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_6195814.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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_6195814.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6195814.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.75, per 1000 atoms: 0.26 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.743 distance_ideal: 2.720 ideal - model: -0.023 slack: 0.000 delta_slack: -0.023 sigma: 10.0000 bond: atom 1: "ATOM 160 OE2 GLU A 14 .*. O " atom 2: "ATOM 3408 OD2 ASP B 23 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 bond: atom 1: "ATOM 3408 OD2 ASP B 23 .*. O " atom 2: "ATOM 187 OG1 THR A 16 .*. O " symmetry operation: x,y,z distance_model: 2.683 distance_ideal: 2.710 ideal - model: 0.027 slack: 0.000 delta_slack: 0.027 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 147.2 milliseconds Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.76 - 0.99: 485 0.99 - 1.23: 2642 1.23 - 1.46: 1477 1.46 - 1.70: 1296 1.70 - 1.93: 34 Bond restraints: 5934 Sorted by residual: bond pdb=" NE ARG A 97 " pdb=" CZ ARG A 97 " ideal model delta sigma weight residual 1.326 1.559 -0.233 1.10e-02 8.26e+03 4.48e+02 bond pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " ideal model delta sigma weight residual 1.529 1.298 0.231 1.13e-02 7.83e+03 4.18e+02 bond pdb=" N ILE B 30 " pdb=" CA ILE B 30 " ideal model delta sigma weight residual 1.458 1.220 0.238 1.20e-02 6.94e+03 3.94e+02 bond pdb=" N ILE A 70 " pdb=" CA ILE A 70 " ideal model delta sigma weight residual 1.458 1.689 -0.230 1.17e-02 7.31e+03 3.87e+02 bond pdb=" C VAL B 69 " pdb=" O VAL B 69 " ideal model delta sigma weight residual 1.236 1.428 -0.193 1.01e-02 9.80e+03 3.63e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.54: 6036 4.54 - 9.08: 3547 9.08 - 13.62: 1084 13.62 - 18.16: 132 18.16 - 22.70: 11 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O VAL A 62 " pdb=" C VAL A 62 " pdb=" N ALA A 63 " ideal model delta sigma weight residual 122.06 104.86 17.20 9.90e-01 1.02e+00 3.02e+02 angle pdb=" C PHE A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta sigma weight residual 119.56 136.08 -16.52 1.01e+00 9.80e-01 2.68e+02 angle pdb=" O ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 121.55 134.20 -12.65 7.80e-01 1.64e+00 2.63e+02 angle pdb=" O PHE A 119 " pdb=" C PHE A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 121.34 107.40 13.94 8.90e-01 1.26e+00 2.45e+02 angle pdb=" O VAL A 7 " pdb=" C VAL A 7 " pdb=" N CYS A 8 " ideal model delta sigma weight residual 122.97 142.78 -19.81 1.32e+00 5.74e-01 2.25e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 1848 17.18 - 34.35: 131 34.35 - 51.52: 45 51.52 - 68.69: 23 68.69 - 85.86: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 155.63 24.37 0 5.00e+00 4.00e-02 2.38e+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 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 240 0.247 - 0.494: 158 0.494 - 0.741: 66 0.741 - 0.988: 23 0.988 - 1.235: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA LEU B 130 " pdb=" N LEU B 130 " pdb=" C LEU B 130 " pdb=" CB LEU B 130 " both_signs ideal model delta sigma weight residual False 2.51 3.75 -1.23 2.00e-01 2.50e+01 3.81e+01 chirality pdb=" CA ILE A 70 " pdb=" N ILE A 70 " pdb=" C ILE A 70 " pdb=" CB ILE A 70 " both_signs ideal model delta sigma weight residual False 2.43 3.56 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CA LEU B 6 " pdb=" N LEU B 6 " pdb=" C LEU B 6 " pdb=" CB LEU B 6 " both_signs ideal model delta sigma weight residual False 2.51 3.62 -1.11 2.00e-01 2.50e+01 3.06e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " 0.073 2.00e-02 2.50e+03 6.90e-02 1.43e+02 pdb=" CG TYR B 67 " -0.125 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " 0.037 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " 0.063 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " 0.061 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " -0.120 