Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7450704.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7450704.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7450704.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 2.50, per 1000 atoms: 0.37 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: 2.701 distance_ideal: 2.720 ideal - model: 0.019 slack: 0.000 delta_slack: 0.019 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: 2.720 distance_ideal: 2.710 ideal - model: -0.010 slack: 0.000 delta_slack: -0.010 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: 0.76 Conformation dependent library (CDL) restraints added in 118.9 milliseconds Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.02: 701 1.02 - 1.25: 2541 1.25 - 1.47: 1439 1.47 - 1.70: 1228 1.70 - 1.93: 25 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL B 114 " pdb=" CB VAL B 114 " ideal model delta sigma weight residual 1.539 1.353 0.186 5.40e-03 3.43e+04 1.19e+03 bond pdb=" C SER B 4 " pdb=" O SER B 4 " ideal model delta sigma weight residual 1.234 1.470 -0.236 1.22e-02 6.72e+03 3.74e+02 bond pdb=" N ARG B 27 " pdb=" H ARG B 27 " ideal model delta sigma weight residual 0.860 1.236 -0.376 2.00e-02 2.50e+03 3.54e+02 bond pdb=" N ARG B 97 " pdb=" H ARG B 97 " ideal model delta sigma weight residual 0.860 1.236 -0.376 2.00e-02 2.50e+03 3.54e+02 bond pdb=" CA THR A 111 " pdb=" HA THR A 111 " ideal model delta sigma weight residual 0.970 1.325 -0.355 2.00e-02 2.50e+03 3.15e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 5938 4.42 - 8.85: 3483 8.85 - 13.27: 1183 13.27 - 17.70: 189 17.70 - 22.12: 17 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O PHE B 95 " pdb=" C PHE B 95 " pdb=" N HIS B 96 " ideal model delta sigma weight residual 122.09 103.79 18.30 1.04e+00 9.25e-01 3.09e+02 angle pdb=" C THR A 111 " pdb=" N VAL A 112 " pdb=" CA VAL A 112 " ideal model delta sigma weight residual 122.97 139.29 -16.32 9.80e-01 1.04e+00 2.77e+02 angle pdb=" O GLU A 180 " pdb=" C GLU A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 122.12 138.60 -16.48 1.06e+00 8.90e-01 2.42e+02 angle pdb=" CA VAL A 150 " pdb=" C VAL A 150 " pdb=" O VAL A 150 " ideal model delta sigma weight residual 119.97 105.90 14.07 9.10e-01 1.21e+00 2.39e+02 angle pdb=" N ALA A 57 " pdb=" CA ALA A 57 " pdb=" C ALA A 57 " ideal model delta sigma weight residual 108.13 94.46 13.67 9.00e-01 1.23e+00 2.31e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1866 17.88 - 35.75: 122 35.75 - 53.63: 40 53.63 - 71.51: 18 71.51 - 89.38: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 152.27 27.73 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual 180.00 -154.34 -25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ALA A 35 " pdb=" C ALA A 35 " pdb=" N SER A 36 " pdb=" CA SER A 36 " ideal model delta harmonic sigma weight residual 180.00 155.75 24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.235: 220 0.235 - 0.469: 155 0.469 - 0.703: 91 0.703 - 0.937: 21 0.937 - 1.171: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 92 " pdb=" N VAL A 92 " pdb=" C VAL A 92 " pdb=" CB VAL A 92 " both_signs ideal model delta sigma weight residual False 2.44 3.61 -1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CA VAL A 7 " pdb=" N VAL A 7 " pdb=" C VAL A 7 " pdb=" CB VAL A 7 " both_signs ideal model delta sigma weight residual False 2.44 3.52 -1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" CB ILE A 168 " pdb=" CA ILE A 168 " pdb=" CG1 ILE A 168 " pdb=" CG2 ILE A 168 " both_signs ideal model delta sigma weight residual False 2.64 1.68 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.026 2.00e-02 2.50e+03 7.05e-02 1.99e+02 pdb=" CG TRP B 146 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.098 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.095 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.027 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.046 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.076 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.021 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.107 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.049 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.121 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.025 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.112 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.159 2.00e-02 2.50e+03 7.95e-02 1.90e+02 pdb=" CG PHE A 164 " 0.132 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.118 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.104 2.00e-02 2.50e+03 6.22e-02 1.55e+02 pdb=" CG TRP A 146 " -0.102 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.041 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.117 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.068 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.030 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.024 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.011 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.104 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.037 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.74 - 1.51: 18 1.51 - 2.29: 1609 2.29 - 3.06: 21393 3.06 - 3.83: 33181 3.83 - 4.60: 54030 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110231 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.744 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.904 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.967 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.007 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.149 2.620 ... (remaining 110226 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_7450704_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= 0.1994 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300852 | | target function (ml) not normalized (work): 805605.572096 | | target function (ml) not normalized (free): 16585.798499 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2129 0.1984 6.6887 6.3092| | 2: 2.94 - 2.33 1.00 7339 128 0.1617 0.1476 5.5349 5.5484| | 3: 2.33 - 2.04 0.96 6939 150 0.1602 0.1548 5.1322 5.1382| | 4: 2.04 - 1.85 1.00 7170 155 0.1770 0.1665 4.9625 5.0554| | 5: 1.85 - 1.72 0.99 7113 159 0.1933 0.1661 4.8039 4.7749| | 6: 1.72 - 1.62 0.99 7102 142 0.2017 0.2096 4.6844 4.7562| | 7: 1.62 - 1.54 0.99 7104 148 0.2026 0.1905 4.5686 4.6251| | 8: 1.54 - 1.47 0.96 6798 152 0.2061 0.2228 4.4752 4.5446| | 9: 1.47 - 1.41 0.98 6938 155 0.2089 0.2175 4.3892 4.4726| | 10: 1.41 - 1.36 0.99 7022 150 0.2098 0.1950 4.2971 4.298| | 11: 1.36 - 1.32 0.99 6997 151 0.2076 0.2387 4.2302 4.3334| | 12: 1.32 - 1.28 0.98 6976 149 0.2065 0.2149 4.1691 4.2579| | 13: 1.28 - 1.25 0.98 6907 166 0.2013 0.2207 4.1234 4.2223| | 14: 1.25 - 1.22 0.98 7015 113 0.2081 0.2388 4.0738 4.2543| | 15: 1.22 - 1.19 0.98 6957 137 0.2128 0.1915 4.0587 4.043| | 16: 1.19 - 1.17 0.93 6604 132 0.2137 0.2155 4.0123 4.0589| | 17: 1.17 - 1.14 0.98 6941 135 0.2210 0.1989 3.9681 3.9932| | 18: 1.14 - 1.12 0.98 6875 142 0.2197 0.2255 3.9108 3.9246| | 19: 1.12 - 1.10 0.97 6949 106 0.2272 0.2672 3.8742 4.0315| | 20: 1.10 - 1.08 0.97 6884 147 0.2321 0.2266 3.828 3.8636| | 21: 1.08 - 1.07 0.97 6852 152 0.2466 0.2764 3.7997 3.84| | 22: 1.07 - 1.05 0.97 6838 135 0.2606 0.2872 3.7602 3.795| | 23: 1.05 - 1.03 0.97 6829 159 0.2721 0.2520 3.7377 3.7656| | 24: 1.03 - 1.02 