Starting phenix.refine on Sun Jan 12 15:15:38 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5016558.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5016558.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5016558.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 2.20, per 1000 atoms: 0.33 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: 2.759 distance_ideal: 2.720 ideal - model: -0.039 slack: 0.000 delta_slack: -0.039 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: 2.751 distance_ideal: 2.710 ideal - model: -0.041 slack: 0.000 delta_slack: -0.041 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: 0.83 Conformation dependent library (CDL) restraints added in 141.5 milliseconds Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.02: 710 1.02 - 1.24: 2516 1.24 - 1.46: 1350 1.46 - 1.68: 1310 1.68 - 1.90: 48 Bond restraints: 5934 Sorted by residual: bond pdb=" C ARG B 149 " pdb=" O ARG B 149 " ideal model delta sigma weight residual 1.237 1.469 -0.232 1.17e-02 7.31e+03 3.93e+02 bond pdb=" CA SER B 13 " pdb=" C SER B 13 " ideal model delta sigma weight residual 1.525 1.780 -0.255 1.32e-02 5.74e+03 3.74e+02 bond pdb=" CA PRO B 158 " pdb=" HA PRO B 158 " ideal model delta sigma weight residual 0.970 1.348 -0.378 2.00e-02 2.50e+03 3.58e+02 bond pdb=" N THR A 46 " pdb=" H THR A 46 " ideal model delta sigma weight residual 0.860 1.231 -0.371 2.00e-02 2.50e+03 3.43e+02 bond pdb=" CE1 HIS B 96 " pdb=" NE2 HIS B 96 " ideal model delta sigma weight residual 1.321 1.136 0.185 1.00e-02 1.00e+04 3.41e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 5824 4.33 - 8.65: 3474 8.65 - 12.98: 1262 12.98 - 17.30: 236 17.30 - 21.63: 14 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O VAL B 112 " pdb=" C VAL B 112 " pdb=" N LEU B 113 " ideal model delta sigma weight residual 121.98 136.26 -14.28 8.90e-01 1.26e+00 2.58e+02 angle pdb=" O ILE A 45 " pdb=" C ILE A 45 " pdb=" N THR A 46 " ideal model delta sigma weight residual 123.20 106.28 16.92 1.06e+00 8.90e-01 2.55e+02 angle pdb=" O LEU B 88 " pdb=" C LEU B 88 " pdb=" N VAL B 89 " ideal model delta sigma weight residual 122.09 137.02 -14.93 1.04e+00 9.25e-01 2.06e+02 angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" O ILE A 134 " ideal model delta sigma weight residual 119.19 109.99 9.20 6.50e-01 2.37e+00 2.00e+02 angle pdb=" CD2 HIS B 96 " pdb=" NE2 HIS B 96 " pdb=" CE1 HIS B 96 " ideal model delta sigma weight residual 109.00 122.18 -13.18 1.00e+00 1.00e+00 1.74e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.12: 1825 16.12 - 32.24: 150 32.24 - 48.35: 41 48.35 - 64.47: 29 64.47 - 80.58: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -153.90 -26.10 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL B 32 " pdb=" C VAL B 32 " pdb=" N THR B 33 " pdb=" CA THR B 33 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.221: 206 0.221 - 0.442: 148 0.442 - 0.663: 98 0.663 - 0.884: 33 0.884 - 1.104: 7 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB VAL A 145 " pdb=" CA VAL A 145 " pdb=" CG1 VAL A 145 " pdb=" CG2 VAL A 145 " both_signs ideal model delta sigma weight residual False -2.63 -3.73 1.10 2.00e-01 2.50e+01 3.05e+01 chirality pdb=" CA SER A 85 " pdb=" N SER A 85 " pdb=" C SER A 85 " pdb=" CB SER A 85 " both_signs ideal model delta sigma weight residual False 2.51 3.57 -1.06 2.00e-01 2.50e+01 2.78e+01 chirality pdb=" CA VAL B 89 " pdb=" N VAL B 89 " pdb=" C VAL B 89 " pdb=" CB VAL B 89 " both_signs ideal model delta sigma weight residual False 2.44 3.45 -1.00 2.00e-01 2.50e+01 2.52e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.086 2.00e-02 2.50e+03 6.45e-02 1.67e+02 pdb=" CG TRP B 139 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.081 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.062 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.113 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.126 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " 0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " 0.069 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.016 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.019 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " 0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.055 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.127 2.00e-02 2.50e+03 7.38e-02 1.63e+02 pdb=" CG PHE B 164 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.052 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.079 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.104 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.072 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.111 2.00e-02 2.50e+03 5.98e-02 1.43e+02 pdb=" CG TRP A 146 " 0.088 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.102 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.053 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.012 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.068 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.026 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.034 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.102 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 30 1.64 - 2.38: 2646 2.38 - 3.12: 22457 3.12 - 3.86: 32873 3.86 - 4.60: 52168 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110174 Sorted by model distance: nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.897 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.902 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.939 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.062 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.135 2.620 ... (remaining 110169 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_5016558_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= 0.1991 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303312 | | target function (ml) not normalized (work): 806066.206029 | | target function (ml) not normalized (free): 16599.583190 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2130 0.1885 6.692 6.2882| | 2: 2.94 - 2.33 1.00 7339 128 0.1620 0.1674 5.5313 5.6109| | 3: 2.33 - 2.04 0.96 6939 150 0.1623 0.1547 5.1379 5.1226| | 4: 2.04 - 1.85 1.00 7170 155 0.1745 0.1717 4.9682 5.0708| | 5: 1.85 - 1.72 0.99 7113 159 0.1934 0.1624 4.7953 4.7244| | 6: 1.72 - 1.62 0.99 7102 142 0.1992 0.1977 4.6649 4.736| | 7: 1.62 - 1.54 0.99 7104 148 0.2024 0.1765 4.5655 4.5758| | 8: 1.54 - 1.47 0.96 6798 152 0.2047 0.2270 4.479 4.5675| | 9: 1.47 - 1.41 0.98 6938 155 0.2067 0.2142 4.3968 4.4415| | 10: 1.41 - 1.36 0.99 7022 150 0.2086 0.2155 4.3017 4.3053| | 11: 1.36 - 1.32 0.99 6997 151 0.2099 0.2105 4.2317 4.2582| | 12: 1.32 - 1.28 0.98 6976 149 0.2092 0.1895 4.1758 4.1166| | 13: 1.28 - 1.25 0.98 6907 166 0.2051 0.2175 4.13 4.2482| | 14: 1.25 - 1.22 0.98 7015 113 0.2087 0.2672 4.103 4.3892| | 15: 1.22 - 1.19 0.98 6957 137 0.2115 0.2021 4.0545 4.0469| | 16: 1.19 - 1.17 0.93 6604 132 0.2117 0.2283 4.0186 4.1022| | 17: 1.17 - 1.14 0.98 6941 135 0.2188 0.1978 3.966 4.049| | 18: 1.14 - 1.12 0.98 6875 142 0.2254 0.2505 3.9357 3.9955| | 19: 1.12 - 1.10 0.97 6949 106 0.2279 0.2596 3.8808 4.0055| | 20: 1.10 - 1.08 0.97 6884 147 0.2340 0.2560 3.8375 3.9504| | 21: 1.08 - 1.07 0.97 6852 152 0.2405 0.2557 3.7824 3.8062| | 22: 1.07 - 1.05 0.97 6838 135 0.2553 0.2748 3.7529 3.827| | 23: 1.05 - 1.03 0.97 6829 159 0.2721 0.2588 3.7316 