Starting phenix.refine on Sun Jan 12 15:15:38 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7737413.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7737413.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7737413.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): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.78, per 1000 atoms: 0.27 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: 2.725 distance_ideal: 2.720 ideal - model: -0.005 slack: 0.000 delta_slack: -0.005 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: 2.735 distance_ideal: 2.710 ideal - model: -0.025 slack: 0.000 delta_slack: -0.025 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: 0.70 Conformation dependent library (CDL) restraints added in 222.0 milliseconds Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 0.99: 415 0.99 - 1.22: 2642 1.22 - 1.45: 1459 1.45 - 1.69: 1361 1.69 - 1.92: 57 Bond restraints: 5934 Sorted by residual: bond pdb=" NZ LYS B 151 " pdb=" HZ3 LYS B 151 " ideal model delta sigma weight residual 0.890 1.310 -0.420 2.00e-02 2.50e+03 4.41e+02 bond pdb=" C LYS B 133 " pdb=" N ILE B 134 " ideal model delta sigma weight residual 1.324 1.504 -0.180 8.60e-03 1.35e+04 4.39e+02 bond pdb=" N ARG B 175 " pdb=" CA ARG B 175 " ideal model delta sigma weight residual 1.459 1.201 0.258 1.23e-02 6.61e+03 4.39e+02 bond pdb=" C GLY B 174 " pdb=" O GLY B 174 " ideal model delta sigma weight residual 1.230 1.417 -0.187 9.30e-03 1.16e+04 4.05e+02 bond pdb=" CG HIS B 179 " pdb=" ND1 HIS B 179 " ideal model delta sigma weight residual 1.378 1.597 -0.219 1.10e-02 8.26e+03 3.95e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 5511 4.10 - 8.19: 3637 8.19 - 12.29: 1328 12.29 - 16.38: 297 16.38 - 20.48: 37 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ALA B 161 " pdb=" C ALA B 161 " pdb=" O ALA B 161 " ideal model delta sigma weight residual 120.55 138.66 -18.11 1.06e+00 8.90e-01 2.92e+02 angle pdb=" O VAL B 26 " pdb=" C VAL B 26 " pdb=" N ARG B 27 " ideal model delta sigma weight residual 121.87 106.86 15.01 9.70e-01 1.06e+00 2.40e+02 angle pdb=" O ILE A 118 " pdb=" C ILE A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 121.80 104.86 16.94 1.13e+00 7.83e-01 2.25e+02 angle pdb=" O ILE A 70 " pdb=" C ILE A 70 " pdb=" N VAL A 71 " ideal model delta sigma weight residual 123.14 108.46 14.68 1.02e+00 9.61e-01 2.07e+02 angle pdb=" CA THR B 21 " pdb=" C THR B 21 " pdb=" N ILE B 22 " ideal model delta sigma weight residual 117.39 134.75 -17.36 1.24e+00 6.50e-01 1.96e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 1841 16.57 - 33.14: 128 33.14 - 49.71: 57 49.71 - 66.28: 17 66.28 - 82.85: 7 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 -146.20 -33.80 0 5.00e+00 4.00e-02 4.57e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual 180.00 -155.60 -24.40 0 5.00e+00 4.00e-02 2.38e+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 -156.11 -23.89 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.244: 212 0.244 - 0.487: 180 0.487 - 0.730: 80 0.730 - 0.974: 19 0.974 - 1.217: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB VAL B 60 " pdb=" CA VAL B 60 " pdb=" CG1 VAL B 60 " pdb=" CG2 VAL B 60 " both_signs ideal model delta sigma weight residual False -2.63 -3.85 1.22 2.00e-01 2.50e+01 3.70e+01 chirality pdb=" CA VAL A 173 " pdb=" N VAL A 173 " pdb=" C VAL A 173 " pdb=" CB VAL A 173 " both_signs ideal model delta sigma weight residual False 2.44 1.48 0.96 2.00e-01 2.50e+01 2.31e+01 chirality pdb=" CA ASP B 117 " pdb=" N ASP B 117 " pdb=" C ASP B 117 " pdb=" CB ASP B 117 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.114 2.00e-02 2.50e+03 7.45e-02 1.66e+02 pdb=" CG PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.132 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.127 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.044 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.093 2.00e-02 2.50e+03 5.68e-02 1.29e+02 pdb=" CG TRP B 146 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.073 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.048 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.084 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.088 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.007 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.029 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 82 " 0.049 2.00e-02 2.50e+03 6.36e-02 1.21e+02 pdb=" CG PHE B 82 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE B 82 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE B 82 " -0.090 2.00e-02 2.50e+03 pdb=" CE1 PHE B 82 " -0.087 2.00e-02 2.50e+03 pdb=" CE2 PHE B 82 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE B 82 " 0.026 2.00e-02 2.50e+03 pdb=" HD1 PHE B 82 " 0.096 2.00e-02 2.50e+03 pdb=" HD2 PHE B 82 " -0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE B 82 " -0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE B 82 " 0.100 2.00e-02 2.50e+03 pdb=" HZ PHE B 82 " 0.037 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.89 - 1.63: 27 1.63 - 2.37: 2610 2.37 - 3.12: 22430 3.12 - 3.86: 32875 3.86 - 4.60: 52420 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110362 Sorted by model distance: nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.890 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.908 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.914 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.092 2.620 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.144 2.100 ... (remaining 110357 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_7737413_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= 0.2034 r_free= 0.1985 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298529 | | target function (ml) not normalized (work): 805170.311381 | | target function (ml) not normalized (free): 16592.631230 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2141 0.1983 6.6602 6.3368| | 2: 2.94 - 2.33 1.00 7339 128 0.1620 0.1513 5.5508 5.5833| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1563 5.148 5.141| | 4: 2.04 - 1.85 1.00 7170 155 0.1778 0.1653 4.9706 5.0599| | 5: 1.85 - 1.72 0.99 7113 159 0.1914 0.1815 4.8009 4.8864| | 6: 1.72 - 1.62 0.99 7102 142 0.1965 0.1783 4.6582 4.597| | 7: 1.62 - 1.54 0.99 7104 148 0.2027 0.1781 4.5619 4.5828| | 8: 1.54 - 1.47 0.96 6798 152 0.2031 0.2120 4.467 4.4783| | 9: 1.47 - 1.41 0.98 6938 155 0.2098 0.2011 4.3876 4.4175| | 10: 1.41 - 1.36 0.99 7022 150 0.2101 0.2277 4.2972 4.3726| | 11: 1.36 - 1.32 0.99 6997 151 0.2067 0.2194 4.2177 4.268| | 12: 1.32 - 1.28 0.98 6976 149 0.2067 0.1970 4.1745 4.2315| | 13: 1.28 - 1.25 0.98 6907 166 0.2021 0.1964 4.1138 4.131| | 14: 1.25 - 1.22 0.98 7015 113 0.2068 0.2387 4.0695 4.2769| | 15: 1.22 - 1.19 0.98 6957 137 0.2094 0.2134 4.0402 4.0474| | 16: 1.19 - 1.17 0.93 6604 132 0.2154 0.2337 4.0214 4.0797| | 17: 1.17 - 1.14 0.98 6941 135 0.2177 0.1997 3.9585 4.0317| | 18: 1.14 - 1.12 0.98 6875 142 0.2241 0.2271 3.923 3.9192| | 19: 1.12 - 1.10 0.97 6949 106 0.2275 0.2512 3.8676 4.0344| | 20: 1.10 - 1.08 0.97 6884 147 0.2314 0.2352 3.8263 3.9092| | 21: 1.08 - 1.07 0.97 6852 152 0.2426 0.2607 3.793 3.7675| | 22: 1.07 - 1.05 0.97 6838 135 0.2536 0.2620 3.7506 3.7951| | 23: 1.05 - 1.03 0.97 6829 159 0.2739 0.2764 3.7424 3.8358| | 24: 1.03 - 1.02 0.96 6785 133 0.2835 0.2830 3.7025 3.8222| | 25: 1.02 - 1.01 0.93 6552 130 