Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2328810.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2328810.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2328810.pdb" } 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 2 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.26, per 1000 atoms: 0.34 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.808 distance_ideal: 2.720 ideal - model: -0.088 slack: 0.000 delta_slack: -0.088 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: 2.800 distance_ideal: 2.710 ideal - model: -0.090 slack: 0.000 delta_slack: -0.090 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: 0.77 Conformation dependent library (CDL) restraints added in 143.2 milliseconds Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.04: 1007 1.04 - 1.28: 2445 1.28 - 1.52: 1617 1.52 - 1.75: 853 1.75 - 1.99: 12 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA B 10 " pdb=" CA ALA B 10 " ideal model delta sigma weight residual 1.455 1.634 -0.179 7.00e-03 2.04e+04 6.53e+02 bond pdb=" NH1 ARG B 175 " pdb="HH12 ARG B 175 " ideal model delta sigma weight residual 0.860 1.272 -0.412 2.00e-02 2.50e+03 4.24e+02 bond pdb=" N ILE A 134 " pdb=" CA ILE A 134 " ideal model delta sigma weight residual 1.462 1.659 -0.198 1.04e-02 9.25e+03 3.61e+02 bond pdb=" C VAL B 69 " pdb=" O VAL B 69 " ideal model delta sigma weight residual 1.234 1.020 0.213 1.15e-02 7.56e+03 3.44e+02 bond pdb=" N LYS B 52 " pdb=" H LYS B 52 " ideal model delta sigma weight residual 0.860 1.228 -0.368 2.00e-02 2.50e+03 3.38e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 5671 4.18 - 8.37: 3610 8.37 - 12.55: 1254 12.55 - 16.73: 243 16.73 - 20.91: 32 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ALA B 108 " pdb=" C ALA B 108 " pdb=" O ALA B 108 " ideal model delta sigma weight residual 118.63 134.36 -15.73 9.20e-01 1.18e+00 2.92e+02 angle pdb=" CA HIS B 179 " pdb=" C HIS B 179 " pdb=" O HIS B 179 " ideal model delta sigma weight residual 120.82 137.56 -16.74 1.05e+00 9.07e-01 2.54e+02 angle pdb=" O PHE A 127 " pdb=" C PHE A 127 " pdb=" N PRO A 128 " ideal model delta sigma weight residual 121.31 133.41 -12.10 8.70e-01 1.32e+00 1.93e+02 angle pdb=" O MET B 187 " pdb=" C MET B 187 " pdb=" N ALA B 188 " ideal model delta sigma weight residual 122.96 107.59 15.37 1.13e+00 7.83e-01 1.85e+02 angle pdb=" CA THR A 91 " pdb=" C THR A 91 " pdb=" O THR A 91 " ideal model delta sigma weight residual 120.42 134.68 -14.26 1.06e+00 8.90e-01 1.81e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 1841 17.39 - 34.78: 143 34.78 - 52.17: 50 52.17 - 69.56: 13 69.56 - 86.95: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -149.63 -30.37 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA TRP A 139 " pdb=" C TRP A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 153.62 26.38 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta harmonic sigma weight residual -180.00 -156.25 -23.75 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.210: 204 0.210 - 0.417: 141 0.417 - 0.625: 90 0.625 - 0.833: 48 0.833 - 1.041: 9 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.59 -1.04 2.00e-01 2.50e+01 2.71e+01 chirality pdb=" CB VAL B 173 " pdb=" CA VAL B 173 " pdb=" CG1 VAL B 173 " pdb=" CG2 VAL B 173 " both_signs ideal model delta sigma weight residual False -2.63 -1.62 -1.01 2.00e-01 2.50e+01 2.53e+01 chirality pdb=" CA ALA A 182 " pdb=" N ALA A 182 " pdb=" C ALA A 182 " pdb=" CB ALA A 182 " both_signs ideal model delta sigma weight residual False 2.48 3.46 -0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 82 " -0.032 2.00e-02 2.50e+03 7.95e-02 1.90e+02 pdb=" CG PHE A 82 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 82 " -0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE A 82 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 82 " -0.101 2.00e-02 2.50e+03 pdb=" CE2 PHE A 82 " 0.080 2.00e-02 2.50e+03 pdb=" CZ PHE A 82 " -0.138 2.00e-02 2.50e+03 pdb=" HD1 PHE A 82 " 0.062 2.00e-02 2.50e+03 pdb=" HD2 PHE A 82 " -0.088 2.00e-02 2.50e+03 pdb=" HE1 PHE A 82 " 0.091 2.00e-02 2.50e+03 pdb=" HE2 PHE A 82 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 82 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.066 2.00e-02 2.50e+03 6.54e-02 1.71e+02 pdb=" CG TRP B 146 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.067 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.130 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.094 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.071 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.059 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.062 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.025 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.038 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 119 " -0.034 2.00e-02 2.50e+03 7.45e-02 1.67e+02 pdb=" CG PHE B 119 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE B 119 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE B 119 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE B 119 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 PHE B 119 " 0.052 2.00e-02 2.50e+03 pdb=" CZ PHE B 119 " -0.105 2.00e-02 2.50e+03 pdb=" HD1 PHE B 119 " 0.110 2.00e-02 2.50e+03 pdb=" HD2 PHE B 119 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE B 119 " -0.074 2.00e-02 2.50e+03 pdb=" HE2 PHE B 119 " -0.063 2.00e-02 2.50e+03 pdb=" HZ PHE B 119 " 0.136 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 25 1.62 - 2.37: 2498 2.37 - 3.11: 22304 3.11 - 3.86: 32911 3.86 - 4.60: 52507 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110245 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.877 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.917 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.993 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.015 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.163 2.620 ... (remaining 110240 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_2328810_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= 0.2035 r_free= 0.1994 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301295 | | target function (ml) not normalized (work): 805688.438794 | | target function (ml) not normalized (free): 16556.712823 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2122 0.1977 6.6859 6.3135| | 2: 2.94 - 2.33 1.00 7339 128 0.1632 0.1540 5.5387 5.5735| | 3: 2.33 - 2.04 0.96 6939 150 0.1644 0.1547 5.1432 5.099| | 4: 2.04 - 1.85 1.00 7170 155 0.1731 0.1629 4.9543 5.0773| | 5: 1.85 - 1.72 0.99 7113 159 0.1931 0.1691 4.7953 4.7609| | 6: 1.72 - 1.62 0.99 7102 142 0.1970 0.2054 4.6649 4.6991| | 7: 1.62 - 1.54 0.99 7104 148 0.2028 0.1908 4.5668 4.6564| | 8: 1.54 - 1.47 0.96 6798 152 0.2065 0.2171 4.4889 4.5351| | 9: 1.47 - 1.41 0.98 6938 155 0.2110 0.2258 4.4065 4.4824| | 10: 1.41 - 1.36 0.99 7022 150 0.2120 0.2314 4.3108 4.3937| | 11: 1.36 - 1.32 0.99 6997 151 0.2122 0.2238 4.2406 4.2845| | 12: 1.32 - 1.28 0.98 6976 149 0.2098 0.1972 4.1702 4.2019| | 13: 1.28 - 1.25 0.98 6907 166 0.2041 0.2227 4.1315 4.2155| | 14: 1.25 - 1.22 0.98 7015 113 0.2092 0.2326 4.0771 4.2218| | 15: 1.22 - 1.19 0.98 6957 137 0.2110 0.2086 4.0545 4.0769| | 16: 1.19 - 1.17 0.93 6604 132 0.2148 0.2256 4.0152 4.0495| | 17: 1.17 - 1.14 0.98 6941 135 0.2182 0.1967 3.9643 4.0159| | 18: 1.14 - 1.12 0.98 6875 142 0.2236 0.2348 3.9258 3.9137| | 19: 1.12 - 1.10 