3.796| | 24: 1.03 - 1.02 0.96 6785 133 0.2886 0.2660 3.7064 3.7464| | 25: 1.02 - 1.01 0.93 6552 130 0.3085 0.2814 3.6809 3.7115| | 26: 1.01 - 0.99 0.96 6767 158 0.3196 0.3107 3.6258 3.5894| | 27: 0.99 - 0.98 0.94 6648 131 0.3393 0.3418 3.6307 3.6615| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.11 0.91 0.96 33945.50| | 2: 2.94 - 2.33 7339 128 0.86 20.96 1.08 1.02 14625.16| | 3: 2.33 - 2.04 6939 150 0.93 12.37 1.11 1.05 4084.12| | 4: 2.04 - 1.85 7170 155 0.93 13.01 1.11 1.06 2649.30| | 5: 1.85 - 1.72 7113 159 0.91 14.90 1.12 1.07 1926.83| | 6: 1.72 - 1.62 7102 142 0.90 16.73 1.11 1.08 1619.87| | 7: 1.62 - 1.54 7104 148 0.89 17.61 1.11 1.08 1357.06| | 8: 1.54 - 1.47 6798 152 0.89 18.31 1.10 1.07 1161.40| | 9: 1.47 - 1.41 6938 155 0.88 18.64 1.10 1.07 974.49| | 10: 1.41 - 1.36 7022 150 0.88 19.32 1.09 1.05 798.27| | 11: 1.36 - 1.32 6997 151 0.88 19.20 1.08 1.06 694.31| | 12: 1.32 - 1.28 6976 149 0.88 19.11 1.08 1.05 611.50| | 13: 1.28 - 1.25 6907 166 0.87 19.85 1.07 1.05 613.17| | 14: 1.25 - 1.22 7015 113 0.86 21.49 1.07 1.04 623.41| | 15: 1.22 - 1.19 6957 137 0.85 22.42 1.08 1.02 605.63| | 16: 1.19 - 1.17 6604 132 0.86 22.06 1.07 1.02 558.60| | 17: 1.17 - 1.14 6941 135 0.85 22.64 1.08 1.01 498.50| | 18: 1.14 - 1.12 6875 142 0.84 23.11 1.08 1.00 463.46| | 19: 1.12 - 1.10 6949 106 0.83 24.10 1.07 0.99 437.40| | 20: 1.10 - 1.08 6884 147 0.83 24.72 1.07 0.97 402.71| | 21: 1.08 - 1.07 6852 152 0.82 25.34 1.06 0.98 372.50| | 22: 1.07 - 1.05 6838 135 0.81 26.26 1.05 0.99 349.19| | 23: 1.05 - 1.03 6829 159 0.80 27.31 1.05 0.99 328.17| | 24: 1.03 - 1.02 6785 133 0.79 28.41 1.05 1.00 315.66| | 25: 1.02 - 1.01 6552 130 0.78 29.54 1.03 0.95 294.67| | 26: 1.01 - 0.99 6767 158 0.75 32.59 1.03 0.92 298.77| | 27: 0.99 - 0.98 6648 131 0.71 35.32 1.03 0.87 314.59| |alpha: min = 0.87 max = 1.08 mean = 1.02| |beta: min = 294.67 max = 33945.50 mean = 2748.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.96| |phase err.(test): min = 0.00 max = 89.93 mean = 21.95| |-----------------------------------------------------------------------------| ----------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 0.255 2950 Z= 5.472 Angle : 5.230 16.966 4018 Z= 3.714 Chirality : 0.387 1.104 492 Planarity : 0.033 0.206 512 Dihedral : 12.685 80.581 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % 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: -2.45 (0.37), residues: 386 helix: -2.55 (0.30), residues: 148 sheet: -1.38 (0.48), residues: 86 loop : -0.40 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.021 ARG A 175 TYR 0.100 0.037 TYR A 67 PHE 0.111 0.038 PHE B 164 TRP 0.124 0.045 TRP B 139 HIS 0.101 0.032 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2033 r_free= 0.1991 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303312 | | target function (ml) not normalized (work): 806066.206029 | | target function (ml) not normalized (free): 16599.583190 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2032 0.2033 0.1991 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2032 0.2033 0.1991 n_refl.: 191155 remove outliers: r(all,work,free)=0.2032 0.2033 0.1991 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2032 0.2033 0.1990 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1804 0.1801 0.1929 n_refl.: 191145 remove outliers: r(all,work,free)=0.1802 0.1800 0.1927 n_refl.: 191140 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4198 400.535 295.137 0.434 0.914 0.299 13.296-10.522 100.00 100 1 0.2546 534.497 520.892 0.784 0.915 0.248 10.503-8.327 99.45 178 3 0.2511 565.118 556.221 0.971 0.915 0.223 8.318-6.595 100.00 360 8 0.2507 414.736 402.883 0.969 0.915 0.165 6.588-5.215 100.00 711 7 0.2238 381.101 366.917 0.958 0.915 0.160 5.214-4.128 98.38 1367 28 0.1485 557.435 550.179 1.074 0.915 0.090 4.126-3.266 94.74 2603 46 0.1340 508.132 499.285 1.143 0.915 0.009 3.266-2.585 99.86 5447 97 0.1425 342.774 337.617 1.118 0.915 0.000 2.585-2.046 97.45 10613 204 0.1408 258.603 254.176 1.122 0.914 0.000 2.046-1.619 99.39 21536 464 0.1622 153.054 149.884 1.143 0.913 0.000 1.619-1.281 98.00 42464 925 0.1918 82.395 80.253 1.127 0.911 0.000 1.281-0.980 96.53 101826 2055 0.2323 44.202 41.657 1.112 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0039 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1927 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1800 r_free=0.1927 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.243803 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.850900 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 0.1272 0.1502 0.0230 0.039 1.2 10.7 0.0 0.3 0 11.122 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.02 2.30 1.117 13.109 577.851 0.019 12.96 15.67 2.71 1.252 13.364 577.851 0.017 Individual atomic B min max mean iso aniso Overall: 5.19 73.04 15.06 1.41 435 3274 Protein: 5.19 40.78 11.02 1.41 0 2902 Water: 6.30 73.04 29.61 N/A 435 370 Other: 16.04 29.53 22.78 N/A 0 2 Chain A: 5.29 59.59 13.08 N/A 0 1626 Chain B: 5.19 73.04 12.80 N/A 0 1648 Chain S: 11.48 65.13 31.04 N/A 435 0 Histogram: Values Number of atoms 5.19 - 11.97 2168 11.97 - 18.76 632 18.76 - 25.54 327 25.54 - 32.33 250 32.33 - 39.11 163 39.11 - 45.90 98 45.90 - 52.69 47 52.69 - 59.47 17 59.47 - 66.26 6 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1567 r_work=0.1295 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1295 r_free = 0.1563 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1280 r_free = 0.1554 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1280 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015644 | | target function (ls_wunit_k1) not normalized (work): 2930.142355 | | target function (ls_wunit_k1) not normalized (free): 117.749390 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1285 0.1280 0.1554 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1470 0.1468 0.1630 n_refl.: 191140 remove outliers: r(all,work,free)=0.1470 0.1468 0.1630 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1494 0.1492 0.1640 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1277 0.1272 0.1544 n_refl.: 191140 remove outliers: r(all,work,free)=0.1277 0.1272 0.1544 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3581 402.814 377.775 0.462 1.001 0.269 13.296-10.522 100.00 100 1 0.2139 534.497 526.009 0.713 1.002 0.240 10.503-8.327 99.45 178 3 0.1757 565.118 561.787 0.854 1.002 0.198 8.318-6.595 100.00 360 8 0.1718 414.736 411.656 0.875 1.002 0.160 6.588-5.215 100.00 711 7 0.1531 381.101 373.559 0.855 1.002 0.160 5.214-4.128 98.38 1367 28 0.0905 557.435 555.266 0.940 1.003 0.054 4.126-3.266 94.74 2603 46 0.0833 508.132 504.200 1.004 1.003 0.014 3.266-2.585 99.86 5447 97 0.0924 342.774 340.270 0.987 1.003 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.298 0.997 1.003 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.378 1.015 1.003 0.000 1.619-1.281 98.00 42464 925 0.1272 82.395 81.418 1.007 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1868 44.202 42.185 0.985 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0373 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1272 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1544 | n_water=805 | time (s): 2.750 (total time: 2.750) Filter (dist) r_work=0.1275 r_free=0.1543 | n_water=795 | time (s): 107.080 (total time: 109.830) Filter (q & B) r_work=0.1276 r_free=0.1543 | n_water=791 | time (s): 5.100 (total time: 114.930) Compute maps r_work=0.1276 r_free=0.1543 | n_water=791 | time (s): 2.010 (total time: 116.940) Filter (map) r_work=0.1303 r_free=0.1532 | n_water=649 | time (s): 4.930 (total time: 121.870) Find peaks r_work=0.1303 r_free=0.1532 | n_water=649 | time (s): 0.730 (total time: 122.600) Add new water r_work=0.1324 r_free=0.1556 | n_water=950 | time (s): 3.940 (total time: 126.540) Refine new water occ: r_work=0.1282 r_free=0.1508 adp: r_work=0.1270 r_free=0.1504 occ: r_work=0.1272 r_free=0.1502 adp: r_work=0.1266 r_free=0.1501 occ: r_work=0.1267 r_free=0.1500 adp: r_work=0.1264 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1264 r_free=0.1501 r_work=0.1264 r_free=0.1501 | n_water=950 | time (s): 84.380 (total time: 210.920) Filter (q & B) r_work=0.1268 r_free=0.1508 | n_water=875 | time (s): 5.530 (total time: 216.450) Filter (dist only) r_work=0.1268 r_free=0.1508 | n_water=873 | time (s): 113.170 (total time: 329.