Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8200675.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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8200675.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8200675.pdb" 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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.94, per 1000 atoms: 0.29 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: 2.743 distance_ideal: 2.720 ideal - model: -0.023 slack: 0.000 delta_slack: -0.023 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: 2.654 distance_ideal: 2.710 ideal - model: 0.056 slack: 0.000 delta_slack: 0.056 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: 1.23 Conformation dependent library (CDL) restraints added in 194.2 milliseconds Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.00: 509 1.00 - 1.21: 2514 1.21 - 1.43: 1265 1.43 - 1.64: 1525 1.64 - 1.85: 121 Bond restraints: 5934 Sorted by residual: bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.448 1.665 -0.217 8.80e-03 1.29e+04 6.07e+02 bond pdb=" C SER A 155 " pdb=" O SER A 155 " ideal model delta sigma weight residual 1.234 1.463 -0.229 1.10e-02 8.26e+03 4.35e+02 bond pdb=" CA VAL B 114 " pdb=" CB VAL B 114 " ideal model delta sigma weight residual 1.539 1.648 -0.109 5.40e-03 3.43e+04 4.07e+02 bond pdb=" N THR A 125 " pdb=" H THR A 125 " ideal model delta sigma weight residual 0.860 1.247 -0.387 2.00e-02 2.50e+03 3.74e+02 bond pdb=" CA PHE A 127 " pdb=" C PHE A 127 " ideal model delta sigma weight residual 1.527 1.330 0.197 1.02e-02 9.61e+03 3.74e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 5506 4.12 - 8.24: 3619 8.24 - 12.36: 1383 12.36 - 16.48: 276 16.48 - 20.60: 26 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 175 " pdb=" CZ ARG B 175 " pdb=" NH2 ARG B 175 " ideal model delta sigma weight residual 119.20 104.76 14.44 9.00e-01 1.23e+00 2.57e+02 angle pdb=" CA VAL A 114 " pdb=" C VAL A 114 " pdb=" N PRO A 115 " ideal model delta sigma weight residual 120.83 111.66 9.17 6.10e-01 2.69e+00 2.26e+02 angle pdb=" O ILE B 70 " pdb=" C ILE B 70 " pdb=" N VAL B 71 " ideal model delta sigma weight residual 123.18 138.67 -15.49 1.05e+00 9.07e-01 2.18e+02 angle pdb=" CA GLY B 165 " pdb=" C GLY B 165 " pdb=" N LEU B 166 " ideal model delta sigma weight residual 117.13 132.07 -14.94 1.03e+00 9.43e-01 2.10e+02 angle pdb=" CA LYS B 77 " pdb=" C LYS B 77 " pdb=" O LYS B 77 " ideal model delta sigma weight residual 120.10 135.76 -15.66 1.13e+00 7.83e-01 1.92e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 1848 17.16 - 34.33: 130 34.33 - 51.49: 49 51.49 - 68.65: 18 68.65 - 85.82: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA CYS B 47 " pdb=" C CYS B 47 " pdb=" N SER B 48 " pdb=" CA SER B 48 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+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 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.195: 190 0.195 - 0.389: 133 0.389 - 0.583: 103 0.583 - 0.777: 51 0.777 - 0.971: 15 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 173 " pdb=" N VAL B 173 " pdb=" C VAL B 173 " pdb=" CB VAL B 173 " both_signs ideal model delta sigma weight residual False 2.44 1.47 0.97 2.00e-01 2.50e+01 2.36e+01 chirality pdb=" CA ILE A 121 " pdb=" N ILE A 121 " pdb=" C ILE A 121 " pdb=" CB ILE A 121 " both_signs ideal model delta sigma weight residual False 2.43 3.38 -0.94 2.00e-01 2.50e+01 2.22e+01 chirality pdb=" CA ILE B 118 " pdb=" N ILE B 118 " pdb=" C ILE B 118 " pdb=" CB ILE B 118 " both_signs ideal model delta sigma weight residual False 2.43 3.37 -0.94 2.00e-01 2.50e+01 2.20e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.129 2.00e-02 2.50e+03 7.07e-02 1.50e+02 pdb=" CG PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.086 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.123 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.086 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.076 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 192 " -0.054 2.00e-02 2.50e+03 7.02e-02 1.48e+02 pdb=" CG TYR B 192 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR B 192 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TYR B 192 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR B 192 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR B 192 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR B 192 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR B 192 " 0.004 2.00e-02 2.50e+03 pdb=" HD1 TYR B 192 " 0.121 2.00e-02 2.50e+03 pdb=" HD2 TYR B 192 " -0.072 2.00e-02 2.50e+03 pdb=" HE1 TYR B 192 " -0.142 2.00e-02 2.50e+03 pdb=" HE2 TYR B 192 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " -0.007 2.00e-02 2.50e+03 5.80e-02 1.35e+02 pdb=" CG TRP A 146 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.063 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.103 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.067 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.050 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.048 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.031 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.048 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.032 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.80 - 1.56: 22 1.56 - 2.32: 1935 2.32 - 3.08: 21826 3.08 - 3.84: 33032 3.84 - 4.60: 53473 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110288 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.802 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.915 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.974 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.128 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.201 2.620 ... (remaining 110283 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_8200675_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= 0.2030 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.299360 | | target function (ml) not normalized (work): 805326.021676 | | target function (ml) not normalized (free): 16562.537150 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2132 0.1889 6.6816 6.3089| | 2: 2.94 - 2.33 1.00 7339 128 0.1615 0.1510 5.5293 5.5556| | 3: 2.33 - 2.04 0.96 6939 150 0.1614 0.1505 5.1296 5.0533| | 4: 2.04 - 1.85 1.00 7170 155 0.1751 0.1685 4.9678 5.0556| | 5: 1.85 - 1.72 0.99 7113 159 0.1918 0.1815 4.7896 4.8557| | 6: 1.72 - 1.62 0.99 7102 142 0.1967 0.2031 4.6625 4.733| | 7: 1.62 - 1.54 0.99 7104 148 0.2027 0.1802 4.5634 4.633| | 8: 1.54 - 1.47 0.96 6798 152 0.2022 0.2335 4.4707 4.5493| | 9: 1.47 - 1.41 0.98 6938 155 0.2091 0.2280 4.3927 4.4922| | 10: 1.41 - 1.36 0.99 7022 150 0.2111 0.2055 4.313 4.2955| | 11: 1.36 - 1.32 0.99 6997 151 0.2129 0.2182 4.2401 4.2966| | 12: 1.32 - 1.28 0.98 6976 149 0.2084 0.1990 4.1822 4.2257| | 13: 1.28 - 1.25 0.98 6907 166 0.2027 0.2138 4.114 4.139| | 14: 1.25 - 1.22 0.98 7015 113 0.2082 0.2104 4.0674 4.2193| | 15: 1.22 - 1.19 0.98 6957 137 0.2106 0.1829 4.0463 3.97| | 16: 1.19 - 1.17 0.93 6604 132 0.2108 0.2345 3.9965 4.076| | 17: 1.17 - 1.14 0.98 6941 135 0.2157 0.2150 3.9507 4.0757| | 18: 1.14 - 1.12 0.98 6875 142 0.2215 0.2217 3.9244 3.9013| | 19: 1.12 - 1.10 0.97 6949 106 0.2285 0.2427 3.885 4.0005| | 20: 1.10 - 1.08 0.97 6884 147 0.2324 0.2346 3.8296 3.8626| | 21: 1.08 - 1.07 0.97 6852 152 0.2472 0.2325 3.8077 3.742| | 22: 1.07 - 1.05 0.97 6838 135 0.2556 0.2585 3.7533 3.7814| | 23: 1.05 - 1.03 0.97 6829 159 0.2715 0.2594 3.7291 3.7951| | 24: 1.03 - 1.02 0.96 6785 133 0.2824 0.2719 3.6939 3.7361| | 25: 1.02 - 1.01 0.93 6552 130 0.3142 0.3030 3.6871 3.7599| | 26: 1.01 - 0.99 0.96 6767 158 0.3198 0.3431 3.6276 3.6618| | 27: 0.99 - 0.98 0.94 6648 131 0.3417 0.3567 3.6354 3.6598| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.53 0.91 0.97 35607.70| | 2: 2.94 - 2.33 7339 128 0.86 21.07 1.09 1.02 14777.51| | 3: 2.33 - 2.04 6939 150 0.94 11.78 1.11 1.06 3789.28| | 4: 2.04 - 1.85 7170 155 0.93 13.21 1.11 1.06 2699.61| | 5: 1.85 - 1.72 7113 159 0.90 16.27 1.12 1.07 2177.48| | 6: 1.72 - 1.62 7102 142 0.89 17.65 1.11 1.07 1805.13| | 7: 1.62 - 1.54 7104 148 0.88 18.91 1.12 1.06 1502.99| | 8: 1.54 - 1.47 6798 152 0.87 19.81 1.10 1.06 1285.82| | 9: 1.47 - 1.41 6938 155 0.87 20.02 1.10 1.05 1062.47| | 10: 1.41 - 1.36 7022 150 0.87 20.61 1.09 1.06 900.18| | 11: 1.36 - 1.32 6997 151 0.87 20.20 1.08 1.04 736.41| | 12: 1.32 - 1.28 6976 149 0.88 19.73 1.08 1.04 652.44| | 13: 1.28 - 1.25 6907 166 0.88 19.61 1.07 1.04 587.35| | 14: 1.25 - 1.22 7015 113 0.87 20.32 1.07 1.04 542.93| | 15: 1.22 - 1.19 6957 137 0.87 19.91 1.08 1.04 503.53| | 16: 1.19 - 1.17 6604 132 0.87 20.07 1.08 1.03 467.71| | 17: 1.17 - 1.14 6941 135 0.86 21.29 1.08 1.02 452.66| | 18: 1.14 - 1.12 6875 142 0.86 21.84 1.08 0.99 414.78| | 19: 1.12 - 1.10 6949 106 0.85 22.35 1.08 0.98 377.99| | 20: 1.10 - 1.08 6884 147 0.86 22.14 1.06 0.97 332.39| | 21: 1.08 - 1.07 6852 152 0.85 22.86 1.06 0.97 307.71| | 22: 1.07 - 1.05 6838 135 0.83 24.45 1.06 0.97 304.31| | 23: 1.05 - 1.03 6829 159 0.81 26.95 1.06 0.97 314.05| | 24: 1.03 - 1.02 6785 133 0.78 29.03 1.05 0.98 325.77| | 25: 1.02 - 1.01 6552 130 0.76 31.54 1.02 0.93 323.54| | 26: 1.01 - 0.99 6767 158 0.72 34.57 1.03 0.88 323.18| | 27: 0.99 - 0.98 6648 131 0.70 36.59 1.03 0.85 328.89| |alpha: min = 0.85 max = 1.07 mean = 1.01| |beta: min = 304.31 max = 35607.70 mean = 2827.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.88| |phase err.(test): min = 0.00 max = 89.00 mean = 21.79| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.236 2950 Z= 5.387 Angle : 5.240 16.901 4018 Z= 3.732 Chirality : 0.380 0.971 492 Planarity : 0.032 0.123 512 Dihedral : 12.975 85.818 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.11 % Favored : 96.11 % Rotamer: Outliers : 1.29 % Allowed : 4.19 % Favored : 94.52 % Cbeta Deviations : 33.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.40), residues: 386 helix: -2.36 (0.34), residues: 146 sheet: -0.73 (0.57), residues: 82 loop : -0.86 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.124 0.023 ARG A 27 TYR 0.094 0.035 TYR A 192 PHE 0.121 0.039 PHE A 95 TRP 0.134 0.043 TRP B 139 HIS 0.074 0.033 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2030 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.299360 | | target function (ml) not normalized (work): 805326.021676 | | target function (ml) not normalized (free): 16562.537150 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2028 0.2030 0.1975 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2028 0.2030 0.1975 n_refl.: 191155 remove outliers: r(all,work,free)=0.2028 0.2031 0.1975 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2030 0.2032 0.1975 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1798 0.1795 0.1907 n_refl.: 191145 remove outliers: r(all,work,free)=0.1795 0.1793 0.1907 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 94.06 92 3 0.4025 398.008 292.482 0.424 0.932 0.297 13.296-10.522 99.01 99 1 0.2503 528.187 518.216 0.764 0.933 0.246 10.503-8.327 98.90 177 3 0.2455 564.205 558.641 0.947 0.933 0.223 8.318-6.595 100.00 360 8 0.2523 414.736 402.475 0.949 0.932 0.180 6.588-5.215 100.00 711 7 0.2275 381.101 366.481 0.936 0.932 0.160 5.214-4.128 98.38 1367 28 0.1506 557.435 549.877 1.051 0.932 0.110 4.126-3.266 94.74 2603 46 0.1334 508.132 499.745 1.120 0.931 0.014 3.266-2.585 99.86 5447 97 0.1416 342.774 337.560 1.099 0.928 0.000 2.585-2.046 97.45 10613 204 0.1386 258.603 254.135 1.106 0.925 0.000 2.046-1.619 99.39 21536 464 0.1614 153.054 149.825 1.130 0.919 0.000 1.619-1.281 98.00 42464 925 0.1921 82.395 80.128 1.125 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2314 44.203 41.656 1.125 0.893 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0171 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1793 r_free=0.1907 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1793 r_free=0.1907 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.729097 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 581.488941 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 0.1267 0.1478 0.0211 0.035 1.2 11.0 0.0 0.0 0 11.365 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.67 14.78 2.11 1.118 13.121 581.489 0.018 12.95 15.46 2.51 1.247 13.335 581.489 0.017 Individual atomic B min max mean iso aniso Overall: 5.14 73.05 15.00 1.41 435 3274 Protein: 5.14 40.60 11.01 1.41 0 2902 Water: 6.35 73.05 29.35 N/A 435 370 Other: 16.10 30.49 23.29 N/A 0 2 Chain A: 5.38 60.13 13.06 N/A 0 1626 Chain B: 5.14 73.05 12.78 N/A 0 1648 Chain S: 11.75 63.98 30.63 N/A 435 0 Histogram: Values Number of atoms 5.14 - 11.93 2153 11.93 - 18.72 644 18.72 - 25.52 321 25.52 - 32.31 264 32.31 - 39.10 159 39.10 - 45.89 103 45.89 - 52.68 46 52.68 - 59.47 16 59.47 - 66.26 2 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1546 r_work=0.1294 r_free=0.1540 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1294 r_free = 0.1540 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 = 0.1279 r_free = 0.1525 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1279 r_free= 0.1525 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015619 | | target function (ls_wunit_k1) not normalized (work): 2925.334830 | | target function (ls_wunit_k1) not normalized (free): 111.081629 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1284 0.1279 0.1525 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1471 0.1468 0.1605 n_refl.: 191137 remove outliers: r(all,work,free)=0.1471 0.1468 0.1605 n_refl.: 191137 overall B=0.16 to atoms: r(all,work,free)=0.1494 0.1492 0.1617 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1518 n_refl.: 191137 remove outliers: r(all,work,free)=0.1279 0.1274 0.1517 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3668 398.008 369.915 0.480 0.963 0.289 13.296-10.522 99.01 99 1 0.2076 528.187 521.344 0.737 0.964 0.246 10.503-8.327 98.90 177 3 0.1719 564.205 562.397 0.884 0.964 0.223 8.318-6.595 100.00 360 8 0.1769 414.736 411.144 0.907 0.964 0.160 6.588-5.215 100.00 711 7 0.1581 381.101 373.308 0.888 0.964 0.160 5.214-4.128 98.38 1367 28 0.0933 557.435 553.965 0.976 0.965 0.090 4.126-3.266 94.74 2603 46 0.0854 508.132 504.233 1.044 0.965 0.014 3.266-2.585 99.86 5447 97 0.0928 342.774 340.359 1.026 0.965 0.000 2.585-2.046 97.45 10613 204 0.0942 258.603 256.475 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1075 153.054 151.396 1.056 0.965 0.000 1.619-1.281 98.00 42464 925 0.1273 82.395 81.408 1.048 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.137 1.025 0.964 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0367 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1517 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1517 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1517 | n_water=805 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1276 r_free=0.1520 | n_water=799 | time (s): 99.750 (total time: 102.120) Filter (q & B) r_work=0.1276 r_free=0.1520 | n_water=794 | time (s): 4.920 (total time: 107.040) Compute maps r_work=0.1276 r_free=0.1520 | n_water=794 | time (s): 1.520 (total time: 108.560) Filter (map) r_work=0.1297 r_free=0.1511 | n_water=666 | time (s): 3.940 (total time: 112.500) Find peaks r_work=0.1297 r_free=0.1511 | n_water=666 | time (s): 0.780 (total time: 113.280) Add new water r_work=0.1324 r_free=0.1553 | n_water=969 | time (s): 5.110 (total time: 118.390) Refine new water occ: r_work=0.1280 r_free=0.1501 adp: r_work=0.1267 r_free=0.1495 occ: r_work=0.1270 r_free=0.1491 adp: r_work=0.1263 r_free=0.1488 occ: r_work=0.1264 r_free=0.1486 adp: r_work=0.1262 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1262 r_free=0.1487 r_work=0.1262 r_free=0.1487 | n_water=969 | time (s): 75.640 (total time: 194.030) Filter (q & B) r_work=0.1265 r_free=0.1488 | n_water=907 | time (s): 4.210 (total time: 198.240) Filter (dist only) r_work=0.1265 r_free=0.1488 | n_water=906 | time (s): 117.930 (total time: 316.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.981292 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 585.932098 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 0.1251 0.1501 0.0250 0.041 1.2 18.5 0.0 0.3 0 11.991 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.51 15.01 2.50 2.047 15.293 585.932 0.014 12.28 14.90 2.62 2.406 15.323 585.932 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 68.22 16.47 1.21 537 3273 Protein: 5.42 40.33 11.00 1.21 0 2902 Water: 6.61 68.22 33.99 N/A 537 369 Other: 16.48 32.29 24.39 N/A 0 2 Chain A: 5.55 56.21 13.05 N/A 0 1625 Chain B: 5.42 68.22 12.83 N/A 0 1648 Chain S: 8.69 67.14 38.02 N/A 537 0 Histogram: Values Number of atoms 5.42 - 11.70 2062 11.70 - 17.98 706 17.98 - 24.26 266 24.26 - 30.54 223 30.54 - 36.82 179 36.82 - 43.10 155 43.10 - 49.38 105 49.38 - 55.66 55 55.66 - 61.94 52 61.94 - 68.22 7 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1490 r_work=0.1228 r_free=0.1491 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1228 r_free = 0.1491 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 = 0.1222 r_free = 0.1486 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1222 r_free= 0.1486 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013245 | | target function (ls_wunit_k1) not normalized (work): 2480.801909 | | target function (ls_wunit_k1) not normalized (free): 95.874005 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1228 0.1222 0.1486 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1432 0.1429 0.1576 n_refl.: 191136 remove outliers: r(all,work,free)=0.1432 0.1429 0.1576 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1428 0.1426 0.1575 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1234 0.1229 0.1492 n_refl.: 191136 remove outliers: r(all,work,free)=0.1234 0.1229 0.1492 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3117 398.008 378.727 0.498 0.963 0.281 13.296-10.522 99.01 99 1 0.1905 528.187 519.152 0.757 0.964 0.231 10.503-8.327 98.90 177 3 0.1353 564.205 567.377 0.918 0.964 0.188 8.318-6.595 100.00 360 8 0.1512 414.736 412.992 0.934 0.964 0.154 6.588-5.215 100.00 711 7 0.1366 381.101 376.850 0.912 0.964 0.137 5.214-4.128 98.38 1367 28 0.0822 557.435 556.192 0.995 0.964 0.100 4.126-3.266 94.74 2603 46 0.0756 508.132 505.460 1.059 0.964 0.019 3.266-2.585 99.86 5447 97 0.0856 342.774 341.263 1.046 0.963 0.010 2.585-2.046 97.45 10613 204 0.0892 258.603 256.788 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1040 153.054 151.654 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.359 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.218 1.060 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0580 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1492 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1229 r_free=0.1492 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1492 | n_water=906 | time (s): 3.380 (total time: 3.380) Filter (dist) r_work=0.1232 r_free=0.1495 | n_water=901 | time (s): 120.640 (total time: 124.020) Filter (q & B) r_work=0.1232 r_free=0.1495 | n_water=901 | time (s): 1.930 (total time: 125.950) Compute maps r_work=0.1232 r_free=0.1495 | n_water=901 | time (s): 1.910 (total time: 127.860) Filter (map) r_work=0.1268 r_free=0.1512 | n_water=711 | time (s): 3.900 (total time: 131.760) Find peaks r_work=0.1268 r_free=0.1512 | n_water=711 | time (s): 0.590 (total time: 132.350) Add new water r_work=0.1293 r_free=0.1540 | n_water=1035 | time (s): 4.120 (total time: 136.470) Refine new water occ: r_work=0.1248 r_free=0.1495 adp: r_work=0.1248 r_free=0.1496 occ: r_work=0.1244 r_free=0.1493 adp: r_work=0.1244 r_free=0.1494 occ: r_work=0.1241 r_free=0.1491 adp: r_work=0.1240 r_free=0.1492 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1492 r_work=0.1240 r_free=0.1492 | n_water=1035 | time (s): 260.490 (total time: 396.960) Filter (q & B) r_work=0.1245 r_free=0.1499 | n_water=898 | time (s): 4.410 (total time: 401.370) Filter (dist only) r_work=0.1245 r_free=0.1499 | n_water=897 | time (s): 133.790 (total time: 535.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.678165 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.354010 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 0.1234 0.1432 0.0198 0.034 1.1 7.5 0.0 0.0 0 0.839 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 14.32 1.98 1.937 14.676 16.354 3.937 12.31 13.90 1.60 2.295 14.569 16.354 3.895 Individual atomic B min max mean iso aniso Overall: 5.54 67.65 15.38 1.04 529 3272 Protein: 5.54 35.86 10.72 1.04 0 2902 Water: 6.71 67.65 30.45 N/A 529 368 Other: 13.90 27.72 20.81 N/A 0 2 Chain A: 5.58 54.86 12.77 N/A 0 1625 Chain B: 5.54 67.65 12.51 N/A 0 1647 Chain S: 13.01 60.82 32.37 N/A 529 0 Histogram: Values Number of atoms 5.54 - 11.75 2122 11.75 - 17.96 699 17.96 - 24.17 294 24.17 - 30.38 242 30.38 - 36.60 182 36.60 - 42.81 151 42.81 - 49.02 72 49.02 - 55.23 25 55.23 - 61.44 13 61.44 - 67.65 1 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1391 r_work=0.1231 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1392 target_work(ml) = 3.895 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1388 target_work(ml) = 3.889 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889228 | | target function (ml) not normalized (work): 728432.918289 | | target function (ml) not normalized (free): 15216.632786 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1228 0.1225 0.1388 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1440 0.1439 0.1487 n_refl.: 191136 remove outliers: r(all,work,free)=0.1440 0.1439 0.1487 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1433 0.1432 0.1483 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1224 0.1221 0.1382 n_refl.: 191136 remove outliers: r(all,work,free)=0.1224 0.1221 0.1382 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 0.3880 398.008 360.323 0.416 0.948 0.247 13.296-10.522 99.01 99 1 0.2439 528.187 510.415 0.717 0.949 0.230 10.503-8.327 97.80 175 3 0.1855 554.286 558.379 0.883 0.949 0.178 8.318-6.595 100.00 360 8 0.2063 414.736 409.190 0.895 0.949 0.126 6.588-5.215 100.00 711 7 0.1802 381.101 371.183 0.885 0.949 0.123 5.214-4.128 