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_7307888.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" 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_7307888.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7307888.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.74, per 1000 atoms: 0.26 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: 2.802 distance_ideal: 2.720 ideal - model: -0.082 slack: 0.000 delta_slack: -0.082 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: 2.739 distance_ideal: 2.710 ideal - model: -0.029 slack: 0.000 delta_slack: -0.029 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 131.8 milliseconds Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.04: 904 1.04 - 1.26: 2419 1.26 - 1.48: 1433 1.48 - 1.70: 1144 1.70 - 1.92: 34 Bond restraints: 5934 Sorted by residual: bond pdb=" N TYR B 67 " pdb=" CA TYR B 67 " ideal model delta sigma weight residual 1.455 1.713 -0.258 1.22e-02 6.72e+03 4.46e+02 bond pdb=" N LEU B 172 " pdb=" H LEU B 172 " ideal model delta sigma weight residual 0.860 1.241 -0.381 2.00e-02 2.50e+03 3.64e+02 bond pdb=" N VAL B 181 " pdb=" H VAL B 181 " ideal model delta sigma weight residual 0.860 1.235 -0.375 2.00e-02 2.50e+03 3.51e+02 bond pdb=" C ARG B 175 " pdb=" O ARG B 175 " ideal model delta sigma weight residual 1.236 1.452 -0.215 1.15e-02 7.56e+03 3.50e+02 bond pdb=" N ILE B 45 " pdb=" H ILE B 45 " ideal model delta sigma weight residual 0.860 1.233 -0.373 2.00e-02 2.50e+03 3.47e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 5729 4.18 - 8.37: 3570 8.37 - 12.55: 1292 12.55 - 16.73: 199 16.73 - 20.91: 20 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O PHE A 127 " pdb=" C PHE A 127 " pdb=" N PRO A 128 " ideal model delta sigma weight residual 121.38 136.75 -15.37 8.20e-01 1.49e+00 3.52e+02 angle pdb=" O GLY A 99 " pdb=" C GLY A 99 " pdb=" N ARG A 100 " ideal model delta sigma weight residual 122.45 140.75 -18.30 1.17e+00 7.31e-01 2.45e+02 angle pdb=" O GLY B 78 " pdb=" C GLY B 78 " pdb=" N ALA B 79 " ideal model delta sigma weight residual 122.19 136.76 -14.57 9.60e-01 1.09e+00 2.30e+02 angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.38 109.47 9.91 6.80e-01 2.16e+00 2.12e+02 angle pdb=" O ARG A 143 " pdb=" C ARG A 143 " pdb=" N VAL A 144 " ideal model delta sigma weight residual 122.07 136.67 -14.60 1.03e+00 9.43e-01 2.01e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.48: 1827 16.48 - 32.96: 146 32.96 - 49.44: 53 49.44 - 65.92: 20 65.92 - 82.40: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CG TRP A 146 " pdb=" CD2 TRP A 146 " pdb=" CE3 TRP A 146 " pdb=" HE3 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 -27.28 27.28 0 5.00e+00 4.00e-02 2.98e+01 dihedral pdb=" CB TRP A 139 " pdb=" CG TRP A 139 " pdb=" CD1 TRP A 139 " pdb=" HD1 TRP A 139 " ideal model delta harmonic sigma weight residual 0.00 26.69 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 153.46 26.54 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.251: 236 0.251 - 0.502: 159 0.502 - 0.753: 68 0.753 - 1.004: 26 1.004 - 1.255: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA SER B 13 " pdb=" N SER B 13 " pdb=" C SER B 13 " pdb=" CB SER B 13 " both_signs ideal model delta sigma weight residual False 2.51 3.77 -1.26 2.00e-01 2.50e+01 3.94e+01 chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -3.73 1.10 2.00e-01 2.50e+01 3.05e+01 chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.62e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.129 2.00e-02 2.50e+03 7.38e-02 2.18e+02 pdb=" CG TRP A 146 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.101 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.129 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.109 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.073 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.040 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.058 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.082 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.033 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.045 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.160 2.00e-02 2.50e+03 6.68e-02 1.79e+02 pdb=" CG TRP B 146 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.080 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " -0.036 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.054 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.063 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.006 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.127 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.044 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.060 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.120 2.00e-02 2.50e+03 7.70e-02 1.78e+02 pdb=" CG PHE B 164 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.114 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.085 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.124 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.114 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.040 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.022 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " -0.040 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.62: 31 1.62 - 2.36: 2422 2.36 - 3.11: 22314 3.11 - 3.85: 32918 3.85 - 4.60: 52547 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110232 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.872 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.928 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.038 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.068 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.168 2.620 ... (remaining 110227 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_7307888_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= 0.2028 r_free= 0.1969 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.296318 | | target function (ml) not normalized (work): 804756.294403 | | target function (ml) not normalized (free): 16499.424916 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2135 0.1855 6.7023 6.2924| | 2: 2.94 - 2.33 1.00 7339 128 0.1609 0.1700 5.5308 5.5803| | 3: 2.33 - 2.04 0.96 6939 150 0.1630 0.1611 5.1466 5.1436| | 4: 2.04 - 1.85 1.00 7170 155 0.1765 0.1479 4.9785 5.0043| | 5: 1.85 - 1.72 0.99 7113 159 0.1910 0.1669 4.7871 4.7553| | 6: 1.72 - 1.62 0.99 7102 142 0.1960 0.2149 4.6594 4.8118| | 7: 1.62 - 1.54 0.99 7104 148 0.2000 0.1785 4.5588 4.5919| | 8: 1.54 - 1.47 0.96 6798 152 0.2019 0.2189 4.4635 4.4561| | 9: 1.47 - 1.41 0.98 6938 155 0.2068 0.2196 4.379 4.4317| | 10: 1.41 - 1.36 0.99 7022 150 0.2114 0.2056 4.3034 4.3423| | 11: 1.36 - 1.32 0.99 6997 151 0.2134 0.2149 4.2391 4.2467| | 12: 1.32 - 1.28 0.98 6976 149 0.2050 0.2207 4.159 4.2938| | 13: 1.28 - 1.25 0.98 6907 166 0.2015 0.1899 4.1086 4.0941| | 14: 1.25 - 1.22 0.98 7015 113 0.2077 0.2466 4.0634 4.2601| | 15: 1.22 - 1.19 0.98 6957 137 0.2088 0.1909 4.0296 4.0322| | 16: 1.19 - 1.17 0.93 6604 132 0.2094 0.2037 3.9877 3.9639| | 17: 1.17 - 1.14 0.98 6941 135 0.2162 0.1969 3.955 3.9646| | 18: 1.14 - 1.12 0.98 6875 142 0.2237 0.2330 3.9255 3.8997| | 19: 1.12 - 1.10 0.97 6949 106 0.2302 0.2362 3.8805 3.916| | 20: 1.10 - 1.08 0.97 6884 147 0.2297 0.2253 3.8175 