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_8360863.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8360863.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8360863.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } 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: 2.36, per 1000 atoms: 0.35 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: 2.762 distance_ideal: 2.720 ideal - model: -0.042 slack: 0.000 delta_slack: -0.042 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: 2.761 distance_ideal: 2.710 ideal - model: -0.051 slack: 0.000 delta_slack: -0.051 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: 0.97 Conformation dependent library (CDL) restraints added in 114.4 milliseconds Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.04: 913 1.04 - 1.27: 2452 1.27 - 1.49: 1467 1.49 - 1.72: 1086 1.72 - 1.95: 16 Bond restraints: 5934 Sorted by residual: bond pdb=" N VAL A 69 " pdb=" CA VAL A 69 " ideal model delta sigma weight residual 1.458 1.715 -0.258 1.17e-02 7.31e+03 4.85e+02 bond pdb=" N VAL A 102 " pdb=" CA VAL A 102 " ideal model delta sigma weight residual 1.459 1.215 0.245 1.24e-02 6.50e+03 3.89e+02 bond pdb=" N TYR A 195 " pdb=" H TYR A 195 " ideal model delta sigma weight residual 0.860 1.242 -0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" CB ALA A 110 " pdb=" HB3 ALA A 110 " ideal model delta sigma weight residual 0.970 1.351 -0.381 2.00e-02 2.50e+03 3.64e+02 bond pdb=" N GLU B 66 " pdb=" CA GLU B 66 " ideal model delta sigma weight residual 1.463 1.697 -0.234 1.24e-02 6.50e+03 3.57e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.28: 5697 4.28 - 8.56: 3537 8.56 - 12.85: 1315 12.85 - 17.13: 240 17.13 - 21.41: 21 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O THR A 21 " pdb=" C THR A 21 " pdb=" N ILE A 22 " ideal model delta sigma weight residual 122.15 139.88 -17.73 1.14e+00 7.69e-01 2.42e+02 angle pdb=" CA ALA A 110 " pdb=" C ALA A 110 " pdb=" O ALA A 110 " ideal model delta sigma weight residual 120.10 137.20 -17.10 1.13e+00 7.83e-01 2.29e+02 angle pdb=" O ALA A 108 " pdb=" C ALA A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.32 137.85 -16.53 1.15e+00 7.56e-01 2.07e+02 angle pdb=" NE ARG A 100 " pdb=" CZ ARG A 100 " pdb=" NH1 ARG A 100 " ideal model delta sigma weight residual 121.50 107.26 14.24 1.00e+00 1.00e+00 2.03e+02 angle pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" O GLY B 74 " ideal model delta sigma weight residual 121.64 136.33 -14.69 1.04e+00 9.25e-01 2.00e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.18: 1827 16.18 - 32.35: 139 32.35 - 48.53: 59 48.53 - 64.70: 20 64.70 - 80.88: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ALA A 188 " pdb=" C ALA A 188 " pdb=" N ALA A 189 " pdb=" CA ALA A 189 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLN A 156 " pdb=" C GLN A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual -180.00 -157.23 -22.77 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA VAL B 112 " pdb=" C VAL B 112 " pdb=" N LEU B 113 " pdb=" CA LEU B 113 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.261: 244 0.261 - 0.520: 152 0.520 - 0.779: 77 0.779 - 1.037: 17 1.037 - 1.296: 2 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE A 162 " pdb=" N ILE A 162 " pdb=" C ILE A 162 " pdb=" CB ILE A 162 " both_signs ideal model delta sigma weight residual False 2.43 3.73 -1.30 2.00e-01 2.50e+01 4.20e+01 chirality pdb=" CA LEU A 172 " pdb=" N LEU A 172 " pdb=" C LEU A 172 " pdb=" CB LEU A 172 " both_signs ideal model delta sigma weight residual False 2.51 3.64 -1.13 2.00e-01 2.50e+01 3.19e+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 -1.55 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 179 " 0.083 2.00e-02 2.50e+03 9.23e-02 1.92e+02 pdb=" CG HIS A 179 " -0.167 2.00e-02 2.50e+03 pdb=" ND1 HIS A 179 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 HIS A 179 " 0.062 2.00e-02 2.50e+03 pdb=" CE1 HIS A 179 " -0.128 2.00e-02 2.50e+03 pdb=" NE2 HIS A 179 " 0.124 2.00e-02 2.50e+03 pdb=" HD2 HIS A 179 " -0.034 2.00e-02 2.50e+03 pdb=" HE1 HIS A 179 " 0.049 2.00e-02 2.50e+03 pdb=" HE2 HIS A 179 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " -0.014 2.00e-02 2.50e+03 6.58e-02 1.73e+02 pdb=" CG TRP A 146 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.118 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.081 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.106 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.052 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.018 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.103 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.047 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.081 2.00e-02 2.50e+03 6.12e-02 1.50e+02 pdb=" CG TRP B 146 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.098 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.048 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.037 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.006 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.011 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.151 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.013 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.54: 21 1.54 - 2.31: 1793 2.31 - 3.07: 21660 3.07 - 3.84: 33036 3.84 - 4.60: 53712 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110222 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.778 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.971 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.050 2.620 nonbonded pdb="HG22 VAL A 181 " pdb=" O HOH S1566 " model vdw 1.167 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.180 2.620 ... (remaining 110217 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_8360863_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2034 r_free= 0.2001 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300821 | | target function (ml) not normalized (work): 805599.738569 | | target function (ml) not normalized (free): 16599.470648 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2130 0.1975 6.6792 6.3055| | 2: 2.94 - 2.33 1.00 7339 128 0.1616 0.1622 5.5421 5.5943| | 3: 2.33 - 2.04 0.96 6939 150 0.1627 0.1720 5.136 5.1886| | 4: 2.04 - 1.85 1.00 7170 155 0.1759 0.1629 4.9665 5.0166| | 5: 1.85 - 1.72 0.99 7113 159 0.1932 0.1581 4.8061 4.739| | 6: 1.72 - 1.62 0.99 7102 142 0.2001 0.2080 4.6662 4.7448| | 7: 1.62 - 1.54 0.99 7104 148 0.2005 0.1835 4.5584 4.6103| | 8: 1.54 - 1.47 0.96 6798 152 0.2021 0.2212 4.4607 4.5615| | 9: 1.47 - 1.41 0.98 6938 155 0.2090 0.2174 4.3917 4.4723| | 10: 1.41 - 1.36 0.99 7022 150 0.2131 0.2139 4.3243 4.4111| | 11: 1.36 - 1.32 0.99 6997 151 0.2131 0.2070 4.2489 4.2332| | 12: 1.32 - 1.28 0.98 6976 149 0.2102 0.2167 4.1863 4.347| | 13: 1.28 - 1.25 0.98 6907 166 0.1998 0.2116 4.11 4.1986| | 14: 1.25 - 1.22 0.98 7015 113 0.2045 0.2328 4.0677 4.2445| | 15: 1.22 - 1.19 0.98 6957 137 0.2103 0.1827 4.0472 3.9694| | 16: 1.19 - 1.17 0.93 6604 132 0.2103 0.2309 4.0027 4.1296| | 17: 1.17 - 1.14 0.98 6941 135 0.2174 0.2035 3.9583 4.0282| | 18: 1.14 - 1.12 0.98 6875 142 0.2197 0.2444 3.9153 3.9878| | 19: 1.12 - 1.10 0.97 6949 106 0.2312 0.2550 3.8837 4.0044| | 20: 1.10 - 1.08 0.97 6884 147 0.2339 0.2073 3.8266 3.8021| | 21: 1.08 - 1.07 0.97 6852 152 0.2447 0.2793 3.7926 3.8318| | 22: 1.07 - 1.05 0.97 6838 135 0.2596 