98.38 1367 28 0.1153 557.435 552.282 0.971 0.949 0.080 4.126-3.266 94.74 2603 46 0.1090 508.132 501.207 1.031 0.949 0.015 3.266-2.585 99.86 5447 97 0.1081 342.774 339.237 1.018 0.948 0.005 2.585-2.046 97.45 10613 204 0.0970 258.603 255.688 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0966 153.054 151.418 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1049 82.395 81.497 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.314 1.041 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1142 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1221 r_free=0.1382 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1221 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1382 | n_water=897 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1222 r_free=0.1383 | n_water=896 | time (s): 114.210 (total time: 116.840) Filter (q & B) r_work=0.1222 r_free=0.1381 | n_water=886 | time (s): 4.550 (total time: 121.390) Compute maps r_work=0.1222 r_free=0.1381 | n_water=886 | time (s): 2.010 (total time: 123.400) Filter (map) r_work=0.1245 r_free=0.1390 | n_water=741 | time (s): 4.870 (total time: 128.270) Find peaks r_work=0.1245 r_free=0.1390 | n_water=741 | time (s): 0.620 (total time: 128.890) Add new water r_work=0.1261 r_free=0.1404 | n_water=991 | time (s): 5.030 (total time: 133.920) Refine new water occ: r_work=0.1214 r_free=0.1361 adp: r_work=0.1206 r_free=0.1356 occ: r_work=0.1204 r_free=0.1356 adp: r_work=0.1204 r_free=0.1355 occ: r_work=0.1201 r_free=0.1355 adp: r_work=0.1201 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1354 r_work=0.1201 r_free=0.1354 | n_water=991 | time (s): 257.210 (total time: 391.130) Filter (q & B) r_work=0.1206 r_free=0.1362 | n_water=885 | time (s): 4.830 (total time: 395.960) Filter (dist only) r_work=0.1207 r_free=0.1361 | n_water=884 | time (s): 115.120 (total time: 511.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.586957 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.663801 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 0.1205 0.1357 0.0152 0.035 1.1 6.8 0.0 0.0 0 0.793 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.57 1.52 1.819 14.222 15.664 3.872 11.97 13.56 1.59 1.904 14.191 15.664 3.863 Individual atomic B min max mean iso aniso Overall: 5.52 67.11 15.04 0.99 516 3272 Protein: 5.52 33.04 10.66 0.99 0 2902 Water: 5.92 67.11 29.41 N/A 516 368 Other: 14.04 26.59 20.31 N/A 0 2 Chain A: 5.54 53.66 12.65 N/A 0 1625 Chain B: 5.52 67.11 12.43 N/A 0 1647 Chain S: 5.92 60.58 30.92 N/A 516 0 Histogram: Values Number of atoms 5.52 - 11.68 2105 11.68 - 17.84 738 17.84 - 23.99 293 23.99 - 30.15 252 30.15 - 36.31 171 36.31 - 42.47 134 42.47 - 48.63 64 48.63 - 54.79 23 54.79 - 60.95 7 60.95 - 67.11 1 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1356 r_work=0.1198 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1357 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1352 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861723 | | target function (ml) not normalized (work): 723273.742889 | | target function (ml) not normalized (free): 15128.912626 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1352 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1425 0.1425 0.1473 n_refl.: 191134 remove outliers: r(all,work,free)=0.1425 0.1425 0.1473 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1417 0.1416 0.1468 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1352 n_refl.: 191134 remove outliers: r(all,work,free)=0.1197 0.1193 0.1352 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3771 361.075 322.714 0.414 0.945 0.245 13.296-10.522 98.02 98 1 0.2482 480.352 454.051 0.706 0.946 0.209 10.503-8.327 97.80 175 3 0.2052 501.733 496.373 0.870 0.947 0.158 8.318-6.595 100.00 360 8 0.2139 375.414 369.275 0.896 0.946 0.120 6.588-5.215 100.00 711 7 0.1885 344.968 334.821 0.886 0.946 0.099 5.214-4.128 98.38 1367 28 0.1204 504.583 499.870 0.973 0.947 0.044 4.126-3.266 94.74 2603 46 0.1109 459.955 453.493 1.035 0.947 0.005 3.266-2.585 99.86 5447 97 0.1081 310.274 307.130 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0939 234.084 231.673 1.035 0.947 0.000 2.046-1.619 99.39 21536 464 0.0910 138.543 137.258 1.058 0.946 0.000 1.619-1.281 98.00 42464 925 0.0982 74.583 73.882 1.055 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.011 38.351 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1338 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1351 | n_water=884 | time (s): 2.220 (total time: 2.220) Filter (dist) r_work=0.1194 r_free=0.1353 | n_water=882 | time (s): 111.210 (total time: 113.430) Filter (q & B) r_work=0.1194 r_free=0.1352 | n_water=875 | time (s): 4.530 (total time: 117.960) Compute maps r_work=0.1194 r_free=0.1352 | n_water=875 | time (s): 2.240 (total time: 120.200) Filter (map) r_work=0.1214 r_free=0.1366 | n_water=761 | time (s): 4.980 (total time: 125.180) Find peaks r_work=0.1214 r_free=0.1366 | n_water=761 | time (s): 0.900 (total time: 126.080) Add new water r_work=0.1225 r_free=0.1374 | n_water=989 | time (s): 4.140 (total time: 130.220) Refine new water occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1191 r_free=0.1343 occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1188 r_free=0.1342 occ: r_work=0.1187 r_free=0.1342 adp: r_work=0.1186 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1341 r_work=0.1186 r_free=0.1341 | n_water=989 | time (s): 298.210 (total time: 428.430) Filter (q & B) r_work=0.1191 r_free=0.1345 | n_water=908 | time (s): 5.300 (total time: 433.730) Filter (dist only) r_work=0.1191 r_free=0.1344 | n_water=907 | time (s): 115.680 (total time: 549.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.517407 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.544894 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1347 0.0152 0.036 1.1 7.1 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.47 1.52 1.787 14.182 14.545 3.762 11.99 13.50 1.51 1.826 14.165 14.545 3.760 Individual atomic B min max mean iso aniso Overall: 5.59 66.84 15.06 0.95 540 3271 Protein: 5.59 31.91 10.61 0.95 0 2902 Water: 6.04 66.84 29.29 N/A 540 367 Other: 13.89 25.94 19.91 N/A 0 2 Chain A: 5.64 53.11 12.55 N/A 0 1624 Chain B: 5.59 66.84 12.36 N/A 0 1647 Chain S: 6.04 60.56 30.83 N/A 540 0 Histogram: Values Number of atoms 5.59 - 11.72 2134 11.72 - 17.84 717 17.84 - 23.97 309 23.97 - 30.09 237 30.09 - 36.22 179 36.22 - 42.34 141 42.34 - 48.46 63 48.46 - 54.59 23 54.59 - 60.71 7 60.71 - 66.84 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1350 r_work=0.1199 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1350 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1351 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759534 | | target function (ml) not normalized (work): 704126.960522 | | target function (ml) not normalized (free): 14737.039143 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1350 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1485 n_refl.: 191132 remove outliers: r(all,work,free)=0.1404 0.1403 0.1485 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1396 0.1394 0.1479 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1350 n_refl.: 191132 remove outliers: r(all,work,free)=0.1200 0.1197 0.1350 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 0.3717 361.075 325.610 0.402 0.950 0.222 13.296-10.522 