3.8383| | 21: 1.08 - 1.07 0.97 6852 152 0.2422 0.2649 3.7858 3.7788| | 22: 1.07 - 1.05 0.97 6838 135 0.2550 0.2728 3.7477 3.813| | 23: 1.05 - 1.03 0.97 6829 159 0.2710 0.2582 3.7308 3.7671| | 24: 1.03 - 1.02 0.96 6785 133 0.2900 0.2733 3.7057 3.7622| | 25: 1.02 - 1.01 0.93 6552 130 0.3046 0.2996 3.6737 3.7247| | 26: 1.01 - 0.99 0.96 6767 158 0.3210 0.3329 3.6288 3.6281| | 27: 0.99 - 0.98 0.94 6648 131 0.3435 0.3435 3.6377 3.6058| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.05 0.91 0.97 34216.53| | 2: 2.94 - 2.33 7339 128 0.86 21.05 1.09 1.01 14765.42| | 3: 2.33 - 2.04 6939 150 0.93 12.59 1.11 1.04 4141.60| | 4: 2.04 - 1.85 7170 155 0.93 13.16 1.11 1.06 2644.34| | 5: 1.85 - 1.72 7113 159 0.91 15.02 1.11 1.07 1972.18| | 6: 1.72 - 1.62 7102 142 0.90 16.68 1.11 1.08 1645.48| | 7: 1.62 - 1.54 7104 148 0.89 17.64 1.11 1.08 1352.28| | 8: 1.54 - 1.47 6798 152 0.89 18.16 1.10 1.07 1138.87| | 9: 1.47 - 1.41 6938 155 0.89 18.48 1.11 1.07 945.11| | 10: 1.41 - 1.36 7022 150 0.87 19.58 1.09 1.06 820.17| | 11: 1.36 - 1.32 6997 151 0.88 19.60 1.09 1.04 705.76| | 12: 1.32 - 1.28 6976 149 0.88 19.66 1.08 1.04 638.25| | 13: 1.28 - 1.25 6907 166 0.88 19.54 1.08 1.03 581.22| | 14: 1.25 - 1.22 7015 113 0.87 19.85 1.08 1.03 526.98| | 15: 1.22 - 1.19 6957 137 0.88 19.55 1.08 1.03 480.53| | 16: 1.19 - 1.17 6604 132 0.89 18.89 1.07 1.03 424.77| | 17: 1.17 - 1.14 6941 135 0.88 19.68 1.08 1.04 402.94| | 18: 1.14 - 1.12 6875 142 0.87 20.09 1.08 1.02 370.57| | 19: 1.12 - 1.10 6949 106 0.86 21.27 1.07 1.02 357.43| | 20: 1.10 - 1.08 6884 147 0.86 21.85 1.06 1.00 330.80| | 21: 1.08 - 1.07 6852 152 0.85 23.10 1.06 0.99 321.33| | 22: 1.07 - 1.05 6838 135 0.83 25.04 1.05 0.98 316.92| | 23: 1.05 - 1.03 6829 159 0.81 26.86 1.05 0.98 320.52| | 24: 1.03 - 1.02 6785 133 0.78 29.09 1.04 0.98 323.93| | 25: 1.02 - 1.01 6552 130 0.77 30.38 1.03 0.94 310.27| | 26: 1.01 - 0.99 6767 158 0.74 33.05 1.04 0.91 302.73| | 27: 0.99 - 0.98 6648 131 0.73 34.31 1.04 0.88 297.76| |alpha: min = 0.88 max = 1.08 mean = 1.02| |beta: min = 297.76 max = 34216.53 mean = 2739.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.97 mean = 21.18| |phase err.(test): min = 0.00 max = 89.98 mean = 21.33| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.261 2950 Z= 5.305 Angle : 5.013 18.304 4018 Z= 3.581 Chirality : 0.389 1.255 492 Planarity : 0.034 0.113 512 Dihedral : 12.657 82.402 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 1.61 % Allowed : 2.58 % Favored : 95.81 % Cbeta Deviations : 33.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.37), residues: 386 helix: -2.45 (0.32), residues: 144 sheet: -1.07 (0.52), residues: 86 loop : -0.72 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.018 ARG A 175 TYR 0.127 0.038 TYR A 195 PHE 0.114 0.035 PHE B 164 TRP 0.147 0.048 TRP A 146 HIS 0.065 0.030 HIS B 179 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= 0.2028 r_free= 0.1969 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.296318 | | target function (ml) not normalized (work): 804756.294403 | | target function (ml) not normalized (free): 16499.424916 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2026 0.2028 0.1969 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2026 0.2028 0.1969 n_refl.: 191155 remove outliers: r(all,work,free)=0.2026 0.2028 0.1969 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2026 0.2028 0.1969 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1795 0.1793 0.1903 n_refl.: 191145 remove outliers: r(all,work,free)=0.1793 0.1791 0.1903 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4076 402.814 293.271 0.433 0.913 0.297 13.296-10.522 99.01 99 1 0.2482 528.187 519.067 0.786 0.915 0.248 10.503-8.327 98.90 177 3 0.2497 564.205 558.538 0.973 0.915 0.227 8.318-6.595 100.00 360 8 0.2461 414.736 403.479 0.966 0.915 0.175 6.588-5.215 100.00 711 7 0.2256 381.101 366.365 0.956 0.915 0.160 5.214-4.128 98.38 1367 28 0.1497 557.435 549.638 1.071 0.915 0.070 4.126-3.266 94.74 2603 46 0.1333 508.132 499.188 1.144 0.916 0.038 3.266-2.585 99.86 5447 97 0.1426 342.774 337.517 1.119 0.915 0.010 2.585-2.046 97.45 10613 204 0.1381 258.603 254.500 1.122 0.914 0.000 2.046-1.619 99.39 21536 464 0.1621 153.054 149.904 1.140 0.913 0.000 1.619-1.281 98.00 42464 925 0.1906 82.395 80.223 1.128 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2315 44.203 41.651 1.111 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0018 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1791 r_free=0.1903 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1791 r_free=0.1903 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.814869 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 578.736567 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1503 0.0230 0.039 1.2 10.9 0.0 0.0 0 11.407 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.03 2.30 1.118 13.111 578.737 0.018 12.98 15.70 2.72 1.243 13.327 578.737 0.017 Individual atomic B min max mean iso aniso Overall: 5.14 73.04 14.99 1.40 435 3274 Protein: 5.14 40.32 10.99 1.40 0 2902 Water: 6.34 73.04 29.39 N/A 435 370 Other: 16.07 30.02 23.04 N/A 0 2 Chain A: 5.34 59.92 13.03 N/A 0 1626 Chain B: 5.14 73.04 12.75 N/A 0 1648 Chain S: 11.39 64.26 30.83 N/A 435 0 Histogram: Values Number of atoms 5.14 - 11.93 2160 11.93 - 18.72 643 18.72 - 25.51 313 25.51 - 32.30 271 32.30 - 39.09 153 39.09 - 45.88 106 45.88 - 52.67 39 52.67 - 59.46 19 59.46 - 66.25 4 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1570 r_work=0.1297 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1567 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015534 | | target function (ls_wunit_k1) not normalized (work): 2909.376937 | | target function (ls_wunit_k1) not normalized (free): 116.842711 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1556 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1468 0.1466 0.1631 n_refl.: 191138 remove outliers: r(all,work,free)=0.1468 0.1466 0.1631 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1493 0.1490 0.1641 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1546 n_refl.: 191138 remove outliers: r(all,work,free)=0.1280 0.1275 0.1545 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3613 402.814 380.886 0.470 0.997 0.275 13.296-10.522 99.01 99 1 0.2105 528.187 520.925 0.714 0.999 0.250 10.503-8.327 98.90 177 3 0.1704 564.205 561.820 0.856 0.999 0.203 8.318-6.595 100.00 360 8 0.1717 414.736 411.959 0.876 0.998 0.160 6.588-5.215 100.00 711 7 0.1532 381.101 373.454 0.858 0.999 0.160 5.214-4.128 98.38 1367 28 0.0901 557.435 554.965 0.942 0.999 0.055 4.126-3.266 94.74 2603 46 0.0828 508.132 504.350 1.008 1.000 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.321 0.991 0.999 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.391 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1091 153.054 151.361 1.019 0.999 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.404 1.011 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.167 0.989 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0388 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1545 | n_water=805 | time (s): 2.990 (total time: 2.990) Filter (dist) r_work=0.1279 r_free=0.1550 | n_water=795 | time (s): 100.510 (total time: 103.500) Filter (q & B) r_work=0.1280 r_free=0.1551 | n_water=791 | time (s): 4.350 (total time: 107.850) Compute maps r_work=0.1280 r_free=0.1551 | n_water=791 | time (s): 1.980 (total time: 109.830) Filter (map) r_work=0.1305 r_free=0.1535 | n_water=653 | time (s): 4.140 (total time: 113.970) Find peaks r_work=0.1305 r_free=0.1535 | n_water=653 | time (s): 0.650 (total time: 114.620) Add new water r_work=0.1329 r_free=0.1571 | n_water=960 | time (s): 4.560 (total time: 119.180) Refine new water occ: r_work=0.1285 r_free=0.1515 adp: r_work=0.1272 r_free=0.1512 occ: r_work=0.1275 r_free=0.1508 adp: r_work=0.1268 r_free=0.1508 occ: r_work=0.1269 r_free=0.1503 adp: r_work=0.1266 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1504 r_work=0.1266 r_free=0.1504 | n_water=960 | time (s): 86.220 (total time: 205.400) Filter (q & B) r_work=0.1269 r_free=0.1506 | n_water=897 | time (s): 4.270 (total time: 209.670) Filter (dist only) r_work=0.1270 r_free=0.1505 | n_water=896 | time (s): 112.760 (total time: 322.