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_5942275.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5942275.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5942275.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.56, per 1000 atoms: 0.38 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.790 distance_ideal: 2.720 ideal - model: -0.070 slack: 0.000 delta_slack: -0.070 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.723 distance_ideal: 2.710 ideal - model: -0.013 slack: 0.000 delta_slack: -0.013 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: 0.91 Conformation dependent library (CDL) restraints added in 184.3 milliseconds Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.04: 914 1.04 - 1.26: 2408 1.26 - 1.49: 1468 1.49 - 1.71: 1121 1.71 - 1.94: 23 Bond restraints: 5934 Sorted by residual: bond pdb=" ND1 HIS A 179 " pdb=" CE1 HIS A 179 " ideal model delta sigma weight residual 1.321 1.059 0.262 1.00e-02 1.00e+04 6.87e+02 bond pdb=" CE1 HIS A 96 " pdb=" NE2 HIS A 96 " ideal model delta sigma weight residual 1.321 1.085 0.236 1.00e-02 1.00e+04 5.58e+02 bond pdb=" CA ASN A 123 " pdb=" C ASN A 123 " ideal model delta sigma weight residual 1.523 1.250 0.274 1.24e-02 6.50e+03 4.87e+02 bond pdb=" N PHE A 82 " pdb=" H PHE A 82 " ideal model delta sigma weight residual 0.860 1.251 -0.391 2.00e-02 2.50e+03 3.82e+02 bond pdb=" N ASN A 123 " pdb=" H ASN A 123 " ideal model delta sigma weight residual 0.860 1.233 -0.373 2.00e-02 2.50e+03 3.48e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.82: 6408 4.82 - 9.64: 3385 9.64 - 14.45: 900 14.45 - 19.27: 109 19.27 - 24.09: 8 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O PHE A 119 " pdb=" C PHE A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 121.34 135.59 -14.25 8.90e-01 1.26e+00 2.56e+02 angle pdb=" O MET A 187 " pdb=" C MET A 187 " pdb=" N ALA A 188 " ideal model delta sigma weight residual 122.86 140.73 -17.87 1.18e+00 7.18e-01 2.29e+02 angle pdb=" CA GLN A 94 " pdb=" C GLN A 94 " pdb=" O GLN A 94 " ideal model delta sigma weight residual 120.42 136.35 -15.93 1.06e+00 8.90e-01 2.26e+02 angle pdb=" CA SER A 4 " pdb=" C SER A 4 " pdb=" O SER A 4 " ideal model delta sigma weight residual 121.33 137.49 -16.16 1.08e+00 8.57e-01 2.24e+02 angle pdb=" CA LEU B 25 " pdb=" C LEU B 25 " pdb=" O LEU B 25 " ideal model delta sigma weight residual 119.97 103.47 16.50 1.15e+00 7.56e-01 2.06e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.02: 1844 17.02 - 34.04: 137 34.04 - 51.06: 44 51.06 - 68.07: 21 68.07 - 85.09: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CB TRP A 146 " pdb=" CG TRP A 146 " pdb=" CD1 TRP A 146 " pdb=" HD1 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 25.54 -25.54 0 5.00e+00 4.00e-02 2.61e+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 -156.06 -23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA LEU A 185 " pdb=" C LEU A 185 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.205: 195 0.205 - 0.409: 156 0.409 - 0.613: 84 0.613 - 0.817: 47 0.817 - 1.021: 10 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE A 134 " pdb=" N ILE A 134 " pdb=" C ILE A 134 " pdb=" CB ILE A 134 " both_signs ideal model delta sigma weight residual False 2.43 3.45 -1.02 2.00e-01 2.50e+01 2.61e+01 chirality pdb=" CA VAL A 145 " pdb=" N VAL A 145 " pdb=" C VAL A 145 " pdb=" CB VAL A 145 " both_signs ideal model delta sigma weight residual False 2.44 3.37 -0.93 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CA LEU B 171 " pdb=" N LEU B 171 " pdb=" C LEU B 171 " pdb=" CB LEU B 171 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " -0.042 2.00e-02 2.50e+03 6.74e-02 1.82e+02 pdb=" CG TRP A 146 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.120 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.054 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.061 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.113 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.018 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " 0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.055 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.092 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 95 " -0.068 2.00e-02 2.50e+03 7.01e-02 1.47e+02 pdb=" CG PHE B 95 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 PHE B 95 " 0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE B 95 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 PHE B 95 " -0.086 2.00e-02 2.50e+03 pdb=" CE2 PHE B 95 " -0.110 2.00e-02 2.50e+03 pdb=" CZ PHE B 95 " 0.070 2.00e-02 2.50e+03 pdb=" HD1 PHE B 95 " -0.022 2.00e-02 2.50e+03 pdb=" HD2 PHE B 95 " 0.111 2.00e-02 2.50e+03 pdb=" HE1 PHE B 95 " 0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE B 95 " -0.087 2.00e-02 2.50e+03 pdb=" HZ PHE B 95 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.082 2.00e-02 2.50e+03 6.02e-02 1.45e+02 pdb=" CG TRP B 139 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.091 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.142 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.042 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " -0.061 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.012 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " 0.086 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.064 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.010 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.62: 26 1.62 - 2.36: 2458 2.36 - 3.11: 22334 3.11 - 3.85: 32910 3.85 - 4.60: 52469 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110197 Sorted by model distance: nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.874 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.910 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.026 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.073 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.162 2.620 ... (remaining 110192 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_5942275_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= 0.2033 r_free= 0.2024 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.303903 | | target function (ml) not normalized (work): 806177.029744 | | target function (ml) not normalized (free): 16648.523848 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2133 0.2013 6.6762 6.3244| | 2: 2.94 - 2.33 1.00 7339 128 0.1615 0.1583 5.5446 5.5758| | 3: 2.33 - 2.04 0.96 6939 150 0.1641 0.1492 5.1502 5.1363| | 4: 2.04 - 1.85 1.00 7170 155 0.1746 0.1618 4.9585 5.0048| | 5: 1.85 - 1.72 0.99 7113 159 0.1928 0.1857 4.8064 4.9166| | 6: 1.72 - 1.62 0.99 7102 142 0.1968 0.2061 4.6777 4.7694| | 7: 1.62 - 1.54 0.99 7104 148 0.2029 0.2090 4.589 4.7213| | 8: 1.54 - 1.47 0.96 6798 152 0.2054 0.2292 4.4889 4.5964| | 9: 1.47 - 1.41 0.98 6938 155 0.2089 0.2152 4.4055 4.4853| | 10: 1.41 - 1.36 0.99 7022 150 0.2146 0.2154 4.3186 4.3073| | 11: 1.36 - 1.32 0.99 6997 151 0.2094 0.2052 4.2358 4.2256| | 12: 1.32 - 1.28 0.98 6976 149 0.2113 0.1976 4.1849 4.1842| | 13: 1.28 - 1.25 0.98 6907 166 0.2051 0.2304 4.1285 4.2456| | 14: 1.25 - 1.22 0.98 7015 113 0.2066 0.2353 4.0791 4.2592| | 15: 1.22 - 1.19 0.98 6957 137 0.2091 0.2026 4.0525 4.0524| | 16: 1.19 - 1.17 0.93 6604 132 0.2110 0.2254 4.0034 4.1067| | 17: 1.17 - 1.14 0.98 6941 135 0.2147 0.2057 3.9589 4.0155| | 18: 1.14 - 1.12 0.98 6875 142 0.2208 0.2369 3.9209 3.932| | 19: 1.12 - 1.10 0.97 6949 106 0.2266 