0.97 6949 106 0.2240 0.2473 3.8683 4.0017| | 20: 1.10 - 1.08 0.97 6884 147 0.2304 0.2280 3.8247 3.8291| | 21: 1.08 - 1.07 0.97 6852 152 0.2436 0.2598 3.7899 3.8214| | 22: 1.07 - 1.05 0.97 6838 135 0.2557 0.2339 3.7505 3.7178| | 23: 1.05 - 1.03 0.97 6829 159 0.2696 0.2515 3.7223 3.7424| | 24: 1.03 - 1.02 0.96 6785 133 0.2861 0.2598 3.6972 3.7012| | 25: 1.02 - 1.01 0.93 6552 130 0.3059 0.3114 3.6722 3.7733| | 26: 1.01 - 0.99 0.96 6767 158 0.3207 0.3245 3.6281 3.6019| | 27: 0.99 - 0.98 0.94 6648 131 0.3389 0.3291 3.6346 3.6298| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.36 0.91 0.97 35086.41| | 2: 2.94 - 2.33 7339 128 0.86 21.10 1.08 1.02 14950.26| | 3: 2.33 - 2.04 6939 150 0.93 12.43 1.11 1.05 4069.59| | 4: 2.04 - 1.85 7170 155 0.93 13.30 1.11 1.07 2709.41| | 5: 1.85 - 1.72 7113 159 0.91 15.20 1.12 1.08 1997.30| | 6: 1.72 - 1.62 7102 142 0.90 16.66 1.11 1.08 1657.81| | 7: 1.62 - 1.54 7104 148 0.89 18.13 1.11 1.07 1392.30| | 8: 1.54 - 1.47 6798 152 0.88 18.72 1.10 1.07 1200.03| | 9: 1.47 - 1.41 6938 155 0.88 19.45 1.10 1.08 1024.81| | 10: 1.41 - 1.36 7022 150 0.87 20.16 1.09 1.07 871.00| | 11: 1.36 - 1.32 6997 151 0.87 19.91 1.09 1.06 734.14| | 12: 1.32 - 1.28 6976 149 0.88 19.61 1.08 1.04 628.53| | 13: 1.28 - 1.25 6907 166 0.87 19.87 1.07 1.03 603.31| | 14: 1.25 - 1.22 7015 113 0.86 21.06 1.08 1.03 594.89| | 15: 1.22 - 1.19 6957 137 0.86 21.63 1.08 1.03 573.46| | 16: 1.19 - 1.17 6604 132 0.86 21.19 1.08 1.02 518.21| | 17: 1.17 - 1.14 6941 135 0.86 21.59 1.08 1.02 461.52| | 18: 1.14 - 1.12 6875 142 0.86 21.66 1.08 1.00 411.83| | 19: 1.12 - 1.10 6949 106 0.85 22.38 1.07 0.99 386.40| | 20: 1.10 - 1.08 6884 147 0.85 22.99 1.06 0.96 347.72| | 21: 1.08 - 1.07 6852 152 0.84 23.65 1.06 0.98 326.88| | 22: 1.07 - 1.05 6838 135 0.83 24.29 1.06 0.99 301.86| | 23: 1.05 - 1.03 6829 159 0.82 26.10 1.06 0.98 300.28| | 24: 1.03 - 1.02 6785 133 0.79 28.12 1.05 0.98 305.29| | 25: 1.02 - 1.01 6552 130 0.77 30.34 1.03 0.93 305.49| | 26: 1.01 - 0.99 6767 158 0.74 33.11 1.03 0.90 305.47| | 27: 0.99 - 0.98 6648 131 0.72 34.94 1.03 0.85 301.70| |alpha: min = 0.85 max = 1.08 mean = 1.01| |beta: min = 300.28 max = 35086.41 mean = 2805.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.69| |phase err.(test): min = 0.00 max = 89.14 mean = 21.71| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.233 2950 Z= 5.474 Angle : 5.160 17.570 4018 Z= 3.656 Chirality : 0.380 1.041 492 Planarity : 0.033 0.139 512 Dihedral : 12.782 86.949 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.63 % Favored : 95.85 % Rotamer: Outliers : 0.32 % Allowed : 4.52 % Favored : 95.16 % Cbeta Deviations : 29.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.38), residues: 386 helix: -2.85 (0.30), residues: 142 sheet: -1.18 (0.52), residues: 86 loop : -0.45 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.022 ARG B 100 TYR 0.123 0.038 TYR B 194 PHE 0.082 0.033 PHE A 82 TRP 0.114 0.040 TRP B 146 HIS 0.078 0.024 HIS A 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= 0.2035 r_free= 0.1994 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301295 | | target function (ml) not normalized (work): 805688.438794 | | target function (ml) not normalized (free): 16556.712823 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2035 0.1994 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2035 0.1994 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2035 0.1994 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2034 0.2035 0.1994 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1803 0.1925 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1800 0.1925 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 0.4102 402.814 293.100 0.436 0.910 0.299 13.296-10.522 99.01 99 1 0.2505 528.187 517.555 0.788 0.911 0.246 10.503-8.327 98.90 177 3 0.2510 564.205 557.649 0.977 0.911 0.220 8.318-6.595 100.00 360 8 0.2499 414.736 402.669 0.970 0.911 0.155 6.588-5.215 100.00 711 7 0.2225 381.101 365.867 0.963 0.911 0.150 5.214-4.128 98.38 1367 28 0.1473 557.435 549.998 1.077 0.912 0.080 4.126-3.266 94.74 2603 46 0.1358 508.132 498.580 1.146 0.912 0.019 3.266-2.585 99.86 5447 97 0.1433 342.774 338.195 1.122 0.911 0.005 2.585-2.046 97.45 10613 204 0.1408 258.603 254.057 1.128 0.911 0.000 2.046-1.619 99.39 21536 464 0.1610 153.054 149.879 1.145 0.909 0.000 1.619-1.281 98.00 42464 925 0.1927 82.395 80.096 1.131 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2323 44.203 41.690 1.114 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0018 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1925 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=0.1801 r_free=0.1925 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.965506 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.371438 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1501 0.0229 0.039 1.2 11.2 0.0 0.3 0 11.483 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.01 2.29 1.117 13.110 573.371 0.018 12.99 15.71 2.71 1.272 13.384 573.371 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.04 15.09 1.42 435 3274 Protein: 5.16 40.33 11.03 1.42 0 2902 Water: 6.30 73.04 29.73 N/A 435 370 Other: 16.15 30.50 23.33 N/A 0 2 Chain A: 5.33 59.87 13.10 N/A 0 1626 Chain B: 5.16 73.04 12.82 N/A 0 1648 Chain S: 11.42 65.37 31.19 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2159 11.95 - 18.74 636 18.74 - 25.52 316 25.52 - 32.31 262 32.31 - 39.10 155 39.10 - 45.89 108 45.89 - 52.68 48 52.68 - 59.47 21 59.47 - 66.25 3 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1571 r_work=0.1299 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1567 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1284 r_free = 0.1557 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1284 r_free= 0.1557 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015530 | | target function (ls_wunit_k1) not normalized (work): 2908.695704 | | target function (ls_wunit_k1) not normalized (free): 115.848508 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1284 0.1557 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1632 n_refl.: 191138 remove outliers: r(all,work,free)=0.1470 0.1467 0.1632 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1493 0.1490 0.1643 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1547 n_refl.: 191138 remove outliers: r(all,work,free)=0.1281 0.1276 0.1546 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3621 402.814 381.263 0.470 0.997 0.275 13.296-10.522 99.01 99 1 0.2081 528.187 521.771 0.714 0.998 0.245 10.503-8.327 98.90 177 3 0.1715 564.205 562.194 0.856 0.998 0.198 8.318-6.595 100.00 360 8 0.1709 414.736 412.332 0.877 0.998 0.155 6.588-5.215 100.00 711 7 0.1529 381.101 373.441 0.858 0.998 0.150 5.214-4.128 98.38 1367 28 0.0904 557.435 555.059 0.942 0.999 0.049 4.126-3.266 94.74 2603 46 0.0830 508.132 504.258 1.007 1.000 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.285 0.991 0.999 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.364 1.002 1.000 0.000 2.046-1.619 99.39 21536 464 0.1093 153.054 151.379 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1284 82.395 81.405 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.166 0.988 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0369 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1546 | n_water=805 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1280 r_free=0.1551 | n_water=795 | time (s): 98.380 (total time: 100.870) Filter (q & B) r_work=0.1281 r_free=0.1552 | n_water=790 | time (s): 4.420 (total time: 105.290) Compute maps r_work=0.1281 r_free=0.1552 | n_water=790 | time (s): 1.940 (total time: 107.230) Filter (map) r_work=0.1307 r_free=0.1532 | n_water=653 | time (s): 4.740 (total time: 111.970) Find peaks r_work=0.1307 r_free=0.1532 | n_water=653 | time (s): 0.760 (total time: 112.730) Add new water r_work=0.1329 r_free=0.1562 | n_water=965 | time (s): 4.280 (total time: 117.010) Refine new water occ: r_work=0.1286 r_free=0.1515 adp: r_work=0.1274 r_free=0.1513 occ: r_work=0.1276 r_free=0.1509 adp: r_work=0.1270 r_free=0.1512 occ: r_work=0.1271 r_free=0.1509 adp: r_work=0.1268 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1512 r_work=0.1268 r_free=0.1512 | n_water=965 | time (s): 82.050 (total time: 199.060) Filter (q & B) r_work=0.1272 r_free=0.1511 | n_water=885 | time (s): 5.060 (total time: 204.120) Filter (dist only) r_work=0.1273 r_free=0.1510 | n_water=884 | time (s): 114.860 (total time: 318.