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " -0.029 2.00e-02 2.50e+03 5.62e-02 1.26e+02 pdb=" CG TRP A 146 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.028 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.055 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.070 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.084 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.066 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.056 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " 0.045 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.019 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.082 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 119 " 0.076 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG PHE B 119 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE B 119 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE B 119 " -0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE B 119 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 PHE B 119 " 0.059 2.00e-02 2.50e+03 pdb=" CZ PHE B 119 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE B 119 " 0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE B 119 " -0.064 2.00e-02 2.50e+03 pdb=" HE1 PHE B 119 " -0.129 2.00e-02 2.50e+03 pdb=" HE2 PHE B 119 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE B 119 " 0.065 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 26 1.60 - 2.35: 2294 2.35 - 3.10: 22188 3.10 - 3.85: 32968 3.85 - 4.60: 52851 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110327 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.853 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.974 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.005 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.020 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.168 2.620 ... (remaining 110322 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_6195814_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= 0.2033 r_free= 0.1974 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299082 | | target function (ml) not normalized (work): 805273.934324 | | target function (ml) not normalized (free): 16532.727829 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2141 0.1987 6.6837 6.3138| | 2: 2.94 - 2.33 1.00 7339 128 0.1622 0.1653 5.5454 5.5871| | 3: 2.33 - 2.04 0.96 6939 150 0.1618 0.1491 5.1423 5.1543| | 4: 2.04 - 1.85 1.00 7170 155 0.1760 0.1677 4.9628 5.074| | 5: 1.85 - 1.72 0.99 7113 159 0.1919 0.1750 4.7996 4.803| | 6: 1.72 - 1.62 0.99 7102 142 0.1975 0.1940 4.6618 4.6458| | 7: 1.62 - 1.54 0.99 7104 148 0.2007 0.1779 4.5577 4.5816| | 8: 1.54 - 1.47 0.96 6798 152 0.2064 0.2086 4.4846 4.4536| | 9: 1.47 - 1.41 0.98 6938 155 0.2105 0.2220 4.3952 4.4643| | 10: 1.41 - 1.36 0.99 7022 150 0.2108 0.2031 4.3056 4.3331| | 11: 1.36 - 1.32 0.99 6997 151 0.2126 0.2008 4.2415 4.2445| | 12: 1.32 - 1.28 0.98 6976 149 0.2028 0.2000 4.1534 4.2242| | 13: 1.28 - 1.25 0.98 6907 166 0.2010 0.2190 4.112 4.2081| | 14: 1.25 - 1.22 0.98 7015 113 0.2070 0.2104 4.0715 4.167| | 15: 1.22 - 1.19 0.98 6957 137 0.2100 0.1962 4.0347 4.0036| | 16: 1.19 - 1.17 0.93 6604 132 0.2148 0.2289 4.0152 4.1318| | 17: 1.17 - 1.14 0.98 6941 135 0.2214 0.1993 3.9674 3.9974| | 18: 1.14 - 1.12 0.98 6875 142 0.2216 0.2532 3.9222 3.9447| | 19: 1.12 - 1.10 0.97 6949 106 0.2271 0.2369 3.8657 3.9601| | 20: 1.10 - 1.08 0.97 6884 147 0.2336 0.2124 3.838 3.8329| | 21: 1.08 - 1.07 0.97 6852 152 0.2409 0.2592 3.7862 3.7759| | 22: 1.07 - 1.05 0.97 6838 135 0.2553 0.2324 3.7516 3.7209| | 23: 1.05 - 1.03 0.97 6829 159 0.2730 0.2586 3.7354 3.7565| | 24: 1.03 - 1.02 0.96 6785 133 0.2862 0.3053 3.703 3.8832| | 25: 1.02 - 1.01 0.93 6552 130 0.3050 0.2798 3.6726 3.6977| | 26: 1.01 - 0.99 0.96 6767 158 0.3181 0.3156 3.6218 3.6318| | 27: 0.99 - 0.98 0.94 6648 131 0.3388 0.3242 3.6316 3.6228| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.57 0.91 0.97 35792.46| | 2: 2.94 - 2.33 