0.2545 3.8741 4.0107| | 20: 1.10 - 1.08 0.97 6884 147 0.2305 0.2260 3.8179 3.8836| | 21: 1.08 - 1.07 0.97 6852 152 0.2430 0.2715 3.7951 3.8104| | 22: 1.07 - 1.05 0.97 6838 135 0.2549 0.2781 3.7548 3.7975| | 23: 1.05 - 1.03 0.97 6829 159 0.2723 0.2471 3.7345 3.7884| | 24: 1.03 - 1.02 0.96 6785 133 0.2866 0.2952 3.7001 3.8405| | 25: 1.02 - 1.01 0.93 6552 130 0.3065 0.3109 3.6744 3.7791| | 26: 1.01 - 0.99 0.96 6767 158 0.3187 0.3287 3.6262 3.6391| | 27: 0.99 - 0.98 0.94 6648 131 0.3392 0.3223 3.6347 3.6272| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.74 0.91 0.98 36701.16| | 2: 2.94 - 2.33 7339 128 0.85 21.38 1.09 1.02 15410.40| | 3: 2.33 - 2.04 6939 150 0.93 12.42 1.11 1.05 4099.06| | 4: 2.04 - 1.85 7170 155 0.92 13.73 1.11 1.06 2821.02| | 5: 1.85 - 1.72 7113 159 0.90 16.79 1.12 1.06 2330.93| | 6: 1.72 - 1.62 7102 142 0.89 18.38 1.11 1.06 1930.02| | 7: 1.62 - 1.54 7104 148 0.87 19.69 1.11 1.07 1650.65| | 8: 1.54 - 1.47 6798 152 0.87 19.72 1.11 1.06 1318.43| | 9: 1.47 - 1.41 6938 155 0.87 19.93 1.10 1.08 1085.54| | 10: 1.41 - 1.36 7022 150 0.87 19.96 1.09 1.07 856.21| | 11: 1.36 - 1.32 6997 151 0.88 19.49 1.08 1.06 713.61| | 12: 1.32 - 1.28 6976 149 0.88 19.56 1.08 1.03 634.44| | 13: 1.28 - 1.25 6907 166 0.87 20.22 1.08 1.04 626.16| | 14: 1.25 - 1.22 7015 113 0.86 21.47 1.07 1.04 615.34| | 15: 1.22 - 1.19 6957 137 0.86 21.35 1.08 1.06 574.63| | 16: 1.19 - 1.17 6604 132 0.87 20.87 1.08 1.05 515.75| | 17: 1.17 - 1.14 6941 135 0.86 21.31 1.08 1.04 464.64| | 18: 1.14 - 1.12 6875 142 0.85 22.00 1.08 1.00 429.50| | 19: 1.12 - 1.10 6949 106 0.85 23.05 1.08 0.99 407.10| | 20: 1.10 - 1.08 6884 147 0.83 24.21 1.06 0.97 384.64| | 21: 1.08 - 1.07 6852 152 0.83 25.02 1.06 0.97 362.27| | 22: 1.07 - 1.05 6838 135 0.81 26.74 1.06 0.96 350.41| | 23: 1.05 - 1.03 6829 159 0.78 28.94 1.05 0.94 348.85| | 24: 1.03 - 1.02 6785 133 0.76 31.17 1.05 0.95 361.10| | 25: 1.02 - 1.01 6552 130 0.75 32.53 1.03 0.92 342.40| | 26: 1.01 - 0.99 6767 158 0.73 33.69 1.02 0.91 317.73| | 27: 0.99 - 0.98 6648 131 0.75 32.72 1.03 0.90 281.67| |alpha: min = 0.90 max = 1.08 mean = 1.01| |beta: min = 281.67 max = 36701.16 mean = 2943.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.95 mean = 22.40| |phase err.(test): min = 0.00 max = 89.69 mean = 22.51| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.274 2950 Z= 5.333 Angle : 5.222 17.872 4018 Z= 3.706 Chirality : 0.375 1.021 492 Planarity : 0.031 0.106 512 Dihedral : 13.200 85.091 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.18 % Favored : 94.56 % Rotamer: Outliers : 1.61 % Allowed : 3.23 % Favored : 95.16 % Cbeta Deviations : 32.87 % 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: -2.67 (0.38), residues: 386 helix: -2.55 (0.32), residues: 146 sheet: -1.71 (0.49), residues: 86 loop : -0.61 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.020 ARG A 100 TYR 0.124 0.033 TYR B 67 PHE 0.104 0.032 PHE B 95 TRP 0.123 0.043 TRP B 146 HIS 0.056 0.025 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2033 r_free= 0.2024 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.303903 | | target function (ml) not normalized (work): 806177.029744 | | target function (ml) not normalized (free): 16648.523848 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2032 0.2033 0.2024 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2032 0.2033 0.2024 n_refl.: 191155 remove outliers: r(all,work,free)=0.2032 0.2033 0.2024 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2032 0.2033 0.2024 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1802 0.1798 0.1962 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1796 0.1962 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4096 402.814 291.964 0.434 0.912 0.300 13.296-10.522 99.01 99 1 0.2469 528.187 520.117 0.790 0.913 0.253 10.503-8.327 98.90 177 3 0.2438 564.205 559.154 0.972 0.913 0.231 8.318-6.595 100.00 360 8 0.2449 414.736 402.631 0.972 0.913 0.175 6.588-5.215 100.00 711 7 0.2252 381.101 365.729 0.960 0.913 0.160 5.214-4.128 98.38 1367 28 0.1499 557.435 549.153 1.072 0.913 0.080 4.126-3.266 94.74 2603 46 0.1323 508.132 499.594 1.146 0.914 0.009 3.266-2.585 99.86 5447 97 0.1441 342.774 337.665 1.119 0.913 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 254.379 1.126 0.912 0.000 2.046-1.619 99.39 21536 464 0.1608 153.054 149.800 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1932 82.395 80.197 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2312 44.203 41.702 1.113 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0002 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1796 r_free=0.1962 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1796 r_free=0.1962 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.703773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.893523 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 0.1270 0.1501 0.0232 0.039 1.2 10.9 0.0 0.3 0 11.352 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.01 2.32 1.117 13.111 577.894 0.018 12.94 15.66 2.72 1.229 13.333 577.894 0.017 Individual atomic B min max mean iso aniso Overall: 5.22 73.04 15.00 1.40 435 3274 Protein: 5.22 40.51 10.99 1.40 0 2902 Water: 6.36 73.04 29.44 N/A 435 370 Other: 15.96 29.88 22.92 N/A 0 2 Chain A: 5.33 60.23 13.04 N/A 0 1626 Chain B: 5.22 73.04 12.76 N/A 0 1648 Chain S: 11.68 63.47 30.85 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.00 2170 12.00 - 18.78 638 18.78 - 25.57 314 25.57 - 32.35 261 32.35 - 39.13 158 39.13 - 45.91 102 45.91 - 52.70 42 52.70 - 59.48 18 59.48 - 66.26 5 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1294 r_free=0.1566 r_work=0.1293 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1293 r_free = 0.1561 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1279 r_free = 0.1552 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1279 r_free= 0.1552 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015484 | | target function (ls_wunit_k1) not normalized (work): 2900.051458 | | target function (ls_wunit_k1) not normalized (free): 116.092192 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1284 0.1279 0.1552 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1466 0.1463 0.1629 n_refl.: 191138 remove outliers: r(all,work,free)=0.1466 0.1463 0.1629 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1490 0.1488 0.1639 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1276 0.1271 0.1545 n_refl.: 191138 remove outliers: r(all,work,free)=0.1276 0.1271 0.1544 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 0.3607 402.814 378.534 0.488 0.963 0.281 13.296-10.522 99.01 99 1 0.2079 528.187 524.532 0.745 0.965 0.249 10.503-8.327 98.90 177 3 0.1717 564.205 562.779 0.887 0.965 0.203 8.318-6.595 100.00 360 8 0.1691 414.736 413.475 0.910 0.964 0.160 6.588-5.215 100.00 711 7 0.1532 381.101 373.924 0.888 0.965 0.150 5.214-4.128 98.38 1367 28 0.0903 557.435 554.239 0.975 0.965 0.070 4.126-3.266 94.74 2603 46 0.0831 508.132 504.297 1.043 0.966 0.009 3.266-2.585 99.86 5447 97 0.0921 342.774 340.382 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.408 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.389 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1273 82.395 81.422 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.165 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0384 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1271 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1544 | n_water=805 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1276 r_free=0.1550 | n_water=793 | time (s): 103.480 (total time: 105.930) Filter (q & B) r_work=0.1277 r_free=0.1549 | n_water=790 | time (s): 5.010 (total time: 110.940) Compute maps r_work=0.1277 r_free=0.1549 | n_water=790 | time (s): 1.860 (total time: 112.800) Filter (map) r_work=0.1303 r_free=0.1525 | n_water=652 | time (s): 4.980 (total time: 117.780) Find peaks r_work=0.1303 r_free=0.1525 | n_water=652 | time (s): 0.650 (total time: 118.430) Add new water r_work=0.1327 r_free=0.1556 | n_water=956 | time (s): 4.350 (total time: 122.780) Refine new water occ: r_work=0.1282 r_free=0.1503 adp: r_work=0.1269 r_free=0.1504 occ: r_work=0.1271 r_free=0.1497 adp: r_work=0.1265 r_free=0.1498 occ: r_work=0.1266 r_free=0.1495 adp: r_work=0.1263 r_free=0.1496 ADP+occupancy (water only), MIN, final r_work=0.1263 r_free=0.1496 r_work=0.1263 r_free=0.1496 | n_water=956 | time (s): 94.890 (total time: 217.670) Filter (q & B) r_work=0.1267 r_free=0.1498 | n_water=892 | time (s): 5.140 (total time: 222.810) Filter (dist only) r_work=0.1267 r_free=0.1497 | n_water=891 | time (s): 112.420 (total time: 335.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.964675 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 596.355348 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 0.1252 0.1514 0.0262 0.041 1.1 21.2 0.0 0.0 0 11.482 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.14 2.62 2.042 15.243 596.355 0.014 12.33 15.05 2.72 2.394 15.287 596.355 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 68.38 16.42 1.20 523 3272 Protein: 5.42 40.24 11.00 1.20 0 2902 Water: 6.67 68.38 34.08 N/A 523 368 Other: 16.41 33.56 24.99 N/A 0 2 Chain A: 5.56 56.51 12.99 N/A 0 1624 Chain B: 5.42 68.38 12.84 N/A 0 1648 Chain S: 13.26 65.28 38.40 N/A 523 0 Histogram: Values Number of atoms 5.42 - 11.71 2072 11.71 - 18.01 700 18.01 - 24.31 261 24.31 - 30.60 217 30.60 - 36.90 163 36.90 - 43.20 162 43.20 - 49.49 111 49.49 - 55.79 50 55.79 - 62.09 46 62.09 - 68.38 13 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1505 r_work=0.1234 r_free=0.1506 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1506 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 = 0.1227 r_free = 0.1505 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013380 | | target function (ls_wunit_k1) not normalized (work): 2505.978061 | | target function (ls_wunit_k1) not normalized (free): 103.524367 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1227 0.1505 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1438 0.1435 0.1608 n_refl.: 191137 remove outliers: r(all,work,free)=0.1438 0.1435 0.1608 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1432 0.1606 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1513 n_refl.: 191137 remove outliers: r(all,work,free)=0.1239 0.1234 0.1513 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 0.3234 402.814 377.975 0.492 0.964 0.277 13.296-10.522 99.01 99 1 0.1783 528.187 524.328 0.770 0.965 0.260 10.503-8.327 98.90 177 3 0.1348 564.205 566.218 0.920 0.964 0.174 8.318-6.595 100.00 360 8 0.1564 414.736 414.597 0.933 0.964 0.150 6.588-5.215 100.00 711 7 0.1325 381.101 376.917 0.914 0.964 0.150 5.214-4.128 98.38 1367 28 0.0828 557.435 556.055 0.994 0.964 0.100 4.126-3.266 94.74 2603 46 0.0759 508.132 505.525 1.058 0.964 0.014 3.266-2.585 99.86 5447 97 0.0860 342.774 341.503 1.045 0.963 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.750 1.057 0.962 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.634 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1258 82.395 81.342 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.214 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0516 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1513 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1513 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1513 | n_water=891 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1236 r_free=0.1514 | n_water=886 | time (s): 124.290 (total time: 126.980) Filter (q & B) r_work=0.1236 r_free=0.1514 | n_water=882 | time (s): 4.290 (total time: 131.270) Compute maps r_work=0.1236 r_free=0.1514 | n_water=882 | time (s): 1.960 (total time: 133.230) Filter (map) r_work=0.1273 r_free=0.1523 | n_water=694 | time (s): 4.630 (total time: 137.860) Find peaks r_work=0.1273 r_free=0.1523 | n_water=694 | time (s): 0.930 (total time: 138.790) Add new water r_work=0.1296 r_free=0.1556 | n_water=1000 | time (s): 4.480 (total time: 143.270) Refine new water occ: r_work=0.1253 r_free=0.1521 adp: r_work=0.1254 r_free=0.1522 occ: r_work=0.1249 r_free=0.1519 adp: r_work=0.1249 r_free=0.1519 occ: r_work=0.1246 r_free=0.1516 adp: r_work=0.1245 r_free=0.1516 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1516 r_work=0.1245 r_free=0.1516 | n_water=1000 | time (s): 277.710 (total time: 420.980) Filter (q & B) r_work=0.1250 r_free=0.1518 | n_water=872 | time (s): 4.080 (total time: 425.060) Filter (dist only) r_work=0.1252 r_free=0.1519 | n_water=870 | time (s): 109.110 (total time: 534.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.702737 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.538987 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 0.1443 0.0203 0.035 1.1 7.1 0.0 0.0 0 0.851 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.43 2.03 1.936 14.621 15.539 3.941 12.34 14.03 1.69 2.248 14.520 15.539 3.899 Individual atomic B min max mean iso aniso Overall: 5.53 67.97 15.30 1.05 504 3270 Protein: 5.53 36.43 10.74 1.05 0 2902 Water: 6.72 67.97 30.50 N/A 504 366 Other: 14.19 28.86 21.53 N/A 0 2 Chain A: 5.57 55.62 12.75 N/A 0 1624 Chain B: 5.53 67.97 12.51 N/A 0 1646 Chain S: 13.82 64.01 32.65 N/A 504 0 Histogram: Values Number of atoms 5.53 - 11.77 2133 11.77 - 18.02 690 18.02 - 24.26 294 24.26 - 30.50 225 30.50 - 36.75 171 36.75 - 42.99 139 42.99 - 49.24 79 49.24 - 55.48 26 55.48 - 61.72 12 61.72 - 67.97 5 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1404 r_work=0.1235 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1404 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1396 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1396 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.893176 | | target function (ml) not normalized (work): 729176.336798 | | target function (ml) not normalized (free): 15228.268449 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1230 0.1395 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1446 0.1445 0.1494 n_refl.: 191137 remove outliers: r(all,work,free)=0.1446 0.1445 0.1494 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1439 0.1490 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1226 0.1386 n_refl.: 191137 remove outliers: r(all,work,free)=0.1229 0.1226 0.1386 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3711 398.008 366.305 0.424 0.947 0.240 13.296-10.522 99.01 99 1 0.2497 528.187 508.796 0.706 0.948 0.210 10.503-8.327 97.80 175 3 0.1858 554.286 558.635 0.885 0.948 0.184 8.318-6.595 100.00 360 8 0.2111 414.736 410.037 0.897 0.948 0.139 6.588-5.215 100.00 711 7 0.1864 381.101 370.808 0.887 0.948 0.120 5.214-4.128 98.38 1367 28 0.1178 557.435 552.154 0.972 0.948 0.090 4.126-3.266 94.74 2603 46 0.1093 508.132 501.205 1.033 0.948 0.019 3.266-2.585 99.86 5447 97 0.1085 342.774 339.223 