0.3079 0.3097 3.6805 3.7653| | 26: 1.01 - 0.99 0.96 6767 158 0.3233 0.3625 3.632 3.6584| | 27: 0.99 - 0.98 0.94 6648 131 0.3403 0.3259 3.6334 3.6459| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 21.10 0.91 0.97 37646.71| | 2: 2.94 - 2.33 7339 128 0.85 21.58 1.08 1.02 15687.68| | 3: 2.33 - 2.04 6939 150 0.93 12.32 1.11 1.06 4076.16| | 4: 2.04 - 1.85 7170 155 0.92 13.50 1.11 1.07 2774.61| | 5: 1.85 - 1.72 7113 159 0.91 15.72 1.11 1.08 2092.00| | 6: 1.72 - 1.62 7102 142 0.90 16.32 1.11 1.07 1567.68| | 7: 1.62 - 1.54 7104 148 0.89 17.38 1.11 1.05 1266.79| | 8: 1.54 - 1.47 6798 152 0.89 18.13 1.10 1.05 1092.21| | 9: 1.47 - 1.41 6938 155 0.88 18.91 1.11 1.05 951.11| | 10: 1.41 - 1.36 7022 150 0.87 19.84 1.10 1.05 841.39| | 11: 1.36 - 1.32 6997 151 0.87 19.75 1.08 1.04 713.26| | 12: 1.32 - 1.28 6976 149 0.88 19.56 1.08 1.04 644.36| | 13: 1.28 - 1.25 6907 166 0.87 19.78 1.07 1.03 593.21| | 14: 1.25 - 1.22 7015 113 0.86 21.34 1.07 1.02 589.29| | 15: 1.22 - 1.19 6957 137 0.86 21.56 1.09 1.02 567.49| | 16: 1.19 - 1.17 6604 132 0.86 21.25 1.07 1.03 524.34| | 17: 1.17 - 1.14 6941 135 0.86 21.75 1.08 1.03 474.69| | 18: 1.14 - 1.12 6875 142 0.86 21.91 1.09 1.01 425.58| | 19: 1.12 - 1.10 6949 106 0.85 22.81 1.07 1.01 401.68| | 20: 1.10 - 1.08 6884 147 0.84 23.19 1.06 0.99 367.77| | 21: 1.08 - 1.07 6852 152 0.84 24.03 1.06 0.99 343.98| | 22: 1.07 - 1.05 6838 135 0.82 25.82 1.06 0.98 339.54| | 23: 1.05 - 1.03 6829 159 0.79 28.36 1.06 0.98 350.43| | 24: 1.03 - 1.02 6785 133 0.76 31.13 1.05 0.98 369.29| | 25: 1.02 - 1.01 6552 130 0.74 33.18 1.04 0.93 356.16| | 26: 1.01 - 0.99 6767 158 0.71 35.17 1.03 0.89 335.60| | 27: 0.99 - 0.98 6648 131 0.72 34.95 1.04 0.88 307.03| |alpha: min = 0.88 max = 1.08 mean = 1.01| |beta: min = 307.03 max = 37646.71 mean = 2937.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 22.14| |phase err.(test): min = 0.00 max = 89.32 mean = 22.26| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.258 2950 Z= 5.528 Angle : 5.152 18.108 4018 Z= 3.673 Chirality : 0.378 1.217 492 Planarity : 0.033 0.143 512 Dihedral : 13.172 82.849 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.59 % Favored : 96.89 % Rotamer: Outliers : 1.61 % Allowed : 4.19 % Favored : 94.19 % Cbeta Deviations : 25.84 % 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: -2.72 (0.36), residues: 386 helix: -2.92 (0.29), residues: 144 sheet: -1.25 (0.50), residues: 82 loop : -0.69 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.130 0.022 ARG A 100 TYR 0.098 0.042 TYR B 192 PHE 0.149 0.038 PHE A 164 TRP 0.109 0.041 TRP A 139 HIS 0.082 0.034 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2034 r_free= 0.1985 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298529 | | target function (ml) not normalized (work): 805170.311381 | | target function (ml) not normalized (free): 16592.631230 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2034 0.1985 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2034 0.1985 n_refl.: 191155 remove outliers: r(all,work,free)=0.2033 0.2035 0.1985 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2034 0.2035 0.1985 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1804 0.1802 0.1913 n_refl.: 191145 remove outliers: r(all,work,free)=0.1802 0.1799 0.1912 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 0.4106 402.814 292.160 0.425 0.932 0.301 13.296-10.522 99.01 99 1 0.2495 528.187 519.677 0.770 0.933 0.255 10.503-8.327 99.45 178 3 0.2499 565.118 555.693 0.949 0.933 0.233 8.318-6.595 100.00 360 8 0.2457 414.736 402.864 0.951 0.933 0.180 6.588-5.215 100.00 711 7 0.2248 381.101 365.252 0.943 0.932 0.170 5.214-4.128 98.38 1367 28 0.1484 557.435 550.274 1.054 0.932 0.090 4.126-3.266 94.74 2603 46 0.1352 508.132 499.157 1.119 0.931 0.009 3.266-2.585 99.86 5447 97 0.1456 342.774 337.815 1.099 0.928 0.000 2.585-2.046 97.45 10613 204 0.1402 258.603 254.156 1.107 0.925 0.000 2.046-1.619 99.39 21536 464 0.1629 153.054 149.590 1.128 0.920 0.000 1.619-1.281 98.00 42464 925 0.1907 82.395 80.191 1.125 0.911 0.000 1.281-0.980 96.53 101826 2055 0.2316 44.202 41.674 1.125 0.895 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0068 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1799 r_free=0.1912 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1799 r_free=0.1912 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.196236 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 569.049134 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 0.1268 0.1491 0.0223 0.038 1.2 11.4 0.0 0.0 0 11.098 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.68 14.91 2.23 1.118 13.115 569.049 0.018 12.96 15.62 2.66 1.244 13.339 569.049 0.017 Individual atomic B min max mean iso aniso Overall: 5.26 73.05 15.01 1.40 435 3274 Protein: 5.26 40.32 11.01 1.40 0 2902 Water: 6.35 73.05 29.42 N/A 435 370 Other: 16.02 30.06 23.04 N/A 0 2 Chain A: 5.42 59.66 13.05 N/A 0 1626 Chain B: 5.26 73.05 12.78 N/A 0 1648 Chain S: 11.58 66.90 30.80 N/A 435 0 Histogram: Values Number of atoms 5.26 - 12.04 2180 12.04 - 18.82 629 18.82 - 25.59 318 25.59 - 32.37 259 32.37 - 39.15 154 39.15 - 45.93 105 45.93 - 52.71 42 52.71 - 59.49 18 59.49 - 66.27 2 66.27 - 73.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1562 r_work=0.1296 r_free=0.1557 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1557 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 = 0.1280 r_free = 0.1546 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015600 | | target function (ls_wunit_k1) not normalized (work): 2921.900219 | | target function (ls_wunit_k1) not normalized (free): 115.826636 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1280 0.1546 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1627 n_refl.: 191138 remove outliers: r(all,work,free)=0.1470 0.1467 0.1627 n_refl.: 191138 overall B=0.15 to atoms: r(all,work,free)=0.1492 0.1489 0.1637 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1539 n_refl.: 191138 remove outliers: r(all,work,free)=0.1279 0.1274 0.1539 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 0.3600 402.814 378.712 0.489 0.963 0.281 13.296-10.522 99.01 99 1 0.2071 528.187 525.676 0.745 0.964 0.244 10.503-8.327 99.45 178 3 0.1757 565.118 565.347 0.890 0.964 0.230 8.318-6.595 100.00 360 8 0.1714 414.736 411.802 0.910 0.964 0.165 6.588-5.215 100.00 711 7 0.1533 381.101 373.473 0.890 0.964 0.160 5.214-4.128 98.38 1367 28 0.0906 557.435 555.074 0.977 0.964 0.054 4.126-3.266 94.74 2603 46 0.0835 508.132 504.109 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0925 342.774 340.208 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.319 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.369 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1278 82.395 81.415 1.047 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.175 1.024 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0350 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1539 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1539 | n_water=805 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1279 r_free=0.1546 | n_water=794 | time (s): 102.620 (total time: 105.810) Filter (q & B) r_work=0.1279 r_free=0.1547 | n_water=790 | time (s): 5.280 (total time: 111.090) Compute maps r_work=0.1279 r_free=0.1547 | n_water=790 | time (s): 2.370 (total time: 113.460) Filter (map) r_work=0.1304 r_free=0.1524 | n_water=654 | time (s): 4.090 (total time: 117.550) Find peaks r_work=0.1304 r_free=0.1524 | n_water=654 | time (s): 0.730 (total time: 118.280) Add new water r_work=0.1328 r_free=0.1568 | n_water=966 | time (s): 4.880 (total time: 123.160) Refine new water occ: r_work=0.1285 r_free=0.1510 adp: r_work=0.1272 r_free=0.1506 occ: r_work=0.1275 r_free=0.1504 adp: r_work=0.1268 r_free=0.1500 occ: r_work=0.1270 r_free=0.1501 adp: r_work=0.1266 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1500 r_work=0.1266 r_free=0.1500 | n_water=966 | time (s): 79.590 (total time: 202.750) Filter (q & B) r_work=0.1270 r_free=0.1503 | n_water=901 | time (s): 5.850 (total time: 208.600) Filter (dist only) r_work=0.1270 r_free=0.1503 | n_water=900 | time (s): 117.320 (total time: 325.