0.96 6785 133 0.2864 0.2773 3.6972 3.7583| | 25: 1.02 - 1.01 0.93 6552 130 0.3045 0.3183 3.6692 3.7845| | 26: 1.01 - 0.99 0.96 6767 158 0.3156 0.3075 3.619 3.5882| | 27: 0.99 - 0.98 0.94 6648 131 0.3425 0.3014 3.641 3.5643| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.37 0.91 0.97 35325.22| | 2: 2.94 - 2.33 7339 128 0.86 20.99 1.08 1.02 14867.93| | 3: 2.33 - 2.04 6939 150 0.94 11.91 1.10 1.06 3908.07| | 4: 2.04 - 1.85 7170 155 0.93 13.06 1.12 1.07 2620.91| | 5: 1.85 - 1.72 7113 159 0.91 15.39 1.12 1.08 2019.55| | 6: 1.72 - 1.62 7102 142 0.90 16.99 1.12 1.07 1701.08| | 7: 1.62 - 1.54 7104 148 0.88 18.59 1.11 1.06 1459.42| | 8: 1.54 - 1.47 6798 152 0.88 19.19 1.11 1.05 1219.28| | 9: 1.47 - 1.41 6938 155 0.88 19.23 1.10 1.06 998.84| | 10: 1.41 - 1.36 7022 150 0.87 19.76 1.09 1.05 841.76| | 11: 1.36 - 1.32 6997 151 0.87 20.17 1.07 1.04 741.84| | 12: 1.32 - 1.28 6976 149 0.87 20.56 1.08 1.02 682.12| | 13: 1.28 - 1.25 6907 166 0.87 20.56 1.07 1.04 646.48| | 14: 1.25 - 1.22 7015 113 0.86 21.67 1.08 1.04 617.86| | 15: 1.22 - 1.19 6957 137 0.86 21.29 1.08 1.05 564.71| | 16: 1.19 - 1.17 6604 132 0.87 20.55 1.07 1.04 495.77| | 17: 1.17 - 1.14 6941 135 0.87 20.79 1.08 1.03 432.61| | 18: 1.14 - 1.12 6875 142 0.86 21.03 1.08 1.00 393.15| | 19: 1.12 - 1.10 6949 106 0.85 22.28 1.07 0.99 388.36| | 20: 1.10 - 1.08 6884 147 0.84 23.51 1.06 0.98 371.32| | 21: 1.08 - 1.07 6852 152 0.83 24.92 1.07 0.97 357.76| | 22: 1.07 - 1.05 6838 135 0.81 26.13 1.06 0.98 337.94| | 23: 1.05 - 1.03 6829 159 0.80 27.30 1.05 0.99 333.21| | 24: 1.03 - 1.02 6785 133 0.78 29.33 1.05 0.99 331.01| | 25: 1.02 - 1.01 6552 130 0.77 30.60 1.03 0.93 310.04| | 26: 1.01 - 0.99 6767 158 0.75 32.01 1.03 0.90 287.29| | 27: 0.99 - 0.98 6648 131 0.75 31.90 1.04 0.89 262.94| |alpha: min = 0.89 max = 1.08 mean = 1.01| |beta: min = 262.94 max = 35325.22 mean = 2811.97| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 21.77| |phase err.(test): min = 0.00 max = 89.61 mean = 21.66| |-----------------------------------------------------------------------------| ----------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 0.292 2950 Z= 5.493 Angle : 5.250 18.296 4018 Z= 3.783 Chirality : 0.385 1.171 492 Planarity : 0.032 0.132 512 Dihedral : 12.995 89.383 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.85 % Favored : 96.89 % Rotamer: Outliers : 1.61 % Allowed : 3.87 % Favored : 94.52 % Cbeta Deviations : 30.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.40), residues: 386 helix: -2.15 (0.35), residues: 142 sheet: -0.02 (0.63), residues: 58 loop : 0.13 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.117 0.019 ARG B 100 TYR 0.112 0.038 TYR A 194 PHE 0.169 0.039 PHE A 164 TRP 0.111 0.043 TRP A 146 HIS 0.095 0.033 HIS B 96 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= 0.1994 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300852 | | target function (ml) not normalized (work): 805605.572096 | | target function (ml) not normalized (free): 16585.798499 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2032 0.2033 0.1994 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2032 0.2033 0.1994 n_refl.: 191155 remove outliers: r(all,work,free)=0.2032 0.2034 0.1994 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2032 0.2034 0.1993 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1803 0.1926 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1800 0.1925 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4075 402.814 292.092 0.436 0.913 0.303 13.296-10.522 99.01 99 1 0.2489 528.187 520.401 0.791 0.914 0.258 10.503-8.327 98.90 177 3 0.2492 564.205 559.434 0.972 0.914 0.237 8.318-6.595 100.00 360 8 0.2461 414.736 403.562 0.976 0.914 0.190 6.588-5.215 100.00 711 7 0.2229 381.101 367.364 0.958 0.914 0.160 5.214-4.128 98.38 1367 28 0.1470 557.435 550.153 1.075 0.914 0.090 4.126-3.266 94.74 2603 46 0.1356 508.132 498.787 1.145 0.914 0.019 3.266-2.585 99.86 5447 97 0.1434 342.774 338.216 1.120 0.913 0.000 2.585-2.046 97.45 10613 204 0.1392 258.603 254.390 1.122 0.913 0.000 2.046-1.619 99.39 21536 464 0.1639 153.054 149.771 1.146 0.911 0.000 1.619-1.281 98.00 42464 925 0.1915 82.395 80.189 1.128 0.909 0.000 1.281-0.980 96.53 101826 2055 0.2324 44.202 41.672 1.113 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0019 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1925 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1800 r_free=0.1925 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.114697 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 572.732135 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 0.1273 0.1480 0.0207 0.035 1.2 11.0 0.0 0.0 0 11.057 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 14.80 2.07 1.117 13.110 572.732 0.019 13.03 15.52 2.49 1.263 13.359 572.732 0.018 Individual atomic B min max mean iso aniso Overall: 5.26 73.04 15.05 1.41 435 3274 Protein: 5.26 41.23 11.01 1.41 0 2902 Water: 6.34 73.04 29.58 N/A 435 370 Other: 15.89 31.09 23.49 N/A 0 2 Chain A: 5.26 60.60 13.09 N/A 0 1626 Chain B: 5.29 73.04 12.81 N/A 0 1648 Chain S: 11.53 62.79 30.87 N/A 435 0 Histogram: Values Number of atoms 5.26 - 12.04 2179 12.04 - 18.82 624 18.82 - 25.59 314 25.59 - 32.37 268 32.37 - 39.15 144 39.15 - 45.93 114 45.93 - 52.71 43 52.71 - 59.49 19 59.49 - 66.26 3 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1304 r_free=0.1553 r_work=0.1303 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1303 r_free = 0.1548 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1287 r_free = 0.1536 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1287 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015831 | | target function (ls_wunit_k1) not normalized (work): 2964.993350 | | target function (ls_wunit_k1) not normalized (free): 112.801504 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1287 0.1536 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1473 0.1471 0.1610 n_refl.: 191137 remove outliers: r(all,work,free)=0.1473 0.1471 0.1610 n_refl.: 191137 overall B=0.17 to atoms: r(all,work,free)=0.1497 0.1495 0.1622 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1284 0.1279 0.1528 n_refl.: 191137 remove outliers: r(all,work,free)=0.1284 0.1279 0.1528 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3669 402.814 378.011 0.486 0.962 0.281 13.296-10.522 99.01 99 1 0.2115 528.187 520.767 0.743 0.964 0.260 10.503-8.327 98.90 177 3 0.1718 564.205 561.398 0.886 0.964 0.213 8.318-6.595 100.00 360 8 0.1769 414.736 411.047 0.909 0.964 0.160 6.588-5.215 100.00 711 7 0.1587 381.101 372.940 0.888 0.964 0.150 5.214-4.128 98.38 1367 28 0.0933 557.435 555.087 0.977 0.964 0.059 4.126-3.266 94.74 2603 46 0.0858 508.132 503.979 1.045 0.965 0.014 3.266-2.585 99.86 5447 97 0.0932 342.774 340.139 1.027 0.965 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.347 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1078 153.054 151.356 1.056 0.965 0.000 1.619-1.281 98.00 42464 925 0.1278 82.395 81.405 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1881 44.202 42.166 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0384 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1279 r_free=0.1528 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1279 r_free=0.1528 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1528 | n_water=805 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1281 r_free=0.1530 | n_water=800 | time (s): 100.680 (total time: 103.020) Filter (q & B) r_work=0.1281 r_free=0.1529 | n_water=793 | time (s): 5.510 (total time: 108.530) Compute maps r_work=0.1281 r_free=0.1529 | n_water=793 | time (s): 2.510 (total time: 111.040) Filter (map) r_work=0.1304 r_free=0.1524 | n_water=668 | time (s): 4.380 (total time: 115.420) Find peaks r_work=0.1304 r_free=0.1524 | n_water=668 | time (s): 0.760 (total time: 116.180) Add new water r_work=0.1329 r_free=0.1561 | n_water=1008 | time (s): 4.740 (total time: 120.920) Refine new water occ: r_work=0.1284 r_free=0.1510 adp: r_work=0.1273 r_free=0.1503 occ: r_work=0.1277 r_free=0.1500 adp: r_work=0.1268 r_free=0.1499 occ: r_work=0.1270 r_free=0.1493 adp: r_work=0.1266 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1494 r_work=0.1266 r_free=0.1494 | n_water=1008 | time (s): 80.820 (total time: 201.740) Filter (q & B) r_work=0.1271 r_free=0.1498 | n_water=911 | time (s): 5.970 (total time: 207.710) Filter (dist only) r_work=0.1271 r_free=0.1499 | n_water=910 | time (s): 123.800 (total time: 331.