Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5525287.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5525287.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5525287.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/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.36, per 1000 atoms: 0.35 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.673 distance_ideal: 2.720 ideal - model: 0.047 slack: 0.000 delta_slack: 0.047 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: 2.683 distance_ideal: 2.710 ideal - model: 0.027 slack: 0.000 delta_slack: 0.027 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: 0.67 Conformation dependent library (CDL) restraints added in 114.2 milliseconds Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 1172 1.05 - 1.28: 2253 1.28 - 1.50: 1515 1.50 - 1.72: 977 1.72 - 1.95: 17 Bond restraints: 5934 Sorted by residual: bond pdb=" C ALA A 108 " pdb=" O ALA A 108 " ideal model delta sigma weight residual 1.244 1.453 -0.209 9.80e-03 1.04e+04 4.55e+02 bond pdb=" N THR A 86 " pdb=" H THR A 86 " ideal model delta sigma weight residual 0.860 1.257 -0.397 2.00e-02 2.50e+03 3.95e+02 bond pdb=" N LEU A 87 " pdb=" H LEU A 87 " ideal model delta sigma weight residual 0.860 1.244 -0.384 2.00e-02 2.50e+03 3.69e+02 bond pdb=" NH1 ARG A 49 " pdb="HH11 ARG A 49 " ideal model delta sigma weight residual 0.860 1.237 -0.377 2.00e-02 2.50e+03 3.54e+02 bond pdb=" N GLY B 126 " pdb=" H GLY B 126 " ideal model delta sigma weight residual 0.860 1.235 -0.375 2.00e-02 2.50e+03 3.51e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 5504 4.08 - 8.17: 3554 8.17 - 12.25: 1402 12.25 - 16.34: 319 16.34 - 20.42: 31 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ILE A 118 " pdb=" C ILE A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 121.80 137.97 -16.17 1.13e+00 7.83e-01 2.05e+02 angle pdb=" O PRO A 73 " pdb=" C PRO A 73 " pdb=" N GLY A 74 " ideal model delta sigma weight residual 122.91 140.06 -17.15 1.21e+00 6.83e-01 2.01e+02 angle pdb=" N GLY A 159 " pdb=" CA GLY A 159 " pdb=" C GLY A 159 " ideal model delta sigma weight residual 114.40 129.09 -14.69 1.11e+00 8.12e-01 1.75e+02 angle pdb=" CA PHE A 95 " pdb=" C PHE A 95 " pdb=" O PHE A 95 " ideal model delta sigma weight residual 121.02 136.34 -15.32 1.17e+00 7.31e-01 1.71e+02 angle pdb=" C PHE A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta sigma weight residual 119.19 132.81 -13.62 1.06e+00 8.90e-01 1.65e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.69: 1860 17.69 - 35.38: 124 35.38 - 53.06: 45 53.06 - 70.75: 19 70.75 - 88.43: 2 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 147.62 32.38 0 5.00e+00 4.00e-02 4.19e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual 180.00 -154.60 -25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.224: 211 0.224 - 0.448: 159 0.448 - 0.672: 86 0.672 - 0.896: 30 0.896 - 1.120: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA MET B 187 " pdb=" N MET B 187 " pdb=" C MET B 187 " pdb=" CB MET B 187 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.13e+01 chirality pdb=" CA LEU A 25 " pdb=" N LEU A 25 " pdb=" C LEU A 25 " pdb=" CB LEU A 25 " both_signs ideal model delta sigma weight residual False 2.51 3.56 -1.05 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA MET B 124 " pdb=" N MET B 124 " pdb=" C MET B 124 " pdb=" CB MET B 124 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.067 2.00e-02 2.50e+03 6.51e-02 1.70e+02 pdb=" CG TRP B 139 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.101 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.074 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.073 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " 0.050 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.105 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.119 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.023 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.042 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.038 2.00e-02 2.50e+03 6.03e-02 1.46e+02 pdb=" CG TRP A 146 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.089 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.111 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.056 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.136 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.012 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.087 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.132 2.00e-02 2.50e+03 6.90e-02 1.43e+02 pdb=" CG PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.106 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.040 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.62: 29 1.62 - 2.36: 2453 2.36 - 3.11: 22294 3.11 - 3.85: 32912 3.85 - 4.60: 52633 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110321 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.871 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.938 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.009 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.163 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.200 2.620 ... (remaining 110316 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_5525287_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= 0.2032 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299024 | | target function (ml) not normalized (work): 805263.161616 | | target function (ml) not normalized (free): 16530.644780 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2137 0.1888 6.7032 6.2904| | 2: 2.94 - 2.33 1.00 7339 128 0.1633 0.1663 5.5314 5.591| | 3: 2.33 - 2.04 0.96 6939 150 0.1618 0.1515 5.1344 5.1056| | 4: 2.04 - 1.85 1.00 7170 155 0.1738 0.1602 4.9519 5.0566| | 5: 1.85 - 1.72 0.99 7113 159 0.1951 0.1631 4.8013 4.7368| | 6: 1.72 - 1.62 0.99 7102 142 0.1972 0.2028 4.6604 4.7086| | 7: 1.62 - 1.54 0.99 7104 148 0.1999 0.1740 4.5561 4.5121| | 8: 1.54 - 1.47 0.96 6798 152 0.2020 0.2344 4.468 4.5963| | 9: 1.47 - 1.41 0.98 6938 155 0.2072 0.2184 4.3924 4.4315| | 10: 1.41 - 1.36 0.99 7022 150 0.2117 0.2008 4.3061 4.2709| | 11: 1.36 - 1.32 0.99 6997 151 0.2138 0.2150 4.2542 4.2885| | 12: 1.32 - 1.28 0.98 6976 149 0.2076 0.1946 4.179 4.2644| | 13: 1.28 - 1.25 0.98 6907 166 0.2011 0.2131 4.1156 4.1924| | 14: 1.25 - 1.22 0.98 7015 113 0.2102 0.2246 4.0849 4.2645| | 15: 1.22 - 1.19 0.98 6957 137 0.2087 0.2027 4.0437 4.0628| | 16: 1.19 - 1.17 0.93 6604 132 0.2112 0.2105 4.0045 4.0891| | 17: 1.17 - 1.14 0.98 6941 135 0.2144 0.1767 3.947 3.9888| | 18: 1.14 - 1.12 0.98 6875 142 0.2234 0.2233 3.9299 3.9044| | 19: 1.12 - 1.10 0.97 6949 106 0.2271 0.2392 3.8699 3.9327| | 20: 1.10 - 1.08 0.97 6884 147 0.2333 0.2256 3.8203 3.864| | 21: 1.08 - 1.07 0.97 6852 152 0.2451 0.2562 3.7964 3.7748| | 22: 1.07 - 1.05 0.97 6838 135 0.2582 0.2470 3.7614 3.7257| | 23: 1.05 - 1.03 0.97 6829 159 0.2703 0.2578 3.7248 3.7709| | 24: 1.03 - 1.02 0.96 6785 133 0.2887 0.2596 3.697 3.7548| | 25: 1.02 - 1.01 0.93 6552 130 0.3052 0.2840 3.672 3.7437| | 26: 1.01 - 0.99 0.96 6767 158 0.3184 0.3534 3.6229 3.6887| | 27: 0.99 - 0.98 0.94 6648 131 0.3383 0.3353 3.6306 3.5927| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.01 0.91 0.97 33970.50| | 2: 2.94 - 2.33 7339 128 0.86 20.97 1.09 1.02 14588.96| | 3: 2.33 - 2.04 6939 150 0.93 12.40 1.11 1.05 4049.68| | 4: 2.04 - 1.85 7170 155 0.93 12.98 1.11 1.06 2609.67| | 5: 1.85 - 1.72 7113 159 0.91 14.83 1.12 1.08 1895.43| | 6: 1.72 - 1.62 7102 142 0.90 16.27 1.11 1.09 1572.00| | 7: 1.62 - 1.54 7104 148 0.90 17.26 1.11 1.08 1303.18| | 8: 1.54 - 1.47 6798 152 0.89 18.35 1.10 1.06 1147.29| | 9: 1.47 - 1.41 6938 155 0.89 18.50 1.10 1.07 955.28| | 10: 1.41 - 1.36 7022 150 0.88 19.57 1.09 1.06 823.31| | 11: 1.36 - 1.32 6997 151 0.88 19.53 1.08 1.05 710.46| | 12: 1.32 - 1.28 6976 149 0.87 19.77 1.07 1.04 641.29| | 13: 1.28 - 1.25 6907 166 0.87 20.06 1.07 1.04 616.63| | 14: 1.25 - 1.22 7015 113 0.86 21.09 1.08 1.04 591.12| | 15: 1.22 - 1.19 6957 137 0.86 21.64 1.07 1.03 575.94| | 16: 1.19 - 1.17 6604 132 0.86 21.37 1.07 1.02 518.64| | 17: 1.17 - 1.14 6941 135 0.86 21.50 1.08 1.01 456.89| | 18: 1.14 - 1.12 6875 142 0.87 20.94 1.08 1.00 387.28| | 19: 1.12 - 1.10 6949 106 0.86 21.35 1.07 1.00 357.00| | 20: 1.10 - 1.08 6884 147 0.86 22.08 1.06 0.99 331.36| | 21: 1.08 - 1.07 6852 152 0.85 23.00 1.05 0.99 318.04| | 22: 1.07 - 1.05 6838 135 0.83 24.40 1.05 0.97 304.03| | 23: 1.05 - 1.03 6829 159 0.81 26.62 1.05 0.97 309.86| | 24: 1.03 - 1.02 6785 133 0.78 29.50 1.05 0.96 323.00| | 25: 1.02 - 1.01 6552 130 0.76 31.45 1.03 0.91 320.86| | 26: 1.01 - 0.99 6767 158 0.74 33.19 1.03 0.91 306.31| | 27: 0.99 - 0.98 6648 131 0.75 32.03 1.04 0.94 282.83| |alpha: min = 0.91 max = 1.09 mean = 1.02| |beta: min = 282.83 max = 33970.50 mean = 2724.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.42| |phase err.(test): min = 0.00 max = 89.77 mean = 21.51| |-----------------------------------------------------------------------------| ----------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 0.243 2950 Z= 5.434 Angle : 5.243 18.236 4018 Z= 3.669 Chirality : 0.382 1.120 492 Planarity : 0.033 0.165 512 Dihedral : 12.795 88.432 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.37 % Favored : 96.11 % Rotamer: Outliers : 2.58 % Allowed : 3.55 % Favored : 93.87 % Cbeta Deviations : 34.27 % 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: -2.26 (0.40), residues: 386 helix: -2.90 (0.29), residues: 146 sheet: -0.36 (0.59), residues: 82 loop : -0.40 (0.51), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.019 ARG B 27 TYR 0.087 0.035 TYR A 67 PHE 0.123 0.036 PHE A 164 TRP 0.129 0.039 TRP B 139 HIS 0.060 0.026 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= 0.2032 r_free= 0.1952 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299024 | | target function (ml) not normalized (work): 805263.161616 | | target function (ml) not normalized (free): 16530.644780 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2030 0.2032 0.1952 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2030 0.2032 0.1952 n_refl.: 191155 remove outliers: r(all,work,free)=0.2030 0.2032 0.1952 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2028 0.2030 0.1951 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1799 0.1797 0.1888 n_refl.: 191145 remove outliers: r(all,work,free)=0.1797 0.1795 0.1887 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 0.4079 402.814 292.288 0.421 0.935 0.299 13.296-10.522 98.02 98 1 0.2392 527.329 514.674 0.761 0.936 0.248 10.503-8.327 99.45 178 3 0.2564 565.118 554.270 0.940 0.936 0.223 8.318-6.595 100.00 360 8 0.2481 414.736 403.140 0.935 0.936 0.160 6.588-5.215 100.00 711 7 0.2224 381.101 365.521 0.926 0.936 0.150 5.214-4.128 98.38 1367 28 0.1485 557.435 549.374 1.041 0.937 0.090 4.126-3.266 94.74 2603 46 0.1343 508.132 498.395 1.106 0.937 0.009 3.266-2.585 99.86 5447 97 0.1448 342.774 337.623 1.086 0.937 0.000 2.585-2.046 97.45 10613 204 0.1391 258.603 254.186 1.087 0.937 0.000 2.046-1.619 99.39 21536 464 0.1610 153.054 149.956 1.106 0.936 0.000 1.619-1.281 98.00 42464 925 0.1922 82.395 80.395 1.089 0.935 0.000 1.281-0.980 96.53 101826 2055 0.2313 44.202 41.999 1.078 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0435 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1795 r_free=0.1887 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 r_work=0.1795 r_free=0.1889 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.569073 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.651864 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 0.1270 0.1499 0.0229 0.038 1.2 11.4 0.0 0.3 0 11.285 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 14.99 2.29 1.117 13.095 573.652 0.018 12.99 15.72 2.73 1.246 13.348 573.652 0.017 Individual atomic B min max mean iso aniso Overall: 5.21 73.03 15.04 1.40 435 3274 Protein: 5.21 40.30 11.02 1.40 0 2902 Water: 6.37 73.03 29.54 N/A 435 370 Other: 16.11 30.32 23.21 N/A 0 2 Chain A: 5.32 59.61 13.07 N/A 0 1626 Chain B: 5.21 73.03 12.78 N/A 0 1648 Chain S: 12.10 64.69 30.99 N/A 435 0 Histogram: Values Number of atoms 5.21 - 11.99 2173 11.99 - 18.77 631 18.77 - 25.56 314 25.56 - 32.34 264 32.34 - 39.12 155 39.12 - 45.90 108 45.90 - 52.68 40 52.68 - 59.46 19 59.46 - 66.25 4 66.25 - 73.03 1 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1572 r_work=0.1298 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1567 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1558 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015607 | | target function (ls_wunit_k1) not normalized (work): 2923.181815 | | target function (ls_wunit_k1) not normalized (free): 118.244649 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1558 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1469 0.1466 0.1638 n_refl.: 191137 remove outliers: r(all,work,free)=0.1469 0.1466 0.1638 n_refl.: 191137 overall B=0.16 to atoms: r(all,work,free)=0.1491 0.1489 0.1647 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1549 n_refl.: 191137 remove outliers: r(all,work,free)=0.1281 0.1276 0.1549 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 0.3601 402.814 377.649 0.471 0.997 0.285 13.296-10.522 98.02 98 1 0.2028 527.329 521.259 0.715 0.999 0.238 10.503-8.327 99.45 178 3 0.1779 565.118 562.054 0.855 0.999 0.213 8.318-6.595 100.00 360 8 0.1731 414.736 411.977 0.875 0.999 0.150 6.588-5.215 100.00 711 7 0.1545 381.101 373.188 0.856 0.999 0.150 5.214-4.128 98.38 1367 28 0.0906 557.435 554.287 0.942 0.999 0.070 4.126-3.266 94.74 2603 46 0.0831 508.132 504.392 1.007 1.000 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.446 0.991 1.000 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.432 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1090 153.054 151.427 1.018 1.000 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.411 1.010 1.001 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.125 0.987 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0356 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1549 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1549 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1549 | n_water=805 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1282 r_free=0.1558 | n_water=792 | time (s): 97.690 (total time: 100.110) Filter (q & B) r_work=0.1282 r_free=0.1558 | n_water=787 | time (s): 5.560 (total time: 105.670) Compute maps r_work=0.1282 r_free=0.1558 | n_water=787 | time (s): 2.410 (total time: 108.080) Filter (map) r_work=0.1308 r_free=0.1535 | n_water=647 | time (s): 4.790 (total time: 112.870) Find peaks r_work=0.1308 r_free=0.1535 | n_water=647 | time (s): 0.580 (total time: 113.450) Add new water r_work=0.1332 r_free=0.1565 | n_water=960 | time (s): 4.320 (total time: 117.770) Refine new water occ: r_work=0.1287 r_free=0.1528 adp: r_work=0.1274 r_free=0.1523 occ: r_work=0.1276 r_free=0.1520 adp: r_work=0.1269 r_free=0.1518 occ: r_work=0.1271 r_free=0.1515 adp: r_work=0.1268 r_free=0.1517 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1517 r_work=0.1268 r_free=0.1517 | n_water=960 | time (s): 94.760 (total time: 212.530) Filter (q & B) r_work=0.1271 r_free=0.1518 | n_water=896 | time (s): 4.290 (total time: 216.820) Filter (dist only) r_work=0.1272 r_free=0.1518 | n_water=895 | time (s): 112.060 (total time: 328.