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_8230052.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8230052.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8230052.pdb" 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/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.44, per 1000 atoms: 0.36 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: 2.659 distance_ideal: 2.720 ideal - model: 0.061 slack: 0.000 delta_slack: 0.061 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: 2.703 distance_ideal: 2.710 ideal - model: 0.007 slack: 0.000 delta_slack: 0.007 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: 1.12 Conformation dependent library (CDL) restraints added in 209.6 milliseconds Time building geometry restraints manager: 1.55 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: 739 1.02 - 1.25: 2551 1.25 - 1.49: 1531 1.49 - 1.72: 1088 1.72 - 1.96: 25 Bond restraints: 5934 Sorted by residual: bond pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 1.236 1.001 0.235 1.05e-02 9.07e+03 5.03e+02 bond pdb=" CA VAL B 145 " pdb=" C VAL B 145 " ideal model delta sigma weight residual 1.522 1.786 -0.263 1.29e-02 6.01e+03 4.17e+02 bond pdb=" CA ILE B 134 " pdb=" C ILE B 134 " ideal model delta sigma weight residual 1.523 1.699 -0.176 8.80e-03 1.29e+04 4.01e+02 bond pdb=" N ARG A 149 " pdb=" H ARG A 149 " ideal model delta sigma weight residual 0.860 1.246 -0.386 2.00e-02 2.50e+03 3.72e+02 bond pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " ideal model delta sigma weight residual 1.529 1.746 -0.217 1.13e-02 7.83e+03 3.69e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.40: 5927 4.40 - 8.80: 3502 8.80 - 13.20: 1198 13.20 - 17.60: 174 17.60 - 22.00: 9 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O PHE B 119 " pdb=" C PHE B 119 " pdb=" N PRO B 120 " ideal model delta sigma weight residual 121.34 135.46 -14.12 8.90e-01 1.26e+00 2.52e+02 angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 119.20 105.31 13.89 9.00e-01 1.23e+00 2.38e+02 angle pdb=" O ILE A 70 " pdb=" C ILE A 70 " pdb=" N VAL A 71 " ideal model delta sigma weight residual 122.93 138.49 -15.56 1.06e+00 8.90e-01 2.15e+02 angle pdb=" O ASP B 170 " pdb=" C ASP B 170 " pdb=" N LEU B 171 " ideal model delta sigma weight residual 122.07 106.98 15.09 1.03e+00 9.43e-01 2.15e+02 angle pdb=" CA PHE A 82 " pdb=" C PHE A 82 " pdb=" O PHE A 82 " ideal model delta sigma weight residual 120.90 136.47 -15.57 1.07e+00 8.73e-01 2.12e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 1841 16.92 - 33.84: 134 33.84 - 50.76: 48 50.76 - 67.68: 21 67.68 - 84.60: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA VAL A 32 " pdb=" C VAL A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -153.52 -26.48 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.250: 233 0.250 - 0.496: 163 0.496 - 0.743: 67 0.743 - 0.989: 23 0.989 - 1.235: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA LEU A 140 " pdb=" N LEU A 140 " pdb=" C LEU A 140 " pdb=" CB LEU A 140 " both_signs ideal model delta sigma weight residual False 2.51 3.75 -1.23 2.00e-01 2.50e+01 3.81e+01 chirality pdb=" CA VAL A 181 " pdb=" N VAL A 181 " pdb=" C VAL A 181 " pdb=" CB VAL A 181 " both_signs ideal model delta sigma weight residual False 2.44 1.32 1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CB VAL A 181 " pdb=" CA VAL A 181 " pdb=" CG1 VAL A 181 " pdb=" CG2 VAL A 181 " both_signs ideal model delta sigma weight residual False -2.63 -1.53 -1.10 2.00e-01 2.50e+01 3.04e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.081 2.00e-02 2.50e+03 7.71e-02 1.78e+02 pdb=" CG PHE B 164 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.108 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.106 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.080 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.124 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.028 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.067 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " 0.119 2.00e-02 2.50e+03 7.30e-02 1.60e+02 pdb=" CG TYR B 67 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " -0.102 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " 0.082 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " 0.043 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " 0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " -0.113 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " -0.031 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " -0.104 2.00e-02 2.50e+03 7.05e-02 1.49e+02 pdb=" CG TYR A 192 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " -0.046 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.125 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " 0.132 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " -0.053 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.65: 28 1.65 - 2.38: 2779 2.38 - 3.12: 22547 3.12 - 3.86: 32795 3.86 - 4.60: 52179 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110328 Sorted by model distance: nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.908 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.939 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.951 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.055 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.134 2.620 ... (remaining 110323 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_8230052_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= 0.2042 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.303531 | | target function (ml) not normalized (work): 806107.304005 | | target function (ml) not normalized (free): 16556.895909 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2145 0.1849 6.7024 6.3067| | 2: 2.94 - 2.33 1.00 7339 128 0.1627 0.1603 5.5356 5.5873| | 3: 2.33 - 2.04 0.96 6939 150 0.1631 0.1608 5.1402 5.1525| | 4: 2.04 - 1.85 1.00 7170 155 0.1736 0.1581 4.9668 5.0538| | 5: 1.85 - 1.72 0.99 7113 159 0.1940 0.1911 4.8062 4.8817| | 6: 1.72 - 1.62 0.99 7102 142 0.1986 0.2058 4.6744 4.7782| | 7: 1.62 - 1.54 0.99 7104 148 0.2020 0.1528 4.5669 4.4516| | 8: 1.54 - 1.47 0.96 6798 152 0.2074 0.2149 4.4879 4.4788| | 9: 1.47 - 1.41 0.98 6938 155 0.2131 0.2370 4.4133 4.5633| | 10: 1.41 - 1.36 0.99 7022 150 0.2131 0.2141 4.315 4.3969| | 11: 1.36 - 1.32 0.99 6997 151 0.2097 0.1945 4.2309 4.1405| | 12: 1.32 - 1.28 0.98 6976 149 0.2078 0.1790 4.1631 4.1738| | 13: 1.28 - 1.25 0.98 6907 166 0.2035 0.2074 4.1111 4.1422| | 14: 1.25 - 1.22 0.98 7015 113 0.2101 0.2305 4.09 4.2559| | 15: 1.22 - 1.19 0.98 6957 137 0.2137 0.2103 4.0476 4.0576| | 16: 1.19 - 1.17 0.93 6604 132 0.2125 0.2177 4.0092 4.0658| | 17: 1.17 - 1.14 0.98 6941 135 0.2171 0.1935 3.9706 4.0047| | 18: 1.14 - 1.12 0.98 6875 142 0.2230 0.2505 3.9314 4.0373| | 19: 1.12 - 1.10 0.97 6949 106 0.2294 0.2481 3.8789 3.9865| | 20: 1.10 - 1.08 0.97 6884 147 0.2331 0.2173 3.8288 3.8253| | 21: 1.08 - 1.07 0.97 6852 152 0.2455 0.2604 3.7879 3.7932| | 22: 1.07 - 1.05 0.97 6838 135 0.2610 0.2422 3.7661 3.721| | 23: 1.05 - 1.03 0.97 6829 159 0.2709 0.2737 3.7287 3.8274| | 24: 1.03 - 1.02 0.96 6785 133 0.2893 0.2894 3.6973 3.7773| | 25: 1.02 - 1.01 0.93 6552 130 0.3058 0.2762 3.6693 3.6725| | 26: 1.01 - 0.99 0.96 6767 158 0.3211 0.3257 3.6273 3.6152| | 27: 0.99 - 0.98 0.94 6648 131 