Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9424116.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9424116.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9424116.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.94, per 1000 atoms: 0.29 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.790 distance_ideal: 2.720 ideal - model: -0.070 slack: 0.000 delta_slack: -0.070 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: 2.759 distance_ideal: 2.710 ideal - model: -0.049 slack: 0.000 delta_slack: -0.049 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: 0.67 Conformation dependent library (CDL) restraints added in 125.4 milliseconds Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 1.00: 533 1.00 - 1.24: 2646 1.24 - 1.47: 1510 1.47 - 1.71: 1216 1.71 - 1.94: 29 Bond restraints: 5934 Sorted by residual: bond pdb=" CA LEU A 88 " pdb=" C LEU A 88 " ideal model delta sigma weight residual 1.524 1.790 -0.266 1.29e-02 6.01e+03 4.26e+02 bond pdb=" CG HIS A 96 " pdb=" ND1 HIS A 96 " ideal model delta sigma weight residual 1.378 1.594 -0.216 1.10e-02 8.26e+03 3.84e+02 bond pdb=" C ILE A 191 " pdb=" O ILE A 191 " ideal model delta sigma weight residual 1.237 1.463 -0.226 1.20e-02 6.94e+03 3.53e+02 bond pdb=" N LEU A 53 " pdb=" CA LEU A 53 " ideal model delta sigma weight residual 1.454 1.685 -0.231 1.23e-02 6.61e+03 3.52e+02 bond pdb=" N THR B 16 " pdb=" H THR B 16 " ideal model delta sigma weight residual 0.860 1.230 -0.370 2.00e-02 2.50e+03 3.43e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 5352 3.90 - 7.80: 3600 7.80 - 11.70: 1451 11.70 - 15.60: 362 15.60 - 19.50: 45 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O CYS B 81 " pdb=" C CYS B 81 " pdb=" N PHE B 82 " ideal model delta sigma weight residual 122.12 106.10 16.02 1.06e+00 8.90e-01 2.28e+02 angle pdb=" CA VAL B 102 " pdb=" C VAL B 102 " pdb=" O VAL B 102 " ideal model delta sigma weight residual 120.48 105.31 15.17 1.06e+00 8.90e-01 2.05e+02 angle pdb=" CA LYS A 31 " pdb=" C LYS A 31 " pdb=" O LYS A 31 " ideal model delta sigma weight residual 120.58 104.52 16.06 1.16e+00 7.43e-01 1.92e+02 angle pdb=" O VAL B 92 " pdb=" C VAL B 92 " pdb=" N LYS B 93 " ideal model delta sigma weight residual 121.87 134.89 -13.02 9.70e-01 1.06e+00 1.80e+02 angle pdb=" CA PHE B 95 " pdb=" C PHE B 95 " pdb=" O PHE B 95 " ideal model delta sigma weight residual 121.02 136.72 -15.70 1.17e+00 7.31e-01 1.80e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.93: 1861 17.93 - 35.86: 121 35.86 - 53.79: 53 53.79 - 71.72: 12 71.72 - 89.65: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: 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 -152.32 -27.68 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 197 0.203 - 0.405: 153 0.405 - 0.608: 100 0.608 - 0.810: 31 0.810 - 1.012: 11 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA TYR B 67 " pdb=" N TYR B 67 " pdb=" C TYR B 67 " pdb=" CB TYR B 67 " both_signs ideal model delta sigma weight residual False 2.51 3.52 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" CA ALA A 10 " pdb=" N ALA A 10 " pdb=" C ALA A 10 " pdb=" CB ALA A 10 " both_signs ideal model delta sigma weight residual False 2.48 3.45 -0.96 2.00e-01 2.50e+01 2.32e+01 chirality pdb=" CA MET A 124 " pdb=" N MET A 124 " pdb=" C MET A 124 " pdb=" CB MET A 124 " 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 TYR A 192 " -0.103 2.00e-02 2.50e+03 7.78e-02 1.82e+02 pdb=" CG TYR A 192 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " 0.086 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " 0.077 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " 0.069 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " -0.113 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " 0.074 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.103 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.084 2.00e-02 2.50e+03 7.17e-02 1.54e+02 pdb=" CG PHE A 164 " 0.147 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.088 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.122 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.030 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.048 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.122 2.00e-02 2.50e+03 7.17e-02 1.54e+02 pdb=" CG PHE B 164 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.106 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.037 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " -0.095 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.028 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.012 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.144 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.64: 30 1.64 - 2.38: 2732 2.38 - 3.12: 22483 3.12 - 3.86: 32836 3.86 - 4.60: 52161 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110242 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.905 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.973 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.029 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.046 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.149 2.620 ... (remaining 110237 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_9424116_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2035 r_free= 0.1974 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.300390 | | target function (ml) not normalized (work): 805518.966197 | | target function (ml) not normalized (free): 16538.150090 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2132 0.1901 6.6808 6.3036| | 2: 2.94 - 2.33 1.00 7339 128 0.1623 0.1608 5.5379 5.5745| | 3: 2.33 - 2.04 0.96 6939 150 0.1645 0.1625 5.1501 5.1685| | 4: 2.04 - 1.85 1.00 7170 155 0.1751 0.1657 4.9654 5.0689| | 5: 1.85 - 1.72 0.99 7113 159 0.1899 0.1753 4.7871 4.8345| | 6: 1.72 - 1.62 0.99 7102 142 0.1995 0.1931 4.6708 4.6285| | 7: 1.62 - 1.54 0.99 7104 148 0.2048 0.1799 4.5683 4.6022| | 8: 1.54 - 1.47 0.96 6798 152 0.2030 0.2177 4.4733 4.5017| | 9: 1.47 - 1.41 0.98 6938 155 0.2096 0.2220 4.3917 4.52| | 10: 1.41 - 1.36 0.99 7022 150 0.2133 0.2234 4.3133 4.3961| | 11: 1.36 - 1.32 0.99 6997 151 0.2099 0.2084 4.233 4.28| | 12: 1.32 - 1.28 0.98 6976 149 0.2068 0.1965 4.1585 4.1839| | 13: 1.28 - 1.25 0.98 6907 166 0.2051 0.2031 4.128 4.1369| | 14: 1.25 - 1.22 0.98 7015 113 0.2066 0.2377 4.0761 4.2061| | 15: 1.22 - 1.19 0.98 6957 137 0.2133 0.2117 4.054 4.042| | 16: 1.19 - 1.17 0.93 6604 132 0.2120 0.2234 4.001 4.0784| | 17: 1.17 - 1.14 0.98 6941 135 0.2185 0.1873 3.9667 3.9533| | 18: 1.14 - 1.12 0.98 6875 142 0.2195 0.2248 3.9179 3.8784| | 19: 1.12 - 1.10 0.97 6949 106 0.2243 0.2586 3.8625 4.0444| | 20: 1.10 - 1.08 0.97 6884 147 0.2325 0.2136 3.8211 3.7516| | 21: 1.08 - 1.07 0.97 6852 152 0.2454 0.2484 3.7954 3.7686| | 22: 1.07 - 1.05 0.97 6838 135 0.2568 0.2580 3.7522 3.7936| | 23: 1.05 - 1.03 0.97 6829 159 0.2662 0.2569 3.7206 3.8095| | 24: 1.03 - 1.02 0.96 6785 133 0.2907 0.2707 3.7004 3.7871| | 25: 1.02 - 1.01 0.93 6552 130 0.3080 0.2979 3.6812 3.7451| | 26: 1.01 - 0.99 0.96 6767 158 0.3224 0.3307 3.6332 3.6397| | 27: 0.99 - 0.98 0.94 6648 131 0.3411 0.2952 3.6578 3.5654| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.46 0.91 0.97 35455.27| | 2: 2.94 - 2.33 7339 128 0.85 