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_9137209.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9137209.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9137209.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.50, per 1000 atoms: 0.22 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: 2.818 distance_ideal: 2.720 ideal - model: -0.098 slack: 0.000 delta_slack: -0.098 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: 2.641 distance_ideal: 2.710 ideal - model: 0.069 slack: 0.000 delta_slack: 0.069 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: 1.17 Conformation dependent library (CDL) restraints added in 201.5 milliseconds Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.02: 640 1.02 - 1.24: 2597 1.24 - 1.47: 1446 1.47 - 1.70: 1224 1.70 - 1.93: 27 Bond restraints: 5934 Sorted by residual: bond pdb=" C LEU A 113 " pdb=" N VAL A 114 " ideal model delta sigma weight residual 1.329 1.076 0.253 1.13e-02 7.83e+03 5.01e+02 bond pdb=" NH1 ARG B 100 " pdb="HH11 ARG B 100 " ideal model delta sigma weight residual 0.860 1.268 -0.408 2.00e-02 2.50e+03 4.15e+02 bond pdb=" C LYS A 133 " pdb=" N ILE A 134 " ideal model delta sigma weight residual 1.324 1.497 -0.173 8.60e-03 1.35e+04 4.05e+02 bond pdb=" N HIS A 179 " pdb=" H HIS A 179 " ideal model delta sigma weight residual 0.860 1.260 -0.400 2.00e-02 2.50e+03 4.01e+02 bond pdb=" CD1 TYR A 192 " pdb=" HD1 TYR A 192 " ideal model delta sigma weight residual 0.930 1.323 -0.393 2.00e-02 2.50e+03 3.87e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 5957 4.49 - 8.98: 3535 8.98 - 13.47: 1157 13.47 - 17.96: 151 17.96 - 22.46: 10 Bond angle restraints: 10810 Sorted by residual: angle pdb=" OD1 ASN B 123 " pdb=" CG ASN B 123 " pdb=" ND2 ASN B 123 " ideal model delta sigma weight residual 122.60 141.91 -19.31 1.00e+00 1.00e+00 3.73e+02 angle pdb=" O ILE B 191 " pdb=" C ILE B 191 " pdb=" N TYR B 192 " ideal model delta sigma weight residual 123.18 108.17 15.01 1.05e+00 9.07e-01 2.04e+02 angle pdb=" CD2 HIS A 96 " pdb=" NE2 HIS A 96 " pdb=" CE1 HIS A 96 " ideal model delta sigma weight residual 109.00 122.91 -13.91 1.00e+00 1.00e+00 1.93e+02 angle pdb=" CA PHE B 164 " pdb=" CB PHE B 164 " pdb=" CG PHE B 164 " ideal model delta sigma weight residual 113.80 127.25 -13.45 1.00e+00 1.00e+00 1.81e+02 angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.65 131.38 -9.73 7.30e-01 1.88e+00 1.78e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 1847 17.20 - 34.40: 136 34.40 - 51.60: 39 51.60 - 68.80: 23 68.80 - 86.00: 5 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 -148.64 -31.36 0 5.00e+00 4.00e-02 3.93e+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 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ILE B 101 " pdb=" C ILE B 101 " pdb=" N VAL B 102 " pdb=" CA VAL B 102 " ideal model delta harmonic sigma weight residual 180.00 154.98 25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.234: 202 0.234 - 0.467: 172 0.467 - 0.699: 84 0.699 - 0.932: 29 0.932 - 1.165: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 102 " pdb=" N VAL B 102 " pdb=" C VAL B 102 " pdb=" CB VAL B 102 " both_signs ideal model delta sigma weight residual False 2.44 3.61 -1.17 2.00e-01 2.50e+01 3.39e+01 chirality pdb=" CA VAL B 60 " pdb=" N VAL B 60 " pdb=" C VAL B 60 " pdb=" CB VAL B 60 " both_signs ideal model delta sigma weight residual False 2.44 1.36 1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" CA VAL A 173 " pdb=" N VAL A 173 " pdb=" C VAL A 173 " pdb=" CB VAL A 173 " both_signs ideal model delta sigma weight residual False 2.44 1.37 1.07 2.00e-01 2.50e+01 2.89e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " 0.027 2.00e-02 2.50e+03 7.22e-02 1.57e+02 pdb=" CG TYR A 192 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " -0.082 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " 0.088 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " 0.107 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " -0.075 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " -0.086 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.092 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " 0.053 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " -0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 127 " -0.062 2.00e-02 2.50e+03 7.09e-02 1.51e+02 pdb=" CG PHE B 127 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE B 127 " 0.107 2.00e-02 2.50e+03 pdb=" CD2 PHE B 127 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE B 127 " 0.106 2.00e-02 2.50e+03 pdb=" CE2 PHE B 127 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE B 127 " 0.041 2.00e-02 2.50e+03 pdb=" HD1 PHE B 127 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE B 127 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE B 127 " -0.040 2.00e-02 2.50e+03 pdb=" HE2 PHE B 127 " 0.084 2.00e-02 2.50e+03 pdb=" HZ PHE B 127 " -0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " -0.102 2.00e-02 2.50e+03 6.86e-02 1.41e+02 pdb=" CG PHE A 119 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.103 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.056 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.083 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.59: 25 1.59 - 2.34: 2194 2.34 - 3.10: 22106 3.10 - 3.85: 33061 3.85 - 4.60: 52869 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110255 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.841 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.860 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 1.020 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.143 2.620 ... (remaining 110250 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_9137209_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= 0.2031 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.298826 | | target function (ml) not normalized (work): 805225.927574 | | target function (ml) not normalized (free): 16524.498660 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2124 0.1903 6.6979 6.305| | 2: 2.94 - 2.33 1.00 7339 128 0.1617 0.1624 5.5309 5.5666| | 3: 2.33 - 2.04 0.96 6939 150 0.1630 0.1480 5.1388 5.1062| | 4: 2.04 - 1.85 1.00 7170 155 0.1758 0.1700 4.9516 5.0823| | 5: 1.85 - 1.72 0.99 7113 159 0.1930 0.1689 4.7904 4.772| | 6: 1.72 - 1.62 0.99 7102 142 0.1961 0.1905 4.6577 4.6681| | 7: 1.62 - 1.54 0.99 7104 148 0.2020 0.1748 4.5623 4.6002| | 8: 1.54 - 1.47 0.96 6798 152 0.2021 0.2000 4.4651 4.3781| | 9: 1.47 - 1.41 0.98 6938 155 0.2087 0.2107 4.383 4.4347| | 10: 1.41 - 1.36 0.99 7022 150 0.2133 0.2264 4.3215 4.3856| | 11: 1.36 - 1.32 0.99 6997 151 0.2107 0.2225 4.2339 4.2697| | 12: 1.32 - 1.28 0.98 6976 149 0.2086 0.1937 4.1717 4.2192| | 13: 1.28 - 1.25 0.98 6907 166 0.2012 0.1992 4.116 4.0941| | 14: 1.25 - 1.22 0.98 7015 113 0.2084 0.2224 4.076 4.2766| | 15: 1.22 - 1.19 0.98 6957 137 0.2110 0.2038 4.045 4.0244| | 16: 1.19 - 1.17 0.93 6604 132 0.2140 0.2184 4.015 4.0283| | 17: 1.17 - 1.14 0.98 6941 135 0.2156 0.1775 3.9531 3.9453| | 18: 1.14 - 1.12 0.98 6875 142 0.2240 0.2401 3.9312 3.9235| | 19: 1.12 - 1.10 0.97 6949 106 0.2271 0.2672 3.866 4.0025| | 20: 1.10 - 1.08 0.97 6884 147 0.2324 0.2451 3.831 3.8926| | 21: 1.08 - 1.07 0.97 6852 152 0.2417 0.2759 3.7954 3.8423| | 22: 1.07 - 1.05 0.97 6838 135 0.2579 