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0966 258.603 255.806 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0972 153.054 151.407 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.485 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.317 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1024 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1386 | n_water=870 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1226 r_free=0.1386 | n_water=870 | time (s): 103.060 (total time: 105.730) Filter (q & B) r_work=0.1226 r_free=0.1385 | n_water=862 | time (s): 5.590 (total time: 111.320) Compute maps r_work=0.1226 r_free=0.1385 | n_water=862 | time (s): 1.640 (total time: 112.960) Filter (map) r_work=0.1247 r_free=0.1396 | n_water=713 | time (s): 5.180 (total time: 118.140) Find peaks r_work=0.1247 r_free=0.1396 | n_water=713 | time (s): 0.820 (total time: 118.960) Add new water r_work=0.1264 r_free=0.1412 | n_water=946 | time (s): 4.310 (total time: 123.270) Refine new water occ: r_work=0.1217 r_free=0.1376 adp: r_work=0.1209 r_free=0.1372 occ: r_work=0.1207 r_free=0.1372 adp: r_work=0.1207 r_free=0.1372 occ: r_work=0.1205 r_free=0.1371 adp: r_work=0.1205 r_free=0.1371 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1371 r_work=0.1205 r_free=0.1371 | n_water=946 | time (s): 213.050 (total time: 336.320) Filter (q & B) r_work=0.1209 r_free=0.1368 | n_water=848 | time (s): 4.310 (total time: 340.630) Filter (dist only) r_work=0.1209 r_free=0.1368 | n_water=847 | time (s): 107.300 (total time: 447.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.594048 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.812169 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 0.1208 0.1370 0.0161 0.036 1.1 5.6 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.70 1.61 1.828 14.115 15.812 3.876 12.01 13.68 1.67 1.958 14.067 15.812 3.866 Individual atomic B min max mean iso aniso Overall: 5.51 67.46 14.80 1.00 481 3270 Protein: 5.51 33.13 10.65 1.00 0 2902 Water: 6.09 67.46 29.01 N/A 481 366 Other: 14.03 27.60 20.81 N/A 0 2 Chain A: 5.56 54.37 12.60 N/A 0 1624 Chain B: 5.51 67.46 12.40 N/A 0 1646 Chain S: 6.09 63.90 30.45 N/A 481 0 Histogram: Values Number of atoms 5.51 - 11.70 2119 11.70 - 17.90 728 17.90 - 24.09 308 24.09 - 30.29 235 30.29 - 36.48 145 36.48 - 42.68 124 42.68 - 48.87 62 48.87 - 55.07 22 55.07 - 61.26 5 61.26 - 67.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1368 r_work=0.1201 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1369 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1364 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863734 | | target function (ml) not normalized (work): 723650.244928 | | target function (ml) not normalized (free): 15139.262535 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1364 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1431 0.1430 0.1476 n_refl.: 191134 remove outliers: r(all,work,free)=0.1431 0.1430 0.1476 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1423 0.1423 0.1471 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191134 remove outliers: r(all,work,free)=0.1201 0.1198 0.1363 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3860 360.726 324.372 0.414 0.946 0.250 13.296-10.522 97.03 97 1 0.2366 481.632 455.425 0.697 0.947 0.200 10.503-8.327 97.80 175 3 0.2063 502.365 497.872 0.866 0.948 0.177 8.315-6.595 100.00 359 8 0.2178 374.940 370.214 0.893 0.947 0.136 6.588-5.215 100.00 711 7 0.1937 345.403 335.687 0.888 0.947 0.115 5.214-4.128 98.38 1367 28 0.1220 505.219 500.141 0.974 0.948 0.080 4.126-3.266 94.74 2603 46 0.1116 460.534 454.164 1.033 0.948 0.000 3.266-2.585 99.86 5447 97 0.1097 310.665 307.434 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0940 234.379 231.905 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0911 138.717 137.405 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0986 74.677 73.960 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.061 38.398 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=-0.1181 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1363 | n_water=847 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1199 r_free=0.1364 | n_water=846 | time (s): 106.240 (total time: 108.760) Filter (q & B) r_work=0.1199 r_free=0.1363 | n_water=837 | time (s): 4.320 (total time: 113.080) Compute maps r_work=0.1199 r_free=0.1363 | n_water=837 | time (s): 1.670 (total time: 114.750) Filter (map) r_work=0.1222 r_free=0.1369 | n_water=715 | time (s): 5.210 (total time: 119.960) Find peaks r_work=0.1222 r_free=0.1369 | n_water=715 | time (s): 0.860 (total time: 120.820) Add new water r_work=0.1236 r_free=0.1389 | n_water=945 | time (s): 5.780 (total time: 126.600) Refine new water occ: r_work=0.1196 r_free=0.1349 adp: r_work=0.1197 r_free=0.1348 occ: r_work=0.1194 r_free=0.1348 adp: r_work=0.1194 r_free=0.1346 occ: r_work=0.1192 r_free=0.1347 adp: r_work=0.1192 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1345 r_work=0.1192 r_free=0.1345 | n_water=945 | time (s): 189.200 (total time: 315.800) Filter (q & B) r_work=0.1195 r_free=0.1351 | n_water=863 | time (s): 4.660 (total time: 320.460) Filter (dist only) r_work=0.1196 r_free=0.1351 | n_water=862 | time (s): 107.150 (total time: 427.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540484 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.122493 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1356 0.0157 0.036 1.1 7.0 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.56 1.57 1.787 14.035 15.122 3.764 12.01 13.59 1.58 1.817 14.023 15.122 3.762 Individual atomic B min max mean iso aniso Overall: 5.55 67.26 14.82 0.97 497 3269 Protein: 5.55 32.30 10.60 0.97 0 2902 Water: 5.98 67.26 29.02 N/A 497 365 Other: 13.78 26.93 20.36 N/A 0 2 Chain A: 5.63 53.93 12.52 N/A 0 1623 Chain B: 5.55 67.26 12.34 N/A 0 1646 Chain S: 5.98 63.86 30.56 N/A 497 0 Histogram: Values Number of atoms 5.55 - 11.72 2140 11.72 - 17.89 722 17.89 - 24.06 305 24.06 - 30.23 223 30.23 - 36.41 161 36.41 - 42.58 125 42.58 - 48.75 62 48.75 - 54.92 20 54.92 - 61.09 5 61.09 - 67.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1359 r_work=0.1201 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1360 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 = 0.1359 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760675 | | target function (ml) not normalized (work): 704336.863321 | | target function (ml) not normalized (free): 14736.582561 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1359 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1426 0.1426 0.1482 n_refl.: 191131 remove outliers: r(all,work,free)=0.1426 0.1426 0.1482 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1419 0.1418 0.1477 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1197 0.1359 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3569 356.306 315.496 0.412 0.948 0.246 13.296-10.522 97.03 97 1 0.2326 481.632 464.578 0.704 0.950 0.191 10.503-8.327 97.80 175 3 0.2104 502.365 497.043 0.861 0.950 0.166 8.315-6.595 100.00 359 8 0.2128 374.940 370.139 0.885 0.949 0.105 6.588-5.215 100.00 711 7 0.1926 345.403 335.869 0.886 0.949 0.090 5.214-4.128 98.38 1367 28 0.1223 505.219 499.907 0.973 0.950 0.080 4.126-3.266 94.74 2603 46 0.1133 460.534 453.801 1.032 0.950 0.005 3.266-2.585 99.86 5447 97 0.1102 310.665 307.451 1.020 0.949 0.000 2.585-2.046 97.45 10613 204 0.0948 234.379 