Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6036143.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_6036143.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6036143.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } 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 1 residue(s): 0.01s 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: 2.78, per 1000 atoms: 0.42 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: 2.761 distance_ideal: 2.720 ideal - model: -0.041 slack: 0.000 delta_slack: -0.041 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: 2.805 distance_ideal: 2.710 ideal - model: -0.095 slack: 0.000 delta_slack: -0.095 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 210.2 milliseconds Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.05: 1032 1.05 - 1.29: 2427 1.29 - 1.53: 1743 1.53 - 1.77: 722 1.77 - 2.01: 10 Bond restraints: 5934 Sorted by residual: bond pdb=" N LEU B 6 " pdb=" CA LEU B 6 " ideal model delta sigma weight residual 1.457 1.751 -0.294 1.23e-02 6.61e+03 5.71e+02 bond pdb=" N GLY A 50 " pdb=" H GLY A 50 " ideal model delta sigma weight residual 0.860 1.241 -0.381 2.00e-02 2.50e+03 3.63e+02 bond pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 1.236 1.445 -0.208 1.10e-02 8.26e+03 3.58e+02 bond pdb=" CB ALA A 182 " pdb=" HB3 ALA A 182 " ideal model delta sigma weight residual 0.970 1.343 -0.373 2.00e-02 2.50e+03 3.48e+02 bond pdb=" N GLU B 66 " pdb=" H GLU B 66 " ideal model delta sigma weight residual 0.860 1.233 -0.373 2.00e-02 2.50e+03 3.47e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.99: 6403 4.99 - 9.98: 3433 9.98 - 14.97: 907 14.97 - 19.97: 63 19.97 - 24.96: 4 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O GLY A 190 " pdb=" C GLY A 190 " pdb=" N ILE A 191 " ideal model delta sigma weight residual 122.71 138.56 -15.85 8.00e-01 1.56e+00 3.92e+02 angle pdb=" ND1 HIS A 116 " pdb=" CG HIS A 116 " pdb=" CD2 HIS A 116 " ideal model delta sigma weight residual 106.10 91.02 15.08 1.00e+00 1.00e+00 2.27e+02 angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 119.20 132.60 -13.40 9.00e-01 1.23e+00 2.22e+02 angle pdb=" O GLU A 17 " pdb=" C GLU A 17 " pdb=" N ALA A 18 " ideal model delta sigma weight residual 122.09 106.12 15.97 1.08e+00 8.57e-01 2.19e+02 angle pdb=" O SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " ideal model delta sigma weight residual 123.26 107.77 15.49 1.05e+00 9.07e-01 2.18e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 1823 16.71 - 33.42: 158 33.42 - 50.13: 41 50.13 - 66.84: 24 66.84 - 83.55: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -148.90 -31.10 0 5.00e+00 4.00e-02 3.87e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -150.36 -29.64 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 203 0.216 - 0.431: 148 0.431 - 0.647: 101 0.647 - 0.862: 34 0.862 - 1.078: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -1.51 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.56 -1.03 2.00e-01 2.50e+01 2.63e+01 chirality pdb=" CA ILE B 22 " pdb=" N ILE B 22 " pdb=" C ILE B 22 " pdb=" CB ILE B 22 " both_signs ideal model delta sigma weight residual False 2.43 3.39 -0.95 2.00e-01 2.50e+01 2.28e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.037 2.00e-02 2.50e+03 7.13e-02 2.03e+02 pdb=" CG TRP A 139 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.059 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.132 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.084 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.055 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.063 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.142 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.064 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.031 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.073 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.027 2.00e-02 2.50e+03 6.46e-02 1.67e+02 pdb=" CG TRP A 146 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.097 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.076 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.013 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.084 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.103 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.018 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.125 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 194 " 0.035 2.00e-02 2.50e+03 6.41e-02 1.23e+02 pdb=" CG TYR B 194 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TYR B 194 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR B 194 " 0.106 2.00e-02 2.50e+03 pdb=" CE1 TYR B 194 " -0.092 2.00e-02 2.50e+03 pdb=" CE2 TYR B 194 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 194 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 194 " 0.035 2.00e-02 2.50e+03 pdb=" HD1 TYR B 194 " -0.074 2.00e-02 2.50e+03 pdb=" HD2 TYR B 194 " -0.015 2.00e-02 2.50e+03 pdb=" HE1 TYR B 194 " 0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR B 194 " -0.082 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 25 1.62 - 2.37: 2478 2.37 - 3.11: 22341 3.11 - 3.85: 32869 3.85 - 4.60: 52606 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110319 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.875 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.891 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.930 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.143 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.144 2.620 ... (remaining 110314 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_6036143_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= 0.2038 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.302341 | | target function (ml) not normalized (work): 805884.412426 | | target function (ml) not normalized (free): 16572.718041 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2133 0.1860 6.6847 6.2976| | 2: 2.94 - 2.33 1.00 7339 128 0.1626 0.1642 5.5372 5.6037| | 3: 2.33 - 2.04 0.96 6939 150 0.1638 0.1592 5.1546 5.2334| | 4: 2.04 - 1.85 1.00 7170 155 0.1761 0.1614 4.9638 5.0121| | 5: 1.85 - 1.72 0.99 7113 159 0.1940 0.1796 4.7968 4.835| | 6: 1.72 - 1.62 0.99 7102 142 0.1977 0.2113 4.6711 4.7636| | 7: 1.62 - 1.54 0.99 7104 148 0.2047 0.1763 4.5786 4.5635| | 8: 1.54 - 1.47 0.96 6798 152 0.2040 0.2372 4.481 4.5917| | 9: 1.47 - 1.41 0.98 6938 155 0.2133 0.2079 4.4077 4.4432| | 10: 1.41 - 1.36 0.99 7022 150 0.2134 0.1969 4.3099 4.2746| | 11: 1.36 - 1.32 0.99 6997 151 0.2129 0.2117 4.2373 4.2471| | 12: 1.32 - 1.28 0.98 6976 149 0.2078 0.2012 4.1772 4.247| | 13: 1.28 - 1.25 0.98 6907 166 0.2016 0.2100 4.1302 4.1286| | 14: 1.25 - 1.22 0.98 7015 113 0.2064 0.2261 4.0774 4.2181| | 15: 1.22 - 1.19 0.98 6957 137 0.2081 0.2263 4.0431 4.0738| | 16: 1.19 - 1.17 0.93 6604 132 0.2140 0.2218 4.0158 4.0651| | 17: 1.17 - 1.14 0.98 6941 135 0.2156 0.1968 3.9541 3.9806| | 18: 1.14 - 1.12 0.98 6875 142 0.2217 0.2357 3.9249 3.9094| | 19: 1.12 - 1.10 0.97 6949 106 0.2268 0.2345 3.8731 3.9602| | 20: 1.10 - 1.08 0.97 6884 147 0.2343 0.2370 3.8289 3.9088| | 21: 1.08 - 1.07 0.97 6852 152 0.2442 0.2601 3.7948 3.8141| | 22: 1.07 - 1.05 0.97 6838 135 0.2519 0.2455 3.7451 3.7482| | 23: 1.05 - 1.03 0.97 6829 159 0.2685 0.2729 3.7239 3.8347| | 24: 1.03 - 1.02 0.96 6785 133 0.2861 