21.32 1.09 1.02 15141.83| | 3: 2.33 - 2.04 6939 150 0.93 12.66 1.11 1.06 4248.15| | 4: 2.04 - 1.85 7170 155 0.92 13.58 1.11 1.05 2775.10| | 5: 1.85 - 1.72 7113 159 0.91 15.67 1.11 1.06 2061.84| | 6: 1.72 - 1.62 7102 142 0.90 16.29 1.11 1.06 1561.99| | 7: 1.62 - 1.54 7104 148 0.89 17.54 1.11 1.07 1332.36| | 8: 1.54 - 1.47 6798 152 0.89 18.30 1.10 1.06 1156.99| | 9: 1.47 - 1.41 6938 155 0.87 19.85 1.11 1.05 1054.16| | 10: 1.41 - 1.36 7022 150 0.87 20.62 1.09 1.04 890.63| | 11: 1.36 - 1.32 6997 151 0.86 20.76 1.08 1.02 767.22| | 12: 1.32 - 1.28 6976 149 0.88 19.62 1.08 1.03 627.59| | 13: 1.28 - 1.25 6907 166 0.88 19.23 1.07 1.04 574.75| | 14: 1.25 - 1.22 7015 113 0.88 19.68 1.08 1.06 535.36| | 15: 1.22 - 1.19 6957 137 0.87 20.20 1.08 1.05 515.61| | 16: 1.19 - 1.17 6604 132 0.88 19.94 1.07 1.02 470.01| | 17: 1.17 - 1.14 6941 135 0.87 20.88 1.08 1.00 430.05| | 18: 1.14 - 1.12 6875 142 0.87 20.55 1.08 0.99 377.79| | 19: 1.12 - 1.10 6949 106 0.86 21.18 1.07 0.99 349.75| | 20: 1.10 - 1.08 6884 147 0.86 21.43 1.07 0.99 314.63| | 21: 1.08 - 1.07 6852 152 0.85 22.60 1.06 0.99 310.44| | 22: 1.07 - 1.05 6838 135 0.82 25.21 1.06 0.98 320.13| | 23: 1.05 - 1.03 6829 159 0.80 27.86 1.06 0.96 335.42| | 24: 1.03 - 1.02 6785 133 0.77 30.58 1.05 0.95 343.19| | 25: 1.02 - 1.01 6552 130 0.77 30.85 1.02 0.92 312.86| | 26: 1.01 - 0.99 6767 158 0.76 30.91 1.03 0.93 273.87| | 27: 0.99 - 0.98 6648 131 0.80 28.11 1.04 0.95 223.89| |alpha: min = 0.92 max = 1.07 mean = 1.01| |beta: min = 223.89 max = 35455.27 mean = 2822.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.25| |phase err.(test): min = 0.00 max = 89.50 mean = 21.18| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.266 2950 Z= 5.340 Angle : 5.161 16.481 4018 Z= 3.703 Chirality : 0.364 1.012 492 Planarity : 0.033 0.154 512 Dihedral : 12.921 89.648 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.37 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Cbeta Deviations : 28.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.40), residues: 386 helix: -1.95 (0.34), residues: 144 sheet: -0.94 (0.53), residues: 86 loop : 0.04 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.147 0.030 ARG B 83 TYR 0.144 0.035 TYR A 192 PHE 0.150 0.041 PHE A 164 TRP 0.126 0.036 TRP A 139 HIS 0.062 0.022 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2035 r_free= 0.1974 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.300390 | | target function (ml) not normalized (work): 805518.966197 | | target function (ml) not normalized (free): 16538.150090 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2035 0.1974 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2035 0.1974 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2036 0.1974 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2035 0.2037 0.1974 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1802 0.1800 0.1912 n_refl.: 191145 remove outliers: r(all,work,free)=0.1801 0.1798 0.1912 n_refl.: 191140 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4084 402.814 291.840 0.424 0.935 0.303 13.296-10.522 100.00 100 1 0.2564 534.497 519.881 0.770 0.936 0.256 10.503-8.327 99.45 178 3 0.2533 565.118 556.445 0.945 0.936 0.233 8.318-6.595 100.00 360 8 0.2469 414.736 402.387 0.944 0.935 0.170 6.588-5.215 100.00 711 7 0.2254 381.101 366.243 0.934 0.935 0.160 5.214-4.128 98.38 1367 28 0.1498 557.435 550.098 1.047 0.935 0.080 4.126-3.266 94.74 2603 46 0.1344 508.132 499.224 1.116 0.933 0.060 3.266-2.585 99.86 5447 97 0.1434 342.774 337.477 1.095 0.931 0.000 2.585-2.046 97.45 10613 204 0.1410 258.603 254.008 1.103 0.927 0.000 2.046-1.619 99.39 21536 464 0.1611 153.054 149.969 1.126 0.921 0.000 1.619-1.281 98.00 42464 925 0.1919 82.395 80.254 1.123 0.912 0.000 1.281-0.980 96.53 101826 2056 0.2318 44.203 41.688 1.123 0.894 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0187 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1798 r_free=0.1912 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 r_work=0.1801 r_free=0.1915 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.432138 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 581.058284 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 0.1505 0.0237 0.039 1.1 10.9 0.0 0.3 0 11.216 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.68 15.05 2.37 1.117 13.123 581.058 0.018 12.95 15.80 2.84 1.260 13.356 581.058 0.017 Individual atomic B min max mean iso aniso Overall: 5.17 73.06 15.03 1.42 435 3274 Protein: 5.17 40.33 11.03 1.42 0 2902 Water: 6.38 73.06 29.44 N/A 435 370 Other: 16.18 29.92 23.05 N/A 0 2 Chain A: 5.33 59.49 13.08 N/A 0 1626 Chain B: 5.17 73.06 12.80 N/A 0 1648 Chain S: 11.26 63.57 30.80 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2153 11.96 - 18.75 646 18.75 - 25.53 318 25.53 - 32.32 261 32.32 - 39.11 161 39.11 - 45.90 106 45.90 - 52.69 42 52.69 - 59.48 17 59.48 - 66.27 4 66.27 - 73.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1580 r_work=0.1295 r_free=0.1574 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1574 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1280 r_free = 0.1561 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1561 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015632 | | target function (ls_wunit_k1) not normalized (work): 2927.822041 | | target function (ls_wunit_k1) not normalized (free): 118.134782 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1280 0.1561 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1640 n_refl.: 191140 remove outliers: r(all,work,free)=0.1470 0.1467 0.1640 n_refl.: 191140 overall B=0.15 to atoms: r(all,work,free)=0.1491 0.1488 0.1649 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1552 n_refl.: 191140 remove outliers: r(all,work,free)=0.1280 0.1275 0.1551 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3608 402.814 367.761 0.460 0.997 0.281 13.296-10.522 100.00 100 1 0.2104 534.497 525.608 0.718 0.998 0.244 10.503-8.327 99.45 178 3 0.1779 565.118 564.697 0.861 0.998 0.230 8.318-6.595 100.00 360 8 0.1702 414.736 412.106 0.879 0.998 0.160 6.588-5.215 100.00 711 7 0.1537 381.101 373.830 0.859 0.998 0.150 5.214-4.128 98.38 1367 28 0.0903 557.435 554.386 0.943 0.999 0.060 4.126-3.266 94.74 2603 46 0.0834 508.132 504.141 1.007 0.999 0.023 3.266-2.585 99.86 5447 97 0.0922 342.774 340.563 0.991 0.999 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.328 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1090 153.054 151.407 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1277 82.395 81.387 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.228 0.990 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0335 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1551 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN Total number of N/Q/H flips: 1 r_work=0.1275 r_free=0.1552 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1552 | n_water=805 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1281 r_free=0.1558 | n_water=794 | time (s): 108.910 (total time: 112.100) Filter (q & B) r_work=0.1281 r_free=0.1559 | n_water=790 | time (s): 4.350 (total time: 116.450) Compute maps r_work=0.1281 r_free=0.1559 | n_water=790 | time (s): 2.080 (total time: 118.530) Filter (map) r_work=0.1307 r_free=0.1536 | n_water=651 | time (s): 5.110 (total time: 123.640) Find peaks r_work=0.1307 r_free=0.1536 | n_water=651 | time (s): 0.890 (total time: 124.530) Add new water r_work=0.1330 r_free=0.1566 | n_water=968 | time (s): 5.430 (total time: 129.960) Refine new water occ: r_work=0.1284 r_free=0.1538 adp: r_work=0.1272 r_free=0.1532 occ: r_work=0.1274 r_free=0.1536 adp: r_work=0.1268 r_free=0.1532 occ: r_work=0.1269 r_free=0.1534 adp: r_work=0.1267 r_free=0.1533 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1533 r_work=0.1267 r_free=0.1533 | n_water=968 | time (s): 87.170 (total time: 217.130) Filter (q & B) r_work=0.1271 r_free=0.1540 | n_water=892 | time (s): 5.540 (total time: 222.670) Filter (dist only) r_work=0.1271 r_free=0.1537 | n_water=889 | time (s): 115.810 (total time: 338.