865 Individual atomic B min max mean iso aniso Overall: 5.50 69.27 15.01 0.99 509 3270 Protein: 5.50 32.99 10.63 0.99 0 2902 Water: 5.82 69.27 29.52 N/A 509 366 Other: 13.92 27.32 20.62 N/A 0 2 Chain A: 5.58 54.06 12.60 N/A 0 1624 Chain B: 5.50 67.22 12.38 N/A 0 1646 Chain S: 5.82 69.27 31.22 N/A 509 0 Histogram: Values Number of atoms 5.50 - 11.88 2170 11.88 - 18.26 702 18.26 - 24.64 303 24.64 - 31.01 228 31.01 - 37.39 161 37.39 - 43.77 135 43.77 - 50.14 54 50.14 - 56.52 18 56.52 - 62.90 5 62.90 - 69.27 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1367 r_work=0.1198 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1367 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1365 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862357 | | target function (ml) not normalized (work): 723396.334072 | | target function (ml) not normalized (free): 15141.752388 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1365 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1423 0.1422 0.1471 n_refl.: 191135 remove outliers: r(all,work,free)=0.1423 0.1422 0.1471 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1417 0.1467 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1360 n_refl.: 191135 remove outliers: r(all,work,free)=0.1193 0.1189 0.1360 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 0.3835 361.353 319.618 0.399 0.970 0.241 13.296-10.522 97.03 97 1 0.2318 481.397 452.820 0.680 0.972 0.198 10.503-8.327 98.35 176 3 0.2158 503.006 497.716 0.845 0.972 0.180 8.318-6.595 100.00 360 8 0.2124 375.703 370.213 0.865 0.971 0.110 6.588-5.215 100.00 711 7 0.1882 345.234 335.868 0.860 0.970 0.110 5.214-4.128 98.38 1367 28 0.1177 504.972 500.051 0.947 0.970 0.080 4.126-3.266 94.74 2603 46 0.1120 460.309 453.680 1.007 0.968 0.000 3.266-2.585 99.86 5447 97 0.1098 310.513 307.072 0.997 0.965 0.000 2.585-2.046 97.45 10613 204 0.0928 234.265 231.860 1.014 0.962 0.000 2.046-1.619 99.39 21536 464 0.0910 138.649 137.340 1.042 0.955 0.000 1.619-1.281 98.00 42464 925 0.0977 74.641 73.950 1.050 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.042 38.380 1.054 0.925 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0893 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1360 | n_water=875 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1190 r_free=0.1360 | n_water=875 | time (s): 98.980 (total time: 101.920) Filter (q & B) r_work=0.1190 r_free=0.1360 | n_water=866 | time (s): 5.090 (total time: 107.010) Compute maps r_work=0.1190 r_free=0.1360 | n_water=866 | time (s): 1.910 (total time: 108.920) Filter (map) r_work=0.1210 r_free=0.1357 | n_water=755 | time (s): 4.540 (total time: 113.460) Find peaks r_work=0.1210 r_free=0.1357 | n_water=755 | time (s): 0.660 (total time: 114.120) Add new water r_work=0.1221 r_free=0.1376 | n_water=969 | time (s): 4.550 (total time: 118.670) Refine new water occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1335 occ: r_work=0.1186 r_free=0.1334 adp: r_work=0.1186 r_free=0.1334 occ: r_work=0.1184 r_free=0.1333 adp: r_work=0.1184 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1334 r_work=0.1184 r_free=0.1334 | n_water=969 | time (s): 206.830 (total time: 325.500) Filter (q & B) r_work=0.1188 r_free=0.1346 | n_water=893 | time (s): 5.710 (total time: 331.210) Filter (dist only) r_work=0.1189 r_free=0.1348 | n_water=891 | time (s): 114.820 (total time: 446.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.618719 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.578307 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1351 0.0160 0.036 1.1 5.6 0.0 0.3 0 0.809 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.51 1.60 1.781 14.140 14.578 3.761 11.95 13.54 1.59 1.815 14.127 14.578 3.760 Individual atomic B min max mean iso aniso Overall: 5.59 69.21 15.01 0.95 525 3270 Protein: 5.59 31.87 10.59 0.95 0 2902 Water: 5.89 69.21 29.40 N/A 525 366 Other: 13.82 26.64 20.23 N/A 0 2 Chain A: 5.60 53.56 12.54 N/A 0 1624 Chain B: 5.59 67.01 12.33 N/A 0 1646 Chain S: 5.89 69.21 31.09 N/A 525 0 Histogram: Values Number of atoms 5.59 - 11.95 2192 11.95 - 18.31 695 18.31 - 24.67 300 24.67 - 31.04 228 31.04 - 37.40 166 37.40 - 43.76 134 43.76 - 50.12 56 50.12 - 56.48 17 56.48 - 62.85 4 62.85 - 69.21 3 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1354 r_work=0.1195 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1355 