0.2748 3.6989 3.7595| | 25: 1.02 - 1.01 0.93 6552 130 0.3062 0.2991 3.6759 3.7149| | 26: 1.01 - 0.99 0.96 6767 158 0.3220 0.3277 3.6334 3.6495| | 27: 0.99 - 0.98 0.94 6648 131 0.3397 0.3162 3.6308 3.6076| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.32 0.91 0.96 34819.01| | 2: 2.94 - 2.33 7339 128 0.86 21.16 1.09 1.02 14992.99| | 3: 2.33 - 2.04 6939 150 0.93 12.78 1.11 1.06 4311.70| | 4: 2.04 - 1.85 7170 155 0.92 13.75 1.12 1.07 2848.76| | 5: 1.85 - 1.72 7113 159 0.90 16.19 1.12 1.07 2189.94| | 6: 1.72 - 1.62 7102 142 0.89 17.45 1.11 1.06 1739.49| | 7: 1.62 - 1.54 7104 148 0.88 18.38 1.11 1.06 1412.13| | 8: 1.54 - 1.47 6798 152 0.88 18.70 1.10 1.06 1186.65| | 9: 1.47 - 1.41 6938 155 0.88 18.99 1.10 1.06 974.09| | 10: 1.41 - 1.36 7022 150 0.88 19.43 1.09 1.04 797.36| | 11: 1.36 - 1.32 6997 151 0.88 19.37 1.08 1.05 684.55| | 12: 1.32 - 1.28 6976 149 0.88 18.99 1.08 1.05 612.89| | 13: 1.28 - 1.25 6907 166 0.88 19.34 1.06 1.05 590.89| | 14: 1.25 - 1.22 7015 113 0.87 20.57 1.07 1.05 569.33| | 15: 1.22 - 1.19 6957 137 0.86 20.90 1.07 1.05 550.07| | 16: 1.19 - 1.17 6604 132 0.87 20.50 1.07 1.04 497.89| | 17: 1.17 - 1.14 6941 135 0.86 21.15 1.08 1.02 441.94| | 18: 1.14 - 1.12 6875 142 0.87 20.91 1.08 0.99 392.35| | 19: 1.12 - 1.10 6949 106 0.86 21.99 1.07 0.99 375.40| | 20: 1.10 - 1.08 6884 147 0.85 22.85 1.06 0.99 355.65| | 21: 1.08 - 1.07 6852 152 0.84 23.93 1.06 0.99 342.34| | 22: 1.07 - 1.05 6838 135 0.82 25.27 1.05 0.97 327.02| | 23: 1.05 - 1.03 6829 159 0.80 27.43 1.05 0.98 329.60| | 24: 1.03 - 1.02 6785 133 0.78 29.43 1.06 0.99 332.72| | 25: 1.02 - 1.01 6552 130 0.77 30.38 1.04 0.96 314.88| | 26: 1.01 - 0.99 6767 158 0.75 31.81 1.03 0.95 294.72| | 27: 0.99 - 0.98 6648 131 0.76 31.83 1.04 0.93 275.44| |alpha: min = 0.93 max = 1.07 mean = 1.02| |beta: min = 275.44 max = 34819.01 mean = 2812.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.54| |phase err.(test): min = 0.00 max = 89.85 mean = 21.50| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.294 2950 Z= 5.447 Angle : 5.377 19.087 4018 Z= 3.855 Chirality : 0.381 1.078 492 Planarity : 0.033 0.169 512 Dihedral : 12.966 83.547 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.66 % Favored : 94.82 % Rotamer: Outliers : 0.97 % Allowed : 4.19 % Favored : 94.84 % Cbeta Deviations : 32.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -2.70 (0.38), residues: 386 helix: -2.98 (0.28), residues: 146 sheet: -1.44 (0.50), residues: 82 loop : -0.42 (0.50), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.102 0.019 ARG B 143 TYR 0.092 0.036 TYR B 194 PHE 0.097 0.041 PHE A 82 TRP 0.138 0.044 TRP A 139 HIS 0.066 0.035 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= 0.2038 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.302341 | | target function (ml) not normalized (work): 805884.412426 | | target function (ml) not normalized (free): 16572.718041 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2038 0.1982 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2038 0.1982 n_refl.: 191155 remove outliers: r(all,work,free)=0.2036 0.2038 0.1982 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2037 0.2039 0.1982 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1806 0.1804 0.1913 n_refl.: 191145 remove outliers: r(all,work,free)=0.1804 0.1802 0.1913 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 0.4232 400.535 295.491 0.437 0.910 0.303 13.296-10.522 99.01 99 1 0.2407 528.187 521.644 0.791 0.911 0.255 10.503-8.327 98.90 177 3 0.2490 564.205 558.711 0.971 0.911 0.199 8.318-6.595 100.00 360 8 0.2520 414.736 404.141 0.967 0.911 0.155 6.588-5.215 100.00 711 7 0.2283 381.101 366.233 0.954 0.911 0.140 5.214-4.128 98.38 1367 28 0.1473 557.435 550.177 1.075 0.911 0.090 4.126-3.266 94.74 2603 46 0.1344 508.132 499.334 1.147 0.912 0.018 3.266-2.585 99.86 5447 97 0.1444 342.774 338.045 1.123 0.911 0.000 2.585-2.046 97.45 10613 204 0.1397 258.603 254.400 1.125 0.911 0.000 2.046-1.619 99.39 21536 464 0.1620 153.054 149.780 1.147 0.910 0.000 1.619-1.281 98.00 42464 925 0.1941 82.395 80.085 1.128 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2315 44.203 41.658 1.109 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0101 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1802 r_free=0.1913 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1802 r_free=0.1913 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.289466 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.431314 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 0.1274 0.1505 0.0231 0.039 1.2 10.7 0.0 0.3 0 11.145 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.74 15.05 2.31 1.118 13.117 570.431 0.018 13.00 15.71 2.72 1.221 13.323 570.431 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.05 14.98 1.39 435 3274 Protein: 5.16 40.32 10.98 1.39 0 2902 Water: 6.41 73.05 29.36 N/A 435 370 Other: 16.02 30.80 23.41 N/A 0 2 Chain A: 5.32 60.50 13.01 N/A 0 1626 Chain B: 5.16 73.05 12.74 N/A 0 1648 Chain S: 11.83 63.36 30.83 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2160 11.95 - 18.74 641 18.74 - 25.53 314 25.53 - 32.31 272 32.31 - 39.10 156 39.10 - 45.89 101 45.89 - 52.68 41 52.68 - 59.47 19 59.47 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1571 r_work=0.1299 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1568 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 = 0.1557 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.16 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= 0.1557 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015632 | | target function (ls_wunit_k1) not normalized (work): 2927.753138 | | target function (ls_wunit_k1) not normalized (free): 115.733618 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1284 0.1557 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1473 0.1471 0.1633 n_refl.: 191139 remove outliers: r(all,work,free)=0.1473 0.1471 0.1633 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1497 0.1495 0.1642 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1546 n_refl.: 191139 remove outliers: r(all,work,free)=0.1281 0.1276 0.1545 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3559 402.814 377.446 0.470 0.997 0.279 13.296-10.522 99.01 99 1 0.2081 528.187 524.744 0.714 0.999 0.234 10.503-8.327 98.90 177 3 0.1727 564.205 562.835 0.858 0.999 0.189 8.318-6.595 100.00 360 8 0.1726 414.736 412.818 0.877 0.998 0.150 6.588-5.215 100.00 711 7 0.1547 381.101 373.192 0.854 0.999 0.140 5.214-4.128 98.38 1367 28 0.0903 557.435 554.158 0.942 0.999 0.070 4.126-3.266 94.74 2603 46 0.0833 508.132 504.274 1.007 1.000 0.009 3.266-2.585 99.86 5447 97 0.0921 342.774 340.364 0.991 0.999 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.445 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.411 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.419 1.010 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.162 0.988 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0382 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1545 | n_water=805 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1281 r_free=0.1552 | n_water=793 | time (s): 98.760 (total time: 101.320) Filter (q & B) r_work=0.1282 r_free=0.1552 | n_water=788 | time (s): 6.080 (total time: 107.400) Compute maps r_work=0.1282 r_free=0.1552 | n_water=788 | time (s): 2.330 (total time: 109.730) Filter (map) r_work=0.1307 r_free=0.1540 | n_water=655 | time (s): 4.680 (total time: 114.410) Find peaks r_work=0.1307 r_free=0.1540 | n_water=655 | time (s): 0.560 (total time: 114.970) Add new water r_work=0.1329 r_free=0.1568 | n_water=955 | time (s): 3.800 (total time: 118.770) Refine new water occ: r_work=0.1287 r_free=0.1509 adp: r_work=0.1274 r_free=0.1508 occ: r_work=0.1277 r_free=0.1499 adp: r_work=0.1271 r_free=0.1500 occ: r_work=0.1273 r_free=0.1496 adp: r_work=0.1269 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1269 r_free=0.1498 r_work=0.1269 r_free=0.1498 | n_water=955 | time (s): 76.840 (total time: 195.610) Filter (q & B) r_work=0.1273 r_free=0.1501 | n_water=880 | time (s): 4.890 (total time: 200.500) Filter (dist only) r_work=0.1273 r_free=0.1500 | n_water=879 | time (s): 109.560 (total time: 310.