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.197407 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 592.693465 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 0.1255 0.1522 0.0268 0.040 1.1 19.0 0.0 0.3 0 11.599 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.22 2.68 2.044 15.257 592.693 0.014 12.30 15.06 2.77 2.408 15.302 592.693 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 73.29 16.44 1.21 527 3272 Protein: 5.38 40.87 10.99 1.21 0 2902 Water: 6.66 73.29 34.08 N/A 527 368 Other: 16.34 31.88 24.11 N/A 0 2 Chain A: 5.52 55.64 13.01 N/A 0 1624 Chain B: 5.38 68.18 12.83 N/A 0 1648 Chain S: 10.16 73.29 38.26 N/A 527 0 Histogram: Values Number of atoms 5.38 - 12.17 2165 12.17 - 18.96 661 18.96 - 25.75 262 25.75 - 32.54 222 32.54 - 39.33 177 39.33 - 46.13 150 46.13 - 52.92 83 52.92 - 59.71 52 59.71 - 66.50 22 66.50 - 73.29 5 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1506 r_work=0.1230 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1507 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 = 0.1225 r_free = 0.1507 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1507 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013345 | | target function (ls_wunit_k1) not normalized (work): 2499.503121 | | target function (ls_wunit_k1) not normalized (free): 105.203415 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1225 0.1507 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1611 n_refl.: 191137 remove outliers: r(all,work,free)=0.1434 0.1431 0.1611 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1609 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1514 n_refl.: 191137 remove outliers: r(all,work,free)=0.1237 0.1231 0.1514 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3082 402.814 380.641 0.483 0.962 0.260 13.296-10.522 98.02 98 1 0.1926 527.329 518.607 0.757 0.963 0.212 10.503-8.327 99.45 178 3 0.1405 565.118 567.288 0.919 0.963 0.197 8.318-6.595 100.00 360 8 0.1518 414.736 415.455 0.936 0.963 0.150 6.588-5.215 100.00 711 7 0.1352 381.101 376.299 0.912 0.963 0.140 5.214-4.128 98.38 1367 28 0.0821 557.435 556.427 0.996 0.963 0.090 4.126-3.266 94.74 2603 46 0.0762 508.132 505.568 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0863 342.774 341.282 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0896 258.603 256.736 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.619 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.353 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.217 1.058 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0569 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1514 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1514 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1514 | n_water=895 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1233 r_free=0.1514 | n_water=889 | time (s): 114.850 (total time: 117.430) Filter (q & B) r_work=0.1233 r_free=0.1514 | n_water=889 | time (s): 2.120 (total time: 119.550) Compute maps r_work=0.1233 r_free=0.1514 | n_water=889 | time (s): 1.790 (total time: 121.340) Filter (map) r_work=0.1273 r_free=0.1520 | n_water=687 | time (s): 5.140 (total time: 126.480) Find peaks r_work=0.1273 r_free=0.1520 | n_water=687 | time (s): 0.600 (total time: 127.080) Add new water r_work=0.1296 r_free=0.1547 | n_water=999 | time (s): 4.340 (total time: 131.420) Refine new water occ: r_work=0.1252 r_free=0.1511 adp: r_work=0.1252 r_free=0.1513 occ: r_work=0.1248 r_free=0.1509 adp: r_work=0.1248 r_free=0.1510 occ: r_work=0.1245 r_free=0.1507 adp: r_work=0.1244 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1508 r_work=0.1244 r_free=0.1508 | n_water=999 | time (s): 229.830 (total time: 361.250) Filter (q & B) r_work=0.1249 r_free=0.1518 | n_water=878 | time (s): 6.230 (total time: 367.480) Filter (dist only) r_work=0.1249 r_free=0.1519 | n_water=877 | time (s): 114.010 (total time: 481.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.677148 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.007759 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 0.1240 0.1442 0.0202 0.035 1.1 9.3 0.0 0.0 0 0.839 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.42 2.02 1.937 14.586 16.008 3.938 12.38 14.01 1.63 2.311 14.476 16.008 3.897 Individual atomic B min max mean iso aniso Overall: 5.56 67.63 15.22 1.03 512 3269 Protein: 5.56 36.19 10.70 1.03 0 2902 Water: 6.72 67.63 30.18 N/A 512 365 Other: 13.90 27.28 20.59 N/A 0 2 Chain A: 5.60 54.39 12.71 N/A 0 1623 Chain B: 5.56 67.63 12.49 N/A 0 1646 Chain S: 13.11 65.63 32.00 N/A 512 0 Histogram: Values Number of atoms 5.56 - 11.77 2130 11.77 - 17.98 699 17.98 - 24.18 293 24.18 - 30.39 232 30.39 - 36.60 174 36.60 - 42.80 147 42.80 - 49.01 67 49.01 - 55.22 31 55.22 - 61.42 5 61.42 - 67.63 3 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1402 r_work=0.1239 r_free=0.1402 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1402 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1393 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1232 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891155 | | target function (ml) not normalized (work): 728797.809078 | | target function (ml) not normalized (free): 15216.548550 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1232 0.1393 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1446 0.1445 0.1500 n_refl.: 191137 remove outliers: r(all,work,free)=0.1446 0.1445 0.1500 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1439 0.1438 0.1496 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1228 0.1387 n_refl.: 191137 remove outliers: r(all,work,free)=0.1231 0.1228 0.1387 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3900 398.008 359.739 0.418 0.946 0.241 13.296-10.522 98.02 98 1 0.2432 527.329 508.910 0.713 0.947 0.215 10.503-8.327 98.35 176 3 0.2029 555.265 558.305 0.882 0.947 0.180 8.318-6.595 100.00 360 8 0.2093 414.736 410.589 0.898 0.947 0.131 6.588-5.215 100.00 711 7 0.1841 381.101 370.798 0.885 0.947 0.110 5.214-4.128 98.38 1367 28 0.1168 557.435 552.293 0.973 0.947 0.080 4.126-3.266 94.74 2603 46 0.1104 508.132 501.068 1.034 0.948 0.009 3.266-2.585 99.86 5447 97 0.1096 342.774 339.125 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0974 258.603 255.671 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.400 