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.934770 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 593.742856 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 0.1256 0.1528 0.0272 0.041 1.1 19.0 0.0 0.0 0 11.967 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.28 2.72 2.054 15.256 593.743 0.014 12.34 15.12 2.78 2.417 15.268 593.743 0.014 Individual atomic B min max mean iso aniso Overall: 5.48 69.11 16.36 1.21 516 3272 Protein: 5.48 40.12 11.01 1.21 0 2902 Water: 6.61 69.11 33.90 N/A 516 368 Other: 16.49 32.66 24.57 N/A 0 2 Chain A: 5.56 56.71 13.02 N/A 0 1624 Chain B: 5.48 69.03 12.85 N/A 0 1648 Chain S: 11.43 69.11 38.07 N/A 516 0 Histogram: Values Number of atoms 5.48 - 11.84 2092 11.84 - 18.20 689 18.20 - 24.57 260 24.57 - 30.93 223 30.93 - 37.29 162 37.29 - 43.65 162 43.65 - 50.02 98 50.02 - 56.38 54 56.38 - 62.74 41 62.74 - 69.11 7 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1512 r_work=0.1234 r_free=0.1513 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1513 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1517 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013436 | | target function (ls_wunit_k1) not normalized (work): 2516.506429 | | target function (ls_wunit_k1) not normalized (free): 101.638139 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1228 0.1517 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1438 0.1434 0.1627 n_refl.: 191137 remove outliers: r(all,work,free)=0.1438 0.1434 0.1627 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1431 0.1625 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1235 0.1525 n_refl.: 191137 remove outliers: r(all,work,free)=0.1241 0.1235 0.1525 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3188 402.814 379.990 0.489 0.962 0.265 13.296-10.522 99.01 99 1 0.1922 528.187 519.749 0.756 0.963 0.219 10.503-8.327 98.90 177 3 0.1434 564.205 566.964 0.920 0.963 0.179 8.318-6.595 100.00 360 8 0.1541 414.736 414.897 0.935 0.963 0.138 6.588-5.215 100.00 711 7 0.1346 381.101 377.094 0.913 0.963 0.117 5.214-4.128 98.38 1367 28 0.0831 557.435 555.966 0.993 0.963 0.070 4.126-3.266 94.74 2603 46 0.0768 508.132 505.381 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0853 342.774 341.467 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.747 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1048 153.054 151.606 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1259 82.395 81.340 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.215 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=-0.0511 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1525 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1525 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1525 | n_water=884 | time (s): 3.580 (total time: 3.580) Filter (dist) r_work=0.1239 r_free=0.1529 | n_water=875 | time (s): 115.360 (total time: 118.940) Filter (q & B) r_work=0.1239 r_free=0.1529 | n_water=874 | time (s): 4.600 (total time: 123.540) Compute maps r_work=0.1239 r_free=0.1529 | n_water=874 | time (s): 2.260 (total time: 125.800) Filter (map) r_work=0.1279 r_free=0.1517 | n_water=675 | time (s): 4.910 (total time: 130.710) Find peaks r_work=0.1279 r_free=0.1517 | n_water=675 | time (s): 0.700 (total time: 131.410) Add new water r_work=0.1300 r_free=0.1550 | n_water=1005 | time (s): 4.040 (total time: 135.450) Refine new water occ: r_work=0.1246 r_free=0.1509 adp: r_work=0.1241 r_free=0.1505 occ: r_work=0.1237 r_free=0.1501 adp: r_work=0.1237 r_free=0.1502 occ: r_work=0.1235 r_free=0.1500 adp: r_work=0.1235 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1500 r_work=0.1235 r_free=0.1500 | n_water=1005 | time (s): 311.140 (total time: 446.590) Filter (q & B) r_work=0.1241 r_free=0.1506 | n_water=849 | time (s): 5.990 (total time: 452.580) Filter (dist only) r_work=0.1241 r_free=0.1505 | n_water=848 | time (s): 109.760 (total time: 562.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.612363 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.592484 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 0.1230 0.1427 0.0197 0.034 1.1 6.6 0.0 0.0 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.30 14.27 1.97 1.943 14.454 16.592 3.932 12.21 13.89 1.68 2.265 14.361 16.592 3.885 Individual atomic B min max mean iso aniso Overall: 5.56 68.54 15.00 1.07 482 3270 Protein: 5.56 36.55 10.76 1.07 0 2902 Water: 5.67 68.54 29.53 N/A 482 366 Other: 13.77 28.21 20.99 N/A 0 2 Chain A: 5.57 55.69 12.76 N/A 0 1623 Chain B: 5.56 68.54 12.55 N/A 0 1647 Chain S: 5.67 61.80 30.95 N/A 482 0 Histogram: Values Number of atoms 5.56 - 11.86 2149 11.86 - 18.15 676 18.15 - 24.45 307 24.45 - 30.75 257 30.75 - 37.05 146 37.05 - 43.35 127 43.35 - 49.64 59 49.64 - 55.94 23 55.94 - 62.24 7 62.24 - 68.54 1 =========================== Idealize ADP of riding H ========================== r_work=0.1221 r_free=0.1389 r_work=0.1222 r_free=0.1390 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1222 r_free = 0.1390 target_work(ml) = 3.885 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1217 r_free = 0.1385 target_work(ml) = 3.880 | | 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.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1217 r_free= 0.1385 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.879870 | | target function (ml) not normalized (work): 726684.117196 | | target function (ml) not normalized (free): 15188.479292 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1220 0.1217 0.1384 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1440 0.1439 0.1492 n_refl.: 191137 remove outliers: r(all,work,free)=0.1440 0.1439 0.1492 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1434 0.1433 0.1488 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1216 0.1213 0.1376 n_refl.: 191137 remove outliers: r(all,work,free)=0.1216 0.1212 0.1376 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3921 393.525 360.903 0.415 0.947 0.249 13.296-10.522 99.01 99 1 0.2510 528.187 510.515 0.697 0.948 0.208 10.503-8.327 97.80 175 3 0.2123 554.286 556.033 0.876 0.948 0.187 8.318-6.595 100.00 360 8 0.2167 414.736 409.873 0.892 0.947 0.130 6.588-5.215 100.00 711 7 0.1881 381.101 370.774 0.886 0.948 0.129 5.214-4.128 98.38 1367 28 0.1189 557.435 551.173 0.971 0.948 0.060 4.126-3.266 94.74 2603 46 0.1091 508.132 501.174 