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.348211 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 589.983321 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 0.1256 0.1517 0.0261 0.041 1.1 15.3 0.0 0.3 0 11.674 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.17 2.61 2.034 15.100 589.983 0.015 12.33 14.96 2.63 2.401 15.168 589.983 0.014 Individual atomic B min max mean iso aniso Overall: 5.35 69.84 16.23 1.21 511 3272 Protein: 5.35 40.58 10.97 1.21 0 2902 Water: 6.56 69.84 33.59 N/A 511 368 Other: 16.43 32.89 24.66 N/A 0 2 Chain A: 5.52 56.87 12.98 N/A 0 1624 Chain B: 5.35 68.22 12.80 N/A 0 1648 Chain S: 13.33 69.84 37.63 N/A 511 0 Histogram: Values Number of atoms 5.35 - 11.80 2090 11.80 - 18.25 704 18.25 - 24.70 252 24.70 - 31.15 213 31.15 - 37.60 188 37.60 - 44.05 163 44.05 - 50.50 96 50.50 - 56.95 45 56.95 - 63.40 28 63.40 - 69.84 4 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1497 r_work=0.1233 r_free=0.1498 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1498 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1494 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1494 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013482 | | target function (ls_wunit_k1) not normalized (work): 2525.190664 | | target function (ls_wunit_k1) not normalized (free): 97.259043 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1494 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1437 0.1435 0.1587 n_refl.: 191137 remove outliers: r(all,work,free)=0.1437 0.1435 0.1587 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1432 0.1585 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1501 n_refl.: 191137 remove outliers: r(all,work,free)=0.1239 0.1234 0.1501 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3265 402.814 378.511 0.489 0.962 0.267 13.296-10.522 99.01 99 1 0.1883 528.187 519.971 0.755 0.963 0.223 10.503-8.327 98.90 177 3 0.1409 564.205 566.245 0.918 0.963 0.174 8.318-6.595 100.00 360 8 0.1562 414.736 415.373 0.934 0.963 0.140 6.588-5.215 100.00 711 7 0.1357 381.101 376.473 0.910 0.963 0.130 5.214-4.128 98.38 1367 28 0.0834 557.435 555.977 0.995 0.963 0.090 4.126-3.266 94.74 2603 46 0.0766 508.132 505.446 1.060 0.963 0.009 3.266-2.585 99.86 5447 97 0.0864 342.774 341.362 1.048 0.962 0.000 2.585-2.046 97.45 10613 204 0.0903 258.603 256.784 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.609 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.362 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.219 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=-0.0536 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1501 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1501 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1501 | n_water=879 | time (s): 3.190 (total time: 3.190) Filter (dist) r_work=0.1234 r_free=0.1501 | n_water=876 | time (s): 113.100 (total time: 116.290) Filter (q & B) r_work=0.1234 r_free=0.1501 | n_water=873 | time (s): 4.910 (total time: 121.200) Compute maps r_work=0.1234 r_free=0.1501 | n_water=873 | time (s): 2.150 (total time: 123.350) Filter (map) r_work=0.1273 r_free=0.1522 | n_water=686 | time (s): 4.840 (total time: 128.190) Find peaks r_work=0.1273 r_free=0.1522 | n_water=686 | time (s): 0.810 (total time: 129.000) Add new water r_work=0.1294 r_free=0.1556 | n_water=1010 | time (s): 4.890 (total time: 133.890) Refine new water occ: r_work=0.1252 r_free=0.1508 adp: r_work=0.1252 r_free=0.1510 occ: r_work=0.1249 r_free=0.1505 adp: r_work=0.1249 r_free=0.1507 occ: r_work=0.1246 r_free=0.1501 adp: r_work=0.1245 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1503 r_work=0.1245 r_free=0.1503 | n_water=1010 | time (s): 335.380 (total time: 469.270) Filter (q & B) r_work=0.1251 r_free=0.1511 | n_water=862 | time (s): 4.660 (total time: 473.930) Filter (dist only) r_work=0.1251 r_free=0.1510 | n_water=860 | time (s): 105.600 (total time: 579.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.685983 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.622472 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 0.1241 0.1434 0.0194 0.035 1.1 7.0 0.0 0.0 0 0.843 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.34 1.94 1.929 14.532 15.622 3.938 12.36 13.99 1.63 2.228 14.433 15.622 3.898 Individual atomic B min max mean iso aniso Overall: 5.51 67.77 15.18 1.04 493 3271 Protein: 5.51 36.55 10.73 1.04 0 2902 Water: 6.67 67.77 30.20 N/A 493 367 Other: 14.17 28.35 21.26 N/A 0 2 Chain A: 5.53 55.94 12.74 N/A 0 1624 Chain B: 5.51 67.77 12.52 N/A 0 1647 Chain S: 13.82 62.11 32.12 N/A 493 0 Histogram: Values Number of atoms 5.51 - 11.73 2119 11.73 - 17.96 702 17.96 - 24.19 280 24.19 - 30.41 234 30.41 - 36.64 183 36.64 - 42.86 137 42.86 - 49.09 74 49.09 - 55.32 24 55.32 - 61.54 9 61.54 - 67.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1399 r_work=0.1236 r_free=0.1400 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1400 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1230 r_free = 0.1390 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1230 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891613 | | target function (ml) not normalized (work): 728883.635754 | | target function (ml) not normalized (free): 15218.142127 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1230 0.1390 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1447 0.1447 0.1492 n_refl.: 191137 remove outliers: r(all,work,free)=0.1447 0.1447 0.1492 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1441 0.1441 0.1489 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1388 n_refl.: 191137 remove outliers: r(all,work,free)=0.1229 0.1226 0.1388 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3758 398.895 355.614 0.419 0.946 0.248 13.296-10.522 99.01 99 1 0.2460 528.187 508.403 0.715 0.947 0.229 10.503-8.327 98.35 176 3 0.1938 556.299 558.951 0.881 0.947 0.220 8.318-6.595 100.00 360 8 0.2104 414.736 411.670 0.898 0.947 0.135 6.588-5.215 100.00 711 7 0.1833 381.101 370.662 0.883 0.947 0.104 5.214-4.128 98.38 1367 28 0.1175 557.435 552.169 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1104 508.132 501.101 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1088 342.774 339.004 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0967 258.603 255.740 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0972 153.054 151.409 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.496 