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.488 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.315 1.039 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1112 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1387 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1228 r_free=0.1387 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1387 | n_water=877 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1228 r_free=0.1387 | n_water=876 | time (s): 106.870 (total time: 109.760) Filter (q & B) r_work=0.1228 r_free=0.1389 | n_water=865 | time (s): 4.010 (total time: 113.770) Compute maps r_work=0.1228 r_free=0.1389 | n_water=865 | time (s): 2.440 (total time: 116.210) Filter (map) r_work=0.1252 r_free=0.1387 | n_water=706 | time (s): 4.730 (total time: 120.940) Find peaks r_work=0.1252 r_free=0.1387 | n_water=706 | time (s): 0.800 (total time: 121.740) Add new water r_work=0.1267 r_free=0.1398 | n_water=959 | time (s): 4.910 (total time: 126.650) Refine new water occ: r_work=0.1218 r_free=0.1362 adp: r_work=0.1211 r_free=0.1358 occ: r_work=0.1208 r_free=0.1358 adp: r_work=0.1208 r_free=0.1358 occ: r_work=0.1206 r_free=0.1359 adp: r_work=0.1205 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1359 r_work=0.1205 r_free=0.1359 | n_water=959 | time (s): 317.120 (total time: 443.770) Filter (q & B) r_work=0.1210 r_free=0.1363 | n_water=874 | time (s): 5.230 (total time: 449.000) Filter (dist only) r_work=0.1210 r_free=0.1362 | n_water=872 | time (s): 111.150 (total time: 560.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.564762 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.550844 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 0.1208 0.1363 0.0155 0.037 1.1 6.6 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.63 1.55 1.813 14.182 15.551 3.873 11.99 13.60 1.61 1.916 14.144 15.551 3.863 Individual atomic B min max mean iso aniso Overall: 5.52 67.05 14.98 0.98 508 3268 Protein: 5.52 32.96 10.63 0.98 0 2902 Water: 6.04 67.05 29.45 N/A 508 364 Other: 13.92 25.91 19.92 N/A 0 2 Chain A: 5.59 52.98 12.56 N/A 0 1622 Chain B: 5.52 67.05 12.39 N/A 0 1646 Chain S: 6.04 65.41 31.10 N/A 508 0 Histogram: Values Number of atoms 5.52 - 11.67 2100 11.67 - 17.82 749 17.82 - 23.98 297 23.98 - 30.13 217 30.13 - 36.28 181 36.28 - 42.44 132 42.44 - 48.59 66 48.59 - 54.74 27 54.74 - 60.90 4 60.90 - 67.05 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1360 r_work=0.1199 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1361 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1361 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861866 | | target function (ml) not normalized (work): 723300.479734 | | target function (ml) not normalized (free): 15128.098640 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1425 0.1424 0.1494 n_refl.: 191134 remove outliers: r(all,work,free)=0.1425 0.1424 0.1494 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1418 0.1417 0.1489 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1358 n_refl.: 191134 remove outliers: r(all,work,free)=0.1198 0.1194 0.1358 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 0.3841 361.163 315.080 0.395 0.947 0.221 13.296-10.522 96.04 96 1 0.2361 480.381 451.880 0.708 0.949 0.200 10.503-8.327 98.35 176 3 0.2057 502.742 497.545 0.863 0.949 0.200 8.318-6.595 100.00 360 8 0.2155 375.506 370.546 0.892 0.948 0.118 6.588-5.215 100.00 711 7 0.1894 345.052 335.095 0.883 0.949 0.100 5.214-4.128 98.38 1367 28 0.1184 504.707 499.897 0.974 0.949 0.090 4.126-3.266 94.74 2603 46 0.1122 460.067 453.828 1.035 0.949 0.009 3.266-2.585 99.86 5447 97 0.1093 310.350 307.225 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0937 234.142 231.710 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0912 138.577 137.278 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0983 74.602 73.904 1.055 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.020 38.367 1.043 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1213 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1358 | n_water=872 | time (s): 3.250 (total time: 3.250) Filter (dist) r_work=0.1194 r_free=0.1358 | n_water=872 | time (s): 100.460 (total time: 103.710) Filter (q & B) r_work=0.1195 r_free=0.1359 | n_water=863 | time (s): 5.320 (total time: 109.030) Compute maps r_work=0.1195 r_free=0.1359 | n_water=863 | time (s): 1.720 (total time: 110.750) Filter (map) r_work=0.1218 r_free=0.1361 | n_water=738 | time (s): 5.380 (total time: 116.130) Find peaks r_work=0.1218 r_free=0.1361 | n_water=738 | time (s): 0.700 (total time: 116.830) Add new water r_work=0.1231 r_free=0.1377 | n_water=958 | time (s): 4.400 (total time: 121.230) Refine new water occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1344 occ: r_work=0.1192 r_free=0.1344 adp: r_work=0.1192 r_free=0.1344 occ: r_work=0.1190 r_free=0.1345 adp: r_work=0.1190 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1345 r_work=0.1190 r_free=0.1345 | n_water=958 | time (s): 212.060 (total time: 333.290) Filter (q & B) r_work=0.1193 r_free=0.1349 | n_water=887 | time (s): 5.130 (total time: 338.420) Filter (dist only) r_work=0.1194 r_free=0.1348 | n_water=886 | time (s): 110.740 (total time: 449.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.518657 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.840088 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 0.1356 0.0159 0.037 1.1 5.5 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.56 1.59 1.778 14.087 14.840 3.763 12.01 13.61 1.60 1.822 14.067 14.840 3.761 Individual atomic B min max mean iso aniso Overall: 5.59 66.78 14.92 0.95 522 3268 Protein: 5.59 31.73 10.57 0.95 0 2902 Water: 6.00 66.78 29.14 N/A 522 364 Other: 13.79 25.11 19.45 N/A 0 2 Chain A: 5.62 52.33 12.48 N/A 0 1622 Chain B: 5.59 66.78 12.32 N/A 0 1646 Chain S: 6.00 65.28 30.70 N/A 522 0 Histogram: Values Number of atoms 5.59 - 11.70 2134 11.70 - 17.82 730 17.82 - 23.94 300 23.94 - 30.06 216 30.06 - 36.18 182 36.18 - 42.30 134 42.30 - 48.42 64 48.42 - 54.54 23 54.54 - 60.66 4 60.66 - 66.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1361 r_work=0.1201 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1361 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1364 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760068 | | target function (ml) not normalized (work): 704223.218068 | | target function (ml) not normalized (free): 14744.412542 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1505 n_refl.: 191131 remove outliers: r(all,work,free)=0.1407 0.1405 0.1505 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1399 0.1397 0.1499 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1198 0.1362 n_refl.: 191131 remove outliers: r(all,work,free)=0.1201 0.1198 0.1362 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3923 356.636 321.837 0.360 0.952 0.160 13.296-10.522 96.04 96 1 0.2418 480.381 462.621 0.711 0.953 0.190 10.503-8.327 98.35 176 3 0.2130 502.742 496.130 0.858 0.954 0.157 8.318-6.595 100.00 360 8 0.2177 375.506 370.557 0.886 0.953 0.108 6.588-5.215 100.00 711 7 0.1925 345.052 335.137 0.879 0.953 0.090 5.214-4.128 98.38 1367 28 0.1202 504.707 499.682 0.968 0.954 0.054 4.126-3.266 