0.2544 3.7597 3.7665| | 23: 1.05 - 1.03 0.97 6829 159 0.2717 0.2349 3.7259 3.7188| | 24: 1.03 - 1.02 0.96 6785 133 0.2875 0.2899 3.6957 3.7869| | 25: 1.02 - 1.01 0.93 6552 130 0.3102 0.3091 3.6846 3.7621| | 26: 1.01 - 0.99 0.96 6767 158 0.3223 0.3238 3.6321 3.6284| | 27: 0.99 - 0.98 0.94 6648 131 0.3431 0.3143 3.6404 3.6246| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.59 0.91 0.97 35649.36| | 2: 2.94 - 2.33 7339 128 0.85 21.31 1.09 1.03 15293.89| | 3: 2.33 - 2.04 6939 150 0.93 12.55 1.11 1.07 4220.82| | 4: 2.04 - 1.85 7170 155 0.93 13.22 1.11 1.07 2704.92| | 5: 1.85 - 1.72 7113 159 0.91 14.99 1.11 1.08 1959.87| | 6: 1.72 - 1.62 7102 142 0.90 16.47 1.12 1.07 1619.02| | 7: 1.62 - 1.54 7104 148 0.89 17.55 1.11 1.07 1343.93| | 8: 1.54 - 1.47 6798 152 0.88 18.60 1.10 1.07 1176.40| | 9: 1.47 - 1.41 6938 155 0.88 19.16 1.10 1.06 989.86| | 10: 1.41 - 1.36 7022 150 0.87 20.59 1.09 1.05 900.95| | 11: 1.36 - 1.32 6997 151 0.86 20.80 1.08 1.04 787.17| | 12: 1.32 - 1.28 6976 149 0.86 20.97 1.08 1.03 711.89| | 13: 1.28 - 1.25 6907 166 0.87 20.71 1.07 1.04 648.33| | 14: 1.25 - 1.22 7015 113 0.86 20.99 1.08 1.05 584.99| | 15: 1.22 - 1.19 6957 137 0.86 20.92 1.08 1.06 554.35| | 16: 1.19 - 1.17 6604 132 0.87 20.60 1.07 1.04 502.92| | 17: 1.17 - 1.14 6941 135 0.85 21.95 1.09 1.02 478.21| | 18: 1.14 - 1.12 6875 142 0.86 21.94 1.08 0.99 421.15| | 19: 1.12 - 1.10 6949 106 0.85 22.68 1.07 1.00 392.73| | 20: 1.10 - 1.08 6884 147 0.85 22.44 1.06 0.99 342.34| | 21: 1.08 - 1.07 6852 152 0.84 23.41 1.05 0.98 324.12| | 22: 1.07 - 1.05 6838 135 0.83 24.68 1.05 0.97 302.98| | 23: 1.05 - 1.03 6829 159 0.81 26.44 1.05 0.96 303.64| | 24: 1.03 - 1.02 6785 133 0.79 28.66 1.05 0.98 314.36| | 25: 1.02 - 1.01 6552 130 0.77 30.37 1.03 0.95 309.85| | 26: 1.01 - 0.99 6767 158 0.75 32.29 1.03 0.92 297.51| | 27: 0.99 - 0.98 6648 131 0.75 32.02 1.04 0.91 271.54| |alpha: min = 0.91 max = 1.08 mean = 1.02| |beta: min = 271.54 max = 35649.36 mean = 2846.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 21.66| |phase err.(test): min = 0.00 max = 89.77 mean = 21.48| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.276 2950 Z= 5.510 Angle : 5.292 18.099 4018 Z= 3.773 Chirality : 0.392 1.296 492 Planarity : 0.034 0.120 512 Dihedral : 12.915 80.875 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.61 % Allowed : 4.19 % Favored : 94.19 % Cbeta Deviations : 28.65 % 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: -2.07 (0.39), residues: 386 helix: -2.48 (0.33), residues: 144 sheet: -1.05 (0.52), residues: 82 loop : -0.10 (0.50), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.064 0.014 ARG A 27 TYR 0.095 0.037 TYR A 192 PHE 0.098 0.035 PHE A 164 TRP 0.113 0.037 TRP A 146 HIS 0.136 0.041 HIS A 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= 0.2034 r_free= 0.2001 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300821 | | target function (ml) not normalized (work): 805599.738569 | | target function (ml) not normalized (free): 16599.470648 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2034 0.2001 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2034 0.2001 n_refl.: 191155 remove outliers: r(all,work,free)=0.2033 0.2034 0.2001 n_refl.: 191145 overall B=-0.03 to atoms: r(all,work,free)=0.2029 0.2030 0.1999 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1802 0.1931 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1801 0.1929 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4225 400.535 295.334 0.431 0.915 0.299 13.296-10.522 100.00 100 1 0.2558 534.497 520.388 0.777 0.917 0.250 10.503-8.327 98.90 177 3 0.2494 564.205 557.833 0.963 0.917 0.227 8.318-6.595 100.00 360 8 0.2498 414.736 403.564 0.965 0.917 0.165 6.588-5.215 100.00 711 7 0.2244 381.101 364.737 0.946 0.917 0.150 5.214-4.128 98.38 1367 28 0.1477 557.435 549.613 1.067 0.918 0.080 4.126-3.266 94.74 2603 46 0.1335 508.132 498.502 1.133 0.919 0.030 3.266-2.585 99.86 5447 97 0.1443 342.774 337.141 1.104 0.920 0.000 2.585-2.046 97.45 10613 204 0.1393 258.603 254.398 1.109 0.923 0.000 2.046-1.619 99.39 21536 464 0.1633 153.054 149.972 1.121 0.926 0.000 1.619-1.281 98.00 42464 925 0.1926 82.395 80.463 1.100 0.931 0.000 1.281-0.980 96.53 101826 2055 0.2317 44.202 42.035 1.077 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0733 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1801 r_free=0.1929 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1801 r_free=0.1929 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.392562 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 569.736705 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1273 0.1505 0.0232 0.039 1.2 11.4 0.0 0.3 0 11.196 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.05 2.32 1.118 13.084 569.737 0.018 13.00 15.77 2.77 1.249 13.374 569.737 0.017 Individual atomic B min max mean iso aniso Overall: 5.28 73.02 15.10 1.40 435 3274 Protein: 5.28 40.37 11.04 1.40 0 2902 Water: 6.36 73.02 29.70 N/A 435 370 Other: 16.27 29.78 23.02 N/A 0 2 Chain A: 5.33 59.62 13.10 N/A 0 1626 Chain B: 5.28 73.02 12.83 N/A 0 1648 Chain S: 11.56 68.13 31.16 N/A 435 0 Histogram: Values Number of atoms 5.28 - 12.05 2178 12.05 - 18.83 628 18.83 - 25.60 310 25.60 - 32.38 261 32.38 - 39.15 155 39.15 - 45.92 111 45.92 - 52.70 41 52.70 - 59.47 19 59.47 - 66.24 4 66.24 - 73.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1577 r_work=0.1299 r_free=0.1572 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1572 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 = 0.1284 r_free = 0.1563 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1284 r_free= 0.1563 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015628 | | target function (ls_wunit_k1) not normalized (work): 2927.146662 | | target function (ls_wunit_k1) not normalized (free): 115.685739 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1284 0.1563 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1475 0.1473 0.1638 n_refl.: 191139 remove outliers: r(all,work,free)=0.1475 0.1473 0.1638 n_refl.: 191139 overall B=0.14 to atoms: r(all,work,free)=0.1497 0.1494 0.1646 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1552 n_refl.: 191139 remove outliers: r(all,work,free)=0.1280 0.1275 0.1552 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 0.3595 402.814 375.051 0.464 0.997 0.275 13.296-10.522 100.00 100 1 0.2119 534.497 528.323 0.720 0.998 0.245 10.503-8.327 98.90 177 3 0.1718 564.205 561.593 0.856 0.998 0.198 8.318-6.595 100.00 360 8 0.1711 414.736 412.881 0.878 0.998 0.150 6.588-5.215 100.00 711 7 0.1541 381.101 373.242 0.855 0.998 0.140 5.214-4.128 98.38 1367 28 0.0901 557.435 554.831 0.943 0.999 0.055 4.126-3.266 94.74 2603 46 0.0828 508.132 504.205 1.008 0.999 0.018 3.266-2.585 99.86 5447 97 0.0921 342.774 340.332 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0954 258.603 256.376 1.002 1.000 0.000 2.046-1.619 99.39 21536 464 0.1093 153.054 151.408 1.018 1.000 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.426 1.010 1.001 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.155 0.988 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0328 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1552 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1552 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1552 | n_water=805 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1279 r_free=0.1555 | n_water=794 | time (s): 113.290 (total time: 115.750) Filter (q & B) r_work=0.1280 r_free=0.1556 | n_water=790 | time (s): 5.270 (total time: 121.020) Compute maps r_work=0.1280 r_free=0.1556 | n_water=790 | time (s): 1.830 (total time: 122.850) Filter (map) r_work=0.1306 r_free=0.1534 | n_water=647 | time (s): 4.170 (total time: 127.020) Find peaks r_work=0.1306 r_free=0.1534 | n_water=647 | time (s): 0.610 (total time: 127.630) Add new water r_work=0.1329 r_free=0.1567 | n_water=950 | time (s): 5.040 (total time: 132.670) Refine new water occ: r_work=0.1284 r_free=0.1520 adp: r_work=0.1273 r_free=0.1519 occ: r_work=0.1275 r_free=0.1517 adp: r_work=0.1269 r_free=0.1517 occ: r_work=0.1270 r_free=0.1517 adp: r_work=0.1268 r_free=0.1519 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1519 r_work=0.1268 r_free=0.1519 | n_water=950 | time (s): 99.050 (total time: 231.720) Filter (q & B) r_work=0.1272 r_free=0.1515 | n_water=876 | time (s): 5.480 (total time: 237.200) Filter (dist only) r_work=0.1272 r_free=0.1514 | n_water=875 | time (s): 110.960 (total time: 348.