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1690 44.202 42.321 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=-0.1010 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1388 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1388 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1388 | n_water=860 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1226 r_free=0.1389 | n_water=859 | time (s): 104.900 (total time: 107.410) Filter (q & B) r_work=0.1226 r_free=0.1384 | n_water=848 | time (s): 5.190 (total time: 112.600) Compute maps r_work=0.1226 r_free=0.1384 | n_water=848 | time (s): 1.660 (total time: 114.260) Filter (map) r_work=0.1247 r_free=0.1393 | n_water=715 | time (s): 4.820 (total time: 119.080) Find peaks r_work=0.1247 r_free=0.1393 | n_water=715 | time (s): 0.650 (total time: 119.730) Add new water r_work=0.1262 r_free=0.1416 | n_water=938 | time (s): 4.780 (total time: 124.510) Refine new water occ: r_work=0.1216 r_free=0.1370 adp: r_work=0.1208 r_free=0.1365 occ: r_work=0.1206 r_free=0.1366 adp: r_work=0.1206 r_free=0.1365 occ: r_work=0.1204 r_free=0.1366 adp: r_work=0.1204 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1364 r_work=0.1204 r_free=0.1364 | n_water=938 | time (s): 375.640 (total time: 500.150) Filter (q & B) r_work=0.1208 r_free=0.1369 | n_water=860 | time (s): 4.510 (total time: 504.660) Filter (dist only) r_work=0.1209 r_free=0.1368 | n_water=859 | time (s): 114.240 (total time: 618.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550591 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.983207 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1373 0.0165 0.036 1.1 6.1 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.73 1.65 1.823 14.189 14.983 3.876 12.03 13.71 1.68 1.925 14.148 14.983 3.867 Individual atomic B min max mean iso aniso Overall: 5.52 67.31 14.96 0.99 492 3271 Protein: 5.52 33.37 10.65 0.99 0 2902 Water: 5.91 67.31 29.53 N/A 492 367 Other: 14.03 27.52 20.77 N/A 0 2 Chain A: 5.52 54.93 12.61 N/A 0 1624 Chain B: 5.53 67.31 12.42 N/A 0 1647 Chain S: 5.91 62.24 31.23 N/A 492 0 Histogram: Values Number of atoms 5.52 - 11.70 2124 11.70 - 17.88 726 17.88 - 24.06 283 24.06 - 30.24 231 30.24 - 36.42 170 36.42 - 42.59 128 42.59 - 48.77 69 48.77 - 54.95 22 54.95 - 61.13 8 61.13 - 67.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1371 r_work=0.1203 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1371 target_work(ml) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1371 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865021 | | target function (ml) not normalized (work): 723891.349941 | | target function (ml) not normalized (free): 15140.103443 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1371 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1474 n_refl.: 191134 remove outliers: r(all,work,free)=0.1415 0.1414 0.1474 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1409 0.1408 0.1470 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1364 n_refl.: 191134 remove outliers: r(all,work,free)=0.1199 0.1195 0.1364 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 0.3768 361.420 324.057 0.399 0.973 0.237 13.296-10.522 98.02 98 1 0.2484 479.211 455.616 0.684 0.974 0.220 10.503-8.327 98.35 176 3 0.2055 504.036 498.577 0.835 0.974 0.220 8.318-6.595 100.00 360 8 0.2175 375.773 370.926 0.865 0.973 0.120 6.588-5.215 100.00 711 7 0.1893 345.298 334.950 0.854 0.973 0.094 5.214-4.128 98.38 1367 28 0.1197 505.066 499.886 0.945 0.972 0.080 4.126-3.266 94.74 2603 46 0.1133 460.395 453.391 1.005 0.971 0.000 3.266-2.585 99.86 5447 97 0.1094 310.571 307.193 0.995 0.968 0.000 2.585-2.046 97.45 10613 204 0.0940 234.308 231.785 1.011 0.964 0.000 2.046-1.619 99.39 21536 464 0.0916 138.675 137.339 1.040 0.958 0.000 1.619-1.281 98.00 42464 925 0.0983 74.655 73.943 1.047 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.049 38.380 1.051 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0933 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1365 | n_water=859 | time (s): 3.350 (total time: 3.350) Filter (dist) r_work=0.1196 r_free=0.1365 | n_water=859 | time (s): 102.020 (total time: 105.370) Filter (q & B) r_work=0.1196 r_free=0.1364 | n_water=849 | time (s): 4.260 (total time: 109.630) Compute maps r_work=0.1196 r_free=0.1364 | n_water=849 | time (s): 2.220 (total time: 111.850) Filter (map) r_work=0.1219 r_free=0.1357 | n_water=719 | time (s): 5.430 (total time: 117.280) Find peaks r_work=0.1219 r_free=0.1357 | n_water=719 | time (s): 0.540 (total time: 117.820) Add new water r_work=0.1234 r_free=0.1372 | n_water=957 | time (s): 3.920 (total time: 121.740) Refine new water occ: r_work=0.1196 r_free=0.1348 adp: r_work=0.1196 r_free=0.1347 occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1193 r_free=0.1349 occ: r_work=0.1191 r_free=0.1352 adp: r_work=0.1190 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1351 r_work=0.1190 r_free=0.1351 | n_water=957 | time (s): 288.860 (total time: 410.600) Filter (q & B) r_work=0.1194 r_free=0.1358 | n_water=883 | time (s): 5.520 (total time: 416.120) Filter (dist only) r_work=0.1194 r_free=0.1356 | n_water=882 | time (s): 113.660 (total time: 529.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.509646 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.090938 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 0.1364 0.0167 0.037 1.1 7.7 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.64 1.67 1.784 14.141 15.091 3.765 12.01 13.67 1.66 1.870 14.103 15.091 3.763 Individual atomic B min max mean iso aniso Overall: 5.57 66.85 14.96 0.94 518 3268 Protein: 5.57 31.53 10.57 0.94 0 2902 Water: 6.09 66.85 29.40 N/A 518 364 Other: 13.88 25.75 19.81 N/A 0 2 Chain A: 5.57 53.81 12.49 N/A 0 1623 Chain B: 5.59 66.85 12.29 N/A 0 1645 Chain S: 6.09 62.31 31.20 N/A 518 0 Histogram: Values Number of atoms 5.57 - 11.69 2136 11.69 - 17.82 730 17.82 - 23.95 283 23.95 - 30.08 221 30.08 - 36.21 181 36.21 - 42.34 130 42.34 - 48.46 72 48.46 - 54.59 24 54.59 - 60.72 7 60.72 - 66.85 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1367 r_work=0.1201 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1367 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1373 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762063 | | target function (ml) not normalized (work): 704604.325934 | | target function (ml) not normalized (free): 14754.149751 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1199 0.1372 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1416 0.1415 0.1498 n_refl.: 191133 remove outliers: r(all,work,free)=0.1416 0.1415 0.1498 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1409 0.1408 0.1494 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1372 n_refl.: 191133 remove outliers: r(all,work,free)=0.1202 0.1198 0.1372 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3792 361.420 324.102 0.395 0.973 0.231 13.296-10.522 98.02 98 1 0.2421 479.211 461.868 0.678 0.975 0.188 10.503-8.327 97.80 175 3 0.2098 502.213 498.066 0.837 0.975 0.163 8.318-6.595 100.00 360 8 0.2182 375.773 371.405 0.863 0.974 0.118 6.588-5.215 100.00 711 7 0.1920 345.298 335.681 0.857 0.974 0.097 5.214-4.128 98.38 1367 28 0.1202 505.066 499.891 0.945 0.973 0.080 4.126-3.266 94.74 2603 46 