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.400361 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 593.267983 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 0.1254 0.1523 0.0268 0.042 1.1 18.7 0.0 0.0 0 11.700 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.23 2.68 2.043 15.224 593.268 0.014 12.32 15.13 2.82 2.414 15.269 593.268 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.20 16.39 1.21 532 3272 Protein: 5.38 40.40 10.98 1.21 0 2902 Water: 6.75 68.20 33.79 N/A 532 368 Other: 16.45 31.49 23.97 N/A 0 2 Chain A: 5.57 55.98 12.99 N/A 0 1624 Chain B: 5.38 68.20 12.83 N/A 0 1648 Chain S: 14.08 65.09 37.77 N/A 532 0 Histogram: Values Number of atoms 5.38 - 11.67 2060 11.67 - 17.95 709 17.95 - 24.23 265 24.23 - 30.51 207 30.51 - 36.79 180 36.79 - 43.07 182 43.07 - 49.36 104 49.36 - 55.64 53 55.64 - 61.92 36 61.92 - 68.20 8 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1514 r_work=0.1232 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1515 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 = 0.1226 r_free = 0.1514 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1514 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013381 | | target function (ls_wunit_k1) not normalized (work): 2506.236930 | | target function (ls_wunit_k1) not normalized (free): 101.906187 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1514 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1609 n_refl.: 191138 remove outliers: r(all,work,free)=0.1436 0.1433 0.1609 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1430 0.1607 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1232 0.1518 n_refl.: 191138 remove outliers: r(all,work,free)=0.1238 0.1232 0.1518 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 0.3209 402.814 377.456 0.493 0.963 0.271 13.296-10.522 99.01 99 1 0.1877 528.187 520.009 0.760 0.964 0.229 10.503-8.327 99.45 178 3 0.1402 565.118 566.788 0.924 0.964 0.184 8.318-6.595 100.00 360 8 0.1543 414.736 414.347 0.939 0.963 0.160 6.588-5.215 100.00 711 7 0.1345 381.101 376.509 0.913 0.963 0.160 5.214-4.128 98.38 1367 28 0.0824 557.435 556.295 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0762 508.132 505.534 1.059 0.963 0.013 3.266-2.585 99.86 5447 97 0.0855 342.774 341.366 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.760 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.617 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.353 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.221 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0554 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1518 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1518 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1518 | n_water=900 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1234 r_free=0.1517 | n_water=897 | time (s): 124.040 (total time: 126.610) Filter (q & B) r_work=0.1234 r_free=0.1517 | n_water=894 | time (s): 4.930 (total time: 131.540) Compute maps r_work=0.1234 r_free=0.1517 | n_water=894 | time (s): 1.950 (total time: 133.490) Filter (map) r_work=0.1274 r_free=0.1517 | n_water=690 | time (s): 5.350 (total time: 138.840) Find peaks r_work=0.1274 r_free=0.1517 | n_water=690 | time (s): 0.700 (total time: 139.540) Add new water r_work=0.1297 r_free=0.1553 | n_water=1007 | time (s): 4.180 (total time: 143.720) Refine new water occ: r_work=0.1251 r_free=0.1517 adp: r_work=0.1251 r_free=0.1519 occ: r_work=0.1247 r_free=0.1515 adp: r_work=0.1247 r_free=0.1516 occ: r_work=0.1245 r_free=0.1512 adp: r_work=0.1244 r_free=0.1513 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1513 r_work=0.1244 r_free=0.1513 | n_water=1007 | time (s): 185.760 (total time: 329.480) Filter (q & B) r_work=0.1249 r_free=0.1512 | n_water=882 | time (s): 4.760 (total time: 334.240) Filter (dist only) r_work=0.1249 r_free=0.1513 | n_water=881 | time (s): 118.990 (total time: 453.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.730599 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.898976 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 0.1238 0.1432 0.0193 0.036 1.1 7.1 0.0 0.0 0 0.865 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.32 1.93 1.934 14.586 15.899 3.939 12.34 13.90 1.57 2.209 14.499 15.899 3.897 Individual atomic B min max mean iso aniso Overall: 5.52 67.85 15.28 1.06 514 3271 Protein: 5.52 36.85 10.76 1.06 0 2902 Water: 6.69 67.85 30.16 N/A 514 367 Other: 14.07 27.73 20.90 N/A 0 2 Chain A: 5.56 55.21 12.78 N/A 0 1624 Chain B: 5.52 67.85 12.56 N/A 0 1647 Chain S: 14.27 61.80 31.89 N/A 514 0 Histogram: Values Number of atoms 5.52 - 11.75 2129 11.75 - 17.99 678 17.99 - 24.22 301 24.22 - 30.45 251 30.45 - 36.68 177 36.68 - 42.92 153 42.92 - 49.15 63 49.15 - 55.38 22 55.38 - 61.61 9 61.61 - 67.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1391 r_work=0.1234 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1392 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1386 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1386 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891587 | | target function (ml) not normalized (work): 728882.625124 | | target function (ml) not normalized (free): 15224.897271 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1386 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1441 0.1481 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1441 0.1481 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1435 0.1478 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1225 0.1381 n_refl.: 191138 remove outliers: r(all,work,free)=0.1228 0.1225 0.1381 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3805 398.008 364.033 0.432 0.945 0.257 13.296-10.522 99.01 99 1 0.2436 528.187 506.324 0.709 0.946 0.214 10.503-8.327 98.35 176 3 0.1975 555.265 555.771 0.890 0.946 0.175 8.318-6.595 100.00 360 8 0.2076 414.736 409.674 0.901 0.946 0.141 6.588-5.215 100.00 711 7 0.1829 381.101 370.642 0.888 0.946 0.123 5.214-4.128 98.38 1367 28 0.1181 557.435 551.766 0.971 0.946 0.054 4.126-3.266 94.74 2603 46 0.1088 508.132 501.094 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1081 342.774 339.066 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0968 258.603 255.709 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.381 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.473 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.316 1.037 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1021 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1381 | n_water=881 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1225 r_free=0.1381 | n_water=881 | time (s): 100.760 (total time: 102.990) Filter (q & B) r_work=0.1226 r_free=0.1379 | n_water=871 | time (s): 4.480 (total time: 107.470) Compute maps r_work=0.1226 r_free=0.1379 | n_water=871 | time (s): 2.110 (total time: 109.580) Filter (map) r_work=0.1248 r_free=0.1382 | n_water=720 | time (s): 4.920 (total time: 114.500) Find peaks r_work=0.1248 r_free=0.1382 | n_water=720 | time (s): 0.740 (total time: 115.240) Add new water r_work=0.1263 r_free=0.1401 | n_water=967 | time (s): 4.720 (total time: 119.960) Refine new water occ: r_work=0.1214 r_free=0.1355 adp: r_work=0.1206 r_free=0.1351 occ: r_work=0.1203 r_free=0.1351 adp: r_work=0.1203 r_free=0.1350 occ: r_work=0.1202 r_free=0.1351 adp: r_work=0.1201 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1350 r_work=0.1201 r_free=0.1350 | n_water=967 | time (s): 280.840 (total time: 400.800) Filter (q & B) r_work=0.1207 r_free=0.1358 | n_water=869 | time (s): 4.420 (total time: 405.220) Filter (dist only) r_work=0.1207 r_free=0.1356 | n_water=867 | time (s): 108.910 (total time: 514.