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.780969 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 589.804743 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 0.1541 0.0287 0.042 1.1 17.8 0.0 0.3 0 11.890 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.41 2.87 2.053 15.147 589.805 0.014 12.32 15.32 3.00 2.439 15.250 589.805 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 72.48 16.33 1.21 521 3272 Protein: 5.39 40.80 10.99 1.21 0 2902 Water: 6.60 72.48 33.76 N/A 521 368 Other: 16.34 33.29 24.82 N/A 0 2 Chain A: 5.53 55.16 13.01 N/A 0 1624 Chain B: 5.39 68.20 12.83 N/A 0 1648 Chain S: 12.32 72.48 37.74 N/A 521 0 Histogram: Values Number of atoms 5.39 - 12.09 2146 12.09 - 18.80 676 18.80 - 25.51 249 25.51 - 32.22 234 32.22 - 38.93 182 38.93 - 45.64 160 45.64 - 52.35 74 52.35 - 59.06 44 59.06 - 65.77 21 65.77 - 72.48 7 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1532 r_work=0.1232 r_free=0.1533 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1533 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 = 0.1531 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1531 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013430 | | target function (ls_wunit_k1) not normalized (work): 2515.461879 | | target function (ls_wunit_k1) not normalized (free): 105.422175 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1531 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1441 0.1438 0.1626 n_refl.: 191139 remove outliers: r(all,work,free)=0.1441 0.1438 0.1626 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1438 0.1435 0.1624 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1536 n_refl.: 191139 remove outliers: r(all,work,free)=0.1238 0.1233 0.1536 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3246 402.814 376.061 0.485 0.962 0.267 13.296-10.522 100.00 100 1 0.1889 534.497 527.393 0.767 0.963 0.228 10.503-8.327 99.45 178 3 0.1423 565.118 566.740 0.923 0.963 0.189 8.318-6.595 100.00 360 8 0.1498 414.736 414.952 0.940 0.962 0.165 6.588-5.215 100.00 711 7 0.1358 381.101 376.247 0.916 0.962 0.160 5.214-4.128 98.38 1367 28 0.0824 557.435 556.360 0.996 0.962 0.090 4.126-3.266 94.74 2603 46 0.0768 508.132 505.464 1.060 0.962 0.019 3.266-2.585 99.86 5447 97 0.0857 342.774 341.410 1.047 0.961 0.010 2.585-2.046 97.45 10613 204 0.0900 258.603 256.749 1.059 0.960 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.617 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.354 1.075 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.219 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0567 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1536 | n_water=889 | time (s): 3.310 (total time: 3.310) Filter (dist) r_work=0.1234 r_free=0.1537 | n_water=883 | time (s): 112.560 (total time: 115.870) Filter (q & B) r_work=0.1234 r_free=0.1538 | n_water=880 | time (s): 4.050 (total time: 119.920) Compute maps r_work=0.1234 r_free=0.1538 | n_water=880 | time (s): 2.040 (total time: 121.960) Filter (map) r_work=0.1276 r_free=0.1534 | n_water=684 | time (s): 5.900 (total time: 127.860) Find peaks r_work=0.1276 r_free=0.1534 | n_water=684 | time (s): 0.940 (total time: 128.800) Add new water r_work=0.1302 r_free=0.1578 | n_water=987 | time (s): 4.750 (total time: 133.550) Refine new water occ: r_work=0.1255 r_free=0.1531 adp: r_work=0.1256 r_free=0.1531 occ: r_work=0.1252 r_free=0.1526 adp: r_work=0.1252 r_free=0.1526 occ: r_work=0.1248 r_free=0.1523 adp: r_work=0.1248 r_free=0.1523 ADP+occupancy (water only), MIN, final r_work=0.1248 r_free=0.1523 r_work=0.1248 r_free=0.1523 | n_water=987 | time (s): 232.430 (total time: 365.980) Filter (q & B) r_work=0.1253 r_free=0.1532 | n_water=867 | time (s): 5.900 (total time: 371.880) Filter (dist only) r_work=0.1253 r_free=0.1532 | n_water=866 | time (s): 126.590 (total time: 498.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.773011 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.977994 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1243 0.1445 0.0202 0.036 1.1 7.5 0.0 0.0 0 0.887 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.43 14.45 2.02 1.935 14.551 15.978 3.940 12.37 14.04 1.67 2.231 14.454 15.978 3.899 Individual atomic B min max mean iso aniso Overall: 5.53 67.79 15.20 1.05 499 3271 Protein: 5.53 36.97 10.75 1.05 0 2902 Water: 6.67 67.79 30.09 N/A 499 367 Other: 14.08 29.32 21.70 N/A 0 2 Chain A: 5.57 54.30 12.78 N/A 0 1624 Chain B: 5.53 67.79 12.55 N/A 0 1647 Chain S: 14.66 63.76 31.80 N/A 499 0 Histogram: Values Number of atoms 5.53 - 11.76 2135 11.76 - 17.99 684 17.99 - 24.21 290 24.21 - 30.44 243 30.44 - 36.66 175 36.66 - 42.89 139 42.89 - 49.12 66 49.12 - 55.34 28 55.34 - 61.57 8 61.57 - 67.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1405 r_work=0.1238 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1406 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1391 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1391 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892836 | | target function (ml) not normalized (work): 729120.490703 | | target function (ml) not normalized (free): 15233.296027 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1231 0.1391 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1447 0.1446 0.1483 n_refl.: 191139 remove outliers: r(all,work,free)=0.1447 0.1446 0.1483 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1440 0.1479 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1227 0.1385 n_refl.: 191139 remove outliers: r(all,work,free)=0.1230 0.1227 0.1385 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3833 398.008 362.103 0.425 0.946 0.250 13.296-10.522 98.02 98 1 0.2472 528.900 510.347 0.714 0.947 0.220 10.503-8.327 98.35 176 3 0.2076 555.265 555.575 0.883 0.947 0.190 8.318-6.595 100.00 360 8 0.2082 414.736 409.412 0.901 0.947 0.139 6.588-5.215 100.00 711 7 0.1885 381.101 369.395 0.886 0.947 0.117 5.214-4.128 98.38 1367 28 0.1177 557.435 551.867 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1101 508.132 500.927 1.033 0.947 0.014 3.266-2.585 99.86 5447 97 0.1088 342.774 338.996 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0965 258.603 255.748 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.399 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.481 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.319 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1041 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1385 