0.1152 460.395 453.399 1.007 0.972 0.000 3.266-2.585 99.86 5447 97 0.1116 310.571 307.184 0.995 0.969 0.000 2.585-2.046 97.45 10613 204 0.0952 234.308 231.749 1.010 0.966 0.000 2.046-1.619 99.39 21536 464 0.0918 138.675 137.315 1.039 0.959 0.000 1.619-1.281 98.00 42464 925 0.0974 74.655 73.940 1.047 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1645 40.049 38.366 1.051 0.932 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1106 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1372 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1372 | n_water=882 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1199 r_free=0.1371 | n_water=881 | time (s): 121.590 (total time: 124.820) Filter (q & B) r_work=0.1199 r_free=0.1371 | n_water=868 | time (s): 4.210 (total time: 129.030) Compute maps r_work=0.1199 r_free=0.1371 | n_water=868 | time (s): 1.980 (total time: 131.010) Filter (map) r_work=0.1221 r_free=0.1364 | n_water=739 | time (s): 4.030 (total time: 135.040) Find peaks r_work=0.1221 r_free=0.1364 | n_water=739 | time (s): 0.830 (total time: 135.870) Add new water r_work=0.1233 r_free=0.1377 | n_water=961 | time (s): 4.620 (total time: 140.490) Refine new water occ: r_work=0.1196 r_free=0.1350 adp: r_work=0.1196 r_free=0.1350 occ: r_work=0.1193 r_free=0.1349 adp: r_work=0.1193 r_free=0.1349 occ: r_work=0.1192 r_free=0.1349 adp: r_work=0.1192 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1349 r_work=0.1192 r_free=0.1349 | n_water=961 | time (s): 235.570 (total time: 376.060) Filter (q & B) r_work=0.1196 r_free=0.1355 | n_water=889 | time (s): 4.700 (total time: 380.760) Filter (dist only) r_work=0.1196 r_free=0.1354 | n_water=888 | time (s): 117.920 (total time: 498.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.516309 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.468506 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1357 0.0158 0.037 1.1 5.8 0.0 0.3 0 0.758 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.57 1.58 1.751 14.023 14.469 3.761 12.00 13.60 1.59 1.863 13.984 14.469 3.759 Individual atomic B min max mean iso aniso Overall: 5.60 65.81 14.84 0.90 524 3268 Protein: 5.60 29.37 10.48 0.90 0 2902 Water: 5.97 65.81 29.09 N/A 524 364 Other: 13.86 23.17 18.51 N/A 0 2 Chain A: 5.65 52.29 12.36 N/A 0 1623 Chain B: 5.60 65.81 12.18 N/A 0 1645 Chain S: 5.97 62.57 30.91 N/A 524 0 Histogram: Values Number of atoms 5.60 - 11.62 2116 11.62 - 17.64 770 17.64 - 23.66 277 23.66 - 29.68 211 29.68 - 35.70 183 35.70 - 41.72 122 41.72 - 47.75 74 47.75 - 53.77 28 53.77 - 59.79 8 59.79 - 65.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1360 r_work=0.1201 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1360 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1359 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757995 | | target function (ml) not normalized (work): 703838.706908 | | target function (ml) not normalized (free): 14727.600823 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1359 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1493 n_refl.: 191132 remove outliers: r(all,work,free)=0.1415 0.1414 0.1493 n_refl.: 191132 overall B=-0.20 to atoms: r(all,work,free)=0.1381 0.1380 0.1471 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191132 remove outliers: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3826 361.420 324.360 0.390 0.973 0.209 13.296-10.522 97.03 97 1 0.2368 481.486 458.232 0.689 0.975 0.166 10.503-8.327 97.80 175 3 0.2139 502.213 496.458 0.857 0.975 0.143 8.318-6.595 100.00 360 8 0.2191 375.773 371.596 0.882 0.974 0.108 6.588-5.215 100.00 711 7 0.1934 345.298 335.429 0.879 0.974 0.087 5.214-4.128 98.38 1367 28 0.1214 505.066 499.626 0.969 0.973 0.070 4.126-3.266 94.74 2603 46 0.1156 460.395 453.425 1.033 0.972 0.000 3.266-2.585 99.86 5447 97 0.1117 310.571 307.226 1.018 0.970 0.000 2.585-2.046 97.45 10613 204 0.0957 234.308 231.766 1.030 0.966 0.000 2.046-1.619 99.39 21536 464 0.0914 138.675 137.353 1.054 0.960 0.000 1.619-1.281 98.00 42464 925 0.0966 74.655 73.961 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1642 40.049 38.373 1.043 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0442 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1357 | n_water=888 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1198 r_free=0.1357 | n_water=888 | time (s): 109.870 (total time: 112.450) Filter (q & B) r_work=0.1199 r_free=0.1358 | n_water=880 | time (s): 4.840 (total time: 117.290) Compute maps r_work=0.1199 r_free=0.1358 | n_water=880 | time (s): 2.450 (total time: 119.740) Filter (map) r_work=0.1222 r_free=0.1370 | n_water=754 | time (s): 4.360 (total time: 124.100) Find peaks r_work=0.1222 r_free=0.1370 | n_water=754 | time (s): 0.760 (total time: 124.860) Add new water r_work=0.1233 r_free=0.1386 | n_water=973 | time (s): 4.720 (total time: 129.580) Refine new water occ: r_work=0.1196 r_free=0.1352 adp: r_work=0.1196 r_free=0.1353 occ: r_work=0.1194 r_free=0.1352 adp: r_work=0.1194 r_free=0.1352 occ: r_work=0.1192 r_free=0.1351 adp: r_work=0.1192 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1352 r_work=0.1192 r_free=0.1352 | n_water=973 | time (s): 257.440 (total time: 387.020) Filter (q & B) r_work=0.1196 r_free=0.1357 | n_water=896 | time (s): 4.340 (total time: 391.360) Filter (dist only) r_work=0.1196 r_free=0.1356 | n_water=895 | time (s): 114.320 (total time: 505.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.579271 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.963827 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1363 0.0164 0.038 1.1 5.1 0.0 0.3 0 0.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.63 1.64 1.715 13.733 13.964 3.759 12.02 13.66 1.64 1.766 13.706 13.964 3.757 Individual atomic B min max mean iso aniso Overall: 5.42 64.53 14.58 0.87 531 3268 Protein: 5.42 28.32 10.26 0.87 0 2902 Water: 5.82 64.53 28.59 N/A 531 364 Other: 13.73 21.85 17.79 N/A 0 2 Chain A: 5.49 51.66 12.10 N/A 0 1623 Chain B: 5.42 64.53 11.93 N/A 0 1645 Chain S: 5.82 62.66 30.39 N/A 531 0 Histogram: Values Number of atoms 5.42 - 11.34 2093 11.34 - 17.25 793 17.25 - 23.16 280 23.16 - 29.07 211 29.07 - 34.98 183 34.98 - 40.89 124 40.89 - 46.80 73 46.80 - 52.71 31 52.71 - 58.62 6 58.62 - 64.53 5 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1366 r_work=0.1202 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1365 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756865 | | target function (ml) not normalized (work): 703623.200055 | | target function (ml) not normalized (free): 14732.624157 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1365 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1386 0.1384 0.1482 n_refl.: 191131 remove outliers: r(all,work,free)=0.1386 0.1384 0.1482 n_refl.: 191131 overall B=0.05 to atoms: r(all,work,free)=0.1394 0.1392 0.1487 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1359 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1359 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3811 361.420 323.317 0.380 0.993 0.203 13.296-10.522 97.03 97 1 0.2383 481.486 462.357 0.682 0.994 0.156 10.503-8.327 97.80 175 3 0.2192 502.213 493.781 0.845 0.995 0.133 8.318-6.595 100.00 360 8 0.2200 375.773 372.011 0.867 0.994 0.080 6.588-5.215 100.00 711 7 0.1948 345.298 334.820 