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.812917 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 596.467565 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 0.1525 0.0272 0.042 1.1 18.4 0.0 0.0 0 11.406 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.25 2.72 2.052 15.193 596.468 0.015 12.34 15.17 2.83 2.394 15.209 596.468 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 68.98 16.27 1.21 505 3272 Protein: 5.39 40.09 11.01 1.21 0 2902 Water: 6.61 68.98 33.70 N/A 505 368 Other: 16.41 32.49 24.45 N/A 0 2 Chain A: 5.54 56.03 13.02 N/A 0 1624 Chain B: 5.39 68.98 12.85 N/A 0 1648 Chain S: 12.53 65.55 37.84 N/A 505 0 Histogram: Values Number of atoms 5.39 - 11.75 2072 11.75 - 18.11 699 18.11 - 24.47 272 24.47 - 30.83 215 30.83 - 37.18 168 37.18 - 43.54 159 43.54 - 49.90 91 49.90 - 56.26 51 56.26 - 62.62 47 62.62 - 68.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1517 r_work=0.1235 r_free=0.1518 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1518 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 = 0.1230 r_free = 0.1510 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013590 | | target function (ls_wunit_k1) not normalized (work): 2545.401466 | | target function (ls_wunit_k1) not normalized (free): 100.826290 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1230 0.1510 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1440 0.1437 0.1601 n_refl.: 191139 remove outliers: r(all,work,free)=0.1440 0.1437 0.1601 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1437 0.1435 0.1599 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1237 0.1519 n_refl.: 191139 remove outliers: r(all,work,free)=0.1242 0.1237 0.1519 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3273 402.814 377.326 0.492 0.963 0.271 13.296-10.522 100.00 100 1 0.1958 534.497 529.647 0.774 0.964 0.250 10.503-8.327 99.45 178 3 0.1445 565.118 567.784 0.917 0.963 0.180 8.318-6.595 100.00 360 8 0.1586 414.736 413.880 0.938 0.963 0.170 6.588-5.215 100.00 711 7 0.1354 381.101 376.338 0.912 0.963 0.160 5.214-4.128 98.38 1367 28 0.0832 557.435 555.955 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0764 508.132 505.583 1.060 0.963 0.009 3.266-2.585 99.86 5447 97 0.0859 342.774 341.268 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.766 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1049 153.054 151.613 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1259 82.395 81.353 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.216 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=-0.0499 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1237 r_free=0.1519 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1237 r_free=0.1519 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1237 r_free=0.1519 | n_water=873 | time (s): 3.440 (total time: 3.440) Filter (dist) r_work=0.1239 r_free=0.1521 | n_water=868 | time (s): 115.980 (total time: 119.420) Filter (q & B) r_work=0.1239 r_free=0.1521 | n_water=867 | time (s): 4.780 (total time: 124.200) Compute maps r_work=0.1239 r_free=0.1521 | n_water=867 | time (s): 1.720 (total time: 125.920) Filter (map) r_work=0.1276 r_free=0.1527 | n_water=687 | time (s): 4.680 (total time: 130.600) Find peaks r_work=0.1276 r_free=0.1527 | n_water=687 | time (s): 0.710 (total time: 131.310) Add new water r_work=0.1299 r_free=0.1558 | n_water=1007 | time (s): 4.420 (total time: 135.730) Refine new water occ: r_work=0.1255 r_free=0.1524 adp: r_work=0.1255 r_free=0.1524 occ: r_work=0.1251 r_free=0.1522 adp: r_work=0.1251 r_free=0.1522 occ: r_work=0.1248 r_free=0.1521 adp: r_work=0.1248 r_free=0.1521 ADP+occupancy (water only), MIN, final r_work=0.1248 r_free=0.1521 r_work=0.1248 r_free=0.1521 | n_water=1007 | time (s): 255.680 (total time: 391.410) Filter (q & B) r_work=0.1251 r_free=0.1530 | n_water=863 | time (s): 5.760 (total time: 397.170) Filter (dist only) r_work=0.1252 r_free=0.1530 | n_water=862 | time (s): 124.730 (total time: 521.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.763631 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.074038 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1243 0.1443 0.0201 0.035 1.1 7.8 0.0 0.0 0 0.882 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.43 14.43 2.01 1.943 14.566 16.074 3.941 12.36 14.03 1.68 2.260 14.464 16.074 3.898 Individual atomic B min max mean iso aniso Overall: 5.56 68.58 15.18 1.06 496 3270 Protein: 5.56 36.59 10.76 1.06 0 2902 Water: 6.68 68.58 30.06 N/A 496 366 Other: 14.17 28.22 21.19 N/A 0 2 Chain A: 5.56 55.12 12.77 N/A 0 1624 Chain B: 5.57 68.58 12.53 N/A 0 1646 Chain S: 14.39 62.46 31.87 N/A 496 0 Histogram: Values Number of atoms 5.56 - 11.86 2154 11.86 - 18.16 670 18.16 - 24.47 300 24.47 - 30.77 241 30.77 - 37.07 169 37.07 - 43.37 131 43.37 - 49.68 67 49.68 - 55.98 25 55.98 - 62.28 7 62.28 - 68.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1404 r_work=0.1236 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1404 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1395 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.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892508 | | target function (ml) not normalized (work): 729058.877224 | | target function (ml) not normalized (free): 15231.324000 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1395 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1448 0.1448 0.1490 n_refl.: 191139 remove outliers: r(all,work,free)=0.1448 0.1448 0.1490 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1442 0.1442 0.1487 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1387 n_refl.: 191139 remove outliers: r(all,work,free)=0.1230 0.1227 0.1387 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3876 398.008 361.079 0.422 0.946 0.241 13.296-10.522 99.01 99 1 0.2436 528.187 511.234 0.715 0.947 0.215 10.503-8.327 98.90 177 3 0.2008 557.261 556.967 0.885 0.947 0.184 8.318-6.595 100.00 360 8 0.2094 414.736 409.872 0.899 0.947 0.139 6.588-5.215 100.00 711 7 0.1834 381.101 370.854 0.884 0.947 0.120 5.214-4.128 98.38 1367 28 0.1178 557.435 551.752 0.973 0.947 0.090 4.126-3.266 94.74 2603 46 0.1106 508.132 501.399 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1091 342.774 338.979 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0967 258.603 255.691 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0974 153.054 151.384 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.480 