231.922 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0915 138.717 137.421 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0974 74.677 73.973 1.054 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.061 38.391 1.042 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1245 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1359 | n_water=862 | time (s): 3.110 (total time: 3.110) Filter (dist) r_work=0.1197 r_free=0.1359 | n_water=861 | time (s): 105.380 (total time: 108.490) Filter (q & B) r_work=0.1198 r_free=0.1358 | n_water=849 | time (s): 4.170 (total time: 112.660) Compute maps r_work=0.1198 r_free=0.1358 | n_water=849 | time (s): 1.930 (total time: 114.590) Filter (map) r_work=0.1218 r_free=0.1362 | n_water=742 | time (s): 5.660 (total time: 120.250) Find peaks r_work=0.1218 r_free=0.1362 | n_water=742 | time (s): 0.610 (total time: 120.860) Add new water r_work=0.1229 r_free=0.1376 | n_water=949 | time (s): 4.500 (total time: 125.360) Refine new water occ: r_work=0.1196 r_free=0.1354 adp: r_work=0.1196 r_free=0.1354 occ: r_work=0.1194 r_free=0.1352 adp: r_work=0.1194 r_free=0.1351 occ: r_work=0.1192 r_free=0.1349 adp: r_work=0.1192 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1350 r_work=0.1192 r_free=0.1350 | n_water=949 | time (s): 192.940 (total time: 318.300) Filter (q & B) r_work=0.1195 r_free=0.1349 | n_water=871 | time (s): 4.710 (total time: 323.010) Filter (dist only) r_work=0.1196 r_free=0.1348 | n_water=870 | time (s): 111.930 (total time: 434.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.557600 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.051294 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 0.1353 0.0156 0.037 1.1 6.8 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.53 1.56 1.768 13.984 15.051 3.761 12.01 13.57 1.56 1.900 13.941 15.051 3.759 Individual atomic B min max mean iso aniso Overall: 5.56 66.16 14.73 0.91 505 3269 Protein: 5.56 29.88 10.50 0.91 0 2902 Water: 5.95 66.16 28.83 N/A 505 365 Other: 13.88 24.13 19.00 N/A 0 2 Chain A: 5.64 51.47 12.39 N/A 0 1623 Chain B: 5.56 66.16 12.22 N/A 0 1646 Chain S: 5.95 63.76 30.46 N/A 505 0 Histogram: Values Number of atoms 5.56 - 11.62 2119 11.62 - 17.68 769 17.68 - 23.74 281 23.74 - 29.80 211 29.80 - 35.86 169 35.86 - 41.92 128 41.92 - 47.98 65 47.98 - 54.04 24 54.04 - 60.10 5 60.10 - 66.16 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1357 r_work=0.1201 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1358 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1358 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757703 | | target function (ml) not normalized (work): 703772.699854 | | target function (ml) not normalized (free): 14729.155583 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1358 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1415 0.1415 0.1480 n_refl.: 191129 remove outliers: r(all,work,free)=0.1415 0.1415 0.1480 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1408 0.1407 0.1475 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191129 remove outliers: r(all,work,free)=0.1200 0.1197 0.1355 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 91.09 89 3 0.3559 357.080 326.709 0.418 0.949 0.229 13.296-10.522 97.03 97 1 0.2331 481.632 465.071 0.694 0.950 0.166 10.503-8.327 97.80 175 3 0.2154 502.365 496.844 0.857 0.951 0.137 8.315-6.595 100.00 359 8 0.2141 374.940 371.074 0.884 0.950 0.101 6.588-5.215 100.00 711 7 0.1918 345.403 336.273 0.885 0.950 0.075 5.214-4.128 98.38 1367 28 0.1238 505.219 499.771 0.972 0.951 0.070 4.126-3.266 94.74 2603 46 0.1143 460.534 453.839 1.033 0.951 0.005 3.266-2.585 99.86 5447 97 0.1115 310.665 307.304 1.019 0.950 0.000 2.585-2.046 97.45 10613 204 0.0956 234.379 231.888 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0909 138.717 137.418 1.054 0.949 0.000 1.619-1.281 98.00 42464 925 0.0969 74.677 73.982 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.061 38.401 1.039 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1339 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1355 | n_water=870 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1197 r_free=0.1355 | n_water=870 | time (s): 103.620 (total time: 106.100) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=864 | time (s): 4.430 (total time: 110.530) Compute maps r_work=0.1198 r_free=0.1356 | n_water=864 | time (s): 2.130 (total time: 112.660) Filter (map) r_work=0.1219 r_free=0.1358 | n_water=754 | time (s): 4.710 (total time: 117.370) Find peaks r_work=0.1219 r_free=0.1358 | n_water=754 | time (s): 0.900 (total time: 118.270) Add new water r_work=0.1228 r_free=0.1370 | n_water=959 | time (s): 4.210 (total time: 122.480) Refine new water occ: r_work=0.1196 r_free=0.1337 adp: r_work=0.1196 r_free=0.1338 occ: r_work=0.1194 r_free=0.1335 adp: r_work=0.1194 r_free=0.1336 occ: r_work=0.1192 r_free=0.1334 adp: r_work=0.1192 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1334 r_work=0.1192 r_free=0.1334 | n_water=959 | time (s): 249.760 (total time: 372.240) Filter (q & B) r_work=0.1196 r_free=0.1341 | n_water=887 | time (s): 4.460 (total time: 376.700) Filter (dist only) r_work=0.1196 r_free=0.1341 | n_water=886 | time (s): 109.960 (total time: 486.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.548159 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.042736 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1351 0.0152 0.038 1.1 6.8 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.51 1.52 1.726 13.883 14.043 3.759 12.02 13.56 1.54 1.798 13.853 14.043 3.758 Individual atomic B min max mean iso aniso Overall: 5.58 64.97 14.69 0.88 521 3269 Protein: 5.58 28.61 10.43 0.88 0 2902 Water: 6.04 64.97 28.64 N/A 521 365 Other: 13.87 22.34 18.10 N/A 0 2 Chain A: 5.63 51.02 12.27 N/A 0 1623 Chain B: 5.58 64.97 12.12 N/A 0 1646 Chain S: 6.04 63.58 30.34 N/A 521 0 Histogram: Values Number of atoms 5.58 - 11.52 2105 11.52 - 17.46 783 17.46 - 23.40 276 23.40 - 29.34 217 29.34 - 35.28 173 35.28 - 41.22 125 41.22 - 47.16 73 47.16 - 53.09 29 53.09 - 59.03 5 59.03 - 64.97 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1356 r_work=0.1202 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1357 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1356 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757827 | | target function (ml) not normalized (work): 703792.094670 | | target function (ml) not normalized (free): 14738.275129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1356 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1482 n_refl.: 191128 remove outliers: r(all,work,free)=0.1398 0.1396 0.1482 n_refl.: 191128 overall B=-0.01 to atoms: r(all,work,free)=0.1396 0.1395 0.1481 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1191 0.1343 n_refl.: 191128 remove outliers: r(all,work,free)=0.1193 0.1191 0.1343 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 91.09 89 3 0.3617 357.080 328.902 0.407 0.973 0.209 13.296-10.522 97.03 97 1 0.2362 481.632 462.982 0.686 0.974 0.147 10.503-8.327 97.80 175 3 0.2183 502.365 495.332 0.852 0.975 0.120 8.315-6.595 100.00 359 8 0.2131 374.940 370.265 0.881 0.975 0.093 6.588-5.215 100.00 711 7 0.1930 345.403 335.866 0.882 0.975 0.073 5.214-4.128 98.38 1367 28 0.1236 505.219 499.117 0.970 0.976 0.070 4.126-3.266 94.74 2603 46 0.1158 460.534 452.964 1.030 0.977 0.005 3.266-2.585 99.86 5447 97 0.1123 310.665 