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.763903 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 584.785494 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 0.1254 0.1529 0.0274 0.041 1.1 15.5 0.0 0.3 0 11.882 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.29 2.74 2.049 15.211 584.785 0.015 12.33 15.11 2.78 2.447 15.249 584.785 0.014 Individual atomic B min max mean iso aniso Overall: 5.41 72.92 16.33 1.20 507 3272 Protein: 5.41 40.69 10.98 1.20 0 2902 Water: 6.52 72.92 34.07 N/A 507 368 Other: 16.48 32.72 24.60 N/A 0 2 Chain A: 5.54 55.30 13.01 N/A 0 1624 Chain B: 5.41 68.16 12.85 N/A 0 1648 Chain S: 9.54 72.92 38.30 N/A 507 0 Histogram: Values Number of atoms 5.41 - 12.16 2170 12.16 - 18.91 661 18.91 - 25.66 251 25.66 - 32.41 209 32.41 - 39.16 171 39.16 - 45.91 153 45.91 - 52.67 88 52.67 - 59.42 52 59.42 - 66.17 20 66.17 - 72.92 4 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1511 r_work=0.1234 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1512 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1508 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1508 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013490 | | target function (ls_wunit_k1) not normalized (work): 2526.640970 | | target function (ls_wunit_k1) not normalized (free): 102.180360 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1228 0.1508 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1600 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1436 0.1600 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1432 0.1598 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1235 0.1516 n_refl.: 191138 remove outliers: r(all,work,free)=0.1240 0.1235 0.1516 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 0.3280 402.814 374.889 0.484 0.962 0.266 13.296-10.522 100.00 100 1 0.1881 534.497 530.789 0.776 0.963 0.248 10.503-8.327 98.90 177 3 0.1392 564.205 565.706 0.916 0.963 0.169 8.318-6.595 100.00 360 8 0.1569 414.736 415.293 0.934 0.963 0.150 6.588-5.215 100.00 711 7 0.1350 381.101 376.645 0.912 0.963 0.140 5.214-4.128 98.38 1367 28 0.0834 557.435 555.836 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0763 508.132 505.498 1.061 0.963 0.014 3.266-2.585 99.86 5447 97 0.0858 342.774 341.308 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.796 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1048 153.054 151.618 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.348 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.212 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0565 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1516 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1516 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1516 | n_water=875 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1237 r_free=0.1516 | n_water=867 | time (s): 110.990 (total time: 113.390) Filter (q & B) r_work=0.1237 r_free=0.1516 | n_water=866 | time (s): 5.090 (total time: 118.480) Compute maps r_work=0.1237 r_free=0.1516 | n_water=866 | time (s): 1.900 (total time: 120.380) Filter (map) r_work=0.1274 r_free=0.1518 | n_water=688 | time (s): 5.270 (total time: 125.650) Find peaks r_work=0.1274 r_free=0.1518 | n_water=688 | time (s): 0.620 (total time: 126.270) Add new water r_work=0.1296 r_free=0.1547 | n_water=1019 | time (s): 3.820 (total time: 130.090) Refine new water occ: r_work=0.1251 r_free=0.1510 adp: r_work=0.1251 r_free=0.1510 occ: r_work=0.1247 r_free=0.1506 adp: r_work=0.1247 r_free=0.1507 occ: r_work=0.1244 r_free=0.1503 adp: r_work=0.1243 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1504 r_work=0.1243 r_free=0.1504 | n_water=1019 | time (s): 214.460 (total time: 344.550) Filter (q & B) r_work=0.1248 r_free=0.1515 | n_water=885 | time (s): 5.700 (total time: 350.250) Filter (dist only) r_work=0.1249 r_free=0.1515 | n_water=883 | time (s): 122.470 (total time: 472.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.715981 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.878849 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 0.1239 0.1431 0.0193 0.034 1.1 6.6 0.0 0.0 0 0.858 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.31 1.93 1.930 14.625 15.879 3.939 12.30 13.91 1.61 2.159 14.546 15.879 3.897 Individual atomic B min max mean iso aniso Overall: 5.53 67.86 15.37 1.07 517 3270 Protein: 5.53 37.55 10.78 1.07 0 2902 Water: 6.68 67.86 30.43 N/A 517 366 Other: 14.11 29.25 21.68 N/A 0 2 Chain A: 5.53 54.64 12.82 N/A 0 1624 Chain B: 5.53 67.86 12.59 N/A 0 1646 Chain S: 12.34 58.81 32.23 N/A 517 0 Histogram: Values Number of atoms 5.53 - 11.76 2120 11.76 - 17.99 698 17.99 - 24.23 293 24.23 - 30.46 224 30.46 - 36.69 189 36.69 - 42.93 148 42.93 - 49.16 74 49.16 - 55.39 35 55.39 - 61.63 5 61.63 - 67.86 1 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1391 r_work=0.1231 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1392 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1382 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1382 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891623 | | target function (ml) not normalized (work): 728889.228756 | | target function (ml) not normalized (free): 15223.668570 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1227 0.1382 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1441 0.1494 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1441 0.1494 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1435 0.1490 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1375 n_refl.: 191138 remove outliers: r(all,work,free)=0.1225 0.1222 0.1375 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3676 398.895 359.115 0.413 0.946 0.231 13.296-10.522 99.01 99 1 0.2531 528.187 513.117 0.713 0.947 0.205 10.503-8.327 97.80 175 3 0.1981 554.286 555.711 0.881 0.947 0.176 8.318-6.595 100.00 360 8 0.2075 414.736 410.269 0.897 0.947 0.135 6.588-5.215 100.00 711 7 0.1812 381.101 371.559 0.888 0.947 0.117 5.214-4.128 98.38 1367 28 0.1153 557.435 551.820 0.974 0.947 0.090 4.126-3.266 94.74 2603 46 0.1091 508.132 501.571 1.035 0.947 0.014 3.266-2.585 99.86 5447 97 0.1081 342.774 339.052 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0958 258.603 255.796 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0972 