Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9524401.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" 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_9524401.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9524401.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.19, per 1000 atoms: 0.33 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: 2.616 distance_ideal: 2.720 ideal - model: 0.104 slack: 0.000 delta_slack: 0.104 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: 2.753 distance_ideal: 2.710 ideal - model: -0.043 slack: 0.000 delta_slack: -0.043 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 133.9 milliseconds Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.01: 614 1.01 - 1.23: 2526 1.23 - 1.46: 1468 1.46 - 1.69: 1287 1.69 - 1.92: 39 Bond restraints: 5934 Sorted by residual: bond pdb=" C VAL B 69 " pdb=" O VAL B 69 " ideal model delta sigma weight residual 1.234 1.002 0.232 1.16e-02 7.43e+03 3.98e+02 bond pdb=" N LEU B 54 " pdb=" H LEU B 54 " ideal model delta sigma weight residual 0.860 1.235 -0.375 2.00e-02 2.50e+03 3.52e+02 bond pdb=" NH1 ARG A 175 " pdb="HH11 ARG A 175 " ideal model delta sigma weight residual 0.860 1.228 -0.368 2.00e-02 2.50e+03 3.39e+02 bond pdb=" N ARG B 175 " pdb=" H ARG B 175 " ideal model delta sigma weight residual 0.860 1.228 -0.368 2.00e-02 2.50e+03 3.38e+02 bond pdb=" CG2 VAL A 150 " pdb="HG23 VAL A 150 " ideal model delta sigma weight residual 0.970 1.334 -0.364 2.00e-02 2.50e+03 3.31e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 5555 4.07 - 8.14: 3546 8.14 - 12.21: 1406 12.21 - 16.28: 271 16.28 - 20.35: 32 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O VAL B 89 " pdb=" C VAL B 89 " pdb=" N GLU B 90 " ideal model delta sigma weight residual 121.87 136.45 -14.58 9.70e-01 1.06e+00 2.26e+02 angle pdb=" O THR A 21 " pdb=" C THR A 21 " pdb=" N ILE A 22 " ideal model delta sigma weight residual 122.07 107.50 14.57 1.03e+00 9.43e-01 2.00e+02 angle pdb=" N PRO B 11 " pdb=" CA PRO B 11 " pdb=" CB PRO B 11 " ideal model delta sigma weight residual 103.19 115.02 -11.83 9.00e-01 1.23e+00 1.73e+02 angle pdb=" CG HIS B 96 " pdb=" CD2 HIS B 96 " pdb=" NE2 HIS B 96 " ideal model delta sigma weight residual 107.20 94.16 13.04 1.00e+00 1.00e+00 1.70e+02 angle pdb=" CA LEU B 113 " pdb=" C LEU B 113 " pdb=" O LEU B 113 " ideal model delta sigma weight residual 121.00 134.42 -13.42 1.05e+00 9.07e-01 1.63e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.75: 1842 16.75 - 33.51: 133 33.51 - 50.26: 43 50.26 - 67.01: 27 67.01 - 83.77: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 152.82 27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -155.46 -24.54 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -155.93 -24.07 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.249: 207 0.249 - 0.496: 157 0.496 - 0.742: 89 0.742 - 0.989: 32 0.989 - 1.236: 7 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.35 -1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CA PRO B 109 " pdb=" N PRO B 109 " pdb=" C PRO B 109 " pdb=" CB PRO B 109 " both_signs ideal model delta sigma weight residual False 2.72 1.61 1.11 2.00e-01 2.50e+01 3.09e+01 chirality pdb=" CB ILE A 169 " pdb=" CA ILE A 169 " pdb=" CG1 ILE A 169 " pdb=" CG2 ILE A 169 " both_signs ideal model delta sigma weight residual False 2.64 1.54 1.10 2.00e-01 2.50e+01 3.05e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " 0.016 2.00e-02 2.50e+03 8.12e-02 1.98e+02 pdb=" CG TYR A 192 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " 0.075 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " -0.138 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " 0.045 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " 0.129 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " -0.016 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.115 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " -0.025 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 95 " 0.006 2.00e-02 2.50e+03 6.76e-02 1.37e+02 pdb=" CG PHE B 95 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 PHE B 95 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 95 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE B 95 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 PHE B 95 " 0.056 2.00e-02 2.50e+03 pdb=" CZ PHE B 95 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE B 95 " 0.036 2.00e-02 2.50e+03 pdb=" HD2 PHE B 95 " -0.061 2.00e-02 2.50e+03 pdb=" HE1 PHE B 95 " 0.076 2.00e-02 2.50e+03 pdb=" HE2 PHE B 95 " 0.089 2.00e-02 2.50e+03 pdb=" HZ PHE B 95 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.125 2.00e-02 2.50e+03 5.75e-02 1.32e+02 pdb=" CG TRP A 146 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.066 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.085 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.073 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.069 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.081 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.045 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.040 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.043 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.006 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.056 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 27 1.61 - 2.36: 2372 2.36 - 3.10: 22141 3.10 - 3.85: 33064 3.85 - 4.60: 52762 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110366 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.861 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.016 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.018 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.061 2.620 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.181 2.100 ... (remaining 110361 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_9524401_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= 0.2039 r_free= 0.2013 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302528 | | target function (ml) not normalized (work): 805919.335768 | | target function (ml) not normalized (free): 16573.238581 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2135 0.1954 6.6719 6.3024| | 2: 2.94 - 2.33 1.00 7339 128 0.1629 0.1772 5.538 5.6337| | 3: 2.33 - 2.04 0.96 6939 150 0.1636 0.1493 5.1455 5.0771| | 4: 2.04 - 1.85 1.00 7170 155 0.1748 0.1679 4.9717 5.0557| | 5: 1.85 - 1.72 0.99 7113 159 0.1937 0.1721 4.8079 4.7747| | 6: 1.72 - 1.62 0.99 7102 142 0.1968 0.1995 4.6698 4.7287| | 7: 1.62 - 1.54 0.99 7104 148 0.2026 0.1895 4.572 4.6242| | 8: 1.54 - 1.47 0.96 6798 152 0.2030 0.2365 4.4682 4.569| | 9: 1.47 - 1.41 0.98 6938 155 0.2091 0.2155 4.3844 4.3972| | 10: 1.41 - 1.36 0.99 7022 150 0.2143 0.1917 4.3088 4.2961| | 11: 1.36 - 1.32 0.99 6997 151 0.2129 0.2264 4.2342 4.2814| | 12: 1.32 - 1.28 0.98 6976 149 0.2083 0.2070 4.1773 4.2428| | 13: 1.28 - 1.25 0.98 6907 166 0.2031 0.2145 4.1229 4.1733| | 14: 1.25 - 1.22 0.98 7015 113 0.2084 0.2454 4.0817 4.2917| | 15: 1.22 - 1.19 0.98 6957 137 0.2120 0.2020 4.0493 4.0252| | 16: 1.19 - 1.17 0.93 6604 132 0.2133 0.2161 4.0106 4.053| | 17: 1.17 - 1.14 0.98 6941 135 0.2194 0.1844 3.9657 3.9537| | 18: 1.14 - 1.12 0.98 6875 142 0.2240 0.2476 3.9316 3.9545| | 19: 1.12 - 1.10 0.97 6949 106 0.2278 0.2582 3.8719 4.0329| | 20: 1.10 - 1.08 0.97 6884 147 0.2340 0.2201 3.8303 3.8587| | 21: 1.08 - 1.07 0.97 6852 152 0.2441 0.2949 3.7915 3.8872| | 22: 1.07 - 