1.054 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.316 1.040 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0997 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1387 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1387 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1387 | n_water=862 | time (s): 3.170 (total time: 3.170) Filter (dist) r_work=0.1229 r_free=0.1390 | n_water=860 | time (s): 106.550 (total time: 109.720) Filter (q & B) r_work=0.1229 r_free=0.1387 | n_water=850 | time (s): 5.180 (total time: 114.900) Compute maps r_work=0.1229 r_free=0.1387 | n_water=850 | time (s): 1.960 (total time: 116.860) Filter (map) r_work=0.1250 r_free=0.1392 | n_water=711 | time (s): 4.920 (total time: 121.780) Find peaks r_work=0.1250 r_free=0.1392 | n_water=711 | time (s): 0.690 (total time: 122.470) Add new water r_work=0.1266 r_free=0.1402 | n_water=954 | time (s): 4.810 (total time: 127.280) Refine new water occ: r_work=0.1218 r_free=0.1358 adp: r_work=0.1211 r_free=0.1354 occ: r_work=0.1208 r_free=0.1355 adp: r_work=0.1208 r_free=0.1355 occ: r_work=0.1208 r_free=0.1355 adp: r_work=0.1208 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1355 r_work=0.1208 r_free=0.1355 | n_water=954 | time (s): 214.870 (total time: 342.150) Filter (q & B) r_work=0.1212 r_free=0.1368 | n_water=855 | time (s): 4.560 (total time: 346.710) Filter (dist only) r_work=0.1213 r_free=0.1367 | n_water=852 | time (s): 109.390 (total time: 456.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.611091 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.276698 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 0.1211 0.1370 0.0159 0.033 1.1 6.1 0.0 0.0 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 13.70 1.59 1.838 14.086 16.277 3.876 12.02 13.66 1.64 1.994 14.041 16.277 3.865 Individual atomic B min max mean iso aniso Overall: 5.49 67.96 14.73 1.00 486 3270 Protein: 5.49 33.11 10.66 1.00 0 2902 Water: 5.81 67.96 28.61 N/A 486 366 Other: 13.87 26.75 20.31 N/A 0 2 Chain A: 5.58 53.54 12.61 N/A 0 1624 Chain B: 5.49 67.96 12.41 N/A 0 1646 Chain S: 5.81 62.53 29.71 N/A 486 0 Histogram: Values Number of atoms 5.49 - 11.73 2119 11.73 - 17.98 733 17.98 - 24.23 343 24.23 - 30.47 220 30.47 - 36.72 136 36.72 - 42.97 120 42.97 - 49.21 56 49.21 - 55.46 21 55.46 - 61.71 6 61.71 - 67.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1366 r_work=0.1202 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1366 target_work(ml) = 3.865 | | 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) = 3.863 | | 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.=191136 (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): 3.862733 | | target function (ml) not normalized (work): 723470.649720 | | target function (ml) not normalized (free): 15131.978873 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1364 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1433 0.1432 0.1481 n_refl.: 191136 remove outliers: r(all,work,free)=0.1433 0.1432 0.1481 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1425 0.1424 0.1476 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1361 n_refl.: 191136 remove outliers: r(all,work,free)=0.1201 0.1198 0.1361 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3786 357.205 316.307 0.404 0.945 0.237 13.296-10.522 99.01 99 1 0.2574 478.406 456.011 0.691 0.947 0.188 10.503-8.327 98.35 176 3 0.2224 502.932 494.989 0.865 0.947 0.167 8.318-6.595 100.00 360 8 0.2265 375.648 370.408 0.890 0.946 0.120 6.588-5.215 100.00 711 7 0.1928 345.183 335.243 0.880 0.947 0.100 5.214-4.128 98.38 1367 28 0.1221 504.897 498.995 0.975 0.947 0.090 4.126-3.266 94.74 2603 46 0.1132 460.241 453.713 1.035 0.947 0.000 3.266-2.585 99.86 5447 97 0.1084 310.468 307.265 1.023 0.947 0.000 2.585-2.046 97.45 10613 204 0.0938 234.230 231.769 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0908 138.629 137.332 1.058 0.945 0.000 1.619-1.281 98.00 42464 925 0.0984 74.630 73.913 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1660 40.036 38.371 1.040 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1198 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1361 | n_water=852 | time (s): 2.290 (total time: 2.290) Filter (dist) r_work=0.1198 r_free=0.1361 | n_water=852 | time (s): 100.190 (total time: 102.480) Filter (q & B) r_work=0.1199 r_free=0.1360 | n_water=842 | time (s): 4.610 (total time: 107.090) Compute maps r_work=0.1199 r_free=0.1360 | n_water=842 | time (s): 1.770 (total time: 108.860) Filter (map) r_work=0.1219 r_free=0.1359 | n_water=722 | time (s): 4.580 (total time: 113.440) Find peaks r_work=0.1219 r_free=0.1359 | n_water=722 | time (s): 0.870 (total time: 114.310) Add new water r_work=0.1231 r_free=0.1376 | n_water=943 | time (s): 4.910 (total time: 119.220) Refine new water occ: r_work=0.1196 r_free=0.1345 adp: r_work=0.1196 r_free=0.1345 occ: r_work=0.1194 r_free=0.1345 adp: r_work=0.1194 r_free=0.1345 occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1191 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1345 r_work=0.1191 r_free=0.1345 | n_water=943 | time (s): 247.440 (total time: 366.660) Filter (q & B) r_work=0.1195 r_free=0.1352 | n_water=872 | time (s): 4.360 (total time: 371.020) Filter (dist only) r_work=0.1196 r_free=0.1352 | n_water=871 | time (s): 111.820 (total time: 482.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.526254 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.906777 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1360 0.0161 0.036 1.1 6.1 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.60 1.61 1.791 14.037 14.907 3.764 12.04 13.65 1.61 1.835 14.017 14.907 3.763 Individual atomic B min max mean iso aniso Overall: 5.58 67.70 14.80 0.96 505 3270 Protein: 5.58 31.98 10.60 0.96 0 2902 Water: 5.88 67.70 28.80 N/A 505 366 Other: 13.77 25.98 19.88 N/A 0 2 Chain A: 5.60 52.97 12.53 N/A 0 1624 Chain B: 5.58 67.70 12.34 N/A 0 1646 Chain S: 5.88 62.53 30.14 N/A 505 0 Histogram: Values Number of atoms 5.58 - 11.79 2158 11.79 - 18.00 711 18.00 - 24.21 307 24.21 - 30.43 230 30.43 - 36.64 164 36.64 - 42.85 126 42.85 - 49.06 56 49.06 - 55.28 17 55.28 - 61.49 4 61.49 - 67.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1365 r_work=0.1205 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1366 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1370 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762123 | | target function (ml) not normalized (work): 704615.626753 | | target function (ml) not normalized (free): 14754.717673 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1370 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1502 n_refl.: 191133 remove outliers: r(all,work,free)=0.1415 0.1414 0.1502 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1408 0.1406 0.1496 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1201 0.1367 n_refl.: 191133 remove outliers: r(all,work,free)=0.1205 0.1201 0.1367 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3859 357.205 316.891 0.388 0.951 0.217 13.296-10.522 98.02 98 1 0.2479 479.052 453.241 0.680 0.952 0.171 10.503-8.327 98.35 176 3 0.2238 502.932 494.097 0.857 0.952 0.147 8.318-6.595 100.00 360 8 0.2239 375.648 370.318 0.883 0.952 0.108 6.588-5.215 100.00 711 7 0.1910 345.183 335.460 0.877 0.952 0.090 5.214-4.128 98.38 1367 28 0.1223 504.897 499.349 0.971 0.952 0.080 4.126-3.266 