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1385 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1385 | n_water=866 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1227 r_free=0.1383 | n_water=863 | time (s): 111.970 (total time: 114.620) Filter (q & B) r_work=0.1227 r_free=0.1380 | n_water=852 | time (s): 4.150 (total time: 118.770) Compute maps r_work=0.1227 r_free=0.1380 | n_water=852 | time (s): 1.770 (total time: 120.540) Filter (map) r_work=0.1251 r_free=0.1398 | n_water=702 | time (s): 5.460 (total time: 126.000) Find peaks r_work=0.1251 r_free=0.1398 | n_water=702 | time (s): 0.670 (total time: 126.670) Add new water r_work=0.1268 r_free=0.1421 | n_water=971 | time (s): 4.380 (total time: 131.050) Refine new water occ: r_work=0.1216 r_free=0.1372 adp: r_work=0.1208 r_free=0.1366 occ: r_work=0.1205 r_free=0.1368 adp: r_work=0.1205 r_free=0.1366 occ: r_work=0.1203 r_free=0.1368 adp: r_work=0.1203 r_free=0.1366 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1366 r_work=0.1203 r_free=0.1366 | n_water=971 | time (s): 314.820 (total time: 445.870) Filter (q & B) r_work=0.1208 r_free=0.1372 | n_water=867 | time (s): 5.410 (total time: 451.280) Filter (dist only) r_work=0.1209 r_free=0.1372 | n_water=865 | time (s): 111.860 (total time: 563.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.627126 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.723133 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1373 0.0165 0.036 1.1 7.0 0.0 0.0 0 0.814 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.73 1.65 1.830 14.199 15.723 3.876 12.00 13.68 1.68 1.945 14.156 15.723 3.866 Individual atomic B min max mean iso aniso Overall: 5.50 67.28 14.95 1.00 498 3271 Protein: 5.50 33.56 10.66 1.00 0 2902 Water: 5.85 67.28 29.35 N/A 498 367 Other: 13.94 28.05 21.00 N/A 0 2 Chain A: 5.56 53.09 12.64 N/A 0 1624 Chain B: 5.50 67.28 12.45 N/A 0 1647 Chain S: 5.85 63.84 30.80 N/A 498 0 Histogram: Values Number of atoms 5.50 - 11.68 2110 11.68 - 17.86 732 17.86 - 24.03 290 24.03 - 30.21 247 30.21 - 36.39 167 36.39 - 42.57 132 42.57 - 48.75 58 48.75 - 54.93 25 54.93 - 61.11 6 61.11 - 67.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1368 r_work=0.1200 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1368 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1370 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863889 | | target function (ml) not normalized (work): 723679.299791 | | target function (ml) not normalized (free): 15140.866009 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1369 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1425 0.1425 0.1468 n_refl.: 191134 remove outliers: r(all,work,free)=0.1425 0.1425 0.1468 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1417 0.1464 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1196 0.1367 n_refl.: 191134 remove outliers: r(all,work,free)=0.1199 0.1196 0.1367 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3985 361.187 312.041 0.392 0.946 0.221 13.296-10.522 98.02 98 1 0.2575 478.901 458.895 0.702 0.948 0.187 10.503-8.327 98.35 176 3 0.2112 502.774 496.367 0.868 0.948 0.170 8.318-6.595 100.00 360 8 0.2148 375.530 369.723 0.895 0.947 0.120 6.588-5.215 100.00 711 7 0.1928 345.075 334.542 0.884 0.948 0.089 5.214-4.128 98.38 1367 28 0.1188 504.739 499.695 0.974 0.948 0.070 4.126-3.266 94.74 2603 46 0.1116 460.097 453.665 1.034 0.948 0.009 3.266-2.585 99.86 5447 97 0.1083 310.370 307.187 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0933 234.157 231.726 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0915 138.586 137.275 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0987 74.606 73.892 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.023 38.364 1.039 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1218 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1367 | n_water=865 | time (s): 2.700 (total time: 2.700) Filter (dist) r_work=0.1196 r_free=0.1367 | n_water=865 | time (s): 105.500 (total time: 108.200) Filter (q & B) r_work=0.1197 r_free=0.1367 | n_water=852 | time (s): 5.140 (total time: 113.340) Compute maps r_work=0.1197 r_free=0.1367 | n_water=852 | time (s): 1.730 (total time: 115.070) Filter (map) r_work=0.1217 r_free=0.1366 | n_water=737 | time (s): 4.730 (total time: 119.800) Find peaks r_work=0.1217 r_free=0.1366 | n_water=737 | time (s): 0.610 (total time: 120.410) Add new water r_work=0.1229 r_free=0.1386 | n_water=964 | time (s): 5.230 (total time: 125.640) Refine new water occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1349 occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1190 r_free=0.1347 occ: r_work=0.1189 r_free=0.1346 adp: r_work=0.1189 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1347 r_work=0.1189 r_free=0.1347 | n_water=964 | time (s): 168.940 (total time: 294.580) Filter (q & B) r_work=0.1193 r_free=0.1361 | n_water=880 | time (s): 4.780 (total time: 299.360) Filter (dist only) r_work=0.1193 r_free=0.1360 | n_water=879 | time (s): 117.940 (total time: 417.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.528408 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.266696 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 0.1365 0.0168 0.037 1.1 6.6 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.65 1.68 1.791 14.116 15.267 3.765 12.02 13.68 1.66 1.852 14.090 15.267 3.763 Individual atomic B min max mean iso aniso Overall: 5.58 66.96 14.93 0.96 512 3271 Protein: 5.58 32.22 10.59 0.96 0 2902 Water: 6.02 66.96 29.22 N/A 512 367 Other: 13.76 26.98 20.37 N/A 0 2 Chain A: 5.59 52.32 12.54 N/A 0 1624 Chain B: 5.58 66.96 12.36 N/A 0 1647 Chain S: 6.02 63.86 30.73 N/A 512 0 Histogram: Values Number of atoms 5.58 - 11.72 2142 11.72 - 17.85 718 17.85 - 23.99 294 23.99 - 30.13 232 30.13 - 36.27 168 36.27 - 42.41 137 42.41 - 48.54 59 48.54 - 54.68 25 54.68 - 60.82 6 60.82 - 66.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1368 r_work=0.1202 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1369 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1369 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762331 | | target function (ml) not normalized (work): 704654.428751 | | target function (ml) not normalized (free): 14756.261836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1369 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1469 n_refl.: 191133 remove outliers: r(all,work,free)=0.1409 0.1408 0.1469 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1401 0.1400 0.1464 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1199 0.1368 n_refl.: 191133 remove outliers: r(all,work,free)=0.1202 0.1199 0.1368 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3729 360.883 308.973 0.395 0.951 0.224 13.296-10.522 98.02 98 1 0.2531 478.901 460.179 0.696 0.952 0.186 10.503-8.327 98.35 176 3 0.2156 502.774 496.256 0.862 0.952 0.163 8.318-6.595 100.00 360 8 0.2161 375.530 369.459 0.890 0.952 0.119 6.588-5.215 100.00 711 7 0.1934 345.075 334.517 0.880 0.952 0.093 5.214-4.128 98.38 1367 28 0.1203 504.739 499.732 0.969 0.952 0.060 4.126-3.266 94.74 2603 46 0.1142 460.097 453.641 1.031 0.953 0.009 3.266-2.585 99.86 5447 97 0.1100 310.370 307.120 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0945 