1.05 0.97 6838 135 0.2568 0.2418 3.758 3.7212| | 23: 1.05 - 1.03 0.97 6829 159 0.2702 0.2532 3.7268 3.7926| | 24: 1.03 - 1.02 0.96 6785 133 0.2912 0.2914 3.7136 3.8102| | 25: 1.02 - 1.01 0.93 6552 130 0.3057 0.2816 3.6759 3.7118| | 26: 1.01 - 0.99 0.96 6767 158 0.3194 0.3503 3.6322 3.6696| | 27: 0.99 - 0.98 0.94 6648 131 0.3420 0.3277 3.6443 3.6097| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.66 0.91 0.97 35942.71| | 2: 2.94 - 2.33 7339 128 0.86 21.19 1.09 1.02 15063.64| | 3: 2.33 - 2.04 6939 150 0.93 12.03 1.11 1.06 3929.14| | 4: 2.04 - 1.85 7170 155 0.92 13.49 1.11 1.06 2730.95| | 5: 1.85 - 1.72 7113 159 0.91 15.74 1.11 1.06 2090.27| | 6: 1.72 - 1.62 7102 142 0.89 17.49 1.11 1.05 1731.40| | 7: 1.62 - 1.54 7104 148 0.89 18.25 1.11 1.06 1425.90| | 8: 1.54 - 1.47 6798 152 0.88 18.74 1.10 1.06 1185.76| | 9: 1.47 - 1.41 6938 155 0.88 18.64 1.11 1.07 962.74| | 10: 1.41 - 1.36 7022 150 0.87 19.79 1.10 1.04 820.09| | 11: 1.36 - 1.32 6997 151 0.87 20.13 1.08 1.04 734.04| | 12: 1.32 - 1.28 6976 149 0.87 20.49 1.07 1.02 679.10| | 13: 1.28 - 1.25 6907 166 0.87 20.73 1.07 1.04 647.04| | 14: 1.25 - 1.22 7015 113 0.86 21.32 1.08 1.03 601.69| | 15: 1.22 - 1.19 6957 137 0.86 21.02 1.08 1.04 555.62| | 16: 1.19 - 1.17 6604 132 0.87 20.42 1.08 1.02 486.16| | 17: 1.17 - 1.14 6941 135 0.87 20.84 1.09 1.02 437.85| | 18: 1.14 - 1.12 6875 142 0.86 21.07 1.08 1.00 399.80| | 19: 1.12 - 1.10 6949 106 0.85 22.67 1.08 1.01 398.33| | 20: 1.10 - 1.08 6884 147 0.84 23.23 1.07 0.99 363.45| | 21: 1.08 - 1.07 6852 152 0.83 24.54 1.06 0.98 349.20| | 22: 1.07 - 1.05 6838 135 0.82 25.37 1.05 0.97 324.17| | 23: 1.05 - 1.03 6829 159 0.80 27.19 1.05 0.98 329.09| | 24: 1.03 - 1.02 6785 133 0.78 29.50 1.05 0.99 332.76| | 25: 1.02 - 1.01 6552 130 0.77 30.88 1.03 0.94 320.00| | 26: 1.01 - 0.99 6767 158 0.74 33.02 1.03 0.90 305.10| | 27: 0.99 - 0.98 6648 131 0.73 33.77 1.03 0.85 283.37| |alpha: min = 0.85 max = 1.07 mean = 1.01| |beta: min = 283.37 max = 35942.71 mean = 2847.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.85| |phase err.(test): min = 0.00 max = 89.15 mean = 21.98| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.233 2950 Z= 5.479 Angle : 5.132 15.955 4018 Z= 3.603 Chirality : 0.428 1.236 492 Planarity : 0.032 0.137 512 Dihedral : 12.999 83.768 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.11 % Favored : 96.63 % Rotamer: Outliers : 0.65 % Allowed : 3.87 % Favored : 95.48 % Cbeta Deviations : 37.08 % 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: -2.67 (0.38), residues: 386 helix: -2.85 (0.29), residues: 148 sheet: -1.19 (0.51), residues: 86 loop : -0.59 (0.52), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.021 ARG A 97 TYR 0.145 0.041 TYR A 192 PHE 0.097 0.032 PHE B 95 TRP 0.113 0.037 TRP A 146 HIS 0.081 0.031 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2039 r_free= 0.2013 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302528 | | target function (ml) not normalized (work): 805919.335768 | | target function (ml) not normalized (free): 16573.238581 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2037 0.2039 0.2013 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2037 0.2039 0.2013 n_refl.: 191155 remove outliers: r(all,work,free)=0.2038 0.2039 0.2013 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2037 0.2038 0.2013 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1809 0.1806 0.1946 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1805 0.1946 n_refl.: 191141 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4230 400.535 296.948 0.436 0.911 0.299 13.296-10.522 100.00 100 1 0.2494 534.497 521.070 0.787 0.912 0.248 10.503-8.327 99.45 178 3 0.2509 565.118 555.710 0.973 0.912 0.223 8.318-6.595 100.00 360 8 0.2528 414.736 401.962 0.968 0.912 0.170 6.588-5.215 100.00 711 7 0.2261 381.101 366.366 0.960 0.912 0.160 5.214-4.128 98.38 1367 28 0.1467 557.435 550.564 1.077 0.912 0.080 4.126-3.266 94.74 2603 46 0.1343 508.132 499.446 1.148 0.913 0.040 3.266-2.585 99.86 5447 97 0.1442 342.774 337.573 1.122 0.912 0.019 2.585-2.046 97.45 10613 204 0.1412 258.603 254.293 1.128 0.911 0.000 2.046-1.619 99.39 21536 464 0.1629 153.054 149.693 1.144 0.910 0.000 1.619-1.281 98.00 42464 925 0.1922 82.395 80.178 1.131 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2327 44.203 41.694 1.115 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0073 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1805 r_free=0.1946 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1805 r_free=0.1946 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.506913 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.378695 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1270 0.1477 0.0207 0.035 1.2 12.1 0.0 0.6 0 11.253 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 14.77 2.07 1.117 13.108 571.379 0.019 13.01 15.48 2.47 1.276 13.361 571.379 0.018 Individual atomic B min max mean iso aniso Overall: 5.20 73.04 15.05 1.41 435 3274 Protein: 5.20 40.57 11.03 1.41 0 2902 Water: 6.39 73.04 29.55 N/A 435 370 Other: 15.91 30.89 23.40 N/A 0 2 Chain A: 5.36 59.93 13.10 N/A 0 1626 Chain B: 5.20 73.04 12.82 N/A 0 1648 Chain S: 11.35 65.89 30.85 N/A 435 0 Histogram: Values Number of atoms 5.20 - 11.98 2169 11.98 - 18.76 629 18.76 - 25.55 316 25.55 - 32.33 256 32.33 - 39.12 165 39.12 - 45.90 104 45.90 - 52.69 48 52.69 - 59.47 18 59.47 - 66.26 3 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1302 r_free=0.1549 r_work=0.1300 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1300 r_free = 0.1544 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1285 r_free = 0.1531 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.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1285 r_free= 0.1531 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015875 | | target function (ls_wunit_k1) not normalized (work): 2973.347492 | | target function (ls_wunit_k1) not normalized (free): 112.882903 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1285 0.1531 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1477 0.1475 0.1607 n_refl.: 191141 remove outliers: r(all,work,free)=0.1477 0.1475 0.1607 n_refl.: 191141 overall B=0.16 to atoms: r(all,work,free)=0.1501 0.1499 0.1618 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1282 0.1278 0.1523 n_refl.: 191141 remove outliers: r(all,work,free)=0.1282 0.1277 0.1522 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3675 402.814 361.286 0.449 1.001 0.287 13.296-10.522 100.00 100 1 0.2124 534.497 525.357 0.712 1.003 0.243 10.503-8.327 99.45 178 3 0.1786 565.118 565.560 0.858 1.003 0.220 8.318-6.595 100.00 360 8 0.1762 414.736 410.936 0.872 1.003 0.155 6.588-5.215 100.00 711 7 0.1577 381.101 373.829 0.855 1.003 0.150 5.214-4.128 98.38 1367 28 0.0933 557.435 554.115 0.939 1.003 0.070 4.126-3.266 94.74 2603 46 0.0857 508.132 504.102 1.005 1.004 0.029 3.266-2.585 99.86 5447 97 0.0927 342.774 340.495 0.988 1.003 0.020 2.585-2.046 97.45 10613 204 0.0945 258.603 256.338 0.998 1.003 0.000 2.046-1.619 99.39 21536 464 0.1079 153.054 151.399 1.015 1.003 0.000 1.619-1.281 98.00 42464 925 0.1277 82.395 81.342 1.007 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.182 0.987 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0370 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1522 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1522 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1522 | n_water=805 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1279 r_free=0.1524 | n_water=799 | time (s): 96.330 (total time: 98.750) Filter (q & B) r_work=0.1280 r_free=0.1524 | n_water=796 | time (s): 4.270 (total time: 103.020) Compute maps r_work=0.1280 r_free=0.1524 | n_water=796 | time (s): 1.980 (total time: 105.000) Filter (map) r_work=0.1303 r_free=0.1513 | n_water=666 | time (s): 4.090 (total time: 109.090) Find peaks r_work=0.1303 r_free=0.1513 | n_water=666 | time (s): 0.720 (total time: 109.810) Add new water r_work=0.1327 r_free=0.1544 | n_water=985 | time (s): 4.750 (total time: 114.560) Refine new water occ: r_work=0.1283 r_free=0.1494 adp: r_work=0.1272 r_free=0.1490 occ: r_work=0.1274 r_free=0.1484 adp: r_work=0.1268 r_free=0.1484 occ: r_work=0.1269 r_free=0.1479 adp: r_work=0.1266 r_free=0.1480 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1480 r_work=0.1266 r_free=0.1480 | n_water=985 | time (s): 88.580 (total time: 203.140) Filter (q & B) r_work=0.1269 r_free=0.1486 | n_water=909 | time (s): 5.260 (total time: 208.400) Filter (dist only) r_work=0.1270 r_free=0.1486 | n_water=908 | time (s): 117.970 (total time: 326.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.752951 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 594.490745 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1254 0.1506 0.0251 0.038 1.1 19.7 0.0 0.3 0 11.876 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.06 2.51 2.055 15.344 594.491 0.014 12.30 14.91 2.61 2.417 15.363 594.491 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 68.20 16.52 1.21 540 3272 Protein: 5.42 40.54 11.02 1.21 0 2902 Water: 6.61 68.20 34.07 N/A 540 368 Other: 16.26 32.40 24.33 N/A 0 2 Chain A: 5.58 56.02 13.05 N/A 0 1624 Chain B: 5.42 68.20 12.85 N/A 0 1648 Chain S: 13.43 63.98 38.16 N/A 540 0 Histogram: Values Number of atoms 5.42 - 11.69 2043 11.69 - 17.97 719 17.97 - 24.25 283 24.25 - 30.53 210 30.53 - 36.81 170 36.81 - 43.09 160 43.09 - 49.37 111 49.37 - 55.65 59 55.65 - 61.92 49 61.92 - 68.20 8 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1492 r_work=0.1231 r_free=0.1493 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1493 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1487 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1487 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013369 | | target function (ls_wunit_k1) not normalized (work): 2503.932754 | | target function (ls_wunit_k1) not normalized (free): 98.664969 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1224 0.1487 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1437 0.1435 0.1588 n_refl.: 191139 remove outliers: r(all,work,free)=0.1437 0.1435 0.1588 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1431 0.1586 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1231 0.1494 n_refl.: 191139 remove outliers: r(all,work,free)=0.1236 0.1231 0.1494 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3197 402.814 380.513 0.489 0.962 0.271 13.296-10.522 100.00 100 1 0.1908 534.497 528.050 0.769 0.963 0.250 10.503-8.327 99.45 178 3 0.1426 565.118 567.025 0.925 0.963 0.184 8.318-6.595 100.00 360 8 0.1520 414.736 413.221 0.936 0.963 0.160 6.588-5.215 100.00 711 7 0.1337 381.101 376.794 0.913 0.963 0.140 5.214-4.128 98.38 1367 28 0.0835 557.435 556.036 0.994 0.963 0.090 4.126-3.266 94.74 2603 46 0.0757 508.132 505.403 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0860 342.774 341.288 1.047 0.962 0.010 2.585-2.046 97.45 10613 204 0.0888 258.603 256.801 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1038 153.054 151.644 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.356 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.217 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0520 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1493 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1493 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1493 | n_water=908 | time (s): 3.870 (total time: 3.870) Filter (dist) r_work=0.1232 r_free=0.1494 | n_water=907 | time (s): 116.980 (total time: 120.850) Filter (q & B) r_work=0.1232 r_free=0.1493 | n_water=905 | time (s): 5.570 (total time: 126.420) Compute maps r_work=0.1232 r_free=0.1493 | n_water=905 | time (s): 2.250 (total time: 128.670) Filter (map) r_work=0.1270 r_free=0.1498 | n_water=713 | time (s): 5.680 (total time: 134.350) Find peaks r_work=0.1270 r_free=0.1498 | n_water=713 | time (s): 0.770 (total time: 135.120) Add new water r_work=0.1294 r_free=0.1532 | n_water=1040 | time (s): 4.430 (total time: 139.550) Refine new water occ: r_work=0.1249 r_free=0.1491 adp: r_work=0.1249 r_free=0.1492 occ: r_work=0.1245 r_free=0.1488 adp: r_work=0.1244 r_free=0.1490 occ: r_work=0.1241 r_free=0.1487 adp: r_work=0.1240 r_free=0.1488 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1488 r_work=0.1240 r_free=0.1488 | n_water=1040 | time (s): 193.360 (total time: 332.910) Filter (q & B) r_work=0.1245 r_free=0.1497 | n_water=900 | time (s): 5.100 (total time: 338.010) Filter (dist only) r_work=0.1245 r_free=0.1497 | n_water=899 | time (s): 126.640 (total time: 464.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.701366 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.278022 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 0.1236 0.1428 0.0192 0.034 1.1 9.2 0.0 0.0 0 0.851 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.28 1.92 1.944 14.737 17.278 3.940 12.29 13.87 1.58 2.260 14.634 17.278 3.894 Individual atomic B min max mean iso aniso Overall: 5.54 67.78 15.47 1.08 531 3272 Protein: 5.54 36.80 10.77 1.08 0 2902 Water: 6.71 67.78 30.62 N/A 531 368 Other: 13.91 27.82 20.87 N/A 0 2 Chain A: 5.56 55.01 12.80 N/A 0 1624 Chain B: 5.54 67.78 12.58 N/A 0 1648 Chain S: 13.41 62.39 32.60 N/A 531 0 Histogram: Values Number of atoms 5.54 - 11.76 2128 11.76 - 17.98 682 17.98 - 24.21 300 24.21 - 30.43 237 30.43 - 36.66 188 36.66 - 42.88 148 42.88 - 49.11 83 49.11 - 55.33 25 55.33 - 61.55 10 61.55 - 67.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1388 r_work=0.1229 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1389 target_work(ml) = 3.895 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1386 target_work(ml) = 3.889 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1386 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889404 | | target function (ml) not normalized (work): 728477.609937 | | target function (ml) not normalized (free): 15222.940108 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1227 0.1224 0.1386 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1438 0.1437 0.1501 n_refl.: 191139 remove outliers: r(all,work,free)=0.1438 0.1437 0.1501 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1432 0.1431 0.1497 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1223 0.1220 0.1380 n_refl.: 191139 remove outliers: r(all,work,free)=0.1222 0.1219 0.1380 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 0.3753 398.008 362.651 0.430 0.947 0.256 13.296-10.522 98.02 98 1 0.2291 528.900 509.263 0.718 0.948 0.219 10.503-8.327 98.35 176 3 0.1985 555.265 556.868 0.892 0.948 0.174 8.318-6.595 100.00 360 8 0.2037 414.736 410.613 0.895 0.948 0.130 6.588-5.215 100.00 711 7 0.1802 381.101 371.444 0.887 0.948 0.120 5.214-4.128 98.38 1367 28 0.1151 557.435 552.495 0.970 0.948 0.059 4.126-3.266 94.74 2603 46 0.1085 508.132 501.241 1.031 0.948 0.014 3.266-2.585 