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.462173 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 566.719267 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1253 0.1505 0.0251 0.039 1.2 18.4 0.0 0.3 0 11.731 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.05 2.51 2.052 15.307 566.719 0.014 12.34 14.96 2.62 2.421 15.331 566.719 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 68.21 16.47 1.20 540 3274 Protein: 5.39 40.64 11.00 1.20 0 2902 Water: 6.58 68.21 33.92 N/A 540 370 Other: 16.41 30.97 23.69 N/A 0 2 Chain A: 5.51 57.31 13.07 N/A 0 1626 Chain B: 5.39 68.21 12.84 N/A 0 1648 Chain S: 11.72 65.18 37.80 N/A 540 0 Histogram: Values Number of atoms 5.39 - 11.67 2051 11.67 - 17.95 714 17.95 - 24.23 278 24.23 - 30.52 216 30.52 - 36.80 178 36.80 - 43.08 162 43.08 - 49.36 111 49.36 - 55.65 45 55.65 - 61.93 49 61.93 - 68.21 10 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1496 r_work=0.1234 r_free=0.1498 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1498 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 = 0.1228 r_free = 0.1491 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1491 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013407 | | target function (ls_wunit_k1) not normalized (work): 2511.058570 | | target function (ls_wunit_k1) not normalized (free): 94.820215 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1228 0.1491 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1430 0.1427 0.1591 n_refl.: 191137 remove outliers: r(all,work,free)=0.1430 0.1427 0.1591 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1427 0.1425 0.1590 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1235 0.1498 n_refl.: 191137 remove outliers: r(all,work,free)=0.1240 0.1235 0.1498 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 0.3228 398.008 380.842 0.492 0.964 0.275 13.296-10.522 99.01 99 1 0.1932 528.187 518.765 0.753 0.965 0.227 10.503-8.327 98.90 177 3 0.1360 564.205 566.621 0.921 0.965 0.181 8.318-6.595 100.00 360 8 0.1538 414.736 413.209 0.933 0.964 0.141 6.588-5.215 100.00 711 7 0.1375 381.101 376.580 0.910 0.964 0.120 5.214-4.128 98.38 1367 28 0.0824 557.435 555.864 0.993 0.964 0.070 4.126-3.266 94.74 2603 46 0.0761 508.132 505.307 1.058 0.964 0.014 3.266-2.585 99.86 5447 97 0.0855 342.774 341.150 1.045 0.963 0.000 2.585-2.046 97.45 10613 204 0.0895 258.603 256.702 1.057 0.962 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.638 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.349 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1881 44.202 42.208 1.058 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0477 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1498 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1498 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1498 | n_water=910 | time (s): 3.560 (total time: 3.560) Filter (dist) r_work=0.1237 r_free=0.1502 | n_water=905 | time (s): 123.930 (total time: 127.490) Filter (q & B) r_work=0.1237 r_free=0.1503 | n_water=904 | time (s): 4.420 (total time: 131.910) Compute maps r_work=0.1237 r_free=0.1503 | n_water=904 | time (s): 1.890 (total time: 133.800) Filter (map) r_work=0.1277 r_free=0.1500 | n_water=701 | time (s): 4.220 (total time: 138.020) Find peaks r_work=0.1277 r_free=0.1500 | n_water=701 | time (s): 0.590 (total time: 138.610) Add new water r_work=0.1298 r_free=0.1516 | n_water=1017 | time (s): 4.370 (total time: 142.980) Refine new water occ: r_work=0.1255 r_free=0.1483 adp: r_work=0.1255 r_free=0.1484 occ: r_work=0.1251 r_free=0.1482 adp: r_work=0.1251 r_free=0.1483 occ: r_work=0.1248 r_free=0.1482 adp: r_work=0.1248 r_free=0.1482 ADP+occupancy (water only), MIN, final r_work=0.1248 r_free=0.1482 r_work=0.1248 r_free=0.1482 | n_water=1017 | time (s): 321.680 (total time: 464.660) Filter (q & B) r_work=0.1252 r_free=0.1488 | n_water=885 | time (s): 6.560 (total time: 471.220) Filter (dist only) r_work=0.1253 r_free=0.1487 | n_water=884 | time (s): 111.510 (total time: 582.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.718813 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.338075 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 0.1426 0.0183 0.035 1.1 6.8 0.0 0.0 0 0.859 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.43 14.26 1.83 1.936 14.633 16.338 3.943 12.34 13.81 1.47 2.256 14.533 16.338 3.896 Individual atomic B min max mean iso aniso Overall: 5.53 67.73 15.32 1.06 517 3271 Protein: 5.53 36.94 10.75 1.06 0 2902 Water: 6.70 67.73 30.31 N/A 517 367 Other: 14.10 27.27 20.69 N/A 0 2 Chain A: 5.54 56.33 12.81 N/A 0 1625 Chain B: 5.53 67.73 12.53 N/A 0 1646 Chain S: 14.24 61.88 32.10 N/A 517 0 Histogram: Values Number of atoms 5.53 - 11.75 2131 11.75 - 17.97 673 17.97 - 24.19 305 24.19 - 30.41 238 30.41 - 36.63 181 36.63 - 42.85 156 42.85 - 49.07 70 49.07 - 55.29 23 55.29 - 61.51 9 61.51 - 67.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1382 r_work=0.1235 r_free=0.1382 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1382 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1377 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890824 | | target function (ml) not normalized (work): 728731.796327 | | target function (ml) not normalized (free): 15215.325768 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1376 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1438 0.1437 0.1481 n_refl.: 191136 remove outliers: r(all,work,free)=0.1438 0.1437 0.1481 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1432 0.1431 0.1477 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1369 n_refl.: 191136 remove outliers: r(all,work,free)=0.1227 0.1225 0.1369 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 93.07 91 3 0.3797 398.895 352.932 0.412 0.947 0.241 13.296-10.522 98.02 98 1 0.2394 528.900 504.732 0.708 0.948 0.220 10.503-8.327 97.80 175 3 0.1935 554.286 557.944 0.883 0.948 0.184 8.318-6.595 100.00 360 8 0.2093 414.736 407.969 0.898 0.948 0.124 6.588-5.215 100.00 711 7 0.1872 381.101 370.269 0.882 0.948 0.100 5.214-4.128 98.38 1367 28 0.1162 557.435 552.016 0.970 0.948 0.044 4.126-3.266 94.74 2603 46 0.1095 508.132 501.252 1.032 0.948 0.009 3.266-2.585 99.86 5447 97 0.1087 342.774 339.181 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0965 