0.2405 3.7549 3.7318| | 23: 1.05 - 1.03 0.97 6829 159 0.2710 0.2764 3.7242 3.833| | 24: 1.03 - 1.02 0.96 6785 133 0.2878 0.3010 3.7052 3.8139| | 25: 1.02 - 1.01 0.93 6552 130 0.3044 0.2936 3.6677 3.7356| | 26: 1.01 - 0.99 0.96 6767 158 0.3185 0.3136 3.6289 3.6263| | 27: 0.99 - 0.98 0.94 6648 131 0.3419 0.3367 3.6415 3.6318| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.12 0.91 0.98 34588.70| | 2: 2.94 - 2.33 7339 128 0.86 20.93 1.09 1.03 14732.13| | 3: 2.33 - 2.04 6939 150 0.93 12.35 1.11 1.06 4060.63| | 4: 2.04 - 1.85 7170 155 0.93 13.33 1.12 1.07 2722.69| | 5: 1.85 - 1.72 7113 159 0.91 15.43 1.12 1.07 2019.92| | 6: 1.72 - 1.62 7102 142 0.90 16.19 1.11 1.07 1536.01| | 7: 1.62 - 1.54 7104 148 0.90 16.79 1.11 1.07 1212.66| | 8: 1.54 - 1.47 6798 152 0.90 16.88 1.10 1.07 1004.04| | 9: 1.47 - 1.41 6938 155 0.89 18.35 1.11 1.07 922.48| | 10: 1.41 - 1.36 7022 150 0.87 19.68 1.09 1.06 838.58| | 11: 1.36 - 1.32 6997 151 0.87 19.99 1.08 1.06 738.55| | 12: 1.32 - 1.28 6976 149 0.88 19.43 1.08 1.05 631.70| | 13: 1.28 - 1.25 6907 166 0.88 18.93 1.07 1.06 569.28| | 14: 1.25 - 1.22 7015 113 0.87 19.92 1.08 1.05 540.64| | 15: 1.22 - 1.19 6957 137 0.87 20.03 1.08 1.06 508.36| | 16: 1.19 - 1.17 6604 132 0.88 19.67 1.07 1.05 465.73| | 17: 1.17 - 1.14 6941 135 0.87 20.22 1.08 1.04 421.16| | 18: 1.14 - 1.12 6875 142 0.86 21.26 1.09 0.99 392.61| | 19: 1.12 - 1.10 6949 106 0.85 22.97 1.08 0.98 393.89| | 20: 1.10 - 1.08 6884 147 0.84 23.84 1.06 0.96 368.48| | 21: 1.08 - 1.07 6852 152 0.83 24.64 1.06 0.97 356.73| | 22: 1.07 - 1.05 6838 135 0.81 26.22 1.05 0.97 335.88| | 23: 1.05 - 1.03 6829 159 0.79 28.25 1.06 0.96 343.37| | 24: 1.03 - 1.02 6785 133 0.77 30.20 1.05 0.97 347.39| | 25: 1.02 - 1.01 6552 130 0.76 31.72 1.03 0.92 326.45| | 26: 1.01 - 0.99 6767 158 0.74 33.12 1.03 0.90 305.80| | 27: 0.99 - 0.98 6648 131 0.74 33.47 1.03 0.87 283.48| |alpha: min = 0.87 max = 1.07 mean = 1.02| |beta: min = 283.48 max = 34588.70 mean = 2752.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.54| |phase err.(test): min = 0.00 max = 89.79 mean = 21.60| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.271 2950 Z= 5.362 Angle : 5.083 19.310 4018 Z= 3.615 Chirality : 0.391 1.165 492 Planarity : 0.033 0.117 512 Dihedral : 12.782 85.998 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.89 % Favored : 95.34 % Rotamer: Outliers : 0.65 % Allowed : 3.87 % Favored : 95.48 % Cbeta Deviations : 29.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.39), residues: 386 helix: -3.02 (0.30), residues: 146 sheet: -1.28 (0.48), residues: 86 loop : 0.18 (0.52), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.140 0.030 ARG B 143 TYR 0.118 0.040 TYR B 67 PHE 0.096 0.034 PHE B 164 TRP 0.102 0.038 TRP A 139 HIS 0.103 0.043 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2031 r_free= 0.1963 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.298826 | | target function (ml) not normalized (work): 805225.927574 | | target function (ml) not normalized (free): 16524.498660 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2029 0.2031 0.1963 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2029 0.2031 0.1963 n_refl.: 191155 remove outliers: r(all,work,free)=0.2029 0.2031 0.1963 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2031 0.2032 0.1964 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1798 0.1796 0.1901 n_refl.: 191145 remove outliers: r(all,work,free)=0.1796 0.1794 0.1900 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4079 402.814 291.017 0.423 0.933 0.303 13.296-10.522 99.01 99 1 0.2490 528.187 520.604 0.769 0.933 0.253 10.503-8.327 98.90 177 3 0.2474 564.205 559.079 0.948 0.933 0.227 8.318-6.595 100.00 360 8 0.2451 414.736 403.557 0.951 0.933 0.169 6.588-5.215 100.00 711 7 0.2295 381.101 366.051 0.936 0.932 0.133 5.214-4.128 98.38 1367 28 0.1492 557.435 550.602 1.047 0.932 0.070 4.126-3.266 94.74 2603 46 0.1319 508.132 499.545 1.118 0.931 0.023 3.266-2.585 99.86 5447 97 0.1448 342.774 337.248 1.095 0.929 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 254.319 1.106 0.926 0.000 2.046-1.619 99.39 21536 464 0.1607 153.054 149.918 1.131 0.920 0.000 1.619-1.281 98.00 42464 925 0.1911 82.395 80.158 1.124 0.911 0.000 1.281-0.980 96.53 101826 2055 0.2315 44.202 41.685 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=0.0160 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1794 r_free=0.1900 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1794 r_free=0.1900 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.026229 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 576.455069 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 0.1265 0.1493 0.0228 0.038 1.1 11.2 0.0 0.3 0 11.513 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.65 14.93 2.28 1.119 13.121 576.455 0.018 12.91 15.59 2.68 1.225 13.338 576.455 0.017 Individual atomic B min max mean iso aniso Overall: 5.23 73.05 15.00 1.40 435 3274 Protein: 5.23 40.55 11.01 1.40 0 2902 Water: 6.37 73.05 29.38 N/A 435 370 Other: 16.08 29.75 22.92 N/A 0 2 Chain A: 5.33 59.95 13.04 N/A 0 1626 Chain B: 5.23 73.05 12.77 N/A 0 1648 Chain S: 11.67 63.65 30.78 N/A 435 0 Histogram: Values Number of atoms 5.23 - 12.01 2171 12.01 - 18.79 635 18.79 - 25.58 316 25.58 - 32.36 269 32.36 - 39.14 151 39.14 - 45.92 103 45.92 - 52.71 41 52.71 - 59.49 18 59.49 - 66.27 4 66.27 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1291 r_free=0.1559 r_work=0.1290 r_free=0.1555 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1290 r_free = 0.1555 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 = 0.1276 r_free = 0.1543 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1276 r_free= 0.1543 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015466 | | target function (ls_wunit_k1) not normalized (work): 2896.680054 | | target function (ls_wunit_k1) not normalized (free): 114.577901 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1281 0.1276 0.1543 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1465 0.1462 0.1624 n_refl.: 191137 remove outliers: r(all,work,free)=0.1465 0.1462 0.1624 n_refl.: 191137 overall B=0.16 to atoms: r(all,work,free)=0.1488 0.1485 0.1633 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1276 0.1270 0.1536 n_refl.: 191137 remove outliers: r(all,work,free)=0.1276 0.1270 0.1536 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3605 402.814 381.437 0.487 0.963 0.275 13.296-10.522 99.01 99 1 0.2110 528.187 522.279 0.739 0.965 0.239 10.503-8.327 98.90 177 3 0.1728 564.205 562.809 0.889 0.965 0.193 8.318-6.595 100.00 360 8 0.1729 414.736 411.886 0.908 0.964 0.155 6.588-5.215 100.00 711 7 0.1548 381.101 373.234 0.887 0.965 0.150 5.214-4.128 98.38 1367 28 0.0905 557.435 554.921 0.975 0.965 0.049 4.126-3.266 94.74 2603 46 0.0830 508.132 504.253 1.042 0.966 0.014 3.266-2.585 99.86 5447 97 0.0919 342.774 340.312 1.024 0.965 0.000 2.585-2.046 97.45 10613 204 0.0947 258.603 256.369 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1081 153.054 151.403 1.055 0.966 0.000 1.619-1.281 98.00 42464 925 0.1272 82.395 81.429 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.173 1.024 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0353 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1536 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1270 