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_1852271.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1852271.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_1852271.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.81, per 1000 atoms: 0.27 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.721 distance_ideal: 2.720 ideal - model: -0.001 slack: 0.000 delta_slack: -0.001 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: 2.593 distance_ideal: 2.710 ideal - model: 0.117 slack: 0.000 delta_slack: 0.117 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 123.5 milliseconds Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.06: 1167 1.06 - 1.29: 2329 1.29 - 1.53: 1647 1.53 - 1.76: 779 1.76 - 1.99: 12 Bond restraints: 5934 Sorted by residual: bond pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta sigma weight residual 1.458 1.703 -0.245 1.19e-02 7.06e+03 4.25e+02 bond pdb=" CA LEU A 152 " pdb=" C LEU A 152 " ideal model delta sigma weight residual 1.521 1.752 -0.231 1.17e-02 7.31e+03 3.89e+02 bond pdb=" CA VAL B 112 " pdb=" C VAL B 112 " ideal model delta sigma weight residual 1.524 1.729 -0.205 1.06e-02 8.90e+03 3.75e+02 bond pdb=" N THR B 86 " pdb=" H THR B 86 " ideal model delta sigma weight residual 0.860 1.247 -0.387 2.00e-02 2.50e+03 3.74e+02 bond pdb=" N ILE A 168 " pdb=" CA ILE A 168 " ideal model delta sigma weight residual 1.461 1.690 -0.229 1.19e-02 7.06e+03 3.71e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 5838 4.31 - 8.62: 3461 8.62 - 12.94: 1285 12.94 - 17.25: 208 17.25 - 21.56: 18 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O VAL B 37 " pdb=" C VAL B 37 " pdb=" N ALA B 38 " ideal model delta sigma weight residual 122.05 142.87 -20.82 1.05e+00 9.07e-01 3.93e+02 angle pdb=" CA ILE A 30 " pdb=" C ILE A 30 " pdb=" N LYS A 31 " ideal model delta sigma weight residual 116.36 132.72 -16.36 9.70e-01 1.06e+00 2.85e+02 angle pdb=" O LYS A 52 " pdb=" C LYS A 52 " pdb=" N LEU A 53 " ideal model delta sigma weight residual 123.05 140.16 -17.11 1.19e+00 7.06e-01 2.07e+02 angle pdb=" O VAL B 112 " pdb=" C VAL B 112 " pdb=" N LEU B 113 " ideal model delta sigma weight residual 121.98 133.02 -11.04 7.70e-01 1.69e+00 2.06e+02 angle pdb=" N VAL B 19 " pdb=" CA VAL B 19 " pdb=" C VAL B 19 " ideal model delta sigma weight residual 110.42 124.06 -13.64 9.60e-01 1.09e+00 2.02e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 1833 17.22 - 34.44: 148 34.44 - 51.67: 50 51.67 - 68.89: 13 68.89 - 86.11: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ILE B 105 " pdb=" C ILE B 105 " pdb=" N CYS B 106 " pdb=" CA CYS B 106 " ideal model delta harmonic sigma weight residual 180.00 152.54 27.46 0 5.00e+00 4.00e-02 3.02e+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 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ALA B 44 " pdb=" C ALA B 44 " pdb=" N ILE B 45 " pdb=" CA ILE B 45 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.228: 208 0.228 - 0.454: 165 0.454 - 0.680: 94 0.680 - 0.906: 20 0.906 - 1.132: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE A 121 " pdb=" N ILE A 121 " pdb=" C ILE A 121 " pdb=" CB ILE A 121 " both_signs ideal model delta sigma weight residual False 2.43 3.57 -1.13 2.00e-01 2.50e+01 3.20e+01 chirality pdb=" CG LEU A 171 " pdb=" CB LEU A 171 " pdb=" CD1 LEU A 171 " pdb=" CD2 LEU A 171 " both_signs ideal model delta sigma weight residual False -2.59 -3.71 1.12 2.00e-01 2.50e+01 3.13e+01 chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.50 -1.09 2.00e-01 2.50e+01 2.97e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 192 " 0.076 2.00e-02 2.50e+03 6.98e-02 1.46e+02 pdb=" CG TYR B 192 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR B 192 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 TYR B 192 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR B 192 " -0.048 2.00e-02 2.50e+03 pdb=" CE2 TYR B 192 " 0.127 2.00e-02 2.50e+03 pdb=" CZ TYR B 192 " -0.035 2.00e-02 2.50e+03 pdb=" OH TYR B 192 " 0.086 2.00e-02 2.50e+03 pdb=" HD1 TYR B 192 " 0.065 2.00e-02 2.50e+03 pdb=" HD2 TYR B 192 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR B 192 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR B 192 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 195 " -0.106 2.00e-02 2.50e+03 6.62e-02 1.32e+02 pdb=" CG TYR A 195 " 0.112 2.00e-02 2.50e+03 pdb=" CD1 TYR A 195 " 0.103 2.00e-02 2.50e+03 pdb=" CD2 TYR A 195 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 195 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 195 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR A 195 " -0.058 2.00e-02 2.50e+03 pdb=" OH TYR A 195 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 TYR A 195 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 195 " -0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR A 195 " -0.042 2.00e-02 2.50e+03 pdb=" HE2 TYR A 195 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.006 2.00e-02 2.50e+03 5.65e-02 1.28e+02 pdb=" CG TRP A 139 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.106 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.068 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.099 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.010 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.050 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.101 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " -0.020 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.66: 33 1.66 - 2.39: 2864 2.39 - 3.13: 22591 3.13 - 3.86: 32754 3.86 - 4.60: 52007 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110249 Sorted by model distance: nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.919 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.953 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.953 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.135 2.620 nonbonded pdb="HG22 VAL A 181 " pdb=" O HOH S1566 " model vdw 1.185 2.620 ... (remaining 110244 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_1852271_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2034 r_free= 0.1971 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.302775 | | target function (ml) not normalized (work): 805965.742148 | | target function (ml) not normalized (free): 16603.220559 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2142 0.1844 6.7078 6.2845| | 2: 2.94 - 2.33 1.00 7339 128 0.1637 0.1560 5.5236 5.5679| | 3: 2.33 - 2.04 0.96 6939 150 0.1621 0.1486 5.1411 5.0764| | 4: 2.04 - 1.85 1.00 7170 155 0.1730 0.1669 4.9572 5.0892| | 5: 1.85 - 1.72 0.99 7113 159 0.1897 0.1764 4.7906 4.84| | 6: 1.72 - 1.62 0.99 7102 142 0.1982 0.2002 4.6673 4.7219| | 7: 1.62 - 1.54 0.99 7104 148 0.2054 0.1776 4.5777 4.5889| | 8: 1.54 - 1.47 0.96 6798 152 0.2021 0.2070 4.4611 4.4867| | 9: 1.47 - 1.41 0.98 6938 155 0.2111 0.2107 4.4006 4.4289| | 10: 1.41 - 1.36 0.99 7022 150 0.2120 0.2272 4.3128 4.3729| | 11: 1.36 - 1.32 0.99 6997 151 0.2084 0.2224 4.235 4.3202| | 12: 1.32 - 1.28 0.98 6976 149 0.2086 0.2139 4.1901 4.2976| | 13: 1.28 - 1.25 0.98 6907 166 0.2050 0.2138 4.1336 4.1735| | 14: 1.25 - 1.22 0.98 7015 113 0.2071 0.2394 4.0795 4.2597| | 15: 1.22 - 1.19 0.98 6957 137 0.2116 0.2021 4.0466 3.9879| | 16: 1.19 - 1.17 0.93 6604 132 0.2135 0.2325 4.0148 4.0863| | 