258.603 255.753 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0970 153.054 151.455 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1056 82.395 81.488 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.322 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0991 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1369 | n_water=884 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1226 r_free=0.1370 | n_water=883 | time (s): 110.230 (total time: 112.940) Filter (q & B) r_work=0.1226 r_free=0.1368 | n_water=872 | time (s): 4.470 (total time: 117.410) Compute maps r_work=0.1226 r_free=0.1368 | n_water=872 | time (s): 1.930 (total time: 119.340) Filter (map) r_work=0.1246 r_free=0.1371 | n_water=727 | time (s): 4.520 (total time: 123.860) Find peaks r_work=0.1246 r_free=0.1371 | n_water=727 | time (s): 0.710 (total time: 124.570) Add new water r_work=0.1258 r_free=0.1385 | n_water=967 | time (s): 4.820 (total time: 129.390) Refine new water occ: r_work=0.1224 r_free=0.1363 adp: r_work=0.1224 r_free=0.1363 occ: r_work=0.1221 r_free=0.1361 adp: r_work=0.1221 r_free=0.1362 occ: r_work=0.1219 r_free=0.1360 adp: r_work=0.1219 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1219 r_free=0.1360 r_work=0.1219 r_free=0.1360 | n_water=967 | time (s): 224.860 (total time: 354.250) Filter (q & B) r_work=0.1224 r_free=0.1364 | n_water=885 | time (s): 5.730 (total time: 359.980) Filter (dist only) r_work=0.1224 r_free=0.1365 | n_water=884 | time (s): 118.090 (total time: 478.070) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.634881 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.608529 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 0.1222 0.1366 0.0143 0.036 1.1 6.1 0.0 0.0 0 0.817 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 13.66 1.43 1.837 14.300 15.609 3.885 12.16 13.66 1.50 1.920 14.267 15.609 3.878 Individual atomic B min max mean iso aniso Overall: 5.51 67.37 15.14 1.01 518 3270 Protein: 5.51 34.05 10.68 1.01 0 2902 Water: 6.71 67.37 29.74 N/A 518 366 Other: 14.04 26.78 20.41 N/A 0 2 Chain A: 5.51 55.47 12.68 N/A 0 1624 Chain B: 5.51 67.37 12.45 N/A 0 1646 Chain S: 13.62 61.83 31.38 N/A 518 0 Histogram: Values Number of atoms 5.51 - 11.70 2115 11.70 - 17.88 717 17.88 - 24.07 296 24.07 - 30.26 238 30.26 - 36.44 179 36.44 - 42.63 148 42.63 - 48.81 65 48.81 - 55.00 21 55.00 - 61.19 7 61.19 - 67.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1216 r_free=0.1366 r_work=0.1216 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1216 r_free = 0.1366 target_work(ml) = 3.878 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1214 r_free = 0.1361 target_work(ml) = 3.876 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1214 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.876485 | | target function (ml) not normalized (work): 726030.736246 | | target function (ml) not normalized (free): 15168.885737 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1214 0.1361 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1413 0.1412 0.1473 n_refl.: 191132 remove outliers: r(all,work,free)=0.1413 0.1412 0.1473 n_refl.: 191132 overall B=-0.03 to atoms: r(all,work,free)=0.1406 0.1406 0.1469 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1212 0.1362 n_refl.: 191132 remove outliers: r(all,work,free)=0.1215 0.1212 0.1362 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 91.09 89 3 0.3515 356.664 315.819 0.414 0.949 0.243 13.296-10.522 97.03 97 1 0.2336 481.071 457.072 0.704 0.951 0.195 10.503-8.327 97.80 175 3 0.2101 501.780 495.487 0.865 0.951 0.139 8.318-6.595 100.00 360 8 0.2158 375.449 370.096 0.890 0.951 0.105 6.588-5.215 100.00 711 7 0.1902 345.000 334.896 0.884 0.951 0.100 5.214-4.128 98.38 1367 28 0.1183 504.630 499.432 0.970 0.951 0.070 4.126-3.266 94.74 2603 46 0.1101 459.998 453.759 1.030 0.951 0.005 3.266-2.585 99.86 5447 97 0.1094 310.303 307.120 1.017 0.951 0.000 2.585-2.046 97.45 10613 204 0.0953 234.106 231.713 1.030 0.950 0.000 2.046-1.619 99.39 21536 464 0.0948 138.556 137.215 1.053 0.949 0.000 1.619-1.281 98.00 42464 925 0.1018 74.590 73.864 1.049 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1674 40.014 38.346 1.035 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1149 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1212 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1212 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1212 r_free=0.1361 | n_water=884 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1212 r_free=0.1360 | n_water=882 | time (s): 106.580 (total time: 109.820) Filter (q & B) r_work=0.1213 r_free=0.1361 | n_water=876 | time (s): 5.210 (total time: 115.030) Compute maps r_work=0.1213 r_free=0.1361 | n_water=876 | time (s): 1.740 (total time: 116.770) Filter (map) r_work=0.1231 r_free=0.1370 | n_water=768 | time (s): 5.020 (total time: 121.790) Find peaks r_work=0.1231 r_free=0.1370 | n_water=768 | time (s): 0.640 (total time: 122.430) Add new water r_work=0.1241 r_free=0.1378 | n_water=994 | time (s): 4.650 (total time: 127.080) Refine new water occ: r_work=0.1198 r_free=0.1343 adp: r_work=0.1190 r_free=0.1337 occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1188 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1338 r_work=0.1188 r_free=0.1338 | n_water=994 | time (s): 124.500 (total time: 251.580) Filter (q & B) r_work=0.1194 r_free=0.1352 | n_water=870 | time (s): 4.060 (total time: 255.640) Filter (dist only) r_work=0.1194 r_free=0.1352 | n_water=869 | time (s): 107.040 (total time: 362.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.525299 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.702537 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1353 0.0156 0.035 1.1 5.1 0.0 0.0 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.53 1.56 1.802 14.097 14.703 3.766 12.01 13.58 1.57 1.880 14.070 14.703 3.763 Individual atomic B min max mean iso aniso Overall: 5.58 66.96 14.86 0.96 503 3270 Protein: 5.58 32.68 10.61 0.96 0 2902 Water: 5.76 66.96 29.04 N/A 503 366 Other: 13.77 25.67 19.72 N/A 0 2 Chain A: 5.58 54.62 12.58 N/A 0 1624 Chain B: 5.58 66.96 12.36 N/A 0 1646 Chain S: 5.76 61.79 30.42 N/A 503 0 Histogram: Values Number of atoms 5.58 - 11.72 2142 11.72 - 17.86 711 17.86 - 24.00 336 24.00 - 30.13 194 30.13 - 36.27 165 36.27 - 42.41 129 42.41 - 48.55 65 48.55 - 54.68 23 54.68 - 60.82 6 60.82 - 66.