97.03 97 1 0.2423 481.026 454.756 0.682 0.951 0.148 10.503-8.327 97.80 175 3 0.2155 501.733 494.158 0.865 0.951 0.120 8.318-6.595 100.00 360 8 0.2156 375.414 369.271 0.888 0.951 0.095 6.588-5.215 100.00 711 7 0.1904 344.968 334.920 0.881 0.951 0.080 5.214-4.128 98.38 1367 28 0.1209 504.583 499.408 0.972 0.952 0.070 4.126-3.266 94.74 2603 46 0.1127 459.955 453.134 1.031 0.952 0.000 3.266-2.585 99.86 5447 97 0.1094 310.274 306.982 1.018 0.952 0.000 2.585-2.046 97.45 10613 204 0.0947 234.084 231.670 1.030 0.952 0.000 2.046-1.619 99.39 21536 464 0.0914 138.543 137.260 1.053 0.952 0.000 1.619-1.281 98.00 42464 925 0.0976 74.583 73.885 1.050 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1657 40.011 38.344 1.035 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1471 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1350 | n_water=907 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1197 r_free=0.1350 | n_water=906 | time (s): 113.260 (total time: 115.770) Filter (q & B) r_work=0.1197 r_free=0.1350 | n_water=893 | time (s): 5.570 (total time: 121.340) Compute maps r_work=0.1197 r_free=0.1350 | n_water=893 | time (s): 2.520 (total time: 123.860) Filter (map) r_work=0.1216 r_free=0.1362 | n_water=787 | time (s): 4.990 (total time: 128.850) Find peaks r_work=0.1216 r_free=0.1362 | n_water=787 | time (s): 0.640 (total time: 129.490) Add new water r_work=0.1224 r_free=0.1371 | n_water=992 | time (s): 4.730 (total time: 134.220) Refine new water occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1193 r_free=0.1348 occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1191 r_free=0.1348 occ: r_work=0.1190 r_free=0.1348 adp: r_work=0.1190 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1348 r_work=0.1190 r_free=0.1348 | n_water=992 | time (s): 274.230 (total time: 408.450) Filter (q & B) r_work=0.1194 r_free=0.1349 | n_water=916 | time (s): 4.190 (total time: 412.640) Filter (dist only) r_work=0.1194 r_free=0.1348 | n_water=915 | time (s): 117.600 (total time: 530.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.516937 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.388496 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1354 0.0155 0.036 1.1 8.5 0.0 0.3 0 0.758 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.54 1.55 1.762 14.115 14.388 3.761 12.02 13.58 1.56 1.896 14.068 14.388 3.759 Individual atomic B min max mean iso aniso Overall: 5.60 65.76 14.95 0.90 548 3271 Protein: 5.60 29.30 10.49 0.90 0 2902 Water: 5.98 65.76 29.09 N/A 548 367 Other: 13.89 23.57 18.73 N/A 0 2 Chain A: 5.67 51.52 12.40 N/A 0 1624 Chain B: 5.60 65.76 12.22 N/A 0 1647 Chain S: 5.98 60.59 30.72 N/A 548 0 Histogram: Values Number of atoms 5.60 - 11.62 2113 11.62 - 17.63 770 17.63 - 23.65 281 23.65 - 29.67 228 29.67 - 35.68 184 35.68 - 41.70 135 41.70 - 47.71 70 47.71 - 53.73 30 53.73 - 59.75 6 59.75 - 65.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1358 r_work=0.1202 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1358 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758092 | | target function (ml) not normalized (work): 703853.101058 | | target function (ml) not normalized (free): 14735.130110 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1358 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1496 n_refl.: 191131 remove outliers: r(all,work,free)=0.1403 0.1401 0.1496 n_refl.: 191131 overall B=-0.25 to atoms: r(all,work,free)=0.1363 0.1361 0.1471 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3760 361.075 325.216 0.396 0.949 0.196 13.296-10.522 97.03 97 1 0.2436 481.026 458.550 0.710 0.950 0.150 10.503-8.327 97.80 175 3 0.2115 501.733 495.289 0.889 0.951 0.119 8.318-6.595 100.00 360 8 0.2151 375.414 369.667 0.911 0.951 0.090 6.588-5.215 100.00 711 7 0.1931 344.968 334.877 0.906 0.951 0.085 5.214-4.128 98.38 1367 28 0.1224 504.583 499.327 0.996 0.951 0.044 4.126-3.266 94.74 2603 46 0.1145 459.955 452.782 1.058 0.952 0.005 3.266-2.585 99.86 5447 97 0.1110 310.274 307.036 1.041 0.952 0.000 2.585-2.046 97.45 10613 204 0.0955 234.084 231.598 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0911 138.543 137.256 1.064 0.953 0.000 1.619-1.281 98.00 42464 925 0.0971 74.583 73.884 1.049 0.954 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.011 38.341 1.016 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0550 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1357 | n_water=915 | time (s): 3.410 (total time: 3.410) Filter (dist) r_work=0.1200 r_free=0.1358 | n_water=914 | time (s): 130.400 (total time: 133.810) Filter (q & B) r_work=0.1201 r_free=0.1358 | n_water=903 | time (s): 5.530 (total time: 139.340) Compute maps r_work=0.1201 r_free=0.1358 | n_water=903 | time (s): 1.900 (total time: 141.240) Filter (map) r_work=0.1221 r_free=0.1366 | n_water=787 | time (s): 5.250 (total time: 146.490) Find peaks r_work=0.1221 r_free=0.1366 | n_water=787 | time (s): 0.580 (total time: 147.070) Add new water r_work=0.1229 r_free=0.1375 | n_water=989 | time (s): 4.180 (total time: 151.250) Refine new water occ: r_work=0.1197 r_free=0.1350 adp: r_work=0.1198 r_free=0.1351 occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1351 occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1193 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1352 r_work=0.1193 r_free=0.1352 | n_water=989 | time (s): 295.770 (total time: 447.020) Filter (q & B) r_work=0.1198 r_free=0.1357 | n_water=918 | time (s): 5.330 (total time: 452.350) Filter (dist only) r_work=0.1198 r_free=0.1355 | n_water=917 | time (s): 117.400 (total time: 569.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558071 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.365170 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 0.1202 0.1360 0.0158 0.037 1.1 9.0 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.60 1.58 1.719 13.767 13.365 3.759 12.05 13.65 1.60 1.781 13.744 13.365 3.759 Individual atomic B min max mean iso aniso Overall: 5.41 64.38 14.67 0.87 550 3271 Protein: 5.41 28.05 10.22 0.87 0 2902 Water: 5.82 64.38 28.74 N/A 550 367 Other: 13.67 22.09 17.88 N/A 0 2 Chain A: 5.44 51.22 12.09 N/A 0 1624 Chain B: 5.41 64.38 11.92 N/A 0 1647 Chain S: 5.82 60.38 30.51 N/A 550 0 Histogram: Values Number of atoms 5.41 - 11.31 2098 11.31 - 17.21 784 17.21 - 23.10 274 23.10 - 29.00 214 29.00 - 34.89 202 34.89 - 40.79 133 40.79 - 46.69 71 46.69 - 52.58 36 52.58 - 58.48 6 58.48 - 64.38 3 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1366 r_work=0.1206 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1366 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1366 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758901 | | target function (ml) not normalized (work): 704004.649218 | | target function (ml) not normalized (free): 14740.817197 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1366 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1373 0.1371 0.1485 n_refl.: 191131 remove outliers: r(all,work,free)=0.1373 0.1371 0.1485 n_refl.: 191131 overall B=0.07 to atoms: r(all,work,free)=0.1382 0.1380 0.1490 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1194 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3804 361.075 322.990 0.431 0.907 0.226 13.296-10.522 97.03 97 1 0.2369 481.026 459.974 0.752 0.908 0.159 10.503-8.327 97.80 175 3 0.2158 501.733 