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1357 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759015 | | target function (ml) not normalized (work): 704029.644027 | | target function (ml) not normalized (free): 14741.849979 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1357 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1406 0.1405 0.1476 n_refl.: 191132 remove outliers: r(all,work,free)=0.1406 0.1405 0.1476 n_refl.: 191132 overall B=-0.03 to atoms: r(all,work,free)=0.1399 0.1398 0.1471 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1355 n_refl.: 191132 remove outliers: r(all,work,free)=0.1195 0.1192 0.1355 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 93.07 91 3 0.3830 361.353 324.396 0.379 0.974 0.207 13.296-10.522 96.04 96 1 0.2369 480.634 456.078 0.682 0.975 0.185 10.503-8.327 98.35 176 3 0.2153 503.006 495.278 0.841 0.975 0.154 8.318-6.595 100.00 360 8 0.2135 375.703 370.151 0.862 0.974 0.113 6.588-5.215 100.00 711 7 0.1898 345.234 336.013 0.856 0.974 0.097 5.214-4.128 98.38 1367 28 0.1191 504.972 499.920 0.946 0.974 0.080 4.126-3.266 94.74 2603 46 0.1132 460.309 453.631 1.006 0.972 0.000 3.266-2.585 99.86 5447 97 0.1110 310.513 306.988 0.994 0.970 0.000 2.585-2.046 97.45 10613 204 0.0940 234.265 231.787 1.010 0.966 0.000 2.046-1.619 99.39 21536 464 0.0914 138.649 137.323 1.039 0.960 0.000 1.619-1.281 98.00 42464 925 0.0970 74.641 73.938 1.047 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1644 40.042 38.364 1.052 0.931 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1116 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1193 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1356 | n_water=891 | time (s): 2.620 (total time: 2.620) Filter (dist) r_work=0.1193 r_free=0.1356 | n_water=891 | time (s): 115.150 (total time: 117.770) Filter (q & B) r_work=0.1193 r_free=0.1356 | n_water=881 | time (s): 5.610 (total time: 123.380) Compute maps r_work=0.1193 r_free=0.1356 | n_water=881 | time (s): 2.410 (total time: 125.790) Filter (map) r_work=0.1212 r_free=0.1361 | n_water=769 | time (s): 4.250 (total time: 130.040) Find peaks r_work=0.1212 r_free=0.1361 | n_water=769 | time (s): 0.830 (total time: 130.870) Add new water r_work=0.1224 r_free=0.1379 | n_water=977 | time (s): 4.470 (total time: 135.340) Refine new water occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1342 occ: r_work=0.1189 r_free=0.1339 adp: r_work=0.1189 r_free=0.1340 occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1187 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1339 r_work=0.1187 r_free=0.1339 | n_water=977 | time (s): 269.370 (total time: 404.710) Filter (q & B) r_work=0.1190 r_free=0.1351 | n_water=898 | time (s): 4.680 (total time: 409.390) Filter (dist only) r_work=0.1190 r_free=0.1349 | n_water=897 | time (s): 111.700 (total time: 521.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.562941 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.563403 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 0.1355 0.0161 0.037 1.1 6.8 0.0 0.3 0 0.781 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.55 1.61 1.758 14.118 14.563 3.761 11.95 13.57 1.62 1.838 14.088 14.563 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 69.05 15.00 0.91 531 3270 Protein: 5.59 29.96 10.53 0.91 0 2902 Water: 5.95 69.05 29.47 N/A 531 366 Other: 13.84 24.69 19.26 N/A 0 2 Chain A: 5.64 51.88 12.44 N/A 0 1624 Chain B: 5.59 66.35 12.24 N/A 0 1646 Chain S: 5.95 69.05 31.42 N/A 531 0 Histogram: Values Number of atoms 5.59 - 11.94 2194 11.94 - 18.28 722 18.28 - 24.63 278 24.63 - 30.97 217 30.97 - 37.32 166 37.32 - 43.67 138 43.67 - 50.01 62 50.01 - 56.36 17 56.36 - 62.70 4 62.70 - 69.05 3 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1357 r_work=0.1195 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1358 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1355 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757216 | | target function (ml) not normalized (work): 703688.986491 | | target function (ml) not normalized (free): 14735.960884 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1355 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1405 0.1403 0.1494 n_refl.: 191131 remove outliers: r(all,work,free)=0.1405 0.1403 0.1494 n_refl.: 191131 overall B=-0.20 to atoms: r(all,work,free)=0.1370 0.1369 0.1469 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191131 remove outliers: r(all,work,free)=0.1195 0.1192 0.1354 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 93.07 91 3 0.3809 361.353 324.512 0.398 0.974 0.223 13.296-10.522 96.04 96 1 0.2344 480.634 462.523 0.705 0.975 0.172 10.503-8.327 98.35 176 3 0.2135 503.006 495.642 0.862 0.975 0.147 8.318-6.595 100.00 360 8 0.2112 375.703 370.141 0.885 0.975 0.108 6.588-5.215 100.00 711 7 0.1882 345.234 336.276 0.878 0.975 0.090 5.214-4.128 98.38 1367 28 0.1202 504.972 499.765 0.971 0.974 0.080 4.126-3.266 94.74 2603 46 0.1134 460.309 453.343 1.030 0.973 0.000 3.266-2.585 99.86 5447 97 0.1114 310.513 306.997 1.017 0.970 0.000 2.585-2.046 97.45 10613 204 0.0945 234.265 231.761 1.030 0.967 0.000 2.046-1.619 99.39 21536 464 0.0916 138.649 137.300 1.054 0.961 0.000 1.619-1.281 98.00 42464 925 0.0965 74.641 73.933 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1641 40.042 38.357 1.044 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0440 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1355 | n_water=897 | time (s): 3.170 (total time: 3.170) Filter (dist) r_work=0.1192 r_free=0.1355 | n_water=897 | time (s): 121.950 (total time: 125.120) Filter (q & B) r_work=0.1193 r_free=0.1354 | n_water=892 | time (s): 5.490 (total time: 130.610) Compute maps r_work=0.1193 r_free=0.1354 | n_water=892 | time (s): 1.760 (total time: 132.370) Filter (map) r_work=0.1213 r_free=0.1351 | n_water=778 | time (s): 4.250 (total time: 136.620) Find peaks r_work=0.1213 r_free=0.1351 | n_water=778 | time (s): 0.550 (total time: 137.170) Add new water r_work=0.1223 r_free=0.1365 | n_water=988 | time (s): 4.180 (total time: 141.350) Refine new water occ: r_work=0.1191 r_free=0.1336 adp: r_work=0.1191 r_free=0.1337 occ: r_work=0.1189 r_free=0.1335 adp: r_work=0.1189 r_free=0.1336 occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1335 r_work=0.1187 r_free=0.1335 | n_water=988 | time (s): 334.900 (total time: 476.250) Filter (q & B) r_work=0.1191 r_free=0.1347 | n_water=911 | time (s): 5.910 (total time: 482.160) Filter (dist only) r_work=0.1191 r_free=0.1346 | n_water=910 | time (s): 120.000 (total time: 602.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.548077 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.093776 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 0.0158 0.037 1.1 6.1 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.52 1.58 1.729 13.878 14.094 3.758 11.95 13.55 1.60 1.798 13.855 14.094 3.757 Individual atomic B min max mean iso aniso Overall: 5.46 68.69 14.79 0.88 544 3270 Protein: 5.46 28.53 10.30 0.88 0 2902 Water: 5.84 68.69 29.13 N/A 544 366 Other: 13.73 22.52 18.12 N/A 0 2 Chain A: 5.47 50.23 12.17 N/A 0 1624 Chain B: 5.46 65.10 11.99 N/A 0 1646 Chain S: 5.84 68.69 31.12 N/A 544 0 Histogram: Values Number of atoms 5.46 - 11.78 2201 11.78 - 18.10 730 18.10 - 24.43 269 24.43 - 30.75 223 30.75 - 37.07 173 37.07 - 43.40 131 43.40 - 49.72 64 49.72 - 56.04 18 56.04 - 62.37 2 62.37 - 68.69 3 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1356 r_work=0.1195 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1356 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1356 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756350 | | target function (ml) not normalized (work): 703526.778397 | | target function (ml) not normalized (free): 14733.595232 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1375 0.1373 0.1479 n_refl.: 191131 remove outliers: r(all,work,free)=0.1375 0.1373 0.1479 n_refl.: 191131 overall B=0.03 to atoms: r(all,work,free)=0.1380 0.1378 0.1482 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1347 n_refl.: 191131 remove outliers: r(all,work,free)=0.1191 0.1187 0.1347 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3883 356.824 323.833 0.356 0.996 0.160 13.296-10.522 96.04 96 1 0.2351 480.634 461.026 0.695 0.997 0.155 10.503-8.327 98.35 176 3 0.2149 503.006 495.954 0.853 0.998 0.151 8.318-6.595 100.00 360 8 0.2096 375.703 370.201 0.874 0.998 0.101 6.588-5.215 100.00 711 7 0.1883 345.234 335.934 0.870 0.998 0.087 5.214-4.128 98.38 1367 28 0.1213 504.972 499.352 0.958 0.999 0.039 4.126-3.266 94.74 2603 46 0.1135 460.309 453.007 1.017 1.000 0.000 3.266-2.585 99.86 5447 97 0.1119 310.513 306.791 1.001 1.000 