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1358 r_work=0.1201 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1359 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762306 | | target function (ml) not normalized (work): 704634.767957 | | target function (ml) not normalized (free): 14749.704968 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1358 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1398 0.1397 0.1483 n_refl.: 191129 remove outliers: r(all,work,free)=0.1398 0.1397 0.1483 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1390 0.1389 0.1478 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1356 n_refl.: 191129 remove outliers: r(all,work,free)=0.1202 0.1199 0.1356 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 91.09 89 3 0.3472 356.664 332.031 0.423 0.952 0.231 13.296-10.522 97.03 97 1 0.2315 481.071 461.443 0.702 0.953 0.181 10.503-8.327 97.80 175 3 0.2133 501.780 494.998 0.859 0.953 0.145 8.318-6.595 100.00 360 8 0.2196 375.449 369.165 0.889 0.953 0.113 6.588-5.215 100.00 711 7 0.1935 345.000 334.493 0.882 0.953 0.093 5.214-4.128 98.38 1367 28 0.1206 504.630 499.358 0.970 0.954 0.070 4.126-3.266 94.74 2603 46 0.1127 459.998 453.279 1.029 0.954 0.000 3.266-2.585 99.86 5447 97 0.1101 310.303 307.020 1.016 0.954 0.000 2.585-2.046 97.45 10613 204 0.0942 234.106 231.655 1.028 0.954 0.000 2.046-1.619 99.39 21536 464 0.0923 138.556 137.252 1.050 0.954 0.000 1.619-1.281 98.00 42464 925 0.0985 74.590 73.876 1.046 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1656 40.014 38.356 1.033 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1399 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1356 | n_water=869 | time (s): 3.120 (total time: 3.120) Filter (dist) r_work=0.1199 r_free=0.1356 | n_water=868 | time (s): 104.440 (total time: 107.560) Filter (q & B) r_work=0.1199 r_free=0.1354 | n_water=859 | time (s): 4.700 (total time: 112.260) Compute maps r_work=0.1199 r_free=0.1354 | n_water=859 | time (s): 2.290 (total time: 114.550) Filter (map) r_work=0.1219 r_free=0.1353 | n_water=763 | time (s): 5.460 (total time: 120.010) Find peaks r_work=0.1219 r_free=0.1353 | n_water=763 | time (s): 0.670 (total time: 120.680) Add new water r_work=0.1229 r_free=0.1371 | n_water=997 | time (s): 4.600 (total time: 125.280) Refine new water occ: r_work=0.1193 r_free=0.1341 adp: r_work=0.1193 r_free=0.1341 occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1340 occ: r_work=0.1189 r_free=0.1341 adp: r_work=0.1189 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1341 r_work=0.1189 r_free=0.1341 | n_water=997 | time (s): 261.060 (total time: 386.340) Filter (q & B) r_work=0.1194 r_free=0.1346 | n_water=915 | time (s): 4.330 (total time: 390.670) Filter (dist only) r_work=0.1194 r_free=0.1346 | n_water=914 | time (s): 117.570 (total time: 508.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560377 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.618997 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1349 0.0152 0.036 1.1 6.5 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.49 1.52 1.768 14.082 14.619 3.762 11.99 13.53 1.54 1.906 14.045 14.619 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 65.83 14.90 0.91 548 3270 Protein: 5.58 29.71 10.50 0.91 0 2902 Water: 5.81 65.83 28.86 N/A 548 366 Other: 13.84 23.57 18.70 N/A 0 2 Chain A: 5.61 52.56 12.43 N/A 0 1624 Chain B: 5.58 65.83 12.23 N/A 0 1646 Chain S: 5.81 61.56 30.27 N/A 548 0 Histogram: Values Number of atoms 5.58 - 11.60 2112 11.60 - 17.63 759 17.63 - 23.65 301 23.65 - 29.68 240 29.68 - 35.70 173 35.70 - 41.73 128 41.73 - 47.75 69 47.75 - 53.78 27 53.78 - 59.80 6 59.80 - 65.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1353 r_work=0.1200 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1353 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758472 | | target function (ml) not normalized (work): 703916.791499 | | target function (ml) not normalized (free): 14743.378162 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1390 0.1388 0.1482 n_refl.: 191129 remove outliers: r(all,work,free)=0.1390 0.1388 0.1482 n_refl.: 191129 overall B=-0.23 to atoms: r(all,work,free)=0.1355 0.1353 0.1457 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1352 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1196 0.1352 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 91.09 89 3 0.3488 356.664 329.960 0.420 0.954 0.215 13.296-10.522 97.03 97 1 0.2361 481.071 460.281 0.710 0.955 0.152 10.503-8.327 97.80 175 3 0.2134 501.780 495.353 0.880 0.955 0.126 8.318-6.595 100.00 360 8 0.2166 375.449 369.713 0.910 0.955 0.104 6.588-5.215 100.00 711 7 0.1924 345.000 334.891 0.904 0.955 0.087 5.214-4.128 98.38 1367 28 0.1200 504.630 499.276 0.993 0.955 0.060 4.126-3.266 94.74 2603 46 0.1138 459.998 453.158 1.052 0.955 0.000 3.266-2.585 99.86 5447 97 0.1111 310.303 306.945 1.037 0.955 0.000 2.585-2.046 97.45 10613 204 0.0946 234.106 231.666 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0917 138.556 137.243 1.062 0.954 0.000 1.619-1.281 98.00 42464 925 0.0973 74.590 73.883 1.050 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.014 38.353 1.022 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0511 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1352 | n_water=914 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1197 r_free=0.1352 | n_water=914 | time (s): 110.010 (total time: 112.590) Filter (q & B) r_work=0.1197 r_free=0.1353 | n_water=903 | time (s): 5.340 (total time: 117.930) Compute maps r_work=0.1197 r_free=0.1353 | n_water=903 | time (s): 2.140 (total time: 120.070) Filter (map) r_work=0.1217 r_free=0.1355 | n_water=794 | time (s): 4.470 (total time: 124.540) Find peaks r_work=0.1217 r_free=0.1355 | n_water=794 | time (s): 0.580 (total time: 125.120) Add new water r_work=0.1224 r_free=0.1364 | n_water=1005 | time (s): 4.360 (total time: 129.480) Refine new water occ: r_work=0.1193 r_free=0.1338 adp: r_work=0.1193 r_free=0.1338 occ: r_work=0.1191 r_free=0.1338 adp: r_work=0.1191 r_free=0.1337 occ: r_work=0.1190 r_free=0.1337 adp: r_work=0.1190 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1337 r_work=0.1190 r_free=0.1337 | n_water=1005 | time (s): 200.860 (total time: 330.340) Filter (q & B) r_work=0.1194 r_free=0.1345 | n_water=925 | time (s): 4.480 (total time: 334.820) Filter (dist only) r_work=0.1194 r_free=0.1345 | n_water=924 | time (s): 118.740 (total time: 453.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.545736 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.249564 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1349 0.0152 0.036 1.1 5.5 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.49 1.52 1.724 13.803 14.250 3.759 11.99 13.52 1.53 1.784 13.780 14.250 3.757 Individual atomic B min max mean iso aniso Overall: 5.38 64.41 14.70 0.88 558 3270 Protein: 5.38 28.38 10.25 0.88 0 2902 Water: 5.73 64.41 28.69 N/A 558 366 Other: 13.66 22.18 17.92 N/A 0 2 Chain A: 5.44 52.26 12.13 N/A 0 1624 Chain B: 5.38 64.41 11.95 N/A 0 1646 Chain S: 5.73 61.22 30.32 N/A 558 0 Histogram: Values Number of atoms 5.38 - 11.28 2084 11.28 - 17.19 789 17.19 - 23.09 282 23.09 - 28.99 239 28.99 - 34.89 185 34.89 - 40.80 127 40.80 - 46.70 82 46.70 - 52.60 30 52.60 - 58.50 6 58.50 - 64.41 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1352 r_work=0.1199 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1352 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1354 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756925 | | target function (ml) not normalized (work): 703626.905577 | | target function (ml) not normalized (free): 14738.533005 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1354 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1361 0.1359 0.1474 n_refl.: 191129 remove outliers: r(all,work,free)=0.1361 0.1359 0.1474 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1368 0.1366 0.1479 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1188 0.1344 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1188 0.1344 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 91.09 89 3 0.3537 356.664 328.817 0.407 0.976 0.206 13.296-10.522 97.03 97 1 0.2407 481.071 459.327 0.701 0.977 0.156 10.503-8.327 97.80 175 3 0.2118 501.780 495.312 0.867 0.978 0.125 8.318-6.595 100.00 360 8 0.2156 375.449 369.363 0.895 0.977 