494.210 0.934 0.909 0.121 8.318-6.595 100.00 360 8 0.2159 375.414 368.662 0.962 0.908 0.096 6.588-5.215 100.00 711 7 0.1932 344.968 334.610 0.955 0.909 0.080 5.214-4.128 98.38 1367 28 0.1232 504.583 498.559 1.053 0.910 0.039 4.126-3.266 94.74 2603 46 0.1160 459.955 452.192 1.119 0.911 0.005 3.266-2.585 99.86 5447 97 0.1116 310.274 306.688 1.100 0.911 0.000 2.585-2.046 97.45 10613 204 0.0963 234.084 231.437 1.109 0.913 0.000 2.046-1.619 99.39 21536 464 0.0913 138.543 137.166 1.126 0.915 0.000 1.619-1.281 98.00 42464 925 0.0951 74.583 73.920 1.113 0.919 0.000 1.281-0.980 96.53 101826 2055 0.1633 40.011 38.311 1.076 0.926 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0618 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1357 | n_water=917 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1194 r_free=0.1357 | n_water=917 | time (s): 113.320 (total time: 116.410) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=903 | time (s): 5.310 (total time: 121.720) Compute maps r_work=0.1194 r_free=0.1356 | n_water=903 | time (s): 2.110 (total time: 123.830) Filter (map) r_work=0.1214 r_free=0.1357 | n_water=799 | time (s): 5.280 (total time: 129.110) Find peaks r_work=0.1214 r_free=0.1357 | n_water=799 | time (s): 0.750 (total time: 129.860) Add new water r_work=0.1221 r_free=0.1366 | n_water=1001 | time (s): 4.640 (total time: 134.500) Refine new water 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=0.1343 occ: r_work=0.1188 r_free=0.1343 adp: r_work=0.1188 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1343 r_work=0.1188 r_free=0.1343 | n_water=1001 | time (s): 279.310 (total time: 413.810) Filter (q & B) r_work=0.1193 r_free=0.1351 | n_water=917 | time (s): 4.900 (total time: 418.710) Filter (dist only) r_work=0.1193 r_free=0.1350 | n_water=916 | time (s): 118.890 (total time: 537.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.551506 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.274542 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1360 0.0165 0.038 1.1 5.6 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.60 1.65 1.667 13.747 14.275 3.757 11.94 13.61 1.67 1.680 13.736 14.275 3.753 Individual atomic B min max mean iso aniso Overall: 5.49 63.36 14.68 0.87 549 3271 Protein: 5.49 28.10 10.29 0.87 0 2902 Water: 5.97 63.36 28.58 N/A 549 367 Other: 13.77 22.11 17.94 N/A 0 2 Chain A: 5.57 51.19 12.13 N/A 0 1624 Chain B: 5.49 63.36 11.97 N/A 0 1647 Chain S: 5.97 60.43 30.38 N/A 549 0 Histogram: Values Number of atoms 5.49 - 11.28 2061 11.28 - 17.06 823 17.06 - 22.85 266 22.85 - 28.64 210 28.64 - 34.42 206 34.42 - 40.21 126 40.21 - 46.00 82 46.00 - 51.78 36 51.78 - 57.57 6 57.57 - 63.36 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1361 r_work=0.1194 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1361 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1361 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752816 | | target function (ml) not normalized (work): 702864.827167 | | target function (ml) not normalized (free): 14724.183055 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1361 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1386 0.1384 0.1500 n_refl.: 191131 remove outliers: r(all,work,free)=0.1386 0.1384 0.1500 n_refl.: 191131 overall B=0.02 to atoms: r(all,work,free)=0.1389 0.1387 0.1501 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1360 n_refl.: 191131 remove outliers: r(all,work,free)=0.1194 0.1190 0.1360 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 0.3656 360.771 310.869 0.390 0.974 0.217 13.296-10.522 97.03 97 1 0.2415 481.026 459.821 0.694 0.976 0.152 10.503-8.327 97.80 175 3 0.2185 501.733 493.316 0.864 0.977 0.116 8.318-6.595 100.00 360 8 0.2174 375.414 369.376 0.891 0.976 0.091 6.588-5.215 100.00 711 7 0.1950 344.968 334.474 0.886 0.977 0.073 5.214-4.128 98.38 1367 28 0.1242 504.583 498.660 0.978 0.978 0.034 4.126-3.266 94.74 2603 46 0.1165 459.955 452.162 1.040 0.979 0.005 3.266-2.585 99.86 5447 97 0.1123 310.274 306.647 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0959 234.084 231.487 1.032 0.982 0.000 2.046-1.619 99.39 21536 464 0.0906 138.543 137.220 1.048 0.985 0.000 1.619-1.281 98.00 42464 925 0.0942 74.583 73.952 1.039 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.011 38.310 1.006 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0238 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1360 | n_water=916 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1190 r_free=0.1360 | n_water=916 | time (s): 108.570 (total time: 111.150) Filter (q & B) r_work=0.1191 r_free=0.1357 | n_water=908 | time (s): 4.590 (total time: 115.740) Compute maps r_work=0.1191 r_free=0.1357 | n_water=908 | time (s): 1.740 (total time: 117.480) Filter (map) r_work=0.1209 r_free=0.1357 | n_water=809 | time (s): 4.870 (total time: 122.350) Find peaks r_work=0.1209 r_free=0.1357 | n_water=809 | time (s): 0.670 (total time: 123.020) Add new water r_work=0.1216 r_free=0.1364 | n_water=1010 | time (s): 4.220 (total time: 127.240) Refine new water occ: r_work=0.1187 r_free=0.1342 adp: r_work=0.1187 r_free=0.1342 occ: r_work=0.1185 r_free=0.1342 adp: r_work=0.1185 r_free=0.1343 occ: r_work=0.1184 r_free=0.1343 adp: r_work=0.1184 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1343 r_work=0.1184 r_free=0.1343 | n_water=1010 | time (s): 182.860 (total time: 310.100) Filter (q & B) r_work=0.1189 r_free=0.1356 | n_water=925 | time (s): 4.140 (total time: 314.240) Filter (dist only) r_work=0.1189 r_free=0.1354 | n_water=924 | time (s): 117.790 (total time: 432.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.538289 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.654566 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 0.1192 0.1361 0.0170 0.038 1.1 7.2 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.61 1.70 1.675 13.784 13.655 3.753 11.93 13.65 1.71 1.675 13.781 13.655 3.753 Individual atomic B min max mean iso aniso Overall: 5.52 63.09 14.73 0.86 557 3271 Protein: 5.52 27.96 10.32 0.86 0 2902 Water: 5.98 63.09 28.57 N/A 557 367 Other: 13.81 22.14 17.98 N/A 0 2 Chain A: 5.59 51.17 12.13 N/A 0 1624 Chain B: 5.52 63.09 11.99 N/A 0 1647 Chain S: 5.98 60.41 30.42 N/A 557 0 Histogram: Values Number of atoms 5.52 - 11.27 2056 11.27 - 17.03 829 17.03 - 22.79 272 22.79 - 28.55 204 28.55 - 34.30 212 34.30 - 40.06 124 40.06 - 45.82 84 45.82 - 51.57 35 51.57 - 57.33 8 57.33 - 63.09 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1365 r_work=0.1194 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1365 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1366 target_work(ml) = 3.753 | | 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= 0.1192 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753185 | | target function (ml) not normalized (work): 702930.328389 | | target function (ml) not normalized (free): 14730.266566 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1388 0.1386 0.1509 n_refl.: 191130 remove outliers: r(all,work,free)=0.1388 0.1386 0.1509 n_refl.: 191130 overall B=-0.00 to atoms: r(all,work,free)=0.1387 0.1385 0.1509 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1365 n_refl.: 191130 remove outliers: r(all,work,free)=0.1194 0.1191 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 0.3662 360.771 329.800 0.402 0.994 0.211 13.296-10.522 97.03 