99.86 5447 97 0.1084 342.774 339.124 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0960 258.603 255.757 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0966 153.054 151.422 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.481 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.311 1.038 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1063 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1219 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1219 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1219 r_free=0.1380 | n_water=899 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1220 r_free=0.1384 | n_water=897 | time (s): 112.850 (total time: 116.090) Filter (q & B) r_work=0.1221 r_free=0.1384 | n_water=889 | time (s): 4.110 (total time: 120.200) Compute maps r_work=0.1221 r_free=0.1384 | n_water=889 | time (s): 1.760 (total time: 121.960) Filter (map) r_work=0.1243 r_free=0.1380 | n_water=753 | time (s): 4.220 (total time: 126.180) Find peaks r_work=0.1243 r_free=0.1380 | n_water=753 | time (s): 0.620 (total time: 126.800) Add new water r_work=0.1257 r_free=0.1392 | n_water=996 | time (s): 4.790 (total time: 131.590) Refine new water occ: r_work=0.1211 r_free=0.1359 adp: r_work=0.1203 r_free=0.1356 occ: r_work=0.1201 r_free=0.1356 adp: r_work=0.1200 r_free=0.1356 occ: r_work=0.1199 r_free=0.1356 adp: r_work=0.1198 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1356 r_work=0.1198 r_free=0.1356 | n_water=996 | time (s): 296.850 (total time: 428.440) Filter (q & B) r_work=0.1204 r_free=0.1366 | n_water=889 | time (s): 5.040 (total time: 433.480) Filter (dist only) r_work=0.1205 r_free=0.1366 | n_water=888 | time (s): 112.780 (total time: 546.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.557736 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.926847 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1367 0.0164 0.034 1.1 6.1 0.0 0.0 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.67 1.64 1.845 14.336 15.927 3.873 11.97 13.64 1.67 1.952 14.297 15.927 3.866 Individual atomic B min max mean iso aniso Overall: 5.50 67.33 15.17 1.01 520 3272 Protein: 5.50 33.63 10.69 1.01 0 2902 Water: 5.92 67.33 29.79 N/A 520 368 Other: 14.01 27.07 20.54 N/A 0 2 Chain A: 5.54 53.93 12.66 N/A 0 1624 Chain B: 5.50 67.33 12.49 N/A 0 1648 Chain S: 5.92 62.34 31.50 N/A 520 0 Histogram: Values Number of atoms 5.50 - 11.68 2109 11.68 - 17.86 726 17.86 - 24.05 302 24.05 - 30.23 233 30.23 - 36.41 180 36.41 - 42.60 138 42.60 - 48.78 72 48.78 - 54.96 24 54.96 - 61.15 6 61.15 - 67.33 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1364 r_work=0.1197 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1365 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1362 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863887 | | target function (ml) not normalized (work): 723678.943823 | | target function (ml) not normalized (free): 15136.576063 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1362 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1419 0.1418 0.1477 n_refl.: 191134 remove outliers: r(all,work,free)=0.1419 0.1418 0.1477 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1412 0.1411 0.1472 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1362 n_refl.: 191134 remove outliers: r(all,work,free)=0.1197 0.1194 0.1362 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3786 360.518 326.877 0.415 0.946 0.244 13.296-10.522 97.03 97 1 0.2380 481.355 455.545 0.711 0.947 0.208 10.503-8.327 98.35 176 3 0.2088 502.962 495.763 0.875 0.948 0.156 8.318-6.595 100.00 360 8 0.2136 375.671 370.117 0.891 0.947 0.105 6.588-5.215 100.00 711 7 0.1867 345.204 336.041 0.885 0.947 0.090 5.214-4.128 98.38 1367 28 0.1171 504.928 500.210 0.973 0.948 0.080 4.126-3.266 94.74 2603 46 0.1103 460.269 453.899 1.033 0.948 0.009 3.266-2.585 99.86 5447 97 0.1083 310.486 307.268 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0937 234.244 231.820 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0912 138.637 137.342 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0990 74.634 73.913 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1664 40.038 38.368 1.039 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1219 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1362 | n_water=888 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1194 r_free=0.1362 | n_water=888 | time (s): 107.540 (total time: 110.670) Filter (q & B) r_work=0.1194 r_free=0.1362 | n_water=883 | time (s): 4.500 (total time: 115.170) Compute maps r_work=0.1194 r_free=0.1362 | n_water=883 | time (s): 1.920 (total time: 117.090) Filter (map) r_work=0.1216 r_free=0.1366 | n_water=762 | time (s): 4.670 (total time: 121.760) Find peaks r_work=0.1216 r_free=0.1366 | n_water=762 | time (s): 0.560 (total time: 122.320) Add new water r_work=0.1228 r_free=0.1377 | n_water=996 | time (s): 4.230 (total time: 126.550) Refine new water occ: r_work=0.1191 r_free=0.1351 adp: r_work=0.1191 r_free=0.1351 occ: r_work=0.1188 r_free=0.1351 adp: r_work=0.1188 r_free=0.1351 occ: r_work=0.1186 r_free=0.1351 adp: r_work=0.1185 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1350 r_work=0.1185 r_free=0.1350 | n_water=996 | time (s): 267.340 (total time: 393.890) Filter (q & B) r_work=0.1191 r_free=0.1356 | n_water=910 | time (s): 4.400 (total time: 398.290) Filter (dist only) r_work=0.1191 r_free=0.1355 | n_water=909 | time (s): 117.130 (total time: 515.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.539509 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.772383 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 0.1366 0.0172 0.036 1.1 6.3 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.66 1.72 1.802 14.282 15.772 3.765 12.00 13.68 1.68 1.903 14.238 15.772 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 66.87 15.15 0.96 542 3271 Protein: 5.58 31.83 10.60 0.96 0 2902 Water: 6.16 66.87 29.68 N/A 542 367 Other: 13.79 25.40 19.60 N/A 0 2 Chain A: 5.58 52.78 12.52 N/A 0 1623 Chain B: 5.58 66.87 12.37 N/A 0 1648 Chain S: 6.16 62.27 31.48 N/A 542 0 Histogram: Values Number of atoms 5.58 - 11.71 2134 11.71 - 17.84 724 17.84 - 23.97 293 23.97 - 30.10 232 30.10 - 36.23 174 36.23 - 42.36 148 42.36 - 48.49 78 48.49 - 54.61 22 54.61 - 60.74 6 60.74 - 66.87 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1368 r_work=0.1200 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1369 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1371 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1371 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760835 | | target function (ml) not normalized (work): 704374.283197 | | target function (ml) not normalized (free): 14754.829162 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1371 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1417 0.1417 0.1479 n_refl.: 191133 remove outliers: r(all,work,free)=0.1417 0.1417 0.1479 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1409 0.1408 0.1474 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1197 0.1370 n_refl.: 191133 remove outliers: r(all,work,free)=0.1200 0.1197 0.1370 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 0.3638 360.208 314.179 0.407 0.947 0.243 13.296-10.522 97.03 97 1 0.2343 481.355 459.925 0.706 0.948 0.184 10.503-8.327 98.35 176 3 0.2132 502.962 495.115 0.874 0.948 0.156 8.318-6.595 100.00 360 8 0.2113 375.671 370.105 0.891 0.948 