0.099 6.588-5.215 100.00 711 7 0.1909 345.000 335.250 0.893 0.978 0.087 5.214-4.128 98.38 1367 28 0.1213 504.630 498.721 0.980 0.979 0.070 4.126-3.266 94.74 2603 46 0.1147 459.998 452.323 1.037 0.980 0.000 3.266-2.585 99.86 5447 97 0.1116 310.303 306.653 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0951 234.106 231.538 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0912 138.556 137.170 1.046 0.985 0.000 1.619-1.281 98.00 42464 925 0.0952 74.590 73.927 1.034 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.014 38.328 1.000 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0639 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1344 | n_water=924 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1189 r_free=0.1346 | n_water=923 | time (s): 116.090 (total time: 118.700) Filter (q & B) r_work=0.1189 r_free=0.1347 | n_water=915 | time (s): 4.130 (total time: 122.830) Compute maps r_work=0.1189 r_free=0.1347 | n_water=915 | time (s): 1.710 (total time: 124.540) Filter (map) r_work=0.1209 r_free=0.1346 | n_water=806 | time (s): 5.390 (total time: 129.930) Find peaks r_work=0.1209 r_free=0.1346 | n_water=806 | time (s): 0.590 (total time: 130.520) Add new water r_work=0.1216 r_free=0.1352 | n_water=993 | time (s): 4.140 (total time: 134.660) Refine new water occ: r_work=0.1186 r_free=0.1325 adp: r_work=0.1186 r_free=0.1325 occ: r_work=0.1185 r_free=0.1325 adp: r_work=0.1185 r_free=0.1325 occ: r_work=0.1183 r_free=0.1325 adp: r_work=0.1183 r_free=0.1324 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1324 r_work=0.1183 r_free=0.1324 | n_water=993 | time (s): 260.380 (total time: 395.040) Filter (q & B) r_work=0.1187 r_free=0.1339 | n_water=926 | time (s): 4.810 (total time: 399.850) Filter (dist only) r_work=0.1187 r_free=0.1339 | n_water=925 | time (s): 117.570 (total time: 517.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.604370 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.915994 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1343 0.0154 0.037 1.1 6.5 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.43 1.54 1.678 13.801 13.916 3.755 11.90 13.47 1.57 1.705 13.791 13.916 3.754 Individual atomic B min max mean iso aniso Overall: 5.49 63.45 14.75 0.87 559 3270 Protein: 5.49 28.01 10.31 0.87 0 2902 Water: 5.88 63.45 28.68 N/A 559 366 Other: 13.74 22.21 17.98 N/A 0 2 Chain A: 5.54 52.11 12.15 N/A 0 1624 Chain B: 5.49 63.45 11.98 N/A 0 1646 Chain S: 5.88 61.11 30.45 N/A 559 0 Histogram: Values Number of atoms 5.49 - 11.28 2062 11.28 - 17.08 815 17.08 - 22.88 271 22.88 - 28.67 231 28.67 - 34.47 194 34.47 - 40.26 125 40.26 - 46.06 86 46.06 - 51.86 33 51.86 - 57.65 9 57.65 - 63.45 3 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1347 r_work=0.1191 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1347 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1348 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753550 | | target function (ml) not normalized (work): 702994.798325 | | target function (ml) not normalized (free): 14729.021972 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1348 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1374 0.1372 0.1486 n_refl.: 191129 remove outliers: r(all,work,free)=0.1374 0.1372 0.1486 n_refl.: 191129 overall B=0.02 to atoms: r(all,work,free)=0.1377 0.1375 0.1487 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1345 n_refl.: 191129 remove outliers: r(all,work,free)=0.1191 0.1188 0.1345 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 91.09 89 3 0.3524 356.664 328.140 0.393 0.996 0.196 13.296-10.522 97.03 97 1 0.2377 481.071 459.984 0.681 0.997 0.139 10.503-8.327 97.80 175 3 0.2146 501.780 494.934 0.847 0.997 0.123 8.318-6.595 100.00 360 8 0.2153 375.449 369.444 0.874 0.997 0.090 6.588-5.215 100.00 711 7 0.1910 345.000 335.124 0.874 0.997 0.083 5.214-4.128 98.38 1367 28 0.1213 504.630 498.742 0.960 0.998 0.070 4.126-3.266 94.74 2603 46 0.1152 459.998 452.333 1.018 1.000 0.005 3.266-2.585 99.86 5447 97 0.1122 310.303 306.705 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0956 234.106 231.524 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0911 138.556 137.182 1.026 1.006 0.000 1.619-1.281 98.00 42464 925 0.0946 74.590 73.939 1.017 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.014 38.315 0.986 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0230 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1345 | n_water=925 | time (s): 2.920 (total time: 2.920) Filter (dist) r_work=0.1188 r_free=0.1345 | n_water=925 | time (s): 111.370 (total time: 114.290) Filter (q & B) r_work=0.1188 r_free=0.1345 | n_water=916 | time (s): 3.920 (total time: 118.210) Compute maps r_work=0.1188 r_free=0.1345 | n_water=916 | time (s): 1.880 (total time: 120.090) Filter (map) r_work=0.1207 r_free=0.1343 | n_water=816 | time (s): 5.530 (total time: 125.620) Find peaks r_work=0.1207 r_free=0.1343 | n_water=816 | time (s): 0.880 (total time: 126.500) Add new water r_work=0.1214 r_free=0.1347 | n_water=1004 | time (s): 5.040 (total time: 131.540) Refine new water occ: r_work=0.1186 r_free=0.1320 adp: r_work=0.1186 r_free=0.1320 occ: r_work=0.1184 r_free=0.1320 adp: r_work=0.1184 r_free=0.1319 occ: r_work=0.1183 r_free=0.1319 adp: r_work=0.1183 r_free=0.1319 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1319 r_work=0.1183 r_free=0.1319 | n_water=1004 | time (s): 171.510 (total time: 303.050) Filter (q & B) r_work=0.1187 r_free=0.1334 | n_water=936 | time (s): 4.910 (total time: 307.960) Filter (dist only) r_work=0.1187 r_free=0.1334 | n_water=934 | time (s): 118.200 (total time: 426.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.552711 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.531919 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 0.1191 0.1344 0.0153 0.038 1.1 5.6 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.44 1.53 1.677 13.785 13.532 3.755 11.92 13.47 1.55 1.681 13.783 13.532 3.754 Individual atomic B min max mean iso aniso Overall: 5.49 62.96 14.72 0.86 568 3270 Protein: 5.49 27.87 10.33 0.86 0 2902 Water: 5.97 62.96 28.34 N/A 568 366 Other: 13.80 22.18 17.99 N/A 0 2 Chain A: 5.59 52.04 12.15 N/A 0 1624 Chain B: 5.49 62.96 11.99 N/A 0 1646 Chain S: 5.97 61.04 29.99 N/A 568 0 Histogram: Values Number of atoms 5.49 - 11.23 2047 11.23 - 16.98 830 16.98 - 22.73 281 22.73 - 28.48 240 28.48 - 34.22 190 34.22 - 39.97 115 39.97 - 45.72 88 45.72 - 51.47 31 51.47 - 57.22 12 57.22 - 62.96 4 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1347 r_work=0.1192 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1348 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1350 target_work(ml) = 3.754 | | 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= 0.1192 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754064 | | target function (ml) not normalized (work): 703091.133625 | | target function (ml) not normalized (free): 14734.306282 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1387 0.1385 0.1498 n_refl.: 191129 remove outliers: r(all,work,free)=0.1387 0.1385 0.1498 n_refl.: 191129 overall B=-0.01 to atoms: r(all,work,free)=0.1386 0.1384 0.1498 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1349 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1349 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 90.10 88 3 0.3480 351.990 326.386 0.389 