0.3406 0.3220 3.6336 3.6479| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.21 0.91 0.98 34799.60| | 2: 2.94 - 2.33 7339 128 0.86 21.04 1.09 1.03 14884.14| | 3: 2.33 - 2.04 6939 150 0.93 12.67 1.11 1.05 4197.79| | 4: 2.04 - 1.85 7170 155 0.92 13.87 1.11 1.06 2911.09| | 5: 1.85 - 1.72 7113 159 0.90 16.18 1.12 1.07 2188.23| | 6: 1.72 - 1.62 7102 142 0.90 16.89 1.11 1.06 1657.95| | 7: 1.62 - 1.54 7104 148 0.90 16.95 1.11 1.07 1246.34| | 8: 1.54 - 1.47 6798 152 0.89 17.81 1.10 1.06 1099.37| | 9: 1.47 - 1.41 6938 155 0.88 19.36 1.11 1.07 1014.42| | 10: 1.41 - 1.36 7022 150 0.87 20.25 1.09 1.04 863.37| | 11: 1.36 - 1.32 6997 151 0.88 19.32 1.08 1.04 684.68| | 12: 1.32 - 1.28 6976 149 0.89 18.35 1.07 1.03 561.78| | 13: 1.28 - 1.25 6907 166 0.88 18.93 1.07 1.04 553.69| | 14: 1.25 - 1.22 7015 113 0.87 20.30 1.07 1.03 559.91| | 15: 1.22 - 1.19 6957 137 0.86 21.17 1.08 1.03 546.17| | 16: 1.19 - 1.17 6604 132 0.87 20.83 1.08 1.01 497.62| | 17: 1.17 - 1.14 6941 135 0.86 21.46 1.08 1.01 459.00| | 18: 1.14 - 1.12 6875 142 0.85 22.16 1.09 0.99 427.11| | 19: 1.12 - 1.10 6949 106 0.85 22.61 1.08 1.00 396.44| | 20: 1.10 - 1.08 6884 147 0.85 22.47 1.06 0.99 344.60| | 21: 1.08 - 1.07 6852 152 0.84 23.28 1.06 0.99 321.30| | 22: 1.07 - 1.05 6838 135 0.83 25.09 1.06 0.97 310.17| | 23: 1.05 - 1.03 6829 159 0.81 26.95 1.05 0.98 322.66| | 24: 1.03 - 1.02 6785 133 0.78 29.03 1.05 0.98 318.26| | 25: 1.02 - 1.01 6552 130 0.77 30.06 1.03 0.96 303.59| | 26: 1.01 - 0.99 6767 158 0.75 32.12 1.03 0.93 294.26| | 27: 0.99 - 0.98 6648 131 0.73 33.93 1.04 0.90 300.20| |alpha: min = 0.90 max = 1.07 mean = 1.01| |beta: min = 294.26 max = 34799.60 mean = 2794.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.52| |phase err.(test): min = 0.00 max = 89.90 mean = 21.52| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.271 2950 Z= 5.461 Angle : 5.215 17.180 4018 Z= 3.693 Chirality : 0.390 1.235 492 Planarity : 0.034 0.145 512 Dihedral : 13.253 84.605 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.60 % Rotamer: Outliers : 0.97 % Allowed : 3.87 % Favored : 95.16 % Cbeta Deviations : 29.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.38), residues: 386 helix: -2.20 (0.35), residues: 146 sheet: -0.63 (0.55), residues: 62 loop : -0.47 (0.43), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.017 ARG B 143 TYR 0.111 0.035 TYR B 67 PHE 0.105 0.038 PHE B 95 TRP 0.104 0.036 TRP B 146 HIS 0.075 0.034 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2042 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.303531 | | target function (ml) not normalized (work): 806107.304005 | | target function (ml) not normalized (free): 16556.895909 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2040 0.2042 0.1961 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2040 0.2042 0.1961 n_refl.: 191155 remove outliers: r(all,work,free)=0.2040 0.2042 0.1961 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2041 0.2043 0.1961 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1812 0.1810 0.1901 n_refl.: 191145 remove outliers: r(all,work,free)=0.1809 0.1808 0.1901 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4216 400.535 295.239 0.422 0.934 0.298 13.296-10.522 99.01 99 1 0.2476 528.187 520.688 0.769 0.935 0.249 10.503-8.327 98.90 177 3 0.2489 564.205 558.174 0.945 0.935 0.227 8.318-6.595 100.00 360 8 0.2480 414.736 403.665 0.950 0.934 0.169 6.588-5.215 100.00 711 7 0.2245 381.101 366.255 0.940 0.934 0.150 5.214-4.128 98.38 1367 28 0.1502 557.435 549.448 1.052 0.933 0.090 4.126-3.266 94.74 2603 46 0.1356 508.132 498.872 1.119 0.932 0.014 3.266-2.585 99.86 5447 97 0.1452 342.774 337.364 1.099 0.930 0.000 2.585-2.046 97.45 10613 204 0.1403 258.603 254.045 1.105 0.927 0.000 2.046-1.619 99.39 21536 464 0.1624 153.054 149.811 1.127 0.921 0.000 1.619-1.281 98.00 42464 925 0.1934 82.395 80.075 1.122 0.912 0.000 1.281-0.980 96.53 101826 2056 0.2327 44.203 41.684 1.123 0.896 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0103 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1808 r_free=0.1901 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1808 r_free=0.1901 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.976978 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 574.716958 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 0.1269 0.1499 0.0230 0.039 1.2 10.5 0.0 0.0 0 10.988 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.69 14.99 2.30 1.118 13.117 574.717 0.018 12.95 15.67 2.72 1.220 13.298 574.717 0.017 Individual atomic B min max mean iso aniso Overall: 5.13 73.05 14.93 1.39 435 3274 Protein: 5.13 40.38 10.96 1.39 0 2902 Water: 6.33 73.05 29.22 N/A 435 370 Other: 16.00 30.38 23.19 N/A 0 2 Chain A: 5.35 60.50 12.99 N/A 0 1626 Chain B: 5.13 73.05 12.71 N/A 0 1648 Chain S: 12.05 62.35 30.65 N/A 435 0 Histogram: Values Number of atoms 5.13 - 11.92 2161 11.92 - 18.72 647 18.72 - 25.51 312 25.51 - 32.30 276 32.30 - 39.09 148 39.09 - 45.88 102 45.88 - 52.67 38 52.67 - 59.47 20 59.47 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1295 r_free=0.1567 r_work=0.1294 r_free=0.1562 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1294 r_free = 0.1562 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 = 0.1279 r_free = 0.1553 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1279 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015522 | | target function (ls_wunit_k1) not normalized (work): 2907.138314 | | target function (ls_wunit_k1) not normalized (free): 116.698537 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1285 0.1279 0.1553 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1631 n_refl.: 191139 remove outliers: r(all,work,free)=0.1470 0.1467 0.1631 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1494 0.1492 0.1640 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1546 n_refl.: 191139 remove outliers: r(all,work,free)=0.1279 0.1273 0.1545 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 0.3609 402.814 374.901 0.480 0.963 0.275 13.296-10.522 99.01 99 1 0.2107 528.187 520.887 0.741 0.964 0.250 10.503-8.327 98.90 177 3 0.1711 564.205 561.937 0.886 0.964 0.203 8.318-6.595 100.00 360 8 0.1713 414.736 412.611 0.911 0.964 0.155 6.588-5.215 100.00 711 7 0.1531 381.101 373.937 0.890 0.964 0.150 5.214-4.128 98.38 1367 28 0.0899 557.435 554.420 0.977 0.965 0.070 4.126-3.266 94.74 2603 46 0.0828 508.132 504.492 1.044 0.965 0.014 3.266-2.585 99.86 5447 97 0.0919 342.774 340.491 1.027 0.965 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.416 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.405 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.411 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.155 1.025 0.964 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0381 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1545 | n_water=805 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1278 r_free=0.1548 | n_water=794 | time (s): 102.830 (total time: 105.410) Filter (q & B) r_work=0.1278 r_free=0.1547 | n_water=791 | time (s): 5.630 (total time: 111.040) Compute maps r_work=0.1278 r_free=0.1547 | n_water=791 | time (s): 2.090 (total time: 113.130) Filter (map) r_work=0.1305 r_free=0.1533 | n_water=654 | time (s): 3.860 (total time: 116.990) Find peaks r_work=0.1305 r_free=0.1533 | n_water=654 | time (s): 0.640 (total time: 117.630) Add new water r_work=0.1328 r_free=0.1558 | n_water=953 | time (s): 3.980 (total time: 121.610) Refine new water occ: r_work=0.1284 r_free=0.1509 adp: r_work=0.1271 r_free=0.1508 occ: r_work=0.1274 r_free=0.1505 adp: r_work=0.1267 r_free=0.1506 occ: r_work=0.1269 r_free=0.1504 adp: r_work=0.1266 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1504 r_work=0.1266 r_free=0.1504 | n_water=953 | time (s): 81.750 (total time: 203.360) Filter (q & B) r_work=0.1270 r_free=0.1506 | n_water=884 | time (s): 5.230 (total time: 208.590) Filter (dist only) r_work=0.1270 r_free=0.1505 | n_water=882 | time (s): 112.480 (total time: 321.