17: 1.17 - 1.14 0.98 6941 135 0.2148 0.2062 3.9536 4.0283| | 18: 1.14 - 1.12 0.98 6875 142 0.2211 0.2261 3.9254 3.9562| | 19: 1.12 - 1.10 0.97 6949 106 0.2267 0.2482 3.8814 3.9753| | 20: 1.10 - 1.08 0.97 6884 147 0.2317 0.2378 3.8331 3.9231| | 21: 1.08 - 1.07 0.97 6852 152 0.2399 0.2890 3.7917 3.865| | 22: 1.07 - 1.05 0.97 6838 135 0.2576 0.2714 3.7625 3.8479| | 23: 1.05 - 1.03 0.97 6829 159 0.2687 0.2599 3.721 3.8128| | 24: 1.03 - 1.02 0.96 6785 133 0.2917 0.2662 3.712 3.7449| | 25: 1.02 - 1.01 0.93 6552 130 0.3094 0.3010 3.6849 3.7504| | 26: 1.01 - 0.99 0.96 6767 158 0.3161 0.2962 3.6195 3.5925| | 27: 0.99 - 0.98 0.94 6648 131 0.3412 0.3350 3.6373 3.6325| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.95 0.91 0.97 33595.54| | 2: 2.94 - 2.33 7339 128 0.86 20.43 1.09 1.02 14179.15| | 3: 2.33 - 2.04 6939 150 0.94 11.91 1.11 1.05 3872.21| | 4: 2.04 - 1.85 7170 155 0.92 13.52 1.11 1.06 2788.21| | 5: 1.85 - 1.72 7113 159 0.90 16.08 1.11 1.07 2155.58| | 6: 1.72 - 1.62 7102 142 0.90 17.12 1.11 1.06 1708.82| | 7: 1.62 - 1.54 7104 148 0.89 17.87 1.11 1.05 1351.72| | 8: 1.54 - 1.47 6798 152 0.88 18.64 1.10 1.03 1125.52| | 9: 1.47 - 1.41 6938 155 0.88 19.15 1.10 1.05 984.55| | 10: 1.41 - 1.36 7022 150 0.87 20.63 1.10 1.06 904.65| | 11: 1.36 - 1.32 6997 151 0.86 21.04 1.08 1.06 814.77| | 12: 1.32 - 1.28 6976 149 0.86 20.91 1.08 1.04 719.65| | 13: 1.28 - 1.25 6907 166 0.87 20.42 1.07 1.03 633.74| | 14: 1.25 - 1.22 7015 113 0.86 20.81 1.07 1.04 582.34| | 15: 1.22 - 1.19 6957 137 0.87 20.79 1.08 1.04 539.17| | 16: 1.19 - 1.17 6604 132 0.87 20.75 1.07 1.03 504.04| | 17: 1.17 - 1.14 6941 135 0.86 21.79 1.08 1.01 469.74| | 18: 1.14 - 1.12 6875 142 0.85 22.50 1.08 0.99 441.28| | 19: 1.12 - 1.10 6949 106 0.84 23.70 1.07 0.99 428.19| | 20: 1.10 - 1.08 6884 147 0.83 24.91 1.06 0.97 408.49| | 21: 1.08 - 1.07 6852 152 0.81 26.17 1.06 0.97 394.12| | 22: 1.07 - 1.05 6838 135 0.80 27.07 1.06 0.98 367.51| | 23: 1.05 - 1.03 6829 159 0.80 27.83 1.06 0.98 341.77| | 24: 1.03 - 1.02 6785 133 0.79 28.79 1.06 1.00 321.48| | 25: 1.02 - 1.01 6552 130 0.78 29.59 1.04 0.96 298.48| | 26: 1.01 - 0.99 6767 158 0.76 31.47 1.04 0.94 286.49| | 27: 0.99 - 0.98 6648 131 0.75 32.60 1.05 0.91 280.78| |alpha: min = 0.91 max = 1.07 mean = 1.01| |beta: min = 280.78 max = 33595.54 mean = 2731.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.01| |phase err.(test): min = 0.00 max = 89.76 mean = 21.98| |-----------------------------------------------------------------------------| ----------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 0.250 2950 Z= 5.525 Angle : 5.197 20.815 4018 Z= 3.698 Chirality : 0.373 1.132 492 Planarity : 0.034 0.163 512 Dihedral : 12.916 86.109 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.89 % Favored : 95.60 % Rotamer: Outliers : 0.32 % Allowed : 6.45 % Favored : 93.23 % Cbeta Deviations : 28.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.41), residues: 386 helix: -2.67 (0.29), residues: 144 sheet: -0.89 (0.54), residues: 86 loop : 0.40 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.092 0.022 ARG A 100 TYR 0.115 0.047 TYR B 195 PHE 0.108 0.033 PHE A 95 TRP 0.124 0.044 TRP B 146 HIS 0.081 0.037 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= 0.2034 r_free= 0.1971 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.302775 | | target function (ml) not normalized (work): 805965.742148 | | target function (ml) not normalized (free): 16603.220559 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2031 0.2034 0.1971 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2031 0.2034 0.1971 n_refl.: 191155 remove outliers: r(all,work,free)=0.2031 0.2034 0.1971 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2032 0.2034 0.1971 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1802 0.1800 0.1923 n_refl.: 191145 remove outliers: r(all,work,free)=0.1800 0.1797 0.1923 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 0.4074 402.814 291.546 0.422 0.936 0.297 13.296-10.522 98.02 98 1 0.2430 527.329 512.582 0.762 0.937 0.246 10.503-8.327 98.90 177 3 0.2458 564.205 558.672 0.950 0.937 0.223 8.318-6.595 100.00 360 8 0.2481 414.736 404.831 0.947 0.936 0.175 6.588-5.215 100.00 711 7 0.2257 381.101 365.536 0.929 0.936 0.123 5.214-4.128 98.38 1367 28 0.1502 557.435 549.745 1.046 0.936 0.080 4.126-3.266 94.74 2603 46 0.1354 508.132 499.211 1.117 0.935 0.023 3.266-2.585 99.86 5447 97 0.1447 342.774 337.716 1.096 0.932 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 254.412 1.102 0.929 0.000 2.046-1.619 99.39 21536 464 0.1607 153.054 149.801 1.124 0.923 0.000 1.619-1.281 98.00 42464 925 0.1918 82.395 80.231 1.121 0.915 0.000 1.281-0.980 96.53 101826 2056 0.2315 44.203 41.694 1.120 0.898 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0079 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1923 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.1797 r_free=0.1923 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.594276 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 579.075710 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1265 0.1490 0.0225 0.038 1.2 11.0 0.0 0.0 0 11.297 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.65 14.90 2.25 1.117 13.115 579.076 0.018 12.96 15.65 2.69 1.257 13.362 579.076 0.017 Individual atomic B min max mean iso aniso Overall: 5.12 73.05 15.05 1.40 435 3274 Protein: 5.12 40.34 11.02 1.40 0 2902 Water: 6.33 73.05 29.57 N/A 435 370 Other: 15.98 30.42 23.20 N/A 0 2 Chain A: 5.32 60.26 13.07 N/A 0 1626 Chain B: 5.12 73.05 12.80 N/A 0 1648 Chain S: 11.52 65.47 31.01 N/A 435 0 Histogram: Values Number of atoms 5.12 - 11.91 2150 11.91 - 18.70 649 18.70 - 25.50 316 25.50 - 32.29 268 32.29 - 39.08 153 39.08 - 45.88 105 45.88 - 52.67 43 52.67 - 59.46 19 59.46 - 66.26 5 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1565 r_work=0.1295 r_free=0.1560 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1560 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1280 r_free = 0.1551 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015466 | | target function (ls_wunit_k1) not normalized (work): 2896.638410 | | target function (ls_wunit_k1) not normalized (free): 114.074474 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1285 0.1280 0.1551 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1467 0.1464 0.1631 n_refl.: 191137 remove outliers: r(all,work,free)=0.1467 0.1464 0.1631 n_refl.: 191137 overall B=0.16 to atoms: r(all,work,free)=0.1489 0.1487 0.1641 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1547 n_refl.: 191137 remove outliers: r(all,work,free)=0.1279 0.1274 0.1546 n_refl.: 191136 ======================== 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 0.3614 402.814 378.922 0.487 0.963 0.281 13.296-10.522 98.02 98 1 0.2027 527.329 523.407 0.750 0.964 0.249 10.503-8.327 98.90 177 3 0.1714 564.205 562.537 0.888 0.964 0.198 8.318-6.595 100.00 360 8 0.1725 414.736 412.560 0.909 0.964 0.150 6.588-5.215 100.00 711 7 0.1535 381.101 373.609 0.887 0.964 0.140 5.214-4.128 98.38 1367 28 0.0903 557.435 555.066 0.975 0.965 0.049 4.126-3.266 94.74 2603 46 0.0827 508.132 504.199 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0917 342.774 340.350 1.026 0.965 0.000 2.585-2.046 97.45 10613 204 0.0947 258.603 