r_free=0.1536 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1270 r_free=0.1536 | n_water=805 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1275 r_free=0.1541 | n_water=795 | time (s): 98.570 (total time: 101.060) Filter (q & B) r_work=0.1275 r_free=0.1542 | n_water=791 | time (s): 5.160 (total time: 106.220) Compute maps r_work=0.1275 r_free=0.1542 | n_water=791 | time (s): 2.350 (total time: 108.570) Filter (map) r_work=0.1299 r_free=0.1525 | n_water=664 | time (s): 4.700 (total time: 113.270) Find peaks r_work=0.1299 r_free=0.1525 | n_water=664 | time (s): 0.760 (total time: 114.030) Add new water r_work=0.1321 r_free=0.1557 | n_water=964 | time (s): 5.020 (total time: 119.050) Refine new water occ: r_work=0.1280 r_free=0.1499 adp: r_work=0.1268 r_free=0.1495 occ: r_work=0.1272 r_free=0.1493 adp: r_work=0.1264 r_free=0.1493 occ: r_work=0.1267 r_free=0.1490 adp: r_work=0.1261 r_free=0.1491 ADP+occupancy (water only), MIN, final r_work=0.1261 r_free=0.1491 r_work=0.1261 r_free=0.1491 | n_water=964 | time (s): 71.000 (total time: 190.050) Filter (q & B) r_work=0.1265 r_free=0.1494 | n_water=895 | time (s): 5.220 (total time: 195.270) Filter (dist only) r_work=0.1265 r_free=0.1493 | n_water=894 | time (s): 112.810 (total time: 308.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.286589 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 592.974188 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 0.1516 0.0263 0.041 1.1 18.0 0.0 0.0 0 11.643 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.16 2.63 2.041 15.099 592.974 0.015 12.33 15.08 2.75 2.421 15.145 592.974 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 68.21 16.17 1.20 526 3272 Protein: 5.39 40.89 10.98 1.20 0 2902 Water: 6.61 68.21 33.00 N/A 526 368 Other: 16.32 32.15 24.24 N/A 0 2 Chain A: 5.53 55.72 12.99 N/A 0 1624 Chain B: 5.39 68.21 12.82 N/A 0 1648 Chain S: 11.75 63.77 36.47 N/A 526 0 Histogram: Values Number of atoms 5.39 - 11.68 2062 11.68 - 17.96 712 17.96 - 24.24 264 24.24 - 30.52 212 30.52 - 36.80 194 36.80 - 43.08 177 43.08 - 49.36 97 49.36 - 55.65 58 55.65 - 61.93 18 61.93 - 68.21 4 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1508 r_work=0.1234 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1509 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 = 0.1503 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.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1503 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013422 | | target function (ls_wunit_k1) not normalized (work): 2513.912747 | | target function (ls_wunit_k1) not normalized (free): 99.865814 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1503 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1432 0.1430 0.1586 n_refl.: 191137 remove outliers: r(all,work,free)=0.1432 0.1430 0.1586 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1429 0.1427 0.1585 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1511 n_refl.: 191137 remove outliers: r(all,work,free)=0.1238 0.1233 0.1511 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3297 402.814 376.588 0.495 0.963 0.281 13.296-10.522 99.01 99 1 0.1893 528.187 519.461 0.749 0.964 0.222 10.503-8.327 98.90 177 3 0.1395 564.205 567.236 0.919 0.964 0.169 8.318-6.595 100.00 360 8 0.1566 414.736 413.864 0.935 0.964 0.150 6.588-5.215 100.00 711 7 0.1350 381.101 376.488 0.914 0.964 0.150 5.214-4.128 98.38 1367 28 0.0828 557.435 556.093 0.993 0.964 0.080 4.126-3.266 94.74 2603 46 0.0757 508.132 505.366 1.059 0.964 0.014 3.266-2.585 99.86 5447 97 0.0857 342.774 341.400 1.046 0.963 0.000 2.585-2.046 97.45 10613 204 0.0900 258.603 256.776 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.626 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.346 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.218 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0519 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1511 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1511 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1511 | n_water=894 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1235 r_free=0.1516 | n_water=886 | time (s): 115.390 (total time: 117.810) Filter (q & B) r_work=0.1236 r_free=0.1517 | n_water=883 | time (s): 5.390 (total time: 123.200) Compute maps r_work=0.1236 r_free=0.1517 | n_water=883 | time (s): 2.180 (total time: 125.380) Filter (map) r_work=0.1274 r_free=0.1527 | n_water=689 | time (s): 5.120 (total time: 130.500) Find peaks r_work=0.1274 r_free=0.1527 | n_water=689 | time (s): 0.640 (total time: 131.140) Add new water r_work=0.1297 r_free=0.1561 | n_water=1016 | time (s): 5.340 (total time: 136.480) Refine new water occ: r_work=0.1251 r_free=0.1514 adp: r_work=0.1252 r_free=0.1516 occ: r_work=0.1247 r_free=0.1510 adp: r_work=0.1247 r_free=0.1512 occ: r_work=0.1244 r_free=0.1507 adp: r_work=0.1244 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1509 r_work=0.1244 r_free=0.1509 | n_water=1016 | time (s): 261.660 (total time: 398.140) Filter (q & B) r_work=0.1249 r_free=0.1510 | n_water=879 | time (s): 4.450 (total time: 402.590) Filter (dist only) r_work=0.1249 r_free=0.1510 | n_water=878 | time (s): 108.830 (total time: 511.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.743683 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.606045 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 0.1237 0.1430 0.0193 0.036 1.1 6.6 0.0 0.0 0 0.872 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.30 1.93 1.929 14.540 16.606 3.939 12.30 13.88 1.58 2.185 14.457 16.606 3.896 Individual atomic B min max mean iso aniso Overall: 5.52 67.84 15.22 1.07 511 3271 Protein: 5.52 37.45 10.76 1.07 0 2902 Water: 6.67 67.84 29.93 N/A 511 367 Other: 14.17 28.16 21.16 N/A 0 2 Chain A: 5.55 54.95 12.78 N/A 0 1624 Chain B: 5.52 67.84 12.56 N/A 0 1647 Chain S: 14.33 62.28 31.51 N/A 511 0 Histogram: Values Number of atoms 5.52 - 11.76 2130 11.76 - 17.99 685 17.99 - 24.22 300 24.22 - 30.45 235 30.45 - 36.68 186 36.68 - 42.92 147 42.92 - 49.15 68 49.15 - 55.38 24 55.38 - 61.61 5 61.61 - 67.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1388 r_work=0.1231 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1389 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1392 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890257 | | target function (ml) not normalized (work): 728629.590072 | | target function (ml) not normalized (free): 15218.952739 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1225 0.1391 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1440 0.1439 0.1483 n_refl.: 191137 remove outliers: r(all,work,free)=0.1440 0.1439 0.1483 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1434 0.1433 0.1479 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1222 0.1383 n_refl.: 191137 remove outliers: r(all,work,free)=0.1224 0.1221 0.1383 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 94.06 92 3 0.3728 398.008 361.998 0.424 0.946 0.246 13.296-10.522 97.03 97 1 0.2241 531.410 502.022 0.705 0.947 0.213 10.503-8.327 97.80 175 3 0.1914 554.286 558.513 0.883 0.947 0.172 8.318-6.595 100.00 360 8 0.2135 414.736 409.603 0.898 0.947 0.135 6.588-5.215 100.00 711 7 0.1844 381.101 370.637 0.889 0.947 0.130 5.214-4.128 98.38 1367 