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.889271 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 590.023367 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 0.1253 0.1521 0.0268 0.042 1.1 17.2 0.0 0.0 0 11.945 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.21 2.68 2.031 15.103 590.023 0.014 12.30 15.04 2.74 2.384 15.192 590.023 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 70.73 16.29 1.21 514 3272 Protein: 5.42 40.51 10.96 1.21 0 2902 Water: 6.64 70.73 33.81 N/A 514 368 Other: 16.30 33.01 24.66 N/A 0 2 Chain A: 5.52 56.40 12.97 N/A 0 1624 Chain B: 5.42 68.22 12.81 N/A 0 1648 Chain S: 9.21 70.73 37.94 N/A 514 0 Histogram: Values Number of atoms 5.42 - 11.95 2128 11.95 - 18.48 682 18.48 - 25.01 258 25.01 - 31.54 208 31.54 - 38.07 169 38.07 - 44.60 174 44.60 - 51.13 86 51.13 - 57.67 45 57.67 - 64.20 25 64.20 - 70.73 11 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1504 r_work=0.1231 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1505 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 = 0.1225 r_free = 0.1502 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 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= 0.1225 r_free= 0.1502 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013415 | | target function (ls_wunit_k1) not normalized (work): 2512.527136 | | target function (ls_wunit_k1) not normalized (free): 101.093696 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1225 0.1502 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1598 n_refl.: 191137 remove outliers: r(all,work,free)=0.1435 0.1432 0.1598 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1596 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1232 0.1510 n_refl.: 191137 remove outliers: r(all,work,free)=0.1237 0.1232 0.1510 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 0.3294 402.814 379.563 0.490 0.962 0.270 13.296-10.522 99.01 99 1 0.1870 528.187 522.220 0.765 0.963 0.255 10.503-8.327 98.90 177 3 0.1506 564.205 566.422 0.917 0.963 0.182 8.318-6.595 100.00 360 8 0.1577 414.736 414.344 0.937 0.963 0.145 6.588-5.215 100.00 711 7 0.1341 381.101 376.983 0.915 0.963 0.125 5.214-4.128 98.38 1367 28 0.0828 557.435 556.299 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0759 508.132 505.503 1.060 0.963 0.009 3.266-2.585 99.86 5447 97 0.0862 342.774 341.529 1.047 0.961 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.729 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.602 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1251 82.395 81.351 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1867 44.202 42.221 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0525 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1510 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1510 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1510 | n_water=882 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1234 r_free=0.1513 | n_water=874 | time (s): 123.950 (total time: 127.040) Filter (q & B) r_work=0.1234 r_free=0.1513 | n_water=873 | time (s): 5.730 (total time: 132.770) Compute maps r_work=0.1234 r_free=0.1513 | n_water=873 | time (s): 2.420 (total time: 135.190) Filter (map) r_work=0.1273 r_free=0.1518 | n_water=685 | time (s): 5.580 (total time: 140.770) Find peaks r_work=0.1273 r_free=0.1518 | n_water=685 | time (s): 0.750 (total time: 141.520) Add new water r_work=0.1294 r_free=0.1544 | n_water=1002 | time (s): 5.810 (total time: 147.330) Refine new water occ: r_work=0.1250 r_free=0.1503 adp: r_work=0.1250 r_free=0.1504 occ: r_work=0.1247 r_free=0.1502 adp: r_work=0.1246 r_free=0.1503 occ: r_work=0.1244 r_free=0.1502 adp: r_work=0.1243 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1502 r_work=0.1243 r_free=0.1502 | n_water=1002 | time (s): 263.480 (total time: 410.810) Filter (q & B) r_work=0.1247 r_free=0.1506 | n_water=867 | time (s): 4.530 (total time: 415.340) Filter (dist only) r_work=0.1248 r_free=0.1506 | n_water=866 | time (s): 118.480 (total time: 533.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.746805 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.860333 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1235 0.1430 0.0195 0.035 1.1 7.3 0.0 0.0 0 0.873 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.30 1.95 1.930 14.512 15.860 3.936 12.31 13.93 1.62 2.203 14.426 15.860 3.896 Individual atomic B min max mean iso aniso Overall: 5.55 67.86 15.17 1.05 499 3271 Protein: 5.55 36.89 10.74 1.05 0 2902 Water: 6.71 67.86 29.98 N/A 499 367 Other: 14.06 29.09 21.57 N/A 0 2 Chain A: 5.57 55.58 12.76 N/A 0 1624 Chain B: 5.55 67.86 12.54 N/A 0 1647 Chain S: 12.87 62.63 31.65 N/A 499 0 Histogram: Values Number of atoms 5.55 - 11.78 2135 11.78 - 18.01 689 18.01 - 24.24 297 24.24 - 30.47 234 30.47 - 36.70 173 36.70 - 42.93 139 42.93 - 49.16 72 49.16 - 55.39 23 55.39 - 61.63 6 61.63 - 67.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1393 r_work=0.1232 r_free=0.1394 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1394 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1387 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890290 | | target function (ml) not normalized (work): 728635.796127 | | target function (ml) not normalized (free): 15212.722647 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1226 0.1387 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1443 0.1442 0.1477 n_refl.: 191137 remove outliers: r(all,work,free)=0.1443 0.1442 0.1477 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1437 0.1474 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1222 0.1379 n_refl.: 191137 remove outliers: r(all,work,free)=0.1225 0.1222 0.1379 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3758 398.008 362.188 0.424 0.946 0.251 13.296-10.522 99.01 99 1 0.2473 528.187 509.577 0.703 0.947 0.219 10.503-8.327 97.80 175 3 0.1940 554.286 556.360 0.883 0.947 0.174 8.318-6.595 100.00 360 8 0.2099 414.736 410.423 0.899 0.947 0.130 6.588-5.215 100.00 711 7 0.1825 381.101 370.857 0.888 0.947 0.120 5.214-4.128 98.38 1367 28 0.1164 557.435 552.082 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1090 508.132 501.329 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1081 342.774 339.191 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0959 258.603 255.781 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0974 153.054 151.393 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.488 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.314 1.037 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0967 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1379 