256.374 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.381 1.054 0.966 0.000 1.619-1.281 98.00 42464 925 0.1283 82.395 81.410 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.164 1.023 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0364 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1546 | n_water=805 | time (s): 2.810 (total time: 2.810) Filter (dist) r_work=0.1279 r_free=0.1551 | n_water=794 | time (s): 99.310 (total time: 102.120) Filter (q & B) r_work=0.1279 r_free=0.1550 | n_water=789 | time (s): 4.300 (total time: 106.420) Compute maps r_work=0.1279 r_free=0.1550 | n_water=789 | time (s): 1.780 (total time: 108.200) Filter (map) r_work=0.1306 r_free=0.1537 | n_water=651 | time (s): 4.060 (total time: 112.260) Find peaks r_work=0.1306 r_free=0.1537 | n_water=651 | time (s): 0.580 (total time: 112.840) Add new water r_work=0.1329 r_free=0.1571 | n_water=968 | time (s): 4.360 (total time: 117.200) Refine new water occ: r_work=0.1285 r_free=0.1520 adp: r_work=0.1272 r_free=0.1516 occ: r_work=0.1274 r_free=0.1514 adp: r_work=0.1268 r_free=0.1512 occ: r_work=0.1269 r_free=0.1512 adp: r_work=0.1266 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1512 r_work=0.1266 r_free=0.1512 | n_water=968 | time (s): 85.470 (total time: 202.670) Filter (q & B) r_work=0.1270 r_free=0.1510 | n_water=884 | time (s): 4.810 (total time: 207.480) Filter (dist only) r_work=0.1271 r_free=0.1509 | n_water=883 | time (s): 112.050 (total time: 319.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.135075 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 602.061634 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1256 0.1531 0.0275 0.041 1.1 17.3 0.0 0.0 0 12.068 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.31 2.75 2.047 15.213 602.062 0.014 12.31 15.10 2.79 2.431 15.253 602.062 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.33 16.35 1.21 515 3272 Protein: 5.38 40.80 10.98 1.21 0 2902 Water: 6.62 68.33 33.97 N/A 515 368 Other: 16.35 32.44 24.39 N/A 0 2 Chain A: 5.55 56.39 13.00 N/A 0 1624 Chain B: 5.38 68.21 12.83 N/A 0 1648 Chain S: 8.93 68.33 38.18 N/A 515 0 Histogram: Values Number of atoms 5.38 - 11.68 2057 11.68 - 17.97 720 17.97 - 24.27 252 24.27 - 30.56 218 30.56 - 36.86 171 36.86 - 43.15 156 43.15 - 49.45 107 49.45 - 55.74 56 55.74 - 62.04 32 62.04 - 68.33 18 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1510 r_work=0.1232 r_free=0.1511 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1511 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 = 0.1224 r_free = 0.1511 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1511 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013351 | | target function (ls_wunit_k1) not normalized (work): 2500.593004 | | target function (ls_wunit_k1) not normalized (free): 102.884322 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1224 0.1511 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1431 0.1428 0.1599 n_refl.: 191136 remove outliers: r(all,work,free)=0.1431 0.1428 0.1599 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1428 0.1425 0.1597 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1519 n_refl.: 191136 remove outliers: r(all,work,free)=0.1237 0.1231 0.1519 n_refl.: 191136 ======================== 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 0.3237 402.814 380.331 0.491 0.963 0.271 13.296-10.522 98.02 98 1 0.1841 527.329 518.295 0.762 0.964 0.223 10.503-8.327 98.90 177 3 0.1449 564.205 567.146 0.916 0.964 0.169 8.318-6.595 100.00 360 8 0.1566 414.736 415.349 0.934 0.964 0.140 6.588-5.215 100.00 711 7 0.1346 381.101 376.942 0.913 0.964 0.140 5.214-4.128 98.38 1367 28 0.0827 557.435 556.260 0.993 0.964 0.070 4.126-3.266 94.74 2603 46 0.0756 508.132 505.472 1.059 0.964 0.014 3.266-2.585 99.86 5447 97 0.0857 342.774 341.466 1.046 0.963 0.000 2.585-2.046 97.45 10613 204 0.0898 258.603 256.763 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.645 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.354 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.220 1.058 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0534 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1518 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1518 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1518 | n_water=883 | time (s): 3.530 (total time: 3.530) Filter (dist) r_work=0.1233 r_free=0.1519 | n_water=878 | time (s): 108.450 (total time: 111.980) Filter (q & B) r_work=0.1233 r_free=0.1520 | n_water=874 | time (s): 5.230 (total time: 117.210) Compute maps r_work=0.1233 r_free=0.1520 | n_water=874 | time (s): 1.650 (total time: 118.860) Filter (map) r_work=0.1273 r_free=0.1527 | n_water=683 | time (s): 5.320 (total time: 124.180) Find peaks r_work=0.1273 r_free=0.1527 | n_water=683 | time (s): 0.680 (total time: 124.860) Add new water r_work=0.1294 r_free=0.1565 | n_water=1005 | time (s): 4.540 (total time: 129.400) Refine new water occ: r_work=0.1250 r_free=0.1518 adp: r_work=0.1251 r_free=0.1520 occ: r_work=0.1247 r_free=0.1514 adp: r_work=0.1247 r_free=0.1516 occ: r_work=0.1244 r_free=0.1510 adp: r_work=0.1244 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1510 r_work=0.1244 r_free=0.1510 | n_water=1005 | time (s): 165.130 (total time: 294.530) Filter (q & B) r_work=0.1250 r_free=0.1514 | n_water=871 | time (s): 5.100 (total time: 299.630) Filter (dist only) r_work=0.1250 r_free=0.1513 | n_water=870 | time (s): 122.080 (total time: 421.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.656776 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.303895 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 0.1240 0.1440 0.0200 0.035 1.1 7.5 0.0 0.0 0 0.828 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.40 2.00 1.934 14.485 16.304 3.939 12.38 14.01 1.63 2.255 14.388 16.304 3.897 Individual atomic B min max mean iso aniso Overall: 5.56 67.73 15.08 1.05 503 3271 Protein: 5.56 36.74 10.73 1.05 0 2902 Water: 6.71 67.73 29.60 N/A 503 367 Other: 13.96 28.14 21.05 N/A 0 2 Chain A: 5.56 55.38 12.75 N/A 0 1624 Chain B: 5.57 67.73 12.53 N/A 0 1647 Chain S: 12.77 62.85 30.98 N/A 503 0 Histogram: Values Number of atoms 5.56 - 11.77 2139 11.77 - 17.99 686 17.99 - 24.21 308 24.21 - 30.42 256 30.42 - 36.64 156 36.64 - 42.86 129 42.86 - 49.07 68 49.07 - 55.29 24 55.29 - 61.51 4 61.51 - 67.73 4 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1401 r_work=0.1239 r_free=0.1402 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1402 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1234 r_free = 0.1394 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1234 r_free= 0.1394 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891678 | | target function (ml) not normalized (work): 728891.834101 | | target function (ml) not normalized (free): 15219.464787 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1234 0.1393 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1449 0.1449 0.1480 n_refl.: 191136 remove outliers: r(all,work,free)=0.1449 0.1449 0.1480 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1443 0.1443 0.1477 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1233 0.1230 0.1384 n_refl.: 191136 remove outliers: r(all,work,free)=0.1232 0.1229 0.1384 