0.987 0.188 13.296-10.522 97.03 97 1 0.2387 481.071 459.194 0.680 0.988 0.121 10.503-8.327 97.80 175 3 0.2176 501.780 494.359 0.855 0.988 0.108 8.318-6.595 100.00 360 8 0.2145 375.449 369.610 0.880 0.988 0.084 6.588-5.215 100.00 711 7 0.1940 345.000 335.196 0.881 0.989 0.080 5.214-4.128 98.38 1367 28 0.1229 504.630 498.743 0.968 0.991 0.060 4.126-3.266 94.74 2603 46 0.1162 459.998 452.316 1.027 0.992 0.000 3.266-2.585 99.86 5447 97 0.1129 310.303 306.678 1.011 0.994 0.000 2.585-2.046 97.45 10613 204 0.0958 234.106 231.476 1.018 0.998 0.000 2.046-1.619 99.39 21536 464 0.0912 138.556 137.174 1.032 1.005 0.000 1.619-1.281 98.00 42464 925 0.0946 74.590 73.936 1.019 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.014 38.316 0.983 1.032 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0204 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1349 After: r_work=0.1192 r_free=0.1349 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1349 | n_water=934 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1192 r_free=0.1350 | n_water=933 | time (s): 124.530 (total time: 127.090) Filter (q & B) r_work=0.1193 r_free=0.1350 | n_water=922 | time (s): 4.990 (total time: 132.080) Compute maps r_work=0.1193 r_free=0.1350 | n_water=922 | time (s): 2.030 (total time: 134.110) Filter (map) r_work=0.1212 r_free=0.1349 | n_water=810 | time (s): 4.320 (total time: 138.430) Find peaks r_work=0.1212 r_free=0.1349 | n_water=810 | time (s): 0.840 (total time: 139.270) Add new water r_work=0.1218 r_free=0.1355 | n_water=1010 | time (s): 4.050 (total time: 143.320) Refine new water occ: r_work=0.1189 r_free=0.1331 adp: r_work=0.1189 r_free=0.1331 occ: r_work=0.1188 r_free=0.1330 adp: r_work=0.1188 r_free=0.1329 occ: r_work=0.1187 r_free=0.1328 adp: r_work=0.1187 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1328 r_work=0.1187 r_free=0.1328 | n_water=1010 | time (s): 235.080 (total time: 378.400) Filter (q & B) r_work=0.1191 r_free=0.1342 | n_water=931 | time (s): 5.310 (total time: 383.710) Filter (dist only) r_work=0.1191 r_free=0.1341 | n_water=929 | time (s): 120.460 (total time: 504.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.500601 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.746317 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 0.1194 0.1347 0.0152 0.038 1.1 6.8 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.47 1.52 1.675 13.786 13.746 3.757 11.95 13.48 1.54 1.676 13.787 13.746 3.755 Individual atomic B min max mean iso aniso Overall: 5.56 62.01 14.72 0.85 563 3270 Protein: 5.56 27.80 10.34 0.85 0 2902 Water: 6.00 62.01 28.40 N/A 563 366 Other: 13.85 22.22 18.04 N/A 0 2 Chain A: 5.66 51.92 12.13 N/A 0 1624 Chain B: 5.56 62.01 11.98 N/A 0 1646 Chain S: 6.00 60.92 30.22 N/A 563 0 Histogram: Values Number of atoms 5.56 - 11.20 2035 11.20 - 16.85 836 16.85 - 22.49 276 22.49 - 28.14 216 28.14 - 33.79 202 33.79 - 39.43 126 39.43 - 45.08 91 45.08 - 50.72 35 50.72 - 56.37 12 56.37 - 62.01 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1348 r_work=0.1195 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1348 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1348 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755475 | | target function (ml) not normalized (work): 703351.626407 | | target function (ml) not normalized (free): 14737.918287 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1352 0.1425 5.6777 5.7641| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1296 5.075 5.1568| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1192 4.6593 4.752| | 4: 2.04 - 1.85 1.00 7170 155 0.0908 0.1088 4.4005 4.6092| | 5: 1.85 - 1.72 0.99 7113 159 0.0938 0.1004 4.1567 4.2453| | 6: 1.72 - 1.62 0.99 7102 142 0.0897 0.1089 3.9502 4.0813| | 7: 1.62 - 1.54 0.99 7104 148 0.0894 0.0952 3.8011 3.929| | 8: 1.54 - 1.47 0.96 6798 152 0.0894 0.1317 3.704 3.9091| | 9: 1.47 - 1.41 0.98 6938 155 0.0930 0.1124 3.6249 3.7611| | 10: 1.41 - 1.36 0.99 7022 150 0.0981 0.1180 3.5586 3.6787| | 11: 1.36 - 1.32 0.99 6997 151 0.0997 0.1130 3.4875 3.5855| | 12: 1.32 - 1.28 0.98 6975 149 0.1038 0.1127 3.4607 3.58| | 13: 1.28 - 1.25 0.98 6907 166 0.1047 0.1240 3.4398 3.568| | 14: 1.25 - 1.22 0.98 7015 112 0.1111 0.1592 3.435 3.6805| | 15: 1.22 - 1.19 0.98 6956 137 0.1175 0.1258 3.4517 3.5004| | 16: 1.19 - 1.17 0.93 6604 132 0.1253 0.1554 3.4672 3.6613| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1236 3.4345 3.4459| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1710 3.4384 3.531| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1758 3.4201 3.5989| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1581 3.4109 3.4395| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2139 3.4186 3.502| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1960 3.4129 3.4145| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2016 3.4329 3.4843| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2251 3.4357 3.5091| | 25: 1.02 - 1.01 0.93 6552 130 0.2619 0.2503 3.4492 3.5235| | 26: 1.01 - 0.99 0.96 6767 158 0.2760 0.2867 3.4156 3.4237| | 27: 0.99 - 0.98 0.94 6647 131 0.3046 0.2805 3.4689 3.3948| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.54 1.00 0.95 11021.21| | 2: 2.94 - 2.33 7339 128 0.93 12.81 0.99 0.95 5090.78| | 3: 2.33 - 2.04 6939 150 0.96 7.73 1.01 0.95 1730.25| | 4: 2.04 - 1.85 7170 155 0.96 7.87 1.00 0.95 1037.06| | 5: 1.85 - 1.72 7113 159 0.96 8.21 1.00 0.96 647.19| | 6: 1.72 - 1.62 7102 142 0.96 8.06 1.00 0.96 448.74| | 7: 1.62 - 1.54 7104 148 0.96 8.18 1.01 0.97 338.68| | 8: 1.54 - 1.47 6798 152 0.96 8.35 1.01 0.97 282.38| | 9: 1.47 - 1.41 6938 155 0.96 8.54 1.00 0.97 233.33| | 10: 1.41 - 1.36 7022 150 0.96 8.99 1.00 0.97 204.02| | 11: 1.36 - 1.32 6997 151 0.96 8.95 0.99 0.96 175.21| | 12: 1.32 - 1.28 6975 149 0.96 8.96 0.98 0.95 160.47| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.96 158.80| | 14: 1.25 - 1.22 7015 112 0.95 10.79 1.01 0.96 164.56| | 15: 1.22 - 1.19 6956 137 0.94 11.36 1.01 0.98 168.78| | 16: 1.19 - 1.17 6604 132 0.95 11.52 1.01 0.96 161.95| | 17: 1.17 - 1.14 6940 135 0.94 12.30 1.01 0.96 154.95| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.94 148.10| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.94 151.65| | 20: 1.10 - 1.08 6884 147 0.92 15.27 1.00 0.93 150.88| | 21: 1.08 - 1.07 6852 152 0.91 16.69 1.00 0.93 153.72| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.92 154.93| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.92 164.35| | 24: 1.03 - 1.02 6784 133 0.85 23.14 0.99 0.92 178.74| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.97 0.89 181.75| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.88 176.41| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.98 0.87 160.89| |alpha: min = 0.87 max = 0.98 mean = 0.94| |beta: min = 148.10 max = 11021.21 mean = 920.57| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.33| |phase err.