0.111 6.588-5.215 100.00 711 7 0.1896 345.204 335.447 0.887 0.948 0.093 5.214-4.128 98.38 1367 28 0.1198 504.928 500.170 0.975 0.949 0.080 4.126-3.266 94.74 2603 46 0.1125 460.269 453.691 1.034 0.949 0.020 3.266-2.585 99.86 5447 97 0.1111 310.486 307.190 1.020 0.949 0.010 2.585-2.046 97.45 10613 204 0.0949 234.244 231.768 1.033 0.949 0.000 2.046-1.619 99.39 21536 464 0.0914 138.637 137.357 1.056 0.949 0.000 1.619-1.281 98.00 42464 925 0.0980 74.634 73.927 1.052 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.038 38.368 1.037 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1391 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1370 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1370 | n_water=909 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1197 r_free=0.1370 | n_water=908 | time (s): 113.640 (total time: 116.580) Filter (q & B) r_work=0.1197 r_free=0.1369 | n_water=898 | time (s): 4.980 (total time: 121.560) Compute maps r_work=0.1197 r_free=0.1369 | n_water=898 | time (s): 1.600 (total time: 123.160) Filter (map) r_work=0.1219 r_free=0.1365 | n_water=776 | time (s): 5.130 (total time: 128.290) Find peaks r_work=0.1219 r_free=0.1365 | n_water=776 | time (s): 0.610 (total time: 128.900) Add new water r_work=0.1230 r_free=0.1375 | n_water=981 | time (s): 4.530 (total time: 133.430) Refine new water occ: r_work=0.1197 r_free=0.1356 adp: r_work=0.1197 r_free=0.1356 occ: r_work=0.1195 r_free=0.1355 adp: r_work=0.1195 r_free=0.1355 occ: r_work=0.1193 r_free=0.1355 adp: r_work=0.1193 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1355 r_work=0.1193 r_free=0.1355 | n_water=981 | time (s): 299.600 (total time: 433.030) Filter (q & B) r_work=0.1196 r_free=0.1363 | n_water=917 | time (s): 4.460 (total time: 437.490) Filter (dist only) r_work=0.1197 r_free=0.1363 | n_water=915 | time (s): 118.540 (total time: 556.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.645867 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.379797 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1365 0.0166 0.036 1.1 6.0 0.0 0.3 0 0.823 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.65 1.66 1.763 14.158 15.380 3.760 11.99 13.68 1.69 1.883 14.116 15.380 3.757 Individual atomic B min max mean iso aniso Overall: 5.59 65.83 15.05 0.91 548 3271 Protein: 5.59 29.42 10.50 0.91 0 2902 Water: 5.99 65.83 29.47 N/A 548 367 Other: 13.86 23.07 18.47 N/A 0 2 Chain A: 5.62 51.05 12.38 N/A 0 1623 Chain B: 5.59 65.83 12.25 N/A 0 1648 Chain S: 5.99 62.17 31.37 N/A 548 0 Histogram: Values Number of atoms 5.59 - 11.61 2113 11.61 - 17.63 767 17.63 - 23.66 285 23.66 - 29.68 223 29.68 - 35.71 167 35.71 - 41.73 146 41.73 - 47.75 77 47.75 - 53.78 31 53.78 - 59.80 7 59.80 - 65.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1368 r_work=0.1200 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1368 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1370 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756744 | | target function (ml) not normalized (work): 703604.322213 | | target function (ml) not normalized (free): 14739.590909 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1370 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1481 n_refl.: 191132 remove outliers: r(all,work,free)=0.1409 0.1408 0.1481 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1401 0.1400 0.1476 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1367 n_refl.: 191132 remove outliers: r(all,work,free)=0.1199 0.1195 0.1367 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 92.08 90 3 0.3536 361.018 327.478 0.419 0.949 0.231 13.296-10.522 97.03 97 1 0.2380 481.355 460.435 0.702 0.950 0.174 10.503-8.327 98.35 176 3 0.2100 502.962 496.243 0.870 0.950 0.150 8.318-6.595 100.00 360 8 0.2081 375.671 369.947 0.886 0.950 0.105 6.588-5.215 100.00 711 7 0.1908 345.204 335.790 0.885 0.950 0.095 5.214-4.128 98.38 1367 28 0.1211 504.928 499.971 0.973 0.951 0.090 4.126-3.266 94.74 2603 46 0.1143 460.269 453.335 1.033 0.951 0.024 3.266-2.585 99.86 5447 97 0.1119 310.486 307.154 1.019 0.950 0.005 2.585-2.046 97.45 10613 204 0.0955 234.244 231.721 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0909 138.637 137.338 1.054 0.950 0.000 1.619-1.281 98.00 42464 925 0.0966 74.634 73.937 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.038 38.373 1.039 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1368 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1368 | n_water=915 | time (s): 3.340 (total time: 3.340) Filter (dist) r_work=0.1195 r_free=0.1368 | n_water=914 | time (s): 119.760 (total time: 123.100) Filter (q & B) r_work=0.1196 r_free=0.1369 | n_water=907 | time (s): 4.230 (total time: 127.330) Compute maps r_work=0.1196 r_free=0.1369 | n_water=907 | time (s): 1.980 (total time: 129.310) Filter (map) r_work=0.1212 r_free=0.1363 | n_water=803 | time (s): 5.280 (total time: 134.590) Find peaks r_work=0.1212 r_free=0.1363 | n_water=803 | time (s): 0.550 (total time: 135.140) Add new water r_work=0.1223 r_free=0.1368 | n_water=999 | time (s): 4.490 (total time: 139.630) Refine new water occ: r_work=0.1193 r_free=0.1346 adp: r_work=0.1193 r_free=0.1347 occ: r_work=0.1191 r_free=0.1344 adp: r_work=0.1191 r_free=0.1345 occ: r_work=0.1189 r_free=0.1343 adp: r_work=0.1189 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1345 r_work=0.1189 r_free=0.1345 | n_water=999 | time (s): 208.900 (total time: 348.530) Filter (q & B) r_work=0.1193 r_free=0.1356 | n_water=935 | time (s): 5.010 (total time: 353.540) Filter (dist only) r_work=0.1194 r_free=0.1356 | n_water=934 | time (s): 124.830 (total time: 478.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.498633 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.584899 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 0.1360 0.0162 0.036 1.1 7.2 0.0 0.3 0 0.749 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.60 1.62 1.725 14.059 14.585 3.758 12.01 13.64 1.63 1.778 14.042 14.585 3.757 Individual atomic B min max mean iso aniso Overall: 5.60 64.70 15.02 0.89 567 3271 Protein: 5.60 28.61 10.44 0.89 0 2902 Water: 6.06 64.70 29.27 N/A 567 367 Other: 13.84 22.28 18.06 N/A 0 2 Chain A: 5.63 50.63 12.28 N/A 0 1623 Chain B: 5.60 64.70 12.17 N/A 0 1648 Chain S: 6.06 62.06 31.17 N/A 567 0 Histogram: Values Number of atoms 5.60 - 11.51 2092 11.51 - 17.42 790 17.42 - 23.33 281 23.33 - 29.24 214 29.24 - 35.15 181 35.15 - 41.06 148 41.06 - 46.97 93 46.97 - 52.88 29 52.88 - 58.79 6 58.79 - 64.70 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1364 r_work=0.1201 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1364 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1364 target_work(ml) = 3.756 | | 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= 0.1199 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756343 | | target function (ml) not normalized (work): 703525.484430 | | target function (ml) not normalized (free): 14736.142480 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1364 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1392 0.1390 0.1487 n_refl.: 191131 remove outliers: r(all,work,free)=0.1392 0.1390 0.1487 n_refl.: 191131 overall B=-0.01 to atoms: r(all,work,free)=0.1390 0.1388 0.1485 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1352 n_refl.: 191131 remove outliers: r(all,work,free)=0.1192 0.1189 0.1352 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 92.08 90 3 0.3593 