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.260785 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 599.836398 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1253 0.1521 0.0268 0.041 1.1 19.2 0.0 0.0 0 11.630 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.21 2.68 2.041 15.210 599.836 0.014 12.30 15.07 2.77 2.408 15.264 599.836 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 69.73 16.39 1.20 528 3272 Protein: 5.40 40.27 10.98 1.20 0 2902 Water: 6.61 69.73 33.87 N/A 528 368 Other: 16.40 32.44 24.42 N/A 0 2 Chain A: 5.57 56.32 12.99 N/A 0 1624 Chain B: 5.40 68.21 12.82 N/A 0 1648 Chain S: 9.83 69.73 37.98 N/A 528 0 Histogram: Values Number of atoms 5.40 - 11.83 2099 11.83 - 18.27 694 18.27 - 24.70 255 24.70 - 31.13 222 31.13 - 37.56 175 37.56 - 44.00 160 44.00 - 50.43 106 50.43 - 56.86 46 56.86 - 63.30 35 63.30 - 69.73 8 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1508 r_work=0.1230 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1509 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1505 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013299 | | target function (ls_wunit_k1) not normalized (work): 2490.903070 | | target function (ls_wunit_k1) not normalized (free): 99.843249 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1224 0.1505 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1435 0.1433 0.1585 n_refl.: 191137 remove outliers: r(all,work,free)=0.1435 0.1433 0.1585 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1430 0.1584 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1231 0.1514 n_refl.: 191137 remove outliers: r(all,work,free)=0.1236 0.1231 0.1514 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 0.3230 402.814 379.826 0.490 0.962 0.273 13.296-10.522 99.01 99 1 0.1916 528.187 520.235 0.758 0.963 0.233 10.503-8.327 98.90 177 3 0.1425 564.205 567.085 0.921 0.963 0.191 8.318-6.595 100.00 360 8 0.1523 414.736 413.673 0.936 0.963 0.149 6.588-5.215 100.00 711 7 0.1342 381.101 376.822 0.911 0.963 0.127 5.214-4.128 98.38 1367 28 0.0820 557.435 556.185 0.993 0.963 0.070 4.126-3.266 94.74 2603 46 0.0759 508.132 505.639 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0853 342.774 341.443 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0896 258.603 256.784 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.622 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.343 1.074 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.217 1.060 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0506 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1515 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1515 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1515 | n_water=896 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1232 r_free=0.1512 | n_water=890 | time (s): 112.440 (total time: 115.450) Filter (q & B) r_work=0.1233 r_free=0.1512 | n_water=888 | time (s): 5.860 (total time: 121.310) Compute maps r_work=0.1233 r_free=0.1512 | n_water=888 | time (s): 1.860 (total time: 123.170) Filter (map) r_work=0.1271 r_free=0.1519 | n_water=698 | time (s): 4.670 (total time: 127.840) Find peaks r_work=0.1271 r_free=0.1519 | n_water=698 | time (s): 0.900 (total time: 128.740) Add new water r_work=0.1294 r_free=0.1549 | n_water=1037 | time (s): 5.040 (total time: 133.780) Refine new water occ: r_work=0.1240 r_free=0.1503 adp: r_work=0.1235 r_free=0.1499 occ: r_work=0.1230 r_free=0.1496 adp: r_work=0.1230 r_free=0.1497 occ: r_work=0.1228 r_free=0.1495 adp: r_work=0.1227 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1495 r_work=0.1227 r_free=0.1495 | n_water=1037 | time (s): 397.090 (total time: 530.870) Filter (q & B) r_work=0.1233 r_free=0.1496 | n_water=875 | time (s): 4.390 (total time: 535.260) Filter (dist only) r_work=0.1234 r_free=0.1496 | n_water=874 | time (s): 113.650 (total time: 648.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.642606 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.464117 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 0.1219 0.1417 0.0198 0.035 1.1 9.3 0.0 0.0 0 0.821 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.19 14.17 1.98 1.931 14.568 16.464 3.927 12.14 13.83 1.69 2.280 14.464 16.464 3.883 Individual atomic B min max mean iso aniso Overall: 5.57 67.60 15.22 1.05 507 3271 Protein: 5.57 35.88 10.71 1.05 0 2902 Water: 5.75 67.60 30.17 N/A 507 367 Other: 13.86 28.06 20.96 N/A 0 2 Chain A: 5.58 54.99 12.72 N/A 0 1624 Chain B: 5.57 67.60 12.49 N/A 0 1647 Chain S: 5.75 63.42 32.05 N/A 507 0 Histogram: Values Number of atoms 5.57 - 11.77 2134 11.77 - 17.97 693 17.97 - 24.18 283 24.18 - 30.38 248 30.38 - 36.58 178 36.58 - 42.79 129 42.79 - 48.99 74 48.99 - 55.19 26 55.19 - 61.40 9 61.40 - 67.60 4 =========================== Idealize ADP of riding H ========================== r_work=0.1214 r_free=0.1384 r_work=0.1215 r_free=0.1384 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1215 r_free = 0.1384 target_work(ml) = 3.883 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1209 r_free = 0.1376 target_work(ml) = 3.877 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1209 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.877355 | | target function (ml) not normalized (work): 726213.167251 | | target function (ml) not normalized (free): 15174.835398 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1209 0.1376 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1428 0.1427 0.1472 n_refl.: 191137 remove outliers: r(all,work,free)=0.1428 0.1427 0.1472 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1422 0.1421 0.1468 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1205 0.1368 n_refl.: 191137 remove outliers: r(all,work,free)=0.1208 0.1205 0.1368 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3789 398.008 365.439 0.426 0.947 0.246 13.296-10.522 99.01 99 1 0.2544 528.187 505.466 0.703 0.948 0.204 10.503-8.327 97.80 175 3 0.1973 554.286 557.586 0.882 0.948 0.190 8.318-6.595 100.00 360 8 0.2091 414.736 410.806 0.896 0.947 0.120 6.588-5.215 100.00 711 7 0.1820 381.101 371.094 0.885 0.947 0.110 5.214-4.128 98.38 1367 28 0.1138 557.435 551.719 0.972 0.948 0.060 4.126-3.266 94.74 2603 46 0.1081 508.132 501.211 1.033 0.948 0.009 3.266-2.585 99.86 5447 97 0.1071 342.774 339.196 