1.032 0.948 0.005 3.266-2.585 99.86 5447 97 0.1078 342.774 339.194 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0954 258.603 255.673 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0948 153.054 151.467 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1027 82.395 81.496 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1674 44.202 42.318 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1028 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1213 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1213 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1213 r_free=0.1376 | n_water=848 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1214 r_free=0.1378 | n_water=845 | time (s): 100.800 (total time: 103.570) Filter (q & B) r_work=0.1214 r_free=0.1374 | n_water=829 | time (s): 4.240 (total time: 107.810) Compute maps r_work=0.1214 r_free=0.1374 | n_water=829 | time (s): 1.790 (total time: 109.600) Filter (map) r_work=0.1235 r_free=0.1368 | n_water=698 | time (s): 4.420 (total time: 114.020) Find peaks r_work=0.1235 r_free=0.1368 | n_water=698 | time (s): 0.710 (total time: 114.730) Add new water r_work=0.1250 r_free=0.1389 | n_water=954 | time (s): 5.060 (total time: 119.790) Refine new water occ: r_work=0.1210 r_free=0.1364 adp: r_work=0.1210 r_free=0.1364 occ: r_work=0.1207 r_free=0.1364 adp: r_work=0.1206 r_free=0.1363 occ: r_work=0.1204 r_free=0.1364 adp: r_work=0.1204 r_free=0.1363 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1363 r_work=0.1204 r_free=0.1363 | n_water=954 | time (s): 334.140 (total time: 453.930) Filter (q & B) r_work=0.1207 r_free=0.1367 | n_water=885 | time (s): 5.480 (total time: 459.410) Filter (dist only) r_work=0.1207 r_free=0.1365 | n_water=884 | time (s): 109.810 (total time: 569.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.608540 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.324724 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 0.1206 0.1372 0.0167 0.036 1.1 7.7 0.0 0.0 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.72 1.67 1.840 14.256 15.325 3.872 12.00 13.71 1.70 1.942 14.217 15.325 3.867 Individual atomic B min max mean iso aniso Overall: 5.54 68.12 15.04 1.00 519 3269 Protein: 5.54 33.43 10.68 1.00 0 2902 Water: 5.62 68.12 29.36 N/A 519 365 Other: 14.00 27.46 20.73 N/A 0 2 Chain A: 5.56 54.69 12.63 N/A 0 1623 Chain B: 5.54 68.12 12.44 N/A 0 1646 Chain S: 5.62 61.65 30.84 N/A 519 0 Histogram: Values Number of atoms 5.54 - 11.79 2144 11.79 - 18.05 712 18.05 - 24.31 298 24.31 - 30.57 256 30.57 - 36.83 153 36.83 - 43.08 132 43.08 - 49.34 64 49.34 - 55.60 21 55.60 - 61.86 7 61.86 - 68.12 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1371 r_work=0.1200 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1371 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1368 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864727 | | target function (ml) not normalized (work): 723832.362401 | | target function (ml) not normalized (free): 15143.908524 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1368 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1424 0.1423 0.1478 n_refl.: 191133 remove outliers: r(all,work,free)=0.1424 0.1423 0.1478 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1416 0.1415 0.1473 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1368 n_refl.: 191133 remove outliers: r(all,work,free)=0.1198 0.1195 0.1368 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3587 356.674 306.411 0.401 0.947 0.241 13.296-10.522 96.04 96 1 0.2392 480.322 451.299 0.697 0.948 0.209 10.503-8.327 97.80 175 3 0.2090 501.793 497.188 0.861 0.948 0.200 8.318-6.595 100.00 360 8 0.2189 375.459 371.209 0.888 0.948 0.105 6.588-5.215 100.00 711 7 0.1919 345.010 334.975 0.883 0.948 0.090 5.214-4.128 98.38 1367 28 0.1186 504.644 499.696 0.974 0.948 0.080 4.126-3.266 94.74 2603 46 0.1101 460.010 453.918 1.034 0.949 0.005 3.266-2.585 99.86 5447 97 0.1086 310.312 307.342 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0931 234.113 231.768 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0913 138.559 137.325 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0992 74.592 73.895 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1664 40.016 38.361 1.038 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1211 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1368 | n_water=884 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1195 r_free=0.1368 | n_water=884 | time (s): 109.900 (total time: 113.040) Filter (q & B) r_work=0.1195 r_free=0.1367 | n_water=871 | time (s): 4.760 (total time: 117.800) Compute maps r_work=0.1195 r_free=0.1367 | n_water=871 | time (s): 1.930 (total time: 119.730) Filter (map) r_work=0.1220 r_free=0.1369 | n_water=740 | time (s): 4.470 (total time: 124.200) Find peaks r_work=0.1220 r_free=0.1369 | n_water=740 | time (s): 0.570 (total time: 124.770) Add new water r_work=0.1230 r_free=0.1387 | n_water=954 | time (s): 5.010 (total time: 129.780) Refine new water occ: r_work=0.1195 r_free=0.1356 adp: r_work=0.1195 r_free=0.1356 occ: r_work=0.1193 r_free=0.1355 adp: r_work=0.1193 r_free=0.1355 occ: r_work=0.1191 r_free=0.1355 adp: r_work=0.1191 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1355 r_work=0.1191 r_free=0.1355 | n_water=954 | time (s): 221.720 (total time: 351.500) Filter (q & B) r_work=0.1194 r_free=0.1358 | n_water=879 | time (s): 5.390 (total time: 356.890) Filter (dist only) r_work=0.1194 r_free=0.1357 | n_water=878 | time (s): 111.410 (total time: 468.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507696 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.506280 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1363 0.0165 0.037 1.1 6.5 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.63 1.65 1.796 14.113 14.506 3.766 12.03 13.69 1.66 1.881 14.079 14.506 3.764 Individual atomic B min max mean iso aniso Overall: 5.58 67.70 14.89 0.95 513 3269 Protein: 5.58 32.03 10.59 0.95 0 2902 Water: 5.70 67.70 29.07 N/A 513 365 Other: 13.85 26.16 20.00 N/A 0 2 Chain A: 5.58 53.76 12.52 N/A 0 1623 Chain B: 5.58 67.70 12.34 N/A 0 1646 Chain S: 5.70 61.49 30.58 N/A 513 0 Histogram: Values Number of atoms 5.58 - 11.79 2161 11.79 - 18.00 710 18.00 - 24.21 294 24.21 - 30.43 241 30.43 - 36.64 159 36.64 - 42.85 133 42.85 - 49.07 59 49.07 - 55.28 17 55.28 - 61.49 7 61.49 - 67.70 1 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1369 r_work=0.1204 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1370 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1368 target_work(ml) = 3.763 | | 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.