153.054 151.398 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.480 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1690 44.202 42.312 1.037 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1000 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1375 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1375 | n_water=883 | time (s): 3.030 (total time: 3.030) Filter (dist) r_work=0.1223 r_free=0.1378 | n_water=882 | time (s): 113.200 (total time: 116.230) Filter (q & B) r_work=0.1224 r_free=0.1372 | n_water=867 | time (s): 4.570 (total time: 120.800) Compute maps r_work=0.1224 r_free=0.1372 | n_water=867 | time (s): 2.160 (total time: 122.960) Filter (map) r_work=0.1243 r_free=0.1382 | n_water=722 | time (s): 4.570 (total time: 127.530) Find peaks r_work=0.1243 r_free=0.1382 | n_water=722 | time (s): 0.870 (total time: 128.400) Add new water r_work=0.1259 r_free=0.1397 | n_water=963 | time (s): 4.500 (total time: 132.900) Refine new water occ: r_work=0.1212 r_free=0.1362 adp: r_work=0.1204 r_free=0.1356 occ: r_work=0.1201 r_free=0.1357 adp: r_work=0.1201 r_free=0.1356 occ: r_work=0.1200 r_free=0.1357 adp: r_work=0.1200 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1356 r_work=0.1200 r_free=0.1356 | n_water=963 | time (s): 244.490 (total time: 377.390) Filter (q & B) r_work=0.1204 r_free=0.1358 | n_water=874 | time (s): 4.480 (total time: 381.870) Filter (dist only) r_work=0.1205 r_free=0.1357 | n_water=873 | time (s): 115.340 (total time: 497.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558005 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.474491 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 0.1354 0.0151 0.034 1.1 6.0 0.0 0.0 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.54 1.51 1.846 14.274 16.474 3.874 11.96 13.49 1.53 2.013 14.215 16.474 3.864 Individual atomic B min max mean iso aniso Overall: 5.50 67.26 15.01 1.01 507 3270 Protein: 5.50 33.84 10.66 1.01 0 2902 Water: 5.84 67.26 29.49 N/A 507 366 Other: 13.92 27.64 20.78 N/A 0 2 Chain A: 5.57 53.93 12.64 N/A 0 1624 Chain B: 5.50 67.26 12.44 N/A 0 1646 Chain S: 5.84 58.88 30.97 N/A 507 0 Histogram: Values Number of atoms 5.50 - 11.68 2110 11.68 - 17.85 733 17.85 - 24.03 299 24.03 - 30.20 226 30.20 - 36.38 174 36.38 - 42.55 131 42.55 - 48.73 69 48.73 - 54.90 27 54.90 - 61.08 7 61.08 - 67.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1350 r_work=0.1197 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1350 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1347 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861915 | | target function (ml) not normalized (work): 723305.691590 | | target function (ml) not normalized (free): 15123.956271 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1347 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1467 n_refl.: 191133 remove outliers: r(all,work,free)=0.1404 0.1403 0.1467 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1397 0.1396 0.1462 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1346 n_refl.: 191133 remove outliers: r(all,work,free)=0.1195 0.1192 0.1346 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 0.3731 356.788 324.544 0.400 0.949 0.217 13.296-10.522 97.03 97 1 0.2435 481.349 452.928 0.700 0.951 0.199 10.503-8.327 97.80 175 3 0.2042 502.069 497.657 0.862 0.951 0.198 8.318-6.595 100.00 360 8 0.2158 375.666 370.803 0.886 0.950 0.105 6.588-5.215 100.00 711 7 0.1868 345.199 335.894 0.883 0.951 0.095 5.214-4.128 98.38 1367 28 0.1171 504.921 499.883 0.971 0.951 0.090 4.126-3.266 94.74 2603 46 0.1105 460.263 453.960 1.031 0.951 0.000 3.266-2.585 99.86 5447 97 0.1080 310.482 307.237 1.017 0.951 0.000 2.585-2.046 97.45 10613 204 0.0933 234.241 231.843 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0916 138.636 137.330 1.052 0.950 0.000 1.619-1.281 98.00 42464 925 0.0986 74.633 73.920 1.048 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.038 38.371 1.032 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1124 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1346 | n_water=873 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1192 r_free=0.1346 | n_water=873 | time (s): 106.640 (total time: 108.870) Filter (q & B) r_work=0.1192 r_free=0.1347 | n_water=865 | time (s): 5.240 (total time: 114.110) Compute maps r_work=0.1192 r_free=0.1347 | n_water=865 | time (s): 1.980 (total time: 116.090) Filter (map) r_work=0.1212 r_free=0.1350 | n_water=752 | time (s): 4.340 (total time: 120.430) Find peaks r_work=0.1212 r_free=0.1350 | n_water=752 | time (s): 0.540 (total time: 120.970) Add new water r_work=0.1223 r_free=0.1365 | n_water=968 | time (s): 4.430 (total time: 125.400) Refine new water occ: r_work=0.1189 r_free=0.1340 adp: r_work=0.1190 r_free=0.1340 occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1187 r_free=0.1340 occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1185 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1341 r_work=0.1185 r_free=0.1341 | n_water=968 | time (s): 207.430 (total time: 332.830) Filter (q & B) r_work=0.1190 r_free=0.1346 | n_water=897 | time (s): 5.200 (total time: 338.030) Filter (dist only) r_work=0.1190 r_free=0.1344 | n_water=896 | time (s): 117.700 (total time: 455.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.460326 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.927733 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1348 0.0155 0.035 1.1 8.0 0.0 0.0 0 0.730 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.48 1.55 1.795 14.177 14.928 3.763 11.97 13.51 1.54 1.822 14.165 14.928 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 67.07 15.06 0.97 530 3270 Protein: 5.57 33.02 10.61 0.97 0 2902 Water: 5.90 67.07 29.43 N/A 530 366 Other: 13.78 27.16 20.47 N/A 0 2 Chain A: 5.62 53.83 12.58 N/A 0 1624 Chain B: 5.57 67.07 12.39 N/A 0 1646 Chain S: 5.90 58.88 30.94 N/A 530 0 Histogram: Values Number of atoms 5.57 - 11.72 2138 11.72 - 17.87 721 17.87 - 24.02 298 24.02 - 30.17 217 30.17 - 36.32 185 36.32 - 42.47 137 42.47 - 48.62 72 48.62 - 54.77 26 54.77 - 60.92 5 60.92 - 67.07 1 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1351 r_work=0.1197 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1351 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1355 target_work(ml) = 3.761 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761175 | | target function (ml) not normalized (work): 704426.780192 | | target function (ml) not normalized (free): 14740.605329 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1355 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1400 0.1399 0.1479 n_refl.: 191130 remove outliers: r(all,work,free)=0.1400 0.1399 0.1479 n_refl.: 191130 overall B=-0.03 to atoms: r(all,work,free)=0.1394 0.1392 0.1474 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1355 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1194 0.1355 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3720 356.788 321.297 0.387 0.951 0.213 13.296-10.522 97.03 97 1 0.2476 481.349 460.148 0.703 0.953 0.195 10.503-8.327 97.80 175 3 0.2068 502.069 494.911 0.862 0.953 0.161 8.315-6.595 100.00 359 8 0.2098 374.719 370.420 0.885 0.953 0.116 6.588-5.215 100.00 711 7 0.1895 345.199 335.843 0.882 0.953 0.100 5.214-4.128 98.38 1367 28 0.1186 504.921 499.630 0.971 0.953 0.090 4.126-3.266 94.74 2603 46 0.1117 460.263 453.561 