7339 128 0.85 21.45 1.08 1.02 15304.74| | 3: 2.33 - 2.04 6939 150 0.93 12.71 1.11 1.05 4276.73| | 4: 2.04 - 1.85 7170 155 0.92 13.56 1.12 1.07 2808.44| | 5: 1.85 - 1.72 7113 159 0.91 15.47 1.11 1.09 2058.78| | 6: 1.72 - 1.62 7102 142 0.91 16.09 1.12 1.09 1561.91| | 7: 1.62 - 1.54 7104 148 0.90 16.89 1.11 1.09 1261.60| | 8: 1.54 - 1.47 6798 152 0.89 17.61 1.10 1.08 1071.05| | 9: 1.47 - 1.41 6938 155 0.89 18.34 1.10 1.07 928.61| | 10: 1.41 - 1.36 7022 150 0.88 19.19 1.09 1.05 804.49| | 11: 1.36 - 1.32 6997 151 0.88 19.42 1.08 1.04 697.01| | 12: 1.32 - 1.28 6976 149 0.88 19.56 1.08 1.03 634.87| | 13: 1.28 - 1.25 6907 166 0.87 19.88 1.07 1.03 600.23| | 14: 1.25 - 1.22 7015 113 0.87 20.51 1.07 1.04 565.04| | 15: 1.22 - 1.19 6957 137 0.87 20.56 1.08 1.04 523.69| | 16: 1.19 - 1.17 6604 132 0.87 20.16 1.07 1.04 482.53| | 17: 1.17 - 1.14 6941 135 0.86 21.04 1.09 1.03 443.48| | 18: 1.14 - 1.12 6875 142 0.86 21.34 1.08 1.00 403.48| | 19: 1.12 - 1.10 6949 106 0.86 21.81 1.07 0.99 367.27| | 20: 1.10 - 1.08 6884 147 0.86 22.13 1.06 0.96 326.90| | 21: 1.08 - 1.07 6852 152 0.85 22.80 1.06 0.97 306.72| | 22: 1.07 - 1.05 6838 135 0.83 24.62 1.05 0.97 307.96| | 23: 1.05 - 1.03 6829 159 0.81 27.08 1.05 0.99 324.59| | 24: 1.03 - 1.02 6785 133 0.78 29.35 1.04 0.98 334.66| | 25: 1.02 - 1.01 6552 130 0.77 30.79 1.03 0.93 315.16| | 26: 1.01 - 0.99 6767 158 0.74 32.85 1.03 0.90 298.67| | 27: 0.99 - 0.98 6648 131 0.73 33.70 1.04 0.87 286.00| |alpha: min = 0.87 max = 1.09 mean = 1.02| |beta: min = 286.00 max = 35792.46 mean = 2835.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.38| |phase err.(test): min = 0.00 max = 89.34 mean = 21.15| |-----------------------------------------------------------------------------| ----------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 0.246 2950 Z= 5.320 Angle : 5.167 19.810 4018 Z= 3.622 Chirality : 0.380 1.235 492 Planarity : 0.031 0.126 512 Dihedral : 12.818 85.862 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.08 % Rotamer: Outliers : 1.29 % Allowed : 3.87 % Favored : 94.84 % Cbeta Deviations : 31.74 % 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: -2.20 (0.39), residues: 386 helix: -2.52 (0.30), residues: 146 sheet: -1.10 (0.50), residues: 82 loop : -0.24 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.090 0.021 ARG A 143 TYR 0.132 0.030 TYR B 67 PHE 0.117 0.036 PHE A 164 TRP 0.110 0.034 TRP A 139 HIS 0.071 0.031 HIS B 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= 0.2033 r_free= 0.1974 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299082 | | target function (ml) not normalized (work): 805273.934324 | | target function (ml) not normalized (free): 16532.727829 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2031 0.2033 0.1974 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2031 0.2033 0.1974 n_refl.: 191155 remove outliers: r(all,work,free)=0.2031 0.2033 0.1974 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2032 0.2034 0.1974 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1803 0.1902 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1801 0.1902 n_refl.: 191140 ======================== 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 0.4234 400.535 295.525 0.432 0.912 0.299 13.296-10.522 100.00 100 1 0.2513 534.497 521.362 0.785 0.913 0.248 10.503-8.327 98.90 177 3 0.2473 564.205 557.808 0.973 0.913 0.223 8.318-6.595 100.00 360 8 0.2530 414.736 402.640 0.971 0.913 0.165 6.588-5.215 100.00 711 7 0.2279 381.101 365.829 0.959 0.913 0.160 5.214-4.128 98.38 1367 28 0.1502 557.435 550.320 1.075 0.913 0.090 4.126-3.266 94.74 2603 46 0.1346 508.132 499.803 1.145 0.913 0.009 3.266-2.585 99.86 5447 97 0.1456 342.774 337.575 1.120 0.912 0.000 2.585-2.046 97.45 10613 204 0.1397 258.603 254.341 1.123 0.912 0.000 2.046-1.619 99.39 21536 464 0.1612 153.054 149.887 1.146 0.910 0.000 1.619-1.281 98.00 42464 925 0.1918 82.395 80.176 1.128 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2322 44.203 