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762636 | | target function (ml) not normalized (work): 704692.782206 | | target function (ml) not normalized (free): 14751.261483 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1369 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1488 n_refl.: 191128 remove outliers: r(all,work,free)=0.1401 0.1400 0.1488 n_refl.: 191128 overall B=-0.04 to atoms: r(all,work,free)=0.1394 0.1392 0.1482 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1367 n_refl.: 191128 remove outliers: r(all,work,free)=0.1203 0.1200 0.1367 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3578 356.674 331.637 0.430 0.953 0.241 13.296-10.522 96.04 96 1 0.2389 480.322 463.066 0.707 0.954 0.193 10.503-8.327 97.80 175 3 0.2119 501.793 496.495 0.856 0.955 0.170 8.318-6.595 100.00 360 8 0.2200 375.459 370.501 0.886 0.954 0.110 6.588-5.215 100.00 711 7 0.1915 345.010 335.164 0.881 0.954 0.100 5.214-4.128 98.38 1367 28 0.1211 504.644 499.296 0.968 0.954 0.080 4.126-3.266 94.74 2603 46 0.1134 460.010 453.334 1.028 0.955 0.000 3.266-2.585 99.86 5447 97 0.1100 310.312 307.027 1.015 0.954 0.000 2.585-2.046 97.45 10613 204 0.0949 234.113 231.580 1.027 0.953 0.000 2.046-1.619 99.39 21536 464 0.0921 138.559 137.228 1.050 0.952 0.000 1.619-1.281 98.00 42464 925 0.0984 74.592 73.868 1.048 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.016 38.351 1.037 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1332 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1367 | n_water=878 | time (s): 2.830 (total time: 2.830) Filter (dist) r_work=0.1200 r_free=0.1367 | n_water=878 | time (s): 105.460 (total time: 108.290) Filter (q & B) r_work=0.1200 r_free=0.1364 | n_water=867 | time (s): 4.940 (total time: 113.230) Compute maps r_work=0.1200 r_free=0.1364 | n_water=867 | time (s): 1.770 (total time: 115.000) Filter (map) r_work=0.1221 r_free=0.1368 | n_water=751 | time (s): 5.260 (total time: 120.260) Find peaks r_work=0.1221 r_free=0.1368 | n_water=751 | time (s): 0.720 (total time: 120.980) Add new water r_work=0.1232 r_free=0.1382 | n_water=957 | time (s): 5.010 (total time: 125.990) Refine new water occ: r_work=0.1199 r_free=0.1354 adp: r_work=0.1199 r_free=0.1354 occ: r_work=0.1197 r_free=0.1352 adp: r_work=0.1197 r_free=0.1352 occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1351 r_work=0.1195 r_free=0.1351 | n_water=957 | time (s): 228.740 (total time: 354.730) Filter (q & B) r_work=0.1199 r_free=0.1359 | n_water=888 | time (s): 4.530 (total time: 359.260) Filter (dist only) r_work=0.1199 r_free=0.1358 | n_water=887 | time (s): 110.870 (total time: 470.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.504774 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.335604 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1368 0.0165 0.037 1.1 7.5 0.0 0.3 0 0.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.68 1.65 1.760 14.017 15.336 3.763 12.02 13.69 1.67 1.883 13.973 15.336 3.759 Individual atomic B min max mean iso aniso Overall: 5.57 66.49 14.80 0.91 522 3269 Protein: 5.57 29.60 10.50 0.91 0 2902 Water: 5.83 66.49 28.87 N/A 522 365 Other: 13.87 23.57 18.72 N/A 0 2 Chain A: 5.63 52.38 12.38 N/A 0 1623 Chain B: 5.57 66.49 12.22 N/A 0 1646 Chain S: 5.83 61.05 30.49 N/A 522 0 Histogram: Values Number of atoms 5.57 - 11.66 2129 11.66 - 17.76 765 17.76 - 23.85 277 23.85 - 29.94 230 29.94 - 36.03 167 36.03 - 42.12 132 42.12 - 48.22 58 48.22 - 54.31 25 54.31 - 60.40 5 60.40 - 66.49 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1369 r_work=0.1202 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1369 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757679 | | target function (ml) not normalized (work): 703764.346313 | | target function (ml) not normalized (free): 14737.003176 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1367 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1398 0.1397 0.1491 n_refl.: 191128 remove outliers: r(all,work,free)=0.1398 0.1397 0.1491 n_refl.: 191128 overall B=-0.23 to atoms: r(all,work,free)=0.1363 0.1361 0.1467 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1365 n_refl.: 191128 remove outliers: r(all,work,free)=0.1202 0.1199 0.1365 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3572 356.674 330.528 0.433 0.953 0.231 13.296-10.522 96.04 96 1 0.2365 480.322 464.630 0.720 0.954 0.172 10.503-8.327 97.80 175 3 0.2182 501.793 494.586 0.876 0.954 0.147 8.318-6.595 100.00 360 8 0.2189 375.459 370.444 0.909 0.954 0.116 6.588-5.215 100.00 711 7 0.1949 345.010 334.670 0.903 0.954 0.100 5.214-4.128 98.38 1367 28 0.1230 504.644 499.250 0.995 0.954 0.100 4.126-3.266 94.74 2603 46 0.1153 460.010 453.008 1.054 0.955 0.000 3.266-2.585 99.86 5447 97 0.1118 310.312 306.943 1.037 0.954 0.000 2.585-2.046 97.45 10613 204 0.0948 234.113 231.595 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0914 138.559 137.243 1.063 0.953 0.000 1.619-1.281 98.00 42464 925 0.0971 74.592 73.887 1.051 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.016 38.356 1.022 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0504 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1366 | n_water=887 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1200 r_free=0.1366 | n_water=886 | time (s): 112.290 (total time: 114.720) Filter (q & B) r_work=0.1200 r_free=0.1365 | n_water=875 | time (s): 4.580 (total time: 119.300) Compute maps r_work=0.1200 r_free=0.1365 | n_water=875 | time (s): 1.920 (total time: 121.220) Filter (map) r_work=0.1223 r_free=0.1366 | n_water=748 | time (s): 5.170 (total time: 126.390) Find peaks r_work=0.1223 r_free=0.1366 | n_water=748 | time (s): 0.550 (total time: 126.940) Add new water r_work=0.1234 r_free=0.1372 | n_water=954 | time (s): 3.990 (total time: 130.930) Refine new water occ: r_work=0.1198 r_free=0.1345 adp: r_work=0.1198 r_free=0.1345 occ: r_work=0.1196 r_free=0.1345 adp: r_work=0.1196 r_free=0.1345 occ: r_work=0.1195 r_free=0.1345 adp: r_work=0.1195 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1346 r_work=0.1195 r_free=0.1346 | n_water=954 | time (s): 193.060 (total time: 323.990) Filter (q & B) r_work=0.1198 r_free=0.1355 | n_water=885 | time (s): 5.580 (total time: 329.570) Filter (dist only) r_work=0.1198 r_free=0.1354 | n_water=884 | time (s): 110.810 (total time: 440.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.572681 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.679637 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 0.1201 0.1363 0.0162 0.038 1.1 7.5 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.63 1.62 1.724 13.682 14.680 3.759 12.03 13.66 1.63 1.768 13.664 14.680 3.758 Individual atomic B min max mean iso aniso Overall: 5.38 65.34 14.51 0.89 519 3269 Protein: 5.38 28.68 10.25 0.89 0 2902 Water: 5.74 65.34 28.47 N/A 519 365 Other: 13.68 22.45 18.06 N/A 0 2 Chain A: 5.46 51.84 12.09 N/A 0 1623 Chain B: 5.38 65.34 11.95 N/A 0 1646 Chain S: 5.74 60.52 30.20 N/A 519 0 Histogram: Values Number of atoms 5.38 - 11.37 2110 11.37 - 17.37 781 17.37 - 23.37 273 23.37 - 29.36 226 29.36 - 35.36 171 35.36 - 41.36 130 41.36 - 47.35 59 47.35 - 53.35 30 53.35 - 59.34 4 59.34 - 65.34 4 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1366 r_work=0.1204 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1368 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756946 | | target function (ml) not normalized (work): 703627.067459 | | target function (ml) not normalized (free): 14734.870386 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1368 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1372 0.1371 0.1474 n_refl.: 191128 remove outliers: r(all,work,free)=0.1372 0.1371 0.1474 n_refl.: 191128 overall B=0.06 to atoms: r(all,work,free)=0.1379 0.1378 0.1478 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1357 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1357 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3587 356.674 329.825 0.425 0.973 0.227 13.296-10.522 96.04 96 1 0.2354 480.322 464.600 0.710 0.974 0.166 10.503-8.327 97.80 175 3 0.2172 501.793 493.802 0.865 0.975 0.140 