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3740 398.895 357.778 0.407 0.946 0.231 13.296-10.522 96.04 96 1 0.2253 530.568 501.716 0.708 0.947 0.206 10.503-8.327 97.80 175 3 0.2092 554.286 556.598 0.877 0.947 0.165 8.318-6.595 100.00 360 8 0.2147 414.736 410.245 0.897 0.947 0.125 6.588-5.215 100.00 711 7 0.1858 381.101 370.455 0.886 0.947 0.120 5.214-4.128 98.38 1367 28 0.1194 557.435 551.748 0.972 0.947 0.070 4.126-3.266 94.74 2603 46 0.1110 508.132 501.438 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1095 342.774 339.128 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0972 258.603 255.744 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.432 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.499 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.324 1.040 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1072 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1229 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1384 | n_water=870 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1229 r_free=0.1384 | n_water=870 | time (s): 101.150 (total time: 104.300) Filter (q & B) r_work=0.1230 r_free=0.1381 | n_water=852 | time (s): 5.360 (total time: 109.660) Compute maps r_work=0.1230 r_free=0.1381 | n_water=852 | time (s): 2.300 (total time: 111.960) Filter (map) r_work=0.1250 r_free=0.1390 | n_water=720 | time (s): 4.750 (total time: 116.710) Find peaks r_work=0.1250 r_free=0.1390 | n_water=720 | time (s): 0.550 (total time: 117.260) Add new water r_work=0.1264 r_free=0.1405 | n_water=966 | time (s): 3.940 (total time: 121.200) Refine new water occ: r_work=0.1215 r_free=0.1370 adp: r_work=0.1207 r_free=0.1365 occ: r_work=0.1205 r_free=0.1366 adp: r_work=0.1205 r_free=0.1365 occ: r_work=0.1203 r_free=0.1366 adp: r_work=0.1203 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1365 r_work=0.1203 r_free=0.1365 | n_water=966 | time (s): 304.890 (total time: 426.090) Filter (q & B) r_work=0.1209 r_free=0.1369 | n_water=864 | time (s): 4.230 (total time: 430.320) Filter (dist only) r_work=0.1209 r_free=0.1369 | n_water=863 | time (s): 111.270 (total time: 541.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.585670 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.036339 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1369 0.0162 0.036 1.1 6.6 0.0 0.3 0 0.793 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.69 1.62 1.826 14.160 15.036 3.874 12.00 13.68 1.67 1.902 14.132 15.036 3.867 Individual atomic B min max mean iso aniso Overall: 5.55 67.37 14.93 1.00 496 3271 Protein: 5.55 33.68 10.67 1.00 0 2902 Water: 5.91 67.37 29.25 N/A 496 367 Other: 13.94 27.46 20.70 N/A 0 2 Chain A: 5.55 54.49 12.64 N/A 0 1624 Chain B: 5.56 67.37 12.45 N/A 0 1647 Chain S: 5.91 62.77 30.66 N/A 496 0 Histogram: Values Number of atoms 5.55 - 11.74 2128 11.74 - 17.92 716 17.92 - 24.10 288 24.10 - 30.28 258 30.28 - 36.46 164 36.46 - 42.64 120 42.64 - 48.82 63 48.82 - 55.01 24 55.01 - 61.19 2 61.19 - 67.37 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1368 r_work=0.1200 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1368 target_work(ml) = 3.868 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1366 target_work(ml) = 3.866 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865689 | | target function (ml) not normalized (work): 724000.950697 | | target function (ml) not normalized (free): 15148.178041 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1406 0.1405 0.1477 n_refl.: 191130 remove outliers: r(all,work,free)=0.1406 0.1405 0.1477 n_refl.: 191130 overall B=-0.03 to atoms: r(all,work,free)=0.1399 0.1398 0.1473 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3843 361.285 322.857 0.391 0.951 0.211 13.296-10.522 96.04 96 1 0.2337 480.543 460.515 0.710 0.953 0.190 10.503-8.327 97.80 175 3 0.2142 502.024 495.998 0.854 0.953 0.190 8.318-6.595 100.00 360 8 0.2178 375.632 371.207 0.889 0.953 0.118 6.588-5.215 100.00 711 7 0.1899 345.168 335.464 0.880 0.953 0.097 5.214-4.128 98.38 1367 28 0.1197 504.876 499.551 0.968 0.953 0.060 4.126-3.266 94.74 2603 46 0.1120 460.222 453.851 1.029 0.953 0.005 3.266-2.585 99.86 5447 97 0.1085 310.455 307.238 1.016 0.952 0.000 2.585-2.046 97.45 10613 204 0.0934 234.220 231.735 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0918 138.623 137.306 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0991 74.627 73.897 1.050 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.034 38.368 1.039 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1363 | n_water=863 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1198 r_free=0.1366 | n_water=861 | time (s): 106.800 (total time: 109.210) Filter (q & B) r_work=0.1199 r_free=0.1366 | n_water=849 | time (s): 5.040 (total time: 114.250) Compute maps r_work=0.1199 r_free=0.1366 | n_water=849 | time (s): 1.850 (total time: 116.100) Filter (map) r_work=0.1219 r_free=0.1364 | n_water=729 | time (s): 5.130 (total time: 121.230) Find peaks r_work=0.1219 r_free=0.1364 | n_water=729 | time (s): 0.560 (total time: 121.790) Add new water r_work=0.1231 r_free=0.1379 | n_water=954 | time (s): 4.610 (total time: 126.400) Refine new water occ: r_work=0.1195 r_free=0.1342 adp: r_work=0.1195 r_free=0.1342 occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1190 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1343 r_work=0.1190 r_free=0.1343 | n_water=954 | time (s): 192.300 (total time: 318.700) Filter (q & B) r_work=0.1194 r_free=0.1350 | n_water=881 | time (s): 4.550 (total time: 323.250) Filter (dist only) r_work=0.1194 r_free=0.1349 | n_water=880 | time (s): 109.670 (total time: 432.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.546657 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.274999 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 0.1359 0.0162 0.036 1.1 7.5 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.59 1.62 1.792 14.130 15.275 3.766 12.00 13.62 1.62 1.886 14.094 15.275 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 66.90 14.93 0.95 513 3271 Protein: 5.58 31.95 10.58 0.95 0 2902 Water: 6.09 66.90 29.24 N/A 513 367 Other: 13.86 25.95 19.90 N/A 0 2 Chain A: 5.58 53.36 12.52 N/A 0 1624 Chain B: 5.58 66.90 12.35 N/A 0 1647 Chain S: 6.09 62.73 30.82 N/A 513 0 Histogram: Values Number of atoms 5.58 - 11.71 2140 11.71 - 17.84 728 17.84 - 23.98 289 23.98 - 30.11 231 30.11 - 36.24 168 36.24 - 42.37 131 42.37 - 48.51 67 48.51 - 54.64 22 54.64 - 60.77 4 60.77 - 66.90 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1363 r_work=0.1201 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1367 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761615 | | target function (ml) not normalized (work): 704509.183257 | | target function (ml) not normalized (free): 14753.847857 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1368 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1409 0.1407 0.1484 n_refl.: 191130 remove outliers: r(all,work,free)=0.1409 0.1407 0.1484 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1401 0.1399 0.1479 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1369 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1369 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3853 361.285 322.342 0.389 0.949 0.211 13.296-10.522 96.04 