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1379 | n_water=866 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1222 r_free=0.1380 | n_water=864 | time (s): 119.950 (total time: 123.100) Filter (q & B) r_work=0.1223 r_free=0.1379 | n_water=853 | time (s): 5.650 (total time: 128.750) Compute maps r_work=0.1223 r_free=0.1379 | n_water=853 | time (s): 1.630 (total time: 130.380) Filter (map) r_work=0.1246 r_free=0.1379 | n_water=711 | time (s): 4.800 (total time: 135.180) Find peaks r_work=0.1246 r_free=0.1379 | n_water=711 | time (s): 0.560 (total time: 135.740) Add new water r_work=0.1261 r_free=0.1396 | n_water=963 | time (s): 3.860 (total time: 139.600) Refine new water occ: r_work=0.1212 r_free=0.1364 adp: r_work=0.1204 r_free=0.1360 occ: r_work=0.1202 r_free=0.1360 adp: r_work=0.1202 r_free=0.1360 occ: r_work=0.1202 r_free=0.1360 adp: r_work=0.1202 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1360 r_work=0.1202 r_free=0.1360 | n_water=963 | time (s): 261.970 (total time: 401.570) Filter (q & B) r_work=0.1207 r_free=0.1370 | n_water=834 | time (s): 4.760 (total time: 406.330) Filter (dist only) r_work=0.1208 r_free=0.1369 | n_water=833 | time (s): 105.980 (total time: 512.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.541795 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.628336 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 0.1209 0.1369 0.0159 0.036 1.1 5.4 0.0 0.0 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 13.69 1.59 1.830 14.063 15.628 3.875 12.04 13.67 1.63 1.959 14.015 15.628 3.867 Individual atomic B min max mean iso aniso Overall: 5.49 67.37 14.71 0.99 466 3271 Protein: 5.49 33.46 10.64 0.99 0 2902 Water: 5.97 67.37 28.86 N/A 466 367 Other: 13.97 27.76 20.87 N/A 0 2 Chain A: 5.55 54.42 12.61 N/A 0 1624 Chain B: 5.49 67.37 12.43 N/A 0 1647 Chain S: 5.97 61.26 30.07 N/A 466 0 Histogram: Values Number of atoms 5.49 - 11.68 2119 11.68 - 17.87 728 17.87 - 24.05 336 24.05 - 30.24 200 30.24 - 36.43 142 36.43 - 42.62 119 42.62 - 48.80 63 48.80 - 54.99 23 54.99 - 61.18 5 61.18 - 67.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1367 r_work=0.1204 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1368 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1365 target_work(ml) = 3.865 | | 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.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864895 | | target function (ml) not normalized (work): 723867.807947 | | target function (ml) not normalized (free): 15140.795488 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1365 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1435 0.1434 0.1479 n_refl.: 191134 remove outliers: r(all,work,free)=0.1435 0.1434 0.1479 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1427 0.1427 0.1474 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1362 n_refl.: 191134 remove outliers: r(all,work,free)=0.1204 0.1201 0.1362 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3918 360.430 324.134 0.412 0.947 0.249 13.296-10.522 99.01 99 1 0.2524 478.319 460.047 0.694 0.948 0.210 10.503-8.327 97.80 175 3 0.2106 501.953 495.008 0.858 0.948 0.164 8.318-6.595 100.00 360 8 0.2246 375.579 368.946 0.889 0.948 0.125 6.588-5.215 100.00 711 7 0.1944 345.120 334.549 0.882 0.948 0.110 5.214-4.128 98.38 1367 28 0.1218 504.805 499.835 0.972 0.948 0.070 4.126-3.266 94.74 2603 46 0.1140 460.157 453.686 1.034 0.948 0.009 3.266-2.585 99.86 5447 97 0.1095 310.411 307.198 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0934 234.187 231.722 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0917 138.604 137.286 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.0986 74.616 73.895 1.055 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.028 38.362 1.044 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1138 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1362 | n_water=833 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1201 r_free=0.1362 | n_water=833 | time (s): 109.710 (total time: 112.120) Filter (q & B) r_work=0.1201 r_free=0.1364 | n_water=822 | time (s): 4.490 (total time: 116.610) Compute maps r_work=0.1201 r_free=0.1364 | n_water=822 | time (s): 1.650 (total time: 118.260) Filter (map) r_work=0.1224 r_free=0.1368 | n_water=703 | time (s): 4.240 (total time: 122.500) Find peaks r_work=0.1224 r_free=0.1368 | n_water=703 | time (s): 0.690 (total time: 123.190) Add new water r_work=0.1237 r_free=0.1392 | n_water=938 | time (s): 5.130 (total time: 128.320) Refine new water occ: r_work=0.1197 r_free=0.1361 adp: r_work=0.1198 r_free=0.1360 occ: r_work=0.1195 r_free=0.1360 adp: r_work=0.1195 r_free=0.1359 occ: r_work=0.1193 r_free=0.1359 adp: r_work=0.1193 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1358 r_work=0.1193 r_free=0.1358 | n_water=938 | time (s): 264.260 (total time: 392.580) Filter (q & B) r_work=0.1198 r_free=0.1370 | n_water=856 | time (s): 4.260 (total time: 396.840) Filter (dist only) r_work=0.1199 r_free=0.1368 | n_water=855 | time (s): 108.820 (total time: 505.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.574273 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.951485 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1368 0.0167 0.036 1.1 6.1 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.68 1.67 1.786 14.013 14.951 3.765 12.06 13.74 1.68 1.843 13.989 14.951 3.763 Individual atomic B min max mean iso aniso Overall: 5.59 67.03 14.77 0.95 489 3270 Protein: 5.59 31.95 10.58 0.95 0 2902 Water: 6.03 67.03 28.96 N/A 489 366 Other: 13.80 26.74 20.27 N/A 0 2 Chain A: 5.59 53.70 12.51 N/A 0 1623 Chain B: 5.59 67.03 12.35 N/A 0 1647 Chain S: 6.03 61.10 30.41 N/A 489 0 Histogram: Values Number of atoms 5.59 - 11.73 2145 11.73 - 17.88 718 17.88 - 24.02 304 24.02 - 30.17 212 30.17 - 36.31 169 36.31 - 42.45 124 42.45 - 48.60 54 48.60 - 54.74 27 54.74 - 60.89 4 60.89 - 67.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1374 r_work=0.1206 r_free=0.1374 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1374 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1377 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1205 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762185 | | target function (ml) not normalized (work): 704630.948452 | | target function (ml) not normalized (free): 14750.231609 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1205 0.1376 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1436 0.1435 0.1484 n_refl.: 191134 remove outliers: r(all,work,free)=0.1436 0.1435 0.1484 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1428 0.1427 0.1479 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1204 0.1373 n_refl.: 191134 remove outliers: r(all,work,free)=0.1207 0.1203 0.1373 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3914 360.430 320.613 0.407 0.946 0.241 13.296-10.522 98.02 98 1 0.2530 478.964 456.298 0.687 0.948 0.189 10.503-8.327 97.80 175 3 0.2140 501.953 495.218 0.858 0.948 0.163 8.318-6.595 100.00 360 8 0.2236 375.579 369.588 0.890 0.948 0.116 6.588-5.215 100.00 711 7 0.1937 345.120 334.581 0.883 0.948 0.093 5.214-4.128 98.38 1367 28 0.1219 504.805 499.601 0.974 0.948 0.070 4.126-3.266 94.74 2603 46 0.1168 460.157 453.347 1.036 0.948 0.009 3.266-2.585 99.86 5447 97 0.1116 310.411 307.153 1.022 0.948 0.000 2.585-2.046 97.45 