28 0.1177 557.435 552.249 0.971 0.947 0.080 4.126-3.266 94.74 2603 46 0.1088 508.132 501.144 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1083 342.774 338.968 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0957 258.603 255.792 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0969 153.054 151.419 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.501 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.326 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0974 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1221 r_free=0.1383 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1221 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1383 | n_water=878 | time (s): 2.250 (total time: 2.250) Filter (dist) r_work=0.1221 r_free=0.1383 | n_water=878 | time (s): 102.470 (total time: 104.720) Filter (q & B) r_work=0.1222 r_free=0.1378 | n_water=864 | time (s): 5.470 (total time: 110.190) Compute maps r_work=0.1222 r_free=0.1378 | n_water=864 | time (s): 2.010 (total time: 112.200) Filter (map) r_work=0.1243 r_free=0.1382 | n_water=726 | time (s): 5.650 (total time: 117.850) Find peaks r_work=0.1243 r_free=0.1382 | n_water=726 | time (s): 0.690 (total time: 118.540) Add new water r_work=0.1257 r_free=0.1400 | n_water=974 | time (s): 4.070 (total time: 122.610) Refine new water occ: r_work=0.1210 r_free=0.1364 adp: r_work=0.1203 r_free=0.1358 occ: r_work=0.1200 r_free=0.1359 adp: r_work=0.1200 r_free=0.1359 occ: r_work=0.1200 r_free=0.1359 adp: r_work=0.1200 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1359 r_work=0.1200 r_free=0.1359 | n_water=974 | time (s): 185.440 (total time: 308.050) Filter (q & B) r_work=0.1205 r_free=0.1371 | n_water=855 | time (s): 4.470 (total time: 312.520) Filter (dist only) r_work=0.1205 r_free=0.1370 | n_water=854 | time (s): 113.070 (total time: 425.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.593702 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.322729 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 0.1204 0.1371 0.0167 0.033 1.1 6.0 0.0 0.0 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.71 1.67 1.840 14.120 16.323 3.874 11.98 13.70 1.72 1.990 14.068 16.323 3.864 Individual atomic B min max mean iso aniso Overall: 5.48 67.32 14.78 1.00 487 3271 Protein: 5.48 33.64 10.65 1.00 0 2902 Water: 5.92 67.32 28.78 N/A 487 367 Other: 13.92 26.94 20.43 N/A 0 2 Chain A: 5.57 53.59 12.62 N/A 0 1624 Chain B: 5.48 67.32 12.43 N/A 0 1647 Chain S: 5.92 62.11 29.90 N/A 487 0 Histogram: Values Number of atoms 5.48 - 11.66 2109 11.66 - 17.85 734 17.85 - 24.03 326 24.03 - 30.22 232 30.22 - 36.40 139 36.40 - 42.58 131 42.58 - 48.77 57 48.77 - 54.95 23 54.95 - 61.14 5 61.14 - 67.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1370 r_work=0.1198 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1370 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1369 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862187 | | target function (ml) not normalized (work): 723352.774101 | | target function (ml) not normalized (free): 15132.719676 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1369 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1424 0.1424 0.1475 n_refl.: 191132 remove outliers: r(all,work,free)=0.1424 0.1424 0.1475 n_refl.: 191132 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1416 0.1470 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1368 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1194 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 94.06 92 3 0.3757 360.364 324.906 0.408 0.948 0.240 13.296-10.522 97.03 97 1 0.2374 481.150 462.670 0.709 0.949 0.210 10.503-8.327 97.80 175 3 0.2058 501.862 496.620 0.856 0.950 0.168 8.318-6.595 100.00 360 8 0.2212 375.510 368.664 0.888 0.949 0.120 6.588-5.215 100.00 711 7 0.1926 345.056 334.865 0.882 0.949 0.094 5.214-4.128 98.38 1367 28 0.1206 504.713 499.960 0.969 0.949 0.039 4.126-3.266 94.74 2603 46 0.1120 460.073 453.700 1.033 0.950 0.000 3.266-2.585 99.86 5447 97 0.1084 310.354 306.984 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0937 234.144 231.694 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0910 138.578 137.265 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.0983 74.603 73.894 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1658 40.021 38.363 1.043 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1148 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1368 | n_water=854 | time (s): 3.120 (total time: 3.120) Filter (dist) r_work=0.1194 r_free=0.1368 | n_water=854 | time (s): 112.850 (total time: 115.970) Filter (q & B) r_work=0.1195 r_free=0.1366 | n_water=844 | time (s): 5.590 (total time: 121.560) Compute maps r_work=0.1195 r_free=0.1366 | n_water=844 | time (s): 2.340 (total time: 123.900) Filter (map) r_work=0.1216 r_free=0.1359 | n_water=728 | time (s): 4.830 (total time: 128.730) Find peaks r_work=0.1216 r_free=0.1359 | n_water=728 | time (s): 0.580 (total time: 129.310) Add new water r_work=0.1228 r_free=0.1373 | n_water=973 | time (s): 3.820 (total time: 133.130) Refine new water occ: r_work=0.1190 r_free=0.1347 adp: r_work=0.1190 r_free=0.1346 occ: r_work=0.1188 r_free=0.1348 adp: r_work=0.1187 r_free=0.1347 occ: r_work=0.1186 r_free=0.1349 adp: r_work=0.1185 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1348 r_work=0.1185 r_free=0.1348 | n_water=973 | time (s): 212.860 (total time: 345.990) Filter (q & B) r_work=0.1189 r_free=0.1352 | n_water=893 | time (s): 4.430 (total time: 350.420) Filter (dist only) r_work=0.1189 r_free=0.1350 | n_water=892 | time (s): 118.080 (total time: 468.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524144 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.038301 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1360 0.0167 0.036 1.1 9.4 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.60 1.67 1.791 14.124 15.038 3.762 11.97 13.64 1.67 1.831 14.107 15.038 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 67.10 14.96 0.96 527 3269 Protein: 5.58 32.52 10.60 0.96 0 2902 Water: 5.92 67.10 29.12 N/A 527 365 Other: 13.75 26.14 19.95 N/A 0 2 Chain A: 5.58 53.07 12.53 N/A 0 1623 Chain B: 5.58 67.10 12.35 N/A 0 1646 Chain S: 5.92 62.03 30.58 N/A 527 0 Histogram: Values Number of atoms 5.58 - 11.73 2149 11.73 - 17.88 712 17.88 - 24.03 299 24.03 - 30.19 237 30.19 - 36.34 169 36.34 - 42.49 139 42.49 - 48.64 62 48.64 - 54.79 22 54.79 - 60.95 4 60.95 - 67.10 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1365 r_work=0.1197 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1365 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1368 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759664 | | target function (ml) not normalized (work): 704151.300521 | | target function (ml) not normalized (free): 14748.637143 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1367 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1417 0.1416 0.1484 n_refl.: 191132 remove outliers: r(all,work,free)=0.1417 0.1416 0.1484 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1410 0.1409 0.1479 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1365 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1195 0.1365 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3688 355.877 