306.992 1.015 0.978 0.000 2.585-2.046 97.45 10613 204 0.0961 234.379 231.707 1.025 0.980 0.000 2.046-1.619 99.39 21536 464 0.0908 138.717 137.297 1.043 0.983 0.000 1.619-1.281 98.00 42464 925 0.0948 74.677 74.022 1.037 0.987 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.061 38.363 1.010 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0251 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1343 | n_water=886 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1191 r_free=0.1343 | n_water=885 | time (s): 104.240 (total time: 106.740) Filter (q & B) r_work=0.1191 r_free=0.1344 | n_water=876 | time (s): 3.980 (total time: 110.720) Compute maps r_work=0.1191 r_free=0.1344 | n_water=876 | time (s): 1.830 (total time: 112.550) Filter (map) r_work=0.1214 r_free=0.1357 | n_water=757 | time (s): 4.970 (total time: 117.520) Find peaks r_work=0.1214 r_free=0.1357 | n_water=757 | time (s): 0.870 (total time: 118.390) Add new water r_work=0.1222 r_free=0.1365 | n_water=960 | time (s): 5.360 (total time: 123.750) Refine new water occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1190 r_free=0.1334 occ: r_work=0.1188 r_free=0.1332 adp: r_work=0.1188 r_free=0.1332 occ: r_work=0.1187 r_free=0.1331 adp: r_work=0.1187 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1331 r_work=0.1187 r_free=0.1331 | n_water=960 | time (s): 198.570 (total time: 322.320) Filter (q & B) r_work=0.1190 r_free=0.1337 | n_water=893 | time (s): 4.320 (total time: 326.640) Filter (dist only) r_work=0.1190 r_free=0.1337 | n_water=892 | time (s): 110.240 (total time: 436.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.547315 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.814288 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 0.1342 0.0149 0.038 1.1 5.8 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.42 1.49 1.699 13.820 14.814 3.757 11.91 13.44 1.53 1.712 13.816 14.814 3.753 Individual atomic B min max mean iso aniso Overall: 5.60 63.83 14.69 0.88 527 3269 Protein: 5.60 28.56 10.43 0.88 0 2902 Water: 5.98 63.83 28.51 N/A 527 365 Other: 13.88 22.31 18.10 N/A 0 2 Chain A: 5.67 50.49 12.24 N/A 0 1623 Chain B: 5.60 63.83 12.09 N/A 0 1646 Chain S: 5.98 63.44 30.31 N/A 527 0 Histogram: Values Number of atoms 5.60 - 11.42 2065 11.42 - 17.24 820 17.24 - 23.07 270 23.07 - 28.89 222 28.89 - 34.71 175 34.71 - 40.54 121 40.54 - 46.36 74 46.36 - 52.18 37 52.18 - 58.01 6 58.01 - 63.83 6 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1344 r_work=0.1191 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1344 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1343 target_work(ml) = 3.752 | | 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= 0.1189 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752340 | | target function (ml) not normalized (work): 702764.590907 | | target function (ml) not normalized (free): 14718.418581 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1343 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1492 n_refl.: 191128 remove outliers: r(all,work,free)=0.1404 0.1402 0.1492 n_refl.: 191128 overall B=-0.02 to atoms: r(all,work,free)=0.1401 0.1399 0.1489 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1339 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1339 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 91.09 89 3 0.3621 357.080 328.520 0.424 0.918 0.203 13.296-10.522 97.03 97 1 0.2374 481.632 463.304 0.720 0.919 0.137 10.503-8.327 97.80 175 3 0.2210 502.365 495.537 0.898 0.920 0.110 8.315-6.595 100.00 359 8 0.2136 374.940 370.373 0.928 0.920 0.070 6.588-5.215 100.00 711 7 0.1946 345.403 335.521 0.933 0.920 0.070 5.214-4.128 98.38 1367 28 0.1257 505.219 498.793 1.027 0.921 0.050 4.126-3.266 94.74 2603 46 0.1160 460.534 452.978 1.092 0.922 0.000 3.266-2.585 99.86 5447 97 0.1123 310.665 307.010 1.077 0.923 0.000 2.585-2.046 97.45 10613 204 0.0961 234.379 231.709 1.086 0.925 0.000 2.046-1.619 99.39 21536 464 0.0904 138.717 137.331 1.106 0.928 0.000 1.619-1.281 98.00 42464 925 0.0940 74.677 74.030 1.100 0.933 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.061 38.353 1.073 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0462 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1339 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1339 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1339 | n_water=892 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1189 r_free=0.1339 | n_water=892 | time (s): 113.040 (total time: 115.930) Filter (q & B) r_work=0.1189 r_free=0.1340 | n_water=882 | time (s): 4.440 (total time: 120.370) Compute maps r_work=0.1189 r_free=0.1340 | n_water=882 | time (s): 2.210 (total time: 122.580) Filter (map) r_work=0.1211 r_free=0.1357 | n_water=774 | time (s): 4.950 (total time: 127.530) Find peaks r_work=0.1211 r_free=0.1357 | n_water=774 | time (s): 0.540 (total time: 128.070) Add new water r_work=0.1218 r_free=0.1363 | n_water=966 | time (s): 4.710 (total time: 132.780) Refine new water occ: r_work=0.1186 r_free=0.1330 adp: r_work=0.1186 r_free=0.1330 occ: r_work=0.1185 r_free=0.1329 adp: r_work=0.1185 r_free=0.1329 occ: r_work=0.1183 r_free=0.1328 adp: r_work=0.1183 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1328 r_work=0.1183 r_free=0.1328 | n_water=966 | time (s): 256.020 (total time: 388.800) Filter (q & B) r_work=0.1187 r_free=0.1335 | n_water=895 | time (s): 4.150 (total time: 392.950) Filter (dist only) r_work=0.1187 r_free=0.1334 | n_water=894 | time (s): 115.300 (total time: 508.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.482988 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.399185 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1343 0.0151 0.039 1.1 6.3 0.0 0.3 0 0.741 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.43 1.51 1.697 13.792 14.399 3.754 11.93 13.48 1.55 1.696 13.791 14.399 3.754 Individual atomic B min max mean iso aniso Overall: 5.60 63.50 14.65 0.87 529 3269 Protein: 5.60 28.39 10.43 0.87 0 2902 Water: 6.05 63.50 28.32 N/A 529 365 Other: 13.86 22.24 18.05 N/A 0 2 Chain A: 5.66 50.36 12.21 N/A 0 1623 Chain B: 5.60 63.50 12.08 N/A 0 1646 Chain S: 6.05 63.36 30.11 N/A 529 0 Histogram: Values Number of atoms 5.60 - 11.39 2057 11.39 - 17.18 831 17.18 - 22.97 279 22.97 - 28.76 216 28.76 - 34.55 173 34.55 - 40.34 119 40.34 - 46.13 71 46.13 - 51.92 40 51.92 - 57.71 6 57.71 - 63.50 6 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1348 r_work=0.1193 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1348 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1350 target_work(ml) = 3.753 | | 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= 0.1192 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753480 | | target function (ml) not normalized (work): 702978.061242 | | target function (ml) not normalized (free): 14727.319244 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1501 n_refl.: 191128 remove outliers: r(all,work,free)=0.1411 0.1410 0.1501 n_refl.: 191128 overall B=-0.02 to atoms: r(all,work,free)=0.1407 0.1405 0.1497 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1347 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1347 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 91.09 89 3 0.3636 357.080 327.282 0.417 0.918 0.193 13.296-10.522 97.03 97 1 0.2410 481.632 461.524 0.719 0.920 0.138 10.503-8.327 97.80 175 3 0.2205 502.365 495.458 0.898 0.920 0.119 8.315-6.595 