1.029 0.953 0.000 3.266-2.585 99.86 5447 97 0.1091 310.482 307.199 1.015 0.952 0.000 2.585-2.046 97.45 10613 204 0.0941 234.241 231.742 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0918 138.636 137.313 1.051 0.951 0.000 1.619-1.281 98.00 42464 925 0.0980 74.633 73.908 1.049 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1655 40.038 38.356 1.036 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1183 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1355 | n_water=896 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1194 r_free=0.1356 | n_water=895 | time (s): 113.420 (total time: 116.570) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=885 | time (s): 4.600 (total time: 121.170) Compute maps r_work=0.1194 r_free=0.1356 | n_water=885 | time (s): 1.920 (total time: 123.090) Filter (map) r_work=0.1215 r_free=0.1355 | n_water=774 | time (s): 3.820 (total time: 126.910) Find peaks r_work=0.1215 r_free=0.1355 | n_water=774 | time (s): 0.540 (total time: 127.450) Add new water r_work=0.1225 r_free=0.1371 | n_water=963 | time (s): 3.920 (total time: 131.370) Refine new water occ: r_work=0.1194 r_free=0.1345 adp: r_work=0.1194 r_free=0.1344 occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1192 r_free=0.1344 occ: r_work=0.1190 r_free=0.1346 adp: r_work=0.1190 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1345 r_work=0.1190 r_free=0.1345 | n_water=963 | time (s): 284.240 (total time: 415.610) Filter (q & B) r_work=0.1194 r_free=0.1354 | n_water=895 | time (s): 4.920 (total time: 420.530) Filter (dist only) r_work=0.1194 r_free=0.1352 | n_water=894 | time (s): 111.610 (total time: 532.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560081 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.225048 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1357 0.0160 0.036 1.1 6.5 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.57 1.60 1.774 14.103 14.225 3.762 12.02 13.65 1.63 1.937 14.045 14.225 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 66.00 14.90 0.90 528 3270 Protein: 5.58 29.74 10.49 0.90 0 2902 Water: 5.87 66.00 29.20 N/A 528 366 Other: 13.84 24.12 18.98 N/A 0 2 Chain A: 5.60 53.33 12.42 N/A 0 1624 Chain B: 5.58 66.00 12.24 N/A 0 1646 Chain S: 5.87 55.95 30.82 N/A 528 0 Histogram: Values Number of atoms 5.58 - 11.62 2116 11.62 - 17.66 770 17.66 - 23.71 278 23.71 - 29.75 200 29.75 - 35.79 191 35.79 - 41.83 132 41.83 - 47.87 73 47.87 - 53.91 31 53.91 - 59.96 6 59.96 - 66.00 1 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1365 r_work=0.1203 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1369 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761113 | | target function (ml) not normalized (work): 704411.311107 | | target function (ml) not normalized (free): 14751.049440 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1369 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1489 n_refl.: 191129 remove outliers: r(all,work,free)=0.1407 0.1406 0.1489 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1400 0.1399 0.1484 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1361 n_refl.: 191129 remove outliers: r(all,work,free)=0.1203 0.1200 0.1361 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3712 356.463 318.333 0.321 0.951 0.090 13.296-10.522 97.03 97 1 0.2502 481.349 458.577 0.685 0.952 0.134 10.503-8.327 97.80 175 3 0.2172 502.069 495.263 0.861 0.953 0.135 8.315-6.595 100.00 359 8 0.2132 374.719 369.552 0.882 0.952 0.115 6.588-5.215 100.00 711 7 0.1923 345.199 335.584 0.882 0.952 0.100 5.214-4.128 98.38 1367 28 0.1217 504.921 499.617 0.973 0.953 0.090 4.126-3.266 94.74 2603 46 0.1139 460.263 453.506 1.031 0.953 0.000 3.266-2.585 99.86 5447 97 0.1113 310.482 307.192 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0950 234.241 231.745 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0916 138.636 137.333 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0976 74.633 73.931 1.049 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.038 38.373 1.036 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1317 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1361 | n_water=894 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1200 r_free=0.1361 | n_water=894 | time (s): 105.740 (total time: 108.170) Filter (q & B) r_work=0.1200 r_free=0.1363 | n_water=888 | time (s): 5.560 (total time: 113.730) Compute maps r_work=0.1200 r_free=0.1363 | n_water=888 | time (s): 2.230 (total time: 115.960) Filter (map) r_work=0.1219 r_free=0.1349 | n_water=774 | time (s): 5.150 (total time: 121.110) Find peaks r_work=0.1219 r_free=0.1349 | n_water=774 | time (s): 0.610 (total time: 121.720) Add new water r_work=0.1230 r_free=0.1363 | n_water=961 | time (s): 4.210 (total time: 125.930) Refine new water occ: r_work=0.1199 r_free=0.1341 adp: r_work=0.1199 r_free=0.1341 occ: r_work=0.1197 r_free=0.1341 adp: r_work=0.1197 r_free=0.1341 occ: r_work=0.1195 r_free=0.1342 adp: r_work=0.1195 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1342 r_work=0.1195 r_free=0.1342 | n_water=961 | time (s): 249.420 (total time: 375.350) Filter (q & B) r_work=0.1198 r_free=0.1348 | n_water=904 | time (s): 4.420 (total time: 379.770) Filter (dist only) r_work=0.1198 r_free=0.1347 | n_water=903 | time (s): 119.320 (total time: 499.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.603228 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.830226 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1348 0.0148 0.036 1.1 5.8 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.48 1.48 1.721 13.958 14.830 3.761 11.99 13.50 1.51 1.776 13.936 14.830 3.756 Individual atomic B min max mean iso aniso Overall: 5.57 64.81 14.85 0.89 537 3270 Protein: 5.57 29.00 10.43 0.89 0 2902 Water: 5.92 64.81 29.03 N/A 537 366 Other: 13.88 22.17 18.03 N/A 0 2 Chain A: 5.64 52.87 12.32 N/A 0 1624 Chain B: 5.57 64.81 12.15 N/A 0 1646 Chain S: 5.92 55.54 30.76 N/A 537 0 Histogram: Values Number of atoms 5.57 - 11.50 2090 11.50 - 17.42 794 17.42 - 23.34 277 23.34 - 29.27 205 29.27 - 35.19 183 35.19 - 41.12 130 41.12 - 47.04 85 47.04 - 52.96 35 52.96 - 58.89 7 58.89 - 64.81 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1350 r_work=0.1199 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1350 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 = 0.1350 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755789 | | target function (ml) not normalized (work): 703410.446354 | | target function (ml) not normalized (free): 14729.698250 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1350 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1394 0.1392 0.1472 n_refl.: 191128 remove outliers: r(all,work,free)=0.1394 0.1392 0.1472 n_refl.: 191128 overall B=-0.01 to atoms: r(all,work,free)=0.1393 0.1391 0.1471 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1335 n_refl.: 191128 remove outliers: r(all,work,free)=0.1190 0.1187 0.1335 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3625 356.230 324.309 0.318 0.985 0.070 13.296-10.522 96.04 96 1 0.2404 480.468 452.113 0.663 0.986 0.103 10.503-8.327 97.80 175 3 0.2183 502.069 494.121 0.846 0.987 0.114 8.315-6.595 100.00 359 8 0.2147 374.719 370.318 0.868 0.987 0.108 6.588-5.215 100.00 711 7 0.1911 345.199 335.531 0.870 0.987 0.105 5.214-4.128 98.38 1367 28 0.1240 504.921 499.051 0.959 0.988 0.066 4.126-3.266 