94.74 2603 46 0.1140 460.241 453.622 1.031 0.953 0.000 3.266-2.585 99.86 5447 97 0.1116 310.468 307.119 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0950 234.230 231.740 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0915 138.629 137.329 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0975 74.630 73.923 1.052 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.036 38.367 1.041 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1303 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1367 | n_water=871 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1202 r_free=0.1365 | n_water=869 | time (s): 103.870 (total time: 106.560) Filter (q & B) r_work=0.1202 r_free=0.1365 | n_water=859 | time (s): 4.360 (total time: 110.920) Compute maps r_work=0.1202 r_free=0.1365 | n_water=859 | time (s): 1.930 (total time: 112.850) Filter (map) r_work=0.1222 r_free=0.1367 | n_water=746 | time (s): 4.950 (total time: 117.800) Find peaks r_work=0.1222 r_free=0.1367 | n_water=746 | time (s): 0.700 (total time: 118.500) Add new water r_work=0.1233 r_free=0.1381 | n_water=957 | time (s): 4.250 (total time: 122.750) Refine new water occ: r_work=0.1199 r_free=0.1360 adp: r_work=0.1199 r_free=0.1361 occ: r_work=0.1197 r_free=0.1358 adp: r_work=0.1197 r_free=0.1359 occ: r_work=0.1195 r_free=0.1357 adp: r_work=0.1194 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1358 r_work=0.1194 r_free=0.1358 | n_water=957 | time (s): 208.740 (total time: 331.490) Filter (q & B) r_work=0.1198 r_free=0.1365 | n_water=883 | time (s): 5.030 (total time: 336.520) Filter (dist only) r_work=0.1199 r_free=0.1366 | n_water=880 | time (s): 114.280 (total time: 450.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.583507 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.254693 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 0.1202 0.1375 0.0173 0.037 1.1 5.1 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.75 1.73 1.764 13.970 14.255 3.762 12.08 13.79 1.71 1.932 13.911 14.255 3.762 Individual atomic B min max mean iso aniso Overall: 5.59 66.42 14.69 0.89 514 3270 Protein: 5.59 28.97 10.47 0.89 0 2902 Water: 5.96 66.42 28.58 N/A 514 366 Other: 13.80 22.83 18.32 N/A 0 2 Chain A: 5.63 51.65 12.36 N/A 0 1624 Chain B: 5.59 66.42 12.19 N/A 0 1646 Chain S: 5.96 62.70 30.03 N/A 514 0 Histogram: Values Number of atoms 5.59 - 11.67 2137 11.67 - 17.75 758 17.75 - 23.84 291 23.84 - 29.92 222 29.92 - 36.00 157 36.00 - 42.08 130 42.08 - 48.17 60 48.17 - 54.25 23 54.25 - 60.33 4 60.33 - 66.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1379 r_work=0.1208 r_free=0.1380 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1208 r_free = 0.1380 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1380 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1380 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761033 | | target function (ml) not normalized (work): 704407.697746 | | target function (ml) not normalized (free): 14757.614597 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1206 0.1380 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1413 0.1411 0.1505 n_refl.: 191132 remove outliers: r(all,work,free)=0.1413 0.1411 0.1505 n_refl.: 191132 overall B=-0.23 to atoms: r(all,work,free)=0.1375 0.1373 0.1480 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1205 0.1378 n_refl.: 191132 remove outliers: r(all,work,free)=0.1208 0.1205 0.1378 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 92.08 90 3 0.3855 357.205 317.442 0.387 0.950 0.201 13.296-10.522 97.03 97 1 0.2508 481.326 455.835 0.699 0.952 0.153 10.503-8.327 98.35 176 3 0.2250 502.932 493.443 0.882 0.952 0.130 8.318-6.595 100.00 360 8 0.2223 375.648 370.305 0.906 0.952 0.105 6.588-5.215 100.00 711 7 0.1925 345.183 335.447 0.902 0.952 0.090 5.214-4.128 98.38 1367 28 0.1237 504.897 499.386 0.994 0.952 0.044 4.126-3.266 94.74 2603 46 0.1160 460.241 453.428 1.057 0.953 0.000 3.266-2.585 99.86 5447 97 0.1133 310.468 306.995 1.041 0.952 0.000 2.585-2.046 97.45 10613 204 0.0960 234.230 231.687 1.048 0.951 0.000 2.046-1.619 99.39 21536 464 0.0915 138.629 137.323 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0970 74.630 73.923 1.055 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.036 38.366 1.027 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0504 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1205 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1378 | n_water=880 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1206 r_free=0.1379 | n_water=879 | time (s): 110.510 (total time: 113.660) Filter (q & B) r_work=0.1206 r_free=0.1380 | n_water=870 | time (s): 4.350 (total time: 118.010) Compute maps r_work=0.1206 r_free=0.1380 | n_water=870 | time (s): 1.570 (total time: 119.580) Filter (map) r_work=0.1227 r_free=0.1371 | n_water=751 | time (s): 4.360 (total time: 123.940) Find peaks r_work=0.1227 r_free=0.1371 | n_water=751 | time (s): 0.680 (total time: 124.620) Add new water r_work=0.1236 r_free=0.1382 | n_water=968 | time (s): 3.960 (total time: 128.580) Refine new water occ: r_work=0.1203 r_free=0.1358 adp: r_work=0.1203 r_free=0.1357 occ: r_work=0.1200 r_free=0.1357 adp: r_work=0.1200 r_free=0.1358 occ: r_work=0.1199 r_free=0.1357 adp: r_work=0.1198 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1357 r_work=0.1198 r_free=0.1357 | n_water=968 | time (s): 309.310 (total time: 437.890) Filter (q & B) r_work=0.1203 r_free=0.1369 | n_water=891 | time (s): 4.100 (total time: 441.990) Filter (dist only) r_work=0.1203 r_free=0.1370 | n_water=889 | time (s): 115.850 (total time: 557.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.522043 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.678807 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1377 0.0170 0.038 1.1 4.3 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.77 1.70 1.712 13.651 14.679 3.762 12.06 13.77 1.72 1.751 13.631 14.679 3.759 Individual atomic B min max mean iso aniso Overall: 5.38 65.00 14.48 0.88 523 3270 Protein: 5.38 28.30 10.24 0.88 0 2902 Water: 5.83 65.00 28.34 N/A 523 366 Other: 13.67 21.80 17.74 N/A 0 2 Chain A: 5.45 51.10 12.08 N/A 0 1624 Chain B: 5.38 65.00 11.92 N/A 0 1646 Chain S: 5.83 62.74 29.99 N/A 523 0 Histogram: Values Number of atoms 5.38 - 11.34 2101 11.34 - 17.30 791 17.30 - 23.27 276 23.27 - 29.23 229 29.23 - 35.19 161 35.19 - 41.15 132 41.15 - 47.11 70 47.11 - 53.07 26 53.07 - 59.03 5 59.03 - 65.