361.018 332.247 0.417 0.973 0.221 13.296-10.522 97.03 97 1 0.2373 481.355 460.052 0.693 0.975 0.154 10.503-8.327 98.35 176 3 0.2137 502.962 494.804 0.868 0.975 0.123 8.318-6.595 100.00 360 8 0.2069 375.671 369.522 0.884 0.975 0.106 6.588-5.215 100.00 711 7 0.1921 345.204 335.527 0.881 0.975 0.092 5.214-4.128 98.38 1367 28 0.1217 504.928 499.640 0.968 0.976 0.049 4.126-3.266 94.74 2603 46 0.1149 460.269 452.596 1.028 0.977 0.005 3.266-2.585 99.86 5447 97 0.1127 310.486 306.713 1.013 0.978 0.000 2.585-2.046 97.45 10613 204 0.0962 234.244 231.571 1.024 0.980 0.000 2.046-1.619 99.39 21536 464 0.0907 138.637 137.240 1.042 0.983 0.000 1.619-1.281 98.00 42464 925 0.0946 74.634 73.978 1.036 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.038 38.334 1.009 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0266 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1352 | n_water=934 | time (s): 2.760 (total time: 2.760) Filter (dist) r_work=0.1189 r_free=0.1352 | n_water=933 | time (s): 111.800 (total time: 114.560) Filter (q & B) r_work=0.1189 r_free=0.1353 | n_water=922 | time (s): 4.530 (total time: 119.090) Compute maps r_work=0.1189 r_free=0.1353 | n_water=922 | time (s): 2.130 (total time: 121.220) Filter (map) r_work=0.1208 r_free=0.1352 | n_water=800 | time (s): 5.020 (total time: 126.240) Find peaks r_work=0.1208 r_free=0.1352 | n_water=800 | time (s): 0.530 (total time: 126.770) Add new water r_work=0.1217 r_free=0.1361 | n_water=1015 | time (s): 4.940 (total time: 131.710) Refine new water occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1334 occ: r_work=0.1185 r_free=0.1333 adp: r_work=0.1185 r_free=0.1333 occ: r_work=0.1183 r_free=0.1333 adp: r_work=0.1182 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1333 r_work=0.1182 r_free=0.1333 | n_water=1015 | time (s): 264.630 (total time: 396.340) Filter (q & B) r_work=0.1186 r_free=0.1346 | n_water=943 | time (s): 5.460 (total time: 401.800) Filter (dist only) r_work=0.1187 r_free=0.1345 | n_water=942 | time (s): 119.710 (total time: 521.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.541422 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.257168 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 0.1189 0.1355 0.0166 0.037 1.1 7.0 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.55 1.66 1.702 14.027 14.257 3.755 11.91 13.59 1.68 1.732 14.012 14.257 3.754 Individual atomic B min max mean iso aniso Overall: 5.63 63.60 15.01 0.87 575 3271 Protein: 5.63 28.06 10.42 0.87 0 2902 Water: 6.00 63.60 29.14 N/A 575 367 Other: 13.85 22.26 18.06 N/A 0 2 Chain A: 5.71 50.26 12.23 N/A 0 1623 Chain B: 5.63 63.60 12.13 N/A 0 1648 Chain S: 6.00 61.86 31.13 N/A 575 0 Histogram: Values Number of atoms 5.63 - 11.43 2064 11.43 - 17.22 819 17.22 - 23.02 280 23.02 - 28.82 206 28.82 - 34.61 182 34.61 - 40.41 146 40.41 - 46.21 103 46.21 - 52.00 33 52.00 - 57.80 9 57.80 - 63.60 4 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1359 r_work=0.1191 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1358 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753497 | | target function (ml) not normalized (work): 702992.536760 | | target function (ml) not normalized (free): 14738.093259 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1358 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1512 n_refl.: 191131 remove outliers: r(all,work,free)=0.1398 0.1396 0.1512 n_refl.: 191131 overall B=-0.02 to atoms: r(all,work,free)=0.1395 0.1393 0.1509 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1354 n_refl.: 191131 remove outliers: r(all,work,free)=0.1191 0.1188 0.1354 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 92.08 90 3 0.3617 361.018 331.035 0.391 0.994 0.195 13.296-10.522 97.03 97 1 0.2383 481.355 459.816 0.669 0.996 0.136 10.503-8.327 98.35 176 3 0.2114 502.962 496.257 0.850 0.996 0.113 8.318-6.595 100.00 360 8 0.2068 375.671 369.449 0.864 0.996 0.100 6.588-5.215 100.00 711 7 0.1925 345.204 335.290 0.862 0.997 0.090 5.214-4.128 98.38 1367 28 0.1224 504.928 499.671 0.948 0.997 0.039 4.126-3.266 94.74 2603 46 0.1151 460.269 452.745 1.007 0.999 0.000 3.266-2.585 99.86 5447 97 0.1130 310.486 306.776 0.993 1.000 0.000 2.585-2.046 97.45 10613 204 0.0962 234.244 231.554 1.003 1.002 0.000 2.046-1.619 99.39 21536 464 0.0907 138.637 137.253 1.021 1.006 0.000 1.619-1.281 98.00 42464 925 0.0942 74.634 73.986 1.015 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.038 38.324 0.990 1.022 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0509 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1354 | n_water=942 | time (s): 3.300 (total time: 3.300) Filter (dist) r_work=0.1188 r_free=0.1354 | n_water=942 | time (s): 114.160 (total time: 117.460) Filter (q & B) r_work=0.1189 r_free=0.1354 | n_water=933 | time (s): 4.640 (total time: 122.100) Compute maps r_work=0.1189 r_free=0.1354 | n_water=933 | time (s): 2.130 (total time: 124.230) Filter (map) r_work=0.1209 r_free=0.1349 | n_water=809 | time (s): 5.440 (total time: 129.670) Find peaks r_work=0.1209 r_free=0.1349 | n_water=809 | time (s): 0.680 (total time: 130.350) Add new water r_work=0.1217 r_free=0.1355 | n_water=1018 | time (s): 4.700 (total time: 135.050) Refine new water occ: r_work=0.1187 r_free=0.1329 adp: r_work=0.1188 r_free=0.1330 occ: r_work=0.1185 r_free=0.1329 adp: r_work=0.1185 r_free=0.1330 occ: r_work=0.1183 r_free=0.1329 adp: r_work=0.1183 r_free=0.1330 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1330 r_work=0.1183 r_free=0.1330 | n_water=1018 | time (s): 294.280 (total time: 429.330) Filter (q & B) r_work=0.1186 r_free=0.1343 | n_water=947 | time (s): 5.140 (total time: 434.470) Filter (dist only) r_work=0.1187 r_free=0.1343 | n_water=945 | time (s): 124.370 (total time: 558.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.477202 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.186336 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 0.1191 0.1347 0.0156 0.037 1.1 7.3 0.0 0.3 0 0.739 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.47 1.56 1.691 13.987 14.186 3.754 11.90 13.49 1.59 1.691 13.985 14.186 3.753 Individual atomic B min max mean iso aniso Overall: 5.61 63.05 14.99 0.86 578 3271 Protein: 5.61 28.04 10.42 0.86 0 2902 Water: 6.02 63.05 29.01 N/A 578 367 Other: 13.88 22.24 18.06 N/A 0 2 Chain A: 5.69 50.11 12.20 N/A 0 1623 Chain B: 5.61 63.05 12.11 N/A 0 1648 Chain S: 6.02 61.76 31.05 N/A 578 0 Histogram: Values Number of atoms 5.61 - 11.35 2050 11.35 - 17.09 828 17.09 - 22.84 283 22.84 - 28.58 207 28.58 - 34.33 181 34.33 - 40.07 146 40.07 - 45.82 104 45.82 - 51.56 36 51.56 - 57.31 9 57.31 - 63.05 5 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1350 r_work=0.1190 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1349 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752766 | | target function (ml) not normalized (work): 702855.450568 | | target function (ml) not normalized (free): 14731.839605 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1349 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1519 n_refl.: 191131 remove outliers: r(all,work,free)=0.1401 0.1399 0.1519 n_refl.: 191131 overall B=-0.02 to atoms: r(all,work,free)=0.1396 0.1394 0.1515 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1349 n_refl.: 191131 remove outliers: r(all,work,free)=0.1191 0.1188 0.1349 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 92.08 90 3 0.3632 361.018 