234.157 231.729 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0918 138.586 137.278 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0981 74.606 73.898 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.023 38.363 1.039 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1288 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1368 | n_water=879 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1199 r_free=0.1368 | n_water=879 | time (s): 110.370 (total time: 113.390) Filter (q & B) r_work=0.1199 r_free=0.1367 | n_water=870 | time (s): 4.620 (total time: 118.010) Compute maps r_work=0.1199 r_free=0.1367 | n_water=870 | time (s): 2.420 (total time: 120.430) Filter (map) r_work=0.1220 r_free=0.1369 | n_water=753 | time (s): 4.590 (total time: 125.020) Find peaks r_work=0.1220 r_free=0.1369 | n_water=753 | time (s): 0.680 (total time: 125.700) Add new water r_work=0.1231 r_free=0.1385 | n_water=962 | time (s): 4.760 (total time: 130.460) Refine new water occ: r_work=0.1196 r_free=0.1351 adp: r_work=0.1196 r_free=0.1351 occ: r_work=0.1194 r_free=0.1352 adp: r_work=0.1194 r_free=0.1351 occ: r_work=0.1193 r_free=0.1353 adp: r_work=0.1193 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1353 r_work=0.1193 r_free=0.1353 | n_water=962 | time (s): 213.100 (total time: 343.560) Filter (q & B) r_work=0.1197 r_free=0.1362 | n_water=891 | time (s): 4.250 (total time: 347.810) Filter (dist only) r_work=0.1197 r_free=0.1360 | n_water=890 | time (s): 114.660 (total time: 462.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.615291 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.388029 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1360 0.0161 0.037 1.1 7.0 0.0 0.3 0 0.808 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.60 1.61 1.762 14.042 14.388 3.762 12.04 13.67 1.63 1.917 13.989 14.388 3.761 Individual atomic B min max mean iso aniso Overall: 5.58 65.69 14.83 0.89 523 3271 Protein: 5.58 29.21 10.47 0.89 0 2902 Water: 5.90 65.69 29.03 N/A 523 367 Other: 13.78 23.64 18.71 N/A 0 2 Chain A: 5.63 51.30 12.39 N/A 0 1624 Chain B: 5.58 65.69 12.22 N/A 0 1647 Chain S: 5.90 64.16 30.64 N/A 523 0 Histogram: Values Number of atoms 5.58 - 11.59 2111 11.59 - 17.60 775 17.60 - 23.61 273 23.61 - 29.62 215 29.62 - 35.63 183 35.63 - 41.65 133 41.65 - 47.66 67 47.66 - 53.67 29 53.67 - 59.68 6 59.68 - 65.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1367 r_work=0.1204 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1368 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1369 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760301 | | target function (ml) not normalized (work): 704270.480060 | | target function (ml) not normalized (free): 14754.062277 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1370 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1400 0.1399 0.1485 n_refl.: 191132 remove outliers: r(all,work,free)=0.1400 0.1399 0.1485 n_refl.: 191132 overall B=-0.22 to atoms: r(all,work,free)=0.1366 0.1364 0.1464 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1368 n_refl.: 191132 remove outliers: r(all,work,free)=0.1204 0.1201 0.1368 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3728 360.883 329.372 0.425 0.952 0.217 13.296-10.522 98.02 98 1 0.2539 478.901 458.741 0.708 0.954 0.171 10.503-8.327 98.35 176 3 0.2184 502.774 496.068 0.882 0.954 0.142 8.318-6.595 100.00 360 8 0.2145 375.530 369.682 0.910 0.954 0.111 6.588-5.215 100.00 711 7 0.1929 345.075 334.836 0.903 0.954 0.087 5.214-4.128 98.38 1367 28 0.1216 504.739 499.922 0.992 0.954 0.040 4.126-3.266 94.74 2603 46 0.1153 460.097 453.294 1.055 0.954 0.009 3.266-2.585 99.86 5447 97 0.1121 310.370 306.998 1.038 0.954 0.000 2.585-2.046 97.45 10613 204 0.0952 234.157 231.670 1.046 0.953 0.000 2.046-1.619 99.39 21536 464 0.0915 138.586 137.268 1.064 0.953 0.000 1.619-1.281 98.00 42464 925 0.0974 74.606 73.892 1.052 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.023 38.359 1.024 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0490 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1369 | n_water=890 | time (s): 3.350 (total time: 3.350) Filter (dist) r_work=0.1201 r_free=0.1369 | n_water=890 | time (s): 118.360 (total time: 121.710) Filter (q & B) r_work=0.1202 r_free=0.1370 | n_water=882 | time (s): 4.480 (total time: 126.190) Compute maps r_work=0.1202 r_free=0.1370 | n_water=882 | time (s): 1.620 (total time: 127.810) Filter (map) r_work=0.1223 r_free=0.1367 | n_water=769 | time (s): 4.370 (total time: 132.180) Find peaks r_work=0.1223 r_free=0.1367 | n_water=769 | time (s): 0.590 (total time: 132.770) Add new water r_work=0.1234 r_free=0.1380 | n_water=985 | time (s): 5.130 (total time: 137.900) Refine new water occ: r_work=0.1197 r_free=0.1351 adp: r_work=0.1197 r_free=0.1352 occ: r_work=0.1195 r_free=0.1352 adp: r_work=0.1195 r_free=0.1352 occ: r_work=0.1193 r_free=0.1352 adp: r_work=0.1193 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1353 r_work=0.1193 r_free=0.1353 | n_water=985 | time (s): 234.700 (total time: 372.600) Filter (q & B) r_work=0.1198 r_free=0.1361 | n_water=912 | time (s): 4.730 (total time: 377.330) Filter (dist only) r_work=0.1198 r_free=0.1360 | n_water=911 | time (s): 117.410 (total time: 494.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507120 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.283414 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1365 0.0162 0.038 1.1 7.0 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.65 1.62 1.714 13.745 14.283 3.762 12.03 13.65 1.63 1.750 13.728 14.283 3.759 Individual atomic B min max mean iso aniso Overall: 5.39 64.55 14.64 0.88 545 3270 Protein: 5.39 28.59 10.24 0.88 0 2902 Water: 5.76 64.55 28.66 N/A 545 366 Other: 13.65 22.21 17.93 N/A 0 2 Chain A: 5.48 50.77 12.12 N/A 0 1624 Chain B: 5.39 64.55 11.94 N/A 0 1646 Chain S: 5.76 64.14 30.32 N/A 545 0 Histogram: Values Number of atoms 5.39 - 11.30 2091 11.30 - 17.22 789 17.22 - 23.14 278 23.14 - 29.05 218 29.05 - 34.97 199 34.97 - 40.89 126 40.89 - 46.80 73 46.80 - 52.72 30 52.72 - 58.64 9 58.64 - 64.55 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1366 r_work=0.1203 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1368 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758335 | | target function (ml) not normalized (work): 703902.230792 | | target function (ml) not normalized (free): 14744.525267 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1368 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1368 0.1366 0.1468 n_refl.: 191132 remove outliers: r(all,work,free)=0.1368 0.1366 0.1468 n_refl.: 191132 overall B=0.06 to atoms: r(all,work,free)=0.1375 0.1374 0.1473 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1356 n_refl.: 191132 remove outliers: r(all,work,free)=0.1195 0.1192 0.1356 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3711 360.883 329.949 0.406 0.975 0.199 13.296-10.522 98.02 98 1 0.2515 478.901 458.562 0.685 0.977 0.148 10.503-8.327 98.35 176 3 0.2197 502.774 495.936 0.868 0.978 0.120 8.318-6.595 100.00 360 8 0.2139 375.530 369.884 0.894 0.977 0.096 6.588-5.215 100.00 711 7 0.1944 345.075 334.513 0.889 0.978 0.077 5.214-4.128 98.38 1367 28 0.1222 504.739 499.389 