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.538457 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.471395 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1354 0.0149 0.036 1.1 6.3 0.0 0.0 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.54 1.49 1.836 14.212 15.471 3.874 11.98 13.53 1.55 1.947 14.173 15.471 3.866 Individual atomic B min max mean iso aniso Overall: 5.52 67.42 14.97 1.01 501 3270 Protein: 5.52 33.65 10.67 1.01 0 2902 Water: 5.89 67.42 29.33 N/A 501 366 Other: 13.98 27.04 20.51 N/A 0 2 Chain A: 5.55 54.14 12.63 N/A 0 1623 Chain B: 5.52 67.42 12.46 N/A 0 1647 Chain S: 5.89 61.82 30.80 N/A 501 0 Histogram: Values Number of atoms 5.52 - 11.71 2123 11.71 - 17.90 719 17.90 - 24.09 291 24.09 - 30.28 254 30.28 - 36.47 166 36.47 - 42.66 131 42.66 - 48.85 57 48.85 - 55.04 22 55.04 - 61.23 5 61.23 - 67.42 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1353 r_work=0.1198 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1353 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1347 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863466 | | target function (ml) not normalized (work): 723603.958017 | | target function (ml) not normalized (free): 15126.559668 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1347 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1421 0.1421 0.1447 n_refl.: 191135 remove outliers: r(all,work,free)=0.1421 0.1421 0.1447 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1414 0.1414 0.1443 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1346 n_refl.: 191135 remove outliers: r(all,work,free)=0.1196 0.1193 0.1346 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3454 356.317 311.793 0.414 0.946 0.245 13.296-10.522 96.04 96 1 0.2304 480.431 448.156 0.703 0.947 0.209 10.503-8.327 98.35 176 3 0.2053 502.794 495.409 0.872 0.947 0.158 8.318-6.595 100.00 360 8 0.2148 375.545 369.737 0.893 0.947 0.115 6.588-5.215 100.00 711 7 0.1886 345.088 335.201 0.888 0.947 0.110 5.214-4.128 98.38 1367 28 0.1183 504.759 499.668 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1096 460.115 454.074 1.035 0.948 0.009 3.266-2.585 99.86 5447 97 0.1079 310.382 307.350 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0936 234.166 231.813 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0918 138.591 137.336 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0989 74.609 73.916 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1664 40.025 38.373 1.037 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1345 | n_water=867 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1193 r_free=0.1345 | n_water=867 | time (s): 111.320 (total time: 113.820) Filter (q & B) r_work=0.1194 r_free=0.1346 | n_water=858 | time (s): 4.350 (total time: 118.170) Compute maps r_work=0.1194 r_free=0.1346 | n_water=858 | time (s): 1.880 (total time: 120.050) Filter (map) r_work=0.1212 r_free=0.1353 | n_water=751 | time (s): 3.890 (total time: 123.940) Find peaks r_work=0.1212 r_free=0.1353 | n_water=751 | time (s): 0.840 (total time: 124.780) Add new water r_work=0.1226 r_free=0.1359 | n_water=986 | time (s): 4.360 (total time: 129.140) Refine new water occ: r_work=0.1190 r_free=0.1326 adp: r_work=0.1190 r_free=0.1326 occ: r_work=0.1187 r_free=0.1326 adp: r_work=0.1187 r_free=0.1325 occ: r_work=0.1185 r_free=0.1327 adp: r_work=0.1184 r_free=0.1326 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1326 r_work=0.1184 r_free=0.1326 | n_water=986 | time (s): 265.510 (total time: 394.650) Filter (q & B) r_work=0.1189 r_free=0.1335 | n_water=900 | time (s): 5.180 (total time: 399.830) Filter (dist only) r_work=0.1189 r_free=0.1335 | n_water=899 | time (s): 113.590 (total time: 513.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.526934 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.276710 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1342 0.0151 0.037 1.1 6.1 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.42 1.51 1.796 14.202 15.277 3.763 11.98 13.47 1.49 1.901 14.165 15.277 3.761 Individual atomic B min max mean iso aniso Overall: 5.54 66.92 15.04 0.95 533 3270 Protein: 5.54 31.57 10.58 0.95 0 2902 Water: 6.05 66.92 29.42 N/A 533 366 Other: 13.88 25.29 19.58 N/A 0 2 Chain A: 5.60 52.85 12.50 N/A 0 1623 Chain B: 5.54 66.92 12.35 N/A 0 1647 Chain S: 6.05 61.87 31.08 N/A 533 0 Histogram: Values Number of atoms 5.54 - 11.68 2132 11.68 - 17.82 725 17.82 - 23.96 294 23.96 - 30.09 239 30.09 - 36.23 177 36.23 - 42.37 143 42.37 - 48.50 64 48.50 - 54.64 21 54.64 - 60.78 5 60.78 - 66.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1347 r_work=0.1198 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1347 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1349 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760300 | | target function (ml) not normalized (work): 704259.125153 | | target function (ml) not normalized (free): 14740.444815 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1349 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1388 0.1387 0.1456 n_refl.: 191129 remove outliers: r(all,work,free)=0.1388 0.1387 0.1456 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1381 0.1380 0.1452 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1347 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1347 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3476 356.317 329.283 0.417 0.951 0.223 13.296-10.522 96.04 96 1 0.2340 480.431 460.486 0.704 0.953 0.167 10.503-8.327 98.35 176 3 0.2132 502.794 495.094 0.867 0.953 0.143 8.318-6.595 100.00 360 8 0.2130 375.545 370.176 0.889 0.953 0.117 6.588-5.215 100.00 711 7 0.1865 345.088 335.275 0.884 0.953 0.099 5.214-4.128 98.38 1367 28 0.1186 504.759 499.474 0.968 0.953 0.050 4.126-3.266 94.74 2603 46 0.1116 460.115 453.300 1.029 0.954 0.014 3.266-2.585 99.86 5447 97 0.1088 310.382 307.201 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0950 234.166 231.673 1.027 0.953 0.000 2.046-1.619 99.39 21536 464 0.0920 138.591 137.272 1.050 0.953 0.000 1.619-1.281 98.00 42464 925 0.0982 74.609 73.891 1.046 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.025 38.360 1.031 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1340 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1347 | n_water=899 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1195 r_free=0.1346 | n_water=898 | time (s): 118.670 (total time: 121.100) Filter (q & B) r_work=0.1195 r_free=0.1346 | n_water=890 | time (s): 5.040 (total time: 126.140) Compute maps r_work=0.1195 r_free=0.1346 | n_water=890 | time (s): 1.960 (total time: 128.100) Filter (map) r_work=0.1215 r_free=0.1348 | n_water=779 | time (s): 4.220 (total time: 132.320) Find peaks r_work=0.1215 r_free=0.1348 | n_water=779 | time (s): 0.530 (total time: 132.850) Add new water r_work=0.1225 r_free=0.1354 | n_water=983 | time (s): 4.950 (total time: 137.800) Refine new water occ: r_work=0.1194 r_free=0.1327 adp: r_work=0.1194 r_free=0.1327 occ: r_work=0.1192 r_free=0.1327 adp: r_work=0.1192 r_free=0.1327 occ: r_work=0.1190 r_free=0.1328 adp: r_work=0.1190 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1328 r_work=0.1190 r_free=0.1328 | n_water=983 | time (s): 227.280 (total time: 365.080) Filter (q & B) r_work=0.1193 r_free=0.1333 | n_water=918 | time (s): 4.540 (total time: 369.620) Filter (dist only) r_work=0.1194 r_free=0.1333 | n_water=917 | time (s): 116.500 (total time: 486.