330.295 0.400 0.974 0.201 13.296-10.522 97.03 97 1 0.2406 481.355 459.554 0.681 0.976 0.134 10.503-8.327 98.35 176 3 0.2151 502.962 496.220 0.866 0.976 0.103 8.318-6.595 100.00 360 8 0.2052 375.671 370.105 0.879 0.976 0.088 6.588-5.215 100.00 711 7 0.1907 345.204 335.393 0.878 0.977 0.077 5.214-4.128 98.38 1367 28 0.1219 504.928 499.299 0.967 0.978 0.039 4.126-3.266 94.74 2603 46 0.1156 460.269 452.658 1.028 0.979 0.005 3.266-2.585 99.86 5447 97 0.1129 310.486 306.860 1.013 0.980 0.000 2.585-2.046 97.45 10613 204 0.0963 234.244 231.574 1.023 0.983 0.000 2.046-1.619 99.39 21536 464 0.0907 138.637 137.246 1.042 0.987 0.000 1.619-1.281 98.00 42464 925 0.0941 74.634 73.984 1.036 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.038 38.315 1.010 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0631 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1188 r_free=0.1349 After: r_work=0.1188 r_free=0.1349 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1349 | n_water=945 | time (s): 3.040 (total time: 3.040) Filter (dist) r_work=0.1188 r_free=0.1351 | n_water=944 | time (s): 121.930 (total time: 124.970) Filter (q & B) r_work=0.1189 r_free=0.1351 | n_water=933 | time (s): 6.100 (total time: 131.070) Compute maps r_work=0.1189 r_free=0.1351 | n_water=933 | time (s): 1.950 (total time: 133.020) Filter (map) r_work=0.1208 r_free=0.1350 | n_water=818 | time (s): 4.530 (total time: 137.550) Find peaks r_work=0.1208 r_free=0.1350 | n_water=818 | time (s): 0.750 (total time: 138.300) Add new water r_work=0.1215 r_free=0.1358 | n_water=1027 | time (s): 5.210 (total time: 143.510) Refine new water occ: r_work=0.1187 r_free=0.1336 adp: r_work=0.1187 r_free=0.1336 occ: r_work=0.1185 r_free=0.1335 adp: r_work=0.1185 r_free=0.1336 occ: r_work=0.1183 r_free=0.1335 adp: r_work=0.1183 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1336 r_work=0.1183 r_free=0.1336 | n_water=1027 | time (s): 326.420 (total time: 469.930) Filter (q & B) r_work=0.1187 r_free=0.1347 | n_water=948 | time (s): 5.640 (total time: 475.570) Filter (dist only) r_work=0.1188 r_free=0.1349 | n_water=945 | time (s): 125.730 (total time: 601.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.564189 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.575145 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 0.1189 0.1352 0.0163 0.037 1.2 9.7 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.52 1.63 1.688 13.954 14.575 3.754 11.89 13.53 1.64 1.689 13.951 14.575 3.752 Individual atomic B min max mean iso aniso Overall: 5.65 61.85 14.94 0.86 578 3271 Protein: 5.65 28.05 10.42 0.86 0 2902 Water: 6.06 61.85 28.82 N/A 578 367 Other: 13.89 22.24 18.07 N/A 0 2 Chain A: 5.71 49.84 12.17 N/A 0 1623 Chain B: 5.65 61.85 12.08 N/A 0 1648 Chain S: 6.06 61.59 30.86 N/A 578 0 Histogram: Values Number of atoms 5.65 - 11.27 2029 11.27 - 16.89 845 16.89 - 22.51 287 22.51 - 28.13 197 28.13 - 33.75 187 33.75 - 39.37 142 39.37 - 44.99 102 44.99 - 50.61 43 50.61 - 56.23 13 56.23 - 61.85 4 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1353 r_work=0.1189 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1353 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1354 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752222 | | target function (ml) not normalized (work): 702753.596162 | | target function (ml) not normalized (free): 14732.852900 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1346 0.1442 5.6771 5.76| | 2: 2.94 - 2.33 1.00 7339 128 0.1076 0.1402 5.0785 5.2002| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1176 4.6592 4.7613| | 4: 2.04 - 1.85 1.00 7170 155 0.0895 0.1027 4.3898 4.5446| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.1024 4.1489 4.2659| | 6: 1.72 - 1.62 0.99 7102 142 0.0890 0.1083 3.941 4.08| | 7: 1.62 - 1.54 0.99 7104 148 0.0879 0.0938 3.7923 3.9166| | 8: 1.54 - 1.47 0.96 6798 152 0.0887 0.1298 3.696 3.8998| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1137 3.6177 3.7602| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1194 3.5538 3.6741| | 11: 1.36 - 1.32 0.99 6997 151 0.0987 0.1111 3.4832 3.5838| | 12: 1.32 - 1.28 0.98 6975 149 0.1027 0.1121 3.4569 3.5809| | 13: 1.28 - 1.25 0.98 6907 166 0.1035 0.1242 3.4345 3.5683| | 14: 1.25 - 1.22 0.98 7015 112 0.1101 0.1588 3.4322 3.6823| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1248 3.4482 3.496| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1548 3.4642 3.656| | 17: 1.17 - 1.14 0.98 6940 135 0.1296 0.1230 3.4315 3.4451| | 18: 1.14 - 1.12 0.98 6875 142 0.1380 0.1696 3.4357 3.5274| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1760 3.4183 3.6025| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1577 3.4094 3.4371| | 21: 1.08 - 1.07 0.97 6852 152 0.1725 0.2147 3.4171 3.5054| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1956 3.4127 3.4132| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2024 3.4325 3.484| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2254 3.4351 3.511| | 25: 1.02 - 1.01 0.93 6552 130 0.2610 0.2519 3.449 3.5249| | 26: 1.01 - 0.99 0.96 6767 158 0.2753 0.2873 3.4156 3.4267| | 27: 0.99 - 0.98 0.94 6647 131 0.3039 0.2803 3.4687 3.3955| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7399 127 0.93 11.55 1.00 0.97 11092.66| | 2: 2.94 - 2.33 7339 128 0.93 12.82 0.99 0.96 5121.90| | 3: 2.33 - 2.04 6939 150 0.96 7.80 1.01 0.96 1731.85| | 4: 2.04 - 1.85 7170 155 0.96 7.70 1.00 0.97 1012.93| | 5: 1.85 - 1.72 7113 159 0.96 8.13 1.00 0.97 638.75| | 6: 1.72 - 1.62 7102 142 0.96 8.03 1.00 0.97 443.19| | 7: 1.62 - 1.54 7104 148 0.96 8.08 1.01 0.98 334.13| | 8: 1.54 - 1.47 6798 152 0.96 8.22 1.01 0.98 277.50| | 9: 1.47 - 1.41 6938 155 0.96 8.47 1.00 0.99 231.13| | 10: 1.41 - 1.36 7022 150 0.96 8.93 1.00 0.98 203.05| | 11: 1.36 - 1.32 6997 151 0.96 8.92 0.99 0.97 175.00| | 12: 1.32 - 1.28 6975 149 0.96 8.96 0.98 0.96 160.46| | 13: 1.28 - 1.25 6907 166 0.96 9.53 1.01 0.97 158.63| | 14: 1.25 - 1.22 7015 112 0.95 10.74 1.01 0.98 164.11| | 15: 1.22 - 1.19 6956 137 0.95 11.30 1.01 0.99 167.82| | 16: 1.19 - 1.17 6604 132 0.95 11.46 1.01 0.97 160.99| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.97 154.11| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.96 147.68| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.96 151.39| | 20: 1.10 - 1.08 6884 147 0.92 15.24 1.00 0.95 150.67| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.94 153.59| | 22: 1.07 - 1.05 6836 135 0.89 18.29 1.00 0.94 154.81| | 23: 1.05 - 1.03 6827 159 0.87 20.50 1.00 0.93 164.60| | 24: 1.03 - 1.02 6784 133 0.85 23.19 1.00 0.94 179.38| | 25: 1.02 - 1.01 6552 130 0.83 25.22 0.98 0.91 182.89| | 26: 1.01 - 0.99 6767 158 0.81 26.69 0.98 0.90 177.44| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.99 0.89 161.30| |alpha: min = 0.89 max = 0.99 mean = 0.96| |beta: min = 147.68 max = 11092.66 mean = 922.86| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.93 mean = 13.31| |phase err.