0.978 0.979 0.035 4.126-3.266 94.74 2603 46 0.1159 460.097 452.688 1.040 0.980 0.009 3.266-2.585 99.86 5447 97 0.1120 310.370 306.709 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0955 234.157 231.537 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0910 138.586 137.205 1.047 0.984 0.000 1.619-1.281 98.00 42464 925 0.0953 74.606 73.933 1.035 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.023 38.332 1.001 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0588 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1356 | n_water=911 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1192 r_free=0.1355 | n_water=910 | time (s): 116.600 (total time: 119.040) Filter (q & B) r_work=0.1193 r_free=0.1355 | n_water=899 | time (s): 5.110 (total time: 124.150) Compute maps r_work=0.1193 r_free=0.1355 | n_water=899 | time (s): 1.880 (total time: 126.030) Filter (map) r_work=0.1216 r_free=0.1352 | n_water=784 | time (s): 4.790 (total time: 130.820) Find peaks r_work=0.1216 r_free=0.1352 | n_water=784 | time (s): 0.630 (total time: 131.450) Add new water r_work=0.1223 r_free=0.1361 | n_water=991 | time (s): 4.790 (total time: 136.240) Refine new water occ: r_work=0.1189 r_free=0.1336 adp: r_work=0.1189 r_free=0.1336 occ: r_work=0.1187 r_free=0.1337 adp: r_work=0.1187 r_free=0.1337 occ: r_work=0.1186 r_free=0.1338 adp: r_work=0.1186 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1339 r_work=0.1186 r_free=0.1339 | n_water=991 | time (s): 183.980 (total time: 320.220) Filter (q & B) r_work=0.1191 r_free=0.1348 | n_water=911 | time (s): 4.710 (total time: 324.930) Filter (dist only) r_work=0.1191 r_free=0.1348 | n_water=910 | time (s): 115.910 (total time: 440.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.515854 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.727888 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1354 0.0159 0.038 1.1 6.6 0.0 0.3 0 0.758 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.54 1.59 1.676 13.750 13.728 3.757 11.97 13.58 1.61 1.704 13.735 13.728 3.756 Individual atomic B min max mean iso aniso Overall: 5.49 64.44 14.66 0.86 544 3270 Protein: 5.49 28.06 10.30 0.86 0 2902 Water: 5.90 64.44 28.56 N/A 544 366 Other: 13.76 22.00 17.88 N/A 0 2 Chain A: 5.57 50.47 12.14 N/A 0 1624 Chain B: 5.49 63.63 11.98 N/A 0 1646 Chain S: 5.90 64.44 30.30 N/A 544 0 Histogram: Values Number of atoms 5.49 - 11.39 2090 11.39 - 17.28 804 17.28 - 23.18 272 23.18 - 29.07 216 29.07 - 34.97 197 34.97 - 40.86 119 40.86 - 46.76 73 46.76 - 52.65 32 52.65 - 58.55 9 58.55 - 64.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1358 r_work=0.1197 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1358 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1360 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756059 | | target function (ml) not normalized (work): 703476.121534 | | target function (ml) not normalized (free): 14738.918633 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1360 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1386 0.1384 0.1484 n_refl.: 191132 remove outliers: r(all,work,free)=0.1386 0.1384 0.1484 n_refl.: 191132 overall B=0.01 to atoms: r(all,work,free)=0.1388 0.1386 0.1485 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191132 remove outliers: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3752 360.883 327.476 0.421 0.913 0.187 13.296-10.522 98.02 98 1 0.2509 478.901 459.400 0.728 0.914 0.145 10.503-8.327 98.35 176 3 0.2201 502.774 495.894 0.923 0.914 0.119 8.318-6.595 100.00 360 8 0.2154 375.530 369.343 0.952 0.914 0.092 6.588-5.215 100.00 711 7 0.1966 345.075 334.140 0.947 0.915 0.071 5.214-4.128 98.38 1367 28 0.1242 504.739 499.105 1.044 0.916 0.030 4.126-3.266 94.74 2603 46 0.1170 460.097 452.438 1.111 0.917 0.009 3.266-2.585 99.86 5447 97 0.1129 310.370 306.640 1.094 0.917 0.000 2.585-2.046 97.45 10613 204 0.0959 234.157 231.506 1.102 0.919 0.000 2.046-1.619 99.39 21536 464 0.0910 138.586 137.229 1.120 0.922 0.000 1.619-1.281 98.00 42464 925 0.0949 74.606 73.944 1.109 0.927 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.023 38.317 1.076 0.936 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0186 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1358 | n_water=910 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1195 r_free=0.1357 | n_water=908 | time (s): 124.060 (total time: 127.290) Filter (q & B) r_work=0.1196 r_free=0.1357 | n_water=893 | time (s): 5.470 (total time: 132.760) Compute maps r_work=0.1196 r_free=0.1357 | n_water=893 | time (s): 2.500 (total time: 135.260) Filter (map) r_work=0.1218 r_free=0.1355 | n_water=780 | time (s): 4.330 (total time: 139.590) Find peaks r_work=0.1218 r_free=0.1355 | n_water=780 | time (s): 0.670 (total time: 140.260) Add new water r_work=0.1225 r_free=0.1363 | n_water=980 | time (s): 4.220 (total time: 144.480) Refine new water occ: r_work=0.1192 r_free=0.1337 adp: r_work=0.1192 r_free=0.1338 occ: r_work=0.1190 r_free=0.1337 adp: r_work=0.1190 r_free=0.1338 occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1188 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1338 r_work=0.1188 r_free=0.1338 | n_water=980 | time (s): 282.620 (total time: 427.100) Filter (q & B) r_work=0.1193 r_free=0.1344 | n_water=905 | time (s): 4.820 (total time: 431.920) Filter (dist only) r_work=0.1193 r_free=0.1344 | n_water=904 | time (s): 116.820 (total time: 548.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.553207 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.208101 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1352 0.0156 0.039 1.1 7.2 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.52 1.56 1.673 13.724 14.208 3.757 11.94 13.53 1.58 1.671 13.720 14.208 3.754 Individual atomic B min max mean iso aniso Overall: 5.53 64.57 14.63 0.86 538 3270 Protein: 5.53 28.12 10.33 0.86 0 2902 Water: 5.96 64.57 28.41 N/A 538 366 Other: 13.76 22.10 17.93 N/A 0 2 Chain A: 5.62 50.31 12.14 N/A 0 1624 Chain B: 5.53 63.09 11.98 N/A 0 1646 Chain S: 5.96 64.57 30.23 N/A 538 0 Histogram: Values Number of atoms 5.53 - 11.43 2092 11.43 - 17.33 809 17.33 - 23.24 266 23.24 - 29.14 219 29.14 - 35.05 198 35.05 - 40.95 119 40.95 - 46.85 65 46.85 - 52.76 29 52.76 - 58.66 9 58.66 - 64.