8.318-6.595 100.00 360 8 0.2187 375.459 370.006 0.892 0.975 0.095 6.588-5.215 100.00 711 7 0.1959 345.010 334.374 0.891 0.975 0.090 5.214-4.128 98.38 1367 28 0.1239 504.644 498.679 0.983 0.976 0.090 4.126-3.266 94.74 2603 46 0.1170 460.010 452.452 1.043 0.977 0.000 3.266-2.585 99.86 5447 97 0.1122 310.312 306.735 1.025 0.978 0.000 2.585-2.046 97.45 10613 204 0.0955 234.113 231.479 1.033 0.979 0.000 2.046-1.619 99.39 21536 464 0.0913 138.559 137.158 1.049 0.982 0.000 1.619-1.281 98.00 42464 925 0.0950 74.592 73.927 1.037 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.016 38.330 1.003 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0622 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1357 | n_water=884 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1193 r_free=0.1357 | n_water=884 | time (s): 106.300 (total time: 108.990) Filter (q & B) r_work=0.1193 r_free=0.1357 | n_water=874 | time (s): 4.980 (total time: 113.970) Compute maps r_work=0.1193 r_free=0.1357 | n_water=874 | time (s): 1.910 (total time: 115.880) Filter (map) r_work=0.1217 r_free=0.1357 | n_water=754 | time (s): 4.200 (total time: 120.080) Find peaks r_work=0.1217 r_free=0.1357 | n_water=754 | time (s): 0.560 (total time: 120.640) Add new water r_work=0.1228 r_free=0.1371 | n_water=968 | time (s): 3.810 (total time: 124.450) Refine new water occ: r_work=0.1191 r_free=0.1344 adp: r_work=0.1191 r_free=0.1344 occ: r_work=0.1189 r_free=0.1343 adp: r_work=0.1189 r_free=0.1343 occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1187 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1343 r_work=0.1187 r_free=0.1343 | n_water=968 | time (s): 278.750 (total time: 403.200) Filter (q & B) r_work=0.1191 r_free=0.1349 | n_water=896 | time (s): 5.670 (total time: 408.870) Filter (dist only) r_work=0.1191 r_free=0.1349 | n_water=895 | time (s): 115.280 (total time: 524.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.492950 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.207317 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 0.1362 0.0167 0.038 1.1 6.5 0.0 0.3 0 0.746 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.62 1.67 1.681 13.707 13.207 3.756 11.98 13.65 1.68 1.689 13.701 13.207 3.757 Individual atomic B min max mean iso aniso Overall: 5.46 65.12 14.59 0.86 530 3269 Protein: 5.46 28.40 10.32 0.86 0 2902 Water: 5.91 65.12 28.43 N/A 530 365 Other: 13.75 22.37 18.06 N/A 0 2 Chain A: 5.53 51.81 12.13 N/A 0 1623 Chain B: 5.46 65.12 11.99 N/A 0 1646 Chain S: 5.91 60.45 30.16 N/A 530 0 Histogram: Values Number of atoms 5.46 - 11.43 2109 11.43 - 17.40 788 17.40 - 23.36 277 23.36 - 29.33 222 29.33 - 35.29 170 35.29 - 41.26 132 41.26 - 47.22 64 47.22 - 53.19 29 53.19 - 59.16 3 59.16 - 65.12 5 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1366 r_work=0.1198 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1366 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1365 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756451 | | target function (ml) not normalized (work): 703534.443597 | | target function (ml) not normalized (free): 14737.804630 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1365 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1388 0.1386 0.1488 n_refl.: 191128 remove outliers: r(all,work,free)=0.1388 0.1386 0.1488 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1390 0.1388 0.1490 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1362 n_refl.: 191128 remove outliers: r(all,work,free)=0.1198 0.1195 0.1362 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3597 356.674 328.051 0.412 0.974 0.209 13.296-10.522 96.04 96 1 0.2336 480.322 464.579 0.702 0.975 0.151 10.503-8.327 97.80 175 3 0.2197 501.793 492.938 0.862 0.976 0.127 8.318-6.595 100.00 360 8 0.2184 375.459 370.275 0.890 0.975 0.090 6.588-5.215 100.00 711 7 0.1956 345.010 334.334 0.890 0.976 0.090 5.214-4.128 98.38 1367 28 0.1244 504.644 498.717 0.982 0.977 0.080 4.126-3.266 94.74 2603 46 0.1179 460.010 452.452 1.042 0.978 0.000 3.266-2.585 99.86 5447 97 0.1129 310.312 306.734 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0958 234.113 231.482 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0915 138.559 137.179 1.050 0.984 0.000 1.619-1.281 98.00 42464 925 0.0950 74.592 73.935 1.039 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.016 38.313 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0205 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1362 | n_water=895 | time (s): 3.210 (total time: 3.210) Filter (dist) r_work=0.1195 r_free=0.1362 | n_water=895 | time (s): 106.140 (total time: 109.350) Filter (q & B) r_work=0.1196 r_free=0.1359 | n_water=882 | time (s): 5.080 (total time: 114.430) Compute maps r_work=0.1196 r_free=0.1359 | n_water=882 | time (s): 1.790 (total time: 116.220) Filter (map) r_work=0.1220 r_free=0.1369 | n_water=765 | time (s): 5.590 (total time: 121.810) Find peaks r_work=0.1220 r_free=0.1369 | n_water=765 | time (s): 0.650 (total time: 122.460) Add new water r_work=0.1229 r_free=0.1380 | n_water=973 | time (s): 4.100 (total time: 126.560) Refine new water occ: r_work=0.1193 r_free=0.1354 adp: r_work=0.1193 r_free=0.1354 occ: r_work=0.1191 r_free=0.1352 adp: r_work=0.1191 r_free=0.1352 occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1190 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1351 r_work=0.1190 r_free=0.1351 | n_water=973 | time (s): 180.560 (total time: 307.120) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=901 | time (s): 4.460 (total time: 311.580) Filter (dist only) r_work=0.1194 r_free=0.1357 | n_water=900 | time (s): 113.930 (total time: 425.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.547667 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.298301 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1362 0.0165 0.039 1.1 6.8 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.62 1.65 1.679 13.715 14.298 3.757 11.95 13.61 1.67 1.684 13.714 14.298 3.754 Individual atomic B min max mean iso aniso Overall: 5.54 64.47 14.59 0.87 535 3269 Protein: 5.54 28.24 10.35 0.87 0 2902 Water: 5.95 64.47 28.27 N/A 535 365 Other: 13.80 22.23 18.02 N/A 0 2 Chain A: 5.61 51.57 12.13 N/A 0 1623 Chain B: 5.54 64.47 12.01 N/A 0 1646 Chain S: 5.95 60.40 30.01 N/A 535 0 Histogram: Values Number of atoms 5.54 - 11.43 2091 11.43 - 17.32 807 17.32 - 23.22 274 23.22 - 29.11 231 29.11 - 35.00 172 35.00 - 40.90 124 40.90 - 46.79 67 46.79 - 52.68 30 52.68 - 58.58 3 58.58 - 64.47 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1362 r_work=0.1195 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1362 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1362 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753322 | | target function (ml) not normalized (work): 702948.362807 | | target function (ml) not normalized (free): 14730.066422 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1193 0.1362 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1496 n_refl.: 191128 remove outliers: r(all,work,free)=0.1395 0.1393 0.1496 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1394 0.1393 0.1496 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1192 0.1360 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1192 0.1360 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3611 356.674 327.570 0.435 0.914 0.209 13.296-10.522 96.04 96 1 0.2345 