94.74 2603 46 0.1146 460.067 453.314 1.031 0.954 0.014 3.266-2.585 99.86 5447 97 0.1109 310.350 307.092 1.017 0.953 0.000 2.585-2.046 97.45 10613 204 0.0945 234.142 231.616 1.028 0.953 0.000 2.046-1.619 99.39 21536 464 0.0913 138.577 137.263 1.052 0.952 0.000 1.619-1.281 98.00 42464 925 0.0976 74.602 73.887 1.050 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.020 38.346 1.038 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1343 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1362 | n_water=886 | time (s): 3.320 (total time: 3.320) Filter (dist) r_work=0.1198 r_free=0.1362 | n_water=886 | time (s): 105.340 (total time: 108.660) Filter (q & B) r_work=0.1199 r_free=0.1364 | n_water=871 | time (s): 5.240 (total time: 113.900) Compute maps r_work=0.1199 r_free=0.1364 | n_water=871 | time (s): 1.880 (total time: 115.780) Filter (map) r_work=0.1220 r_free=0.1360 | n_water=754 | time (s): 4.310 (total time: 120.090) Find peaks r_work=0.1220 r_free=0.1360 | n_water=754 | time (s): 0.800 (total time: 120.890) Add new water r_work=0.1231 r_free=0.1368 | n_water=971 | time (s): 4.520 (total time: 125.410) Refine new water occ: r_work=0.1196 r_free=0.1340 adp: r_work=0.1196 r_free=0.1340 occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1192 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1345 r_work=0.1192 r_free=0.1345 | n_water=971 | time (s): 224.800 (total time: 350.210) Filter (q & B) r_work=0.1196 r_free=0.1353 | n_water=900 | time (s): 5.430 (total time: 355.640) Filter (dist only) r_work=0.1196 r_free=0.1352 | n_water=899 | time (s): 116.230 (total time: 471.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.499719 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.356750 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 0.1200 0.1360 0.0160 0.037 1.1 6.5 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.60 1.60 1.753 14.041 14.357 3.761 12.04 13.63 1.59 1.885 13.997 14.357 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 65.65 14.86 0.89 535 3268 Protein: 5.58 28.99 10.47 0.89 0 2902 Water: 5.92 65.65 29.05 N/A 535 364 Other: 13.85 22.53 18.19 N/A 0 2 Chain A: 5.66 51.32 12.33 N/A 0 1622 Chain B: 5.58 65.65 12.19 N/A 0 1646 Chain S: 5.92 64.80 30.75 N/A 535 0 Histogram: Values Number of atoms 5.58 - 11.59 2113 11.59 - 17.60 772 17.60 - 23.60 280 23.60 - 29.61 208 29.61 - 35.62 185 35.62 - 41.62 138 41.62 - 47.63 67 47.63 - 53.63 32 53.63 - 59.64 4 59.64 - 65.65 4 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1364 r_work=0.1204 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1364 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1367 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758906 | | target function (ml) not normalized (work): 704001.673295 | | target function (ml) not normalized (free): 14739.861759 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1202 0.1367 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1503 n_refl.: 191130 remove outliers: r(all,work,free)=0.1407 0.1405 0.1503 n_refl.: 191130 overall B=-0.24 to atoms: r(all,work,free)=0.1370 0.1368 0.1480 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1365 n_refl.: 191130 remove outliers: r(all,work,free)=0.1206 0.1203 0.1365 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3929 356.636 321.469 0.345 0.950 0.120 13.296-10.522 96.04 96 1 0.2477 480.381 461.456 0.706 0.952 0.127 10.503-8.327 98.35 176 3 0.2211 502.742 495.164 0.882 0.952 0.125 8.318-6.595 100.00 360 8 0.2166 375.506 371.179 0.908 0.952 0.098 6.588-5.215 100.00 711 7 0.1941 345.052 335.277 0.903 0.952 0.080 5.214-4.128 98.38 1367 28 0.1217 504.707 499.766 0.995 0.953 0.039 4.126-3.266 94.74 2603 46 0.1156 460.067 453.043 1.058 0.953 0.005 3.266-2.585 99.86 5447 97 0.1124 310.350 307.157 1.040 0.953 0.000 2.585-2.046 97.45 10613 204 0.0954 234.142 231.614 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0912 138.577 137.303 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0974 74.602 73.899 1.048 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.020 38.346 1.015 0.957 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0534 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1365 | n_water=899 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1204 r_free=0.1364 | n_water=898 | time (s): 112.100 (total time: 114.990) Filter (q & B) r_work=0.1204 r_free=0.1365 | n_water=887 | time (s): 4.190 (total time: 119.180) Compute maps r_work=0.1204 r_free=0.1365 | n_water=887 | time (s): 1.860 (total time: 121.040) Filter (map) r_work=0.1228 r_free=0.1370 | n_water=757 | time (s): 4.330 (total time: 125.370) Find peaks r_work=0.1228 r_free=0.1370 | n_water=757 | time (s): 0.620 (total time: 125.990) Add new water r_work=0.1237 r_free=0.1380 | n_water=972 | time (s): 5.190 (total time: 131.180) Refine new water occ: r_work=0.1202 r_free=0.1345 adp: r_work=0.1202 r_free=0.1346 occ: r_work=0.1200 r_free=0.1344 adp: r_work=0.1200 r_free=0.1345 occ: r_work=0.1198 r_free=0.1344 adp: r_work=0.1198 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1344 r_work=0.1198 r_free=0.1344 | n_water=972 | time (s): 280.560 (total time: 411.740) Filter (q & B) r_work=0.1202 r_free=0.1354 | n_water=893 | time (s): 4.540 (total time: 416.280) Filter (dist only) r_work=0.1203 r_free=0.1355 | n_water=890 | time (s): 112.820 (total time: 529.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.529468 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.379942 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 0.1206 0.1360 0.0153 0.038 1.1 5.5 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.60 1.53 1.711 13.621 14.380 3.761 12.06 13.62 1.56 1.755 13.616 14.380 3.758 Individual atomic B min max mean iso aniso Overall: 5.39 64.11 14.47 0.88 526 3268 Protein: 5.39 28.33 10.21 0.88 0 2902 Water: 5.77 64.11 28.35 N/A 526 364 Other: 13.65 21.85 17.75 N/A 0 2 Chain A: 5.42 50.60 12.04 N/A 0 1622 Chain B: 5.39 64.07 11.91 N/A 0 1646 Chain S: 5.77 64.11 29.99 N/A 526 0 Histogram: Values Number of atoms 5.39 - 11.26 2085 11.26 - 17.14 802 17.14 - 23.01 277 23.01 - 28.88 207 28.88 - 34.75 193 34.75 - 40.62 117 40.62 - 46.50 73 46.50 - 52.37 30 52.37 - 58.24 5 58.24 - 64.11 5 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1362 r_work=0.1206 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1362 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1205 r_free = 0.1361 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1205 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757221 | | target function (ml) not normalized (work): 703686.226894 | | target function (ml) not normalized (free): 14731.179768 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1205 0.1361 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1378 0.1376 0.1484 n_refl.: 191130 remove outliers: r(all,work,free)=0.1378 0.1376 0.1484 n_refl.: 191130 overall B=0.07 to atoms: r(all,work,free)=0.1388 0.1386 0.1490 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1351 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1194 0.1351 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3960 356.636 318.211 0.344 0.979 0.139 13.296-10.522 96.04 96 1 0.2450 480.381 461.340 