0.000 2.585-2.046 97.45 10613 204 0.0952 234.265 231.656 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0912 138.649 137.251 1.026 1.004 0.000 1.619-1.281 98.00 42464 925 0.0951 74.641 73.967 1.016 1.008 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.042 38.331 0.984 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0525 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1347 | n_water=910 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1188 r_free=0.1348 | n_water=909 | time (s): 118.040 (total time: 121.170) Filter (q & B) r_work=0.1188 r_free=0.1349 | n_water=903 | time (s): 4.480 (total time: 125.650) Compute maps r_work=0.1188 r_free=0.1349 | n_water=903 | time (s): 1.640 (total time: 127.290) Filter (map) r_work=0.1207 r_free=0.1344 | n_water=802 | time (s): 5.090 (total time: 132.380) Find peaks r_work=0.1207 r_free=0.1344 | n_water=802 | time (s): 0.690 (total time: 133.070) Add new water r_work=0.1214 r_free=0.1355 | n_water=1005 | time (s): 4.960 (total time: 138.030) Refine new water occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1185 r_free=0.1333 occ: r_work=0.1182 r_free=0.1330 adp: r_work=0.1182 r_free=0.1331 occ: r_work=0.1181 r_free=0.1328 adp: r_work=0.1181 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1329 r_work=0.1181 r_free=0.1329 | n_water=1005 | time (s): 215.010 (total time: 353.040) Filter (q & B) r_work=0.1187 r_free=0.1339 | n_water=925 | time (s): 4.600 (total time: 357.640) Filter (dist only) r_work=0.1187 r_free=0.1338 | n_water=924 | time (s): 118.020 (total time: 475.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.528644 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.893540 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1347 0.0157 0.038 1.1 5.1 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.47 1.57 1.684 13.860 14.894 3.756 11.88 13.48 1.60 1.696 13.855 14.894 3.752 Individual atomic B min max mean iso aniso Overall: 5.52 64.33 14.84 0.88 558 3270 Protein: 5.52 28.44 10.34 0.88 0 2902 Water: 5.90 64.33 28.95 N/A 558 366 Other: 13.77 22.13 17.95 N/A 0 2 Chain A: 5.57 49.92 12.18 N/A 0 1624 Chain B: 5.52 64.33 12.01 N/A 0 1646 Chain S: 5.90 63.47 30.90 N/A 558 0 Histogram: Values Number of atoms 5.52 - 11.40 2085 11.40 - 17.28 809 17.28 - 23.16 262 23.16 - 29.04 219 29.04 - 34.93 189 34.93 - 40.81 138 40.81 - 46.69 80 46.69 - 52.57 37 52.57 - 58.45 6 58.45 - 64.33 3 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1348 r_work=0.1188 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1348 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1349 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1187 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752157 | | target function (ml) not normalized (work): 702737.712333 | | target function (ml) not normalized (free): 14728.539702 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1187 0.1349 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1386 0.1384 0.1490 n_refl.: 191130 remove outliers: r(all,work,free)=0.1386 0.1384 0.1490 n_refl.: 191130 overall B=0.01 to atoms: r(all,work,free)=0.1387 0.1385 0.1491 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1185 0.1344 n_refl.: 191130 remove outliers: r(all,work,free)=0.1189 0.1185 0.1344 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 0.3905 356.824 321.225 0.325 0.982 0.100 13.296-10.522 96.04 96 1 0.2404 480.634 459.081 0.689 0.984 0.113 10.503-8.327 98.35 176 3 0.2172 503.006 494.379 0.862 0.985 0.114 8.318-6.595 100.00 360 8 0.2105 375.703 370.373 0.882 0.984 0.095 6.588-5.215 100.00 711 7 0.1911 345.234 335.936 0.880 0.985 0.080 5.214-4.128 98.38 1367 28 0.1213 504.972 498.971 0.972 0.986 0.070 4.126-3.266 94.74 2603 46 0.1143 460.309 452.879 1.031 0.987 0.000 3.266-2.585 99.86 5447 97 0.1124 310.513 306.838 1.015 0.988 0.000 2.585-2.046 97.45 10613 204 0.0952 234.265 231.656 1.024 0.990 0.000 2.046-1.619 99.39 21536 464 0.0906 138.649 137.286 1.041 0.993 0.000 1.619-1.281 98.00 42464 925 0.0942 74.641 73.986 1.033 0.997 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.042 38.324 1.002 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0117 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1344 | n_water=924 | time (s): 3.420 (total time: 3.420) Filter (dist) r_work=0.1185 r_free=0.1344 | n_water=924 | time (s): 120.770 (total