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0950 258.603 255.738 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0946 153.054 151.475 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1022 82.395 81.519 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1674 44.202 42.328 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1025 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1205 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1205 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1205 r_free=0.1369 | n_water=874 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1205 r_free=0.1369 | n_water=873 | time (s): 109.480 (total time: 112.080) Filter (q & B) r_work=0.1205 r_free=0.1368 | n_water=861 | time (s): 5.020 (total time: 117.100) Compute maps r_work=0.1205 r_free=0.1368 | n_water=861 | time (s): 1.790 (total time: 118.890) Filter (map) r_work=0.1229 r_free=0.1370 | n_water=724 | time (s): 4.290 (total time: 123.180) Find peaks r_work=0.1229 r_free=0.1370 | n_water=724 | time (s): 0.550 (total time: 123.730) Add new water r_work=0.1243 r_free=0.1390 | n_water=995 | time (s): 4.080 (total time: 127.810) Refine new water occ: r_work=0.1203 r_free=0.1350 adp: r_work=0.1203 r_free=0.1349 occ: r_work=0.1200 r_free=0.1350 adp: r_work=0.1200 r_free=0.1349 occ: r_work=0.1197 r_free=0.1350 adp: r_work=0.1197 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1349 r_work=0.1197 r_free=0.1349 | n_water=995 | time (s): 241.010 (total time: 368.820) Filter (q & B) r_work=0.1203 r_free=0.1358 | n_water=895 | time (s): 4.470 (total time: 373.290) Filter (dist only) r_work=0.1203 r_free=0.1357 | n_water=894 | time (s): 114.790 (total time: 488.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.531804 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.322676 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 0.1203 0.1360 0.0157 0.037 1.1 7.8 0.0 0.3 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.60 1.57 1.819 14.265 15.323 3.870 11.98 13.60 1.61 1.912 14.228 15.323 3.864 Individual atomic B min max mean iso aniso Overall: 5.53 67.10 15.11 0.99 527 3271 Protein: 5.53 32.91 10.64 0.99 0 2902 Water: 5.64 67.10 29.61 N/A 527 367 Other: 13.98 26.97 20.48 N/A 0 2 Chain A: 5.56 53.84 12.60 N/A 0 1624 Chain B: 5.53 67.10 12.41 N/A 0 1647 Chain S: 5.64 62.60 31.29 N/A 527 0 Histogram: Values Number of atoms 5.53 - 11.68 2106 11.68 - 17.84 740 17.84 - 24.00 297 24.00 - 30.16 242 30.16 - 36.31 180 36.31 - 42.47 125 42.47 - 48.63 73 48.63 - 54.79 26 54.79 - 60.94 6 60.94 - 67.10 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1360 r_work=0.1198 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1360 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1361 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862589 | | target function (ml) not normalized (work): 723435.905346 | | target function (ml) not normalized (free): 15135.637207 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1361 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1420 0.1419 0.1481 n_refl.: 191134 remove outliers: r(all,work,free)=0.1420 0.1419 0.1481 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1413 0.1412 0.1476 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1359 n_refl.: 191134 remove outliers: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3772 361.193 319.500 0.396 0.949 0.221 13.296-10.522 97.03 97 1 0.2466 481.183 452.186 0.687 0.951 0.175 10.503-8.327 97.80 175 3 0.2065 501.897 496.901 0.866 0.951 0.159 8.318-6.595 100.00 360 8 0.2140 375.537 370.829 0.886 0.951 0.109 6.588-5.215 100.00 711 7 0.1920 345.080 334.912 0.881 0.951 0.093 5.214-4.128 98.38 1367 28 0.1179 504.748 499.505 0.970 0.951 0.060 4.126-3.266 94.74 2603 46 0.1115 460.105 453.928 1.031 0.951 0.005 3.266-2.585 99.86 5447 97 0.1093 310.376 307.163 1.018 0.950 0.000 2.585-2.046 97.45 10613 204 0.0934 234.161 231.768 1.031 0.949 0.000 2.046-1.619 99.39 21536 464 0.0912 138.588 137.303 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0984 74.608 73.907 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.024 38.370 1.044 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1175 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1359 | n_water=894 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1194 r_free=0.1360 | n_water=893 | time (s): 110.640 (total time: 113.330) Filter (q & B) r_work=0.1195 r_free=0.1361 | n_water=881 | time (s): 4.800 (total time: 118.130) Compute maps r_work=0.1195 r_free=0.1361 | n_water=881 | time (s): 1.980 (total time: 120.110) Filter (map) r_work=0.1218 r_free=0.1371 | n_water=759 | time (s): 4.260 (total time: 124.370) Find peaks r_work=0.1218 r_free=0.1371 | n_water=759 | time (s): 0.690 (total time: 125.060) Add new water r_work=0.1228 r_free=0.1382 | n_water=983 | time (s): 4.300 (total time: 129.360) Refine new water occ: r_work=0.1192 r_free=0.1354 adp: r_work=0.1193 r_free=0.1354 occ: r_work=0.1190 r_free=0.1353 adp: r_work=0.1190 r_free=0.1353 occ: r_work=0.1188 r_free=0.1353 adp: r_work=0.1188 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1353 r_work=0.1188 r_free=0.1353 | n_water=983 | time (s): 262.640 (total time: 392.000) Filter (q & B) r_work=0.1192 r_free=0.1361 | n_water=901 | time (s): 4.900 (total time: 396.900) Filter (dist only) r_work=0.1193 r_free=0.1360 | n_water=899 | time (s): 112.850 (total time: 509.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.605146 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.103861 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 0.1361 0.0166 0.036 1.1 7.3 0.0 0.3 0 0.803 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.61 1.66 1.781 14.148 15.104 3.762 11.97 13.64 1.67 1.839 14.123 15.104 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 66.76 15.00 0.95 533 3270 Protein: 5.58 31.55 10.58 0.95 0 2902 Water: 5.70 66.76 29.28 N/A 533 366 Other: 13.83 25.88 19.86 N/A 0 2 Chain A: 5.58 53.02 12.51 N/A 0 1624 Chain B: 5.58 66.76 12.31 N/A 0 1646 Chain S: 5.70 62.47 30.92 N/A 533 0 Histogram: Values Number of atoms 5.58 - 11.69 2134 11.69 - 17.81 732 17.81 - 23.93 294 23.93 - 30.05 232 30.05 - 36.17 178 36.17 - 42.29 131 42.29 - 48.40 71 48.40 - 54.52 24 54.52 - 60.64 4 60.64 - 66.76 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1364 r_work=0.1198 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1366 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758927 | | target function (ml) not normalized (work): 704009.371047 | | target function (ml) not normalized (free): 14740.181948 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1366 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1495 n_refl.: 191131 remove outliers: r(all,work,free)=0.1404 0.1403 0.1495 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1396 0.1395 0.1489 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1366 n_refl.: 191131 remove outliers: r(all,work,free)=0.1198 0.1195 0.1366 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3806 361.193 324.475 0.396 0.952 0.215 13.296-10.522 97.03 97 1 0.2364 481.183 461.795 0.692 0.954 0.161 10.503-8.327 97.80 175 3 0.2101 501.897 494.819 0.857 0.954 0.137 8.318-6.595 100.00 360 8 0.2160 375.537 370.813 0.882 0.954 0.103 6.588-5.215 100.00 711 7 0.1922 345.080 