96 1 0.2373 480.543 462.998 0.708 0.950 0.177 10.503-8.327 97.80 175 3 0.2115 502.024 495.316 0.858 0.951 0.160 8.318-6.595 100.00 360 8 0.2161 375.632 370.909 0.890 0.950 0.115 6.588-5.215 100.00 711 7 0.1898 345.168 335.327 0.884 0.951 0.100 5.214-4.128 98.38 1367 28 0.1206 504.876 499.123 0.974 0.951 0.090 4.126-3.266 94.74 2603 46 0.1141 460.222 453.446 1.033 0.952 0.000 3.266-2.585 99.86 5447 97 0.1103 310.455 307.173 1.018 0.951 0.000 2.585-2.046 97.45 10613 204 0.0946 234.220 231.742 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0918 138.623 137.311 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0980 74.627 73.912 1.048 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.034 38.359 1.034 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1384 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1369 | n_water=880 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1199 r_free=0.1368 | n_water=879 | time (s): 111.510 (total time: 114.530) Filter (q & B) r_work=0.1199 r_free=0.1369 | n_water=869 | time (s): 5.590 (total time: 120.120) Compute maps r_work=0.1199 r_free=0.1369 | n_water=869 | time (s): 1.870 (total time: 121.990) Filter (map) r_work=0.1219 r_free=0.1367 | n_water=756 | time (s): 4.240 (total time: 126.230) Find peaks r_work=0.1219 r_free=0.1367 | n_water=756 | time (s): 0.840 (total time: 127.070) Add new water r_work=0.1230 r_free=0.1383 | n_water=970 | time (s): 4.200 (total time: 131.270) Refine new water occ: r_work=0.1197 r_free=0.1355 adp: r_work=0.1197 r_free=0.1354 occ: r_work=0.1195 r_free=0.1355 adp: r_work=0.1195 r_free=0.1355 occ: r_work=0.1193 r_free=0.1357 adp: r_work=0.1193 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1357 r_work=0.1193 r_free=0.1357 | n_water=970 | time (s): 231.480 (total time: 362.750) Filter (q & B) r_work=0.1197 r_free=0.1359 | n_water=896 | time (s): 5.500 (total time: 368.250) Filter (dist only) r_work=0.1197 r_free=0.1358 | n_water=894 | time (s): 114.630 (total time: 482.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.574768 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.037685 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 0.1361 0.0161 0.036 1.1 5.8 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 13.61 1.61 1.757 14.013 15.038 3.762 12.02 13.65 1.63 1.873 13.976 15.038 3.760 Individual atomic B min max mean iso aniso Overall: 5.59 65.80 14.82 0.90 527 3271 Protein: 5.59 29.59 10.49 0.90 0 2902 Water: 6.00 65.80 28.87 N/A 527 367 Other: 13.85 23.26 18.56 N/A 0 2 Chain A: 5.63 52.46 12.39 N/A 0 1624 Chain B: 5.59 65.80 12.23 N/A 0 1647 Chain S: 6.00 61.79 30.41 N/A 527 0 Histogram: Values Number of atoms 5.59 - 11.61 2113 11.61 - 17.63 775 17.63 - 23.65 286 23.65 - 29.67 214 29.67 - 35.69 174 35.69 - 41.71 131 41.71 - 47.73 72 47.73 - 53.76 26 53.76 - 59.78 4 59.78 - 65.80 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1365 r_work=0.1203 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1369 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759133 | | target function (ml) not normalized (work): 704044.174643 | | target function (ml) not normalized (free): 14746.581188 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1369 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1482 n_refl.: 191130 remove outliers: r(all,work,free)=0.1407 0.1405 0.1482 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1371 0.1369 0.1462 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1368 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1368 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3893 361.285 321.936 0.390 0.950 0.201 13.296-10.522 96.04 96 1 0.2394 480.543 463.059 0.717 0.952 0.156 10.503-8.327 97.80 175 3 0.2211 502.024 494.364 0.878 0.952 0.137 8.318-6.595 100.00 360 8 0.2145 375.632 370.629 0.907 0.952 0.095 6.588-5.215 100.00 711 7 0.1921 345.168 335.401 0.903 0.952 0.090 5.214-4.128 98.38 1367 28 0.1215 504.876 499.091 0.997 0.953 0.080 4.126-3.266 94.74 2603 46 0.1148 460.222 453.372 1.057 0.953 0.000 3.266-2.585 99.86 5447 97 0.1116 310.455 307.165 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0953 234.220 231.713 1.047 0.952 0.000 2.046-1.619 99.39 21536 464 0.0914 138.623 137.328 1.066 0.952 0.000 1.619-1.281 98.00 42464 925 0.0970 74.627 73.921 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.034 38.363 1.024 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0508 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1368 | n_water=894 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1199 r_free=0.1369 | n_water=893 | time (s): 111.170 (total time: 113.800) Filter (q & B) r_work=0.1200 r_free=0.1369 | n_water=883 | time (s): 5.400 (total time: 119.200) Compute maps r_work=0.1200 r_free=0.1369 | n_water=883 | time (s): 1.750 (total time: 120.950) Filter (map) r_work=0.1220 r_free=0.1365 | n_water=765 | time (s): 4.440 (total time: 125.390) Find peaks r_work=0.1220 r_free=0.1365 | n_water=765 | time (s): 0.740 (total time: 126.130) Add new water r_work=0.1231 r_free=0.1375 | n_water=993 | time (s): 4.700 (total time: 130.830) Refine new water occ: r_work=0.1196 r_free=0.1355 adp: r_work=0.1196 r_free=0.1355 occ: r_work=0.1194 r_free=0.1355 adp: r_work=0.1194 r_free=0.1355 occ: r_work=0.1192 r_free=0.1355 adp: r_work=0.1192 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1356 r_work=0.1192 r_free=0.1356 | n_water=993 | time (s): 265.050 (total time: 395.880) Filter (q & B) r_work=0.1197 r_free=0.1361 | n_water=908 | time (s): 5.140 (total time: 401.020) Filter (dist only) r_work=0.1197 r_free=0.1361 | n_water=906 | time (s): 115.630 (total time: 516.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558192 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.623737 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 0.1362 0.0161 0.037 1.1 6.0 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.62 1.61 1.719 13.725 14.624 3.760 12.02 13.66 1.64 1.764 13.711 14.624 3.758 Individual atomic B min max mean iso aniso Overall: 5.40 64.51 14.61 0.88 539 3271 Protein: 5.40 28.62 10.24 0.88 0 2902 Water: 5.70 64.51 28.58 N/A 539 367 Other: 13.68 21.93 17.80 N/A 0 2 Chain A: 5.44 51.79 12.10 N/A 0 1624 Chain B: 5.40 64.51 11.95 N/A 0 1647 Chain S: 5.70 61.29 30.24 N/A 539 0 Histogram: Values Number of atoms 5.40 - 11.31 2097 11.31 - 17.22 786 17.22 - 23.13 285 23.13 - 29.04 215 29.04 - 34.96 181 34.96 - 40.87 124 40.87 - 46.78 82 46.78 - 52.69 33 52.69 - 58.60 3 58.60 - 64.51 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1366 r_work=0.1202 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757511 | | target function (ml) not normalized (work): 703740.484613 | | target function (ml) not normalized (free): 14738.189987 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1367 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1377 0.1375 0.1467 n_refl.: 191130 remove outliers: r(all,work,free)=0.1377 0.1375 0.1467 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1377 0.1375 0.1467 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1191 0.1353 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3959 356.756 322.170 0.335 0.981 0.130 13.296-10.522 96.04 96 1 0.2402 480.543 462.426 0.678 0.982 0.129 10.503-8.327 97.80 175 3 0.2233 