time: 124.190) Filter (q & B) r_work=0.1186 r_free=0.1345 | n_water=914 | time (s): 5.400 (total time: 129.590) Compute maps r_work=0.1186 r_free=0.1345 | n_water=914 | time (s): 2.310 (total time: 131.900) Filter (map) r_work=0.1207 r_free=0.1353 | n_water=808 | time (s): 4.300 (total time: 136.200) Find peaks r_work=0.1207 r_free=0.1353 | n_water=808 | time (s): 0.730 (total time: 136.930) Add new water r_work=0.1213 r_free=0.1360 | n_water=1000 | time (s): 4.800 (total time: 141.730) Refine new water occ: r_work=0.1184 r_free=0.1335 adp: r_work=0.1184 r_free=0.1335 occ: r_work=0.1182 r_free=0.1333 adp: r_work=0.1182 r_free=0.1334 occ: r_work=0.1180 r_free=0.1331 adp: r_work=0.1180 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1331 r_work=0.1180 r_free=0.1331 | n_water=1000 | time (s): 291.610 (total time: 433.340) Filter (q & B) r_work=0.1184 r_free=0.1343 | n_water=929 | time (s): 4.430 (total time: 437.770) Filter (dist only) r_work=0.1184 r_free=0.1342 | n_water=928 | time (s): 122.550 (total time: 560.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.578987 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.565103 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 0.1187 0.1348 0.0161 0.039 1.1 7.2 0.0 0.3 0 0.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 13.48 1.61 1.687 13.832 13.565 3.753 11.90 13.52 1.62 1.690 13.832 13.565 3.754 Individual atomic B min max mean iso aniso Overall: 5.55 64.04 14.78 0.86 562 3270 Protein: 5.55 28.20 10.36 0.86 0 2902 Water: 5.99 64.04 28.57 N/A 562 366 Other: 13.80 22.09 17.94 N/A 0 2 Chain A: 5.60 49.83 12.18 N/A 0 1624 Chain B: 5.55 64.04 12.01 N/A 0 1646 Chain S: 5.99 63.50 30.37 N/A 562 0 Histogram: Values Number of atoms 5.55 - 11.40 2084 11.40 - 17.25 814 17.25 - 23.10 267 23.10 - 28.95 227 28.95 - 34.80 194 34.80 - 40.65 121 40.65 - 46.50 80 46.50 - 52.35 34 52.35 - 58.20 8 58.20 - 64.04 3 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1352 r_work=0.1190 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1352 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753892 | | target function (ml) not normalized (work): 703062.680986 | | target function (ml) not normalized (free): 14736.244941 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1353 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1501 n_refl.: 191130 remove outliers: r(all,work,free)=0.1398 0.1396 0.1501 n_refl.: 191130 overall B=-0.01 to atoms: r(all,work,free)=0.1397 0.1395 0.1500 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1352 n_refl.: 191130 remove outliers: r(all,work,free)=0.1191 0.1188 0.1352 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 0.3941 356.824 320.236 0.318 0.984 0.090 13.296-10.522 96.04 96 1 0.2393 480.634 458.057 0.680 0.985 0.100 10.503-8.327 98.35 176 3 0.2192 503.006 494.512 0.857 0.986 0.101 8.318-6.595 100.00 360 8 0.2126 375.703 369.716 0.880 0.986 0.090 6.588-5.215 100.00 711 7 0.1934 345.234 335.622 0.878 0.986 0.080 5.214-4.128 98.38 1367 28 0.1220 504.972 499.206 0.969 0.987 0.034 4.126-3.266 94.74 2603 46 0.1149 460.309 452.938 1.030 0.989 0.000 3.266-2.585 99.86 5447 97 0.1125 310.513 306.769 1.014 0.990 0.000 2.585-2.046 97.45 10613 204 0.0956 234.265 231.620 1.023 0.992 0.000 2.046-1.619 99.39 21536 464 0.0909 138.649 137.274 1.041 0.995 0.000 1.619-1.281 98.00 42464 925 0.0942 74.641 73.989 1.032 1.001 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.042 38.320 1.003 1.011 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0180 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1188 r_free=0.1352 After: r_work=0.1189 r_free=0.1352 ================================== NQH flips ================================== r_work=0.1189 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1352 | n_water=928 | time (s): 2.860 (total time: 2.860) Filter (dist) r_work=0.1189 r_free=0.1352 | n_water=928 | time (s): 117.550 (total time: 120.410) Filter (q & B) r_work=0.1190 r_free=0.1354 | n_water=916 | time (s): 4.560 (total time: 124.970) Compute maps r_work=0.1190 r_free=0.1354 | n_water=916 | time (s): 1.940 (total time: 126.910) Filter (map) r_work=0.1209 r_free=0.1355 | n_water=823 | time (s): 4.200 (total time: 131.110) Find peaks r_work=0.1209 r_free=0.1355 | n_water=823 | time (s): 0.580 (total time: 131.690) Add new water r_work=0.1214 r_free=0.1359 | n_water=1017 | time (s): 4.990 (total time: 136.680) Refine new water occ: r_work=0.1185 r_free=0.1338 adp: r_work=0.1185 r_free=0.1338 occ: r_work=0.1184 r_free=0.1338 adp: r_work=0.1184 r_free=0.1339 occ: r_work=0.1183 r_free=0.1339 adp: r_work=0.1183 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1339 r_work=0.1183 r_free=0.1339 | n_water=1017 | time (s): 234.270 (total time: 370.950) Filter (q & B) r_work=0.1188 r_free=0.1350 | n_water=929 | time (s): 4.810 (total time: 375.760) Filter (dist only) r_work=0.1188 r_free=0.1349 | n_water=927 | time (s): 125.630 (total time: 501.