0.870 0.994 0.080 5.214-4.128 98.38 1367 28 0.1241 505.066 498.732 0.960 0.994 0.080 4.126-3.266 94.74 2603 46 0.1171 460.395 452.701 1.022 0.994 0.005 3.266-2.585 99.86 5447 97 0.1124 310.571 306.937 1.006 0.993 0.000 2.585-2.046 97.45 10613 204 0.0964 234.308 231.574 1.017 0.992 0.000 2.046-1.619 99.39 21536 464 0.0910 138.675 137.263 1.038 0.991 0.000 1.619-1.281 98.00 42464 925 0.0945 74.655 73.994 1.035 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.049 38.347 1.015 0.984 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0593 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1359 | n_water=895 | time (s): 2.880 (total time: 2.880) Filter (dist) r_work=0.1193 r_free=0.1359 | n_water=895 | time (s): 104.190 (total time: 107.070) Filter (q & B) r_work=0.1194 r_free=0.1359 | n_water=886 | time (s): 5.230 (total time: 112.300) Compute maps r_work=0.1194 r_free=0.1359 | n_water=886 | time (s): 1.810 (total time: 114.110) Filter (map) r_work=0.1215 r_free=0.1358 | n_water=764 | time (s): 5.230 (total time: 119.340) Find peaks r_work=0.1215 r_free=0.1358 | n_water=764 | time (s): 0.570 (total time: 119.910) Add new water r_work=0.1224 r_free=0.1368 | n_water=970 | time (s): 4.060 (total time: 123.970) Refine new water occ: r_work=0.1191 r_free=0.1350 adp: r_work=0.1191 r_free=0.1349 occ: r_work=0.1189 r_free=0.1351 adp: r_work=0.1189 r_free=0.1350 occ: r_work=0.1187 r_free=0.1352 adp: r_work=0.1187 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1351 r_work=0.1187 r_free=0.1351 | n_water=970 | time (s): 169.030 (total time: 293.000) Filter (q & B) r_work=0.1191 r_free=0.1356 | n_water=898 | time (s): 4.600 (total time: 297.600) Filter (dist only) r_work=0.1192 r_free=0.1355 | n_water=897 | time (s): 116.910 (total time: 414.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.579645 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.859880 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1364 0.0169 0.038 1.1 4.9 0.0 0.3 0 0.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.64 1.69 1.674 13.728 13.860 3.757 11.96 13.65 1.69 1.697 13.710 13.860 3.755 Individual atomic B min max mean iso aniso Overall: 5.52 63.53 14.61 0.86 533 3268 Protein: 5.52 27.91 10.32 0.86 0 2902 Water: 5.94 63.53 28.48 N/A 533 364 Other: 13.79 21.99 17.89 N/A 0 2 Chain A: 5.60 51.29 12.12 N/A 0 1623 Chain B: 5.52 63.53 11.95 N/A 0 1645 Chain S: 5.94 59.74 30.38 N/A 533 0 Histogram: Values Number of atoms 5.52 - 11.32 2066 11.32 - 17.12 823 17.12 - 22.92 271 22.92 - 28.72 210 28.72 - 34.52 190 34.52 - 40.32 119 40.32 - 46.12 77 46.12 - 51.93 33 51.93 - 57.73 8 57.73 - 63.53 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1365 r_work=0.1196 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1365 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1367 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754654 | | target function (ml) not normalized (work): 703209.055690 | | target function (ml) not normalized (free): 14730.495288 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1367 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1497 n_refl.: 191131 remove outliers: r(all,work,free)=0.1402 0.1401 0.1497 n_refl.: 191131 overall B=0.00 to atoms: r(all,work,free)=0.1403 0.1401 0.1497 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1364 n_refl.: 191131 remove outliers: r(all,work,free)=0.1198 0.1195 0.1364 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3840 361.420 321.633 0.384 0.974 0.201 13.296-10.522 97.03 97 1 0.2404 481.486 461.558 0.694 0.975 0.153 10.503-8.327 97.80 175 3 0.2189 502.213 493.911 0.862 0.976 0.130 8.318-6.595 100.00 360 8 0.2218 375.773 370.534 0.888 0.976 0.100 6.588-5.215 100.00 711 7 0.1973 345.298 334.591 0.886 0.976 0.082 5.214-4.128 98.38 1367 28 0.1256 505.066 498.944 0.977 0.977 0.044 4.126-3.266 94.74 2603 46 0.1175 460.395 452.534 1.043 0.978 0.005 3.266-2.585 99.86 5447 97 0.1130 310.571 306.904 1.024 0.979 0.000 2.585-2.046 97.45 10613 204 0.0966 234.308 231.584 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0907 138.675 137.309 1.050 0.985 0.000 1.619-1.281 98.00 42464 925 0.0943 74.655 74.000 1.041 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.049 38.333 1.010 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0029 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1364 | n_water=897 | time (s): 2.830 (total time: 2.830) Filter (dist) r_work=0.1195 r_free=0.1365 | n_water=896 | time (s): 112.440 (total time: 115.270) Filter (q & B) r_work=0.1195 r_free=0.1364 | n_water=887 | time (s): 4.370 (total time: 119.640) Compute maps r_work=0.1195 r_free=0.1364 | n_water=887 | time (s): 1.620 (total time: 121.260) Filter (map) r_work=0.1218 r_free=0.1364 | n_water=763 | time (s): 5.290 (total time: 126.550) Find peaks r_work=0.1218 r_free=0.1364 | n_water=763 | time (s): 0.840 (total time: 127.390) Add new water r_work=0.1226 r_free=0.1373 | n_water=974 | time (s): 4.560 (total time: 131.950) Refine new water occ: r_work=0.1192 r_free=0.1341 adp: r_work=0.1192 r_free=0.1340 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1341 occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1342 r_work=0.1189 r_free=0.1342 | n_water=974 | time (s): 227.870 (total time: 359.820) Filter (q & B) r_work=0.1193 r_free=0.1354 | n_water=904 | time (s): 4.630 (total time: 364.450) Filter (dist only) r_work=0.1193 r_free=0.1353 | n_water=903 | time (s): 114.970 (total time: 479.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540751 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.385077 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1360 0.0164 0.039 1.1 6.7 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.60 1.64 1.674 13.731 13.385 3.756 11.97 13.63 1.66 1.674 13.727 13.385 3.755 Individual atomic B min max mean iso aniso Overall: 5.52 63.23 14.63 0.85 539 3268 Protein: 5.52 27.83 10.33 0.85 0 2902 Water: 6.00 63.23 28.44 N/A 539 364 Other: 13.79 21.98 17.88 N/A 0 2 Chain A: 5.64 51.21 12.11 N/A 0 1623 Chain B: 5.52 63.23 11.95 N/A 0 1645 Chain S: 6.00 59.71 30.39 N/A 539 0 Histogram: Values Number of atoms 5.52 - 11.29 2061 11.29 - 17.06 825 17.06 - 22.83 272 22.83 - 28.60 205 28.60 - 34.37 199 34.37 - 40.14 124 40.14 - 45.91 75 45.91 - 51.69 33 51.69 - 57.46 9 57.46 - 63.23 4 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1363 r_work=0.1197 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1363 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1367 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754875 | | target function (ml) not normalized (work): 703250.515185 | | target function (ml) not normalized (free): 14732.094103 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1367 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1410 0.1408 0.1508 n_refl.: 191131 remove outliers: r(all,work,free)=0.1410 0.1408 0.1508 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1404 0.1402 0.1504 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1366 n_refl.: 191131 remove outliers: r(all,work,free)=0.1199 0.1195 0.1366 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3867 361.420 319.356 0.375 0.973 0.199 13.296-10.522 97.03 97 1 0.2386 481.486 460.353 0.675 0.975 0.148 10.503-8.327 97.80 175 3 0.2183 502.213 494.251 0.842 0.976 0.123 