502.024 493.453 0.843 0.983 0.128 8.315-6.595 100.00 359 8 0.2123 374.686 370.138 0.870 0.983 0.099 6.588-5.215 100.00 711 7 0.1936 345.168 334.848 0.865 0.983 0.077 5.214-4.128 98.38 1367 28 0.1238 504.876 498.614 0.959 0.984 0.060 4.126-3.266 94.74 2603 46 0.1161 460.222 452.665 1.016 0.985 0.000 3.266-2.585 99.86 5447 97 0.1120 310.455 306.797 0.999 0.986 0.000 2.585-2.046 97.45 10613 204 0.0956 234.220 231.599 1.005 0.987 0.000 2.046-1.619 99.39 21536 464 0.0906 138.623 137.256 1.019 0.990 0.000 1.619-1.281 98.00 42464 925 0.0951 74.627 73.962 1.004 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.034 38.335 0.965 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1353 | n_water=906 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1191 r_free=0.1353 | n_water=906 | time (s): 104.960 (total time: 107.680) Filter (q & B) r_work=0.1192 r_free=0.1353 | n_water=898 | time (s): 4.870 (total time: 112.550) Compute maps r_work=0.1192 r_free=0.1353 | n_water=898 | time (s): 2.510 (total time: 115.060) Filter (map) r_work=0.1214 r_free=0.1348 | n_water=774 | time (s): 4.420 (total time: 119.480) Find peaks r_work=0.1214 r_free=0.1348 | n_water=774 | time (s): 0.760 (total time: 120.240) Add new water r_work=0.1222 r_free=0.1356 | n_water=987 | time (s): 4.260 (total time: 124.500) Refine new water occ: r_work=0.1189 r_free=0.1339 adp: r_work=0.1190 r_free=0.1339 occ: r_work=0.1188 r_free=0.1339 adp: r_work=0.1188 r_free=0.1340 occ: r_work=0.1186 r_free=0.1340 adp: r_work=0.1186 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1341 r_work=0.1186 r_free=0.1341 | n_water=987 | time (s): 177.840 (total time: 302.340) Filter (q & B) r_work=0.1191 r_free=0.1342 | n_water=907 | time (s): 4.180 (total time: 306.520) Filter (dist only) r_work=0.1191 r_free=0.1342 | n_water=906 | time (s): 117.770 (total time: 424.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.553036 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.103291 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 0.1193 0.1350 0.0157 0.037 1.1 5.5 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.50 1.57 1.676 13.659 14.103 3.756 11.94 13.53 1.59 1.690 13.652 14.103 3.754 Individual atomic B min max mean iso aniso Overall: 5.40 63.88 14.56 0.87 539 3271 Protein: 5.40 28.33 10.25 0.87 0 2902 Water: 5.74 63.88 28.35 N/A 539 367 Other: 13.68 21.92 17.80 N/A 0 2 Chain A: 5.49 51.51 12.08 N/A 0 1624 Chain B: 5.40 63.88 11.94 N/A 0 1647 Chain S: 5.74 61.10 30.04 N/A 539 0 Histogram: Values Number of atoms 5.40 - 11.25 2067 11.25 - 17.10 820 17.10 - 22.94 274 22.94 - 28.79 220 28.79 - 34.64 187 34.64 - 40.49 122 40.49 - 46.34 82 46.34 - 52.18 27 52.18 - 58.03 6 58.03 - 63.88 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1353 r_work=0.1194 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1353 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754141 | | target function (ml) not normalized (work): 703101.736306 | | target function (ml) not normalized (free): 14721.750152 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1354 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1386 0.1384 0.1473 n_refl.: 191128 remove outliers: r(all,work,free)=0.1386 0.1384 0.1473 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1386 0.1384 0.1473 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3988 356.756 317.801 0.356 0.909 0.129 13.296-10.522 96.04 96 1 0.2411 480.543 462.300 0.728 0.910 0.126 10.503-8.327 97.80 175 3 0.2230 502.024 493.861 0.907 0.911 0.116 8.315-6.595 100.00 359 8 0.2137 374.686 369.582 0.934 0.911 0.095 6.588-5.215 100.00 711 7 0.1949 345.168 335.365 0.933 0.911 0.080 5.214-4.128 98.38 1367 28 0.1250 504.876 498.581 1.033 0.912 0.053 4.126-3.266 94.74 2603 46 0.1163 460.222 452.843 1.097 0.913 0.000 3.266-2.585 99.86 5447 97 0.1120 310.455 306.858 1.078 0.914 0.000 2.585-2.046 97.45 10613 204 0.0958 234.220 231.622 1.085 0.916 0.000 2.046-1.619 99.39 21536 464 0.0908 138.623 137.284 1.101 0.919 0.000 1.619-1.281 98.00 42464 925 0.0947 74.627 73.979 1.086 0.924 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.034 38.327 1.047 0.932 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0838 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1353 | n_water=906 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1192 r_free=0.1353 | n_water=906 | time (s): 108.430 (total time: 111.490) Filter (q & B) r_work=0.1192 r_free=0.1353 | n_water=895 | time (s): 4.880 (total time: 116.370) Compute maps r_work=0.1192 r_free=0.1353 | n_water=895 | time (s): 1.780 (total time: 118.150) Filter (map) r_work=0.1213 r_free=0.1353 | n_water=789 | time (s): 4.360 (total time: 122.510) Find peaks r_work=0.1213 r_free=0.1353 | n_water=789 | time (s): 0.890 (total time: 123.400) Add new water r_work=0.1220 r_free=0.1363 | n_water=981 | time (s): 4.760 (total time: 128.160) Refine new water occ: r_work=0.1190 r_free=0.1344 adp: r_work=0.1190 r_free=0.1344 occ: r_work=0.1188 r_free=0.1343 adp: r_work=0.1188 r_free=0.1344 occ: r_work=0.1187 r_free=0.1343 adp: r_work=0.1187 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1344 r_work=0.1187 r_free=0.1344 | n_water=981 | time (s): 241.840 (total time: 370.000) Filter (q & B) r_work=0.1190 r_free=0.1349 | n_water=906 | time (s): 5.340 (total time: 375.340) Filter (dist only) r_work=0.1191 r_free=0.1350 | n_water=903 | time (s): 115.950 (total time: 491.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.551196 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.474592 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1357 0.0162 0.038 1.1 5.8 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.57 1.62 1.670 13.648 13.475 3.755 11.96 13.61 1.65 1.682 13.641 13.475 3.755 Individual atomic B min max mean iso aniso Overall: 5.45 63.20 14.54 0.85 536 3271 Protein: 5.45 27.95 10.26 0.85 0 2902 Water: 5.82 63.20 28.30 N/A 536 367 Other: 13.72 21.97 17.85 N/A 0 2 Chain A: 5.53 51.22 12.06 N/A 0 1624 Chain B: 5.45 63.20 11.92 N/A 0 1647 Chain S: 5.82 60.87 30.12 N/A 536 0 Histogram: Values Number of atoms 5.45 - 11.22 2062 11.22 - 17.00 831 17.00 - 22.77 263 22.77 - 28.55 211 28.55 - 34.33 201 34.33 - 40.10 117 40.10 - 45.88 78 45.88 - 51.65 32 51.65 - 57.43 7 57.43 - 63.20 5 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1361 r_work=0.1197 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1361 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1363 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.