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.508342 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.832929 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 0.1195 0.1358 0.0163 0.039 1.2 9.4 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.58 1.63 1.681 13.847 13.833 3.759 11.96 13.59 1.63 1.688 13.847 13.833 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 63.55 14.80 0.85 561 3270 Protein: 5.59 27.93 10.37 0.85 0 2902 Water: 6.03 63.55 28.68 N/A 561 366 Other: 13.84 22.00 17.92 N/A 0 2 Chain A: 5.67 49.60 12.16 N/A 0 1624 Chain B: 5.59 63.16 12.00 N/A 0 1646 Chain S: 6.03 63.55 30.67 N/A 561 0 Histogram: Values Number of atoms 5.59 - 11.38 2070 11.38 - 17.18 829 17.18 - 22.97 265 22.97 - 28.77 212 28.77 - 34.57 203 34.57 - 40.36 120 40.36 - 46.16 83 46.16 - 51.95 34 51.95 - 57.75 12 57.75 - 63.55 3 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1359 r_work=0.1196 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757807 | | target function (ml) not normalized (work): 703795.853748 | | target function (ml) not normalized (free): 14745.437897 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1350 0.1431 5.6816 5.7471| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1410 5.0801 5.2162| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1190 4.6646 4.756| | 4: 2.04 - 1.85 1.00 7170 155 0.0907 0.1070 4.4022 4.5856| | 5: 1.85 - 1.72 0.99 7113 159 0.0939 0.1006 4.1585 4.2562| | 6: 1.72 - 1.62 0.99 7102 142 0.0902 0.1104 3.9544 4.0933| | 7: 1.62 - 1.54 0.99 7104 148 0.0898 0.0952 3.8087 3.9309| | 8: 1.54 - 1.47 0.96 6798 152 0.0900 0.1338 3.7103 3.9266| | 9: 1.47 - 1.41 0.98 6938 155 0.0933 0.1126 3.6287 3.7536| | 10: 1.41 - 1.36 0.99 7022 150 0.0982 0.1183 3.5609 3.6656| | 11: 1.36 - 1.32 0.99 6997 151 0.0998 0.1128 3.4892 3.592| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1126 3.4618 3.5825| | 13: 1.28 - 1.25 0.98 6907 166 0.1046 0.1249 3.4414 3.572| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1582 3.4357 3.6796| | 15: 1.22 - 1.19 0.98 6956 137 0.1172 0.1242 3.4525 3.4889| | 16: 1.19 - 1.17 0.93 6604 132 0.1254 0.1545 3.4675 3.6553| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1233 3.4354 3.4464| | 18: 1.14 - 1.12 0.98 6875 142 0.1388 0.1706 3.4404 3.5327| | 19: 1.12 - 1.10 0.97 6948 106 0.1474 0.1777 3.4217 3.6036| | 20: 1.10 - 1.08 0.97 6884 147 0.1587 0.1584 3.4122 3.4371| | 21: 1.08 - 1.07 0.97 6852 152 0.1732 0.2150 3.4204 3.5068| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1962 3.4143 3.4161| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2025 3.4339 3.49| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2254 3.4367 3.5132| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2504 3.4504 3.5198| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2854 3.416 3.4223| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2803 3.4699 3.3966| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 11.54 1.00 0.95 10948.46| | 2: 2.94 - 2.33 7339 128 0.93 12.79 0.99 0.95 5113.68| | 3: 2.33 - 2.04 6939 150 0.96 7.87 1.01 0.96 1774.67| | 4: 2.04 - 1.85 7170 155 0.96 7.82 1.00 0.96 1035.44| | 5: 1.85 - 1.72 7113 159 0.96 8.19 1.00 0.96 646.66| | 6: 1.72 - 1.62 7102 142 0.96 8.13 1.00 0.96 452.06| | 7: 1.62 - 1.54 7104 148 0.96 8.25 1.01 0.97 343.16| | 8: 1.54 - 1.47 6798 152 0.96 8.37 1.01 0.97 284.31| | 9: 1.47 - 1.41 6938 155 0.96 8.57 1.00 0.98 233.80| | 10: 1.41 - 1.36 7022 150 0.96 8.93 1.00 0.97 203.34| | 11: 1.36 - 1.32 6997 151 0.96 8.95 0.99 0.96 175.20| | 12: 1.32 - 1.28 6975 149 0.96 8.99 0.98 0.95 161.20| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.96 159.28| | 14: 1.25 - 1.22 7015 112 0.95 10.74 1.01 0.96 164.11| | 15: 1.22 - 1.19 6956 137 0.95 11.28 1.01 0.98 