324.793 0.399 0.949 0.227 13.296-10.522 97.03 97 1 0.2399 481.150 460.568 0.691 0.951 0.158 10.503-8.327 97.80 175 3 0.2137 501.862 494.318 0.857 0.951 0.133 8.318-6.595 100.00 360 8 0.2179 375.510 369.988 0.889 0.951 0.115 6.588-5.215 100.00 711 7 0.1882 345.056 335.310 0.883 0.951 0.084 5.214-4.128 98.38 1367 28 0.1193 504.713 500.092 0.969 0.951 0.034 4.126-3.266 94.74 2603 46 0.1128 460.073 453.687 1.033 0.951 0.005 3.266-2.585 99.86 5447 97 0.1099 310.354 306.956 1.018 0.950 0.000 2.585-2.046 97.45 10613 204 0.0948 234.144 231.607 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0915 138.578 137.256 1.055 0.948 0.000 1.619-1.281 98.00 42464 925 0.0975 74.603 73.893 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.021 38.353 1.042 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1269 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1365 | n_water=892 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1195 r_free=0.1365 | n_water=892 | time (s): 120.260 (total time: 122.790) Filter (q & B) r_work=0.1195 r_free=0.1365 | n_water=878 | time (s): 5.160 (total time: 127.950) Compute maps r_work=0.1195 r_free=0.1365 | n_water=878 | time (s): 1.930 (total time: 129.880) Filter (map) r_work=0.1219 r_free=0.1373 | n_water=743 | time (s): 4.220 (total time: 134.100) Find peaks r_work=0.1219 r_free=0.1373 | n_water=743 | time (s): 0.840 (total time: 134.940) Add new water r_work=0.1229 r_free=0.1381 | n_water=985 | time (s): 5.080 (total time: 140.020) Refine new water occ: r_work=0.1192 r_free=0.1351 adp: r_work=0.1192 r_free=0.1351 occ: r_work=0.1190 r_free=0.1350 adp: r_work=0.1190 r_free=0.1350 occ: r_work=0.1188 r_free=0.1349 adp: r_work=0.1188 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1349 r_work=0.1188 r_free=0.1349 | n_water=985 | time (s): 256.160 (total time: 396.180) Filter (q & B) r_work=0.1192 r_free=0.1359 | n_water=908 | time (s): 4.820 (total time: 401.000) Filter (dist only) r_work=0.1192 r_free=0.1358 | n_water=907 | time (s): 116.230 (total time: 517.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558751 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.467244 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 0.1355 0.0161 0.037 1.1 8.4 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.55 1.61 1.767 14.079 14.467 3.760 11.99 13.59 1.60 1.926 14.025 14.467 3.758 Individual atomic B min max mean iso aniso Overall: 5.57 65.97 14.88 0.90 542 3269 Protein: 5.57 29.42 10.48 0.90 0 2902 Water: 5.97 65.97 28.92 N/A 542 365 Other: 13.84 23.23 18.53 N/A 0 2 Chain A: 5.63 51.68 12.37 N/A 0 1623 Chain B: 5.57 65.97 12.21 N/A 0 1646 Chain S: 5.97 61.70 30.47 N/A 542 0 Histogram: Values Number of atoms 5.57 - 11.61 2117 11.61 - 17.65 771 17.65 - 23.69 278 23.69 - 29.73 228 29.73 - 35.77 179 35.77 - 41.81 139 41.81 - 47.85 64 47.85 - 53.89 28 53.89 - 59.93 4 59.93 - 65.97 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1359 r_work=0.1200 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1361 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757312 | | target function (ml) not normalized (work): 703706.934214 | | target function (ml) not normalized (free): 14735.749058 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1489 n_refl.: 191131 remove outliers: r(all,work,free)=0.1415 0.1414 0.1489 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1407 0.1406 0.1483 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3780 355.877 320.239 0.390 0.949 0.222 13.296-10.522 97.03 97 1 0.2377 481.150 461.610 0.691 0.950 0.158 10.503-8.327 97.80 175 3 0.2121 501.862 494.875 0.860 0.950 0.121 8.318-6.595 100.00 360 8 0.2168 375.510 370.270 0.886 0.950 0.105 6.588-5.215 100.00 711 7 0.1895 345.056 335.717 0.886 0.950 0.100 5.214-4.128 98.38 1367 28 0.1198 504.713 499.817 0.971 0.950 0.034 4.126-3.266 94.74 2603 46 0.1132 460.073 453.455 1.035 0.951 0.000 3.266-2.585 99.86 5447 97 0.1108 310.354 306.858 1.020 0.950 0.000 2.585-2.046 97.45 10613 204 0.0957 234.144 231.597 1.032 0.950 0.000 2.046-1.619 99.39 21536 464 0.0912 138.578 137.271 1.055 0.949 0.000 1.619-1.281 98.00 42464 925 0.0970 74.603 73.895 1.052 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.021 38.352 1.040 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1360 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1361 | n_water=907 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1196 r_free=0.1361 | n_water=907 | time (s): 111.400 (total time: 114.050) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=899 | time (s): 4.760 (total time: 118.810) Compute maps r_work=0.1196 r_free=0.1362 | n_water=899 | time (s): 2.150 (total time: 120.960) Filter (map) r_work=0.1218 r_free=0.1364 | n_water=779 | time (s): 5.680 (total time: 126.640) Find peaks r_work=0.1218 r_free=0.1364 | n_water=779 | time (s): 0.700 (total time: 127.340) Add new water r_work=0.1227 r_free=0.1376 | n_water=991 | time (s): 3.980 (total time: 131.320) Refine new water occ: r_work=0.1194 r_free=0.1346 adp: r_work=0.1195 r_free=0.1345 occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1192 r_free=0.1345 occ: r_work=0.1190 r_free=0.1345 adp: r_work=0.1190 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1344 r_work=0.1190 r_free=0.1344 | n_water=991 | time (s): 236.680 (total time: 368.000) Filter (q & B) r_work=0.1194 r_free=0.1353 | n_water=916 | time (s): 4.530 (total time: 372.530) Filter (dist only) r_work=0.1194 r_free=0.1353 | n_water=914 | time (s): 117.580 (total time: 490.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.557759 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.442484 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 0.1361 0.0164 0.037 1.1 9.5 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.61 1.64 1.718 13.942 14.442 3.759 11.98 13.62 1.64 1.768 13.916 14.442 3.756 Individual atomic B min max mean iso aniso Overall: 5.59 64.85 14.82 0.88 549 3269 Protein: 5.59 28.70 10.43 0.88 0 2902 Water: 6.04 64.85 28.76 N/A 549 365 Other: 13.86 21.96 17.91 N/A 0 2 Chain A: 5.63 51.33 12.28 N/A 0 1623 Chain B: 5.59 64.85 12.12 N/A 0 1646 Chain S: 6.04 61.27 30.42 N/A 549 0 Histogram: Values Number of atoms 5.59 - 11.51 2095 11.51 - 17.44 786 17.44 - 23.37 278 23.37 - 29.29 234 29.29 - 35.22 176 35.22 - 41.14 136 41.14 - 47.07 72 47.07 - 53.00 34 53.00 - 58.92 4 58.92 - 64.85 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1362 r_work=0.1199 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1362 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755281 | | target function (ml) not normalized (work): 703326.626494 | | target function (ml) not normalized (free): 14735.471546 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1362 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1481 n_refl.: 191131 remove outliers: r(all,work,free)=0.1415 0.1414 0.1481 n_refl.: 191131 overall B=-0.23 to atoms: r(all,work,free)=0.1377 0.1376 0.1461 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3753 356.641 314.798 0.388 0.947 0.204 13.296-10.522 97.03 97 1 0.2377 481.150 462.375 0.706 0.949 0.142 10.503-8.327 97.80 175 3 0.2132 501.862 495.040 0.884 0.949 0.111 8.318-6.595 100.00 360 8 0.2154 375.510 370.942 0.907 0.949 0.090 6.588-5.215 100.00 711 7 0.1913 345.056 335.681 0.909 