335.069 0.876 0.954 0.083 5.214-4.128 98.38 1367 28 0.1201 504.748 499.164 0.969 0.954 0.060 4.126-3.266 94.74 2603 46 0.1135 460.105 453.608 1.029 0.954 0.000 3.266-2.585 99.86 5447 97 0.1100 310.376 307.121 1.015 0.954 0.000 2.585-2.046 97.45 10613 204 0.0947 234.161 231.719 1.028 0.953 0.000 2.046-1.619 99.39 21536 464 0.0912 138.588 137.284 1.052 0.952 0.000 1.619-1.281 98.00 42464 925 0.0972 74.608 73.900 1.050 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.024 38.356 1.039 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1338 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1366 | n_water=899 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1195 r_free=0.1366 | n_water=899 | time (s): 111.530 (total time: 114.770) Filter (q & B) r_work=0.1195 r_free=0.1366 | n_water=889 | time (s): 4.700 (total time: 119.470) Compute maps r_work=0.1195 r_free=0.1366 | n_water=889 | time (s): 2.070 (total time: 121.540) Filter (map) r_work=0.1215 r_free=0.1360 | n_water=781 | time (s): 4.680 (total time: 126.220) Find peaks r_work=0.1215 r_free=0.1360 | n_water=781 | time (s): 0.550 (total time: 126.770) Add new water r_work=0.1224 r_free=0.1367 | n_water=994 | time (s): 3.670 (total time: 130.440) Refine new water occ: r_work=0.1191 r_free=0.1352 adp: r_work=0.1191 r_free=0.1351 occ: r_work=0.1189 r_free=0.1351 adp: r_work=0.1189 r_free=0.1351 occ: r_work=0.1188 r_free=0.1352 adp: r_work=0.1188 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1352 r_work=0.1188 r_free=0.1352 | n_water=994 | time (s): 258.950 (total time: 389.390) Filter (q & B) r_work=0.1192 r_free=0.1357 | n_water=911 | time (s): 4.290 (total time: 393.680) Filter (dist only) r_work=0.1192 r_free=0.1357 | n_water=909 | time (s): 114.870 (total time: 508.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.532173 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.023572 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1361 0.0164 0.037 1.1 5.5 0.0 0.3 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.61 1.64 1.755 14.065 15.024 3.760 11.98 13.64 1.66 1.871 14.030 15.024 3.757 Individual atomic B min max mean iso aniso Overall: 5.59 65.62 14.91 0.90 543 3270 Protein: 5.59 29.25 10.48 0.90 0 2902 Water: 5.79 65.62 29.05 N/A 543 366 Other: 13.87 23.25 18.56 N/A 0 2 Chain A: 5.64 52.12 12.38 N/A 0 1624 Chain B: 5.59 65.62 12.20 N/A 0 1646 Chain S: 5.79 62.09 30.74 N/A 543 0 Histogram: Values Number of atoms 5.59 - 11.59 2104 11.59 - 17.59 782 17.59 - 23.60 278 23.60 - 29.60 220 29.60 - 35.60 183 35.60 - 41.61 137 41.61 - 47.61 73 47.61 - 53.61 29 53.61 - 59.62 5 59.62 - 65.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1364 r_work=0.1199 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1364 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756510 | | target function (ml) not normalized (work): 703556.673336 | | target function (ml) not normalized (free): 14728.225203 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1493 n_refl.: 191131 remove outliers: r(all,work,free)=0.1402 0.1401 0.1493 n_refl.: 191131 overall B=-0.23 to atoms: r(all,work,free)=0.1365 0.1363 0.1468 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3835 361.193 323.195 0.398 0.951 0.206 13.296-10.522 97.03 97 1 0.2370 481.183 461.860 0.704 0.953 0.141 10.503-8.327 97.80 175 3 0.2153 501.897 493.865 0.879 0.953 0.114 8.318-6.595 100.00 360 8 0.2162 375.537 371.131 0.903 0.953 0.088 6.588-5.215 100.00 711 7 0.1928 345.080 335.281 0.899 0.953 0.073 5.214-4.128 98.38 1367 28 0.1208 504.748 499.115 0.994 0.953 0.034 4.126-3.266 94.74 2603 46 0.1146 460.105 453.209 1.056 0.953 0.000 3.266-2.585 99.86 5447 97 0.1110 310.376 307.032 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0950 234.161 231.681 1.047 0.952 0.000 2.046-1.619 99.39 21536 464 0.0907 138.588 137.297 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0967 74.608 73.910 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.024 38.360 1.025 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0509 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1362 | n_water=909 | time (s): 3.410 (total time: 3.410) Filter (dist) r_work=0.1196 r_free=0.1362 | n_water=909 | time (s): 111.980 (total time: 115.390) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=904 | time (s): 5.070 (total time: 120.460) Compute maps r_work=0.1196 r_free=0.1362 | n_water=904 | time (s): 1.730 (total time: 122.190) Filter (map) r_work=0.1218 r_free=0.1358 | n_water=790 | time (s): 5.200 (total time: 127.390) Find peaks r_work=0.1218 r_free=0.1358 | n_water=790 | time (s): 0.780 (total time: 128.170) Add new water r_work=0.1225 r_free=0.1366 | n_water=1009 | time (s): 4.690 (total time: 132.860) Refine new water occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1348 occ: r_work=0.1191 r_free=0.1348 adp: r_work=0.1191 r_free=0.1348 occ: r_work=0.1189 r_free=0.1350 adp: r_work=0.1189 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1350 r_work=0.1189 r_free=0.1350 | n_water=1009 | time (s): 211.630 (total time: 344.490) Filter (q & B) r_work=0.1193 r_free=0.1358 | n_water=926 | time (s): 5.140 (total time: 349.630) Filter (dist only) r_work=0.1193 r_free=0.1357 | n_water=925 | time (s): 116.540 (total time: 466.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.614694 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.371077 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1365 0.0169 0.038 1.1 6.8 0.0 0.3 0 0.807 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.65 1.69 1.718 13.785 14.371 3.757 11.99 13.68 1.69 1.761 13.763 14.371 3.756 Individual atomic B min max mean iso aniso Overall: 5.40 64.51 14.70 0.88 559 3270 Protein: 5.40 28.30 10.24 0.88 0 2902 Water: 5.69 64.51 28.67 N/A 559 366 Other: 13.67 22.14 17.90 N/A 0 2 Chain A: 5.48 51.66 12.09 N/A 0 1624 Chain B: 5.40 64.51 11.92 N/A 0 1646 Chain S: 5.69 61.53 30.42 N/A 559 0 Histogram: Values Number of atoms 5.40 - 11.31 2094 11.31 - 17.22 792 17.22 - 23.13 278 23.13 - 29.04 213 29.04 - 34.95 200 34.95 - 40.86 126 40.86 - 46.77 87 46.77 - 52.68 32 52.68 - 58.59 2 58.59 - 64.51 5 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1368 r_work=0.1199 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1368 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1369 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755854 | | target function (ml) not normalized (work): 703433.889710 | | target function (ml) not normalized (free): 14733.991894 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1369 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1371 0.1369 0.1483 n_refl.: 191131 remove outliers: r(all,work,free)=0.1371 0.1369 0.1483 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1378 0.1376 0.1488 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1359 n_refl.: 191131 remove outliers: r(all,work,free)=0.1192 0.1189 0.1359 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3938 361.193 320.011 0.375 0.975 0.183 13.296-10.522 97.03 97 1 0.2390 481.183 460.922 0.687 0.977 0.129 10.503-8.327 97.80 175 3 0.2171 501.897 493.278 0.862 0.977 0.107 8.318-6.595 100.00 360 8 0.2148 375.537 370.810 0.883 0.977 0.070 6.588-5.215 100.00 711 7 0.1933 345.080 334.781 0.886 0.978 0.070 5.214-4.128 98.38 1367 28 