167.48| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.01 0.96 161.02| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.96 154.80| | 18: 1.14 - 1.12 6875 142 0.94 12.81 1.01 0.95 148.70| | 19: 1.12 - 1.10 6948 106 0.93 14.21 1.00 0.95 152.38| | 20: 1.10 - 1.08 6884 147 0.92 15.31 1.00 0.94 151.47| | 21: 1.08 - 1.07 6852 152 0.91 16.72 1.00 0.93 154.51| | 22: 1.07 - 1.05 6836 135 0.89 18.38 0.99 0.93 156.04| | 23: 1.05 - 1.03 6827 159 0.87 20.55 0.99 0.92 165.62| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.93 179.39| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.98 0.90 181.86| | 26: 1.01 - 0.99 6767 158 0.81 26.60 0.98 0.89 176.35| | 27: 0.99 - 0.98 6647 131 0.82 26.32 0.99 0.87 161.22| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.70 max = 10948.46 mean = 920.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.35| |phase err.(test): min = 0.00 max = 89.64 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1360 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1518 n_refl.: 191130 remove outliers: r(all,work,free)=0.1407 0.1405 0.1518 n_refl.: 191130 overall B=-0.07 to atoms: r(all,work,free)=0.1397 0.1395 0.1509 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1194 0.1360 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 0.3924 356.824 319.724 0.305 0.985 0.080 13.296-10.522 96.04 96 1 0.2382 480.634 460.197 0.671 0.986 0.130 10.503-8.327 98.35 176 3 0.2148 503.006 495.408 0.834 0.987 0.111 8.318-6.595 100.00 360 8 0.2115 375.703 369.698 0.855 0.987 0.080 6.588-5.215 100.00 711 7 0.1940 345.234 335.419 0.854 0.988 0.067 5.214-4.128 98.38 1367 28 0.1231 504.972 499.046 0.944 0.989 0.024 4.126-3.266 94.74 2603 46 0.1153 460.309 452.614 1.005 0.990 0.000 3.266-2.585 99.86 5447 97 0.1127 310.513 306.828 0.989 0.991 0.000 2.585-2.046 97.45 10613 204 0.0965 234.265 231.616 0.996 0.993 0.000 2.046-1.619 99.39 21536 464 0.0917 138.649 137.258 1.011 0.998 0.000 1.619-1.281 98.00 42464 925 0.0952 74.641 73.976 1.001 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.042 38.309 0.969 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0144 ================= 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 : 0.2029 0.1980 0.081 5.217 5.2 78.0 14.6 805 0.000 1_bss: 0.1792 0.1919 0.081 5.217 5.2 78.1 14.6 805 0.000 1_settarget: 0.1792 0.1919 0.081 5.217 5.2 78.1 14.6 805 0.000 1_nqh: 0.1793 0.1921 0.081 5.217 5.2 78.1 14.6 805 0.002 1_weight: 0.1793 0.1921 0.081 5.217 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1270 0.1497 0.037 1.155 5.2 78.1 14.6 805 0.154 1_adp: 0.1296 0.1566 0.037 1.155 5.1 73.1 14.9 805 0.154 1_regHadp: 0.1295 0.1561 0.037 1.155 5.1 73.1 14.9 805 0.154 1_occ: 0.1281 0.1551 0.037 1.155 5.1 73.1 14.9 805 0.154 2_bss: 0.1275 0.1545 0.037 1.155 5.3 73.2 15.1 805 0.154 2_settarget: 0.1275 0.1545 0.037 1.155 5.3 73.2 15.1 805 0.154 2_updatecdl: 0.1275 0.1545 0.037 1.163 5.3 73.2 15.1 805 0.154 2_nqh: 0.1275 0.1545 0.037 1.163 5.3 73.2 15.1 805 0.154 2_sol: 0.1269 0.1508 0.037 1.163 5.3 73.2 16.2 886 n/a 2_weight: 0.1269 0.1508 0.037 1.163 5.3 73.2 16.2 886 n/a 2_xyzrec: 0.1255 0.1525 0.039 1.148 5.3 73.2 16.2 886 n/a 2_adp: 0.1230 0.1509 0.039 1.148 5.4 71.6 16.4 886 n/a 2_regHadp: 0.1231 0.1510 0.039 1.148 5.4 71.6 16.4 886 n/a 2_occ: 0.1224 0.1510 0.039 1.148 5.4 71.6 16.4 886 n/a 3_bss: 0.1231 0.1515 0.039 1.148 5.4 71.5 16.4 886 n/a 3_settarget: 0.1231 0.1515 0.039 1.148 5.4 71.5 16.4 886 n/a 3_updatecdl: 0.1231 0.1515 0.039 1.148 5.4 71.5 16.4 886 n/a 3_nqh: 0.1231 0.1515 0.039 1.148 5.4 71.5 16.4 886 n/a 3_sol: 0.1247 0.1501 0.039 1.148 5.4 69.5 15.5 878 n/a 3_weight: 0.1247 0.1501 0.039 1.148 5.4 69.5 15.5 878 n/a 3_xyzrec: 0.1235 0.1431 0.034 1.106 5.4 69.5 15.5 878 n/a 3_adp: 0.1235 0.1399 0.034 1.106 5.5 69.4 15.3 878 n/a 3_regHadp: 0.1235 0.1401 0.034 1.106 5.5 69.4 15.3 878 n/a 3_occ: 0.1229 0.1394 0.034 1.106 5.5 69.4 15.3 878 n/a 4_bss: 0.1225 0.1385 0.034 1.106 5.5 69.4 15.3 878 n/a 4_settarget: 0.1225 0.1385 0.034 1.106 5.5 69.4 15.3 878 n/a 4_updatecdl: 0.1225 0.1385 0.034 1.111 5.5 69.4 15.3 878 n/a 4_nqh: 0.1225 0.1385 0.034 1.111 5.5 69.4 15.3 878 n/a 4_sol: 0.1209 0.1369 0.034 1.111 5.5 69.4 15.1 875 n/a 4_weight: 0.1209 0.1369 0.034 1.111 5.5 69.4 15.1 875 n/a 4_xyzrec: 0.1207 0.1372 0.036 1.118 5.5 69.4 15.1 875 n/a 4_adp: 0.1198 0.1367 0.036 1.118 5.5 69.3 15.0 875 n/a 4_regHadp: 