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.564358 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.115100 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 0.1346 0.0149 0.037 1.1 6.3 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.46 1.49 1.756 14.119 14.115 3.761 11.99 13.47 1.49 1.847 14.087 14.115 3.759 Individual atomic B min max mean iso aniso Overall: 5.56 66.09 15.01 0.90 551 3270 Protein: 5.56 29.61 10.50 0.90 0 2902 Water: 6.00 66.09 29.29 N/A 551 366 Other: 13.86 23.46 18.66 N/A 0 2 Chain A: 5.66 51.27 12.39 N/A 0 1623 Chain B: 5.56 66.09 12.24 N/A 0 1647 Chain S: 6.00 61.92 31.03 N/A 551 0 Histogram: Values Number of atoms 5.56 - 11.62 2118 11.62 - 17.67 766 17.67 - 23.72 283 23.72 - 29.77 228 29.77 - 35.83 182 35.83 - 41.88 137 41.88 - 47.93 71 47.93 - 53.98 28 53.98 - 60.04 4 60.04 - 66.09 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1347 r_work=0.1199 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1348 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1348 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758465 | | target function (ml) not normalized (work): 703915.391236 | | target function (ml) not normalized (free): 14734.872193 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1348 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1390 0.1389 0.1468 n_refl.: 191129 remove outliers: r(all,work,free)=0.1390 0.1389 0.1468 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1382 0.1381 0.1463 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1346 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1196 0.1346 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3692 356.317 326.606 0.379 0.953 0.170 13.296-10.522 96.04 96 1 0.2294 480.431 461.486 0.697 0.954 0.149 10.503-8.327 98.35 176 3 0.2137 502.794 494.716 0.864 0.955 0.137 8.318-6.595 100.00 360 8 0.2113 375.545 370.856 0.883 0.954 0.108 6.588-5.215 100.00 711 7 0.1899 345.088 335.839 0.881 0.955 0.093 5.214-4.128 98.38 1367 28 0.1208 504.759 499.342 0.967 0.955 0.039 4.126-3.266 94.74 2603 46 0.1127 460.115 453.297 1.029 0.955 0.005 3.266-2.585 99.86 5447 97 0.1107 310.382 307.111 1.016 0.955 0.000 2.585-2.046 97.45 10613 204 0.0954 234.166 231.631 1.026 0.954 0.000 2.046-1.619 99.39 21536 464 0.0916 138.591 137.282 1.050 0.954 0.000 1.619-1.281 98.00 42464 925 0.0974 74.609 73.902 1.047 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.025 38.362 1.034 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1425 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1346 | n_water=917 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1197 r_free=0.1347 | n_water=916 | time (s): 112.400 (total time: 115.120) Filter (q & B) r_work=0.1197 r_free=0.1347 | n_water=905 | time (s): 5.290 (total time: 120.410) Compute maps r_work=0.1197 r_free=0.1347 | n_water=905 | time (s): 2.320 (total time: 122.730) Filter (map) r_work=0.1217 r_free=0.1340 | n_water=795 | time (s): 5.340 (total time: 128.070) Find peaks r_work=0.1217 r_free=0.1340 | n_water=795 | time (s): 0.570 (total time: 128.640) Add new water r_work=0.1225 r_free=0.1345 | n_water=1009 | time (s): 4.070 (total time: 132.710) Refine new water occ: r_work=0.1194 r_free=0.1326 adp: r_work=0.1194 r_free=0.1326 occ: r_work=0.1191 r_free=0.1327 adp: r_work=0.1191 r_free=0.1327 occ: r_work=0.1190 r_free=0.1330 adp: r_work=0.1189 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1329 r_work=0.1189 r_free=0.1329 | n_water=1009 | time (s): 245.310 (total time: 378.020) Filter (q & B) r_work=0.1194 r_free=0.1334 | n_water=930 | time (s): 4.530 (total time: 382.550) Filter (dist only) r_work=0.1194 r_free=0.1334 | n_water=929 | time (s): 120.480 (total time: 503.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.518147 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.397030 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 0.1342 0.0145 0.038 1.1 6.0 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.42 1.45 1.722 14.028 14.397 3.759 11.98 13.44 1.46 1.777 14.009 14.397 3.756 Individual atomic B min max mean iso aniso Overall: 5.57 64.97 14.97 0.89 563 3270 Protein: 5.57 28.76 10.44 0.89 0 2902 Water: 5.98 64.97 29.11 N/A 563 366 Other: 13.89 22.22 18.05 N/A 0 2 Chain A: 5.63 50.86 12.29 N/A 0 1623 Chain B: 5.57 64.97 12.16 N/A 0 1647 Chain S: 5.98 61.93 30.91 N/A 563 0 Histogram: Values Number of atoms 5.57 - 11.51 2094 11.51 - 17.45 792 17.45 - 23.39 273 23.39 - 29.33 230 29.33 - 35.27 185 35.27 - 41.21 140 41.21 - 47.15 78 47.15 - 53.09 33 53.09 - 59.03 4 59.03 - 64.97 4 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1344 r_work=0.1198 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1344 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1346 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755937 | | target function (ml) not normalized (work): 703441.902359 | | target function (ml) not normalized (free): 14726.590035 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1346 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1390 0.1389 0.1470 n_refl.: 191129 remove outliers: r(all,work,free)=0.1390 0.1389 0.1470 n_refl.: 191129 overall B=-0.01 to atoms: r(all,work,free)=0.1388 0.1387 0.1468 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1335 n_refl.: 191129 remove outliers: r(all,work,free)=0.1189 0.1186 0.1335 n_refl.: 191127 ======================== 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 89.11 87 3 0.3454 355.745 314.006 0.335 0.982 0.100 13.296-10.522 96.04 96 1 0.2326 480.431 460.325 0.678 0.983 0.113 10.503-8.327 98.35 176 3 0.2154 502.794 493.299 0.856 0.984 0.114 8.318-6.595 100.00 360 8 0.2103 375.545 370.315 0.873 0.984 0.098 6.588-5.215 100.00 711 7 0.1924 345.088 335.041 0.872 0.984 0.083 5.214-4.128 98.38 1367 28 0.1230 504.759 498.693 0.959 0.985 0.034 4.126-3.266 94.74 2603 46 0.1137 460.115 452.778 1.021 0.986 0.005 3.266-2.585 99.86 5447 97 0.1106 310.382 306.859 1.006 0.987 0.000 2.585-2.046 97.45 10613 204 0.0957 234.166 231.564 1.015 0.989 0.000 2.046-1.619 99.39 21536 464 0.0909 138.591 137.221 1.034 0.993 0.000 1.619-1.281 98.00 42464 925 0.0949 74.609 73.968 1.027 0.998 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.025 38.336 1.000 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0299 