97 1 0.2397 481.026 459.510 0.678 0.996 0.142 10.503-8.327 97.80 175 3 0.2186 501.733 493.513 0.846 0.996 0.105 8.318-6.595 100.00 360 8 0.2150 375.414 369.580 0.873 0.996 0.081 6.588-5.215 100.00 711 7 0.1941 344.968 334.508 0.868 0.997 0.067 5.214-4.128 98.38 1367 28 0.1244 504.583 498.376 0.959 0.997 0.035 4.126-3.266 94.74 2603 46 0.1165 459.955 452.128 1.021 0.999 0.009 3.266-2.585 99.86 5447 97 0.1127 310.274 306.564 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0962 234.084 231.428 1.012 1.002 0.000 2.046-1.619 99.39 21536 464 0.0908 138.543 137.182 1.028 1.006 0.000 1.619-1.281 98.00 42464 925 0.0941 74.583 73.937 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.011 38.303 0.989 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0081 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1365 After: r_work=0.1192 r_free=0.1365 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1365 | n_water=924 | time (s): 2.120 (total time: 2.120) Filter (dist) r_work=0.1192 r_free=0.1366 | n_water=923 | time (s): 122.610 (total time: 124.730) Filter (q & B) r_work=0.1193 r_free=0.1366 | n_water=911 | time (s): 5.620 (total time: 130.350) Compute maps r_work=0.1193 r_free=0.1366 | n_water=911 | time (s): 1.860 (total time: 132.210) Filter (map) r_work=0.1214 r_free=0.1371 | n_water=803 | time (s): 4.650 (total time: 136.860) Find peaks r_work=0.1214 r_free=0.1371 | n_water=803 | time (s): 0.870 (total time: 137.730) Add new water r_work=0.1221 r_free=0.1383 | n_water=1001 | time (s): 4.820 (total time: 142.550) Refine new water occ: r_work=0.1192 r_free=0.1352 adp: r_work=0.1192 r_free=0.1352 occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1190 r_free=0.1351 occ: r_work=0.1188 r_free=0.1349 adp: r_work=0.1188 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1350 r_work=0.1188 r_free=0.1350 | n_water=1001 | time (s): 199.330 (total time: 341.880) Filter (q & B) r_work=0.1193 r_free=0.1360 | n_water=920 | time (s): 5.700 (total time: 347.580) Filter (dist only) r_work=0.1193 r_free=0.1358 | n_water=919 | time (s): 123.780 (total time: 471.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.557801 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.123424 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 0.1362 0.0167 0.038 1.2 9.2 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.62 1.67 1.673 13.756 14.123 3.755 11.95 13.63 1.68 1.676 13.751 14.123 3.753 Individual atomic B min max mean iso aniso Overall: 5.57 62.18 14.67 0.86 552 3271 Protein: 5.57 27.87 10.33 0.86 0 2902 Water: 6.02 62.18 28.35 N/A 552 367 Other: 13.84 22.06 17.95 N/A 0 2 Chain A: 5.65 51.07 12.12 N/A 0 1624 Chain B: 5.57 62.18 11.98 N/A 0 1647 Chain S: 6.02 60.38 30.19 N/A 552 0 Histogram: Values Number of atoms 5.57 - 11.23 2040 11.23 - 16.89 839 16.89 - 22.55 274 22.55 - 28.21 208 28.21 - 33.87 207 33.87 - 39.54 117 39.54 - 45.20 82 45.20 - 50.86 41 50.86 - 56.52 10 56.52 - 62.18 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1363 r_work=0.1195 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1363 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1361 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753333 | | target function (ml) not normalized (work): 702958.066757 | | target function (ml) not normalized (free): 14728.114512 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1369 0.1479 5.6963 5.7807| | 2: 2.94 - 2.33 1.00 7339 128 0.1079 0.1393 5.0886 5.1965| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1171 4.6594 4.7408| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1069 4.3956 4.5837| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.1004 4.1506 4.255| | 6: 1.72 - 1.62 0.99 7102 142 0.0893 0.1085 3.9437 4.0719| | 7: 1.62 - 1.54 0.99 7104 148 0.0885 0.0960 3.7932 3.9253| | 8: 1.54 - 1.47 0.96 6798 152 0.0887 0.1277 3.6937 3.8805| | 9: 1.47 - 1.41 0.98 6938 155 0.0922 0.1121 3.6155 3.7461| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1192 3.5516 3.6759| | 11: 1.36 - 1.32 0.99 6997 151 0.0988 0.1110 3.4808 3.5786| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1128 3.4561 3.5836| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1248 3.4358 3.57| | 14: 1.25 - 1.22 0.98 7015 112 0.1103 0.1569 3.4311 3.6689| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1246 3.4462 3.4929| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1551 3.4635 3.6588| | 17: 1.17 - 1.14 0.98 6940 135 0.1297 0.1224 3.4316 3.4407| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1714 3.4375 3.5337| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1747 3.4187 3.5925| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1576 3.409 3.434| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2138 3.417 3.5045| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1956 3.4124 3.4137| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2025 3.4325 3.4858| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2247 3.435 3.5085| | 25: 1.02 - 1.01 0.93 6552 130 0.2615 0.2518 3.4488 3.5241| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2872 3.4147 3.4252| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2801 3.4685 3.3945| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.05 1.00 0.95 11704.02| | 2: 2.94 - 2.33 7339 128 0.92 13.12 0.99 0.95 5314.75| | 3: 2.33 - 2.04 6939 150 0.96 7.74 1.01 0.95 1724.14| | 4: 2.04 - 1.85 7170 155 0.96 7.77 1.00 0.95 1025.17| | 5: 1.85 - 1.72 7113 159 0.96 8.19 1.00 0.96 642.63| | 6: 1.72 - 1.62 7102 142 0.96 8.02 1.00 0.96 443.16| | 7: 1.62 - 1.54 7104 148 0.96 8.03 1.01 0.97 332.03| | 8: 1.54 - 1.47 6798 152 0.96 8.14 1.01 0.97 273.62| | 9: 1.47 - 1.41 6938 155 0.96 8.36 1.00 0.97 226.66| | 10: 1.41 - 1.36 7022 150 0.96 8.83 1.00 0.97 199.90| | 11: 1.36 - 1.32 6997 151 0.96 8.89 0.99 0.96 173.40| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.98 0.95 160.22| | 13: 1.28 - 1.25 6907 166 0.96 9.55 1.01 0.96 158.41| | 14: 1.25 - 1.22 7015 112 0.95 10.72 1.01 0.96 163.37| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 0.97 166.61| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.96 160.02| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.96 153.59| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.94 147.44| | 19: 1.12 - 1.10 6948 106 0.93 14.15 1.00 0.94 150.88| | 20: 1.10 - 1.08 6884 147 0.92 15.22 1.00 0.94 150.16| | 21: 1.08 - 1.07 6852 152 0.91 16.65 1.00 0.93 153.21| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.93 154.65| | 23: 1.05 - 1.03 6827 159 0.87 20.49 0.99 0.92 164.35| | 24: 1.03 - 1.02 6784 133 0.85 23.16 0.99 0.93 178.77| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.97 0.90 182.14| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.88 176.62| | 27: 0.99 - 0.98 6647 131 0.82 26.26 0.99 0.87 160.54| |alpha: min = 0.87 max = 0.97 mean = 0.94| |beta: min = 147.44 max = 11704.02 mean = 953.95| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.31| |phase err.