(test): min = 0.00 max = 89.08 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1354 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1406 0.1403 0.1527 n_refl.: 191131 remove outliers: r(all,work,free)=0.1406 0.1403 0.1527 n_refl.: 191131 overall B=-0.13 to atoms: r(all,work,free)=0.1384 0.1382 0.1510 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1354 n_refl.: 191131 remove outliers: r(all,work,free)=0.1190 0.1187 0.1354 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 92.08 90 3 0.3622 361.018 330.060 0.419 0.919 0.206 13.296-10.522 97.03 97 1 0.2445 481.355 458.337 0.710 0.920 0.134 10.503-8.327 98.35 176 3 0.2137 502.962 496.743 0.902 0.921 0.093 8.318-6.595 100.00 360 8 0.2053 375.671 370.487 0.918 0.921 0.075 6.588-5.215 100.00 711 7 0.1904 345.204 335.905 0.917 0.921 0.070 5.214-4.128 98.38 1367 28 0.1229 504.928 499.148 1.010 0.922 0.034 4.126-3.266 94.74 2603 46 0.1160 460.269 452.497 1.075 0.923 0.005 3.266-2.585 99.86 5447 97 0.1125 310.486 306.945 1.057 0.925 0.000 2.585-2.046 97.45 10613 204 0.0964 234.244 231.566 1.065 0.927 0.000 2.046-1.619 99.39 21536 464 0.0906 138.637 137.259 1.081 0.932 0.000 1.619-1.281 98.00 42464 925 0.0940 74.634 73.989 1.069 0.938 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.038 38.316 1.034 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0283 ================= 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 : 0.2039 0.2013 0.081 5.132 5.2 78.0 14.6 805 0.000 1_bss: 0.1805 0.1946 0.081 5.132 5.2 78.0 14.6 805 0.000 1_settarget: 0.1805 0.1946 0.081 5.132 5.2 78.0 14.6 805 0.000 1_nqh: 0.1805 0.1946 0.081 5.132 5.2 78.0 14.6 805 0.000 1_weight: 0.1805 0.1946 0.081 5.132 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1477 0.035 1.168 5.2 78.0 14.6 805 0.140 1_adp: 0.1302 0.1549 0.035 1.168 5.2 73.0 15.1 805 0.140 1_regHadp: 0.1300 0.1544 0.035 1.168 5.2 73.0 15.1 805 0.140 1_occ: 0.1285 0.1531 0.035 1.168 5.2 73.0 15.1 805 0.140 2_bss: 0.1277 0.1522 0.035 1.168 5.4 73.2 15.2 805 0.140 2_settarget: 0.1277 0.1522 0.035 1.168 5.4 73.2 15.2 805 0.140 2_updatecdl: 0.1277 0.1522 0.035 1.177 5.4 73.2 15.2 805 0.140 2_nqh: 0.1277 0.1522 0.035 1.177 5.4 73.2 15.2 805 0.140 2_sol: 0.1270 0.1486 0.035 1.177 5.4 73.2 16.5 908 n/a 2_weight: 0.1270 0.1486 0.035 1.177 5.4 73.2 16.5 908 n/a 2_xyzrec: 0.1254 0.1506 0.038 1.139 5.4 73.2 16.5 908 n/a 2_adp: 0.1231 0.1492 0.038 1.139 5.4 68.2 16.5 908 n/a 2_regHadp: 0.1231 0.1493 0.038 1.139 5.4 68.2 16.5 908 n/a 2_occ: 0.1224 0.1487 0.038 1.139 5.4 68.2 16.5 908 n/a 3_bss: 0.1231 0.1493 0.038 1.139 5.4 68.2 16.5 908 n/a 3_settarget: 0.1231 0.1493 0.038 1.139 5.4 68.2 16.5 908 n/a 3_updatecdl: 0.1231 0.1493 0.038 1.145 5.4 68.2 16.5 908 n/a 3_nqh: 0.1231 0.1493 0.038 1.145 5.4 68.2 16.5 908 n/a 3_sol: 0.1245 0.1497 0.038 1.145 5.4 68.2 15.7 899 n/a 3_weight: 0.1245 0.1497 0.038 1.145 5.4 68.2 15.7 899 n/a 3_xyzrec: 0.1236 0.1428 0.034 1.103 5.4 68.2 15.7 899 n/a 3_adp: 0.1229 0.1388 0.034 1.103 5.5 67.8 15.5 899 n/a 3_regHadp: 0.1229 0.1389 0.034 1.103 5.5 67.8 15.5 899 n/a 3_occ: 0.1224 0.1386 0.034 1.103 5.5 67.8 15.5 899 n/a 4_bss: 0.1219 0.1380 0.034 1.103 5.5 67.7 15.4 899 n/a 4_settarget: 0.1219 0.1380 0.034 1.103 5.5 67.7 15.4 899 n/a 4_updatecdl: 0.1219 0.1380 0.034 1.104 5.5 67.7 15.4 899 n/a 4_nqh: 0.1219 0.1380 0.034 1.104 5.5 67.7 15.4 899 n/a 4_sol: 0.1205 0.1366 0.034 1.104 5.5 67.7 15.2 888 n/a 4_weight: 0.1205 0.1366 0.034 1.104 5.5 67.7 15.2 888 n/a 4_xyzrec: 0.1203 0.1367 0.034 1.127 5.5 67.7 15.2 888 n/a 4_adp: 0.1197 0.1364 0.034 1.127 5.5 67.3 15.2 888 n/a 4_regHadp: 0.1197 0.1365 0.034 1.127 5.5 67.3 15.2 888 n/a 4_occ: 0.1195 0.1362 0.034 1.127 5.5 67.3 15.2 888 n/a 5_bss: 0.1194 0.1362 0.034 1.127 5.5 67.3 15.1 888 n/a 5_settarget: 0.1194 0.1362 0.034 1.127 5.5 67.3 15.1 888 n/a 5_updatecdl: 0.1194 0.1362 0.034 1.127 5.5 67.3 15.1 888 n/a 5_nqh: 0.1194 0.1362 0.034 1.127 5.5 67.3 15.1 888 n/a 5_sol: 0.1191 0.1355 0.034 1.127 5.5 67.3 15.2 909 n/a 5_weight: 0.1191 0.1355 0.034 1.127 5.5 67.3 15.2 909 n/a 5_xyzrec: 0.1194 0.1366 0.036 1.124 5.5 67.3 15.2 909 n/a 5_adp: 0.1200 0.1368 0.036 1.124 5.6 66.9 15.2 909 n/a 5_regHadp: 0.1200 0.1369 0.036 1.124 5.6 66.9 15.2 909 n/a 5_occ: 0.1198 0.1371 0.036 1.124 5.6 66.9 15.2 909 n/a 6_bss: 0.1197 0.1370 0.036 1.124 5.5 66.8 15.1 909 n/a 6_settarget: 0.1197 0.1370 0.036 1.124 5.5 66.8 15.1 909 n/a 6_updatecdl: 0.1197 0.1370 0.036 1.124 5.5 66.8 15.1 909 n/a 6_nqh: 0.1197 0.1370 0.036 1.124 5.5 66.8 15.1 909 n/a 6_sol: 0.1197 0.1363 0.036 1.124 5.5 66.8 15.1 915 n/a 6_weight: 0.1197 0.1363 0.036 1.124 5.5 66.8 15.1 915 n/a 6_xyzrec: 0.1199 0.1365 0.036 1.138 5.5 66.8 15.1 915 n/a 6_adp: 0.1199 0.1368 0.036 1.138 5.6 65.8 15.0 915 n/a 6_regHadp: 0.1200 0.1368 0.036 1.138 5.6 65.8 15.0 915 n/a 6_occ: 0.1197 0.1370 0.036 1.138 5.6 65.8 15.0 915 n/a 7_bss: 0.1195 0.1368 0.036 1.138 5.5 65.8 15.0 915 n/a 7_settarget: 0.1195 0.1368 0.036 1.138 5.5 65.8 15.0 915 n/a 7_updatecdl: 0.1195 0.1368 0.036 1.139 5.5 65.8 15.0 915 n/a 7_nqh: 0.1195 0.1368 0.036 1.139 5.5 65.8 15.0 915 n/a 7_sol: 0.1194 0.1356 0.036 1.139 5.5 65.8 15.1 934 n/a 7_weight: 0.1194 0.1356 0.036 1.139 5.5 65.8 15.1 934 n/a 7_xyzrec: 0.1198 0.1360 0.036 1.128 5.5 65.8 15.1 934 n/a 7_adp: 0.1201 0.1364 0.036 1.128 5.6 64.7 15.0 934 n/a 7_regHadp: 0.1201 0.1364 0.036 1.128 5.6 64.7 15.0 934 n/a 7_occ: 0.1199 0.1364 0.036 1.128 5.6 64.7 15.0 934 n/a 8_bss: 0.1189 0.1352 0.036 1.128 5.6 64.7 15.0 934 n/a 8_settarget: 0.1189 0.1352 0.036 1.128 5.6 64.7 15.0 934 n/a 8_updatecdl: 0.1189 0.1352 0.036 1.128 5.6 64.7 15.0 934 n/a 8_nqh: 0.1189 0.1352 0.036 1.128 5.6 64.7 15.0 934 n/a 8_sol: 0.1187 0.1345 0.036 1.128 5.6 64.7 15.0 942 n/a 8_weight: 0.1187 0.1345 0.036 1.128 5.6 64.7 15.0 942 n/a 8_xyzrec: 0.1189 0.1355 0.037 1.115 5.6 64.7 15.0 942 n/a 8_adp: 0.1191 0.1359 0.037 1.115 5.6 63.6 15.0 942 n/a 8_regHadp: 0.1191 0.1359 0.037 1.115 5.6 63.6 15.0 942 n/a 8_occ: 0.1189 0.1358 0.037 1.115 5.6 63.6 15.0 942 n/a 9_bss: 0.1188 0.1354 0.037 1.115 5.6 63.6 15.0 942 n/a 9_settarget: 0.1188 0.1354 0.037 1.115 5.6 63.6 15.0 942 n/a 9_updatecdl: 0.1188 0.1354 0.037 1.115 5.6 63.6 15.0 942 n/a 9_nqh: 0.1188 0.1354 0.037 1.115 5.6 63.6 15.0 942 n/a 9_sol: 0.1187 0.1343 0.037 1.115 5.6 63.6 15.0 945 n/a 9_weight: 0.1187 0.1343 0.037 1.115 5.6 63.6 15.0 945 n/a 9_xyzrec: 0.1191 0.1347 0.037 1.117 5.6 63.6 15.0 945 n/a 9_adp: 0.1190 0.1350 0.037 1.117 5.6 63.1 15.0 945 n/a 9_regHadp: 0.1190 0.1350 0.037 1.117 5.6 63.1 15.0 945 n/a 9_occ: 0.1188 0.1349 0.037 1.117 5.6 63.1 15.0 945 n/a 10_bss: 0.1188 0.1349 0.037 1.117 5.6 63.0 15.0 945 n/a 10_settarget: 0.1188 0.1349 0.037 1.117 5.6 63.0 15.0 945 n/a 10_updatecdl: 0.1188 0.1349 0.037 1.117 5.6 63.0 15.0 945 n/a 10_setrh: 0.1188 0.1349 0.037 1.117 5.6 63.0 15.0 945 n/a 10_nqh: 0.1188 0.1349 0.037 1.117 5.6 63.0 15.0 945 n/a 10_sol: 0.1188 0.1349 0.037 1.117 5.6 63.0 14.9 945 n/a 10_weight: 0.1188 0.1349 0.037 1.117 5.6 63.0 14.9 945 n/a 10_xyzrec: 0.1189 0.1352 0.037 1.163 5.6 63.0 14.9 945 n/a 10_adp: 0.1189 0.1353 0.037 1.163 5.7 61.9 14.9 945 n/a 10_regHadp: 0.1189 0.1353 0.037 1.163 5.7 61.9 14.9 945 n/a 10_occ: 0.1188 0.1354 0.037 1.163 5.7 61.9 14.9 945 n/a end: 0.1187 0.1354 0.037 1.163 5.5 61.7 14.8 945 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9524401_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9524401_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2100 Refinement macro-cycles (run) : 12356.5600 Write final files (write_after_run_outputs) : 141.8500 Total : 12504.6200 Total CPU time: 3.48 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:45:43 PST -0800 (1736736343.81 s) Start R-work = 0.1805, R-free = 0.1946 Final R-work = 0.1187, R-free = 0.1354 =============================================================================== Job complete usr+sys time: 12777.23 seconds wall clock time: 214 minutes 3.70 seconds (12843.70 seconds total)