100.00 359 8 0.2143 374.940 370.133 0.929 0.920 0.083 6.588-5.215 100.00 711 7 0.1949 345.403 335.305 0.933 0.920 0.079 5.214-4.128 98.38 1367 28 0.1262 505.219 498.910 1.027 0.921 0.049 4.126-3.266 94.74 2603 46 0.1171 460.534 452.996 1.093 0.922 0.005 3.266-2.585 99.86 5447 97 0.1133 310.665 307.012 1.076 0.923 0.000 2.585-2.046 97.45 10613 204 0.0962 234.379 231.684 1.086 0.926 0.000 2.046-1.619 99.39 21536 464 0.0904 138.717 137.331 1.106 0.929 0.000 1.619-1.281 98.00 42464 925 0.0940 74.677 74.032 1.100 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.061 38.345 1.073 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0623 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1347 After: r_work=0.1192 r_free=0.1348 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1348 | n_water=894 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1192 r_free=0.1348 | n_water=894 | time (s): 118.140 (total time: 121.150) Filter (q & B) r_work=0.1193 r_free=0.1347 | n_water=882 | time (s): 5.550 (total time: 126.700) Compute maps r_work=0.1193 r_free=0.1347 | n_water=882 | time (s): 2.150 (total time: 128.850) Filter (map) r_work=0.1216 r_free=0.1360 | n_water=772 | time (s): 4.300 (total time: 133.150) Find peaks r_work=0.1216 r_free=0.1360 | n_water=772 | time (s): 0.540 (total time: 133.690) Add new water r_work=0.1223 r_free=0.1368 | n_water=966 | time (s): 4.870 (total time: 138.560) Refine new water occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1190 r_free=0.1334 occ: r_work=0.1189 r_free=0.1332 adp: r_work=0.1189 r_free=0.1332 occ: r_work=0.1187 r_free=0.1331 adp: r_work=0.1187 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1331 r_work=0.1187 r_free=0.1331 | n_water=966 | time (s): 170.710 (total time: 309.270) Filter (q & B) r_work=0.1191 r_free=0.1338 | n_water=894 | time (s): 4.140 (total time: 313.410) Filter (dist only) r_work=0.1192 r_free=0.1338 | n_water=892 | time (s): 115.600 (total time: 429.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.497177 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.474312 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 0.1344 0.0149 0.039 1.1 8.9 0.0 0.3 0 0.749 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.44 1.49 1.691 13.773 14.474 3.756 11.95 13.46 1.51 1.696 13.771 14.474 3.755 Individual atomic B min max mean iso aniso Overall: 5.62 63.08 14.62 0.86 527 3269 Protein: 5.62 28.21 10.42 0.86 0 2902 Water: 6.09 63.08 28.27 N/A 527 365 Other: 13.88 22.09 17.99 N/A 0 2 Chain A: 5.70 49.95 12.18 N/A 0 1623 Chain B: 5.62 62.45 12.05 N/A 0 1646 Chain S: 6.09 63.08 30.16 N/A 527 0 Histogram: Values Number of atoms 5.62 - 11.36 2054 11.36 - 17.11 832 17.11 - 22.86 281 22.86 - 28.60 210 28.60 - 34.35 180 34.35 - 40.09 112 40.09 - 45.84 75 45.84 - 51.59 39 51.59 - 57.33 7 57.33 - 63.08 6 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1346 r_work=0.1196 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1346 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1344 target_work(ml) = 3.755 | | 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= 0.1195 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754827 | | target function (ml) not normalized (work): 703230.347922 | | target function (ml) not normalized (free): 14727.785849 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1368 0.1395 5.6921 5.7499| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1325 5.0721 5.1557| | 3: 2.33 - 2.04 0.96 6939 150 0.0911 0.1209 4.6643 4.7564| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1060 4.3938 4.5735| | 5: 1.85 - 1.72 0.99 7113 159 0.0933 0.1011 4.1556 4.2626| | 6: 1.72 - 1.62 0.99 7102 142 0.0897 0.1077 3.9487 4.0796| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0959 3.8007 3.9228| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1336 3.7024 3.9151| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1126 3.6224 3.7515| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1172 3.5565 3.6691| | 11: 1.36 - 1.32 0.99 6997 151 0.0990 0.1133 3.4837 3.5926| | 12: 1.32 - 1.28 0.98 6975 149 0.1029 0.1114 3.4586 3.5748| | 13: 1.28 - 1.25 0.98 6907 166 0.1037 0.1246 3.4351 3.5657| | 14: 1.25 - 1.22 0.98 7015 112 0.1100 0.1580 3.4308 3.6757| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1239 3.4474 3.4913| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1548 3.4647 3.6553| | 17: 1.17 - 1.14 0.98 6940 135 0.1296 0.1229 3.4331 3.4448| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1701 3.4384 3.5293| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1764 3.4194 3.595| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1580 3.4105 3.4349| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2124 3.4185 3.5005| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1961 3.414 3.4182| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2020 3.4342 3.4885| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2251 3.4369 3.5117| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2524 3.4502 3.5237| | 26: 1.01 - 0.99 0.96 6767 158 0.2752 0.2843 3.4159 3.4218| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2790 3.4697 3.3968| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.32 1.00 0.96 10692.06| | 2: 2.94 - 2.33 7339 128 0.93 12.57 0.99 0.96 4974.75| | 3: 2.33 - 2.04 6939 150 0.96 7.74 1.01 0.96 1723.04| | 4: 2.04 - 1.85 7170 155 0.96 7.70 1.00 0.96 1015.69| | 5: 1.85 - 1.72 7113 159 0.96 8.15 1.00 0.97 644.60| | 6: 1.72 - 1.62 7102 142 0.96 8.06 1.00 0.98 445.69| | 7: 1.62 - 1.54 7104 148 0.96 8.13 1.01 0.98 337.31| | 8: 1.54 - 1.47 6798 152 0.96 8.24 1.01 0.98 279.36| | 9: 1.47 - 1.41 6938 155 0.96 8.47 1.00 0.99 230.71| | 10: 1.41 - 1.36 7022 150 0.96 8.92 1.00 0.98 202.57| | 11: 1.36 - 1.32 6997 151 0.96 8.90 0.99 0.97 174.27| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.98 0.96 160.43| | 13: 1.28 - 1.25 6907 166 0.96 9.46 1.01 0.97 157.51| | 14: 1.25 - 1.22 7015 112 0.95 10.64 1.01 0.98 162.33| | 15: 1.22 - 1.19 6956 137 0.95 11.19 1.01 0.99 165.90| | 16: 1.19 - 1.17 6604 132 0.95 11.40 1.00 0.97 159.95| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.97 153.94| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.96 147.69| | 19: 1.12 - 1.10 6948 106 0.93 14.13 1.00 0.96 150.98| | 20: 1.10 - 1.08 6884 147 0.92 15.21 1.00 0.95 150.14| | 21: 1.08 - 1.07 6852 152 0.91 16.61 1.00 0.94 153.26| | 22: 1.07 - 1.05 6836 135 0.89 18.31 1.00 0.94 155.34| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.93 165.26| | 24: 1.03 - 1.02 6784 133 0.85 23.16 1.00 0.94 179.39| | 25: 1.02 - 1.01 6552 130 0.83 25.12 0.98 0.91 182.04| | 26: 1.01 - 0.99 6767 158 0.81 26.57 0.98 0.90 176.40| | 27: 0.99 - 0.98 6647 131 0.82 26.26 0.99 0.89 160.98| |alpha: min = 0.89 max = 0.99 mean = 0.96| |beta: min = 147.69 max = 10692.06 mean = 901.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.91 mean = 13.26| |phase err.