10613 204 0.0946 234.187 231.755 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0919 138.604 137.295 1.058 0.946 0.000 1.619-1.281 98.00 42464 925 0.0976 74.616 73.909 1.056 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.028 38.359 1.044 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1322 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1204 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1373 | n_water=855 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1204 r_free=0.1373 | n_water=854 | time (s): 104.460 (total time: 107.030) Filter (q & B) r_work=0.1204 r_free=0.1373 | n_water=845 | time (s): 4.450 (total time: 111.480) Compute maps r_work=0.1204 r_free=0.1373 | n_water=845 | time (s): 1.920 (total time: 113.400) Filter (map) r_work=0.1225 r_free=0.1367 | n_water=730 | time (s): 4.570 (total time: 117.970) Find peaks r_work=0.1225 r_free=0.1367 | n_water=730 | time (s): 0.650 (total time: 118.620) Add new water r_work=0.1236 r_free=0.1385 | n_water=954 | time (s): 5.390 (total time: 124.010) Refine new water occ: r_work=0.1198 r_free=0.1358 adp: r_work=0.1198 r_free=0.1357 occ: r_work=0.1196 r_free=0.1355 adp: r_work=0.1196 r_free=0.1356 occ: r_work=0.1194 r_free=0.1354 adp: r_work=0.1194 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1355 r_work=0.1194 r_free=0.1355 | n_water=954 | time (s): 226.050 (total time: 350.060) Filter (q & B) r_work=0.1199 r_free=0.1365 | n_water=876 | time (s): 5.370 (total time: 355.430) Filter (dist only) r_work=0.1200 r_free=0.1363 | n_water=875 | time (s): 108.650 (total time: 464.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.522619 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.667165 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 0.1365 0.0161 0.037 1.1 6.1 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.65 1.61 1.757 13.976 14.667 3.762 12.06 13.68 1.63 1.884 13.935 14.667 3.760 Individual atomic B min max mean iso aniso Overall: 5.60 65.93 14.74 0.90 509 3270 Protein: 5.60 29.33 10.48 0.90 0 2902 Water: 6.04 65.93 28.87 N/A 509 366 Other: 13.84 23.86 18.85 N/A 0 2 Chain A: 5.63 53.07 12.37 N/A 0 1623 Chain B: 5.60 65.93 12.23 N/A 0 1647 Chain S: 6.04 60.71 30.46 N/A 509 0 Histogram: Values Number of atoms 5.60 - 11.63 2119 11.63 - 17.66 777 17.66 - 23.70 277 23.70 - 29.73 202 29.73 - 35.77 173 35.77 - 41.80 125 41.80 - 47.83 70 47.83 - 53.87 28 53.87 - 59.90 5 59.90 - 65.93 3 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1368 r_work=0.1206 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1369 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1367 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759127 | | target function (ml) not normalized (work): 704054.484515 | | target function (ml) not normalized (free): 14736.998627 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1367 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1430 0.1430 0.1481 n_refl.: 191133 remove outliers: r(all,work,free)=0.1430 0.1430 0.1481 n_refl.: 191133 overall B=-0.23 to atoms: r(all,work,free)=0.1391 0.1390 0.1459 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1366 n_refl.: 191133 remove outliers: r(all,work,free)=0.1206 0.1203 0.1366 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 0.3881 360.430 320.863 0.411 0.947 0.235 13.296-10.522 97.03 97 1 0.2467 478.186 455.001 0.707 0.948 0.176 10.503-8.327 97.80 175 3 0.2148 501.953 495.077 0.881 0.949 0.149 8.318-6.595 100.00 360 8 0.2233 375.579 370.044 0.914 0.948 0.106 6.588-5.215 100.00 711 7 0.1950 345.120 335.091 0.905 0.948 0.086 5.214-4.128 98.38 1367 28 0.1220 504.805 499.777 0.999 0.949 0.060 4.126-3.266 94.74 2603 46 0.1176 460.157 453.204 1.062 0.949 0.005 3.266-2.585 99.86 5447 97 0.1121 310.411 307.118 1.044 0.948 0.000 2.585-2.046 97.45 10613 204 0.0952 234.187 231.745 1.052 0.948 0.000 2.046-1.619 99.39 21536 464 0.0916 138.604 137.321 1.070 0.948 0.000 1.619-1.281 98.00 42464 925 0.0969 74.616 73.917 1.058 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.028 38.357 1.028 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0507 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1366 | n_water=875 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1203 r_free=0.1365 | n_water=874 | time (s): 109.590 (total time: 112.320) Filter (q & B) r_work=0.1204 r_free=0.1365 | n_water=870 | time (s): 5.220 (total time: 117.540) Compute maps r_work=0.1204 r_free=0.1365 | n_water=870 | time (s): 2.110 (total time: 119.650) Filter (map) r_work=0.1229 r_free=0.1367 | n_water=742 | time (s): 5.060 (total time: 124.710) Find peaks r_work=0.1229 r_free=0.1367 | n_water=742 | time (s): 0.830 (total time: 125.540) Add new water r_work=0.1238 r_free=0.1380 | n_water=957 | time (s): 4.240 (total time: 129.780) Refine new water occ: r_work=0.1202 r_free=0.1353 adp: r_work=0.1202 r_free=0.1353 occ: r_work=0.1200 r_free=0.1351 adp: r_work=0.1200 r_free=0.1352 occ: r_work=0.1198 r_free=0.1350 adp: r_work=0.1198 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1351 r_work=0.1198 r_free=0.1351 | n_water=957 | time (s): 244.350 (total time: 374.130) Filter (q & B) r_work=0.1202 r_free=0.1361 | n_water=880 | time (s): 5.100 (total time: 379.230) Filter (dist only) r_work=0.1202 r_free=0.1359 | n_water=879 | time (s): 110.730 (total time: 489.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524113 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.695449 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1365 0.0161 0.038 1.1 6.1 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.65 1.61 1.717 13.682 13.695 3.760 12.08 13.70 1.62 1.773 13.657 13.695 3.760 Individual atomic B min max mean iso aniso Overall: 5.40 64.63 14.52 0.87 514 3269 Protein: 5.40 28.16 10.23 0.87 0 2902 Water: 5.81 64.63 28.66 N/A 514 365 Other: 13.66 22.23 17.95 N/A 0 2 Chain A: 5.44 52.40 12.08 N/A 0 1623 Chain B: 5.40 64.63 11.93 N/A 0 1646 Chain S: 5.81 60.70 30.50 N/A 514 0 Histogram: Values Number of atoms 5.40 - 11.32 2100 11.32 - 17.25 792 17.25 - 23.17 270 23.17 - 29.09 203 29.09 - 35.01 167 35.01 - 40.94 136 40.94 - 46.86 75 46.86 - 52.78 29 52.78 - 58.70 8 58.70 - 64.63 3 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1370 r_work=0.1208 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1370 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1371 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759424 | | target function (ml) not normalized (work): 704106.357092 | | target function (ml) not normalized (free): 14740.563527 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1210 0.1206 0.1371 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1399 0.1398 0.1479 n_refl.: 191132 remove outliers: r(all,work,free)=0.1399 0.1398 0.1479 n_refl.: 191132 overall B=0.06 to atoms: r(all,work,free)=0.1408 0.1407 0.1484 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191132 remove outliers: r(all,work,free)=0.1200 0.1197 0.1362 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 0.3777 361.234 318.891 0.385 0.995 0.218 13.296-10.522 97.03 97 1 0.2459 478.186 459.503 0.679 0.997 0.152 10.503-8.327 97.80 175 3 0.2182 501.953 494.079 0.845 0.998 0.122 8.318-6.595 100.00 360 8 0.2203 375.579 369.801 0.874 0.998 0.098 6.588-5.215 100.00 711 7 0.1941 345.120 335.262 0.868 0.998 0.077 