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1378 r_work=0.1206 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1378 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1378 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758173 | | target function (ml) not normalized (work): 703868.175444 | | target function (ml) not normalized (free): 14753.288686 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1203 0.1378 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1379 0.1378 0.1483 n_refl.: 191131 remove outliers: r(all,work,free)=0.1379 0.1378 0.1483 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1388 0.1386 0.1488 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1368 n_refl.: 191131 remove outliers: r(all,work,free)=0.1198 0.1194 0.1368 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3818 357.205 318.462 0.379 0.975 0.197 13.296-10.522 96.04 96 1 0.2382 480.445 454.693 0.686 0.977 0.135 10.503-8.327 98.35 176 3 0.2276 502.932 492.425 0.866 0.977 0.110 8.318-6.595 100.00 360 8 0.2214 375.648 370.111 0.888 0.977 0.096 6.588-5.215 100.00 711 7 0.1928 345.183 334.991 0.886 0.978 0.083 5.214-4.128 98.38 1367 28 0.1248 504.897 498.774 0.978 0.978 0.039 4.126-3.266 94.74 2603 46 0.1168 460.241 452.797 1.040 0.979 0.000 3.266-2.585 99.86 5447 97 0.1132 310.468 306.774 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0960 234.230 231.589 1.031 0.981 0.000 2.046-1.619 99.39 21536 464 0.0908 138.629 137.265 1.048 0.984 0.000 1.619-1.281 98.00 42464 925 0.0946 74.630 73.980 1.037 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.036 38.346 1.003 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0582 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1368 | n_water=889 | time (s): 2.930 (total time: 2.930) Filter (dist) r_work=0.1195 r_free=0.1369 | n_water=888 | time (s): 107.000 (total time: 109.930) Filter (q & B) r_work=0.1195 r_free=0.1369 | n_water=879 | time (s): 4.270 (total time: 114.200) Compute maps r_work=0.1195 r_free=0.1369 | n_water=879 | time (s): 2.180 (total time: 116.380) Filter (map) r_work=0.1217 r_free=0.1373 | n_water=764 | time (s): 5.560 (total time: 121.940) Find peaks r_work=0.1217 r_free=0.1373 | n_water=764 | time (s): 0.650 (total time: 122.590) Add new water r_work=0.1224 r_free=0.1381 | n_water=980 | time (s): 4.640 (total time: 127.230) Refine new water occ: r_work=0.1191 r_free=0.1354 adp: r_work=0.1192 r_free=0.1354 occ: r_work=0.1190 r_free=0.1354 adp: r_work=0.1190 r_free=0.1354 occ: r_work=0.1189 r_free=0.1355 adp: r_work=0.1188 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1355 r_work=0.1188 r_free=0.1355 | n_water=980 | time (s): 329.590 (total time: 456.820) Filter (q & B) r_work=0.1193 r_free=0.1360 | n_water=888 | time (s): 4.180 (total time: 461.000) Filter (dist only) r_work=0.1193 r_free=0.1360 | n_water=886 | time (s): 111.760 (total time: 572.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.504569 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.512337 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1365 0.0169 0.038 1.1 4.8 0.0 0.3 0 0.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.65 1.69 1.675 13.641 14.512 3.757 11.97 13.68 1.71 1.675 13.637 14.512 3.755 Individual atomic B min max mean iso aniso Overall: 5.46 64.76 14.49 0.87 520 3270 Protein: 5.46 28.16 10.31 0.87 0 2902 Water: 5.90 64.76 28.18 N/A 520 366 Other: 13.73 21.94 17.83 N/A 0 2 Chain A: 5.55 51.08 12.13 N/A 0 1624 Chain B: 5.46 64.76 11.98 N/A 0 1646 Chain S: 5.90 62.86 29.82 N/A 520 0 Histogram: Values Number of atoms 5.46 - 11.39 2094 11.39 - 17.32 802 17.32 - 23.25 275 23.25 - 29.18 229 29.18 - 35.11 165 35.11 - 41.04 121 41.04 - 46.97 71 46.97 - 52.90 26 52.90 - 58.83 5 58.83 - 64.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1368 r_work=0.1197 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1368 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1371 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754834 | | target function (ml) not normalized (work): 703239.047750 | | target function (ml) not normalized (free): 14741.262579 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1371 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1394 0.1392 0.1496 n_refl.: 191130 remove outliers: r(all,work,free)=0.1394 0.1392 0.1496 n_refl.: 191130 overall B=0.01 to atoms: r(all,work,free)=0.1396 0.1394 0.1498 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1370 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1194 0.1370 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 0.3815 357.205 316.993 0.375 0.975 0.194 13.296-10.522 95.05 95 1 0.2355 479.665 458.433 0.701 0.977 0.143 10.503-8.327 98.35 176 3 0.2252 502.932 493.114 0.863 0.977 0.128 8.318-6.595 100.00 360 8 0.2227 375.648 370.148 0.886 0.977 0.099 6.588-5.215 100.00 711 7 0.1944 345.183 335.089 0.886 0.978 0.093 5.214-4.128 98.38 1367 28 0.1255 504.897 498.862 0.978 0.978 0.044 4.126-3.266 94.74 2603 46 0.1179 460.241 452.679 1.040 0.980 0.000 3.266-2.585 99.86 5447 97 0.1134 310.468 306.744 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0961 234.230 231.596 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0907 138.629 137.270 1.049 0.985 0.000 1.619-1.281 98.00 42464 925 0.0942 74.630 73.986 1.039 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.036 38.331 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0198 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1370 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1370 | n_water=886 | time (s): 3.370 (total time: 3.370) Filter (dist) r_work=0.1194 r_free=0.1370 | n_water=886 | time (s): 102.380 (total time: 105.750) Filter (q & B) r_work=0.1194 r_free=0.1368 | n_water=875 | time (s): 4.450 (total time: 110.200) Compute maps r_work=0.1194 r_free=0.1368 | n_water=875 | time (s): 1.910 (total time: 112.110) Filter (map) r_work=0.1216 r_free=0.1370 | n_water=772 | time (s): 5.080 (total time: 117.190) Find peaks r_work=0.1216 r_free=0.1370 | n_water=772 | time (s): 0.570 (total time: 117.760) Add new water r_work=0.1223 r_free=0.1379 | n_water=980 | time (s): 4.230 (total time: 121.990) Refine new water occ: r_work=0.1191 r_free=0.1355 adp: r_work=0.1192 r_free=0.1355 occ: r_work=0.1190 r_free=0.1355 adp: r_work=0.1190 r_free=0.1355 occ: r_work=0.1189 r_free=0.1355 adp: r_work=0.1189 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1355 r_work=0.1189 r_free=0.1355 | n_water=980 | time (s): 268.450 (total time: 390.440) Filter (q & B) r_work=0.1193 r_free=0.1365 | n_water=895 | time (s): 4.460 (total time: 394.900) Filter (dist only) r_work=0.1193 r_free=0.1366 | n_water=893 | time (s): 114.390 (total time: 509.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533954 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.476124 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1369 0.0173 0.039 1.1 7.3 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.69 1.73 1.680 13.674 14.476 3.756 11.97 13.72 1.75 1.692 13.668 14.476 3.754 Individual atomic B min max mean iso aniso Overall: 5.54 63.90 14.52 0.87 527 3270 Protein: 5.54 27.87 10.33 0.87 0 2902 Water: 5.96 63.90 28.09 N/A 527 366 Other: 13.81 22.05 17.93 N/A 0 2 Chain A: 5.61 50.73 12.13 N/A 0 1624 Chain B: 5.54 63.90 11.98 N/A 0 1646 Chain S: 5.96 63.07 29.79 N/A 527 0 Histogram: Values Number of atoms 5.54 - 11.38 2079 11.38 - 17.21 818 17.21 - 23.05 276 23.05 - 28.89 217 28.89 - 34.72 176 34.72 - 40.56 118 40.56 - 46.39 75 46.39 - 52.23 30 52.23 - 58.07 5 58.07 - 63.