94.74 2603 46 0.1138 460.263 452.965 1.018 0.989 0.000 3.266-2.585 99.86 5447 97 0.1116 310.482 306.890 1.002 0.990 0.000 2.585-2.046 97.45 10613 204 0.0953 234.241 231.664 1.012 0.992 0.000 2.046-1.619 99.39 21536 464 0.0906 138.636 137.260 1.030 0.995 0.000 1.619-1.281 98.00 42464 925 0.0947 74.633 73.988 1.023 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.038 38.337 0.996 1.009 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0187 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1335 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1335 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1335 | n_water=903 | time (s): 3.220 (total time: 3.220) Filter (dist) r_work=0.1187 r_free=0.1335 | n_water=903 | time (s): 104.320 (total time: 107.540) Filter (q & B) r_work=0.1187 r_free=0.1337 | n_water=896 | time (s): 4.360 (total time: 111.900) Compute maps r_work=0.1187 r_free=0.1337 | n_water=896 | time (s): 1.640 (total time: 113.540) Filter (map) r_work=0.1208 r_free=0.1338 | n_water=781 | time (s): 4.660 (total time: 118.200) Find peaks r_work=0.1208 r_free=0.1338 | n_water=781 | time (s): 0.580 (total time: 118.780) Add new water r_work=0.1215 r_free=0.1343 | n_water=972 | time (s): 5.060 (total time: 123.840) Refine new water occ: r_work=0.1185 r_free=0.1321 adp: r_work=0.1185 r_free=0.1320 occ: r_work=0.1183 r_free=0.1322 adp: r_work=0.1183 r_free=0.1321 occ: r_work=0.1182 r_free=0.1323 adp: r_work=0.1182 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1323 r_work=0.1182 r_free=0.1323 | n_water=972 | time (s): 212.070 (total time: 335.910) Filter (q & B) r_work=0.1186 r_free=0.1334 | n_water=908 | time (s): 4.580 (total time: 340.490) Filter (dist only) r_work=0.1186 r_free=0.1333 | n_water=906 | time (s): 119.190 (total time: 459.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540296 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.296717 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1338 0.0148 0.037 1.1 6.5 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.38 1.48 1.705 13.910 14.297 3.754 11.91 13.40 1.50 1.711 13.904 14.297 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 64.43 14.83 0.88 540 3270 Protein: 5.56 28.68 10.44 0.88 0 2902 Water: 6.02 64.43 28.88 N/A 540 366 Other: 13.86 22.24 18.05 N/A 0 2 Chain A: 5.66 52.71 12.30 N/A 0 1624 Chain B: 5.56 64.43 12.14 N/A 0 1646 Chain S: 6.02 55.54 30.65 N/A 540 0 Histogram: Values Number of atoms 5.56 - 11.44 2069 11.44 - 17.33 816 17.33 - 23.22 276 23.22 - 29.11 202 29.11 - 34.99 189 34.99 - 40.88 132 40.88 - 46.77 83 46.77 - 52.66 32 52.66 - 58.54 10 58.54 - 64.43 1 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1340 r_work=0.1191 r_free=0.1341 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1341 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1344 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753420 | | target function (ml) not normalized (work): 702959.304892 | | target function (ml) not normalized (free): 14723.639082 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1344 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1495 n_refl.: 191126 remove outliers: r(all,work,free)=0.1393 0.1391 0.1495 n_refl.: 191126 overall B=-0.01 to atoms: r(all,work,free)=0.1390 0.1388 0.1493 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1343 n_refl.: 191126 remove outliers: r(all,work,free)=0.1192 0.1189 0.1343 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3641 356.230 331.595 0.311 0.988 0.040 13.296-10.522 96.04 96 1 0.2390 480.468 459.993 0.668 0.989 0.090 10.503-8.327 97.80 175 3 0.2194 502.069 494.025 0.843 0.990 0.107 8.315-6.595 100.00 359 8 0.2157 374.719 369.272 0.864 0.990 0.106 6.588-5.215 100.00 711 7 0.1940 345.199 335.119 0.867 0.990 0.106 5.214-4.128 98.38 1367 28 0.1249 504.921 498.663 0.957 0.991 0.067 4.126-3.266 94.74 2603 46 0.1151 460.263 452.848 1.016 0.992 0.000 3.266-2.585 99.86 5447 97 0.1119 310.482 306.859 1.000 0.993 0.000 2.585-2.046 97.45 10613 204 0.0956 234.241 231.576 1.010 0.995 0.000 2.046-1.619 99.39 21536 464 0.0908 138.636 137.256 1.028 0.998 0.000 1.619-1.281 98.00 42464 925 0.0944 74.633 73.981 1.022 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.038 38.320 0.996 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0397 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1343 | n_water=906 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1189 r_free=0.1343 | n_water=906 | time (s): 109.310 (total time: 112.040) Filter (q & B) r_work=0.1189 r_free=0.1343 | n_water=895 | time (s): 4.540 (total time: 116.580) Compute maps r_work=0.1189 r_free=0.1343 | n_water=895 | time (s): 2.200 (total time: 118.780) Filter (map) r_work=0.1209 r_free=0.1337 | n_water=782 | time (s): 5.080 (total time: 123.860) Find peaks r_work=0.1209 r_free=0.1337 | n_water=782 | time (s): 0.760 (total time: 124.620) Add new water r_work=0.1217 r_free=0.1343 | n_water=985 | time (s): 4.050 (total time: 128.670) Refine new water occ: r_work=0.1185 r_free=0.1322 adp: r_work=0.1185 r_free=0.1322 occ: r_work=0.1183 r_free=0.1322 adp: r_work=0.1183 r_free=0.1322 occ: r_work=0.1182 r_free=0.1323 adp: r_work=0.1182 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1323 r_work=0.1182 r_free=0.1323 | n_water=985 | time (s): 233.680 (total time: 362.350) Filter (q & B) r_work=0.1186 r_free=0.1333 | n_water=914 | time (s): 5.070 (total time: 367.420) Filter (dist only) r_work=0.1186 r_free=0.1332 | n_water=911 | time (s): 118.530 (total time: 485.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.500690 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.860059 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1338 0.0147 0.037 1.1 6.5 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.38 1.47 1.699 13.898 14.860 3.754 11.90 13.39 1.50 1.708 13.890 14.860 3.752 Individual atomic B min max mean iso aniso Overall: 5.61 63.62 14.81 0.88 545 3270 Protein: 5.61 28.47 10.43 0.88 0 2902 Water: 6.03 63.62 28.74 N/A 545 366 Other: 13.89 22.24 18.06 N/A 0 2 Chain A: 5.68 52.38 12.26 N/A 0 1624 Chain B: 5.61 63.62 12.11 N/A 0 1646 Chain S: 6.03 55.63 30.55 N/A 545 0 Histogram: Values Number of atoms 5.61 - 11.41 2062 11.41 - 17.21 826 17.21 - 23.01 274 23.01 - 28.81 206 28.81 - 34.61 180 34.61 - 40.41 131 40.41 - 46.21 90 46.21 - 52.01 33 52.01 - 57.82 12 57.82 - 63.62 1 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1340 r_work=0.1190 r_free=0.1340 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1340 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1341 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1341 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751572 | | target function (ml) not normalized (work): 702613.213173 | | target function (ml) not normalized (free): 14722.561870 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1341 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1499 n_refl.: 191126 remove outliers: r(all,work,free)=0.1397 0.1395 0.1499 n_refl.: 191126 overall B=-0.02 to atoms: r(all,work,free)=0.1393 0.1391 0.1497 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1343 n_refl.: 191126 remove outliers: r(all,work,free)=0.1190 0.1187 0.1343 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3645 356.230 330.761 0.303 0.995 0.030 13.296-10.522 96.04 96 1 0.2392 480.468 460.751 0.668 0.996 0.100 