0.690 0.981 0.130 10.503-8.327 98.35 176 3 0.2219 502.742 494.144 0.860 0.981 0.123 8.318-6.595 100.00 360 8 0.2197 375.506 369.767 0.886 0.981 0.097 6.588-5.215 100.00 711 7 0.1943 345.052 335.234 0.883 0.982 0.088 5.214-4.128 98.38 1367 28 0.1246 504.707 498.882 0.975 0.983 0.059 4.126-3.266 94.74 2603 46 0.1168 460.067 452.442 1.038 0.984 0.009 3.266-2.585 99.86 5447 97 0.1123 310.350 306.849 1.020 0.984 0.000 2.585-2.046 97.45 10613 204 0.0959 234.142 231.497 1.027 0.986 0.000 2.046-1.619 99.39 21536 464 0.0906 138.577 137.215 1.043 0.989 0.000 1.619-1.281 98.00 42464 925 0.0951 74.602 73.940 1.031 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1631 40.020 38.322 0.996 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0588 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1351 | n_water=890 | time (s): 3.400 (total time: 3.400) Filter (dist) r_work=0.1194 r_free=0.1351 | n_water=890 | time (s): 107.780 (total time: 111.180) Filter (q & B) r_work=0.1195 r_free=0.1351 | n_water=881 | time (s): 5.200 (total time: 116.380) Compute maps r_work=0.1195 r_free=0.1351 | n_water=881 | time (s): 2.300 (total time: 118.680) Filter (map) r_work=0.1215 r_free=0.1349 | n_water=773 | time (s): 4.480 (total time: 123.160) Find peaks r_work=0.1215 r_free=0.1349 | n_water=773 | time (s): 0.750 (total time: 123.910) Add new water r_work=0.1223 r_free=0.1360 | n_water=984 | time (s): 4.640 (total time: 128.550) Refine new water occ: r_work=0.1190 r_free=0.1333 adp: r_work=0.1190 r_free=0.1333 occ: r_work=0.1188 r_free=0.1334 adp: r_work=0.1188 r_free=0.1334 occ: r_work=0.1187 r_free=0.1335 adp: r_work=0.1187 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1335 r_work=0.1187 r_free=0.1335 | n_water=984 | time (s): 222.430 (total time: 350.980) Filter (q & B) r_work=0.1191 r_free=0.1346 | n_water=906 | time (s): 4.480 (total time: 355.460) Filter (dist only) r_work=0.1192 r_free=0.1346 | n_water=904 | time (s): 114.420 (total time: 469.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.599661 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.487884 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 0.1351 0.0156 0.038 1.1 6.0 0.0 0.3 0 0.800 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.51 1.56 1.670 13.700 14.488 3.755 11.94 13.52 1.58 1.670 13.699 14.488 3.753 Individual atomic B min max mean iso aniso Overall: 5.47 64.10 14.62 0.88 540 3268 Protein: 5.47 28.28 10.30 0.88 0 2902 Water: 5.89 64.10 28.45 N/A 540 364 Other: 13.73 22.00 17.87 N/A 0 2 Chain A: 5.53 50.54 12.10 N/A 0 1622 Chain B: 5.47 63.83 11.98 N/A 0 1646 Chain S: 5.89 64.10 30.21 N/A 540 0 Histogram: Values Number of atoms 5.47 - 11.33 2075 11.33 - 17.20 814 17.20 - 23.06 274 23.06 - 28.92 208 28.92 - 34.78 198 34.78 - 40.65 125 40.65 - 46.51 74 46.51 - 52.37 30 52.37 - 58.24 5 58.24 - 64.10 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1353 r_work=0.1195 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1353 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1355 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 23 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752850 | | target function (ml) not normalized (work): 702867.523637 | | target function (ml) not normalized (free): 14721.513059 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1193 0.1355 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1391 0.1388 0.1505 n_refl.: 191130 remove outliers: r(all,work,free)=0.1391 0.1388 0.1505 n_refl.: 191130 overall B=0.02 to atoms: r(all,work,free)=0.1393 0.1391 0.1507 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3960 356.636 317.985 0.341 0.979 0.135 13.296-10.522 96.04 96 1 0.2447 480.381 460.629 0.685 0.981 0.122 10.503-8.327 98.35 176 3 0.2238 502.742 493.926 0.858 0.982 0.114 8.318-6.595 100.00 360 8 0.2197 375.506 369.660 0.884 0.981 0.097 6.588-5.215 100.00 711 7 0.1946 345.052 335.261 0.881 0.982 0.088 5.214-4.128 98.38 1367 28 0.1246 504.707 498.886 0.974 0.983 0.059 4.126-3.266 94.74 2603 46 0.1171 460.067 452.539 1.036 0.984 0.009 3.266-2.585 99.86 5447 97 0.1128 310.350 306.772 1.019 0.985 0.000 2.585-2.046 97.45 10613 204 0.0959 234.142 231.502 1.027 0.987 0.000 2.046-1.619 99.39 21536 464 0.0904 138.577 137.235 1.043 0.990 0.000 1.619-1.281 98.00 42464 925 0.0943 74.602 73.950 1.033 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.020 38.310 1.001 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0235 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1354 | n_water=904 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1192 r_free=0.1354 | n_water=904 | time (s): 103.450 (total time: 106.030) Filter (q & B) r_work=0.1193 r_free=0.1354 | n_water=892 | time (s): 5.040 (total time: 111.070) Compute maps r_work=0.1193 r_free=0.1354 | n_water=892 | time (s): 2.100 (total time: 113.170) Filter (map) r_work=0.1213 r_free=0.1351 | n_water=783 | time (s): 5.070 (total time: 118.240) Find peaks r_work=0.1213 r_free=0.1351 | n_water=783 | time (s): 0.580 (total time: 118.820) Add new water r_work=0.1222 r_free=0.1367 | n_water=986 | time (s): 4.780 (total time: 123.600) Refine new water occ: r_work=0.1189 r_free=0.1336 adp: r_work=0.1189 r_free=0.1337 occ: r_work=0.1187 r_free=0.1336 adp: r_work=0.1187 r_free=0.1336 occ: r_work=0.1186 r_free=0.1336 adp: r_work=0.1186 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1336 r_work=0.1186 r_free=0.1336 | n_water=986 | time (s): 223.130 (total time: 346.730) Filter (q & B) r_work=0.1190 r_free=0.1346 | n_water=909 | time (s): 4.510 (total time: 351.240) Filter (dist only) r_work=0.1190 r_free=0.1347 | n_water=907 | time (s): 115.810 (total time: 467.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.511395 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.874236 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 0.1353 0.0158 0.039 1.1 6.3 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.53 1.58 1.678 13.731 13.874 3.754 11.97 13.56 1.59 1.692 13.723 13.874 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 63.84 14.62 0.86 543 3268 Protein: 5.56 27.88 10.32 0.86 0 2902 Water: 5.95 63.84 28.37 N/A 543 364 Other: 13.80 22.14 17.97 N/A 0 2 Chain A: 5.64 50.25 12.09 N/A 0 1622 Chain B: 5.56 62.92 11.97 N/A 0 1646 Chain S: 5.95 63.84 30.21 N/A 543 0 Histogram: Values Number of atoms 5.56 - 11.39 2083 11.39 - 17.22 821 17.22 - 23.05 265 23.05 - 28.87 205 28.87 - 34.70 195 34.70 - 40.53 129 40.53 - 46.36 71 46.36 - 52.18 32 52.18 - 58.01 5 58.01 - 63.84 5 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1356 r_work=0.1197 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1356 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754184 | | target function (ml) not normalized (work): 703117.385272 | | target function (ml) not normalized (free): 14731.659795 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1515 n_refl.: 191130 remove outliers: r(all,work,free)=0.1404 0.1402 0.1515 n_refl.: 191130 overall B=-0.00 to atoms: r(all,work,free)=0.1404 0.1402 0.1514 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1358 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3993 356.636 317.287 0.332 0.980 0.120 13.296-10.522 96.04 96 1 0.2442 480.381 