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1372 r_work=0.1197 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1372 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1374 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1374 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754366 | | target function (ml) not normalized (work): 703147.763154 | | target function (ml) not normalized (free): 14741.757784 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1374 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1505 n_refl.: 191129 remove outliers: r(all,work,free)=0.1404 0.1403 0.1505 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1404 0.1402 0.1504 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1373 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1195 0.1373 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 0.3814 357.205 316.946 0.361 0.995 0.184 13.296-10.522 95.05 95 1 0.2324 479.665 465.945 0.691 0.996 0.131 10.503-8.327 98.35 176 3 0.2272 502.932 492.974 0.842 0.997 0.115 8.318-6.595 100.00 360 8 0.2230 375.648 369.667 0.865 0.997 0.088 6.588-5.215 100.00 711 7 0.1960 345.183 334.893 0.865 0.997 0.083 5.214-4.128 98.38 1367 28 0.1278 504.897 498.431 0.958 0.998 0.039 4.126-3.266 94.74 2603 46 0.1186 460.241 452.509 1.019 1.000 0.000 3.266-2.585 99.86 5447 97 0.1139 310.468 306.645 1.004 1.001 0.000 2.585-2.046 97.45 10613 204 0.0963 234.230 231.582 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0906 138.629 137.270 1.029 1.006 0.000 1.619-1.281 98.00 42464 925 0.0940 74.630 73.980 1.020 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.036 38.321 0.991 1.022 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0092 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1373 After: r_work=0.1196 r_free=0.1373 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1373 | n_water=893 | time (s): 2.870 (total time: 2.870) Filter (dist) r_work=0.1196 r_free=0.1373 | n_water=892 | time (s): 120.930 (total time: 123.800) Filter (q & B) r_work=0.1197 r_free=0.1372 | n_water=880 | time (s): 4.970 (total time: 128.770) Compute maps r_work=0.1197 r_free=0.1372 | n_water=880 | time (s): 2.050 (total time: 130.820) Filter (map) r_work=0.1220 r_free=0.1381 | n_water=769 | time (s): 4.390 (total time: 135.210) Find peaks r_work=0.1220 r_free=0.1381 | n_water=769 | time (s): 0.870 (total time: 136.080) Add new water r_work=0.1227 r_free=0.1394 | n_water=971 | time (s): 4.550 (total time: 140.630) Refine new water occ: r_work=0.1194 r_free=0.1359 adp: r_work=0.1194 r_free=0.1358 occ: r_work=0.1192 r_free=0.1358 adp: r_work=0.1192 r_free=0.1357 occ: r_work=0.1191 r_free=0.1357 adp: r_work=0.1191 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1357 r_work=0.1191 r_free=0.1357 | n_water=971 | time (s): 268.180 (total time: 408.810) Filter (q & B) r_work=0.1195 r_free=0.1367 | n_water=889 | time (s): 4.280 (total time: 413.090) Filter (dist only) r_work=0.1195 r_free=0.1367 | n_water=887 | time (s): 113.910 (total time: 527.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.525723 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.651933 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1368 0.0172 0.039 1.1 7.7 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.68 1.72 1.677 13.634 14.652 3.755 11.96 13.69 1.73 1.677 13.633 14.652 3.753 Individual atomic B min max mean iso aniso Overall: 5.58 62.82 14.45 0.87 521 3270 Protein: 5.58 27.89 10.35 0.87 0 2902 Water: 6.02 62.82 27.87 N/A 521 366 Other: 13.86 22.03 17.94 N/A 0 2 Chain A: 5.65 50.31 12.12 N/A 0 1624 Chain B: 5.58 62.82 11.98 N/A 0 1646 Chain S: 6.02 58.64 29.55 N/A 521 0 Histogram: Values Number of atoms 5.58 - 11.31 2053 11.31 - 17.03 839 17.03 - 22.75 268 22.75 - 28.48 216 28.48 - 34.20 183 34.20 - 39.93 113 39.93 - 45.65 81 45.65 - 51.38 30 51.38 - 57.10 6 57.10 - 62.82 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1369 r_work=0.1196 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1369 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1368 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753234 | | target function (ml) not normalized (work): 702935.716269 | | target function (ml) not normalized (free): 14732.154921 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1383 0.1545 5.7101 5.8095| | 2: 2.94 - 2.33 1.00 7339 128 0.1080 0.1359 5.1021 5.1911| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1179 4.654 4.7592| | 4: 2.04 - 1.85 1.00 7170 155 0.0895 0.1070 4.39 4.567| | 5: 1.85 - 1.72 0.99 7113 159 0.0927 0.0986 4.1464 4.2405| | 6: 1.72 - 1.62 0.99 7102 142 0.0890 0.1081 3.9411 4.0749| | 7: 1.62 - 1.54 0.99 7104 148 0.0885 0.0970 3.793 3.9261| | 8: 1.54 - 1.47 0.96 6798 152 0.0882 0.1308 3.6913 3.9044| | 9: 1.47 - 1.41 0.98 6938 155 0.0918 0.1088 3.612 3.729| | 10: 1.41 - 1.36 0.99 7022 150 0.0969 0.1194 3.5488 3.6802| | 11: 1.36 - 1.32 0.99 6997 151 0.0987 0.1118 3.4793 3.579| | 12: 1.32 - 1.28 0.98 6975 149 0.1028 0.1135 3.4557 3.5827| | 13: 1.28 - 1.25 0.98 6907 166 0.1037 0.1250 3.434 3.5717| | 14: 1.25 - 1.22 0.98 7015 112 0.1103 0.1573 3.4314 3.6714| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1239 3.4467 3.4896| | 16: 1.19 - 1.17 0.93 6604 132 0.1246 0.1557 3.4634 3.6622| | 17: 1.17 - 1.14 0.98 6940 135 0.1296 0.1219 3.4316 3.4405| | 18: 1.14 - 1.12 0.98 6875 142 0.1381 0.1701 3.4366 3.5312| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1746 3.4178 3.5973| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1568 3.4085 3.4289| | 21: 1.08 - 1.07 0.97 6852 152 0.1725 0.2138 3.417 3.5042| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1958 3.4124 3.416| | 23: 1.05 - 1.03 0.97 6827 159 0.2116 0.2032 3.4323 3.488| | 24: 1.03 - 1.02 0.96 6784 133 0.2328 0.2249 3.4351 3.5099| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2516 3.4492 3.5266| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2857 3.4158 3.426| | 27: 0.99 - 0.98 0.94 6647 131 0.3038 0.2805 3.4683 3.3943| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7397 127 0.92 12.40 1.00 0.95 12335.33| | 2: 2.94 - 2.33 7339 128 0.92 13.38 0.99 0.95 5517.47| | 3: 2.33 - 2.04 6939 150 0.96 7.70 1.01 0.95 1711.47| | 4: 2.04 - 1.85 7170 155 0.96 7.66 1.00 0.95 1009.39| | 5: 1.85 - 1.72 7113 159 0.96 8.05 1.00 0.96 633.30| | 6: 1.72 - 1.62 7102 142 0.96 7.98 1.00 0.96 440.51| | 7: 1.62 - 1.54 7104 148 0.96 8.08 1.01 0.97 332.85| | 8: 1.54 - 1.47 6798 152 0.96 8.19 1.01 0.97 275.40| | 9: 1.47 - 1.41 6938 155 0.96 8.31 1.00 0.98 226.08| | 10: 1.41 - 1.36 7022 150 0.96 8.80 1.00 0.97 199.27| | 11: 1.36 - 1.32 6997 151 0.96 8.86 0.99 0.96 172.75| | 12: 1.32 - 1.28 6975 149 0.96 8.95 0.98 0.95 160.44| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.01 0.96 158.32| | 14: 1.25 - 1.22 7015 112 0.95 10.72 1.01 0.97 163.59| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 0.98 166.56| | 16: 1.19 - 1.17 6604 132 0.95 11.41 1.01 0.96 160.18| | 17: 1.17 - 1.14 6940 135 0.94 12.22 1.01 0.96 153.59| | 18: 1.14 - 1.12 6875 142 0.94 12.70 1.01 0.95 147.10| | 19: 1.12 - 1.10 6948 106 0.93 14.10 1.00 0.95 150.26| | 20: 1.10 - 1.08 6884 147 0.92 15.15 1.00 0.94 149.41| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.93 153.06| | 22: 1.07 - 1.05 6836 135 0.89 18.30 0.99 0.93 155.08| | 23: 1.05 - 1.03 6827 159 0.87 20.53 0.99 0.92 165.26| | 24: 1.03 - 1.02 6784 133 0.85 23.20 0.99 0.93 179.64| | 25: 1.02 - 1.01 6552 130 0.83 25.19 0.98 0.90 182.69| | 26: 1.01 - 0.99 6767 158 0.81 26.63 0.98 0.89 176.87| | 27: 0.99 - 0.98 6647 131 0.82 26.23 0.99 0.87 160.66| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.10 max = 12335.33 mean = 985.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.32| |phase err.