(test): min = 0.00 max = 88.64 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1361 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1399 0.1396 0.1510 n_refl.: 191130 remove outliers: r(all,work,free)=0.1399 0.1396 0.1510 n_refl.: 191130 overall B=-0.05 to atoms: r(all,work,free)=0.1390 0.1388 0.1505 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1196 0.1193 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 0.3660 360.771 330.066 0.399 0.975 0.212 13.296-10.522 97.03 97 1 0.2411 481.026 461.517 0.671 0.976 0.142 10.503-8.327 97.80 175 3 0.2192 501.733 493.363 0.838 0.977 0.106 8.318-6.595 100.00 360 8 0.2160 375.414 369.013 0.868 0.977 0.088 6.588-5.215 100.00 711 7 0.1974 344.968 334.019 0.863 0.977 0.077 5.214-4.128 98.38 1367 28 0.1266 504.583 498.246 0.955 0.978 0.039 4.126-3.266 94.74 2603 46 0.1168 459.955 451.903 1.016 0.980 0.005 3.266-2.585 99.86 5447 97 0.1127 310.274 306.588 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0965 234.084 231.436 1.005 0.984 0.000 2.046-1.619 99.39 21536 464 0.0909 138.543 137.174 1.020 0.988 0.000 1.619-1.281 98.00 42464 925 0.0942 74.583 73.935 1.010 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.011 38.302 0.977 1.009 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0116 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2030 0.1975 0.080 5.240 5.2 78.0 14.6 805 0.000 1_bss: 0.1793 0.1907 0.080 5.240 5.2 78.1 14.6 805 0.000 1_settarget: 0.1793 0.1907 0.080 5.240 5.2 78.1 14.6 805 0.000 1_nqh: 0.1793 0.1907 0.080 5.240 5.2 78.1 14.6 805 0.000 1_weight: 0.1793 0.1907 0.080 5.240 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1267 0.1478 0.035 1.163 5.2 78.1 14.6 805 0.141 1_adp: 0.1296 0.1546 0.035 1.163 5.1 73.1 15.0 805 0.141 1_regHadp: 0.1294 0.1540 0.035 1.163 5.1 73.1 15.0 805 0.141 1_occ: 0.1279 0.1525 0.035 1.163 5.1 73.1 15.0 805 0.141 2_bss: 0.1274 0.1517 0.035 1.163 5.3 73.2 15.2 805 0.141 2_settarget: 0.1274 0.1517 0.035 1.163 5.3 73.2 15.2 805 0.141 2_updatecdl: 0.1274 0.1517 0.035 1.177 5.3 73.2 15.2 805 0.141 2_nqh: 0.1274 0.1517 0.035 1.177 5.3 73.2 15.2 805 0.141 2_sol: 0.1265 0.1488 0.035 1.177 5.3 73.2 16.4 906 n/a 2_weight: 0.1265 0.1488 0.035 1.177 5.3 73.2 16.4 906 n/a 2_xyzrec: 0.1251 0.1501 0.041 1.160 5.3 73.2 16.4 906 n/a 2_adp: 0.1228 0.1490 0.041 1.160 5.4 68.2 16.5 906 n/a 2_regHadp: 0.1228 0.1491 0.041 1.160 5.4 68.2 16.5 906 n/a 2_occ: 0.1222 0.1486 0.041 1.160 5.4 68.2 16.5 906 n/a 3_bss: 0.1229 0.1492 0.041 1.160 5.4 68.2 16.5 906 n/a 3_settarget: 0.1229 0.1492 0.041 1.160 5.4 68.2 16.5 906 n/a 3_updatecdl: 0.1229 0.1492 0.041 1.162 5.4 68.2 16.5 906 n/a 3_nqh: 0.1229 0.1492 0.041 1.162 5.4 68.2 16.5 906 n/a 3_sol: 0.1245 0.1499 0.041 1.162 5.4 68.2 15.6 897 n/a 3_weight: 0.1245 0.1499 0.041 1.162 5.4 68.2 15.6 897 n/a 3_xyzrec: 0.1234 0.1432 0.034 1.103 5.4 68.2 15.6 897 n/a 3_adp: 0.1231 0.1391 0.034 1.103 5.5 67.6 15.4 897 n/a 3_regHadp: 0.1231 0.1392 0.034 1.103 5.5 67.6 15.4 897 n/a 3_occ: 0.1225 0.1388 0.034 1.103 5.5 67.6 15.4 897 n/a 4_bss: 0.1221 0.1382 0.034 1.103 5.5 67.6 15.3 897 n/a 4_settarget: 0.1221 0.1382 0.034 1.103 5.5 67.6 15.3 897 n/a 4_updatecdl: 0.1221 0.1382 0.034 1.106 5.5 67.6 15.3 897 n/a 4_nqh: 0.1221 0.1382 0.034 1.106 5.5 67.6 15.3 897 n/a 4_sol: 0.1207 0.1361 0.034 1.106 5.5 67.6 15.1 884 n/a 4_weight: 0.1207 0.1361 0.034 1.106 5.5 67.6 15.1 884 n/a 4_xyzrec: 0.1205 0.1357 0.035 1.138 5.5 67.6 15.1 884 n/a 4_adp: 0.1197 0.1356 0.035 1.138 5.5 67.1 15.0 884 n/a 4_regHadp: 0.1198 0.1357 0.035 1.138 5.5 67.1 15.0 884 n/a 4_occ: 0.1195 0.1352 0.035 1.138 5.5 67.1 15.0 884 n/a 5_bss: 0.1193 0.1351 0.035 1.138 5.5 67.1 15.0 884 n/a 5_settarget: 0.1193 0.1351 0.035 1.138 5.5 67.1 15.0 884 n/a 5_updatecdl: 0.1193 0.1351 0.035 1.139 5.5 67.1 15.0 884 n/a 5_nqh: 0.1193 0.1351 0.035 1.139 5.5 67.1 15.0 884 n/a 5_sol: 0.1191 0.1344 0.035 1.139 5.5 67.1 15.1 907 n/a 5_weight: 0.1191 0.1344 0.035 1.139 5.5 67.1 15.1 907 n/a 5_xyzrec: 0.1194 0.1347 0.036 1.129 5.5 67.1 15.1 907 n/a 5_adp: 0.1199 0.1350 0.036 1.129 5.6 66.8 15.1 907 n/a 5_regHadp: 0.1199 0.1350 0.036 1.129 5.6 66.8 15.1 907 n/a 5_occ: 0.1197 0.1351 0.036 1.129 5.6 66.8 15.1 907 n/a 6_bss: 0.1197 0.1350 0.036 1.129 5.6 66.8 15.0 907 n/a 6_settarget: 0.1197 0.1350 0.036 1.129 5.6 66.8 15.0 907 n/a 6_updatecdl: 0.1197 0.1350 0.036 1.128 5.6 66.8 15.0 907 n/a 6_nqh: 0.1197 0.1350 0.036 1.128 5.6 66.8 15.0 907 n/a 6_sol: 0.1194 0.1348 0.036 1.128 5.6 66.8 15.0 915 n/a 6_weight: 0.1194 0.1348 0.036 1.128 5.6 66.8 15.0 915 n/a 6_xyzrec: 0.1198 0.1354 0.036 1.128 5.6 66.8 15.0 915 n/a 6_adp: 0.1202 0.1358 0.036 1.128 5.6 65.8 15.0 915 n/a 6_regHadp: 0.1202 0.1358 0.036 1.128 5.6 65.8 15.0 915 n/a 6_occ: 0.1200 0.1358 0.036 1.128 5.6 65.8 15.0 915 n/a 7_bss: 0.1200 0.1357 0.036 1.128 5.4 65.5 14.7 915 n/a 7_settarget: 0.1200 0.1357 0.036 1.128 5.4 65.5 14.7 915 n/a 7_updatecdl: 0.1200 0.1357 0.036 1.128 5.4 65.5 14.7 915 n/a 7_nqh: 0.1200 0.1357 0.036 1.128 5.4 65.5 14.7 915 n/a 7_sol: 0.1198 0.1355 0.036 1.128 5.4 65.5 14.7 917 n/a 7_weight: 0.1198 0.1355 0.036 1.128 5.4 65.5 14.7 917 n/a 7_xyzrec: 0.1202 0.1360 0.037 1.136 5.4 65.5 14.7 917 n/a 7_adp: 0.1206 0.1366 0.037 1.136 5.4 64.4 14.7 917 n/a 7_regHadp: 0.1206 0.1366 0.037 1.136 5.4 64.4 14.7 917 n/a 7_occ: 0.1204 0.1366 0.037 1.136 5.4 64.4 14.7 917 n/a 8_bss: 0.1194 0.1357 0.037 1.136 5.5 64.4 14.7 917 n/a 8_settarget: 0.1194 0.1357 0.037 1.136 5.5 64.4 14.7 917 n/a 8_updatecdl: 0.1194 0.1357 0.037 1.136 5.5 64.4 14.7 917 n/a 8_nqh: 0.1194 0.1357 0.037 1.136 5.5 64.4 14.7 917 n/a 8_sol: 0.1193 0.1350 0.037 1.136 5.5 64.4 14.7 916 n/a 8_weight: 0.1193 0.1350 0.037 1.136 5.5 64.4 14.7 916 n/a 8_xyzrec: 0.1196 0.1360 0.038 1.122 5.5 64.4 14.7 916 n/a 8_adp: 0.1194 0.1361 0.038 1.122 5.5 63.4 14.7 916 n/a 8_regHadp: 0.1194 0.1361 0.038 1.122 5.5 63.4 14.7 916 n/a 8_occ: 0.1192 0.1361 0.038 1.122 5.5 63.4 14.7 916 n/a 9_bss: 0.1190 0.1360 0.038 1.122 5.5 63.4 14.7 916 n/a 9_settarget: 0.1190 0.1360 0.038 1.122 5.5 63.4 14.7 916 n/a 9_updatecdl: 0.1190 0.1360 0.038 1.121 5.5 63.4 14.7 916 n/a 9_nqh: 0.1190 0.1360 0.038 1.121 5.5 63.4 14.7 916 n/a 9_sol: 0.1189 0.1354 0.038 1.121 5.5 63.4 14.7 924 n/a 9_weight: 0.1189 0.1354 0.038 1.121 5.5 63.4 14.7 924 n/a 9_xyzrec: 0.1192 0.1361 0.038 1.121 5.5 63.4 14.7 924 n/a 9_adp: 0.1193 0.1365 0.038 1.121 5.5 63.1 14.7 924 n/a 9_regHadp: 0.1194 0.1365 0.038 1.121 5.5 63.1 14.7 924 n/a 9_occ: 0.1192 0.1366 0.038 1.121 5.5 63.1 14.7 924 n/a 10_bss: 0.1191 0.1365 0.038 1.121 5.5 63.1 14.7 924 n/a 10_settarget: 0.1191 0.1365 0.038 1.121 5.5 63.1 14.7 924 n/a 10_updatecdl: 0.1191 0.1365 0.038 1.122 5.5 63.1 14.7 924 n/a 10_setrh: 0.1192 0.1365 0.038 1.122 5.5 63.1 14.7 924 n/a 10_nqh: 0.1192 0.1365 0.038 1.122 5.5 63.1 14.7 924 n/a 10_sol: 0.1193 0.1358 0.038 1.122 5.5 63.1 14.7 919 n/a 10_weight: 0.1193 0.1358 0.038 1.122 5.5 63.1 14.7 919 n/a 10_xyzrec: 0.1195 0.1362 0.038 1.155 5.5 63.1 14.7 919 n/a 10_adp: 0.1195 0.1363 0.038 1.155 5.6 62.2 14.7 919 n/a 10_regHadp: 0.1195 0.1363 0.038 1.155 5.6 62.2 14.7 919 n/a 10_occ: 0.1194 0.1361 0.038 1.155 5.6 62.2 14.7 919 n/a end: 0.1193 0.1359 0.038 1.155 5.5 62.1 14.6 919 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8200675_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8200675_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.9500 Refinement macro-cycles (run) : 12166.4500 Write final files (write_after_run_outputs) : 153.1600 Total : 12326.5600 Total CPU time: 3.43 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:43 PST -0800 (1736736163.53 s) Start R-work = 0.1793, R-free = 0.1907 Final R-work = 0.1193, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 12595.66 seconds wall clock time: 210 minutes 59.40 seconds (12659.40 seconds total)