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1353 r_work=0.1195 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1352 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753623 | | target function (ml) not normalized (work): 703019.841525 | | target function (ml) not normalized (free): 14731.802248 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1352 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1396 0.1395 0.1483 n_refl.: 191132 remove outliers: r(all,work,free)=0.1396 0.1395 0.1483 n_refl.: 191132 overall B=-0.00 to atoms: r(all,work,free)=0.1396 0.1394 0.1483 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1351 n_refl.: 191132 remove outliers: r(all,work,free)=0.1195 0.1192 0.1351 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3673 360.883 328.425 0.388 0.994 0.183 13.296-10.522 98.02 98 1 0.2497 478.901 458.236 0.667 0.996 0.145 10.503-8.327 98.35 176 3 0.2191 502.774 496.192 0.845 0.996 0.121 8.318-6.595 100.00 360 8 0.2178 375.530 369.054 0.872 0.996 0.090 6.588-5.215 100.00 711 7 0.1967 345.075 333.866 0.868 0.997 0.077 5.214-4.128 98.38 1367 28 0.1243 504.739 499.136 0.958 0.998 0.034 4.126-3.266 94.74 2603 46 0.1171 460.097 452.528 1.020 0.999 0.005 3.266-2.585 99.86 5447 97 0.1128 310.370 306.743 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0958 234.157 231.498 1.012 1.003 0.000 2.046-1.619 99.39 21536 464 0.0908 138.586 137.219 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0944 74.606 73.949 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.023 38.310 0.990 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0096 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1351 After: r_work=0.1193 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1351 | n_water=904 | time (s): 2.740 (total time: 2.740) Filter (dist) r_work=0.1193 r_free=0.1351 | n_water=904 | time (s): 117.330 (total time: 120.070) Filter (q & B) r_work=0.1193 r_free=0.1351 | n_water=892 | time (s): 5.350 (total time: 125.420) Compute maps r_work=0.1193 r_free=0.1351 | n_water=892 | time (s): 1.630 (total time: 127.050) Filter (map) r_work=0.1215 r_free=0.1358 | n_water=780 | time (s): 5.320 (total time: 132.370) Find peaks r_work=0.1215 r_free=0.1358 | n_water=780 | time (s): 0.600 (total time: 132.970) Add new water r_work=0.1222 r_free=0.1366 | n_water=970 | time (s): 4.100 (total time: 137.070) Refine new water occ: r_work=0.1191 r_free=0.1339 adp: r_work=0.1191 r_free=0.1339 occ: r_work=0.1189 r_free=0.1338 adp: r_work=0.1189 r_free=0.1339 occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1188 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1339 r_work=0.1188 r_free=0.1339 | n_water=970 | time (s): 223.620 (total time: 360.690) Filter (q & B) r_work=0.1192 r_free=0.1347 | n_water=899 | time (s): 4.400 (total time: 365.090) Filter (dist only) r_work=0.1192 r_free=0.1346 | n_water=898 | time (s): 117.230 (total time: 482.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.466638 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.373104 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1350 0.0154 0.039 1.2 8.7 0.0 0.3 0 0.733 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.50 1.54 1.676 13.712 14.373 3.757 11.97 13.53 1.56 1.677 13.710 14.373 3.756 Individual atomic B min max mean iso aniso Overall: 5.55 62.11 14.59 0.86 532 3270 Protein: 5.55 28.07 10.34 0.86 0 2902 Water: 5.88 62.11 28.33 N/A 532 366 Other: 13.83 22.12 17.98 N/A 0 2 Chain A: 5.66 50.03 12.12 N/A 0 1624 Chain B: 5.55 62.11 11.98 N/A 0 1646 Chain S: 5.88 56.65 30.25 N/A 532 0 Histogram: Values Number of atoms 5.55 - 11.20 2031 11.20 - 16.86 842 16.86 - 22.52 272 22.52 - 28.17 209 28.17 - 33.83 197 33.83 - 39.49 110 39.49 - 45.14 87 45.14 - 50.80 36 50.80 - 56.45 16 56.45 - 62.11 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1353 r_work=0.1197 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1353 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1352 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755841 | | target function (ml) not normalized (work): 703435.287658 | | target function (ml) not normalized (free): 14733.915442 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7400 127 0.1370 0.1462 5.6946 5.7543| | 2: 2.94 - 2.33 1.00 7339 128 0.1070 0.1311 5.0696 5.1528| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1153 4.6552 4.7399| | 4: 2.04 - 1.85 1.00 7170 155 0.0898 0.1039 4.3922 4.5631| | 5: 1.85 - 1.72 0.99 7113 159 0.0937 0.1019 4.1571 4.2607| | 6: 1.72 - 1.62 0.99 7102 142 0.0900 0.1082 3.9537 4.0807| | 7: 1.62 - 1.54 0.99 7104 148 0.0896 0.0978 3.8072 3.9452| | 8: 1.54 - 1.47 0.96 6798 152 0.0896 0.1344 3.7075 3.9173| | 9: 1.47 - 1.41 0.98 6938 155 0.0932 0.1126 3.6265 3.7567| | 10: 1.41 - 1.36 0.99 7022 150 0.0980 0.1202 3.56 3.683| | 11: 1.36 - 1.32 0.99 6997 151 0.0997 0.1126 3.4879 3.5839| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1149 3.4611 3.5943| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1232 3.4378 3.558| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1592 3.433 3.6883| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1246 3.4487 3.4958| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1547 3.4653 3.6554| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1224 3.4334 3.4382| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1716 3.4385 3.5357| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1769 3.4206 3.6042| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1587 3.4109 3.4383| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2150 3.4189 3.5052| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1968 3.4135 3.4174| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2019 3.4329 3.4839| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2252 3.4359 3.5089| | 25: 1.02 - 1.01 0.93 6552 130 0.2615 0.2522 3.4493 3.5251| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2863 3.4152 3.424| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2803 3.4691 3.395| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7400 127 0.93 11.35 1.00 0.96 10810.34| | 2: 2.94 - 2.33 7339 128 0.93 12.55 0.99 0.95 4965.76| | 3: 2.33 - 2.04 6939 150 0.96 7.53 1.01 0.95 1671.79| | 4: 2.04 - 1.85 7170 155 0.96 7.65 1.00 0.95 1006.36| | 5: 1.85 - 1.72 7113 159 0.96 8.18 1.00 0.96 646.55| | 6: 1.72 - 1.62 7102 142 0.96 8.16 1.00 0.96 453.51| | 7: 1.62 - 1.54 7104 148 0.96 8.31 1.01 0.97 345.90| | 8: 1.54 - 1.47 6798 152 0.96 8.44 1.01 0.97 286.16| | 9: 1.47 - 1.41 6938 155 0.96 8.62 1.00 0.97 235.56| | 10: 1.41 - 1.36 7022 150 0.96 9.02 1.00 0.97 205.85| | 11: 1.36 - 1.32 6997 151 0.96 9.01 0.99 0.96 176.46| | 12: 1.32 - 1.28 6975 149 0.96 9.03 0.98 0.95 161.89| | 13: 1.28 - 1.25 6907 166 0.96 9.57 1.01 0.96 158.83| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.96 163.79| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.01 0.98 167.16| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.01 0.96 160.58| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.96 154.31| | 18: 1.14 - 1.12 6875 142 0.94 12.80 1.01 0.94 148.44| | 19: 1.12 - 1.10 6948 106 0.93 14.23 1.00 0.94 152.36| | 20: 1.10 - 1.08 6884 147 0.92 15.31 1.00 0.94 151.60| | 21: 1.08 - 1.07 6852 152 0.91 16.72 1.00 0.93 154.27| | 22: 1.07 - 1.05 6836 135 0.89 18.34 0.99 0.93 155.45| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.92 164.90| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.99 0.93 179.16| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.90 182.24| | 26: 1.01 - 0.99 6767 158 0.81 26.63 0.98 0.88 176.63| | 27: 0.99 - 0.98 6647 131 0.82 26.24 0.99 0.87 160.59| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.44 max = 10810.34 mean = 905.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.32| |phase err.