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1335 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1186 r_free=0.1335 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1335 | n_water=929 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1186 r_free=0.1335 | n_water=929 | time (s): 114.390 (total time: 116.830) Filter (q & B) r_work=0.1187 r_free=0.1334 | n_water=915 | time (s): 5.260 (total time: 122.090) Compute maps r_work=0.1187 r_free=0.1334 | n_water=915 | time (s): 1.580 (total time: 123.670) Filter (map) r_work=0.1209 r_free=0.1332 | n_water=805 | time (s): 5.240 (total time: 128.910) Find peaks r_work=0.1209 r_free=0.1332 | n_water=805 | time (s): 0.670 (total time: 129.580) Add new water r_work=0.1215 r_free=0.1336 | n_water=998 | time (s): 4.580 (total time: 134.160) Refine new water occ: r_work=0.1184 r_free=0.1321 adp: r_work=0.1185 r_free=0.1322 occ: r_work=0.1182 r_free=0.1321 adp: r_work=0.1182 r_free=0.1322 occ: r_work=0.1181 r_free=0.1323 adp: r_work=0.1181 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1323 r_work=0.1181 r_free=0.1323 | n_water=998 | time (s): 227.940 (total time: 362.100) Filter (q & B) r_work=0.1185 r_free=0.1327 | n_water=927 | time (s): 4.360 (total time: 366.460) Filter (dist only) r_work=0.1185 r_free=0.1327 | n_water=924 | time (s): 119.390 (total time: 485.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.476618 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.051943 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1334 0.0145 0.039 1.1 7.3 0.0 0.3 0 0.738 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.34 1.45 1.703 13.973 14.052 3.755 11.91 13.36 1.46 1.724 13.962 14.052 3.754 Individual atomic B min max mean iso aniso Overall: 5.61 64.12 14.93 0.87 558 3270 Protein: 5.61 28.33 10.43 0.87 0 2902 Water: 6.02 64.12 29.04 N/A 558 366 Other: 13.92 22.30 18.11 N/A 0 2 Chain A: 5.68 50.60 12.25 N/A 0 1623 Chain B: 5.61 64.12 12.12 N/A 0 1647 Chain S: 6.02 61.95 30.99 N/A 558 0 Histogram: Values Number of atoms 5.61 - 11.46 2075 11.46 - 17.31 807 17.31 - 23.16 273 23.16 - 29.01 215 29.01 - 34.86 198 34.86 - 40.71 133 40.71 - 46.56 80 46.56 - 52.41 38 52.41 - 58.27 5 58.27 - 64.12 4 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1336 r_work=0.1191 r_free=0.1337 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1337 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1337 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1337 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753148 | | target function (ml) not normalized (work): 702912.090091 | | target function (ml) not normalized (free): 14716.169913 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1337 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1382 0.1380 0.1478 n_refl.: 191127 remove outliers: r(all,work,free)=0.1382 0.1380 0.1478 n_refl.: 191127 overall B=-0.02 to atoms: r(all,work,free)=0.1379 0.1377 0.1476 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1189 0.1335 n_refl.: 191127 remove outliers: r(all,work,free)=0.1191 0.1189 0.1335 n_refl.: 191127 ======================== 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 89.11 87 3 0.3472 355.745 331.986 0.342 0.986 0.080 13.296-10.522 96.04 96 1 0.2339 480.431 459.502 0.668 0.987 0.097 10.503-8.327 98.35 176 3 0.2169 502.794 493.103 0.851 0.988 0.100 8.318-6.595 100.00 360 8 0.2112 375.545 370.401 0.866 0.988 0.088 6.588-5.215 100.00 711 7 0.1937 345.088 334.911 0.867 0.988 0.077 5.214-4.128 98.38 1367 28 0.1239 504.759 498.676 0.955 0.989 0.034 4.126-3.266 94.74 2603 46 0.1153 460.115 452.584 1.017 0.990 0.005 3.266-2.585 99.86 5447 97 0.1113 310.382 306.767 1.003 0.991 0.000 2.585-2.046 97.45 10613 204 0.0962 234.166 231.513 1.011 0.994 0.000 2.046-1.619 99.39 21536 464 0.0910 138.591 137.220 1.030 0.997 0.000 1.619-1.281 98.00 42464 925 0.0946 74.609 73.962 1.024 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.025 38.311 0.998 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0495 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1335 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1335 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1335 | n_water=924 | time (s): 3.100 (total time: 3.100) Filter (dist) r_work=0.1189 r_free=0.1335 | n_water=923 | time (s): 120.440 (total time: 123.540) Filter (q & B) r_work=0.1189 r_free=0.1333 | n_water=913 | time (s): 4.530 (total time: 128.070) Compute maps r_work=0.1189 r_free=0.1333 | n_water=913 | time (s): 2.040 (total time: 130.110) Filter (map) r_work=0.1207 r_free=0.1334 | n_water=824 | time (s): 5.160 (total time: 135.270) Find peaks r_work=0.1207 r_free=0.1334 | n_water=824 | time (s): 0.870 (total time: 136.140) Add new water r_work=0.1212 r_free=0.1338 | n_water=1000 | time (s): 5.210 (total time: 141.350) Refine new water occ: r_work=0.1185 r_free=0.1320 adp: r_work=0.1186 r_free=0.1320 occ: r_work=0.1184 r_free=0.1322 adp: r_work=0.1184 r_free=0.1321 occ: r_work=0.1183 r_free=0.1324 adp: r_work=0.1182 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1323 r_work=0.1182 r_free=0.1323 | n_water=1000 | time (s): 294.930 (total time: 436.280) Filter (q & B) r_work=0.1186 r_free=0.1331 | n_water=928 | time (s): 4.180 (total time: 440.460) Filter (dist only) r_work=0.1187 r_free=0.1330 | n_water=925 | time (s): 122.270 (total time: 562.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.496122 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.190113 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1334 0.0144 0.039 1.1 5.8 0.0 0.3 0 0.748 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.34 1.44 1.693 13.931 14.190 3.754 11.89 13.36 1.47 1.702 13.931 14.190 3.752 Individual atomic B min max mean iso aniso Overall: 5.62 63.07 14.89 0.87 559 3270 Protein: 5.62 28.20 10.43 0.87 0 2902 Water: 6.06 63.07 28.90 N/A 559 366 Other: 13.94 22.25 18.10 N/A 0 2 Chain A: 5.71 50.21 12.21 N/A 0 1623 Chain B: 5.62 63.07 12.09 N/A 0 1647 Chain S: 6.06 61.89 30.92 N/A 559 0 Histogram: Values Number of atoms 5.62 - 11.37 2054 11.37 - 17.11 822 17.11 - 22.86 270 22.86 - 28.60 209 28.60 - 34.35 211 34.35 - 40.09 132 40.09 - 45.84 80 45.84 - 51.58 37 51.58 - 57.33 8 57.33 - 63.07 6 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1336 r_work=0.1189 r_free=0.1337 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1337 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1335 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1335 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751861 | | target function (ml) not normalized (work): 702671.004013 | | target function (ml) not normalized (free): 14713.661376 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1335 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1385 0.1383 0.1486 n_refl.: 191127 remove outliers: r(all,work,free)=0.1385 0.1383 0.1486 n_refl.: 191127 overall B=-0.11 to atoms: r(all,work,free)=0.1368 0.1366 0.1474 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1336 n_refl.: 191127 remove outliers: r(all,work,free)=0.1190 0.1187 0.1336 n_refl.: 191127 ======================== 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 89.11 87 3 0.3468 355.745 332.119 0.333 0.986 0.070 13.296-10.522 96.04 96 1 0.2353 480.431 458.787 0.659 0.987 0.100 10.503-8.327 98.35 176 3 0.2154 502.794 493.758 0.838 0.988 0.095 8.318-6.595 