8.318-6.595 100.00 360 8 0.2207 375.773 370.736 0.866 0.976 0.093 6.588-5.215 100.00 711 7 0.1975 345.298 334.743 0.865 0.976 0.077 5.214-4.128 98.38 1367 28 0.1252 505.066 498.957 0.954 0.977 0.039 4.126-3.266 94.74 2603 46 0.1180 460.395 452.712 1.018 0.979 0.005 3.266-2.585 99.86 5447 97 0.1134 310.571 306.937 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0965 234.308 231.576 1.007 0.982 0.000 2.046-1.619 99.39 21536 464 0.0909 138.675 137.294 1.024 0.986 0.000 1.619-1.281 98.00 42464 925 0.0942 74.655 74.006 1.014 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.049 38.331 0.983 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0082 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1366 After: r_work=0.1196 r_free=0.1367 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1367 | n_water=903 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1196 r_free=0.1367 | n_water=903 | time (s): 122.230 (total time: 124.600) Filter (q & B) r_work=0.1197 r_free=0.1366 | n_water=891 | time (s): 4.180 (total time: 128.780) Compute maps r_work=0.1197 r_free=0.1366 | n_water=891 | time (s): 1.820 (total time: 130.600) Filter (map) r_work=0.1220 r_free=0.1365 | n_water=768 | time (s): 5.800 (total time: 136.400) Find peaks r_work=0.1220 r_free=0.1365 | n_water=768 | time (s): 0.840 (total time: 137.240) Add new water r_work=0.1228 r_free=0.1375 | n_water=980 | time (s): 4.100 (total time: 141.340) Refine new water occ: r_work=0.1194 r_free=0.1348 adp: r_work=0.1194 r_free=0.1348 occ: r_work=0.1192 r_free=0.1350 adp: r_work=0.1192 r_free=0.1350 occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1190 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1351 r_work=0.1190 r_free=0.1351 | n_water=980 | time (s): 359.830 (total time: 501.170) Filter (q & B) r_work=0.1195 r_free=0.1361 | n_water=903 | time (s): 4.910 (total time: 506.080) Filter (dist only) r_work=0.1195 r_free=0.1360 | n_water=901 | time (s): 115.610 (total time: 621.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554753 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.258841 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1365 0.0167 0.039 1.2 9.4 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.65 1.67 1.671 13.686 13.259 3.757 11.99 13.67 1.68 1.672 13.683 13.259 3.757 Individual atomic B min max mean iso aniso Overall: 5.53 62.29 14.57 0.84 537 3268 Protein: 5.53 27.68 10.31 0.84 0 2902 Water: 5.97 62.29 28.30 N/A 537 364 Other: 13.82 21.89 17.86 N/A 0 2 Chain A: 5.66 50.88 12.06 N/A 0 1623 Chain B: 5.53 62.29 11.91 N/A 0 1645 Chain S: 5.97 59.61 30.31 N/A 537 0 Histogram: Values Number of atoms 5.53 - 11.20 2035 11.20 - 16.88 852 16.88 - 22.55 267 22.55 - 28.23 204 28.23 - 33.91 197 33.91 - 39.58 117 39.58 - 45.26 78 45.26 - 50.94 39 50.94 - 56.61 10 56.61 - 62.29 6 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1367 r_work=0.1199 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1367 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1369 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756905 | | target function (ml) not normalized (work): 703630.744202 | | target function (ml) not normalized (free): 14734.503453 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1374 0.1525 5.7017 5.7785| | 2: 2.94 - 2.33 1.00 7339 128 0.1079 0.1390 5.0895 5.1981| | 3: 2.33 - 2.04 0.96 6939 150 0.0911 0.1199 4.6636 4.7568| | 4: 2.04 - 1.85 1.00 7170 155 0.0900 0.1051 4.3943 4.5688| | 5: 1.85 - 1.72 0.99 7113 159 0.0937 0.0981 4.1522 4.2324| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1059 3.9463 4.0655| | 7: 1.62 - 1.54 0.99 7104 148 0.0893 0.0975 3.8011 3.9342| | 8: 1.54 - 1.47 0.96 6798 152 0.0897 0.1316 3.7048 3.9196| | 9: 1.47 - 1.41 0.98 6938 155 0.0930 0.1134 3.6253 3.7494| | 10: 1.41 - 1.36 0.99 7022 150 0.0979 0.1178 3.5595 3.6724| | 11: 1.36 - 1.32 0.99 6997 151 0.0996 0.1122 3.4879 3.5935| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1121 3.4624 3.5853| | 13: 1.28 - 1.25 0.98 6907 166 0.1045 0.1242 3.4396 3.5648| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1582 3.4337 3.679| | 15: 1.22 - 1.19 0.98 6956 137 0.1170 0.1244 3.4495 3.4897| | 16: 1.19 - 1.17 0.93 6604 132 0.1253 0.1535 3.4662 3.6521| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1217 3.4334 3.4363| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1718 3.439 3.5352| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1769 3.4208 3.6061| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1582 3.4109 3.4317| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2138 3.4192 3.5017| | 22: 1.07 - 1.05 0.97 6836 135 0.1906 0.1946 3.4144 3.4143| | 23: 1.05 - 1.03 0.97 6827 159 0.2122 0.2027 3.4345 3.4894| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2260 3.4369 3.5127| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2527 3.4507 3.5289| | 26: 1.01 - 0.99 0.96 6767 158 0.2759 0.2845 3.4164 3.4217| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2809 3.4696 3.3996| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7399 127 0.93 11.87 1.00 0.98 11577.01| | 2: 2.94 - 2.33 7339 128 0.92 13.02 0.99 0.98 5279.53| | 3: 2.33 - 2.04 6939 150 0.96 7.72 1.01 0.98 1722.56| | 4: 2.04 - 1.85 7170 155 0.96 7.68 1.00 0.98 1007.80| | 5: 1.85 - 1.72 7113 159 0.96 7.99 1.00 0.98 625.69| | 6: 1.72 - 1.62 7102 142 0.96 7.93 1.00 0.99 437.48| | 7: 1.62 - 1.54 7104 148 0.96 8.12 1.01 0.99 335.35| | 8: 1.54 - 1.47 6798 152 0.96 8.27 1.01 0.99 279.73| | 9: 1.47 - 1.41 6938 155 0.96 8.46 1.00 1.00 231.09| | 10: 1.41 - 1.36 7022 150 0.96 8.93 1.00 0.99 203.19| | 11: 1.36 - 1.32 6997 151 0.96 8.96 0.99 0.98 175.50| | 12: 1.32 - 1.28 6975 149 0.96 9.01 0.98 0.97 161.50| | 13: 1.28 - 1.25 6907 166 0.96 9.53 1.01 0.98 158.62| | 14: 1.25 - 1.22 7015 112 0.95 10.69 1.01 0.99 163.29| | 15: 1.22 - 1.19 6956 137 0.95 11.21 1.01 1.00 166.13| | 16: 1.19 - 1.17 6604 132 0.95 11.38 1.01 0.98 159.33| | 17: 1.17 - 1.14 6940 135 0.94 12.20 1.01 0.98 153.28| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.97 147.75| | 19: 1.12 - 1.10 6948 106 0.93 14.16 1.00 0.97 151.58| | 20: 1.10 - 1.08 6884 147 0.92 15.21 1.00 0.96 150.23| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.95 153.07| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.95 154.87| | 23: 1.05 - 1.03 6827 159 0.87 20.56 0.99 0.94 165.57| | 24: 1.03 - 1.02 6784 133 0.85 23.25 0.99 0.95 180.22| | 25: 1.02 - 1.01 6552 130 0.83 25.24 0.98 0.92 183.35| | 26: 1.01 - 0.99 6767 158 0.81 26.72 0.98 0.91 177.69| | 27: 0.99 - 0.98 6647 131 0.82 26.41 0.99 0.89 162.24| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 147.75 max = 11577.01 mean = 947.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.32| |phase err.