460.816 0.681 0.982 0.113 10.503-8.327 98.35 176 3 0.2244 502.742 493.638 0.857 0.982 0.103 8.318-6.595 100.00 360 8 0.2176 375.506 369.879 0.882 0.982 0.095 6.588-5.215 100.00 711 7 0.1973 345.052 334.979 0.879 0.983 0.090 5.214-4.128 98.38 1367 28 0.1250 504.707 498.655 0.973 0.984 0.063 4.126-3.266 94.74 2603 46 0.1175 460.067 452.430 1.036 0.985 0.009 3.266-2.585 99.86 5447 97 0.1137 310.350 306.739 1.018 0.986 0.000 2.585-2.046 97.45 10613 204 0.0963 234.142 231.495 1.026 0.989 0.000 2.046-1.619 99.39 21536 464 0.0906 138.577 137.232 1.043 0.993 0.000 1.619-1.281 98.00 42464 925 0.0944 74.602 73.951 1.034 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.020 38.301 1.003 1.010 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0091 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1358 After: r_work=0.1196 r_free=0.1358 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1358 | n_water=907 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1196 r_free=0.1358 | n_water=907 | time (s): 110.430 (total time: 113.120) Filter (q & B) r_work=0.1196 r_free=0.1358 | n_water=895 | time (s): 4.550 (total time: 117.670) Compute maps r_work=0.1196 r_free=0.1358 | n_water=895 | time (s): 1.770 (total time: 119.440) Filter (map) r_work=0.1218 r_free=0.1358 | n_water=781 | time (s): 4.270 (total time: 123.710) Find peaks r_work=0.1218 r_free=0.1358 | n_water=781 | time (s): 0.730 (total time: 124.440) Add new water r_work=0.1226 r_free=0.1373 | n_water=987 | time (s): 4.180 (total time: 128.620) Refine new water occ: r_work=0.1193 r_free=0.1342 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1343 occ: r_work=0.1189 r_free=0.1343 adp: r_work=0.1189 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1344 r_work=0.1189 r_free=0.1344 | n_water=987 | time (s): 226.200 (total time: 354.820) Filter (q & B) r_work=0.1193 r_free=0.1353 | n_water=915 | time (s): 5.900 (total time: 360.720) Filter (dist only) r_work=0.1193 r_free=0.1353 | n_water=913 | time (s): 117.500 (total time: 478.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.519946 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.273474 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1357 0.0161 0.039 1.2 10.7 0.0 0.3 0 0.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.57 1.61 1.672 13.725 14.273 3.756 11.96 13.58 1.62 1.669 13.725 14.273 3.754 Individual atomic B min max mean iso aniso Overall: 5.58 63.57 14.63 0.86 549 3268 Protein: 5.58 27.92 10.34 0.86 0 2902 Water: 6.01 63.57 28.24 N/A 549 364 Other: 13.84 22.03 17.93 N/A 0 2 Chain A: 5.69 49.90 12.08 N/A 0 1622 Chain B: 5.58 61.81 11.97 N/A 0 1646 Chain S: 6.01 63.57 30.10 N/A 549 0 Histogram: Values Number of atoms 5.58 - 11.38 2073 11.38 - 17.18 837 17.18 - 22.98 266 22.98 - 28.78 202 28.78 - 34.57 201 34.57 - 40.37 120 40.37 - 46.17 74 46.17 - 51.97 32 51.97 - 57.77 7 57.77 - 63.57 5 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1358 r_work=0.1196 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1358 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754443 | | target function (ml) not normalized (work): 703165.887499 | | target function (ml) not normalized (free): 14729.033483 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1372 0.1482 5.6982 5.7861| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1392 5.0923 5.1984| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1183 4.656 4.7507| | 4: 2.04 - 1.85 1.00 7170 155 0.0895 0.1052 4.3884 4.567| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.0972 4.1469 4.2229| | 6: 1.72 - 1.62 0.99 7102 142 0.0891 0.1062 3.938 4.0608| | 7: 1.62 - 1.54 0.99 7104 148 0.0888 0.0973 3.7946 3.9283| | 8: 1.54 - 1.47 0.96 6798 152 0.0892 0.1296 3.6998 3.8978| | 9: 1.47 - 1.41 0.98 6938 155 0.0925 0.1133 3.6212 3.7614| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1176 3.5561 3.6721| | 11: 1.36 - 1.32 0.99 6997 151 0.0995 0.1131 3.4872 3.5932| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1142 3.4618 3.59| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1258 3.4389 3.5751| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1564 3.4329 3.6692| | 15: 1.22 - 1.19 0.98 6956 137 0.1170 0.1240 3.4475 3.4883| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1531 3.4638 3.6543| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1207 3.4311 3.434| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1695 3.4367 3.5275| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1761 3.4194 3.6019| | 20: 1.10 - 1.08 0.97 6884 147 0.1586 0.1580 3.4108 3.4351| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2148 3.419 3.506| | 22: 1.07 - 1.05 0.97 6836 135 0.1906 0.1956 3.4137 3.416| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2022 3.4333 3.4876| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2253 3.4357 3.5114| | 25: 1.02 - 1.01 0.93 6552 130 0.2615 0.2514 3.4498 3.5251| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2856 3.4155 3.4215| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2793 3.4692 3.3943| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 12.02 1.00 0.96 11810.39| | 2: 2.94 - 2.33 7339 128 0.92 13.07 0.99 0.96 5350.68| | 3: 2.33 - 2.04 6939 150 0.96 7.67 1.01 0.96 1711.89| | 4: 2.04 - 1.85 7170 155 0.96 7.57 1.00 0.95 993.91| | 5: 1.85 - 1.72 7113 159 0.96 7.93 1.00 0.96 618.87| | 6: 1.72 - 1.62 7102 142 0.96 7.89 1.00 0.96 433.20| | 7: 1.62 - 1.54 7104 148 0.96 8.07 1.01 0.97 332.44| | 8: 1.54 - 1.47 6798 152 0.96 8.25 1.01 0.97 278.10| | 9: 1.47 - 1.41 6938 155 0.96 8.46 1.00 0.98 230.98| | 10: 1.41 - 1.36 7022 150 0.96 8.95 1.00 0.97 203.32| | 11: 1.36 - 1.32 6997 151 0.96 9.01 0.99 0.96 176.35| | 12: 1.32 - 1.28 6975 149 0.96 9.09 0.98 0.95 162.93| | 13: 1.28 - 1.25 6907 166 0.96 9.61 1.01 0.96 159.84| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.97 163.67| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 0.98 165.57| | 16: 1.19 - 1.17 6604 132 0.95 11.34 1.01 0.96 158.77| | 17: 1.17 - 1.14 6940 135 0.94 12.14 1.01 0.96 152.24| | 18: 1.14 - 1.12 6875 142 0.94 12.68 1.01 0.95 146.67| | 19: 1.12 - 1.10 6948 106 0.93 14.13 1.00 0.95 150.79| | 20: 1.10 - 1.08 6884 147 0.92 15.26 1.00 0.94 150.59| | 21: 1.08 - 1.07 6852 152 0.91 16.69 1.00 0.93 153.96| | 22: 1.07 - 1.05 6836 135 0.89 18.35 0.99 0.93 155.41| | 23: 1.05 - 1.03 6827 159 0.87 20.55 0.99 0.92 165.21| | 24: 1.03 - 1.02 6784 133 0.85 23.21 0.99 0.93 179.38| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.98 0.90 182.08| | 26: 1.01 - 0.99 6767 158 0.81 26.58 0.98 0.89 176.07| | 27: 0.99 - 0.98 6647 131 0.82 26.16 0.99 0.87 159.89| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.67 max = 11810.39 mean = 957.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.30| |phase err.