0.1215 504.748 498.681 0.979 0.979 0.029 4.126-3.266 94.74 2603 46 0.1155 460.105 452.560 1.040 0.980 0.000 3.266-2.585 99.86 5447 97 0.1117 310.376 306.784 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0955 234.161 231.563 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0906 138.588 137.213 1.047 0.984 0.000 1.619-1.281 98.00 42464 925 0.0946 74.608 73.952 1.035 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.024 38.333 1.001 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0611 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1359 | n_water=925 | time (s): 2.970 (total time: 2.970) Filter (dist) r_work=0.1190 r_free=0.1360 | n_water=922 | time (s): 115.850 (total time: 118.820) Filter (q & B) r_work=0.1190 r_free=0.1361 | n_water=912 | time (s): 5.010 (total time: 123.830) Compute maps r_work=0.1190 r_free=0.1361 | n_water=912 | time (s): 1.780 (total time: 125.610) Filter (map) r_work=0.1213 r_free=0.1351 | n_water=791 | time (s): 5.280 (total time: 130.890) Find peaks r_work=0.1213 r_free=0.1351 | n_water=791 | time (s): 0.810 (total time: 131.700) Add new water r_work=0.1219 r_free=0.1362 | n_water=1006 | time (s): 5.110 (total time: 136.810) Refine new water occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1188 r_free=0.1342 occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1186 r_free=0.1341 occ: r_work=0.1185 r_free=0.1339 adp: r_work=0.1185 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1340 r_work=0.1185 r_free=0.1340 | n_water=1006 | time (s): 180.140 (total time: 316.950) Filter (q & B) r_work=0.1189 r_free=0.1349 | n_water=926 | time (s): 5.270 (total time: 322.220) Filter (dist only) r_work=0.1189 r_free=0.1349 | n_water=924 | time (s): 116.100 (total time: 438.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.522415 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.988202 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 0.1354 0.0160 0.038 1.1 6.5 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.54 1.60 1.674 13.772 13.988 3.756 11.94 13.57 1.63 1.705 13.763 13.988 3.754 Individual atomic B min max mean iso aniso Overall: 5.50 63.40 14.71 0.86 558 3270 Protein: 5.50 27.81 10.29 0.86 0 2902 Water: 5.83 63.40 28.59 N/A 558 366 Other: 13.77 22.14 17.95 N/A 0 2 Chain A: 5.54 51.25 12.11 N/A 0 1624 Chain B: 5.50 63.40 11.95 N/A 0 1646 Chain S: 5.83 61.10 30.44 N/A 558 0 Histogram: Values Number of atoms 5.50 - 11.29 2065 11.29 - 17.08 822 17.08 - 22.87 281 22.87 - 28.66 197 28.66 - 34.45 198 34.45 - 40.24 134 40.24 - 46.03 86 46.03 - 51.82 33 51.82 - 57.61 7 57.61 - 63.40 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1357 r_work=0.1195 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1357 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753898 | | target function (ml) not normalized (work): 703067.511909 | | target function (ml) not normalized (free): 14723.948836 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1354 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1390 0.1388 0.1487 n_refl.: 191131 remove outliers: r(all,work,free)=0.1390 0.1388 0.1487 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1392 0.1391 0.1489 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191131 remove outliers: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3922 361.193 318.955 0.379 0.975 0.196 13.296-10.522 97.03 97 1 0.2367 481.183 462.749 0.685 0.977 0.131 10.503-8.327 97.80 175 3 0.2180 501.897 492.470 0.859 0.977 0.103 8.318-6.595 100.00 360 8 0.2183 375.537 369.881 0.883 0.977 0.083 6.588-5.215 100.00 711 7 0.1942 345.080 335.215 0.883 0.977 0.067 5.214-4.128 98.38 1367 28 0.1243 504.748 498.433 0.978 0.978 0.034 4.126-3.266 94.74 2603 46 0.1162 460.105 452.556 1.041 0.979 0.005 3.266-2.585 99.86 5447 97 0.1130 310.376 306.725 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0960 234.161 231.549 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0907 138.588 137.216 1.049 0.985 0.000 1.619-1.281 98.00 42464 925 0.0943 74.608 73.957 1.039 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.024 38.313 1.007 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0217 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1353 | n_water=924 | time (s): 3.310 (total time: 3.310) Filter (dist) r_work=0.1192 r_free=0.1353 | n_water=923 | time (s): 114.830 (total time: 118.140) Filter (q & B) r_work=0.1193 r_free=0.1352 | n_water=910 | time (s): 4.120 (total time: 122.260) Compute maps r_work=0.1193 r_free=0.1352 | n_water=910 | time (s): 2.370 (total time: 124.630) Filter (map) r_work=0.1215 r_free=0.1362 | n_water=795 | time (s): 4.140 (total time: 128.770) Find peaks r_work=0.1215 r_free=0.1362 | n_water=795 | time (s): 0.640 (total time: 129.410) Add new water r_work=0.1221 r_free=0.1372 | n_water=997 | time (s): 4.040 (total time: 133.450) Refine new water occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1191 r_free=0.1351 occ: r_work=0.1189 r_free=0.1349 adp: r_work=0.1189 r_free=0.1350 occ: r_work=0.1187 r_free=0.1347 adp: r_work=0.1187 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1348 r_work=0.1187 r_free=0.1348 | n_water=997 | time (s): 330.060 (total time: 463.510) Filter (q & B) r_work=0.1191 r_free=0.1355 | n_water=919 | time (s): 4.920 (total time: 468.430) Filter (dist only) r_work=0.1192 r_free=0.1355 | n_water=917 | time (s): 121.970 (total time: 590.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.573057 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.039817 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1357 0.0162 0.038 1.1 6.6 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.57 1.62 1.672 13.742 15.040 3.755 11.94 13.60 1.66 1.672 13.736 15.040 3.752 Individual atomic B min max mean iso aniso Overall: 5.54 62.31 14.66 0.87 551 3270 Protein: 5.54 28.10 10.33 0.87 0 2902 Water: 5.97 62.31 28.36 N/A 551 366 Other: 13.82 22.07 17.94 N/A 0 2 Chain A: 5.63 50.91 12.11 N/A 0 1624 Chain B: 5.54 62.31 11.95 N/A 0 1646 Chain S: 5.97 60.60 30.25 N/A 551 0 Histogram: Values Number of atoms 5.54 - 11.22 2040 11.22 - 16.90 837 16.90 - 22.58 285 22.58 - 28.25 195 28.25 - 33.93 196 33.93 - 39.61 131 39.61 - 45.28 89 45.28 - 50.96 35 50.96 - 56.64 8 56.64 - 62.31 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1360 r_work=0.1194 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1360 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1358 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751618 | | target function (ml) not normalized (work): 702640.504383 | | target function (ml) not normalized (free): 14728.247335 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1358 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1499 n_refl.: 191131 remove outliers: r(all,work,free)=0.1403 0.1401 0.1499 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1402 0.1400 0.1499 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1194 0.1191 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3916 361.193 318.298 0.369 0.994 0.190 13.296-10.522 97.03 97 1 0.2395 481.183 461.038 0.672 0.996 0.129 10.503-8.327 97.80 175 3 0.2189 501.897 492.476 0.838 0.996 0.100 8.318-6.595 100.00 360 8 0.2181 375.537 369.672 0.865 0.996 0.083 6.588-5.215 100.00 711 7 0.1959 345.080 334.998 0.864 