0.1198 0.1367 0.036 1.118 5.5 69.3 15.0 875 n/a 4_occ: 0.1195 0.1365 0.036 1.118 5.5 69.3 15.0 875 n/a 5_bss: 0.1190 0.1360 0.036 1.118 5.5 69.2 15.0 875 n/a 5_settarget: 0.1190 0.1360 0.036 1.118 5.5 69.2 15.0 875 n/a 5_updatecdl: 0.1190 0.1360 0.036 1.119 5.5 69.2 15.0 875 n/a 5_nqh: 0.1190 0.1360 0.036 1.119 5.5 69.2 15.0 875 n/a 5_sol: 0.1189 0.1348 0.036 1.119 5.5 69.2 15.0 891 n/a 5_weight: 0.1189 0.1348 0.036 1.119 5.5 69.2 15.0 891 n/a 5_xyzrec: 0.1190 0.1351 0.036 1.138 5.5 69.2 15.0 891 n/a 5_adp: 0.1195 0.1354 0.036 1.138 5.6 69.2 15.0 891 n/a 5_regHadp: 0.1195 0.1355 0.036 1.138 5.6 69.2 15.0 891 n/a 5_occ: 0.1193 0.1357 0.036 1.138 5.6 69.2 15.0 891 n/a 6_bss: 0.1192 0.1355 0.036 1.138 5.6 69.2 15.0 891 n/a 6_settarget: 0.1192 0.1355 0.036 1.138 5.6 69.2 15.0 891 n/a 6_updatecdl: 0.1192 0.1355 0.036 1.138 5.6 69.2 15.0 891 n/a 6_nqh: 0.1193 0.1356 0.036 1.138 5.6 69.2 15.0 891 n/a 6_sol: 0.1190 0.1349 0.036 1.138 5.6 69.2 15.1 897 n/a 6_weight: 0.1190 0.1349 0.036 1.138 5.6 69.2 15.1 897 n/a 6_xyzrec: 0.1193 0.1355 0.037 1.128 5.6 69.2 15.1 897 n/a 6_adp: 0.1195 0.1357 0.037 1.128 5.6 69.0 15.0 897 n/a 6_regHadp: 0.1195 0.1358 0.037 1.128 5.6 69.0 15.0 897 n/a 6_occ: 0.1193 0.1355 0.037 1.128 5.6 69.0 15.0 897 n/a 7_bss: 0.1192 0.1355 0.037 1.128 5.4 68.8 14.8 897 n/a 7_settarget: 0.1192 0.1355 0.037 1.128 5.4 68.8 14.8 897 n/a 7_updatecdl: 0.1192 0.1355 0.037 1.128 5.4 68.8 14.8 897 n/a 7_nqh: 0.1192 0.1355 0.037 1.128 5.4 68.8 14.8 897 n/a 7_sol: 0.1191 0.1346 0.037 1.128 5.4 68.8 14.8 910 n/a 7_weight: 0.1191 0.1346 0.037 1.128 5.4 68.8 14.8 910 n/a 7_xyzrec: 0.1193 0.1352 0.037 1.134 5.4 68.8 14.8 910 n/a 7_adp: 0.1195 0.1356 0.037 1.134 5.5 68.7 14.8 910 n/a 7_regHadp: 0.1195 0.1356 0.037 1.134 5.5 68.7 14.8 910 n/a 7_occ: 0.1194 0.1356 0.037 1.134 5.5 68.7 14.8 910 n/a 8_bss: 0.1187 0.1347 0.037 1.134 5.5 68.7 14.8 910 n/a 8_settarget: 0.1187 0.1347 0.037 1.134 5.5 68.7 14.8 910 n/a 8_updatecdl: 0.1187 0.1347 0.037 1.134 5.5 68.7 14.8 910 n/a 8_nqh: 0.1187 0.1347 0.037 1.134 5.5 68.7 14.8 910 n/a 8_sol: 0.1187 0.1338 0.037 1.134 5.5 65.1 14.8 924 n/a 8_weight: 0.1187 0.1338 0.037 1.134 5.5 65.1 14.8 924 n/a 8_xyzrec: 0.1189 0.1347 0.038 1.119 5.5 65.1 14.8 924 n/a 8_adp: 0.1188 0.1348 0.038 1.119 5.5 64.3 14.8 924 n/a 8_regHadp: 0.1188 0.1348 0.038 1.119 5.5 64.3 14.8 924 n/a 8_occ: 0.1187 0.1349 0.038 1.119 5.5 64.3 14.8 924 n/a 9_bss: 0.1185 0.1344 0.038 1.119 5.5 64.3 14.8 924 n/a 9_settarget: 0.1185 0.1344 0.038 1.119 5.5 64.3 14.8 924 n/a 9_updatecdl: 0.1185 0.1344 0.038 1.119 5.5 64.3 14.8 924 n/a 9_nqh: 0.1185 0.1344 0.038 1.119 5.5 64.3 14.8 924 n/a 9_sol: 0.1184 0.1342 0.038 1.119 5.5 64.3 14.8 928 n/a 9_weight: 0.1184 0.1342 0.038 1.119 5.5 64.3 14.8 928 n/a 9_xyzrec: 0.1187 0.1348 0.039 1.121 5.5 64.3 14.8 928 n/a 9_adp: 0.1190 0.1352 0.039 1.121 5.6 64.0 14.8 928 n/a 9_regHadp: 0.1190 0.1352 0.039 1.121 5.6 64.0 14.8 928 n/a 9_occ: 0.1189 0.1353 0.039 1.121 5.6 64.0 14.8 928 n/a 10_bss: 0.1188 0.1352 0.039 1.121 5.5 64.0 14.8 928 n/a 10_settarget: 0.1188 0.1352 0.039 1.121 5.5 64.0 14.8 928 n/a 10_updatecdl: 0.1188 0.1352 0.039 1.121 5.5 64.0 14.8 928 n/a 10_setrh: 0.1189 0.1352 0.039 1.121 5.5 64.0 14.8 928 n/a 10_nqh: 0.1189 0.1352 0.039 1.121 5.5 64.0 14.8 928 n/a 10_sol: 0.1188 0.1349 0.039 1.121 5.5 64.0 14.8 927 n/a 10_weight: 0.1188 0.1349 0.039 1.121 5.5 64.0 14.8 927 n/a 10_xyzrec: 0.1195 0.1358 0.039 1.165 5.5 64.0 14.8 927 n/a 10_adp: 0.1196 0.1359 0.039 1.165 5.6 63.5 14.8 927 n/a 10_regHadp: 0.1196 0.1359 0.039 1.165 5.6 63.5 14.8 927 n/a 10_occ: 0.1195 0.1360 0.039 1.165 5.6 63.5 14.8 927 n/a end: 0.1194 0.1361 0.039 1.165 5.5 63.5 14.7 927 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5361003_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5361003_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.7100 Refinement macro-cycles (run) : 12365.4200 Write final files (write_after_run_outputs) : 133.2700 Total : 12504.4000 Total CPU time: 3.48 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:45:35 PST -0800 (1736736335.16 s) Start R-work = 0.1792, R-free = 0.1919 Final R-work = 0.1194, R-free = 0.1361 =============================================================================== Job complete usr+sys time: 12759.30 seconds wall clock time: 213 minutes 38.74 seconds (12818.74 seconds total)