=191128 (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): 3.755178 | | target function (ml) not normalized (work): 703295.932942 | | target function (ml) not normalized (free): 14729.283762 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1363 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1487 n_refl.: 191128 remove outliers: r(all,work,free)=0.1397 0.1395 0.1487 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1397 0.1395 0.1487 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1361 n_refl.: 191128 remove outliers: r(all,work,free)=0.1198 0.1195 0.1361 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.4028 356.756 318.142 0.313 0.983 0.100 13.296-10.522 96.04 96 1 0.2436 480.543 461.834 0.660 0.985 0.109 10.503-8.327 97.80 175 3 0.2232 502.024 492.858 0.832 0.985 0.109 8.315-6.595 100.00 359 8 0.2145 374.686 369.460 0.857 0.985 0.091 6.588-5.215 100.00 711 7 0.1954 345.168 335.240 0.857 0.986 0.080 5.214-4.128 98.38 1367 28 0.1258 504.876 498.786 0.949 0.987 0.039 4.126-3.266 94.74 2603 46 0.1171 460.222 452.704 1.009 0.988 0.000 3.266-2.585 99.86 5447 97 0.1130 310.455 306.806 0.991 0.989 0.000 2.585-2.046 97.45 10613 204 0.0961 234.220 231.597 0.998 0.991 0.000 2.046-1.619 99.39 21536 464 0.0910 138.623 137.273 1.012 0.995 0.000 1.619-1.281 98.00 42464 925 0.0947 74.627 73.978 1.000 1.001 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.034 38.320 0.966 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0443 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1361 After: r_work=0.1196 r_free=0.1361 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1361 | n_water=903 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1196 r_free=0.1361 | n_water=903 | time (s): 111.810 (total time: 114.700) Filter (q & B) r_work=0.1197 r_free=0.1360 | n_water=890 | time (s): 5.330 (total time: 120.030) Compute maps r_work=0.1197 r_free=0.1360 | n_water=890 | time (s): 1.980 (total time: 122.010) Filter (map) r_work=0.1217 r_free=0.1352 | n_water=788 | time (s): 5.450 (total time: 127.460) Find peaks r_work=0.1217 r_free=0.1352 | n_water=788 | time (s): 0.710 (total time: 128.170) Add new water r_work=0.1223 r_free=0.1360 | n_water=984 | time (s): 5.090 (total time: 133.260) Refine new water occ: r_work=0.1193 r_free=0.1340 adp: r_work=0.1193 r_free=0.1340 occ: r_work=0.1191 r_free=0.1340 adp: r_work=0.1191 r_free=0.1340 occ: r_work=0.1190 r_free=0.1340 adp: r_work=0.1190 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1340 r_work=0.1190 r_free=0.1340 | n_water=984 | time (s): 198.340 (total time: 331.600) Filter (q & B) r_work=0.1194 r_free=0.1353 | n_water=901 | time (s): 4.600 (total time: 336.200) Filter (dist only) r_work=0.1195 r_free=0.1353 | n_water=899 | time (s): 117.900 (total time: 454.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.537817 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.420130 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1355 0.0159 0.038 1.1 8.7 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.55 1.59 1.664 13.597 13.420 3.756 11.97 13.57 1.60 1.669 13.599 13.420 3.756 Individual atomic B min max mean iso aniso Overall: 5.51 62.21 14.46 0.85 532 3271 Protein: 5.51 27.78 10.27 0.85 0 2902 Water: 5.94 62.21 28.00 N/A 532 367 Other: 13.78 21.92 17.85 N/A 0 2 Chain A: 5.55 50.85 12.04 N/A 0 1624 Chain B: 5.51 62.21 11.91 N/A 0 1647 Chain S: 5.94 60.56 29.75 N/A 532 0 Histogram: Values Number of atoms 5.51 - 11.18 2042 11.18 - 16.85 843 16.85 - 22.52 267 22.52 - 28.19 210 28.19 - 33.86 204 33.86 - 39.53 115 39.53 - 45.20 74 45.20 - 50.87 35 50.87 - 56.54 8 56.54 - 62.21 5 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1357 r_work=0.1197 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755608 | | target function (ml) not normalized (work): 703376.580984 | | target function (ml) not normalized (free): 14727.360433 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1373 0.1491 5.6989 5.7732| | 2: 2.94 - 2.33 1.00 7339 128 0.1077 0.1339 5.0807 5.1685| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1180 4.6507 4.7335| | 4: 2.04 - 1.85 1.00 7170 155 0.0900 0.1033 4.392 4.5481| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.1010 4.1554 4.2622| | 6: 1.72 - 1.62 0.99 7102 142 0.0899 0.1086 3.954 4.0884| | 7: 1.62 - 1.54 0.99 7104 148 0.0895 0.0972 3.8034 3.932| | 8: 1.54 - 1.47 0.96 6798 152 0.0892 0.1291 3.6988 3.8933| | 9: 1.47 - 1.41 0.98 6938 155 0.0925 0.1109 3.6191 3.7413| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1179 3.5554 3.6759| | 11: 1.36 - 1.32 0.99 6997 151 0.0994 0.1134 3.4864 3.5926| | 12: 1.32 - 1.28 0.98 6975 149 0.1040 0.1150 3.4637 3.5943| | 13: 1.28 - 1.25 0.98 6907 166 0.1048 0.1252 3.4425 3.5677| | 14: 1.25 - 1.22 0.98 7015 112 0.1111 0.1584 3.4355 3.6796| | 15: 1.22 - 1.19 0.98 6956 137 0.1172 0.1238 3.4492 3.4914| | 16: 1.19 - 1.17 0.93 6604 132 0.1253 0.1542 3.4656 3.6598| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1225 3.4342 3.4437| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1700 3.4387 3.5326| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1756 3.4201 3.5959| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1574 3.4104 3.4325| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2140 3.4181 3.5028| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1963 3.4132 3.4155| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2023 3.4329 3.4856| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2252 3.436 3.5094| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2500 3.4495 3.5229| | 26: 1.01 - 0.99 0.96 6767 158 0.2760 0.2878 3.4157 3.4249| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2806 3.4692 3.3946| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.71 1.00 0.98 11303.92| | 2: 2.94 - 2.33 7339 128 0.93 12.79 0.99 0.98 5128.64| | 3: 2.33 - 2.04 6939 150 0.96 7.54 1.01 0.98 1667.45| | 4: 2.04 - 1.85 7170 155 0.96 7.59 1.00 0.98 997.85| | 5: 1.85 - 1.72 7113 159 0.96 8.13 1.00 0.98 643.90| | 6: 1.72 - 1.62 7102 142 0.96 8.12 1.00 0.98 451.27| | 7: 1.62 - 1.54 7104 148 0.96 8.16 1.01 0.99 338.95| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 1.00 277.58| | 9: 1.47 - 1.41 6938 155 0.96 8.37 1.00 1.00 228.05| | 10: 1.41 - 1.36 7022 150 0.96 8.89 1.00 0.99 201.43| | 11: 1.36 - 1.32 6997 151 0.96 8.97 0.99 0.98 175.61| | 12: 1.32 - 1.28 6975 149 0.96 9.08 0.98 0.97 162.80| | 13: 1.28 - 1.25 6907 166 0.96 9.65 1.01 0.98 160.33| | 14: 1.25 - 1.22 7015 112 0.95 10.78 1.01 0.99 164.50| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.01 1.00 167.31| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.98 160.32| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.98 153.97| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.97 147.49| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.97 150.96| | 20: 1.10 - 1.08 6884 147 0.92 15.20 1.00 0.96 149.99| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.95 153.03| | 22: 1.07 - 1.05 6836 135 0.89 18.28 0.99 0.95 154.69| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.94 164.49| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.95 179.00| | 25: 1.02 - 1.01 6552 130 0.83 25.15 0.97 0.92 182.04| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.90 176.53| | 27: 0.99 - 0.98 6647 131 0.82 26.24 0.98 0.89 160.54| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 147.49 max = 11303.92 mean = 928.81| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.88 mean = 13.29| |phase err.