0.949 0.083 5.214-4.128 98.38 1367 28 0.1208 504.713 499.805 0.998 0.949 0.035 4.126-3.266 94.74 2603 46 0.1139 460.073 453.453 1.062 0.950 0.005 3.266-2.585 99.86 5447 97 0.1116 310.354 306.947 1.043 0.949 0.000 2.585-2.046 97.45 10613 204 0.0958 234.144 231.577 1.051 0.949 0.000 2.046-1.619 99.39 21536 464 0.0907 138.578 137.287 1.068 0.949 0.000 1.619-1.281 98.00 42464 925 0.0963 74.603 73.908 1.055 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.021 38.349 1.024 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0512 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1361 | n_water=914 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1196 r_free=0.1361 | n_water=914 | time (s): 114.500 (total time: 117.690) Filter (q & B) r_work=0.1197 r_free=0.1363 | n_water=903 | time (s): 4.370 (total time: 122.060) Compute maps r_work=0.1197 r_free=0.1363 | n_water=903 | time (s): 2.020 (total time: 124.080) Filter (map) r_work=0.1218 r_free=0.1370 | n_water=784 | time (s): 4.270 (total time: 128.350) Find peaks r_work=0.1218 r_free=0.1370 | n_water=784 | time (s): 0.550 (total time: 128.900) Add new water r_work=0.1225 r_free=0.1379 | n_water=994 | time (s): 4.940 (total time: 133.840) Refine new water occ: r_work=0.1193 r_free=0.1343 adp: r_work=0.1193 r_free=0.1344 occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1340 adp: r_work=0.1190 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1341 r_work=0.1190 r_free=0.1341 | n_water=994 | time (s): 178.820 (total time: 312.660) Filter (q & B) r_work=0.1194 r_free=0.1352 | n_water=922 | time (s): 4.980 (total time: 317.640) Filter (dist only) r_work=0.1195 r_free=0.1352 | n_water=919 | time (s): 121.160 (total time: 438.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544600 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.933466 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1361 0.0163 0.038 1.1 8.5 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.61 1.63 1.699 13.672 13.933 3.757 12.00 13.64 1.64 1.721 13.657 13.933 3.756 Individual atomic B min max mean iso aniso Overall: 5.38 63.87 14.57 0.86 554 3269 Protein: 5.38 27.98 10.19 0.86 0 2902 Water: 5.81 63.87 28.38 N/A 554 365 Other: 13.63 21.88 17.76 N/A 0 2 Chain A: 5.46 50.92 12.01 N/A 0 1623 Chain B: 5.38 63.87 11.87 N/A 0 1646 Chain S: 5.81 60.97 30.11 N/A 554 0 Histogram: Values Number of atoms 5.38 - 11.23 2075 11.23 - 17.08 810 17.08 - 22.93 270 22.93 - 28.78 230 28.78 - 34.63 193 34.63 - 40.48 125 40.48 - 46.33 77 46.33 - 52.17 34 52.17 - 58.02 6 58.02 - 63.87 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1364 r_work=0.1201 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1365 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1364 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755953 | | target function (ml) not normalized (work): 703448.625360 | | target function (ml) not normalized (free): 14741.988200 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1372 0.1370 0.1473 n_refl.: 191130 remove outliers: r(all,work,free)=0.1372 0.1370 0.1473 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1372 0.1370 0.1473 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1353 n_refl.: 191130 remove outliers: r(all,work,free)=0.1193 0.1190 0.1353 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3857 356.641 317.777 0.362 0.977 0.180 13.296-10.522 97.03 97 1 0.2372 481.150 462.290 0.676 0.979 0.134 10.503-8.327 97.80 175 3 0.2153 501.862 494.141 0.849 0.980 0.108 8.318-6.595 100.00 360 8 0.2171 375.510 370.852 0.870 0.979 0.090 6.588-5.215 100.00 711 7 0.1934 345.056 335.195 0.873 0.980 0.083 5.214-4.128 98.38 1367 28 0.1211 504.713 499.429 0.960 0.981 0.034 4.126-3.266 94.74 2603 46 0.1149 460.073 452.915 1.020 0.982 0.005 3.266-2.585 99.86 5447 97 0.1120 310.354 306.658 1.002 0.983 0.000 2.585-2.046 97.45 10613 204 0.0962 234.144 231.422 1.008 0.985 0.000 2.046-1.619 99.39 21536 464 0.0907 138.578 137.198 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0946 74.603 73.942 1.006 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.021 38.323 0.967 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1182 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1353 | n_water=919 | time (s): 2.760 (total time: 2.760) Filter (dist) r_work=0.1190 r_free=0.1353 | n_water=919 | time (s): 114.050 (total time: 116.810) Filter (q & B) r_work=0.1190 r_free=0.1353 | n_water=907 | time (s): 4.030 (total time: 120.840) Compute maps r_work=0.1190 r_free=0.1353 | n_water=907 | time (s): 1.680 (total time: 122.520) Filter (map) r_work=0.1211 r_free=0.1362 | n_water=786 | time (s): 4.700 (total time: 127.220) Find peaks r_work=0.1211 r_free=0.1362 | n_water=786 | time (s): 0.820 (total time: 128.040) Add new water r_work=0.1218 r_free=0.1371 | n_water=999 | time (s): 4.220 (total time: 132.260) Refine new water occ: r_work=0.1187 r_free=0.1336 adp: r_work=0.1187 r_free=0.1337 occ: r_work=0.1185 r_free=0.1336 adp: r_work=0.1185 r_free=0.1336 occ: r_work=0.1183 r_free=0.1335 adp: r_work=0.1183 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1335 r_work=0.1183 r_free=0.1335 | n_water=999 | time (s): 207.800 (total time: 340.060) Filter (q & B) r_work=0.1188 r_free=0.1347 | n_water=922 | time (s): 4.280 (total time: 344.340) Filter (dist only) r_work=0.1188 r_free=0.1346 | n_water=920 | time (s): 119.460 (total time: 463.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.607636 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.194589 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1343 0.0153 0.037 1.1 7.7 0.0 0.3 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.43 1.53 1.661 13.643 14.195 3.754 11.89 13.44 1.55 1.665 13.640 14.195 3.751 Individual atomic B min max mean iso aniso Overall: 5.44 62.98 14.59 0.86 555 3269 Protein: 5.44 27.89 10.21 0.86 0 2902 Water: 5.89 62.98 28.38 N/A 555 365 Other: 13.65 21.89 17.77 N/A 0 2 Chain A: 5.49 50.63 12.00 N/A 0 1623 Chain B: 5.44 62.98 11.86 N/A 0 1646 Chain S: 5.89 61.03 30.25 N/A 555 0 Histogram: Values Number of atoms 5.44 - 11.19 2060 11.19 - 16.94 826 16.94 - 22.70 272 22.70 - 28.45 217 28.45 - 34.21 189 34.21 - 39.96 131 39.96 - 45.72 78 45.72 - 51.47 38 51.47 - 57.22 9 57.22 - 62.98 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1345 r_work=0.1190 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1345 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1343 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750892 | | target function (ml) not normalized (work): 702500.729854 | | target function (ml) not normalized (free): 14722.658283 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1343 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1377 0.1376 0.1477 n_refl.: 191130 remove outliers: r(all,work,free)=0.1377 0.1376 0.1477 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1377 0.1376 0.1477 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1342 n_refl.: 191130 remove outliers: r(all,work,free)=0.1190 0.1187 0.1342 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3856 356.641 318.238 0.356 0.977 0.167 13.296-10.522 97.03 97 1 0.2378 481.150 462.388 0.672 0.979 0.128 10.503-8.327 97.80 175 3 0.2131 501.862 494.805 0.849 0.979 0.105 8.318-6.595 100.00 360 8 0.2164 375.510 