0.997 0.070 5.214-4.128 98.38 1367 28 0.1249 504.748 498.369 0.959 0.998 0.048 4.126-3.266 94.74 2603 46 0.1174 460.105 452.445 1.021 0.999 0.014 3.266-2.585 99.86 5447 97 0.1137 310.376 306.760 1.004 1.000 0.003 2.585-2.046 97.45 10613 204 0.0961 234.161 231.520 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0904 138.588 137.213 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0936 74.608 73.966 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.024 38.309 0.989 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0073 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1357 After: r_work=0.1192 r_free=0.1358 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1358 | n_water=917 | time (s): 3.320 (total time: 3.320) Filter (dist) r_work=0.1192 r_free=0.1358 | n_water=917 | time (s): 113.070 (total time: 116.390) Filter (q & B) r_work=0.1193 r_free=0.1357 | n_water=906 | time (s): 4.720 (total time: 121.110) Compute maps r_work=0.1193 r_free=0.1357 | n_water=906 | time (s): 1.760 (total time: 122.870) Filter (map) r_work=0.1214 r_free=0.1357 | n_water=798 | time (s): 5.870 (total time: 128.740) Find peaks r_work=0.1214 r_free=0.1357 | n_water=798 | time (s): 0.680 (total time: 129.420) Add new water r_work=0.1220 r_free=0.1365 | n_water=1001 | time (s): 3.880 (total time: 133.300) Refine new water occ: r_work=0.1189 r_free=0.1347 adp: r_work=0.1189 r_free=0.1347 occ: r_work=0.1188 r_free=0.1348 adp: r_work=0.1188 r_free=0.1347 occ: r_work=0.1186 r_free=0.1348 adp: r_work=0.1186 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1348 r_work=0.1186 r_free=0.1348 | n_water=1001 | time (s): 303.940 (total time: 437.240) Filter (q & B) r_work=0.1190 r_free=0.1357 | n_water=920 | time (s): 5.320 (total time: 442.560) Filter (dist only) r_work=0.1190 r_free=0.1356 | n_water=919 | time (s): 119.690 (total time: 562.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.510310 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.008117 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 0.1361 0.0167 0.039 1.2 8.0 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.61 1.67 1.677 13.746 15.008 3.755 11.94 13.63 1.69 1.670 13.748 15.008 3.753 Individual atomic B min max mean iso aniso Overall: 5.56 62.11 14.66 0.87 553 3270 Protein: 5.56 28.02 10.34 0.87 0 2902 Water: 6.02 62.11 28.29 N/A 553 366 Other: 13.83 22.10 17.96 N/A 0 2 Chain A: 5.63 50.86 12.10 N/A 0 1624 Chain B: 5.56 62.11 11.96 N/A 0 1646 Chain S: 6.02 60.52 30.21 N/A 553 0 Histogram: Values Number of atoms 5.56 - 11.21 2035 11.21 - 16.87 843 16.87 - 22.52 286 22.52 - 28.18 205 28.18 - 33.83 180 33.83 - 39.49 134 39.49 - 45.14 92 45.14 - 50.80 35 50.80 - 56.45 9 56.45 - 62.11 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1363 r_work=0.1194 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1363 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1365 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753114 | | target function (ml) not normalized (work): 702920.792383 | | target function (ml) not normalized (free): 14727.720828 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1371 0.1528 5.6996 5.8009| | 2: 2.94 - 2.33 1.00 7339 128 0.1076 0.1342 5.0924 5.1738| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1185 4.6547 4.7352| | 4: 2.04 - 1.85 1.00 7170 155 0.0895 0.1074 4.3891 4.5833| | 5: 1.85 - 1.72 0.99 7113 159 0.0928 0.0979 4.15 4.2406| | 6: 1.72 - 1.62 0.99 7102 142 0.0895 0.1088 3.949 4.0927| | 7: 1.62 - 1.54 0.99 7104 148 0.0886 0.0981 3.7973 3.9385| | 8: 1.54 - 1.47 0.96 6798 152 0.0885 0.1297 3.6951 3.8831| | 9: 1.47 - 1.41 0.98 6938 155 0.0919 0.1128 3.615 3.7523| | 10: 1.41 - 1.36 0.99 7022 150 0.0969 0.1169 3.55 3.6707| | 11: 1.36 - 1.32 0.99 6997 151 0.0987 0.1127 3.4808 3.5915| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1135 3.457 3.5841| | 13: 1.28 - 1.25 0.98 6907 166 0.1039 0.1234 3.4345 3.5596| | 14: 1.25 - 1.22 0.98 7015 112 0.1103 0.1581 3.4291 3.6743| | 15: 1.22 - 1.19 0.98 6956 137 0.1164 0.1243 3.4435 3.4809| | 16: 1.19 - 1.17 0.93 6604 132 0.1246 0.1527 3.4612 3.6498| | 17: 1.17 - 1.14 0.98 6940 135 0.1295 0.1219 3.4297 3.4385| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1701 3.4365 3.5333| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1758 3.4179 3.5923| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1568 3.4091 3.4312| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2128 3.4174 3.5041| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1950 3.4123 3.4153| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2018 3.4322 3.4862| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2253 3.435 3.5096| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2518 3.4489 3.5251| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2855 3.4153 3.4225| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2812 3.4683 3.397| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7399 127 0.93 12.22 1.00 0.95 11982.71| | 2: 2.94 - 2.33 7339 128 0.92 13.18 0.99 0.95 5369.27| | 3: 2.33 - 2.04 6939 150 0.96 7.59 1.01 0.95 1679.56| | 4: 2.04 - 1.85 7170 155 0.96 7.66 1.00 0.95 1008.26| | 5: 1.85 - 1.72 7113 159 0.96 8.14 1.00 0.96 640.81| | 6: 1.72 - 1.62 7102 142 0.96 8.14 1.00 0.96 450.50| | 7: 1.62 - 1.54 7104 148 0.96 8.18 1.01 0.97 339.47| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 0.97 278.21| | 9: 1.47 - 1.41 6938 155 0.96 8.40 1.00 0.98 228.87| | 10: 1.41 - 1.36 7022 150 0.96 8.87 1.00 0.97 201.15| | 11: 1.36 - 1.32 6997 151 0.96 8.94 0.99 0.96 174.76| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.98 0.95 160.60| | 13: 1.28 - 1.25 6907 166 0.96 9.49 1.01 0.96 157.39| | 14: 1.25 - 1.22 7015 112 0.95 10.64 1.01 0.97 161.52| | 15: 1.22 - 1.19 6956 137 0.95 11.13 1.01 0.98 164.49| | 16: 1.19 - 1.17 6604 132 0.95 11.35 1.01 0.96 158.46| | 17: 1.17 - 1.14 6940 135 0.94 12.17 1.01 0.96 152.54| | 18: 1.14 - 1.12 6875 142 0.94 12.71 1.01 0.95 147.02| | 19: 1.12 - 1.10 6948 106 0.93 14.12 1.00 0.95 150.55| | 20: 1.10 - 1.08 6884 147 0.92 15.21 1.00 0.94 149.98| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.93 153.20| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.93 155.13| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 164.95| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.93 179.28| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.90 182.31| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.88 176.89| | 27: 0.99 - 0.98 6647 131 0.82 26.32 0.99 0.87 161.33| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.02 max = 11982.71 mean = 965.50| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.32| |phase err.