100.00 360 8 0.2125 375.545 370.429 0.853 0.988 0.081 6.588-5.215 100.00 711 7 0.1928 345.088 335.267 0.855 0.988 0.073 5.214-4.128 98.38 1367 28 0.1234 504.759 498.741 0.941 0.989 0.029 4.126-3.266 94.74 2603 46 0.1156 460.115 452.385 1.002 0.990 0.000 3.266-2.585 99.86 5447 97 0.1111 310.382 306.780 0.987 0.992 0.000 2.585-2.046 97.45 10613 204 0.0961 234.166 231.527 0.993 0.994 0.000 2.046-1.619 99.39 21536 464 0.0909 138.591 137.222 1.009 0.998 0.000 1.619-1.281 98.00 42464 925 0.0942 74.609 73.964 0.999 1.005 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.025 38.303 0.967 1.017 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0241 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1336 After: r_work=0.1188 r_free=0.1336 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1336 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1336 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1336 | n_water=925 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1188 r_free=0.1336 | n_water=925 | time (s): 117.290 (total time: 119.880) Filter (q & B) r_work=0.1188 r_free=0.1335 | n_water=917 | time (s): 4.420 (total time: 124.300) Compute maps r_work=0.1188 r_free=0.1335 | n_water=917 | time (s): 2.360 (total time: 126.660) Filter (map) r_work=0.1206 r_free=0.1337 | n_water=829 | time (s): 4.940 (total time: 131.600) Find peaks r_work=0.1206 r_free=0.1337 | n_water=829 | time (s): 0.540 (total time: 132.140) Add new water r_work=0.1210 r_free=0.1344 | n_water=1010 | time (s): 4.050 (total time: 136.190) Refine new water occ: r_work=0.1184 r_free=0.1327 adp: r_work=0.1185 r_free=0.1327 occ: r_work=0.1183 r_free=0.1327 adp: r_work=0.1183 r_free=0.1327 occ: r_work=0.1181 r_free=0.1327 adp: r_work=0.1181 r_free=0.1327 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1327 r_work=0.1181 r_free=0.1327 | n_water=1010 | time (s): 220.750 (total time: 356.940) Filter (q & B) r_work=0.1185 r_free=0.1333 | n_water=938 | time (s): 5.880 (total time: 362.820) Filter (dist only) r_work=0.1186 r_free=0.1333 | n_water=935 | time (s): 116.570 (total time: 479.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.480711 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.106819 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1338 0.0147 0.039 1.2 9.7 0.0 0.3 0 0.740 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.38 1.47 1.689 13.843 13.107 3.755 11.93 13.41 1.48 1.689 13.842 13.107 3.756 Individual atomic B min max mean iso aniso Overall: 5.51 62.67 14.81 0.85 569 3270 Protein: 5.51 27.93 10.33 0.85 0 2902 Water: 6.03 62.67 28.72 N/A 569 366 Other: 13.85 22.11 17.98 N/A 0 2 Chain A: 5.64 50.02 12.09 N/A 0 1623 Chain B: 5.51 62.67 11.98 N/A 0 1647 Chain S: 6.03 61.74 30.76 N/A 569 0 Histogram: Values Number of atoms 5.51 - 11.22 2042 11.22 - 16.94 839 16.94 - 22.66 272 22.66 - 28.37 216 28.37 - 34.09 205 34.09 - 39.81 130 39.81 - 45.52 79 45.52 - 51.24 41 51.24 - 56.96 9 56.96 - 62.67 6 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1342 r_work=0.1193 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1342 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1343 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756181 | | target function (ml) not normalized (work): 703480.167281 | | target function (ml) not normalized (free): 14725.158969 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1339 0.1373 5.6705 5.7189| | 2: 2.94 - 2.33 1.00 7339 128 0.1071 0.1375 5.0603 5.1665| | 3: 2.33 - 2.04 0.96 6939 150 0.0908 0.1164 4.6596 4.7359| | 4: 2.04 - 1.85 1.00 7170 155 0.0908 0.1073 4.3984 4.5811| | 5: 1.85 - 1.72 0.99 7113 159 0.0940 0.1001 4.1564 4.2398| | 6: 1.72 - 1.62 0.99 7102 142 0.0901 0.1107 3.9512 4.0906| | 7: 1.62 - 1.54 0.99 7104 148 0.0894 0.0942 3.8048 3.9211| | 8: 1.54 - 1.47 0.96 6798 152 0.0898 0.1327 3.7067 3.914| | 9: 1.47 - 1.41 0.98 6938 155 0.0934 0.1132 3.6306 3.7637| | 10: 1.41 - 1.36 0.99 7022 150 0.0986 0.1206 3.5654 3.6787| | 11: 1.36 - 1.32 0.99 6997 151 0.0997 0.1140 3.4912 3.594| | 12: 1.32 - 1.28 0.98 6975 149 0.1037 0.1124 3.4642 3.5798| | 13: 1.28 - 1.25 0.98 6907 166 0.1047 0.1230 3.4417 3.5612| | 14: 1.25 - 1.22 0.98 7015 112 0.1108 0.1573 3.4355 3.6815| | 15: 1.22 - 1.19 0.98 6956 137 0.1173 0.1257 3.4527 3.5002| | 16: 1.19 - 1.17 0.93 6604 132 0.1255 0.1537 3.4685 3.6556| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1223 3.435 3.4391| | 18: 1.14 - 1.12 0.98 6875 142 0.1388 0.1702 3.4402 3.5299| | 19: 1.12 - 1.10 0.97 6948 106 0.1473 0.1760 3.4211 3.5949| | 20: 1.10 - 1.08 0.97 6884 147 0.1588 0.1588 3.4123 3.4361| | 21: 1.08 - 1.07 0.97 6852 152 0.1733 0.2132 3.4201 3.5033| | 22: 1.07 - 1.05 0.97 6836 135 0.1907 0.1951 3.4149 3.4147| | 23: 1.05 - 1.03 0.97 6827 159 0.2124 0.2023 3.4344 3.4872| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2256 3.4367 3.5114| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2516 3.4497 3.5234| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2848 3.4164 3.4209| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2779 3.4698 3.3955| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7395 127 0.94 10.90 1.00 0.98 10159.44| | 2: 2.94 - 2.33 7339 128 0.93 12.26 0.99 0.98 4784.77| | 3: 2.33 - 2.04 6939 150 0.96 7.65 1.01 0.98 1702.52| | 4: 2.04 - 1.85 7170 155 0.96 7.69 1.00 0.98 1014.13| | 5: 1.85 - 1.72 7113 159 0.96 8.08 1.00 0.98 636.31| | 6: 1.72 - 1.62 7102 142 0.96 8.03 1.00 0.99 445.49| | 7: 1.62 - 1.54 7104 148 0.96 8.13 1.01 1.00 337.51| | 8: 1.54 - 1.47 6798 152 0.96 8.34 1.01 1.00 281.78| | 9: 1.47 - 1.41 6938 155 0.96 8.59 1.00 1.00 234.94| | 10: 1.41 - 1.36 7022 150 0.96 9.04 1.00 1.00 206.00| | 11: 1.36 - 1.32 6997 151 0.96 9.02 0.99 0.99 177.32| | 12: 1.32 - 1.28 6975 149 0.96 9.01 0.98 0.97 161.56| | 13: 1.28 - 1.25 6907 166 0.96 9.55 1.01 0.98 158.64| | 14: 1.25 - 1.22 7015 112 0.95 10.72 1.01 0.99 163.39| | 15: 1.22 - 1.19 6956 137 0.95 11.30 1.01 1.00 167.46| | 16: 1.19 - 1.17 6604 132 0.95 11.47 1.01 0.99 160.86| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.99 153.92| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.97 147.32| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.97 150.89| | 20: 1.10 - 1.08 6884 147 0.92 15.25 1.00 0.96 150.41| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.96 153.44| | 22: 1.07 - 1.05 6836 135 0.89 18.32 1.00 0.95 155.18| | 23: 1.05 - 1.03 6827 159 0.87 20.53 1.00 0.95 164.96| | 24: 1.03 - 1.02 6784 133 0.85 23.17 1.00 0.96 179.23| | 25: 1.02 - 1.01 6552 130 0.83 25.13 0.98 0.93 181.83| | 26: 1.01 - 0.99 6767 158 0.81 26.58 0.99 0.91 176.04| | 27: 0.99 - 0.98 6647 131 0.82 26.20 0.99 0.90 160.28| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 147.32 max = 10159.44 mean = 872.00| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.26| |phase err.