(test): min = 0.00 max = 88.06 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1369 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1415 0.1413 0.1514 n_refl.: 191131 remove outliers: r(all,work,free)=0.1415 0.1413 0.1514 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1409 0.1407 0.1510 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1368 n_refl.: 191131 remove outliers: r(all,work,free)=0.1201 0.1198 0.1368 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3882 361.420 318.962 0.369 0.974 0.191 13.296-10.522 97.03 97 1 0.2388 481.486 460.290 0.672 0.976 0.145 10.503-8.327 97.80 175 3 0.2166 502.213 494.415 0.841 0.976 0.116 8.318-6.595 100.00 360 8 0.2210 375.773 370.364 0.864 0.976 0.096 6.588-5.215 100.00 711 7 0.1957 345.298 334.755 0.864 0.977 0.083 5.214-4.128 98.38 1367 28 0.1251 505.066 499.197 0.954 0.978 0.039 4.126-3.266 94.74 2603 46 0.1181 460.395 452.730 1.018 0.979 0.000 3.266-2.585 99.86 5447 97 0.1131 310.571 307.048 1.000 0.981 0.000 2.585-2.046 97.45 10613 204 0.0970 234.308 231.582 1.007 0.983 0.000 2.046-1.619 99.39 21536 464 0.0912 138.675 137.286 1.022 0.988 0.000 1.619-1.281 98.00 42464 925 0.0950 74.655 73.999 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.049 38.326 0.979 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0086 ================= 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 : 0.2038 0.1982 0.081 5.377 5.2 78.0 14.6 805 0.000 1_bss: 0.1802 0.1913 0.081 5.377 5.2 78.0 14.6 805 0.000 1_settarget: 0.1802 0.1913 0.081 5.377 5.2 78.0 14.6 805 0.000 1_nqh: 0.1802 0.1913 0.081 5.377 5.2 78.0 14.6 805 0.000 1_weight: 0.1802 0.1913 0.081 5.377 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1274 0.1505 0.039 1.155 5.2 78.0 14.6 805 0.158 1_adp: 0.1300 0.1571 0.039 1.155 5.2 73.0 15.0 805 0.158 1_regHadp: 0.1299 0.1568 0.039 1.155 5.2 73.0 15.0 805 0.158 1_occ: 0.1284 0.1557 0.039 1.155 5.2 73.0 15.0 805 0.158 2_bss: 0.1276 0.1545 0.039 1.155 5.3 73.2 15.1 805 0.158 2_settarget: 0.1276 0.1545 0.039 1.155 5.3 73.2 15.1 805 0.158 2_updatecdl: 0.1276 0.1545 0.039 1.162 5.3 73.2 15.1 805 0.158 2_nqh: 0.1276 0.1545 0.039 1.162 5.3 73.2 15.1 805 0.158 2_sol: 0.1273 0.1500 0.039 1.162 5.3 73.2 16.1 879 n/a 2_weight: 0.1273 0.1500 0.039 1.162 5.3 73.2 16.1 879 n/a 2_xyzrec: 0.1256 0.1517 0.041 1.128 5.3 73.2 16.1 879 n/a 2_adp: 0.1233 0.1497 0.041 1.128 5.4 69.8 16.2 879 n/a 2_regHadp: 0.1233 0.1498 0.041 1.128 5.4 69.8 16.2 879 n/a 2_occ: 0.1227 0.1494 0.041 1.128 5.4 69.8 16.2 879 n/a 3_bss: 0.1234 0.1501 0.041 1.128 5.3 69.8 16.2 879 n/a 3_settarget: 0.1234 0.1501 0.041 1.128 5.3 69.8 16.2 879 n/a 3_updatecdl: 0.1234 0.1501 0.041 1.137 5.3 69.8 16.2 879 n/a 3_nqh: 0.1234 0.1501 0.041 1.137 5.3 69.8 16.2 879 n/a 3_sol: 0.1251 0.1510 0.041 1.137 5.3 68.2 15.4 860 n/a 3_weight: 0.1251 0.1510 0.041 1.137 5.3 68.2 15.4 860 n/a 3_xyzrec: 0.1241 0.1434 0.035 1.094 5.3 68.2 15.4 860 n/a 3_adp: 0.1236 0.1399 0.035 1.094 5.5 67.8 15.2 860 n/a 3_regHadp: 0.1236 0.1400 0.035 1.094 5.5 67.8 15.2 860 n/a 3_occ: 0.1230 0.1390 0.035 1.094 5.5 67.8 15.2 860 n/a 4_bss: 0.1226 0.1388 0.035 1.094 5.5 67.7 15.2 860 n/a 4_settarget: 0.1226 0.1388 0.035 1.094 5.5 67.7 15.2 860 n/a 4_updatecdl: 0.1226 0.1388 0.035 1.098 5.5 67.7 15.2 860 n/a 4_nqh: 0.1226 0.1388 0.035 1.098 5.5 67.7 15.2 860 n/a 4_sol: 0.1209 0.1368 0.035 1.098 5.5 67.7 15.0 859 n/a 4_weight: 0.1209 0.1368 0.035 1.098 5.5 67.7 15.0 859 n/a 4_xyzrec: 0.1207 0.1373 0.036 1.120 5.5 67.7 15.0 859 n/a 4_adp: 0.1203 0.1371 0.036 1.120 5.5 67.3 15.0 859 n/a 4_regHadp: 0.1203 0.1371 0.036 1.120 5.5 67.3 15.0 859 n/a 4_occ: 0.1201 0.1371 0.036 1.120 5.5 67.3 15.0 859 n/a 5_bss: 0.1196 0.1365 0.036 1.120 5.5 67.3 14.9 859 n/a 5_settarget: 0.1196 0.1365 0.036 1.120 5.5 67.3 14.9 859 n/a 5_updatecdl: 0.1196 0.1365 0.036 1.120 5.5 67.3 14.9 859 n/a 5_nqh: 0.1196 0.1365 0.036 1.120 5.5 67.3 14.9 859 n/a 5_sol: 0.1194 0.1356 0.036 1.120 5.5 67.3 15.0 882 n/a 5_weight: 0.1194 0.1356 0.036 1.120 5.5 67.3 15.0 882 n/a 5_xyzrec: 0.1197 0.1364 0.037 1.122 5.5 67.3 15.0 882 n/a 5_adp: 0.1201 0.1367 0.037 1.122 5.6 66.8 15.0 882 n/a 5_regHadp: 0.1201 0.1367 0.037 1.122 5.6 66.8 15.0 882 n/a 5_occ: 0.1199 0.1373 0.037 1.122 5.6 66.8 15.0 882 n/a 6_bss: 0.1198 0.1372 0.037 1.122 5.5 66.8 14.9 882 n/a 6_settarget: 0.1198 0.1372 0.037 1.122 5.5 66.8 14.9 882 n/a 6_updatecdl: 0.1198 0.1372 0.037 1.121 5.5 66.8 14.9 882 n/a 6_nqh: 0.1198 0.1372 0.037 1.121 5.5 66.8 14.9 882 n/a 6_sol: 0.1196 0.1354 0.037 1.121 5.5 66.8 14.9 888 n/a 6_weight: 0.1196 0.1354 0.037 1.121 5.5 66.8 14.9 888 n/a 6_xyzrec: 0.1199 0.1357 0.037 1.130 5.5 66.8 14.9 888 n/a 6_adp: 0.1201 0.1360 0.037 1.130 5.6 65.8 14.8 888 n/a 6_regHadp: 0.1201 0.1360 0.037 1.130 5.6 65.8 14.8 888 n/a 6_occ: 0.1199 0.1359 0.037 1.130 5.6 65.8 14.8 888 n/a 7_bss: 0.1198 0.1357 0.037 1.130 5.4 65.6 14.6 888 n/a 7_settarget: 0.1198 0.1357 0.037 1.130 5.4 65.6 14.6 888 n/a 7_updatecdl: 0.1198 0.1357 0.037 1.130 5.4 65.6 14.6 888 n/a 7_nqh: 0.1198 0.1357 0.037 1.130 5.4 65.6 14.6 888 n/a 7_sol: 0.1196 0.1356 0.037 1.130 5.4 65.6 14.6 895 n/a 7_weight: 0.1196 0.1356 0.037 1.130 5.4 65.6 14.6 895 n/a 7_xyzrec: 0.1199 0.1363 0.038 1.126 5.4 65.6 14.6 895 n/a 7_adp: 0.1202 0.1366 0.038 1.126 5.4 64.5 14.6 895 n/a 7_regHadp: 0.1202 0.1366 0.038 1.126 5.4 64.5 14.6 895 n/a 7_occ: 0.1200 0.1365 0.038 1.126 5.4 64.5 14.6 895 n/a 8_bss: 0.1193 0.1359 0.038 1.126 5.5 64.6 14.6 895 n/a 8_settarget: 0.1193 0.1359 0.038 1.126 5.5 64.6 14.6 895 n/a 8_updatecdl: 0.1193 0.1359 0.038 1.125 5.5 64.6 14.6 895 n/a 8_nqh: 0.1193 0.1359 0.038 1.125 5.5 64.6 14.6 895 n/a 8_sol: 0.1192 0.1355 0.038 1.125 5.5 64.6 14.6 897 n/a 8_weight: 0.1192 0.1355 0.038 1.125 5.5 64.6 14.6 897 n/a 8_xyzrec: 0.1195 0.1364 0.038 1.123 5.5 64.6 14.6 897 n/a 8_adp: 0.1196 0.1365 0.038 1.123 5.5 63.5 14.6 897 n/a 8_regHadp: 0.1196 0.1365 0.038 1.123 5.5 63.5 14.6 897 n/a 8_occ: 0.1195 0.1367 0.038 1.123 5.5 63.5 14.6 897 n/a 9_bss: 0.1195 0.1364 0.038 1.123 5.5 63.5 14.6 897 n/a 9_settarget: 0.1195 0.1364 0.038 1.123 5.5 63.5 14.6 897 n/a 9_updatecdl: 0.1195 0.1364 0.038 1.123 5.5 63.5 14.6 897 n/a 9_nqh: 0.1195 0.1364 0.038 1.123 5.5 63.5 14.6 897 n/a 9_sol: 0.1193 0.1353 0.038 1.123 5.5 63.5 14.6 903 n/a 9_weight: 0.1193 0.1353 0.038 1.123 5.5 63.5 14.6 903 n/a 9_xyzrec: 0.1196 0.1360 0.039 1.114 5.5 63.5 14.6 903 n/a 9_adp: 0.1197 0.1363 0.039 1.114 5.5 63.2 14.6 903 n/a 9_regHadp: 0.1197 0.1363 0.039 1.114 5.5 63.2 14.6 903 n/a 9_occ: 0.1196 0.1367 0.039 1.114 5.5 63.2 14.6 903 n/a 10_bss: 0.1195 0.1366 0.039 1.114 5.5 63.2 14.6 903 n/a 10_settarget: 0.1195 0.1366 0.039 1.114 5.5 63.2 14.6 903 n/a 10_updatecdl: 0.1195 0.1366 0.039 1.115 5.5 63.2 14.6 903 n/a 10_setrh: 0.1196 0.1367 0.039 1.115 5.5 63.2 14.6 903 n/a 10_nqh: 0.1196 0.1367 0.039 1.115 5.5 63.2 14.6 903 n/a 10_sol: 0.1195 0.1360 0.039 1.115 5.5 63.2 14.6 901 n/a 10_weight: 0.1195 0.1360 0.039 1.115 5.5 63.2 14.6 901 n/a 10_xyzrec: 0.1198 0.1365 0.039 1.168 5.5 63.2 14.6 901 n/a 10_adp: 0.1199 0.1367 0.039 1.168 5.5 62.3 14.6 901 n/a 10_regHadp: 0.1199 0.1367 0.039 1.168 5.5 62.3 14.6 901 n/a 10_occ: 0.1198 0.1369 0.039 1.168 5.5 62.3 14.6 901 n/a end: 0.1198 0.1368 0.039 1.168 5.5 62.2 14.5 901 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6036143_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6036143_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.0900 Refinement macro-cycles (run) : 12258.0600 Write final files (write_after_run_outputs) : 157.4300 Total : 12422.5800 Total CPU time: 3.46 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:20 PST -0800 (1736736260.80 s) Start R-work = 0.1802, R-free = 0.1913 Final R-work = 0.1198, R-free = 0.1368 =============================================================================== Job complete usr+sys time: 12692.53 seconds wall clock time: 212 minutes 35.19 seconds (12755.19 seconds total)