10.503-8.327 97.80 175 3 0.2196 502.069 494.691 0.837 0.997 0.103 8.315-6.595 100.00 359 8 0.2160 374.719 369.638 0.856 0.997 0.101 6.588-5.215 100.00 711 7 0.1942 345.199 335.114 0.860 0.997 0.100 5.214-4.128 98.38 1367 28 0.1240 504.921 498.439 0.951 0.998 0.100 4.126-3.266 94.74 2603 46 0.1154 460.263 452.809 1.009 0.999 0.000 3.266-2.585 99.86 5447 97 0.1121 310.482 306.905 0.993 1.000 0.000 2.585-2.046 97.45 10613 204 0.0955 234.241 231.550 1.002 1.003 0.000 2.046-1.619 99.39 21536 464 0.0906 138.636 137.262 1.021 1.007 0.000 1.619-1.281 98.00 42464 925 0.0941 74.633 73.981 1.015 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.038 38.311 0.989 1.023 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0535 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1343 After: r_work=0.1188 r_free=0.1343 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1343 | n_water=911 | time (s): 2.930 (total time: 2.930) Filter (dist) r_work=0.1188 r_free=0.1343 | n_water=911 | time (s): 116.280 (total time: 119.210) Filter (q & B) r_work=0.1189 r_free=0.1345 | n_water=900 | time (s): 4.660 (total time: 123.870) Compute maps r_work=0.1189 r_free=0.1345 | n_water=900 | time (s): 1.610 (total time: 125.480) Filter (map) r_work=0.1207 r_free=0.1334 | n_water=792 | time (s): 4.870 (total time: 130.350) Find peaks r_work=0.1207 r_free=0.1334 | n_water=792 | time (s): 0.640 (total time: 130.990) Add new water r_work=0.1216 r_free=0.1339 | n_water=993 | time (s): 4.720 (total time: 135.710) Refine new water occ: r_work=0.1185 r_free=0.1322 adp: r_work=0.1186 r_free=0.1322 occ: r_work=0.1184 r_free=0.1323 adp: r_work=0.1183 r_free=0.1323 occ: r_work=0.1182 r_free=0.1324 adp: r_work=0.1182 r_free=0.1324 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1324 r_work=0.1182 r_free=0.1324 | n_water=993 | time (s): 191.770 (total time: 327.480) Filter (q & B) r_work=0.1186 r_free=0.1334 | n_water=918 | time (s): 4.850 (total time: 332.330) Filter (dist only) r_work=0.1186 r_free=0.1333 | n_water=916 | time (s): 121.380 (total time: 453.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566882 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.084181 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 0.1188 0.1340 0.0152 0.038 1.2 10.1 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.40 1.52 1.695 13.885 14.084 3.753 11.89 13.42 1.53 1.690 13.886 14.084 3.753 Individual atomic B min max mean iso aniso Overall: 5.62 63.40 14.81 0.87 550 3270 Protein: 5.62 28.38 10.43 0.87 0 2902 Water: 6.08 63.40 28.68 N/A 550 366 Other: 13.91 22.20 18.05 N/A 0 2 Chain A: 5.72 52.28 12.24 N/A 0 1624 Chain B: 5.62 63.40 12.10 N/A 0 1646 Chain S: 6.08 55.61 30.54 N/A 550 0 Histogram: Values Number of atoms 5.62 - 11.40 2058 11.40 - 17.17 833 17.17 - 22.95 268 22.95 - 28.73 213 28.73 - 34.51 181 34.51 - 40.29 131 40.29 - 46.06 89 46.06 - 51.84 33 51.84 - 57.62 13 57.62 - 63.40 1 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1342 r_work=0.1189 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1342 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1344 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752866 | | target function (ml) not normalized (work): 702855.516731 | | target function (ml) not normalized (free): 14723.066289 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7394 127 0.1348 0.1407 5.6776 5.7325| | 2: 2.94 - 2.33 1.00 7339 128 0.1065 0.1337 5.0647 5.1669| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1170 4.6536 4.7454| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1069 4.3919 4.5676| | 5: 1.85 - 1.72 0.99 7113 159 0.0933 0.0989 4.1495 4.2396| | 6: 1.72 - 1.62 0.99 7102 142 0.0895 0.1096 3.9455 4.0846| | 7: 1.62 - 1.54 0.99 7104 148 0.0891 0.0952 3.8019 3.9326| | 8: 1.54 - 1.47 0.96 6798 152 0.0889 0.1312 3.6995 3.9038| | 9: 1.47 - 1.41 0.98 6938 155 0.0922 0.1119 3.6205 3.7521| | 10: 1.41 - 1.36 0.99 7022 150 0.0971 0.1190 3.5542 3.672| | 11: 1.36 - 1.32 0.99 6997 151 0.0991 0.1134 3.4851 3.5872| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1138 3.4599 3.5874| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1247 3.4376 3.5707| | 14: 1.25 - 1.22 0.98 7015 112 0.1103 0.1574 3.4325 3.682| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1239 3.4473 3.4879| | 16: 1.19 - 1.17 0.93 6604 132 0.1248 0.1541 3.464 3.6521| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1225 3.4328 3.4412| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1711 3.4383 3.5345| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1750 3.4192 3.5926| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1580 3.4094 3.4332| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2133 3.4178 3.5045| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1942 3.4128 3.4138| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2021 3.4334 3.4862| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2256 3.436 3.5108| | 25: 1.02 - 1.01 0.93 6552 130 0.2610 0.2514 3.4494 3.5236| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2849 3.4161 3.4228| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2811 3.4682 3.3981| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7394 127 0.93 11.21 1.00 0.97 10545.19| | 2: 2.94 - 2.33 7339 128 0.93 12.42 0.99 0.96 4890.29| | 3: 2.33 - 2.04 6939 150 0.96 7.56 1.01 0.96 1676.64| | 4: 2.04 - 1.85 7170 155 0.96 7.60 1.00 0.96 996.32| | 5: 1.85 - 1.72 7113 159 0.96 8.08 1.00 0.97 631.58| | 6: 1.72 - 1.62 7102 142 0.96 8.04 1.00 0.97 444.22| | 7: 1.62 - 1.54 7104 148 0.96 8.17 1.01 0.98 338.61| | 8: 1.54 - 1.47 6798 152 0.96 8.30 1.01 0.98 280.36| | 9: 1.47 - 1.41 6938 155 0.96 8.47 1.00 0.99 231.52| | 10: 1.41 - 1.36 7022 150 0.96 8.89 1.00 0.98 202.78| | 11: 1.36 - 1.32 6997 151 0.96 8.96 0.99 0.97 175.46| | 12: 1.32 - 1.28 6975 149 0.96 9.02 0.98 0.96 161.61| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.97 159.37| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.97 163.68| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 0.99 166.68| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.97 159.90| | 17: 1.17 - 1.14 6940 135 0.94 12.22 1.01 0.97 153.61| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.96 147.43| | 19: 1.12 - 1.10 6948 106 0.93 14.12 1.00 0.96 150.85| | 20: 1.10 - 1.08 6884 147 0.92 15.21 1.00 0.95 150.05| | 21: 1.08 - 1.07 6852 152 0.91 16.63 1.00 0.94 153.10| | 22: 1.07 - 1.05 6836 135 0.89 18.30 1.00 0.94 154.94| | 23: 1.05 - 1.03 6827 159 0.87 20.51 1.00 0.93 164.78| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.94 179.25| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.91 182.38| | 26: 1.01 - 0.99 6767 158 0.81 26.70 0.98 0.90 177.34| | 27: 0.99 - 0.98 6647 131 0.82 26.43 0.99 0.89 162.37| |alpha: min = 0.89 max = 0.99 mean = 0.96| |beta: min = 147.43 max = 10545.19 mean = 889.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.26| |phase err.