(test): min = 0.00 max = 88.97 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1195 0.1344 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1417 0.1416 0.1501 n_refl.: 191128 remove outliers: r(all,work,free)=0.1417 0.1416 0.1501 n_refl.: 191128 overall B=-0.13 to atoms: r(all,work,free)=0.1396 0.1394 0.1484 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1344 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1194 0.1344 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 91.09 89 3 0.3595 357.080 328.837 0.418 0.919 0.205 13.296-10.522 97.03 97 1 0.2401 481.632 461.819 0.705 0.920 0.130 10.503-8.327 97.80 175 3 0.2215 502.365 495.127 0.882 0.920 0.100 8.315-6.595 100.00 359 8 0.2129 374.940 370.368 0.915 0.920 0.085 6.588-5.215 100.00 711 7 0.1934 345.403 335.437 0.918 0.921 0.070 5.214-4.128 98.38 1367 28 0.1265 505.219 498.944 1.010 0.922 0.034 4.126-3.266 94.74 2603 46 0.1173 460.534 452.953 1.076 0.923 0.000 3.266-2.585 99.86 5447 97 0.1130 310.665 307.050 1.059 0.924 0.000 2.585-2.046 97.45 10613 204 0.0969 234.379 231.669 1.065 0.927 0.000 2.046-1.619 99.39 21536 464 0.0910 138.717 137.330 1.081 0.931 0.000 1.619-1.281 98.00 42464 925 0.0945 74.677 74.027 1.070 0.937 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.061 38.340 1.035 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0277 ================= 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 : 0.2033 0.2024 0.081 5.222 5.2 78.0 14.6 805 0.000 1_bss: 0.1796 0.1962 0.081 5.222 5.2 78.0 14.6 805 0.000 1_settarget: 0.1796 0.1962 0.081 5.222 5.2 78.0 14.6 805 0.000 1_nqh: 0.1796 0.1962 0.081 5.222 5.2 78.0 14.6 805 0.000 1_weight: 0.1796 0.1962 0.081 5.222 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1501 0.039 1.173 5.2 78.0 14.6 805 0.156 1_adp: 0.1294 0.1566 0.039 1.173 5.2 73.0 15.0 805 0.156 1_regHadp: 0.1293 0.1561 0.039 1.173 5.2 73.0 15.0 805 0.156 1_occ: 0.1279 0.1552 0.039 1.173 5.2 73.0 15.0 805 0.156 2_bss: 0.1271 0.1544 0.039 1.173 5.4 73.2 15.2 805 0.156 2_settarget: 0.1271 0.1544 0.039 1.173 5.4 73.2 15.2 805 0.156 2_updatecdl: 0.1271 0.1544 0.039 1.175 5.4 73.2 15.2 805 0.156 2_nqh: 0.1271 0.1544 0.039 1.175 5.4 73.2 15.2 805 0.156 2_sol: 0.1267 0.1497 0.039 1.175 5.4 73.2 16.3 891 n/a 2_weight: 0.1267 0.1497 0.039 1.175 5.4 73.2 16.3 891 n/a 2_xyzrec: 0.1252 0.1514 0.041 1.136 5.4 73.2 16.3 891 n/a 2_adp: 0.1233 0.1505 0.041 1.136 5.4 68.4 16.4 891 n/a 2_regHadp: 0.1234 0.1506 0.041 1.136 5.4 68.4 16.4 891 n/a 2_occ: 0.1227 0.1505 0.041 1.136 5.4 68.4 16.4 891 n/a 3_bss: 0.1234 0.1513 0.041 1.136 5.4 68.4 16.4 891 n/a 3_settarget: 0.1234 0.1513 0.041 1.136 5.4 68.4 16.4 891 n/a 3_updatecdl: 0.1234 0.1513 0.041 1.138 5.4 68.4 16.4 891 n/a 3_nqh: 0.1234 0.1513 0.041 1.138 5.4 68.4 16.4 891 n/a 3_sol: 0.1252 0.1519 0.041 1.138 5.4 68.4 15.5 870 n/a 3_weight: 0.1252 0.1519 0.041 1.138 5.4 68.4 15.5 870 n/a 3_xyzrec: 0.1240 0.1443 0.035 1.105 5.4 68.4 15.5 870 n/a 3_adp: 0.1234 0.1404 0.035 1.105 5.5 68.0 15.3 870 n/a 3_regHadp: 0.1235 0.1404 0.035 1.105 5.5 68.0 15.3 870 n/a 3_occ: 0.1230 0.1396 0.035 1.105 5.5 68.0 15.3 870 n/a 4_bss: 0.1226 0.1386 0.035 1.105 5.5 67.9 15.3 870 n/a 4_settarget: 0.1226 0.1386 0.035 1.105 5.5 67.9 15.3 870 n/a 4_updatecdl: 0.1226 0.1386 0.035 1.107 5.5 67.9 15.3 870 n/a 4_nqh: 0.1226 0.1386 0.035 1.107 5.5 67.9 15.3 870 n/a 4_sol: 0.1209 0.1368 0.035 1.107 5.5 67.9 14.9 847 n/a 4_weight: 0.1209 0.1368 0.035 1.107 5.5 67.9 14.9 847 n/a 4_xyzrec: 0.1208 0.1370 0.036 1.121 5.5 67.9 14.9 847 n/a 4_adp: 0.1201 0.1368 0.036 1.121 5.5 67.5 14.8 847 n/a 4_regHadp: 0.1201 0.1369 0.036 1.121 5.5 67.5 14.8 847 n/a 4_occ: 0.1200 0.1364 0.036 1.121 5.5 67.5 14.8 847 n/a 5_bss: 0.1198 0.1363 0.036 1.121 5.5 67.4 14.8 847 n/a 5_settarget: 0.1198 0.1363 0.036 1.121 5.5 67.4 14.8 847 n/a 5_updatecdl: 0.1198 0.1363 0.036 1.121 5.5 67.4 14.8 847 n/a 5_nqh: 0.1198 0.1363 0.036 1.121 5.5 67.4 14.8 847 n/a 5_sol: 0.1196 0.1351 0.036 1.121 5.5 67.4 14.8 862 n/a 5_weight: 0.1196 0.1351 0.036 1.121 5.5 67.4 14.8 862 n/a 5_xyzrec: 0.1198 0.1356 0.036 1.130 5.5 67.4 14.8 862 n/a 5_adp: 0.1201 0.1359 0.036 1.130 5.6 67.3 14.8 862 n/a 5_regHadp: 0.1201 0.1360 0.036 1.130 5.6 67.3 14.8 862 n/a 5_occ: 0.1199 0.1359 0.036 1.130 5.6 67.3 14.8 862 n/a 6_bss: 0.1197 0.1359 0.036 1.130 5.5 67.2 14.8 862 n/a 6_settarget: 0.1197 0.1359 0.036 1.130 5.5 67.2 14.8 862 n/a 6_updatecdl: 0.1197 0.1359 0.036 1.131 5.5 67.2 14.8 862 n/a 6_nqh: 0.1197 0.1359 0.036 1.131 5.5 67.2 14.8 862 n/a 6_sol: 0.1196 0.1348 0.036 1.131 5.5 67.2 14.8 870 n/a 6_weight: 0.1196 0.1348 0.036 1.131 5.5 67.2 14.8 870 n/a 6_xyzrec: 0.1197 0.1353 0.037 1.130 5.5 67.2 14.8 870 n/a 6_adp: 0.1201 0.1357 0.037 1.130 5.6 66.2 14.7 870 n/a 6_regHadp: 0.1201 0.1358 0.037 1.130 5.6 66.2 14.7 870 n/a 6_occ: 0.1198 0.1358 0.037 1.130 5.6 66.2 14.7 870 n/a 7_bss: 0.1197 0.1355 0.037 1.130 5.5 66.1 14.7 870 n/a 7_settarget: 0.1197 0.1355 0.037 1.130 5.5 66.1 14.7 870 n/a 7_updatecdl: 0.1197 0.1355 0.037 1.130 5.5 66.1 14.7 870 n/a 7_nqh: 0.1197 0.1355 0.037 1.130 5.5 66.1 14.7 870 n/a 7_sol: 0.1196 0.1341 0.037 1.130 5.5 66.1 14.7 886 n/a 7_weight: 0.1196 0.1341 0.037 1.130 5.5 66.1 14.7 886 n/a 7_xyzrec: 0.1199 0.1351 0.038 1.126 5.5 66.1 14.7 886 n/a 7_adp: 0.1202 0.1356 0.038 1.126 5.6 65.0 14.7 886 n/a 7_regHadp: 0.1202 0.1357 0.038 1.126 5.6 65.0 14.7 886 n/a 7_occ: 0.1200 0.1356 0.038 1.126 5.6 65.0 14.7 886 n/a 8_bss: 0.1190 0.1343 0.038 1.126 5.6 65.0 14.7 886 n/a 8_settarget: 0.1190 0.1343 0.038 1.126 5.6 65.0 14.7 886 n/a 8_updatecdl: 0.1190 0.1343 0.038 1.125 5.6 65.0 14.7 886 n/a 8_nqh: 0.1190 0.1343 0.038 1.125 5.6 65.0 14.7 886 n/a 8_sol: 0.1190 0.1337 0.038 1.125 5.6 65.0 14.7 892 n/a 8_weight: 0.1190 0.1337 0.038 1.125 5.6 65.0 14.7 892 n/a 8_xyzrec: 0.1193 0.1342 0.038 1.122 5.6 65.0 14.7 892 n/a 8_adp: 0.1191 0.1344 0.038 1.122 5.6 63.8 14.7 892 n/a 8_regHadp: 0.1191 0.1344 0.038 1.122 5.6 63.8 14.7 892 n/a 8_occ: 0.1189 0.1343 0.038 1.122 5.6 63.8 14.7 892 n/a 9_bss: 0.1189 0.1339 0.038 1.122 5.6 63.8 14.7 892 n/a 9_settarget: 0.1189 0.1339 0.038 1.122 5.6 63.8 14.7 892 n/a 9_updatecdl: 0.1189 0.1339 0.038 1.123 5.6 63.8 14.7 892 n/a 9_nqh: 0.1189 0.1339 0.038 1.123 5.6 63.8 14.7 892 n/a 9_sol: 0.1187 0.1334 0.038 1.123 5.6 63.8 14.6 894 n/a 9_weight: 0.1187 0.1334 0.038 1.123 5.6 63.8 14.6 894 n/a 9_xyzrec: 0.1192 0.1343 0.039 1.103 5.6 63.8 14.6 894 n/a 9_adp: 0.1193 0.1348 0.039 1.103 5.6 63.5 14.6 894 n/a 9_regHadp: 0.1193 0.1348 0.039 1.103 5.6 63.5 14.6 894 n/a 9_occ: 0.1192 0.1350 0.039 1.103 5.6 63.5 14.6 894 n/a 10_bss: 0.1191 0.1347 0.039 1.103 5.6 63.5 14.6 894 n/a 10_settarget: 0.1191 0.1347 0.039 1.103 5.6 63.5 14.6 894 n/a 10_updatecdl: 0.1191 0.1347 0.039 1.103 5.6 63.5 14.6 894 n/a 10_setrh: 0.1192 0.1348 0.039 1.103 5.6 63.5 14.6 894 n/a 10_nqh: 0.1192 0.1348 0.039 1.103 5.6 63.5 14.6 894 n/a 10_sol: 0.1192 0.1338 0.039 1.103 5.6 63.5 14.6 892 n/a 10_weight: 0.1192 0.1338 0.039 1.103 5.6 63.5 14.6 892 n/a 10_xyzrec: 0.1195 0.1344 0.039 1.150 5.6 63.5 14.6 892 n/a 10_adp: 0.1196 0.1346 0.039 1.150 5.6 63.1 14.6 892 n/a 10_regHadp: 0.1196 0.1346 0.039 1.150 5.6 63.1 14.6 892 n/a 10_occ: 0.1195 0.1344 0.039 1.150 5.6 63.1 14.6 892 n/a end: 0.1194 0.1344 0.039 1.150 5.5 63.0 14.5 892 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5942275_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5942275_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.4100 Refinement macro-cycles (run) : 11758.8700 Write final files (write_after_run_outputs) : 165.9900 Total : 11932.2700 Total CPU time: 3.33 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:36:10 PST -0800 (1736735770.03 s) Start R-work = 0.1796, R-free = 0.1962 Final R-work = 0.1194, R-free = 0.1344 =============================================================================== Job complete usr+sys time: 12264.76 seconds wall clock time: 205 minutes 28.19 seconds (12328.19 seconds total)