(test): min = 0.00 max = 85.74 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1352 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1485 n_refl.: 191132 remove outliers: r(all,work,free)=0.1407 0.1406 0.1485 n_refl.: 191132 overall B=-0.05 to atoms: r(all,work,free)=0.1398 0.1397 0.1479 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3614 360.883 329.106 0.387 0.974 0.182 13.296-10.522 98.02 98 1 0.2515 478.901 458.433 0.663 0.976 0.140 10.503-8.327 98.35 176 3 0.2185 502.774 496.364 0.841 0.976 0.121 8.318-6.595 100.00 360 8 0.2189 375.530 368.937 0.868 0.976 0.091 6.588-5.215 100.00 711 7 0.1953 345.075 334.002 0.864 0.977 0.080 5.214-4.128 98.38 1367 28 0.1256 504.739 499.217 0.953 0.978 0.034 4.126-3.266 94.74 2603 46 0.1171 460.097 452.430 1.017 0.979 0.000 3.266-2.585 99.86 5447 97 0.1124 310.370 306.840 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0963 234.157 231.484 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0912 138.586 137.204 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0950 74.606 73.945 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.023 38.306 0.978 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0120 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2035 0.1974 0.081 5.161 5.2 78.0 14.6 805 0.000 1_bss: 0.1798 0.1912 0.081 5.161 5.2 78.1 14.6 805 0.000 1_settarget: 0.1798 0.1912 0.081 5.161 5.2 78.1 14.6 805 0.000 1_nqh: 0.1801 0.1915 0.081 5.161 5.2 78.1 14.6 805 0.002 1_weight: 0.1801 0.1915 0.081 5.161 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1268 0.1505 0.039 1.144 5.2 78.1 14.6 805 0.157 1_adp: 0.1296 0.1580 0.039 1.144 5.2 73.1 15.0 805 0.157 1_regHadp: 0.1295 0.1574 0.039 1.144 5.2 73.1 15.0 805 0.157 1_occ: 0.1280 0.1561 0.039 1.144 5.2 73.1 15.0 805 0.157 2_bss: 0.1275 0.1551 0.039 1.144 5.3 73.2 15.2 805 0.157 2_settarget: 0.1275 0.1551 0.039 1.144 5.3 73.2 15.2 805 0.157 2_updatecdl: 0.1275 0.1551 0.039 1.153 5.3 73.2 15.2 805 0.157 2_nqh: 0.1275 0.1552 0.039 1.153 5.3 73.2 15.2 805 0.156 2_sol: 0.1271 0.1537 0.039 1.153 5.3 73.2 16.1 889 n/a 2_weight: 0.1271 0.1537 0.039 1.153 5.3 73.2 16.1 889 n/a 2_xyzrec: 0.1254 0.1541 0.042 1.132 5.3 73.2 16.1 889 n/a 2_adp: 0.1232 0.1532 0.042 1.132 5.4 72.5 16.3 889 n/a 2_regHadp: 0.1232 0.1533 0.042 1.132 5.4 72.5 16.3 889 n/a 2_occ: 0.1226 0.1531 0.042 1.132 5.4 72.5 16.3 889 n/a 3_bss: 0.1233 0.1536 0.042 1.132 5.4 72.5 16.3 889 n/a 3_settarget: 0.1233 0.1536 0.042 1.132 5.4 72.5 16.3 889 n/a 3_updatecdl: 0.1233 0.1536 0.042 1.135 5.4 72.5 16.3 889 n/a 3_nqh: 0.1233 0.1536 0.042 1.135 5.4 72.5 16.3 889 n/a 3_sol: 0.1253 0.1532 0.042 1.135 5.4 68.2 15.4 866 n/a 3_weight: 0.1253 0.1532 0.042 1.135 5.4 68.2 15.4 866 n/a 3_xyzrec: 0.1243 0.1445 0.036 1.106 5.4 68.2 15.4 866 n/a 3_adp: 0.1238 0.1405 0.036 1.106 5.5 67.8 15.2 866 n/a 3_regHadp: 0.1238 0.1406 0.036 1.106 5.5 67.8 15.2 866 n/a 3_occ: 0.1231 0.1391 0.036 1.106 5.5 67.8 15.2 866 n/a 4_bss: 0.1227 0.1385 0.036 1.106 5.5 67.8 15.2 866 n/a 4_settarget: 0.1227 0.1385 0.036 1.106 5.5 67.8 15.2 866 n/a 4_updatecdl: 0.1227 0.1385 0.036 1.111 5.5 67.8 15.2 866 n/a 4_nqh: 0.1227 0.1385 0.036 1.111 5.5 67.8 15.2 866 n/a 4_sol: 0.1209 0.1372 0.036 1.111 5.5 67.8 15.0 865 n/a 4_weight: 0.1209 0.1372 0.036 1.111 5.5 67.8 15.0 865 n/a 4_xyzrec: 0.1207 0.1373 0.036 1.130 5.5 67.8 15.0 865 n/a 4_adp: 0.1200 0.1368 0.036 1.130 5.5 67.3 15.0 865 n/a 4_regHadp: 0.1200 0.1368 0.036 1.130 5.5 67.3 15.0 865 n/a 4_occ: 0.1197 0.1370 0.036 1.130 5.5 67.3 15.0 865 n/a 5_bss: 0.1196 0.1367 0.036 1.130 5.5 67.3 14.9 865 n/a 5_settarget: 0.1196 0.1367 0.036 1.130 5.5 67.3 14.9 865 n/a 5_updatecdl: 0.1196 0.1367 0.036 1.130 5.5 67.3 14.9 865 n/a 5_nqh: 0.1196 0.1367 0.036 1.130 5.5 67.3 14.9 865 n/a 5_sol: 0.1193 0.1360 0.036 1.130 5.5 67.3 15.0 879 n/a 5_weight: 0.1193 0.1360 0.036 1.130 5.5 67.3 15.0 879 n/a 5_xyzrec: 0.1197 0.1365 0.037 1.125 5.5 67.3 15.0 879 n/a 5_adp: 0.1202 0.1368 0.037 1.125 5.6 67.0 14.9 879 n/a 5_regHadp: 0.1202 0.1369 0.037 1.125 5.6 67.0 14.9 879 n/a 5_occ: 0.1201 0.1369 0.037 1.125 5.6 67.0 14.9 879 n/a 6_bss: 0.1199 0.1368 0.037 1.125 5.5 66.9 14.9 879 n/a 6_settarget: 0.1199 0.1368 0.037 1.125 5.5 66.9 14.9 879 n/a 6_updatecdl: 0.1199 0.1368 0.037 1.125 5.5 66.9 14.9 879 n/a 6_nqh: 0.1199 0.1368 0.037 1.125 5.5 66.9 14.9 879 n/a 6_sol: 0.1197 0.1360 0.037 1.125 5.5 66.9 14.9 890 n/a 6_weight: 0.1197 0.1360 0.037 1.125 5.5 66.9 14.9 890 n/a 6_xyzrec: 0.1199 0.1360 0.037 1.137 5.5 66.9 14.9 890 n/a 6_adp: 0.1204 0.1367 0.037 1.137 5.6 65.7 14.8 890 n/a 6_regHadp: 0.1204 0.1368 0.037 1.137 5.6 65.7 14.8 890 n/a 6_occ: 0.1202 0.1369 0.037 1.137 5.6 65.7 14.8 890 n/a 7_bss: 0.1201 0.1369 0.037 1.137 5.4 65.5 14.6 890 n/a 7_settarget: 0.1201 0.1369 0.037 1.137 5.4 65.5 14.6 890 n/a 7_updatecdl: 0.1201 0.1369 0.037 1.137 5.4 65.5 14.6 890 n/a 7_nqh: 0.1201 0.1369 0.037 1.137 5.4 65.5 14.6 890 n/a 7_sol: 0.1198 0.1360 0.037 1.137 5.4 65.5 14.7 911 n/a 7_weight: 0.1198 0.1360 0.037 1.137 5.4 65.5 14.7 911 n/a 7_xyzrec: 0.1203 0.1365 0.038 1.121 5.4 65.5 14.7 911 n/a 7_adp: 0.1203 0.1366 0.038 1.121 5.4 64.6 14.6 911 n/a 7_regHadp: 0.1203 0.1366 0.038 1.121 5.4 64.6 14.6 911 n/a 7_occ: 0.1201 0.1368 0.038 1.121 5.4 64.6 14.6 911 n/a 8_bss: 0.1192 0.1356 0.038 1.121 5.4 64.6 14.7 911 n/a 8_settarget: 0.1192 0.1356 0.038 1.121 5.4 64.6 14.7 911 n/a 8_updatecdl: 0.1192 0.1356 0.038 1.122 5.4 64.6 14.7 911 n/a 8_nqh: 0.1192 0.1356 0.038 1.122 5.4 64.6 14.7 911 n/a 8_sol: 0.1191 0.1348 0.038 1.122 5.4 64.6 14.7 910 n/a 8_weight: 0.1191 0.1348 0.038 1.122 5.4 64.6 14.7 910 n/a 8_xyzrec: 0.1195 0.1354 0.038 1.116 5.4 64.6 14.7 910 n/a 8_adp: 0.1197 0.1358 0.038 1.116 5.5 64.4 14.7 910 n/a 8_regHadp: 0.1197 0.1358 0.038 1.116 5.5 64.4 14.7 910 n/a 8_occ: 0.1196 0.1360 0.038 1.116 5.5 64.4 14.7 910 n/a 9_bss: 0.1194 0.1358 0.038 1.116 5.5 64.5 14.7 910 n/a 9_settarget: 0.1194 0.1358 0.038 1.116 5.5 64.5 14.7 910 n/a 9_updatecdl: 0.1194 0.1358 0.038 1.116 5.5 64.5 14.7 910 n/a 9_nqh: 0.1194 0.1358 0.038 1.116 5.5 64.5 14.7 910 n/a 9_sol: 0.1193 0.1344 0.038 1.116 5.5 64.5 14.6 904 n/a 9_weight: 0.1193 0.1344 0.038 1.116 5.5 64.5 14.6 904 n/a 9_xyzrec: 0.1196 0.1352 0.039 1.120 5.5 64.5 14.6 904 n/a 9_adp: 0.1195 0.1353 0.039 1.120 5.5 64.6 14.6 904 n/a 9_regHadp: 0.1195 0.1353 0.039 1.120 5.5 64.6 14.6 904 n/a 9_occ: 0.1193 0.1352 0.039 1.120 5.5 64.6 14.6 904 n/a 10_bss: 0.1192 0.1351 0.039 1.120 5.5 64.6 14.6 904 n/a 10_settarget: 0.1192 0.1351 0.039 1.120 5.5 64.6 14.6 904 n/a 10_updatecdl: 0.1192 0.1351 0.039 1.119 5.5 64.6 14.6 904 n/a 10_setrh: 0.1193 0.1351 0.039 1.119 5.5 64.6 14.6 904 n/a 10_nqh: 0.1193 0.1351 0.039 1.119 5.5 64.6 14.6 904 n/a 10_sol: 0.1192 0.1346 0.039 1.119 5.5 63.1 14.6 898 n/a 10_weight: 0.1192 0.1346 0.039 1.119 5.5 63.1 14.6 898 n/a 10_xyzrec: 0.1196 0.1350 0.039 1.151 5.5 63.1 14.6 898 n/a 10_adp: 0.1197 0.1353 0.039 1.151 5.5 62.1 14.6 898 n/a 10_regHadp: 0.1197 0.1353 0.039 1.151 5.5 62.1 14.6 898 n/a 10_occ: 0.1196 0.1352 0.039 1.151 5.5 62.1 14.6 898 n/a end: 0.1195 0.1351 0.039 1.151 5.5 62.1 14.5 898 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9424116_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9424116_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.8400 Refinement macro-cycles (run) : 12212.8300 Write final files (write_after_run_outputs) : 148.1600 Total : 12367.8300 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:23 PST -0800 (1736736203.51 s) Start R-work = 0.1798, R-free = 0.1912 Final R-work = 0.1195, R-free = 0.1351 =============================================================================== Job complete usr+sys time: 12628.63 seconds wall clock time: 211 minutes 31.55 seconds (12691.55 seconds total)