(test): min = 0.00 max = 87.18 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1344 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1402 0.1400 0.1498 n_refl.: 191126 remove outliers: r(all,work,free)=0.1402 0.1400 0.1498 n_refl.: 191126 overall B=-0.12 to atoms: r(all,work,free)=0.1383 0.1381 0.1484 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191126 remove outliers: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3652 356.230 331.072 0.295 0.994 0.020 13.296-10.522 96.04 96 1 0.2336 480.468 462.297 0.658 0.995 0.100 10.503-8.327 97.80 175 3 0.2191 502.069 494.983 0.823 0.996 0.099 8.315-6.595 100.00 359 8 0.2143 374.719 369.591 0.846 0.996 0.095 6.588-5.215 100.00 711 7 0.1933 345.199 334.964 0.847 0.996 0.092 5.214-4.128 98.38 1367 28 0.1243 504.921 498.598 0.937 0.997 0.070 4.126-3.266 94.74 2603 46 0.1152 460.263 452.909 0.995 0.999 0.000 3.266-2.585 99.86 5447 97 0.1115 310.482 307.040 0.978 1.000 0.000 2.585-2.046 97.45 10613 204 0.0960 234.241 231.577 0.985 1.003 0.000 2.046-1.619 99.39 21536 464 0.0910 138.636 137.254 1.000 1.007 0.000 1.619-1.281 98.00 42464 925 0.0944 74.633 73.980 0.990 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.038 38.310 0.957 1.027 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0258 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2034 0.2001 0.082 5.292 5.2 78.0 14.6 805 0.000 1_bss: 0.1801 0.1929 0.082 5.292 5.2 78.0 14.6 805 0.000 1_settarget: 0.1801 0.1929 0.082 5.292 5.2 78.0 14.6 805 0.000 1_nqh: 0.1801 0.1929 0.082 5.292 5.2 78.0 14.6 805 0.000 1_weight: 0.1801 0.1929 0.082 5.292 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1273 0.1505 0.039 1.153 5.2 78.0 14.6 805 0.158 1_adp: 0.1300 0.1577 0.039 1.153 5.3 73.0 15.1 805 0.158 1_regHadp: 0.1299 0.1572 0.039 1.153 5.3 73.0 15.1 805 0.158 1_occ: 0.1284 0.1563 0.039 1.153 5.3 73.0 15.1 805 0.158 2_bss: 0.1275 0.1552 0.039 1.153 5.4 73.2 15.2 805 0.158 2_settarget: 0.1275 0.1552 0.039 1.153 5.4 73.2 15.2 805 0.158 2_updatecdl: 0.1275 0.1552 0.039 1.163 5.4 73.2 15.2 805 0.158 2_nqh: 0.1275 0.1552 0.039 1.163 5.4 73.2 15.2 805 0.158 2_sol: 0.1272 0.1514 0.039 1.163 5.4 73.2 16.3 875 n/a 2_weight: 0.1272 0.1514 0.039 1.163 5.4 73.2 16.3 875 n/a 2_xyzrec: 0.1254 0.1529 0.041 1.149 5.4 73.2 16.3 875 n/a 2_adp: 0.1234 0.1511 0.041 1.149 5.4 72.9 16.3 875 n/a 2_regHadp: 0.1234 0.1512 0.041 1.149 5.4 72.9 16.3 875 n/a 2_occ: 0.1228 0.1508 0.041 1.149 5.4 72.9 16.3 875 n/a 3_bss: 0.1235 0.1516 0.041 1.149 5.4 72.9 16.3 875 n/a 3_settarget: 0.1235 0.1516 0.041 1.149 5.4 72.9 16.3 875 n/a 3_updatecdl: 0.1235 0.1516 0.041 1.147 5.4 72.9 16.3 875 n/a 3_nqh: 0.1235 0.1516 0.041 1.147 5.4 72.9 16.3 875 n/a 3_sol: 0.1249 0.1515 0.041 1.147 5.4 68.1 15.5 883 n/a 3_weight: 0.1249 0.1515 0.041 1.147 5.4 68.1 15.5 883 n/a 3_xyzrec: 0.1239 0.1431 0.034 1.107 5.4 68.1 15.5 883 n/a 3_adp: 0.1231 0.1391 0.034 1.107 5.5 67.9 15.4 883 n/a 3_regHadp: 0.1231 0.1392 0.034 1.107 5.5 67.9 15.4 883 n/a 3_occ: 0.1227 0.1382 0.034 1.107 5.5 67.9 15.4 883 n/a 4_bss: 0.1222 0.1375 0.034 1.107 5.5 67.8 15.3 883 n/a 4_settarget: 0.1222 0.1375 0.034 1.107 5.5 67.8 15.3 883 n/a 4_updatecdl: 0.1222 0.1375 0.034 1.111 5.5 67.8 15.3 883 n/a 4_nqh: 0.1222 0.1375 0.034 1.111 5.5 67.8 15.3 883 n/a 4_sol: 0.1205 0.1357 0.034 1.111 5.5 67.8 15.1 873 n/a 4_weight: 0.1205 0.1357 0.034 1.111 5.5 67.8 15.1 873 n/a 4_xyzrec: 0.1203 0.1354 0.034 1.132 5.5 67.8 15.1 873 n/a 4_adp: 0.1196 0.1350 0.034 1.132 5.5 67.3 15.0 873 n/a 4_regHadp: 0.1197 0.1350 0.034 1.132 5.5 67.3 15.0 873 n/a 4_occ: 0.1194 0.1347 0.034 1.132 5.5 67.3 15.0 873 n/a 5_bss: 0.1192 0.1346 0.034 1.132 5.5 67.2 15.0 873 n/a 5_settarget: 0.1192 0.1346 0.034 1.132 5.5 67.2 15.0 873 n/a 5_updatecdl: 0.1192 0.1346 0.034 1.132 5.5 67.2 15.0 873 n/a 5_nqh: 0.1192 0.1346 0.034 1.132 5.5 67.2 15.0 873 n/a 5_sol: 0.1190 0.1344 0.034 1.132 5.5 67.2 15.1 896 n/a 5_weight: 0.1190 0.1344 0.034 1.132 5.5 67.2 15.1 896 n/a 5_xyzrec: 0.1193 0.1348 0.035 1.122 5.5 67.2 15.1 896 n/a 5_adp: 0.1197 0.1351 0.035 1.122 5.6 67.1 15.1 896 n/a 5_regHadp: 0.1197 0.1351 0.035 1.122 5.6 67.1 15.1 896 n/a 5_occ: 0.1195 0.1355 0.035 1.122 5.6 67.1 15.1 896 n/a 6_bss: 0.1194 0.1355 0.035 1.122 5.5 67.0 15.0 896 n/a 6_settarget: 0.1194 0.1355 0.035 1.122 5.5 67.0 15.0 896 n/a 6_updatecdl: 0.1194 0.1355 0.035 1.122 5.5 67.0 15.0 896 n/a 6_nqh: 0.1194 0.1355 0.035 1.122 5.5 67.0 15.0 896 n/a 6_sol: 0.1194 0.1352 0.035 1.122 5.5 67.0 15.0 894 n/a 6_weight: 0.1194 0.1352 0.035 1.122 5.5 67.0 15.0 894 n/a 6_xyzrec: 0.1197 0.1357 0.036 1.123 5.5 67.0 15.0 894 n/a 6_adp: 0.1202 0.1365 0.036 1.123 5.6 66.0 14.9 894 n/a 6_regHadp: 0.1203 0.1366 0.036 1.123 5.6 66.0 14.9 894 n/a 6_occ: 0.1200 0.1369 0.036 1.123 5.6 66.0 14.9 894 n/a 7_bss: 0.1200 0.1361 0.036 1.123 5.5 66.0 14.9 894 n/a 7_settarget: 0.1200 0.1361 0.036 1.123 5.5 66.0 14.9 894 n/a 7_updatecdl: 0.1200 0.1361 0.036 1.123 5.5 66.0 14.9 894 n/a 7_nqh: 0.1200 0.1361 0.036 1.123 5.5 66.0 14.9 894 n/a 7_sol: 0.1198 0.1347 0.036 1.123 5.5 66.0 14.9 903 n/a 7_weight: 0.1198 0.1347 0.036 1.123 5.5 66.0 14.9 903 n/a 7_xyzrec: 0.1201 0.1348 0.036 1.134 5.5 66.0 14.9 903 n/a 7_adp: 0.1199 0.1350 0.036 1.134 5.6 64.8 14.9 903 n/a 7_regHadp: 0.1199 0.1350 0.036 1.134 5.6 64.8 14.9 903 n/a 7_occ: 0.1197 0.1350 0.036 1.134 5.6 64.8 14.9 903 n/a 8_bss: 0.1187 0.1335 0.036 1.134 5.6 64.8 14.8 903 n/a 8_settarget: 0.1187 0.1335 0.036 1.134 5.6 64.8 14.8 903 n/a 8_updatecdl: 0.1187 0.1335 0.036 1.133 5.6 64.8 14.8 903 n/a 8_nqh: 0.1187 0.1335 0.036 1.133 5.6 64.8 14.8 903 n/a 8_sol: 0.1186 0.1333 0.036 1.133 5.6 64.8 14.8 906 n/a 8_weight: 0.1186 0.1333 0.036 1.133 5.6 64.8 14.8 906 n/a 8_xyzrec: 0.1190 0.1338 0.037 1.120 5.6 64.8 14.8 906 n/a 8_adp: 0.1191 0.1340 0.037 1.120 5.6 64.4 14.8 906 n/a 8_regHadp: 0.1191 0.1341 0.037 1.120 5.6 64.4 14.8 906 n/a 8_occ: 0.1190 0.1344 0.037 1.120 5.6 64.4 14.8 906 n/a 9_bss: 0.1189 0.1343 0.037 1.120 5.5 64.4 14.8 906 n/a 9_settarget: 0.1189 0.1343 0.037 1.120 5.5 64.4 14.8 906 n/a 9_updatecdl: 0.1189 0.1343 0.037 1.120 5.5 64.4 14.8 906 n/a 9_nqh: 0.1189 0.1343 0.037 1.120 5.5 64.4 14.8 906 n/a 9_sol: 0.1186 0.1332 0.037 1.120 5.5 64.4 14.8 911 n/a 9_weight: 0.1186 0.1332 0.037 1.120 5.5 64.4 14.8 911 n/a 9_xyzrec: 0.1190 0.1338 0.037 1.118 5.5 64.4 14.8 911 n/a 9_adp: 0.1190 0.1340 0.037 1.118 5.6 63.6 14.8 911 n/a 9_regHadp: 0.1190 0.1340 0.037 1.118 5.6 63.6 14.8 911 n/a 9_occ: 0.1188 0.1341 0.037 1.118 5.6 63.6 14.8 911 n/a 10_bss: 0.1187 0.1343 0.037 1.118 5.6 63.6 14.8 911 n/a 10_settarget: 0.1187 0.1343 0.037 1.118 5.6 63.6 14.8 911 n/a 10_updatecdl: 0.1187 0.1343 0.037 1.118 5.6 63.6 14.8 911 n/a 10_setrh: 0.1188 0.1343 0.037 1.118 5.6 63.6 14.8 911 n/a 10_nqh: 0.1188 0.1343 0.037 1.118 5.6 63.6 14.8 911 n/a 10_sol: 0.1186 0.1333 0.037 1.118 5.6 63.6 14.8 916 n/a 10_weight: 0.1186 0.1333 0.037 1.118 5.6 63.6 14.8 916 n/a 10_xyzrec: 0.1188 0.1340 0.038 1.172 5.6 63.6 14.8 916 n/a 10_adp: 0.1189 0.1342 0.038 1.172 5.6 63.4 14.8 916 n/a 10_regHadp: 0.1189 0.1342 0.038 1.172 5.6 63.4 14.8 916 n/a 10_occ: 0.1189 0.1344 0.038 1.172 5.6 63.4 14.8 916 n/a end: 0.1188 0.1343 0.038 1.172 5.5 63.3 14.7 916 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8360863_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8360863_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.6400 Refinement macro-cycles (run) : 11926.3800 Write final files (write_after_run_outputs) : 181.4100 Total : 12114.4300 Total CPU time: 3.37 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:39:06 PST -0800 (1736735946.25 s) Start R-work = 0.1801, R-free = 0.1929 Final R-work = 0.1188, R-free = 0.1343 =============================================================================== Job complete usr+sys time: 12439.24 seconds wall clock time: 208 minutes 19.97 seconds (12499.97 seconds total)