(test): min = 0.00 max = 88.85 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1343 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1378 0.1376 0.1480 n_refl.: 191127 remove outliers: r(all,work,free)=0.1378 0.1376 0.1480 n_refl.: 191127 overall B=-0.04 to atoms: r(all,work,free)=0.1373 0.1371 0.1477 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1343 n_refl.: 191127 remove outliers: r(all,work,free)=0.1195 0.1192 0.1343 n_refl.: 191127 ======================== 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 89.11 87 3 0.3452 355.745 332.398 0.331 0.994 0.070 13.296-10.522 96.04 96 1 0.2377 480.431 459.432 0.649 0.995 0.091 10.503-8.327 98.35 176 3 0.2114 502.794 494.163 0.834 0.996 0.088 8.318-6.595 100.00 360 8 0.2101 375.545 370.357 0.847 0.996 0.076 6.588-5.215 100.00 711 7 0.1932 345.088 335.342 0.847 0.996 0.067 5.214-4.128 98.38 1367 28 0.1233 504.759 498.917 0.935 0.997 0.024 4.126-3.266 94.74 2603 46 0.1151 460.115 452.473 0.996 0.999 0.000 3.266-2.585 99.86 5447 97 0.1115 310.382 306.876 0.981 1.000 0.000 2.585-2.046 97.45 10613 204 0.0966 234.166 231.559 0.987 1.003 0.000 2.046-1.619 99.39 21536 464 0.0917 138.591 137.222 1.002 1.008 0.000 1.619-1.281 98.00 42464 925 0.0953 74.609 73.952 0.992 1.015 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.025 38.299 0.960 1.027 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0084 ================= 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 : 0.2034 0.1985 0.083 5.152 5.2 78.0 14.6 805 0.000 1_bss: 0.1799 0.1912 0.083 5.152 5.2 78.0 14.6 805 0.000 1_settarget: 0.1799 0.1912 0.083 5.152 5.2 78.0 14.6 805 0.000 1_nqh: 0.1799 0.1912 0.083 5.152 5.2 78.0 14.6 805 0.000 1_weight: 0.1799 0.1912 0.083 5.152 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1268 0.1491 0.038 1.156 5.2 78.0 14.6 805 0.154 1_adp: 0.1296 0.1562 0.038 1.156 5.3 73.0 15.0 805 0.154 1_regHadp: 0.1296 0.1557 0.038 1.156 5.3 73.0 15.0 805 0.154 1_occ: 0.1280 0.1546 0.038 1.156 5.3 73.0 15.0 805 0.154 2_bss: 0.1274 0.1539 0.038 1.156 5.4 73.2 15.2 805 0.154 2_settarget: 0.1274 0.1539 0.038 1.156 5.4 73.2 15.2 805 0.154 2_updatecdl: 0.1274 0.1539 0.038 1.168 5.4 73.2 15.2 805 0.154 2_nqh: 0.1274 0.1539 0.038 1.168 5.4 73.2 15.2 805 0.154 2_sol: 0.1270 0.1503 0.038 1.168 5.4 73.2 16.3 900 n/a 2_weight: 0.1270 0.1503 0.038 1.168 5.4 73.2 16.3 900 n/a 2_xyzrec: 0.1254 0.1523 0.042 1.144 5.4 73.2 16.3 900 n/a 2_adp: 0.1232 0.1514 0.042 1.144 5.4 68.2 16.4 900 n/a 2_regHadp: 0.1232 0.1515 0.042 1.144 5.4 68.2 16.4 900 n/a 2_occ: 0.1226 0.1514 0.042 1.144 5.4 68.2 16.4 900 n/a 3_bss: 0.1232 0.1518 0.042 1.144 5.4 68.2 16.4 900 n/a 3_settarget: 0.1232 0.1518 0.042 1.144 5.4 68.2 16.4 900 n/a 3_updatecdl: 0.1232 0.1518 0.042 1.145 5.4 68.2 16.4 900 n/a 3_nqh: 0.1232 0.1518 0.042 1.145 5.4 68.2 16.4 900 n/a 3_sol: 0.1249 0.1513 0.042 1.145 5.4 68.2 15.4 881 n/a 3_weight: 0.1249 0.1513 0.042 1.145 5.4 68.2 15.4 881 n/a 3_xyzrec: 0.1238 0.1432 0.036 1.104 5.4 68.2 15.4 881 n/a 3_adp: 0.1234 0.1391 0.036 1.104 5.5 67.8 15.3 881 n/a 3_regHadp: 0.1234 0.1392 0.036 1.104 5.5 67.8 15.3 881 n/a 3_occ: 0.1229 0.1386 0.036 1.104 5.5 67.8 15.3 881 n/a 4_bss: 0.1225 0.1381 0.036 1.104 5.5 67.8 15.3 881 n/a 4_settarget: 0.1225 0.1381 0.036 1.104 5.5 67.8 15.3 881 n/a 4_updatecdl: 0.1225 0.1381 0.036 1.105 5.5 67.8 15.3 881 n/a 4_nqh: 0.1225 0.1381 0.036 1.105 5.5 67.8 15.3 881 n/a 4_sol: 0.1207 0.1356 0.036 1.105 5.5 67.8 15.0 867 n/a 4_weight: 0.1207 0.1356 0.036 1.105 5.5 67.8 15.0 867 n/a 4_xyzrec: 0.1205 0.1354 0.036 1.123 5.5 67.8 15.0 867 n/a 4_adp: 0.1198 0.1353 0.036 1.123 5.5 67.4 15.0 867 n/a 4_regHadp: 0.1198 0.1353 0.036 1.123 5.5 67.4 15.0 867 n/a 4_occ: 0.1196 0.1347 0.036 1.123 5.5 67.4 15.0 867 n/a 5_bss: 0.1193 0.1345 0.036 1.123 5.5 67.4 14.9 867 n/a 5_settarget: 0.1193 0.1345 0.036 1.123 5.5 67.4 14.9 867 n/a 5_updatecdl: 0.1193 0.1345 0.036 1.123 5.5 67.4 14.9 867 n/a 5_nqh: 0.1193 0.1345 0.036 1.123 5.5 67.4 14.9 867 n/a 5_sol: 0.1189 0.1335 0.036 1.123 5.5 67.4 15.1 899 n/a 5_weight: 0.1189 0.1335 0.036 1.123 5.5 67.4 15.1 899 n/a 5_xyzrec: 0.1192 0.1342 0.037 1.128 5.5 67.4 15.1 899 n/a 5_adp: 0.1198 0.1347 0.037 1.128 5.5 66.9 15.0 899 n/a 5_regHadp: 0.1198 0.1347 0.037 1.128 5.5 66.9 15.0 899 n/a 5_occ: 0.1195 0.1349 0.037 1.128 5.5 66.9 15.0 899 n/a 6_bss: 0.1194 0.1347 0.037 1.128 5.5 66.9 15.0 899 n/a 6_settarget: 0.1194 0.1347 0.037 1.128 5.5 66.9 15.0 899 n/a 6_updatecdl: 0.1194 0.1347 0.037 1.128 5.5 66.9 15.0 899 n/a 6_nqh: 0.1194 0.1347 0.037 1.128 5.5 66.9 15.0 899 n/a 6_sol: 0.1194 0.1333 0.037 1.128 5.5 66.9 15.1 917 n/a 6_weight: 0.1194 0.1333 0.037 1.128 5.5 66.9 15.1 917 n/a 6_xyzrec: 0.1197 0.1346 0.037 1.130 5.5 66.9 15.1 917 n/a 6_adp: 0.1199 0.1347 0.037 1.130 5.6 66.1 15.0 917 n/a 6_regHadp: 0.1199 0.1348 0.037 1.130 5.6 66.1 15.0 917 n/a 6_occ: 0.1197 0.1348 0.037 1.130 5.6 66.1 15.0 917 n/a 7_bss: 0.1196 0.1346 0.037 1.130 5.5 66.0 15.0 917 n/a 7_settarget: 0.1196 0.1346 0.037 1.130 5.5 66.0 15.0 917 n/a 7_updatecdl: 0.1196 0.1346 0.037 1.130 5.5 66.0 15.0 917 n/a 7_nqh: 0.1196 0.1346 0.037 1.130 5.5 66.0 15.0 917 n/a 7_sol: 0.1194 0.1334 0.037 1.130 5.5 66.0 15.0 929 n/a 7_weight: 0.1194 0.1334 0.037 1.130 5.5 66.0 15.0 929 n/a 7_xyzrec: 0.1198 0.1342 0.038 1.124 5.5 66.0 15.0 929 n/a 7_adp: 0.1198 0.1344 0.038 1.124 5.6 65.0 15.0 929 n/a 7_regHadp: 0.1198 0.1344 0.038 1.124 5.6 65.0 15.0 929 n/a 7_occ: 0.1196 0.1346 0.038 1.124 5.6 65.0 15.0 929 n/a 8_bss: 0.1186 0.1335 0.038 1.124 5.6 65.0 15.0 929 n/a 8_settarget: 0.1186 0.1335 0.038 1.124 5.6 65.0 15.0 929 n/a 8_updatecdl: 0.1186 0.1335 0.038 1.124 5.6 65.0 15.0 929 n/a 8_nqh: 0.1186 0.1335 0.038 1.124 5.6 65.0 15.0 929 n/a 8_sol: 0.1185 0.1327 0.038 1.124 5.6 65.0 14.9 924 n/a 8_weight: 0.1185 0.1327 0.038 1.124 5.6 65.0 14.9 924 n/a 8_xyzrec: 0.1189 0.1334 0.039 1.111 5.6 65.0 14.9 924 n/a 8_adp: 0.1191 0.1336 0.039 1.111 5.6 64.1 14.9 924 n/a 8_regHadp: 0.1191 0.1337 0.039 1.111 5.6 64.1 14.9 924 n/a 8_occ: 0.1190 0.1337 0.039 1.111 5.6 64.1 14.9 924 n/a 9_bss: 0.1189 0.1335 0.039 1.111 5.6 64.1 14.9 924 n/a 9_settarget: 0.1189 0.1335 0.039 1.111 5.6 64.1 14.9 924 n/a 9_updatecdl: 0.1189 0.1335 0.039 1.111 5.6 64.1 14.9 924 n/a 9_nqh: 0.1189 0.1335 0.039 1.111 5.6 64.1 14.9 924 n/a 9_sol: 0.1187 0.1330 0.039 1.111 5.6 64.1 14.9 925 n/a 9_weight: 0.1187 0.1330 0.039 1.111 5.6 64.1 14.9 925 n/a 9_xyzrec: 0.1190 0.1334 0.039 1.120 5.6 64.1 14.9 925 n/a 9_adp: 0.1189 0.1336 0.039 1.120 5.6 63.1 14.9 925 n/a 9_regHadp: 0.1189 0.1337 0.039 1.120 5.6 63.1 14.9 925 n/a 9_occ: 0.1188 0.1335 0.039 1.120 5.6 63.1 14.9 925 n/a 10_bss: 0.1187 0.1336 0.039 1.120 5.5 63.0 14.8 925 n/a 10_settarget: 0.1187 0.1336 0.039 1.120 5.5 63.0 14.8 925 n/a 10_updatecdl: 0.1187 0.1336 0.039 1.120 5.5 63.0 14.8 925 n/a 10_setrh: 0.1188 0.1336 0.039 1.120 5.5 63.0 14.8 925 n/a 10_nqh: 0.1188 0.1336 0.039 1.120 5.5 63.0 14.8 925 n/a 10_sol: 0.1186 0.1333 0.039 1.120 5.5 63.0 14.8 935 n/a 10_weight: 0.1186 0.1333 0.039 1.120 5.5 63.0 14.8 935 n/a 10_xyzrec: 0.1190 0.1338 0.039 1.173 5.5 63.0 14.8 935 n/a 10_adp: 0.1193 0.1342 0.039 1.173 5.5 62.7 14.8 935 n/a 10_regHadp: 0.1193 0.1342 0.039 1.173 5.5 62.7 14.8 935 n/a 10_occ: 0.1192 0.1343 0.039 1.173 5.5 62.7 14.8 935 n/a end: 0.1192 0.1343 0.039 1.173 5.5 62.6 14.8 935 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7737413_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7737413_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.7700 Refinement macro-cycles (run) : 12054.6500 Write final files (write_after_run_outputs) : 160.7400 Total : 12222.1600 Total CPU time: 3.40 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:51 PST -0800 (1736736051.04 s) Start R-work = 0.1799, R-free = 0.1912 Final R-work = 0.1192, R-free = 0.1343 =============================================================================== Job complete usr+sys time: 12500.30 seconds wall clock time: 209 minutes 18.48 seconds (12558.48 seconds total)