370.860 0.870 0.979 0.087 6.588-5.215 100.00 711 7 0.1938 345.056 335.283 0.873 0.980 0.080 5.214-4.128 98.38 1367 28 0.1219 504.713 499.080 0.959 0.980 0.029 4.126-3.266 94.74 2603 46 0.1147 460.073 452.931 1.021 0.982 0.000 3.266-2.585 99.86 5447 97 0.1122 310.354 306.713 1.003 0.983 0.000 2.585-2.046 97.45 10613 204 0.0960 234.144 231.438 1.009 0.985 0.000 2.046-1.619 99.39 21536 464 0.0905 138.578 137.228 1.023 0.988 0.000 1.619-1.281 98.00 42464 925 0.0940 74.603 73.950 1.010 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.021 38.312 0.972 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0854 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1342 After: r_work=0.1188 r_free=0.1342 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1342 | n_water=920 | time (s): 3.340 (total time: 3.340) Filter (dist) r_work=0.1188 r_free=0.1342 | n_water=919 | time (s): 122.590 (total time: 125.930) Filter (q & B) r_work=0.1189 r_free=0.1343 | n_water=912 | time (s): 4.190 (total time: 130.120) Compute maps r_work=0.1189 r_free=0.1343 | n_water=912 | time (s): 2.030 (total time: 132.150) Filter (map) r_work=0.1211 r_free=0.1360 | n_water=799 | time (s): 5.320 (total time: 137.470) Find peaks r_work=0.1211 r_free=0.1360 | n_water=799 | time (s): 0.530 (total time: 138.000) Add new water r_work=0.1217 r_free=0.1364 | n_water=994 | time (s): 4.790 (total time: 142.790) Refine new water occ: r_work=0.1187 r_free=0.1332 adp: r_work=0.1187 r_free=0.1332 occ: r_work=0.1186 r_free=0.1331 adp: r_work=0.1186 r_free=0.1332 occ: r_work=0.1184 r_free=0.1330 adp: r_work=0.1184 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1331 r_work=0.1184 r_free=0.1331 | n_water=994 | time (s): 335.480 (total time: 478.270) Filter (q & B) r_work=0.1188 r_free=0.1342 | n_water=924 | time (s): 4.220 (total time: 482.490) Filter (dist only) r_work=0.1188 r_free=0.1342 | n_water=922 | time (s): 120.520 (total time: 603.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560276 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.046409 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1342 0.0153 0.037 1.1 9.5 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.42 1.53 1.661 13.641 14.046 3.752 11.89 13.44 1.55 1.655 13.642 14.046 3.751 Individual atomic B min max mean iso aniso Overall: 5.44 62.75 14.58 0.86 557 3269 Protein: 5.44 27.86 10.23 0.86 0 2902 Water: 5.86 62.75 28.25 N/A 557 365 Other: 13.68 21.92 17.80 N/A 0 2 Chain A: 5.51 50.55 11.99 N/A 0 1623 Chain B: 5.44 62.75 11.86 N/A 0 1646 Chain S: 5.86 61.05 30.13 N/A 557 0 Histogram: Values Number of atoms 5.44 - 11.17 2052 11.17 - 16.90 835 16.90 - 22.63 273 22.63 - 28.37 219 28.37 - 34.10 188 34.10 - 39.83 131 39.83 - 45.56 77 45.56 - 51.29 37 51.29 - 57.02 10 57.02 - 62.75 4 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1344 r_work=0.1189 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1344 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1343 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750540 | | target function (ml) not normalized (work): 702434.886620 | | target function (ml) not normalized (free): 14714.966571 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1352 0.1435 5.6847 5.7604| | 2: 2.94 - 2.33 1.00 7339 128 0.1068 0.1325 5.0783 5.1853| | 3: 2.33 - 2.04 0.96 6939 150 0.0902 0.1196 4.6567 4.768| | 4: 2.04 - 1.85 1.00 7170 155 0.0898 0.1048 4.3892 4.5618| | 5: 1.85 - 1.72 0.99 7113 159 0.0926 0.0968 4.1415 4.2248| | 6: 1.72 - 1.62 0.99 7102 142 0.0886 0.1067 3.9342 4.0633| | 7: 1.62 - 1.54 0.99 7104 148 0.0883 0.0974 3.7869 3.9198| | 8: 1.54 - 1.47 0.96 6798 152 0.0881 0.1278 3.6866 3.8868| | 9: 1.47 - 1.41 0.98 6938 155 0.0916 0.1100 3.6103 3.7388| | 10: 1.41 - 1.36 0.99 7022 150 0.0969 0.1171 3.5492 3.6685| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1116 3.4797 3.5802| | 12: 1.32 - 1.28 0.98 6975 149 0.1034 0.1132 3.4572 3.5843| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1231 3.4346 3.5473| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1580 3.4287 3.6742| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1239 3.4449 3.4925| | 16: 1.19 - 1.17 0.93 6604 132 0.1248 0.1557 3.4629 3.6623| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1230 3.4328 3.443| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1713 3.4375 3.5355| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1722 3.4182 3.5897| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1570 3.4093 3.4304| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2139 3.4181 3.5063| | 22: 1.07 - 1.05 0.97 6836 135 0.1906 0.1958 3.4129 3.4146| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2036 3.4326 3.4876| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2250 3.4351 3.5076| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2519 3.4485 3.5278| | 26: 1.01 - 0.99 0.96 6767 158 0.2761 0.2868 3.4158 3.4242| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2815 3.4678 3.3953| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 11.63 1.00 0.97 11207.51| | 2: 2.94 - 2.33 7339 128 0.93 12.84 0.99 0.97 5158.99| | 3: 2.33 - 2.04 6939 150 0.96 7.74 1.01 0.97 1722.33| | 4: 2.04 - 1.85 7170 155 0.96 7.63 1.00 0.97 998.49| | 5: 1.85 - 1.72 7113 159 0.96 7.89 1.00 0.97 617.71| | 6: 1.72 - 1.62 7102 142 0.96 7.82 1.00 0.98 429.40| | 7: 1.62 - 1.54 7104 148 0.96 7.98 1.01 0.99 326.91| | 8: 1.54 - 1.47 6798 152 0.96 8.11 1.01 0.99 271.86| | 9: 1.47 - 1.41 6938 155 0.96 8.29 1.00 0.99 224.48| | 10: 1.41 - 1.36 7022 150 0.96 8.77 1.00 0.98 198.29| | 11: 1.36 - 1.32 6997 151 0.96 8.84 0.99 0.97 172.20| | 12: 1.32 - 1.28 6975 149 0.96 8.89 0.98 0.96 158.82| | 13: 1.28 - 1.25 6907 166 0.96 9.46 1.01 0.98 155.86| | 14: 1.25 - 1.22 7015 112 0.95 10.58 1.02 0.98 160.57| | 15: 1.22 - 1.19 6956 137 0.95 11.14 1.01 0.99 165.06| | 16: 1.19 - 1.17 6604 132 0.95 11.39 1.01 0.98 159.73| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.98 154.10| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.96 147.56| | 19: 1.12 - 1.10 6948 106 0.93 14.11 1.00 0.96 150.62| | 20: 1.10 - 1.08 6884 147 0.92 15.19 1.00 0.95 149.79| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.94 153.12| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.94 154.97| | 23: 1.05 - 1.03 6827 159 0.87 20.50 0.99 0.93 164.91| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.94 179.12| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.97 0.91 182.21| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.97 0.89 176.69| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.98 0.88 161.21| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 147.56 max = 11207.51 mean = 924.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.24| |phase err.