(test): min = 0.00 max = 89.34 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1486 n_refl.: 191128 remove outliers: r(all,work,free)=0.1407 0.1406 0.1486 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1407 0.1406 0.1486 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1357 n_refl.: 191128 remove outliers: r(all,work,free)=0.1199 0.1196 0.1357 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.4043 356.756 318.273 0.306 0.984 0.090 13.296-10.522 96.04 96 1 0.2471 480.543 459.940 0.653 0.986 0.102 10.503-8.327 97.80 175 3 0.2253 502.024 493.231 0.828 0.987 0.102 8.315-6.595 100.00 359 8 0.2136 374.686 369.812 0.852 0.986 0.083 6.588-5.215 100.00 711 7 0.1949 345.168 335.506 0.854 0.987 0.067 5.214-4.128 98.38 1367 28 0.1262 504.876 498.516 0.948 0.988 0.060 4.126-3.266 94.74 2603 46 0.1177 460.222 452.697 1.009 0.989 0.000 3.266-2.585 99.86 5447 97 0.1125 310.455 306.898 0.991 0.991 0.000 2.585-2.046 97.45 10613 204 0.0964 234.220 231.591 0.997 0.993 0.000 2.046-1.619 99.39 21536 464 0.0911 138.623 137.253 1.013 0.997 0.000 1.619-1.281 98.00 42464 925 0.0947 74.627 73.976 1.002 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.034 38.321 0.971 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0117 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2034 0.1971 0.083 5.197 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1923 0.083 5.197 5.2 78.0 14.6 805 0.000 1_settarget: 0.1797 0.1923 0.083 5.197 5.2 78.0 14.6 805 0.000 1_nqh: 0.1797 0.1923 0.083 5.197 5.2 78.0 14.6 805 0.000 1_weight: 0.1797 0.1923 0.083 5.197 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1265 0.1490 0.038 1.152 5.2 78.0 14.6 805 0.154 1_adp: 0.1296 0.1565 0.038 1.152 5.1 73.0 15.1 805 0.154 1_regHadp: 0.1295 0.1560 0.038 1.152 5.1 73.0 15.1 805 0.154 1_occ: 0.1280 0.1551 0.038 1.152 5.1 73.0 15.1 805 0.154 2_bss: 0.1274 0.1546 0.038 1.152 5.3 73.2 15.2 805 0.154 2_settarget: 0.1274 0.1546 0.038 1.152 5.3 73.2 15.2 805 0.154 2_updatecdl: 0.1274 0.1546 0.038 1.166 5.3 73.2 15.2 805 0.154 2_nqh: 0.1274 0.1546 0.038 1.166 5.3 73.2 15.2 805 0.154 2_sol: 0.1271 0.1509 0.038 1.166 5.3 73.2 16.3 883 n/a 2_weight: 0.1271 0.1509 0.038 1.166 5.3 73.2 16.3 883 n/a 2_xyzrec: 0.1256 0.1531 0.041 1.137 5.3 73.2 16.3 883 n/a 2_adp: 0.1231 0.1510 0.041 1.137 5.4 68.3 16.3 883 n/a 2_regHadp: 0.1232 0.1511 0.041 1.137 5.4 68.3 16.3 883 n/a 2_occ: 0.1224 0.1511 0.041 1.137 5.4 68.3 16.3 883 n/a 3_bss: 0.1231 0.1518 0.041 1.137 5.4 68.3 16.3 883 n/a 3_settarget: 0.1231 0.1518 0.041 1.137 5.4 68.3 16.3 883 n/a 3_updatecdl: 0.1231 0.1518 0.041 1.142 5.4 68.3 16.3 883 n/a 3_nqh: 0.1231 0.1518 0.041 1.142 5.4 68.3 16.3 883 n/a 3_sol: 0.1250 0.1513 0.041 1.142 5.4 68.2 15.3 870 n/a 3_weight: 0.1250 0.1513 0.041 1.142 5.4 68.2 15.3 870 n/a 3_xyzrec: 0.1240 0.1440 0.035 1.099 5.4 68.2 15.3 870 n/a 3_adp: 0.1238 0.1401 0.035 1.099 5.6 67.7 15.1 870 n/a 3_regHadp: 0.1239 0.1402 0.035 1.099 5.6 67.7 15.1 870 n/a 3_occ: 0.1234 0.1394 0.035 1.099 5.6 67.7 15.1 870 n/a 4_bss: 0.1229 0.1384 0.035 1.099 5.5 67.7 15.1 870 n/a 4_settarget: 0.1229 0.1384 0.035 1.099 5.5 67.7 15.1 870 n/a 4_updatecdl: 0.1229 0.1384 0.035 1.100 5.5 67.7 15.1 870 n/a 4_nqh: 0.1229 0.1384 0.035 1.100 5.5 67.7 15.1 870 n/a 4_sol: 0.1209 0.1369 0.035 1.100 5.5 67.7 15.0 863 n/a 4_weight: 0.1209 0.1369 0.035 1.100 5.5 67.7 15.0 863 n/a 4_xyzrec: 0.1207 0.1369 0.036 1.121 5.5 67.7 15.0 863 n/a 4_adp: 0.1200 0.1368 0.036 1.121 5.6 67.4 14.9 863 n/a 4_regHadp: 0.1200 0.1368 0.036 1.121 5.6 67.4 14.9 863 n/a 4_occ: 0.1199 0.1366 0.036 1.121 5.6 67.4 14.9 863 n/a 5_bss: 0.1197 0.1363 0.036 1.121 5.5 67.3 14.9 863 n/a 5_settarget: 0.1197 0.1363 0.036 1.121 5.5 67.3 14.9 863 n/a 5_updatecdl: 0.1197 0.1363 0.036 1.122 5.5 67.3 14.9 863 n/a 5_nqh: 0.1197 0.1363 0.036 1.122 5.5 67.3 14.9 863 n/a 5_sol: 0.1194 0.1349 0.036 1.122 5.5 67.3 15.0 880 n/a 5_weight: 0.1194 0.1349 0.036 1.122 5.5 67.3 15.0 880 n/a 5_xyzrec: 0.1197 0.1359 0.036 1.127 5.5 67.3 15.0 880 n/a 5_adp: 0.1201 0.1363 0.036 1.127 5.6 66.9 14.9 880 n/a 5_regHadp: 0.1201 0.1363 0.036 1.127 5.6 66.9 14.9 880 n/a 5_occ: 0.1199 0.1367 0.036 1.127 5.6 66.9 14.9 880 n/a 6_bss: 0.1199 0.1369 0.036 1.127 5.5 66.9 14.9 880 n/a 6_settarget: 0.1199 0.1369 0.036 1.127 5.5 66.9 14.9 880 n/a 6_updatecdl: 0.1199 0.1369 0.036 1.127 5.5 66.9 14.9 880 n/a 6_nqh: 0.1199 0.1369 0.036 1.127 5.5 66.9 14.9 880 n/a 6_sol: 0.1197 0.1358 0.036 1.127 5.5 66.9 14.9 894 n/a 6_weight: 0.1197 0.1358 0.036 1.127 5.5 66.9 14.9 894 n/a 6_xyzrec: 0.1201 0.1361 0.036 1.129 5.5 66.9 14.9 894 n/a 6_adp: 0.1202 0.1365 0.036 1.129 5.6 65.8 14.8 894 n/a 6_regHadp: 0.1203 0.1366 0.036 1.129 5.6 65.8 14.8 894 n/a 6_occ: 0.1200 0.1369 0.036 1.129 5.6 65.8 14.8 894 n/a 7_bss: 0.1199 0.1368 0.036 1.129 5.4 65.6 14.6 894 n/a 7_settarget: 0.1199 0.1368 0.036 1.129 5.4 65.6 14.6 894 n/a 7_updatecdl: 0.1199 0.1368 0.036 1.130 5.4 65.6 14.6 894 n/a 7_nqh: 0.1199 0.1368 0.036 1.130 5.4 65.6 14.6 894 n/a 7_sol: 0.1197 0.1361 0.036 1.130 5.4 65.6 14.6 906 n/a 7_weight: 0.1197 0.1361 0.036 1.130 5.4 65.6 14.6 906 n/a 7_xyzrec: 0.1201 0.1362 0.037 1.130 5.4 65.6 14.6 906 n/a 7_adp: 0.1202 0.1366 0.037 1.130 5.4 64.5 14.6 906 n/a 7_regHadp: 0.1202 0.1366 0.037 1.130 5.4 64.5 14.6 906 n/a 7_occ: 0.1201 0.1367 0.037 1.130 5.4 64.5 14.6 906 n/a 8_bss: 0.1191 0.1353 0.037 1.130 5.4 64.5 14.6 906 n/a 8_settarget: 0.1191 0.1353 0.037 1.130 5.4 64.5 14.6 906 n/a 8_updatecdl: 0.1191 0.1353 0.037 1.130 5.4 64.5 14.6 906 n/a 8_nqh: 0.1191 0.1353 0.037 1.130 5.4 64.5 14.6 906 n/a 8_sol: 0.1191 0.1342 0.037 1.130 5.4 64.5 14.6 906 n/a 8_weight: 0.1191 0.1342 0.037 1.130 5.4 64.5 14.6 906 n/a 8_xyzrec: 0.1193 0.1350 0.037 1.123 5.4 64.5 14.6 906 n/a 8_adp: 0.1194 0.1353 0.037 1.123 5.4 63.9 14.6 906 n/a 8_regHadp: 0.1194 0.1353 0.037 1.123 5.4 63.9 14.6 906 n/a 8_occ: 0.1193 0.1354 0.037 1.123 5.4 63.9 14.6 906 n/a 9_bss: 0.1192 0.1353 0.037 1.123 5.4 63.9 14.6 906 n/a 9_settarget: 0.1192 0.1353 0.037 1.123 5.4 63.9 14.6 906 n/a 9_updatecdl: 0.1192 0.1353 0.037 1.123 5.4 63.9 14.6 906 n/a 9_nqh: 0.1192 0.1353 0.037 1.123 5.4 63.9 14.6 906 n/a 9_sol: 0.1191 0.1350 0.037 1.123 5.4 63.9 14.6 903 n/a 9_weight: 0.1191 0.1350 0.037 1.123 5.4 63.9 14.6 903 n/a 9_xyzrec: 0.1195 0.1357 0.038 1.121 5.4 63.9 14.6 903 n/a 9_adp: 0.1197 0.1361 0.038 1.121 5.4 63.2 14.5 903 n/a 9_regHadp: 0.1197 0.1361 0.038 1.121 5.4 63.2 14.5 903 n/a 9_occ: 0.1196 0.1363 0.038 1.121 5.4 63.2 14.5 903 n/a 10_bss: 0.1195 0.1361 0.038 1.121 5.4 63.2 14.5 903 n/a 10_settarget: 0.1195 0.1361 0.038 1.121 5.4 63.2 14.5 903 n/a 10_updatecdl: 0.1195 0.1361 0.038 1.121 5.4 63.2 14.5 903 n/a 10_setrh: 0.1196 0.1361 0.038 1.121 5.4 63.2 14.5 903 n/a 10_nqh: 0.1196 0.1361 0.038 1.121 5.4 63.2 14.5 903 n/a 10_sol: 0.1195 0.1353 0.038 1.121 5.4 63.2 14.5 899 n/a 10_weight: 0.1195 0.1353 0.038 1.121 5.4 63.2 14.5 899 n/a 10_xyzrec: 0.1196 0.1355 0.038 1.150 5.4 63.2 14.5 899 n/a 10_adp: 0.1197 0.1357 0.038 1.150 5.5 62.2 14.5 899 n/a 10_regHadp: 0.1197 0.1357 0.038 1.150 5.5 62.2 14.5 899 n/a 10_occ: 0.1197 0.1357 0.038 1.150 5.5 62.2 14.5 899 n/a end: 0.1196 0.1357 0.038 1.150 5.5 62.2 14.5 899 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1852271_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_1852271_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.1500 Refinement macro-cycles (run) : 11836.2000 Write final files (write_after_run_outputs) : 163.0800 Total : 12005.4300 Total CPU time: 3.34 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:37:13 PST -0800 (1736735833.71 s) Start R-work = 0.1797, R-free = 0.1923 Final R-work = 0.1196, R-free = 0.1357 =============================================================================== Job complete usr+sys time: 12306.78 seconds wall clock time: 206 minutes 3.82 seconds (12363.82 seconds total)