5.214-4.128 98.38 1367 28 0.1226 504.805 499.391 0.960 0.999 0.060 4.126-3.266 94.74 2603 46 0.1182 460.157 452.578 1.020 1.000 0.005 3.266-2.585 99.86 5447 97 0.1130 310.411 306.775 1.002 1.001 0.000 2.585-2.046 97.45 10613 204 0.0961 234.187 231.586 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0915 138.604 137.232 1.026 1.005 0.000 1.619-1.281 98.00 42464 925 0.0952 74.616 73.959 1.015 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1631 40.028 38.332 0.981 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0586 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1362 | n_water=879 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1197 r_free=0.1362 | n_water=879 | time (s): 104.500 (total time: 106.870) Filter (q & B) r_work=0.1198 r_free=0.1364 | n_water=874 | time (s): 4.620 (total time: 111.490) Compute maps r_work=0.1198 r_free=0.1364 | n_water=874 | time (s): 1.770 (total time: 113.260) Filter (map) r_work=0.1221 r_free=0.1359 | n_water=750 | time (s): 5.440 (total time: 118.700) Find peaks r_work=0.1221 r_free=0.1359 | n_water=750 | time (s): 0.810 (total time: 119.510) Add new water r_work=0.1229 r_free=0.1372 | n_water=969 | time (s): 5.040 (total time: 124.550) Refine new water occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1195 r_free=0.1341 occ: r_work=0.1193 r_free=0.1341 adp: r_work=0.1193 r_free=0.1341 occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1341 r_work=0.1191 r_free=0.1341 | n_water=969 | time (s): 224.850 (total time: 349.400) Filter (q & B) r_work=0.1196 r_free=0.1356 | n_water=895 | time (s): 4.750 (total time: 354.150) Filter (dist only) r_work=0.1196 r_free=0.1356 | n_water=893 | time (s): 115.130 (total time: 469.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.569609 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.058666 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1359 0.0160 0.038 1.1 6.5 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.59 1.60 1.669 13.687 14.059 3.758 11.98 13.61 1.64 1.686 13.679 14.059 3.755 Individual atomic B min max mean iso aniso Overall: 5.50 63.64 14.58 0.87 528 3269 Protein: 5.50 28.08 10.30 0.87 0 2902 Water: 5.85 63.64 28.46 N/A 528 365 Other: 13.78 22.03 17.91 N/A 0 2 Chain A: 5.57 52.00 12.11 N/A 0 1623 Chain B: 5.50 63.64 11.97 N/A 0 1646 Chain S: 5.85 60.95 30.28 N/A 528 0 Histogram: Values Number of atoms 5.50 - 11.31 2067 11.31 - 17.13 824 17.13 - 22.94 266 22.94 - 28.76 203 28.76 - 34.57 186 34.57 - 40.39 128 40.39 - 46.20 81 46.20 - 52.01 31 52.01 - 57.83 8 57.83 - 63.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1361 r_work=0.1198 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1362 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1361 target_work(ml) = 3.754 | | 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.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754465 | | target function (ml) not normalized (work): 703173.772091 | | target function (ml) not normalized (free): 14726.084799 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1361 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1398 0.1397 0.1498 n_refl.: 191131 remove outliers: r(all,work,free)=0.1398 0.1397 0.1498 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1400 0.1399 0.1499 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1198 0.1195 0.1358 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 0.3915 361.234 321.151 0.407 0.910 0.195 13.296-10.522 97.03 97 1 0.2485 478.186 459.126 0.735 0.912 0.139 10.503-8.327 97.80 175 3 0.2190 501.953 494.134 0.919 0.913 0.111 8.318-6.595 100.00 360 8 0.2244 375.579 370.082 0.949 0.913 0.091 6.588-5.215 100.00 711 7 0.1966 345.120 335.241 0.947 0.913 0.073 5.214-4.128 98.38 1367 28 0.1245 504.805 498.805 1.048 0.914 0.060 4.126-3.266 94.74 2603 46 0.1182 460.157 452.491 1.114 0.915 0.005 3.266-2.585 99.86 5447 97 0.1128 310.411 306.672 1.095 0.916 0.000 2.585-2.046 97.45 10613 204 0.0961 234.187 231.562 1.104 0.918 0.000 2.046-1.619 99.39 21536 464 0.0910 138.604 137.251 1.122 0.921 0.000 1.619-1.281 98.00 42464 925 0.0944 74.616 73.966 1.112 0.926 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.028 38.319 1.078 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0182 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1358 | n_water=893 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1195 r_free=0.1358 | n_water=893 | time (s): 103.980 (total time: 106.340) Filter (q & B) r_work=0.1196 r_free=0.1358 | n_water=884 | time (s): 4.540 (total time: 110.880) Compute maps r_work=0.1196 r_free=0.1358 | n_water=884 | time (s): 1.940 (total time: 112.820) Filter (map) r_work=0.1217 r_free=0.1360 | n_water=766 | time (s): 4.820 (total time: 117.640) Find peaks r_work=0.1217 r_free=0.1360 | n_water=766 | time (s): 0.880 (total time: 118.520) Add new water r_work=0.1225 r_free=0.1372 | n_water=973 | time (s): 4.230 (total time: 122.750) Refine new water occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1193 r_free=0.1348 occ: r_work=0.1191 r_free=0.1346 adp: r_work=0.1191 r_free=0.1347 occ: r_work=0.1190 r_free=0.1346 adp: r_work=0.1190 r_free=0.1346 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1346 r_work=0.1190 r_free=0.1346 | n_water=973 | time (s): 234.260 (total time: 357.010) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=895 | time (s): 4.730 (total time: 361.740) Filter (dist only) r_work=0.1194 r_free=0.1357 | n_water=893 | time (s): 120.700 (total time: 482.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.501928 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.040863 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1361 0.0162 0.038 1.1 6.5 0.0 0.3 0 0.751 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.61 1.62 1.674 13.685 14.041 3.756 11.99 13.64 1.65 1.673 13.682 14.041 3.755 Individual atomic B min max mean iso aniso Overall: 5.52 63.33 14.56 0.86 529 3268 Protein: 5.52 27.99 10.33 0.86 0 2902 Water: 5.95 63.33 28.30 N/A 529 364 Other: 13.80 22.08 17.94 N/A 0 2 Chain A: 5.61 51.89 12.11 N/A 0 1623 Chain B: 5.52 63.33 11.96 N/A 0 1645 Chain S: 5.95 61.01 30.15 N/A 529 0 Histogram: Values Number of atoms 5.52 - 11.30 2060 11.30 - 17.08 832 17.08 - 22.86 273 22.86 - 28.64 205 28.64 - 34.42 177 34.42 - 40.20 123 40.20 - 45.98 83 45.98 - 51.77 32 51.77 - 57.55 9 57.55 - 63.33 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1364 r_work=0.1199 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1364 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754657 | | target function (ml) not normalized (work): 703209.668401 | | target function (ml) not normalized (free): 14729.071975 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1365 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1507 n_refl.: 191131 remove outliers: r(all,work,free)=0.1409 0.1408 0.1507 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1409 0.1407 0.1507 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1364 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1364 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 0.3921 361.234 319.525 0.382 0.974 0.205 13.296-10.522 97.03 97 1 0.2436 478.186 459.779 0.690 0.976 0.151 10.503-8.327 97.80 175 3 0.2197 501.953 494.212 0.856 0.976 0.120 8.318-6.595 100.00 360 8 0.2249 375.579 369.948 