480.322 464.129 0.745 0.915 0.149 10.503-8.327 97.80 175 3 0.2196 501.793 492.920 0.916 0.916 0.123 8.318-6.595 100.00 360 8 0.2192 375.459 369.614 0.949 0.916 0.100 6.588-5.215 100.00 711 7 0.1976 345.010 334.554 0.946 0.916 0.083 5.214-4.128 98.38 1367 28 0.1247 504.644 498.685 1.044 0.917 0.070 4.126-3.266 94.74 2603 46 0.1179 460.010 452.441 1.110 0.918 0.000 3.266-2.585 99.86 5447 97 0.1129 310.312 306.692 1.091 0.919 0.000 2.585-2.046 97.45 10613 204 0.0957 234.113 231.479 1.100 0.921 0.000 2.046-1.619 99.39 21536 464 0.0911 138.559 137.182 1.118 0.925 0.000 1.619-1.281 98.00 42464 925 0.0943 74.592 73.940 1.108 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.016 38.306 1.076 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0076 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1360 After: r_work=0.1193 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1361 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=0.1194 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1364 | n_water=900 | time (s): 2.980 (total time: 2.980) Filter (dist) r_work=0.1194 r_free=0.1364 | n_water=899 | time (s): 119.070 (total time: 122.050) Filter (q & B) r_work=0.1195 r_free=0.1361 | n_water=887 | time (s): 5.270 (total time: 127.320) Compute maps r_work=0.1195 r_free=0.1361 | n_water=887 | time (s): 1.780 (total time: 129.100) Filter (map) r_work=0.1219 r_free=0.1370 | n_water=776 | time (s): 5.100 (total time: 134.200) Find peaks r_work=0.1219 r_free=0.1370 | n_water=776 | time (s): 0.760 (total time: 134.960) Add new water r_work=0.1227 r_free=0.1378 | n_water=974 | time (s): 4.920 (total time: 139.880) Refine new water occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1193 r_free=0.1352 occ: r_work=0.1191 r_free=0.1348 adp: r_work=0.1191 r_free=0.1349 occ: r_work=0.1190 r_free=0.1346 adp: r_work=0.1190 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1347 r_work=0.1190 r_free=0.1347 | n_water=974 | time (s): 294.910 (total time: 434.790) Filter (q & B) r_work=0.1193 r_free=0.1354 | n_water=910 | time (s): 5.210 (total time: 440.000) Filter (dist only) r_work=0.1194 r_free=0.1354 | n_water=909 | time (s): 115.100 (total time: 555.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524240 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.679397 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1358 0.0162 0.039 1.2 9.4 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.58 1.62 1.682 13.732 14.679 3.756 11.96 13.58 1.62 1.683 13.733 14.679 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 63.62 14.61 0.87 544 3269 Protein: 5.56 28.19 10.36 0.87 0 2902 Water: 6.03 63.62 28.17 N/A 544 365 Other: 13.83 22.25 18.04 N/A 0 2 Chain A: 5.67 51.26 12.13 N/A 0 1623 Chain B: 5.56 63.62 12.00 N/A 0 1646 Chain S: 6.03 60.32 29.91 N/A 544 0 Histogram: Values Number of atoms 5.56 - 11.37 2069 11.37 - 17.17 826 17.17 - 22.98 272 22.98 - 28.79 238 28.79 - 34.59 170 34.59 - 40.40 125 40.40 - 46.20 71 46.20 - 52.01 32 52.01 - 57.82 4 57.82 - 63.62 6 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1358 r_work=0.1196 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1358 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1356 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753850 | | target function (ml) not normalized (work): 703047.321534 | | target function (ml) not normalized (free): 14724.953715 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1373 0.1501 5.6959 5.7742| | 2: 2.94 - 2.33 1.00 7339 128 0.1071 0.1300 5.0807 5.1708| | 3: 2.33 - 2.04 0.96 6939 150 0.0902 0.1191 4.6502 4.7507| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1031 4.3896 4.5493| | 5: 1.85 - 1.72 0.99 7113 159 0.0937 0.1005 4.1524 4.2495| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1100 3.9466 4.0785| | 7: 1.62 - 1.54 0.99 7104 148 0.0891 0.0956 3.7974 3.918| | 8: 1.54 - 1.47 0.96 6798 152 0.0890 0.1316 3.6989 3.9011| | 9: 1.47 - 1.41 0.98 6938 155 0.0925 0.1127 3.6218 3.759| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1202 3.5575 3.6835| | 11: 1.36 - 1.32 0.99 6997 151 0.0994 0.1126 3.485 3.5875| | 12: 1.32 - 1.28 0.98 6975 149 0.1033 0.1120 3.4587 3.5779| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1241 3.4366 3.5661| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1574 3.432 3.6789| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1245 3.4477 3.4871| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1545 3.4641 3.6561| | 17: 1.17 - 1.14 0.98 6940 135 0.1297 0.1212 3.4315 3.4367| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1713 3.437 3.535| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1756 3.4188 3.5937| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1584 3.4097 3.4342| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2146 3.418 3.5056| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1958 3.4124 3.4175| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2012 3.4326 3.4835| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2247 3.4351 3.5082| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2511 3.4487 3.5224| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2867 3.4149 3.4244| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2797 3.4687 3.3948| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.82 1.00 0.95 11413.10| | 2: 2.94 - 2.33 7339 128 0.93 12.83 0.99 0.95 5161.57| | 3: 2.33 - 2.04 6939 150 0.96 7.53 1.01 0.95 1662.66| | 4: 2.04 - 1.85 7170 155 0.96 7.60 1.00 0.95 995.99| | 5: 1.85 - 1.72 7113 159 0.96 8.09 1.00 0.96 636.82| | 6: 1.72 - 1.62 7102 142 0.96 8.03 1.00 0.96 443.62| | 7: 1.62 - 1.54 7104 148 0.96 8.11 1.01 0.97 334.82| | 8: 1.54 - 1.47 6798 152 0.96 8.25 1.01 0.97 278.79| | 9: 1.47 - 1.41 6938 155 0.96 8.49 1.00 0.98 232.34| | 10: 1.41 - 1.36 7022 150 0.96 8.97 1.00 0.97 204.23| | 11: 1.36 - 1.32 6997 151 0.96 8.95 0.99 0.96 175.29| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.98 0.95 160.43| | 13: 1.28 - 1.25 6907 166 0.96 9.54 1.01 0.96 157.92| | 14: 1.25 - 1.22 7015 112 0.95 10.72 1.01 0.96 163.26| | 15: 1.22 - 1.19 6956 137 0.95 11.25 1.01 0.98 166.44| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.96 159.80| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.96 153.16| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.95 147.37| | 19: 1.12 - 1.10 6948 106 0.93 14.16 1.00 0.94 151.11| | 20: 1.10 - 1.08 6884 147 0.92 15.26 1.00 0.94 150.72| | 21: 1.08 - 1.07 6852 152 0.91 16.68 1.00 0.93 153.74| | 22: 1.07 - 1.05 6836 135 0.89 18.32 0.99 0.93 155.16| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.92 164.32| | 24: 1.03 - 1.02 6784 133 0.85 23.11 0.99 0.93 178.48| | 25: 1.02 - 1.01 6552 130 0.83 25.12 0.98 0.90 181.55| | 26: 1.01 - 0.99 6767 158 0.81 26.60 0.98 0.88 176.29| | 27: 0.99 - 0.98 6647 131 0.82 26.24 0.99 0.87 160.55| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.37 max = 11413.10 mean = 933.46| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.29| |phase err.