(test): min = 0.00 max = 89.09 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1368 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1412 0.1411 0.1506 n_refl.: 191129 remove outliers: r(all,work,free)=0.1412 0.1411 0.1506 n_refl.: 191129 overall B=-0.05 to atoms: r(all,work,free)=0.1404 0.1402 0.1500 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1367 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1367 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 0.3753 352.582 316.830 0.359 0.975 0.186 13.296-10.522 95.05 95 1 0.2368 479.665 464.520 0.689 0.976 0.135 10.503-8.327 98.35 176 3 0.2266 502.932 492.586 0.837 0.977 0.108 8.318-6.595 100.00 360 8 0.2235 375.648 369.555 0.865 0.977 0.096 6.588-5.215 100.00 711 7 0.1955 345.183 334.751 0.860 0.977 0.095 5.214-4.128 98.38 1367 28 0.1283 504.897 498.108 0.954 0.978 0.061 4.126-3.266 94.74 2603 46 0.1183 460.241 452.653 1.015 0.980 0.000 3.266-2.585 99.86 5447 97 0.1133 310.468 306.743 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0963 234.230 231.562 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0905 138.629 137.268 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0939 74.630 73.982 1.012 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.036 38.314 0.980 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0120 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2033 0.1991 0.081 5.230 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1927 0.081 5.230 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1927 0.081 5.230 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1927 0.081 5.230 5.2 78.0 14.6 805 0.000 1_weight: 0.1800 0.1927 0.081 5.230 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1272 0.1502 0.039 1.168 5.2 78.0 14.6 805 0.155 1_adp: 0.1296 0.1567 0.039 1.168 5.2 73.0 15.1 805 0.155 1_regHadp: 0.1295 0.1563 0.039 1.168 5.2 73.0 15.1 805 0.155 1_occ: 0.1280 0.1554 0.039 1.168 5.2 73.0 15.1 805 0.155 2_bss: 0.1272 0.1544 0.039 1.168 5.3 73.2 15.2 805 0.155 2_settarget: 0.1272 0.1544 0.039 1.168 5.3 73.2 15.2 805 0.155 2_updatecdl: 0.1272 0.1544 0.039 1.165 5.3 73.2 15.2 805 0.155 2_nqh: 0.1272 0.1544 0.039 1.165 5.3 73.2 15.2 805 0.155 2_sol: 0.1268 0.1508 0.039 1.165 5.3 73.2 16.2 873 n/a 2_weight: 0.1268 0.1508 0.039 1.165 5.3 73.2 16.2 873 n/a 2_xyzrec: 0.1252 0.1525 0.042 1.125 5.3 73.2 16.2 873 n/a 2_adp: 0.1235 0.1517 0.042 1.125 5.4 69.0 16.3 873 n/a 2_regHadp: 0.1235 0.1518 0.042 1.125 5.4 69.0 16.3 873 n/a 2_occ: 0.1230 0.1510 0.042 1.125 5.4 69.0 16.3 873 n/a 3_bss: 0.1237 0.1519 0.042 1.125 5.4 69.0 16.2 873 n/a 3_settarget: 0.1237 0.1519 0.042 1.125 5.4 69.0 16.2 873 n/a 3_updatecdl: 0.1237 0.1519 0.042 1.129 5.4 69.0 16.2 873 n/a 3_nqh: 0.1237 0.1519 0.042 1.129 5.4 69.0 16.2 873 n/a 3_sol: 0.1252 0.1530 0.042 1.129 5.4 69.0 15.4 862 n/a 3_weight: 0.1252 0.1530 0.042 1.129 5.4 69.0 15.4 862 n/a 3_xyzrec: 0.1243 0.1443 0.035 1.100 5.4 69.0 15.4 862 n/a 3_adp: 0.1236 0.1404 0.035 1.100 5.6 68.6 15.2 862 n/a 3_regHadp: 0.1236 0.1404 0.035 1.100 5.6 68.6 15.2 862 n/a 3_occ: 0.1231 0.1395 0.035 1.100 5.6 68.6 15.2 862 n/a 4_bss: 0.1227 0.1387 0.035 1.100 5.5 68.6 15.2 862 n/a 4_settarget: 0.1227 0.1387 0.035 1.100 5.5 68.6 15.2 862 n/a 4_updatecdl: 0.1227 0.1387 0.035 1.105 5.5 68.6 15.2 862 n/a 4_nqh: 0.1227 0.1387 0.035 1.105 5.5 68.6 15.2 862 n/a 4_sol: 0.1213 0.1367 0.035 1.105 5.5 68.6 14.8 852 n/a 4_weight: 0.1213 0.1367 0.035 1.105 5.5 68.6 14.8 852 n/a 4_xyzrec: 0.1211 0.1370 0.033 1.122 5.5 68.6 14.8 852 n/a 4_adp: 0.1202 0.1366 0.033 1.122 5.5 68.0 14.7 852 n/a 4_regHadp: 0.1202 0.1366 0.033 1.122 5.5 68.0 14.7 852 n/a 4_occ: 0.1200 0.1364 0.033 1.122 5.5 68.0 14.7 852 n/a 5_bss: 0.1198 0.1361 0.033 1.122 5.5 67.9 14.7 852 n/a 5_settarget: 0.1198 0.1361 0.033 1.122 5.5 67.9 14.7 852 n/a 5_updatecdl: 0.1198 0.1361 0.033 1.123 5.5 67.9 14.7 852 n/a 5_nqh: 0.1198 0.1361 0.033 1.123 5.5 67.9 14.7 852 n/a 5_sol: 0.1196 0.1352 0.033 1.123 5.5 67.9 14.8 871 n/a 5_weight: 0.1196 0.1352 0.033 1.123 5.5 67.9 14.8 871 n/a 5_xyzrec: 0.1199 0.1360 0.036 1.121 5.5 67.9 14.8 871 n/a 5_adp: 0.1205 0.1365 0.036 1.121 5.6 67.7 14.8 871 n/a 5_regHadp: 0.1205 0.1366 0.036 1.121 5.6 67.7 14.8 871 n/a 5_occ: 0.1203 0.1370 0.036 1.121 5.6 67.7 14.8 871 n/a 6_bss: 0.1201 0.1367 0.036 1.121 5.5 67.7 14.8 871 n/a 6_settarget: 0.1201 0.1367 0.036 1.121 5.5 67.7 14.8 871 n/a 6_updatecdl: 0.1201 0.1367 0.036 1.121 5.5 67.7 14.8 871 n/a 6_nqh: 0.1201 0.1367 0.036 1.121 5.5 67.7 14.8 871 n/a 6_sol: 0.1199 0.1366 0.036 1.121 5.5 67.7 14.8 880 n/a 6_weight: 0.1199 0.1366 0.036 1.121 5.5 67.7 14.8 880 n/a 6_xyzrec: 0.1202 0.1375 0.037 1.123 5.5 67.7 14.8 880 n/a 6_adp: 0.1208 0.1379 0.037 1.123 5.6 66.4 14.7 880 n/a 6_regHadp: 0.1208 0.1380 0.037 1.123 5.6 66.4 14.7 880 n/a 6_occ: 0.1206 0.1380 0.037 1.123 5.6 66.4 14.7 880 n/a 7_bss: 0.1205 0.1378 0.037 1.123 5.4 66.2 14.5 880 n/a 7_settarget: 0.1205 0.1378 0.037 1.123 5.4 66.2 14.5 880 n/a 7_updatecdl: 0.1205 0.1378 0.037 1.123 5.4 66.2 14.5 880 n/a 7_nqh: 0.1205 0.1378 0.037 1.123 5.4 66.2 14.5 880 n/a 7_sol: 0.1203 0.1370 0.037 1.123 5.4 66.2 14.5 889 n/a 7_weight: 0.1203 0.1370 0.037 1.123 5.4 66.2 14.5 889 n/a 7_xyzrec: 0.1207 0.1377 0.038 1.118 5.4 66.2 14.5 889 n/a 7_adp: 0.1206 0.1378 0.038 1.118 5.4 65.0 14.5 889 n/a 7_regHadp: 0.1206 0.1378 0.038 1.118 5.4 65.0 14.5 889 n/a 7_occ: 0.1203 0.1378 0.038 1.118 5.4 65.0 14.5 889 n/a 8_bss: 0.1194 0.1368 0.038 1.118 5.4 65.1 14.5 889 n/a 8_settarget: 0.1194 0.1368 0.038 1.118 5.4 65.1 14.5 889 n/a 8_updatecdl: 0.1194 0.1368 0.038 1.117 5.4 65.1 14.5 889 n/a 8_nqh: 0.1194 0.1368 0.038 1.117 5.4 65.1 14.5 889 n/a 8_sol: 0.1193 0.1360 0.038 1.117 5.4 65.1 14.5 886 n/a 8_weight: 0.1193 0.1360 0.038 1.117 5.4 65.1 14.5 886 n/a 8_xyzrec: 0.1196 0.1365 0.038 1.108 5.4 65.1 14.5 886 n/a 8_adp: 0.1197 0.1368 0.038 1.108 5.5 64.8 14.5 886 n/a 8_regHadp: 0.1197 0.1368 0.038 1.108 5.5 64.8 14.5 886 n/a 8_occ: 0.1195 0.1371 0.038 1.108 5.5 64.8 14.5 886 n/a 9_bss: 0.1194 0.1370 0.038 1.108 5.5 64.8 14.5 886 n/a 9_settarget: 0.1194 0.1370 0.038 1.108 5.5 64.8 14.5 886 n/a 9_updatecdl: 0.1194 0.1370 0.038 1.108 5.5 64.8 14.5 886 n/a 9_nqh: 0.1194 0.1370 0.038 1.108 5.5 64.8 14.5 886 n/a 9_sol: 0.1193 0.1366 0.038 1.108 5.5 64.8 14.5 893 n/a 9_weight: 0.1193 0.1366 0.038 1.108 5.5 64.8 14.5 893 n/a 9_xyzrec: 0.1196 0.1369 0.039 1.114 5.5 64.8 14.5 893 n/a 9_adp: 0.1197 0.1372 0.039 1.114 5.5 63.9 14.5 893 n/a 9_regHadp: 0.1197 0.1372 0.039 1.114 5.5 63.9 14.5 893 n/a 9_occ: 0.1196 0.1374 0.039 1.114 5.5 63.9 14.5 893 n/a 10_bss: 0.1195 0.1373 0.039 1.114 5.5 63.9 14.5 893 n/a 10_settarget: 0.1195 0.1373 0.039 1.114 5.5 63.9 14.5 893 n/a 10_updatecdl: 0.1195 0.1373 0.039 1.114 5.5 63.9 14.5 893 n/a 10_setrh: 0.1196 0.1373 0.039 1.114 5.5 63.9 14.5 893 n/a 10_nqh: 0.1196 0.1373 0.039 1.114 5.5 63.9 14.5 893 n/a 10_sol: 0.1195 0.1367 0.039 1.114 5.5 63.9 14.5 887 n/a 10_weight: 0.1195 0.1367 0.039 1.114 5.5 63.9 14.5 887 n/a 10_xyzrec: 0.1196 0.1368 0.039 1.129 5.5 63.9 14.5 887 n/a 10_adp: 0.1196 0.1369 0.039 1.129 5.6 62.8 14.5 887 n/a 10_regHadp: 0.1196 0.1369 0.039 1.129 5.6 62.8 14.5 887 n/a 10_occ: 0.1195 0.1368 0.039 1.129 5.6 62.8 14.5 887 n/a end: 0.1194 0.1367 0.039 1.129 5.5 62.8 14.4 887 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5016558_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5016558_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.2000 Refinement macro-cycles (run) : 12081.4100 Write final files (write_after_run_outputs) : 173.2200 Total : 12261.8300 Total CPU time: 3.42 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:31 PST -0800 (1736736091.25 s) Start R-work = 0.1800, R-free = 0.1927 Final R-work = 0.1194, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 12555.05 seconds wall clock time: 210 minutes 14.22 seconds (12614.22 seconds total)