(test): min = 0.00 max = 89.95 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1343 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1385 0.1383 0.1486 n_refl.: 191130 remove outliers: r(all,work,free)=0.1385 0.1383 0.1486 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1385 0.1383 0.1486 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191130 remove outliers: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3828 356.641 318.042 0.356 0.977 0.172 13.296-10.522 97.03 97 1 0.2382 481.150 463.367 0.666 0.979 0.116 10.503-8.327 97.80 175 3 0.2168 501.862 493.399 0.846 0.979 0.092 8.318-6.595 100.00 360 8 0.2145 375.510 371.713 0.869 0.979 0.081 6.588-5.215 100.00 711 7 0.1935 345.056 335.573 0.871 0.980 0.073 5.214-4.128 98.38 1367 28 0.1240 504.713 498.751 0.962 0.980 0.070 4.126-3.266 94.74 2603 46 0.1148 460.073 452.878 1.021 0.982 0.000 3.266-2.585 99.86 5447 97 0.1121 310.354 306.712 1.004 0.983 0.000 2.585-2.046 97.45 10613 204 0.0961 234.144 231.438 1.010 0.985 0.000 2.046-1.619 99.39 21536 464 0.0905 138.578 137.231 1.024 0.989 0.000 1.619-1.281 98.00 42464 925 0.0939 74.603 73.952 1.012 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.021 38.302 0.976 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0567 ================= 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 : 0.2031 0.1963 0.080 5.083 5.2 78.0 14.6 805 0.000 1_bss: 0.1794 0.1900 0.080 5.083 5.2 78.1 14.6 805 0.000 1_settarget: 0.1794 0.1900 0.080 5.083 5.2 78.1 14.6 805 0.000 1_nqh: 0.1794 0.1900 0.080 5.083 5.2 78.1 14.6 805 0.000 1_weight: 0.1794 0.1900 0.080 5.083 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1265 0.1493 0.038 1.147 5.2 78.1 14.6 805 0.155 1_adp: 0.1291 0.1559 0.038 1.147 5.2 73.1 15.0 805 0.155 1_regHadp: 0.1290 0.1555 0.038 1.147 5.2 73.1 15.0 805 0.155 1_occ: 0.1276 0.1543 0.038 1.147 5.2 73.1 15.0 805 0.155 2_bss: 0.1270 0.1536 0.038 1.147 5.4 73.2 15.2 805 0.155 2_settarget: 0.1270 0.1536 0.038 1.147 5.4 73.2 15.2 805 0.155 2_updatecdl: 0.1270 0.1536 0.038 1.167 5.4 73.2 15.2 805 0.155 2_nqh: 0.1270 0.1536 0.038 1.167 5.4 73.2 15.2 805 0.155 2_sol: 0.1265 0.1493 0.038 1.167 5.4 73.2 16.1 894 n/a 2_weight: 0.1265 0.1493 0.038 1.167 5.4 73.2 16.1 894 n/a 2_xyzrec: 0.1254 0.1516 0.041 1.134 5.4 73.2 16.1 894 n/a 2_adp: 0.1233 0.1508 0.041 1.134 5.4 68.2 16.2 894 n/a 2_regHadp: 0.1234 0.1509 0.041 1.134 5.4 68.2 16.2 894 n/a 2_occ: 0.1226 0.1503 0.041 1.134 5.4 68.2 16.2 894 n/a 3_bss: 0.1233 0.1511 0.041 1.134 5.4 68.2 16.1 894 n/a 3_settarget: 0.1233 0.1511 0.041 1.134 5.4 68.2 16.1 894 n/a 3_updatecdl: 0.1233 0.1511 0.041 1.140 5.4 68.2 16.1 894 n/a 3_nqh: 0.1233 0.1511 0.041 1.140 5.4 68.2 16.1 894 n/a 3_sol: 0.1249 0.1510 0.041 1.140 5.4 68.2 15.4 878 n/a 3_weight: 0.1249 0.1510 0.041 1.140 5.4 68.2 15.4 878 n/a 3_xyzrec: 0.1237 0.1430 0.036 1.109 5.4 68.2 15.4 878 n/a 3_adp: 0.1230 0.1388 0.036 1.109 5.5 67.8 15.2 878 n/a 3_regHadp: 0.1231 0.1389 0.036 1.109 5.5 67.8 15.2 878 n/a 3_occ: 0.1225 0.1392 0.036 1.109 5.5 67.8 15.2 878 n/a 4_bss: 0.1221 0.1383 0.036 1.109 5.5 67.8 15.2 878 n/a 4_settarget: 0.1221 0.1383 0.036 1.109 5.5 67.8 15.2 878 n/a 4_updatecdl: 0.1221 0.1383 0.036 1.112 5.5 67.8 15.2 878 n/a 4_nqh: 0.1221 0.1383 0.036 1.112 5.5 67.8 15.2 878 n/a 4_sol: 0.1205 0.1370 0.036 1.112 5.5 67.8 14.9 854 n/a 4_weight: 0.1205 0.1370 0.036 1.112 5.5 67.8 14.9 854 n/a 4_xyzrec: 0.1204 0.1371 0.033 1.120 5.5 67.8 14.9 854 n/a 4_adp: 0.1198 0.1370 0.033 1.120 5.5 67.3 14.8 854 n/a 4_regHadp: 0.1198 0.1370 0.033 1.120 5.5 67.3 14.8 854 n/a 4_occ: 0.1197 0.1369 0.033 1.120 5.5 67.3 14.8 854 n/a 5_bss: 0.1194 0.1368 0.033 1.120 5.4 67.3 14.7 854 n/a 5_settarget: 0.1194 0.1368 0.033 1.120 5.4 67.3 14.7 854 n/a 5_updatecdl: 0.1194 0.1368 0.033 1.120 5.4 67.3 14.7 854 n/a 5_nqh: 0.1194 0.1368 0.033 1.120 5.4 67.3 14.7 854 n/a 5_sol: 0.1189 0.1350 0.033 1.120 5.4 67.3 15.0 892 n/a 5_weight: 0.1189 0.1350 0.033 1.120 5.4 67.3 15.0 892 n/a 5_xyzrec: 0.1192 0.1360 0.036 1.123 5.4 67.3 15.0 892 n/a 5_adp: 0.1197 0.1365 0.036 1.123 5.6 67.1 15.0 892 n/a 5_regHadp: 0.1197 0.1365 0.036 1.123 5.6 67.1 15.0 892 n/a 5_occ: 0.1195 0.1368 0.036 1.123 5.6 67.1 15.0 892 n/a 6_bss: 0.1195 0.1365 0.036 1.123 5.5 67.1 14.9 892 n/a 6_settarget: 0.1195 0.1365 0.036 1.123 5.5 67.1 14.9 892 n/a 6_updatecdl: 0.1195 0.1365 0.036 1.123 5.5 67.1 14.9 892 n/a 6_nqh: 0.1195 0.1365 0.036 1.123 5.5 67.1 14.9 892 n/a 6_sol: 0.1192 0.1358 0.036 1.123 5.5 67.1 15.0 907 n/a 6_weight: 0.1192 0.1358 0.036 1.123 5.5 67.1 15.0 907 n/a 6_xyzrec: 0.1195 0.1355 0.037 1.131 5.5 67.1 15.0 907 n/a 6_adp: 0.1199 0.1359 0.037 1.131 5.6 66.0 14.9 907 n/a 6_regHadp: 0.1200 0.1360 0.037 1.131 5.6 66.0 14.9 907 n/a 6_occ: 0.1197 0.1361 0.037 1.131 5.6 66.0 14.9 907 n/a 7_bss: 0.1196 0.1361 0.037 1.131 5.5 65.9 14.8 907 n/a 7_settarget: 0.1196 0.1361 0.037 1.131 5.5 65.9 14.8 907 n/a 7_updatecdl: 0.1196 0.1361 0.037 1.131 5.5 65.9 14.8 907 n/a 7_nqh: 0.1196 0.1361 0.037 1.131 5.5 65.9 14.8 907 n/a 7_sol: 0.1194 0.1353 0.037 1.131 5.5 65.9 14.9 914 n/a 7_weight: 0.1194 0.1353 0.037 1.131 5.5 65.9 14.9 914 n/a 7_xyzrec: 0.1197 0.1361 0.037 1.122 5.5 65.9 14.9 914 n/a 7_adp: 0.1199 0.1362 0.037 1.122 5.6 64.9 14.8 914 n/a 7_regHadp: 0.1199 0.1362 0.037 1.122 5.6 64.9 14.8 914 n/a 7_occ: 0.1196 0.1362 0.037 1.122 5.6 64.9 14.8 914 n/a 8_bss: 0.1196 0.1361 0.037 1.122 5.4 64.6 14.6 914 n/a 8_settarget: 0.1196 0.1361 0.037 1.122 5.4 64.6 14.6 914 n/a 8_updatecdl: 0.1196 0.1361 0.037 1.122 5.4 64.6 14.6 914 n/a 8_nqh: 0.1196 0.1361 0.037 1.122 5.4 64.6 14.6 914 n/a 8_sol: 0.1195 0.1352 0.037 1.122 5.4 64.6 14.6 919 n/a 8_weight: 0.1195 0.1352 0.037 1.122 5.4 64.6 14.6 919 n/a 8_xyzrec: 0.1198 0.1361 0.038 1.122 5.4 64.6 14.6 919 n/a 8_adp: 0.1201 0.1364 0.038 1.122 5.4 63.9 14.6 919 n/a 8_regHadp: 0.1201 0.1365 0.038 1.122 5.4 63.9 14.6 919 n/a 8_occ: 0.1199 0.1364 0.038 1.122 5.4 63.9 14.6 919 n/a 9_bss: 0.1190 0.1353 0.038 1.122 5.4 63.9 14.6 919 n/a 9_settarget: 0.1190 0.1353 0.038 1.122 5.4 63.9 14.6 919 n/a 9_updatecdl: 0.1190 0.1353 0.038 1.122 5.4 63.9 14.6 919 n/a 9_nqh: 0.1190 0.1353 0.038 1.122 5.4 63.9 14.6 919 n/a 9_sol: 0.1188 0.1346 0.038 1.122 5.4 63.9 14.6 920 n/a 9_weight: 0.1188 0.1346 0.038 1.122 5.4 63.9 14.6 920 n/a 9_xyzrec: 0.1190 0.1343 0.037 1.127 5.4 63.9 14.6 920 n/a 9_adp: 0.1190 0.1345 0.037 1.127 5.4 63.0 14.6 920 n/a 9_regHadp: 0.1190 0.1345 0.037 1.127 5.4 63.0 14.6 920 n/a 9_occ: 0.1188 0.1343 0.037 1.127 5.4 63.0 14.6 920 n/a 10_bss: 0.1187 0.1342 0.037 1.127 5.4 63.0 14.6 920 n/a 10_settarget: 0.1187 0.1342 0.037 1.127 5.4 63.0 14.6 920 n/a 10_updatecdl: 0.1187 0.1342 0.037 1.126 5.4 63.0 14.6 920 n/a 10_setrh: 0.1188 0.1342 0.037 1.126 5.4 63.0 14.6 920 n/a 10_nqh: 0.1188 0.1342 0.037 1.126 5.4 63.0 14.6 920 n/a 10_sol: 0.1188 0.1342 0.037 1.126 5.4 63.0 14.6 922 n/a 10_weight: 0.1188 0.1342 0.037 1.126 5.4 63.0 14.6 922 n/a 10_xyzrec: 0.1189 0.1342 0.037 1.129 5.4 63.0 14.6 922 n/a 10_adp: 0.1189 0.1344 0.037 1.129 5.4 62.7 14.6 922 n/a 10_regHadp: 0.1189 0.1344 0.037 1.129 5.4 62.7 14.6 922 n/a 10_occ: 0.1189 0.1343 0.037 1.129 5.4 62.7 14.6 922 n/a end: 0.1188 0.1342 0.037 1.129 5.4 62.7 14.6 922 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9137209_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9137209_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.1200 Refinement macro-cycles (run) : 12184.0800 Write final files (write_after_run_outputs) : 163.0500 Total : 12353.2500 Total CPU time: 3.44 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:11 PST -0800 (1736736191.16 s) Start R-work = 0.1794, R-free = 0.1900 Final R-work = 0.1188, R-free = 0.1342 =============================================================================== Job complete usr+sys time: 12636.81 seconds wall clock time: 211 minutes 40.12 seconds (12700.12 seconds total)