(test): min = 0.00 max = 88.37 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1495 n_refl.: 191128 remove outliers: r(all,work,free)=0.1403 0.1402 0.1495 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1395 0.1393 0.1489 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1353 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1194 0.1353 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3659 356.674 325.901 0.386 0.974 0.195 13.296-10.522 96.04 96 1 0.2363 480.322 464.151 0.677 0.975 0.140 10.503-8.327 97.80 175 3 0.2206 501.793 492.447 0.837 0.976 0.113 8.318-6.595 100.00 360 8 0.2186 375.459 369.978 0.868 0.976 0.093 6.588-5.215 100.00 711 7 0.1989 345.010 334.766 0.864 0.976 0.077 5.214-4.128 98.38 1367 28 0.1266 504.644 498.534 0.954 0.977 0.034 4.126-3.266 94.74 2603 46 0.1179 460.010 452.222 1.017 0.979 0.000 3.266-2.585 99.86 5447 97 0.1124 310.312 306.817 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0960 234.113 231.495 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0911 138.559 137.186 1.022 0.988 0.000 1.619-1.281 98.00 42464 925 0.0946 74.592 73.944 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.016 38.304 0.978 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0121 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2035 0.1994 0.081 5.160 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1925 0.081 5.160 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1925 0.081 5.160 5.2 78.0 14.6 805 0.000 1_nqh: 0.1801 0.1925 0.081 5.160 5.2 78.0 14.6 805 0.002 1_weight: 0.1801 0.1925 0.081 5.160 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1272 0.1501 0.039 1.159 5.2 78.0 14.6 805 0.157 1_adp: 0.1300 0.1571 0.039 1.159 5.2 73.0 15.1 805 0.157 1_regHadp: 0.1299 0.1567 0.039 1.159 5.2 73.0 15.1 805 0.157 1_occ: 0.1284 0.1557 0.039 1.159 5.2 73.0 15.1 805 0.157 2_bss: 0.1276 0.1546 0.039 1.159 5.3 73.2 15.3 805 0.157 2_settarget: 0.1276 0.1546 0.039 1.159 5.3 73.2 15.3 805 0.157 2_updatecdl: 0.1276 0.1546 0.039 1.167 5.3 73.2 15.3 805 0.157 2_nqh: 0.1276 0.1546 0.039 1.167 5.3 73.2 15.3 805 0.157 2_sol: 0.1273 0.1510 0.039 1.167 5.3 73.2 16.3 884 n/a 2_weight: 0.1273 0.1510 0.039 1.167 5.3 73.2 16.3 884 n/a 2_xyzrec: 0.1256 0.1528 0.041 1.139 5.3 73.2 16.3 884 n/a 2_adp: 0.1234 0.1512 0.041 1.139 5.5 69.1 16.4 884 n/a 2_regHadp: 0.1234 0.1513 0.041 1.139 5.5 69.1 16.4 884 n/a 2_occ: 0.1228 0.1517 0.041 1.139 5.5 69.1 16.4 884 n/a 3_bss: 0.1235 0.1525 0.041 1.139 5.5 69.1 16.3 884 n/a 3_settarget: 0.1235 0.1525 0.041 1.139 5.5 69.1 16.3 884 n/a 3_updatecdl: 0.1235 0.1525 0.041 1.150 5.5 69.1 16.3 884 n/a 3_nqh: 0.1235 0.1525 0.041 1.150 5.5 69.1 16.3 884 n/a 3_sol: 0.1241 0.1505 0.041 1.150 5.5 69.0 15.2 848 n/a 3_weight: 0.1241 0.1505 0.041 1.150 5.5 69.0 15.2 848 n/a 3_xyzrec: 0.1230 0.1427 0.034 1.098 5.5 69.0 15.2 848 n/a 3_adp: 0.1221 0.1389 0.034 1.098 5.6 68.5 15.0 848 n/a 3_regHadp: 0.1222 0.1390 0.034 1.098 5.6 68.5 15.0 848 n/a 3_occ: 0.1217 0.1385 0.034 1.098 5.6 68.5 15.0 848 n/a 4_bss: 0.1213 0.1376 0.034 1.098 5.5 68.5 15.0 848 n/a 4_settarget: 0.1213 0.1376 0.034 1.098 5.5 68.5 15.0 848 n/a 4_updatecdl: 0.1213 0.1376 0.034 1.100 5.5 68.5 15.0 848 n/a 4_nqh: 0.1213 0.1376 0.034 1.100 5.5 68.5 15.0 848 n/a 4_sol: 0.1207 0.1365 0.034 1.100 5.5 68.5 15.1 884 n/a 4_weight: 0.1207 0.1365 0.034 1.100 5.5 68.5 15.1 884 n/a 4_xyzrec: 0.1206 0.1372 0.036 1.129 5.5 68.5 15.1 884 n/a 4_adp: 0.1200 0.1371 0.036 1.129 5.5 68.1 15.0 884 n/a 4_regHadp: 0.1200 0.1371 0.036 1.129 5.5 68.1 15.0 884 n/a 4_occ: 0.1197 0.1368 0.036 1.129 5.5 68.1 15.0 884 n/a 5_bss: 0.1195 0.1368 0.036 1.129 5.5 68.1 15.0 884 n/a 5_settarget: 0.1195 0.1368 0.036 1.129 5.5 68.1 15.0 884 n/a 5_updatecdl: 0.1195 0.1368 0.036 1.129 5.5 68.1 15.0 884 n/a 5_nqh: 0.1195 0.1368 0.036 1.129 5.5 68.1 15.0 884 n/a 5_sol: 0.1194 0.1357 0.036 1.129 5.5 68.1 14.9 878 n/a 5_weight: 0.1194 0.1357 0.036 1.129 5.5 68.1 14.9 878 n/a 5_xyzrec: 0.1198 0.1363 0.037 1.122 5.5 68.1 14.9 878 n/a 5_adp: 0.1203 0.1369 0.037 1.122 5.6 67.7 14.9 878 n/a 5_regHadp: 0.1204 0.1370 0.037 1.122 5.6 67.7 14.9 878 n/a 5_occ: 0.1201 0.1368 0.037 1.122 5.6 67.7 14.9 878 n/a 6_bss: 0.1200 0.1367 0.037 1.122 5.5 67.7 14.8 878 n/a 6_settarget: 0.1200 0.1367 0.037 1.122 5.5 67.7 14.8 878 n/a 6_updatecdl: 0.1200 0.1367 0.037 1.122 5.5 67.7 14.8 878 n/a 6_nqh: 0.1200 0.1367 0.037 1.122 5.5 67.7 14.8 878 n/a 6_sol: 0.1199 0.1358 0.037 1.122 5.5 67.7 14.9 887 n/a 6_weight: 0.1199 0.1358 0.037 1.122 5.5 67.7 14.9 887 n/a 6_xyzrec: 0.1202 0.1368 0.037 1.115 5.5 67.7 14.9 887 n/a 6_adp: 0.1202 0.1369 0.037 1.115 5.6 66.5 14.8 887 n/a 6_regHadp: 0.1202 0.1369 0.037 1.115 5.6 66.5 14.8 887 n/a 6_occ: 0.1200 0.1367 0.037 1.115 5.6 66.5 14.8 887 n/a 7_bss: 0.1200 0.1366 0.037 1.115 5.3 66.3 14.6 887 n/a 7_settarget: 0.1200 0.1366 0.037 1.115 5.3 66.3 14.6 887 n/a 7_updatecdl: 0.1200 0.1366 0.037 1.114 5.3 66.3 14.6 887 n/a 7_nqh: 0.1200 0.1366 0.037 1.114 5.3 66.3 14.6 887 n/a 7_sol: 0.1198 0.1354 0.037 1.114 5.3 66.3 14.5 884 n/a 7_weight: 0.1198 0.1354 0.037 1.114 5.3 66.3 14.5 884 n/a 7_xyzrec: 0.1201 0.1363 0.038 1.125 5.3 66.3 14.5 884 n/a 7_adp: 0.1203 0.1366 0.038 1.125 5.4 65.3 14.5 884 n/a 7_regHadp: 0.1204 0.1367 0.038 1.125 5.4 65.3 14.5 884 n/a 7_occ: 0.1202 0.1368 0.038 1.125 5.4 65.3 14.5 884 n/a 8_bss: 0.1193 0.1357 0.038 1.125 5.4 65.4 14.6 884 n/a 8_settarget: 0.1193 0.1357 0.038 1.125 5.4 65.4 14.6 884 n/a 8_updatecdl: 0.1193 0.1357 0.038 1.125 5.4 65.4 14.6 884 n/a 8_nqh: 0.1193 0.1357 0.038 1.125 5.4 65.4 14.6 884 n/a 8_sol: 0.1191 0.1349 0.038 1.125 5.4 65.4 14.6 895 n/a 8_weight: 0.1191 0.1349 0.038 1.125 5.4 65.4 14.6 895 n/a 8_xyzrec: 0.1195 0.1362 0.038 1.114 5.4 65.4 14.6 895 n/a 8_adp: 0.1198 0.1366 0.038 1.114 5.5 65.1 14.6 895 n/a 8_regHadp: 0.1198 0.1366 0.038 1.114 5.5 65.1 14.6 895 n/a 8_occ: 0.1196 0.1365 0.038 1.114 5.5 65.1 14.6 895 n/a 9_bss: 0.1195 0.1362 0.038 1.114 5.5 65.1 14.6 895 n/a 9_settarget: 0.1195 0.1362 0.038 1.114 5.5 65.1 14.6 895 n/a 9_updatecdl: 0.1195 0.1362 0.038 1.114 5.5 65.1 14.6 895 n/a 9_nqh: 0.1195 0.1362 0.038 1.114 5.5 65.1 14.6 895 n/a 9_sol: 0.1194 0.1357 0.038 1.114 5.5 65.1 14.6 900 n/a 9_weight: 0.1194 0.1357 0.038 1.114 5.5 65.1 14.6 900 n/a 9_xyzrec: 0.1197 0.1362 0.039 1.116 5.5 65.1 14.6 900 n/a 9_adp: 0.1195 0.1362 0.039 1.116 5.5 64.5 14.6 900 n/a 9_regHadp: 0.1195 0.1362 0.039 1.116 5.5 64.5 14.6 900 n/a 9_occ: 0.1193 0.1362 0.039 1.116 5.5 64.5 14.6 900 n/a 10_bss: 0.1192 0.1360 0.039 1.116 5.5 64.5 14.6 900 n/a 10_settarget: 0.1192 0.1360 0.039 1.116 5.5 64.5 14.6 900 n/a 10_updatecdl: 0.1192 0.1360 0.039 1.116 5.5 64.5 14.6 900 n/a 10_setrh: 0.1193 0.1361 0.039 1.116 5.5 64.5 14.6 900 n/a 10_nqh: 0.1194 0.1364 0.039 1.116 5.5 64.5 14.6 900 n/a 10_sol: 0.1194 0.1354 0.039 1.116 5.5 64.5 14.6 909 n/a 10_weight: 0.1194 0.1354 0.039 1.116 5.5 64.5 14.6 909 n/a 10_xyzrec: 0.1196 0.1358 0.039 1.156 5.5 64.5 14.6 909 n/a 10_adp: 0.1196 0.1358 0.039 1.156 5.6 63.6 14.6 909 n/a 10_regHadp: 0.1196 0.1358 0.039 1.156 5.6 63.6 14.6 909 n/a 10_occ: 0.1195 0.1356 0.039 1.156 5.6 63.6 14.6 909 n/a end: 0.1194 0.1353 0.039 1.156 5.5 63.6 14.6 909 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2328810_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2328810_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.6000 Refinement macro-cycles (run) : 12220.1400 Write final files (write_after_run_outputs) : 155.7500 Total : 12381.4900 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:41 PST -0800 (1736736221.23 s) Start R-work = 0.1800, R-free = 0.1925 Final R-work = 0.1194, R-free = 0.1353 =============================================================================== Job complete usr+sys time: 12659.42 seconds wall clock time: 212 minutes 3.74 seconds (12723.74 seconds total)