(test): min = 0.00 max = 89.61 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1348 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1396 0.1394 0.1503 n_refl.: 191128 remove outliers: r(all,work,free)=0.1396 0.1394 0.1503 n_refl.: 191128 overall B=-0.05 to atoms: r(all,work,free)=0.1388 0.1386 0.1497 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1348 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 90.10 88 3 0.3504 351.990 322.960 0.385 0.976 0.200 13.296-10.522 97.03 97 1 0.2387 481.071 458.879 0.673 0.977 0.136 10.503-8.327 97.80 175 3 0.2155 501.780 495.102 0.841 0.978 0.106 8.318-6.595 100.00 360 8 0.2138 375.449 369.982 0.867 0.978 0.087 6.588-5.215 100.00 711 7 0.1930 345.000 335.562 0.867 0.978 0.080 5.214-4.128 98.38 1367 28 0.1231 504.630 498.538 0.955 0.979 0.070 4.126-3.266 94.74 2603 46 0.1166 459.998 452.110 1.014 0.980 0.005 3.266-2.585 99.86 5447 97 0.1126 310.303 306.735 0.998 0.982 0.000 2.585-2.046 97.45 10613 204 0.0963 234.106 231.470 1.005 0.984 0.000 2.046-1.619 99.39 21536 464 0.0916 138.556 137.157 1.020 0.988 0.000 1.619-1.281 98.00 42464 925 0.0948 74.590 73.934 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.014 38.305 0.979 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0116 ================= 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 0.1994 0.081 5.250 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1925 0.081 5.250 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1925 0.081 5.250 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1925 0.081 5.250 5.2 78.0 14.6 805 0.000 1_weight: 0.1800 0.1925 0.081 5.250 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1273 0.1480 0.035 1.167 5.2 78.0 14.6 805 0.140 1_adp: 0.1304 0.1553 0.035 1.167 5.3 73.0 15.0 805 0.140 1_regHadp: 0.1303 0.1548 0.035 1.167 5.3 73.0 15.0 805 0.140 1_occ: 0.1287 0.1536 0.035 1.167 5.3 73.0 15.0 805 0.140 2_bss: 0.1279 0.1528 0.035 1.167 5.4 73.2 15.2 805 0.140 2_settarget: 0.1279 0.1528 0.035 1.167 5.4 73.2 15.2 805 0.140 2_updatecdl: 0.1279 0.1528 0.035 1.183 5.4 73.2 15.2 805 0.140 2_nqh: 0.1279 0.1528 0.035 1.183 5.4 73.2 15.2 805 0.140 2_sol: 0.1271 0.1499 0.035 1.183 5.4 73.2 16.4 910 n/a 2_weight: 0.1271 0.1499 0.035 1.183 5.4 73.2 16.4 910 n/a 2_xyzrec: 0.1253 0.1505 0.039 1.159 5.4 73.2 16.4 910 n/a 2_adp: 0.1234 0.1496 0.039 1.159 5.4 68.2 16.5 910 n/a 2_regHadp: 0.1234 0.1498 0.039 1.159 5.4 68.2 16.5 910 n/a 2_occ: 0.1228 0.1491 0.039 1.159 5.4 68.2 16.5 910 n/a 3_bss: 0.1235 0.1498 0.039 1.159 5.4 68.2 16.5 910 n/a 3_settarget: 0.1235 0.1498 0.039 1.159 5.4 68.2 16.5 910 n/a 3_updatecdl: 0.1235 0.1498 0.039 1.162 5.4 68.2 16.5 910 n/a 3_nqh: 0.1235 0.1498 0.039 1.162 5.4 68.2 16.5 910 n/a 3_sol: 0.1253 0.1487 0.039 1.162 5.4 68.2 15.5 884 n/a 3_weight: 0.1253 0.1487 0.039 1.162 5.4 68.2 15.5 884 n/a 3_xyzrec: 0.1243 0.1426 0.035 1.099 5.4 68.2 15.5 884 n/a 3_adp: 0.1234 0.1382 0.035 1.099 5.5 67.7 15.3 884 n/a 3_regHadp: 0.1235 0.1382 0.035 1.099 5.5 67.7 15.3 884 n/a 3_occ: 0.1229 0.1377 0.035 1.099 5.5 67.7 15.3 884 n/a 4_bss: 0.1225 0.1369 0.035 1.099 5.5 67.7 15.3 884 n/a 4_settarget: 0.1225 0.1369 0.035 1.099 5.5 67.7 15.3 884 n/a 4_updatecdl: 0.1225 0.1369 0.035 1.103 5.5 67.7 15.3 884 n/a 4_nqh: 0.1225 0.1369 0.035 1.103 5.5 67.7 15.3 884 n/a 4_sol: 0.1224 0.1365 0.035 1.103 5.5 67.7 15.2 884 n/a 4_weight: 0.1224 0.1365 0.035 1.103 5.5 67.7 15.2 884 n/a 4_xyzrec: 0.1222 0.1366 0.036 1.125 5.5 67.7 15.2 884 n/a 4_adp: 0.1216 0.1366 0.036 1.125 5.5 67.4 15.1 884 n/a 4_regHadp: 0.1216 0.1366 0.036 1.125 5.5 67.4 15.1 884 n/a 4_occ: 0.1214 0.1361 0.036 1.125 5.5 67.4 15.1 884 n/a 5_bss: 0.1212 0.1361 0.036 1.125 5.5 67.3 15.1 884 n/a 5_settarget: 0.1212 0.1361 0.036 1.125 5.5 67.3 15.1 884 n/a 5_updatecdl: 0.1212 0.1361 0.036 1.125 5.5 67.3 15.1 884 n/a 5_nqh: 0.1212 0.1361 0.036 1.125 5.5 67.3 15.1 884 n/a 5_sol: 0.1194 0.1352 0.036 1.125 5.5 67.3 14.9 869 n/a 5_weight: 0.1194 0.1352 0.036 1.125 5.5 67.3 14.9 869 n/a 5_xyzrec: 0.1197 0.1353 0.035 1.120 5.5 67.3 14.9 869 n/a 5_adp: 0.1201 0.1358 0.035 1.120 5.6 67.0 14.9 869 n/a 5_regHadp: 0.1201 0.1359 0.035 1.120 5.6 67.0 14.9 869 n/a 5_occ: 0.1200 0.1358 0.035 1.120 5.6 67.0 14.9 869 n/a 6_bss: 0.1199 0.1356 0.035 1.120 5.5 66.9 14.8 869 n/a 6_settarget: 0.1199 0.1356 0.035 1.120 5.5 66.9 14.8 869 n/a 6_updatecdl: 0.1199 0.1356 0.035 1.120 5.5 66.9 14.8 869 n/a 6_nqh: 0.1199 0.1356 0.035 1.120 5.5 66.9 14.8 869 n/a 6_sol: 0.1194 0.1346 0.035 1.120 5.5 66.9 15.0 914 n/a 6_weight: 0.1194 0.1346 0.035 1.120 5.5 66.9 15.0 914 n/a 6_xyzrec: 0.1197 0.1349 0.036 1.126 5.5 66.9 15.0 914 n/a 6_adp: 0.1199 0.1353 0.036 1.126 5.6 65.8 14.9 914 n/a 6_regHadp: 0.1200 0.1353 0.036 1.126 5.6 65.8 14.9 914 n/a 6_occ: 0.1198 0.1355 0.036 1.126 5.6 65.8 14.9 914 n/a 7_bss: 0.1197 0.1352 0.036 1.126 5.3 65.6 14.7 914 n/a 7_settarget: 0.1197 0.1352 0.036 1.126 5.3 65.6 14.7 914 n/a 7_updatecdl: 0.1197 0.1352 0.036 1.127 5.3 65.6 14.7 914 n/a 7_nqh: 0.1197 0.1352 0.036 1.127 5.3 65.6 14.7 914 n/a 7_sol: 0.1194 0.1345 0.036 1.127 5.3 65.6 14.7 924 n/a 7_weight: 0.1194 0.1345 0.036 1.127 5.3 65.6 14.7 924 n/a 7_xyzrec: 0.1197 0.1349 0.036 1.122 5.3 65.6 14.7 924 n/a 7_adp: 0.1199 0.1352 0.036 1.122 5.4 64.4 14.7 924 n/a 7_regHadp: 0.1199 0.1352 0.036 1.122 5.4 64.4 14.7 924 n/a 7_occ: 0.1197 0.1354 0.036 1.122 5.4 64.4 14.7 924 n/a 8_bss: 0.1188 0.1344 0.036 1.122 5.4 64.5 14.8 924 n/a 8_settarget: 0.1188 0.1344 0.036 1.122 5.4 64.5 14.8 924 n/a 8_updatecdl: 0.1188 0.1344 0.036 1.123 5.4 64.5 14.8 924 n/a 8_nqh: 0.1188 0.1344 0.036 1.123 5.4 64.5 14.8 924 n/a 8_sol: 0.1187 0.1339 0.036 1.123 5.4 64.5 14.8 925 n/a 8_weight: 0.1187 0.1339 0.036 1.123 5.4 64.5 14.8 925 n/a 8_xyzrec: 0.1190 0.1343 0.037 1.129 5.4 64.5 14.8 925 n/a 8_adp: 0.1190 0.1347 0.037 1.129 5.5 63.4 14.7 925 n/a 8_regHadp: 0.1191 0.1347 0.037 1.129 5.5 63.4 14.7 925 n/a 8_occ: 0.1189 0.1348 0.037 1.129 5.5 63.4 14.7 925 n/a 9_bss: 0.1188 0.1345 0.037 1.129 5.5 63.5 14.8 925 n/a 9_settarget: 0.1188 0.1345 0.037 1.129 5.5 63.5 14.8 925 n/a 9_updatecdl: 0.1188 0.1345 0.037 1.128 5.5 63.5 14.8 925 n/a 9_nqh: 0.1188 0.1345 0.037 1.128 5.5 63.5 14.8 925 n/a 9_sol: 0.1187 0.1334 0.037 1.128 5.5 63.5 14.7 934 n/a 9_weight: 0.1187 0.1334 0.037 1.128 5.5 63.5 14.7 934 n/a 9_xyzrec: 0.1191 0.1344 0.038 1.119 5.5 63.5 14.7 934 n/a 9_adp: 0.1192 0.1347 0.038 1.119 5.5 63.0 14.7 934 n/a 9_regHadp: 0.1192 0.1348 0.038 1.119 5.5 63.0 14.7 934 n/a 9_occ: 0.1192 0.1350 0.038 1.119 5.5 63.0 14.7 934 n/a 10_bss: 0.1191 0.1349 0.038 1.119 5.5 63.0 14.7 934 n/a 10_settarget: 0.1191 0.1349 0.038 1.119 5.5 63.0 14.7 934 n/a 10_updatecdl: 0.1191 0.1349 0.038 1.119 5.5 63.0 14.7 934 n/a 10_setrh: 0.1192 0.1349 0.038 1.119 5.5 63.0 14.7 934 n/a 10_nqh: 0.1192 0.1349 0.038 1.119 5.5 63.0 14.7 934 n/a 10_sol: 0.1191 0.1341 0.038 1.119 5.5 63.0 14.7 929 n/a 10_weight: 0.1191 0.1341 0.038 1.119 5.5 63.0 14.7 929 n/a 10_xyzrec: 0.1194 0.1347 0.038 1.147 5.5 63.0 14.7 929 n/a 10_adp: 0.1195 0.1348 0.038 1.147 5.6 62.0 14.7 929 n/a 10_regHadp: 0.1195 0.1348 0.038 1.147 5.6 62.0 14.7 929 n/a 10_occ: 0.1194 0.1348 0.038 1.147 5.6 62.0 14.7 929 n/a end: 0.1193 0.1348 0.038 1.147 5.5 62.0 14.7 929 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7450704_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7450704_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.6200 Refinement macro-cycles (run) : 11870.4400 Write final files (write_after_run_outputs) : 166.3700 Total : 12044.4300 Total CPU time: 3.36 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:38:02 PST -0800 (1736735882.96 s) Start R-work = 0.1800, R-free = 0.1925 Final R-work = 0.1193, R-free = 0.1348 =============================================================================== Job complete usr+sys time: 12368.05 seconds wall clock time: 207 minutes 12.40 seconds (12432.40 seconds total)