0.887 0.976 0.095 6.588-5.215 100.00 711 7 0.1984 345.120 334.922 0.883 0.977 0.077 5.214-4.128 98.38 1367 28 0.1257 504.805 498.669 0.980 0.978 0.060 4.126-3.266 94.74 2603 46 0.1192 460.157 452.267 1.042 0.979 0.013 3.266-2.585 99.86 5447 97 0.1136 310.411 306.611 1.024 0.980 0.003 2.585-2.046 97.45 10613 204 0.0965 234.187 231.539 1.033 0.982 0.000 2.046-1.619 99.39 21536 464 0.0910 138.604 137.235 1.050 0.986 0.000 1.619-1.281 98.00 42464 925 0.0941 74.616 73.965 1.041 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.028 38.307 1.011 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0089 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1197 r_free=0.1364 After: r_work=0.1198 r_free=0.1365 ================================== NQH flips ================================== r_work=0.1198 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1365 | n_water=893 | time (s): 2.880 (total time: 2.880) Filter (dist) r_work=0.1198 r_free=0.1365 | n_water=893 | time (s): 111.540 (total time: 114.420) Filter (q & B) r_work=0.1198 r_free=0.1363 | n_water=882 | time (s): 5.230 (total time: 119.650) Compute maps r_work=0.1198 r_free=0.1363 | n_water=882 | time (s): 1.970 (total time: 121.620) Filter (map) r_work=0.1220 r_free=0.1367 | n_water=764 | time (s): 5.120 (total time: 126.740) Find peaks r_work=0.1220 r_free=0.1367 | n_water=764 | time (s): 0.640 (total time: 127.380) Add new water r_work=0.1228 r_free=0.1383 | n_water=969 | time (s): 4.290 (total time: 131.670) Refine new water occ: r_work=0.1195 r_free=0.1350 adp: r_work=0.1195 r_free=0.1350 occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1193 r_free=0.1350 occ: r_work=0.1192 r_free=0.1349 adp: r_work=0.1192 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1350 r_work=0.1192 r_free=0.1350 | n_water=969 | time (s): 300.530 (total time: 432.200) Filter (q & B) r_work=0.1196 r_free=0.1361 | n_water=895 | time (s): 5.010 (total time: 437.210) Filter (dist only) r_work=0.1196 r_free=0.1361 | n_water=893 | time (s): 116.400 (total time: 553.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565251 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.506021 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 0.1363 0.0166 0.038 1.1 7.5 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.63 1.66 1.675 13.681 14.506 3.755 11.97 13.63 1.66 1.674 13.680 14.506 3.753 Individual atomic B min max mean iso aniso Overall: 5.57 62.26 14.54 0.86 529 3268 Protein: 5.57 28.00 10.34 0.86 0 2902 Water: 6.05 62.26 28.18 N/A 529 364 Other: 13.87 22.00 17.94 N/A 0 2 Chain A: 5.65 51.48 12.10 N/A 0 1623 Chain B: 5.57 62.26 11.96 N/A 0 1645 Chain S: 6.05 61.16 30.07 N/A 529 0 Histogram: Values Number of atoms 5.57 - 11.24 2040 11.24 - 16.91 841 16.91 - 22.58 277 22.58 - 28.25 193 28.25 - 33.92 191 33.92 - 39.59 118 39.59 - 45.26 93 45.26 - 50.93 27 50.93 - 56.59 13 56.59 - 62.26 4 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1364 r_work=0.1197 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1364 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1363 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753209 | | target function (ml) not normalized (work): 702938.524188 | | target function (ml) not normalized (free): 14724.518549 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1383 0.1533 5.7072 5.8027| | 2: 2.94 - 2.33 1.00 7339 128 0.1079 0.1352 5.095 5.1953| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1174 4.6567 4.7373| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1057 4.3912 4.5709| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0995 4.1467 4.2512| | 6: 1.72 - 1.62 0.99 7102 142 0.0893 0.1077 3.9427 4.0655| | 7: 1.62 - 1.54 0.99 7104 148 0.0886 0.0952 3.792 3.9202| | 8: 1.54 - 1.47 0.96 6798 152 0.0886 0.1302 3.6941 3.8919| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1135 3.6184 3.7512| | 10: 1.41 - 1.36 0.99 7022 150 0.0971 0.1177 3.5512 3.6667| | 11: 1.36 - 1.32 0.99 6997 151 0.0988 0.1119 3.48 3.5828| | 12: 1.32 - 1.28 0.98 6975 149 0.1028 0.1118 3.4544 3.5756| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1236 3.4331 3.5611| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1584 3.4297 3.6737| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1233 3.4445 3.4883| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1551 3.4623 3.6569| | 17: 1.17 - 1.14 0.98 6940 135 0.1297 0.1224 3.4312 3.4399| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1703 3.4365 3.5316| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1739 3.4184 3.5964| | 20: 1.10 - 1.08 0.97 6884 147 0.1580 0.1574 3.4084 3.4296| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2125 3.4171 3.5031| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1953 3.4121 3.4136| | 23: 1.05 - 1.03 0.97 6827 159 0.2116 0.2020 3.4324 3.4873| | 24: 1.03 - 1.02 0.96 6784 133 0.2328 0.2253 3.4348 3.5109| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2522 3.4491 3.5251| | 26: 1.01 - 0.99 0.96 6767 158 0.2754 0.2856 3.4151 3.4238| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2802 3.4687 3.3961| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7399 127 0.93 12.27 1.00 0.95 12054.88| | 2: 2.94 - 2.33 7339 128 0.92 13.23 0.99 0.95 5411.75| | 3: 2.33 - 2.04 6939 150 0.96 7.63 1.01 0.95 1697.86| | 4: 2.04 - 1.85 7170 155 0.96 7.65 1.00 0.95 1005.05| | 5: 1.85 - 1.72 7113 159 0.96 8.04 1.00 0.96 629.87| | 6: 1.72 - 1.62 7102 142 0.96 7.90 1.00 0.96 436.47| | 7: 1.62 - 1.54 7104 148 0.96 7.99 1.01 0.97 330.27| | 8: 1.54 - 1.47 6798 152 0.96 8.16 1.01 0.97 275.03| | 9: 1.47 - 1.41 6938 155 0.96 8.38 1.00 0.98 228.21| | 10: 1.41 - 1.36 7022 150 0.96 8.84 1.00 0.97 199.98| | 11: 1.36 - 1.32 6997 151 0.96 8.81 0.99 0.96 171.96| | 12: 1.32 - 1.28 6975 149 0.96 8.87 0.98 0.95 158.36| | 13: 1.28 - 1.25 6907 166 0.96 9.45 1.01 0.96 156.62| | 14: 1.25 - 1.22 7015 112 0.95 10.65 1.01 0.97 162.02| | 15: 1.22 - 1.19 6956 137 0.95 11.18 1.01 0.98 165.57| | 16: 1.19 - 1.17 6604 132 0.95 11.38 1.01 0.96 159.38| | 17: 1.17 - 1.14 6940 135 0.94 12.20 1.01 0.96 153.33| | 18: 1.14 - 1.12 6875 142 0.94 12.70 1.01 0.95 147.12| | 19: 1.12 - 1.10 6948 106 0.93 14.09 1.00 0.95 150.37| | 20: 1.10 - 1.08 6884 147 0.92 15.15 1.00 0.94 149.31| | 21: 1.08 - 1.07 6852 152 0.91 16.60 1.00 0.93 152.71| | 22: 1.07 - 1.05 6836 135 0.89 18.28 0.99 0.93 154.75| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 164.99| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.99 0.93 179.37| | 25: 1.02 - 1.01 6552 130 0.83 25.19 0.98 0.90 182.45| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.89 176.91| | 27: 0.99 - 0.98 6647 131 0.82 26.32 0.99 0.87 161.30| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.12 max = 12054.88 mean = 968.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.29| |phase err.