(test): min = 0.00 max = 88.85 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1365 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1411 0.1409 0.1507 n_refl.: 191131 remove outliers: r(all,work,free)=0.1411 0.1409 0.1507 n_refl.: 191131 overall B=-0.06 to atoms: r(all,work,free)=0.1402 0.1400 0.1500 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1361 n_refl.: 191131 remove outliers: r(all,work,free)=0.1195 0.1192 0.1361 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3766 356.665 321.281 0.380 0.912 0.161 13.296-10.522 97.03 97 1 0.2475 481.183 459.838 0.706 0.914 0.110 10.503-8.327 97.80 175 3 0.2178 501.897 493.062 0.893 0.915 0.098 8.318-6.595 100.00 360 8 0.2175 375.537 369.679 0.919 0.915 0.080 6.588-5.215 100.00 711 7 0.1946 345.080 334.911 0.919 0.915 0.073 5.214-4.128 98.38 1367 28 0.1245 504.748 498.500 1.019 0.916 0.034 4.126-3.266 94.74 2603 46 0.1172 460.105 452.526 1.085 0.918 0.000 3.266-2.585 99.86 5447 97 0.1133 310.376 306.746 1.067 0.919 0.000 2.585-2.046 97.45 10613 204 0.0964 234.161 231.537 1.073 0.921 0.000 2.046-1.619 99.39 21536 464 0.0907 138.588 137.214 1.090 0.926 0.000 1.619-1.281 98.00 42464 925 0.0940 74.608 73.962 1.079 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.024 38.303 1.043 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0124 ================= 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 : 0.2028 0.1969 0.079 5.013 5.2 78.0 14.6 805 0.000 1_bss: 0.1791 0.1903 0.079 5.013 5.2 78.0 14.6 805 0.000 1_settarget: 0.1791 0.1903 0.079 5.013 5.2 78.0 14.6 805 0.000 1_nqh: 0.1791 0.1903 0.079 5.013 5.2 78.0 14.6 805 0.000 1_weight: 0.1791 0.1903 0.079 5.013 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1272 0.1503 0.039 1.160 5.2 78.0 14.6 805 0.157 1_adp: 0.1298 0.1570 0.039 1.160 5.1 73.0 15.0 805 0.157 1_regHadp: 0.1297 0.1567 0.039 1.160 5.1 73.0 15.0 805 0.157 1_occ: 0.1283 0.1556 0.039 1.160 5.1 73.0 15.0 805 0.157 2_bss: 0.1275 0.1545 0.039 1.160 5.3 73.2 15.2 805 0.157 2_settarget: 0.1275 0.1545 0.039 1.160 5.3 73.2 15.2 805 0.157 2_updatecdl: 0.1275 0.1545 0.039 1.172 5.3 73.2 15.2 805 0.157 2_nqh: 0.1275 0.1545 0.039 1.172 5.3 73.2 15.2 805 0.157 2_sol: 0.1270 0.1505 0.039 1.172 5.3 73.2 16.3 896 n/a 2_weight: 0.1270 0.1505 0.039 1.172 5.3 73.2 16.3 896 n/a 2_xyzrec: 0.1253 0.1521 0.041 1.134 5.3 73.2 16.3 896 n/a 2_adp: 0.1230 0.1508 0.041 1.134 5.4 69.7 16.4 896 n/a 2_regHadp: 0.1230 0.1509 0.041 1.134 5.4 69.7 16.4 896 n/a 2_occ: 0.1224 0.1505 0.041 1.134 5.4 69.7 16.4 896 n/a 3_bss: 0.1231 0.1515 0.041 1.134 5.4 69.7 16.4 896 n/a 3_settarget: 0.1231 0.1515 0.041 1.134 5.4 69.7 16.4 896 n/a 3_updatecdl: 0.1231 0.1515 0.041 1.137 5.4 69.7 16.4 896 n/a 3_nqh: 0.1231 0.1515 0.041 1.137 5.4 69.7 16.4 896 n/a 3_sol: 0.1234 0.1496 0.041 1.137 5.4 68.2 15.4 874 n/a 3_weight: 0.1234 0.1496 0.041 1.137 5.4 68.2 15.4 874 n/a 3_xyzrec: 0.1219 0.1417 0.035 1.100 5.4 68.2 15.4 874 n/a 3_adp: 0.1214 0.1384 0.035 1.100 5.6 67.6 15.2 874 n/a 3_regHadp: 0.1215 0.1384 0.035 1.100 5.6 67.6 15.2 874 n/a 3_occ: 0.1209 0.1376 0.035 1.100 5.6 67.6 15.2 874 n/a 4_bss: 0.1205 0.1369 0.035 1.100 5.5 67.6 15.2 874 n/a 4_settarget: 0.1205 0.1369 0.035 1.100 5.5 67.6 15.2 874 n/a 4_updatecdl: 0.1205 0.1369 0.035 1.100 5.5 67.6 15.2 874 n/a 4_nqh: 0.1205 0.1369 0.035 1.100 5.5 67.6 15.2 874 n/a 4_sol: 0.1203 0.1357 0.035 1.100 5.5 67.6 15.2 894 n/a 4_weight: 0.1203 0.1357 0.035 1.100 5.5 67.6 15.2 894 n/a 4_xyzrec: 0.1203 0.1360 0.037 1.119 5.5 67.6 15.2 894 n/a 4_adp: 0.1198 0.1360 0.037 1.119 5.5 67.1 15.1 894 n/a 4_regHadp: 0.1198 0.1360 0.037 1.119 5.5 67.1 15.1 894 n/a 4_occ: 0.1196 0.1361 0.037 1.119 5.5 67.1 15.1 894 n/a 5_bss: 0.1194 0.1359 0.037 1.119 5.5 67.1 15.1 894 n/a 5_settarget: 0.1194 0.1359 0.037 1.119 5.5 67.1 15.1 894 n/a 5_updatecdl: 0.1194 0.1359 0.037 1.119 5.5 67.1 15.1 894 n/a 5_nqh: 0.1194 0.1359 0.037 1.119 5.5 67.1 15.1 894 n/a 5_sol: 0.1193 0.1360 0.037 1.119 5.5 67.1 15.0 899 n/a 5_weight: 0.1193 0.1360 0.037 1.119 5.5 67.1 15.0 899 n/a 5_xyzrec: 0.1194 0.1361 0.036 1.130 5.5 67.1 15.0 899 n/a 5_adp: 0.1198 0.1364 0.036 1.130 5.6 66.8 15.0 899 n/a 5_regHadp: 0.1198 0.1365 0.036 1.130 5.6 66.8 15.0 899 n/a 5_occ: 0.1196 0.1366 0.036 1.130 5.6 66.8 15.0 899 n/a 6_bss: 0.1195 0.1366 0.036 1.130 5.5 66.7 15.0 899 n/a 6_settarget: 0.1195 0.1366 0.036 1.130 5.5 66.7 15.0 899 n/a 6_updatecdl: 0.1195 0.1366 0.036 1.131 5.5 66.7 15.0 899 n/a 6_nqh: 0.1195 0.1366 0.036 1.131 5.5 66.7 15.0 899 n/a 6_sol: 0.1192 0.1357 0.036 1.131 5.5 66.7 15.0 909 n/a 6_weight: 0.1192 0.1357 0.036 1.131 5.5 66.7 15.0 909 n/a 6_xyzrec: 0.1196 0.1361 0.037 1.132 5.5 66.7 15.0 909 n/a 6_adp: 0.1198 0.1364 0.037 1.132 5.6 65.6 14.9 909 n/a 6_regHadp: 0.1199 0.1364 0.037 1.132 5.6 65.6 14.9 909 n/a 6_occ: 0.1197 0.1363 0.037 1.132 5.6 65.6 14.9 909 n/a 7_bss: 0.1196 0.1362 0.037 1.132 5.4 65.4 14.7 909 n/a 7_settarget: 0.1196 0.1362 0.037 1.132 5.4 65.4 14.7 909 n/a 7_updatecdl: 0.1196 0.1362 0.037 1.132 5.4 65.4 14.7 909 n/a 7_nqh: 0.1196 0.1362 0.037 1.132 5.4 65.4 14.7 909 n/a 7_sol: 0.1193 0.1357 0.037 1.132 5.4 65.4 14.7 925 n/a 7_weight: 0.1193 0.1357 0.037 1.132 5.4 65.4 14.7 925 n/a 7_xyzrec: 0.1196 0.1365 0.038 1.129 5.4 65.4 14.7 925 n/a 7_adp: 0.1199 0.1368 0.038 1.129 5.4 64.5 14.7 925 n/a 7_regHadp: 0.1199 0.1368 0.038 1.129 5.4 64.5 14.7 925 n/a 7_occ: 0.1198 0.1369 0.038 1.129 5.4 64.5 14.7 925 n/a 8_bss: 0.1189 0.1359 0.038 1.129 5.5 64.6 14.8 925 n/a 8_settarget: 0.1189 0.1359 0.038 1.129 5.5 64.6 14.8 925 n/a 8_updatecdl: 0.1189 0.1359 0.038 1.129 5.5 64.6 14.8 925 n/a 8_nqh: 0.1189 0.1359 0.038 1.129 5.5 64.6 14.8 925 n/a 8_sol: 0.1189 0.1349 0.038 1.129 5.5 64.6 14.7 924 n/a 8_weight: 0.1189 0.1349 0.038 1.129 5.5 64.6 14.7 924 n/a 8_xyzrec: 0.1194 0.1354 0.038 1.122 5.5 64.6 14.7 924 n/a 8_adp: 0.1195 0.1357 0.038 1.122 5.5 63.4 14.7 924 n/a 8_regHadp: 0.1195 0.1357 0.038 1.122 5.5 63.4 14.7 924 n/a 8_occ: 0.1193 0.1354 0.038 1.122 5.5 63.4 14.7 924 n/a 9_bss: 0.1192 0.1353 0.038 1.122 5.5 63.4 14.7 924 n/a 9_settarget: 0.1192 0.1353 0.038 1.122 5.5 63.4 14.7 924 n/a 9_updatecdl: 0.1192 0.1353 0.038 1.123 5.5 63.4 14.7 924 n/a 9_nqh: 0.1192 0.1353 0.038 1.123 5.5 63.4 14.7 924 n/a 9_sol: 0.1192 0.1355 0.038 1.123 5.5 63.4 14.7 917 n/a 9_weight: 0.1192 0.1355 0.038 1.123 5.5 63.4 14.7 917 n/a 9_xyzrec: 0.1195 0.1357 0.038 1.120 5.5 63.4 14.7 917 n/a 9_adp: 0.1194 0.1360 0.038 1.120 5.5 62.3 14.7 917 n/a 9_regHadp: 0.1194 0.1360 0.038 1.120 5.5 62.3 14.7 917 n/a 9_occ: 0.1192 0.1358 0.038 1.120 5.5 62.3 14.7 917 n/a 10_bss: 0.1191 0.1357 0.038 1.120 5.5 62.3 14.7 917 n/a 10_settarget: 0.1191 0.1357 0.038 1.120 5.5 62.3 14.7 917 n/a 10_updatecdl: 0.1191 0.1357 0.038 1.120 5.5 62.3 14.7 917 n/a 10_setrh: 0.1192 0.1358 0.038 1.120 5.5 62.3 14.7 917 n/a 10_nqh: 0.1192 0.1358 0.038 1.120 5.5 62.3 14.7 917 n/a 10_sol: 0.1190 0.1356 0.038 1.120 5.5 62.3 14.7 919 n/a 10_weight: 0.1190 0.1356 0.038 1.120 5.5 62.3 14.7 919 n/a 10_xyzrec: 0.1194 0.1361 0.039 1.159 5.5 62.3 14.7 919 n/a 10_adp: 0.1194 0.1363 0.039 1.159 5.6 62.1 14.7 919 n/a 10_regHadp: 0.1194 0.1363 0.039 1.159 5.6 62.1 14.7 919 n/a 10_occ: 0.1193 0.1365 0.039 1.159 5.6 62.1 14.7 919 n/a end: 0.1192 0.1361 0.039 1.159 5.5 62.1 14.6 919 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7307888_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7307888_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3400 Refinement macro-cycles (run) : 12306.1100 Write final files (write_after_run_outputs) : 142.8800 Total : 12455.3300 Total CPU time: 3.47 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:47 PST -0800 (1736736287.45 s) Start R-work = 0.1791, R-free = 0.1903 Final R-work = 0.1192, R-free = 0.1361 =============================================================================== Job complete usr+sys time: 12716.57 seconds wall clock time: 212 minutes 56.42 seconds (12776.42 seconds total)