(test): min = 0.00 max = 88.48 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1411 0.1409 0.1513 n_refl.: 191130 remove outliers: r(all,work,free)=0.1411 0.1409 0.1513 n_refl.: 191130 overall B=-0.06 to atoms: r(all,work,free)=0.1402 0.1400 0.1508 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3986 356.636 316.274 0.328 0.979 0.130 13.296-10.522 96.04 96 1 0.2454 480.381 460.405 0.663 0.981 0.117 10.503-8.327 98.35 176 3 0.2200 502.742 494.484 0.836 0.982 0.100 8.318-6.595 100.00 360 8 0.2143 375.506 369.773 0.859 0.981 0.088 6.588-5.215 100.00 711 7 0.1957 345.052 334.856 0.858 0.982 0.082 5.214-4.128 98.38 1367 28 0.1250 504.707 498.432 0.950 0.983 0.058 4.126-3.266 94.74 2603 46 0.1174 460.067 452.383 1.012 0.985 0.009 3.266-2.585 99.86 5447 97 0.1131 310.350 306.799 0.994 0.986 0.000 2.585-2.046 97.45 10613 204 0.0963 234.142 231.501 1.000 0.989 0.000 2.046-1.619 99.39 21536 464 0.0907 138.577 137.220 1.016 0.993 0.000 1.619-1.281 98.00 42464 925 0.0945 74.602 73.950 1.005 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.020 38.295 0.973 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0121 ================= 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 : 0.2032 0.1952 0.081 5.243 5.2 78.0 14.6 805 0.000 1_bss: 0.1795 0.1887 0.081 5.243 5.2 78.0 14.6 805 0.000 1_settarget: 0.1795 0.1887 0.081 5.243 5.2 78.0 14.6 805 0.000 1_nqh: 0.1795 0.1889 0.081 5.243 5.2 78.0 14.6 805 0.002 1_weight: 0.1795 0.1889 0.081 5.243 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1270 0.1499 0.038 1.150 5.2 78.0 14.6 805 0.157 1_adp: 0.1299 0.1572 0.038 1.150 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1298 0.1567 0.038 1.150 5.2 73.0 15.0 805 0.157 1_occ: 0.1283 0.1558 0.038 1.150 5.2 73.0 15.0 805 0.157 2_bss: 0.1276 0.1549 0.038 1.150 5.4 73.2 15.2 805 0.157 2_settarget: 0.1276 0.1549 0.038 1.150 5.4 73.2 15.2 805 0.157 2_updatecdl: 0.1276 0.1549 0.038 1.163 5.4 73.2 15.2 805 0.157 2_nqh: 0.1276 0.1549 0.038 1.163 5.4 73.2 15.2 805 0.157 2_sol: 0.1272 0.1518 0.038 1.163 5.4 73.2 16.4 895 n/a 2_weight: 0.1272 0.1518 0.038 1.163 5.4 73.2 16.4 895 n/a 2_xyzrec: 0.1255 0.1522 0.040 1.120 5.4 73.2 16.4 895 n/a 2_adp: 0.1230 0.1506 0.040 1.120 5.4 73.3 16.4 895 n/a 2_regHadp: 0.1230 0.1507 0.040 1.120 5.4 73.3 16.4 895 n/a 2_occ: 0.1225 0.1507 0.040 1.120 5.4 73.3 16.4 895 n/a 3_bss: 0.1232 0.1514 0.040 1.120 5.4 73.3 16.4 895 n/a 3_settarget: 0.1232 0.1514 0.040 1.120 5.4 73.3 16.4 895 n/a 3_updatecdl: 0.1232 0.1514 0.040 1.125 5.4 73.3 16.4 895 n/a 3_nqh: 0.1232 0.1514 0.040 1.125 5.4 73.3 16.4 895 n/a 3_sol: 0.1249 0.1519 0.040 1.125 5.4 68.2 15.4 877 n/a 3_weight: 0.1249 0.1519 0.040 1.125 5.4 68.2 15.4 877 n/a 3_xyzrec: 0.1240 0.1442 0.035 1.098 5.4 68.2 15.4 877 n/a 3_adp: 0.1238 0.1402 0.035 1.098 5.6 67.6 15.2 877 n/a 3_regHadp: 0.1239 0.1402 0.035 1.098 5.6 67.6 15.2 877 n/a 3_occ: 0.1232 0.1393 0.035 1.098 5.6 67.6 15.2 877 n/a 4_bss: 0.1228 0.1387 0.035 1.098 5.5 67.6 15.2 877 n/a 4_settarget: 0.1228 0.1387 0.035 1.098 5.5 67.6 15.2 877 n/a 4_updatecdl: 0.1228 0.1387 0.035 1.103 5.5 67.6 15.2 877 n/a 4_nqh: 0.1228 0.1387 0.035 1.103 5.5 67.6 15.2 877 n/a 4_sol: 0.1210 0.1362 0.035 1.103 5.5 67.6 15.1 872 n/a 4_weight: 0.1210 0.1362 0.035 1.103 5.5 67.6 15.1 872 n/a 4_xyzrec: 0.1208 0.1363 0.037 1.123 5.5 67.6 15.1 872 n/a 4_adp: 0.1199 0.1360 0.037 1.123 5.5 67.1 15.0 872 n/a 4_regHadp: 0.1199 0.1361 0.037 1.123 5.5 67.1 15.0 872 n/a 4_occ: 0.1197 0.1361 0.037 1.123 5.5 67.1 15.0 872 n/a 5_bss: 0.1194 0.1358 0.037 1.123 5.5 67.0 14.9 872 n/a 5_settarget: 0.1194 0.1358 0.037 1.123 5.5 67.0 14.9 872 n/a 5_updatecdl: 0.1194 0.1358 0.037 1.123 5.5 67.0 14.9 872 n/a 5_nqh: 0.1194 0.1358 0.037 1.123 5.5 67.0 14.9 872 n/a 5_sol: 0.1194 0.1348 0.037 1.123 5.5 67.0 15.0 886 n/a 5_weight: 0.1194 0.1348 0.037 1.123 5.5 67.0 15.0 886 n/a 5_xyzrec: 0.1197 0.1356 0.037 1.121 5.5 67.0 15.0 886 n/a 5_adp: 0.1201 0.1361 0.037 1.121 5.6 66.8 14.9 886 n/a 5_regHadp: 0.1201 0.1361 0.037 1.121 5.6 66.8 14.9 886 n/a 5_occ: 0.1199 0.1364 0.037 1.121 5.6 66.8 14.9 886 n/a 6_bss: 0.1198 0.1362 0.037 1.121 5.5 66.7 14.9 886 n/a 6_settarget: 0.1198 0.1362 0.037 1.121 5.5 66.7 14.9 886 n/a 6_updatecdl: 0.1198 0.1362 0.037 1.121 5.5 66.7 14.9 886 n/a 6_nqh: 0.1198 0.1362 0.037 1.121 5.5 66.7 14.9 886 n/a 6_sol: 0.1196 0.1352 0.037 1.121 5.5 66.7 14.9 899 n/a 6_weight: 0.1196 0.1352 0.037 1.121 5.5 66.7 14.9 899 n/a 6_xyzrec: 0.1200 0.1360 0.037 1.121 5.5 66.7 14.9 899 n/a 6_adp: 0.1204 0.1364 0.037 1.121 5.6 65.6 14.9 899 n/a 6_regHadp: 0.1204 0.1364 0.037 1.121 5.6 65.6 14.9 899 n/a 6_occ: 0.1202 0.1367 0.037 1.121 5.6 65.6 14.9 899 n/a 7_bss: 0.1203 0.1365 0.037 1.121 5.3 65.4 14.6 899 n/a 7_settarget: 0.1203 0.1365 0.037 1.121 5.3 65.4 14.6 899 n/a 7_updatecdl: 0.1203 0.1365 0.037 1.121 5.3 65.4 14.6 899 n/a 7_nqh: 0.1203 0.1365 0.037 1.121 5.3 65.4 14.6 899 n/a 7_sol: 0.1203 0.1355 0.037 1.121 5.3 65.4 14.5 890 n/a 7_weight: 0.1203 0.1355 0.037 1.121 5.3 65.4 14.5 890 n/a 7_xyzrec: 0.1206 0.1360 0.038 1.125 5.3 65.4 14.5 890 n/a 7_adp: 0.1206 0.1362 0.038 1.125 5.4 64.1 14.5 890 n/a 7_regHadp: 0.1206 0.1362 0.038 1.125 5.4 64.1 14.5 890 n/a 7_occ: 0.1205 0.1361 0.038 1.125 5.4 64.1 14.5 890 n/a 8_bss: 0.1194 0.1351 0.038 1.125 5.5 64.2 14.5 890 n/a 8_settarget: 0.1194 0.1351 0.038 1.125 5.5 64.2 14.5 890 n/a 8_updatecdl: 0.1194 0.1351 0.038 1.125 5.5 64.2 14.5 890 n/a 8_nqh: 0.1194 0.1351 0.038 1.125 5.5 64.2 14.5 890 n/a 8_sol: 0.1192 0.1346 0.038 1.125 5.5 64.2 14.6 904 n/a 8_weight: 0.1192 0.1346 0.038 1.125 5.5 64.2 14.6 904 n/a 8_xyzrec: 0.1195 0.1351 0.038 1.130 5.5 64.2 14.6 904 n/a 8_adp: 0.1195 0.1353 0.038 1.130 5.5 64.1 14.6 904 n/a 8_regHadp: 0.1195 0.1353 0.038 1.130 5.5 64.1 14.6 904 n/a 8_occ: 0.1193 0.1355 0.038 1.130 5.5 64.1 14.6 904 n/a 9_bss: 0.1192 0.1354 0.038 1.130 5.5 64.1 14.6 904 n/a 9_settarget: 0.1192 0.1354 0.038 1.130 5.5 64.1 14.6 904 n/a 9_updatecdl: 0.1192 0.1354 0.038 1.129 5.5 64.1 14.6 904 n/a 9_nqh: 0.1192 0.1354 0.038 1.129 5.5 64.1 14.6 904 n/a 9_sol: 0.1190 0.1347 0.038 1.129 5.5 64.1 14.6 907 n/a 9_weight: 0.1190 0.1347 0.038 1.129 5.5 64.1 14.6 907 n/a 9_xyzrec: 0.1195 0.1353 0.039 1.112 5.5 64.1 14.6 907 n/a 9_adp: 0.1197 0.1356 0.039 1.112 5.6 63.8 14.6 907 n/a 9_regHadp: 0.1197 0.1356 0.039 1.112 5.6 63.8 14.6 907 n/a 9_occ: 0.1196 0.1359 0.039 1.112 5.6 63.8 14.6 907 n/a 10_bss: 0.1195 0.1358 0.039 1.112 5.6 63.8 14.6 907 n/a 10_settarget: 0.1195 0.1358 0.039 1.112 5.6 63.8 14.6 907 n/a 10_updatecdl: 0.1195 0.1358 0.039 1.113 5.6 63.8 14.6 907 n/a 10_setrh: 0.1196 0.1358 0.039 1.113 5.6 63.8 14.6 907 n/a 10_nqh: 0.1196 0.1358 0.039 1.113 5.6 63.8 14.6 907 n/a 10_sol: 0.1193 0.1353 0.039 1.113 5.6 63.8 14.6 913 n/a 10_weight: 0.1193 0.1353 0.039 1.113 5.6 63.8 14.6 913 n/a 10_xyzrec: 0.1197 0.1357 0.039 1.160 5.6 63.8 14.6 913 n/a 10_adp: 0.1196 0.1358 0.039 1.160 5.6 63.6 14.6 913 n/a 10_regHadp: 0.1196 0.1358 0.039 1.160 5.6 63.6 14.6 913 n/a 10_occ: 0.1195 0.1359 0.039 1.160 5.6 63.6 14.6 913 n/a end: 0.1194 0.1359 0.039 1.160 5.5 63.5 14.6 913 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5525287_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5525287_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.3400 Refinement macro-cycles (run) : 11994.2500 Write final files (write_after_run_outputs) : 165.5700 Total : 12167.1600 Total CPU time: 3.39 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:39:59 PST -0800 (1736735999.38 s) Start R-work = 0.1795, R-free = 0.1887 Final R-work = 0.1194, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 12484.02 seconds wall clock time: 209 minutes 4.56 seconds (12544.56 seconds total)