(test): min = 0.00 max = 89.46 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1417 0.1415 0.1514 n_refl.: 191131 remove outliers: r(all,work,free)=0.1417 0.1415 0.1514 n_refl.: 191131 overall B=-0.06 to atoms: r(all,work,free)=0.1408 0.1406 0.1507 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1361 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1195 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 0.3918 361.234 319.435 0.398 0.913 0.207 13.296-10.522 97.03 97 1 0.2442 478.186 460.137 0.719 0.914 0.154 10.503-8.327 97.80 175 3 0.2207 501.953 493.991 0.891 0.915 0.120 8.318-6.595 100.00 360 8 0.2235 375.579 370.039 0.923 0.915 0.095 6.588-5.215 100.00 711 7 0.1987 345.120 334.601 0.920 0.915 0.080 5.214-4.128 98.38 1367 28 0.1250 504.805 498.951 1.018 0.916 0.039 4.126-3.266 94.74 2603 46 0.1192 460.157 452.211 1.085 0.918 0.005 3.266-2.585 99.86 5447 97 0.1132 310.411 306.629 1.066 0.919 0.000 2.585-2.046 97.45 10613 204 0.0965 234.187 231.553 1.073 0.921 0.000 2.046-1.619 99.39 21536 464 0.0908 138.604 137.236 1.090 0.926 0.000 1.619-1.281 98.00 42464 925 0.0941 74.616 73.969 1.079 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.028 38.308 1.044 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0127 ================= 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 : 0.2042 0.1961 0.083 5.215 5.2 78.0 14.6 805 0.000 1_bss: 0.1808 0.1901 0.083 5.215 5.2 78.0 14.6 805 0.000 1_settarget: 0.1808 0.1901 0.083 5.215 5.2 78.0 14.6 805 0.000 1_nqh: 0.1808 0.1901 0.083 5.215 5.2 78.0 14.6 805 0.000 1_weight: 0.1808 0.1901 0.083 5.215 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1269 0.1499 0.039 1.155 5.2 78.0 14.6 805 0.156 1_adp: 0.1295 0.1567 0.039 1.155 5.1 73.0 14.9 805 0.156 1_regHadp: 0.1294 0.1562 0.039 1.155 5.1 73.0 14.9 805 0.156 1_occ: 0.1279 0.1553 0.039 1.155 5.1 73.0 14.9 805 0.156 2_bss: 0.1273 0.1545 0.039 1.155 5.3 73.2 15.1 805 0.156 2_settarget: 0.1273 0.1545 0.039 1.155 5.3 73.2 15.1 805 0.156 2_updatecdl: 0.1273 0.1545 0.039 1.173 5.3 73.2 15.1 805 0.156 2_nqh: 0.1273 0.1545 0.039 1.173 5.3 73.2 15.1 805 0.156 2_sol: 0.1270 0.1505 0.039 1.173 5.3 73.2 16.1 882 n/a 2_weight: 0.1270 0.1505 0.039 1.173 5.3 73.2 16.1 882 n/a 2_xyzrec: 0.1253 0.1521 0.042 1.145 5.3 73.2 16.1 882 n/a 2_adp: 0.1230 0.1504 0.042 1.145 5.4 70.7 16.3 882 n/a 2_regHadp: 0.1231 0.1505 0.042 1.145 5.4 70.7 16.3 882 n/a 2_occ: 0.1225 0.1502 0.042 1.145 5.4 70.7 16.3 882 n/a 3_bss: 0.1232 0.1510 0.042 1.145 5.4 70.7 16.3 882 n/a 3_settarget: 0.1232 0.1510 0.042 1.145 5.4 70.7 16.3 882 n/a 3_updatecdl: 0.1232 0.1510 0.042 1.152 5.4 70.7 16.3 882 n/a 3_nqh: 0.1232 0.1510 0.042 1.152 5.4 70.7 16.3 882 n/a 3_sol: 0.1248 0.1506 0.042 1.152 5.4 68.2 15.3 866 n/a 3_weight: 0.1248 0.1506 0.042 1.152 5.4 68.2 15.3 866 n/a 3_xyzrec: 0.1235 0.1430 0.035 1.108 5.4 68.2 15.3 866 n/a 3_adp: 0.1231 0.1393 0.035 1.108 5.5 67.9 15.2 866 n/a 3_regHadp: 0.1232 0.1394 0.035 1.108 5.5 67.9 15.2 866 n/a 3_occ: 0.1226 0.1387 0.035 1.108 5.5 67.9 15.2 866 n/a 4_bss: 0.1222 0.1379 0.035 1.108 5.5 67.8 15.1 866 n/a 4_settarget: 0.1222 0.1379 0.035 1.108 5.5 67.8 15.1 866 n/a 4_updatecdl: 0.1222 0.1379 0.035 1.108 5.5 67.8 15.1 866 n/a 4_nqh: 0.1222 0.1379 0.035 1.108 5.5 67.8 15.1 866 n/a 4_sol: 0.1208 0.1369 0.035 1.108 5.5 67.8 14.8 833 n/a 4_weight: 0.1208 0.1369 0.035 1.108 5.5 67.8 14.8 833 n/a 4_xyzrec: 0.1209 0.1369 0.036 1.117 5.5 67.8 14.8 833 n/a 4_adp: 0.1204 0.1367 0.036 1.117 5.5 67.4 14.7 833 n/a 4_regHadp: 0.1204 0.1368 0.036 1.117 5.5 67.4 14.7 833 n/a 4_occ: 0.1203 0.1365 0.036 1.117 5.5 67.4 14.7 833 n/a 5_bss: 0.1201 0.1362 0.036 1.117 5.5 67.3 14.7 833 n/a 5_settarget: 0.1201 0.1362 0.036 1.117 5.5 67.3 14.7 833 n/a 5_updatecdl: 0.1201 0.1362 0.036 1.117 5.5 67.3 14.7 833 n/a 5_nqh: 0.1201 0.1362 0.036 1.117 5.5 67.3 14.7 833 n/a 5_sol: 0.1199 0.1368 0.036 1.117 5.5 67.3 14.8 855 n/a 5_weight: 0.1199 0.1368 0.036 1.117 5.5 67.3 14.8 855 n/a 5_xyzrec: 0.1201 0.1368 0.036 1.123 5.5 67.3 14.8 855 n/a 5_adp: 0.1206 0.1374 0.036 1.123 5.6 67.0 14.8 855 n/a 5_regHadp: 0.1206 0.1374 0.036 1.123 5.6 67.0 14.8 855 n/a 5_occ: 0.1205 0.1377 0.036 1.123 5.6 67.0 14.8 855 n/a 6_bss: 0.1204 0.1373 0.036 1.123 5.5 67.0 14.7 855 n/a 6_settarget: 0.1204 0.1373 0.036 1.123 5.5 67.0 14.7 855 n/a 6_updatecdl: 0.1204 0.1373 0.036 1.123 5.5 67.0 14.7 855 n/a 6_nqh: 0.1204 0.1373 0.036 1.123 5.5 67.0 14.7 855 n/a 6_sol: 0.1200 0.1363 0.036 1.123 5.5 67.0 14.8 875 n/a 6_weight: 0.1200 0.1363 0.036 1.123 5.5 67.0 14.8 875 n/a 6_xyzrec: 0.1204 0.1365 0.037 1.123 5.5 67.0 14.8 875 n/a 6_adp: 0.1206 0.1368 0.037 1.123 5.6 65.9 14.7 875 n/a 6_regHadp: 0.1206 0.1369 0.037 1.123 5.6 65.9 14.7 875 n/a 6_occ: 0.1204 0.1367 0.037 1.123 5.6 65.9 14.7 875 n/a 7_bss: 0.1203 0.1366 0.037 1.123 5.4 65.7 14.5 875 n/a 7_settarget: 0.1203 0.1366 0.037 1.123 5.4 65.7 14.5 875 n/a 7_updatecdl: 0.1203 0.1366 0.037 1.125 5.4 65.7 14.5 875 n/a 7_nqh: 0.1203 0.1366 0.037 1.125 5.4 65.7 14.5 875 n/a 7_sol: 0.1202 0.1359 0.037 1.125 5.4 65.7 14.6 879 n/a 7_weight: 0.1202 0.1359 0.037 1.125 5.4 65.7 14.6 879 n/a 7_xyzrec: 0.1205 0.1365 0.038 1.119 5.4 65.7 14.6 879 n/a 7_adp: 0.1208 0.1370 0.038 1.119 5.4 64.6 14.5 879 n/a 7_regHadp: 0.1208 0.1370 0.038 1.119 5.4 64.6 14.5 879 n/a 7_occ: 0.1206 0.1371 0.038 1.119 5.4 64.6 14.5 879 n/a 8_bss: 0.1197 0.1362 0.038 1.119 5.5 64.7 14.6 879 n/a 8_settarget: 0.1197 0.1362 0.038 1.119 5.5 64.7 14.6 879 n/a 8_updatecdl: 0.1197 0.1362 0.038 1.118 5.5 64.7 14.6 879 n/a 8_nqh: 0.1197 0.1362 0.038 1.118 5.5 64.7 14.6 879 n/a 8_sol: 0.1196 0.1356 0.038 1.118 5.5 64.7 14.6 893 n/a 8_weight: 0.1196 0.1356 0.038 1.118 5.5 64.7 14.6 893 n/a 8_xyzrec: 0.1199 0.1359 0.038 1.128 5.5 64.7 14.6 893 n/a 8_adp: 0.1198 0.1361 0.038 1.128 5.5 63.6 14.6 893 n/a 8_regHadp: 0.1198 0.1362 0.038 1.128 5.5 63.6 14.6 893 n/a 8_occ: 0.1196 0.1361 0.038 1.128 5.5 63.6 14.6 893 n/a 9_bss: 0.1195 0.1358 0.038 1.128 5.5 63.7 14.6 893 n/a 9_settarget: 0.1195 0.1358 0.038 1.128 5.5 63.7 14.6 893 n/a 9_updatecdl: 0.1195 0.1358 0.038 1.128 5.5 63.7 14.6 893 n/a 9_nqh: 0.1195 0.1358 0.038 1.128 5.5 63.7 14.6 893 n/a 9_sol: 0.1194 0.1357 0.038 1.128 5.5 63.7 14.6 893 n/a 9_weight: 0.1194 0.1357 0.038 1.128 5.5 63.7 14.6 893 n/a 9_xyzrec: 0.1199 0.1361 0.038 1.112 5.5 63.7 14.6 893 n/a 9_adp: 0.1199 0.1364 0.038 1.112 5.5 63.3 14.6 893 n/a 9_regHadp: 0.1199 0.1364 0.038 1.112 5.5 63.3 14.6 893 n/a 9_occ: 0.1198 0.1365 0.038 1.112 5.5 63.3 14.6 893 n/a 10_bss: 0.1197 0.1364 0.038 1.112 5.5 63.3 14.6 893 n/a 10_settarget: 0.1197 0.1364 0.038 1.112 5.5 63.3 14.6 893 n/a 10_updatecdl: 0.1197 0.1364 0.038 1.112 5.5 63.3 14.6 893 n/a 10_setrh: 0.1198 0.1365 0.038 1.112 5.5 63.3 14.6 893 n/a 10_nqh: 0.1198 0.1365 0.038 1.112 5.5 63.3 14.6 893 n/a 10_sol: 0.1196 0.1361 0.038 1.112 5.5 63.3 14.5 893 n/a 10_weight: 0.1196 0.1361 0.038 1.112 5.5 63.3 14.5 893 n/a 10_xyzrec: 0.1197 0.1363 0.038 1.147 5.5 63.3 14.5 893 n/a 10_adp: 0.1197 0.1364 0.038 1.147 5.6 62.3 14.5 893 n/a 10_regHadp: 0.1197 0.1364 0.038 1.147 5.6 62.3 14.5 893 n/a 10_occ: 0.1196 0.1363 0.038 1.147 5.6 62.3 14.5 893 n/a end: 0.1196 0.1361 0.038 1.147 5.5 62.2 14.5 893 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8230052_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8230052_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.8300 Refinement macro-cycles (run) : 12086.1600 Write final files (write_after_run_outputs) : 161.7600 Total : 12253.7500 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:26 PST -0800 (1736736086.42 s) Start R-work = 0.1808, R-free = 0.1901 Final R-work = 0.1196, R-free = 0.1361 =============================================================================== Job complete usr+sys time: 12538.39 seconds wall clock time: 209 minutes 57.93 seconds (12597.93 seconds total)