41.655 1.112 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0105 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1801 r_free=0.1902 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN Total number of N/Q/H flips: 1 r_work=0.1806 r_free=0.1901 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.593741 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 569.080452 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 0.1497 0.0227 0.037 1.2 11.6 0.0 0.0 0 11.297 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 14.97 2.27 1.118 13.117 569.080 0.018 12.93 15.63 2.70 1.207 13.298 569.080 0.017 Individual atomic B min max mean iso aniso Overall: 5.15 73.05 14.93 1.39 435 3274 Protein: 5.15 40.49 10.96 1.39 0 2902 Water: 6.30 73.05 29.24 N/A 435 370 Other: 15.91 29.65 22.78 N/A 0 2 Chain A: 5.30 60.28 12.99 N/A 0 1626 Chain B: 5.15 73.05 12.72 N/A 0 1648 Chain S: 11.63 62.82 30.62 N/A 435 0 Histogram: Values Number of atoms 5.15 - 11.94 2162 11.94 - 18.73 644 18.73 - 25.52 323 25.52 - 32.31 262 32.31 - 39.10 154 39.10 - 45.89 102 45.89 - 52.68 39 52.68 - 59.47 18 59.47 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1293 r_free=0.1563 r_work=0.1292 r_free=0.1559 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1292 r_free = 0.1559 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1547 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1278 r_free= 0.1547 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015559 | | target function (ls_wunit_k1) not normalized (work): 2914.230643 | | target function (ls_wunit_k1) not normalized (free): 115.470577 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1283 0.1278 0.1547 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1467 0.1465 0.1626 n_refl.: 191140 remove outliers: r(all,work,free)=0.1467 0.1465 0.1626 n_refl.: 191140 overall B=0.17 to atoms: r(all,work,free)=0.1492 0.1490 0.1637 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1275 0.1270 0.1540 n_refl.: 191140 remove outliers: r(all,work,free)=0.1275 0.1270 0.1539 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3633 402.814 371.600 0.462 1.000 0.281 13.296-10.522 100.00 100 1 0.2120 534.497 530.337 0.722 1.002 0.249 10.503-8.327 98.90 177 3 0.1726 564.205 562.574 0.854 1.002 0.198 8.318-6.595 100.00 360 8 0.1722 414.736 412.550 0.875 1.002 0.155 6.588-5.215 100.00 711 7 0.1542 381.101 373.533 0.855 1.002 0.150 5.214-4.128 98.38 1367 28 0.0913 557.435 554.381 0.940 1.002 0.070 4.126-3.266 94.74 2603 46 0.0832 508.132 504.488 1.005 1.003 0.014 3.266-2.585 99.86 5447 97 0.0924 342.774 340.414 0.987 1.002 0.000 2.585-2.046 97.45 10613 204 0.0947 258.603 256.388 0.998 1.003 0.000 2.046-1.619 99.39 21536 464 0.1080 153.054 151.395 1.016 1.002 0.000 1.619-1.281 98.00 42464 925 0.1268 82.395 81.419 1.008 1.002 0.000 1.281-0.980 96.53 101826 2055 0.1867 44.202 42.171 0.987 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0388 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1270 r_free=0.1539 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN Total number of N/Q/H flips: 1 r_work=0.1271 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1541 | n_water=805 | time (s): 2.990 (total time: 2.990) Filter (dist) r_work=0.1275 r_free=0.1546 | n_water=795 | time (s): 98.020 (total time: 101.010) Filter (q & B) r_work=0.1275 r_free=0.1546 | n_water=791 | time (s): 4.490 (total time: 105.500) Compute maps r_work=0.1275 r_free=0.1546 | n_water=791 | time (s): 2.510 (total time: 108.010) Filter (map) r_work=0.1301 r_free=0.1531 | n_water=655 | time (s): 4.280 (total time: 112.290) Find peaks r_work=0.1301 r_free=0.1531 | n_water=655 | time (s): 0.620 (total time: 112.910) Add new water r_work=0.1324 r_free=0.1562 | n_water=955 | time (s): 4.020 (total time: 116.930) Refine new water occ: r_work=0.1280 r_free=0.1522 adp: r_work=0.1268 r_free=0.1516 occ: r_work=0.1270 r_free=0.1516 adp: r_work=0.1264 r_free=0.1514 occ: r_work=0.1265 r_free=0.1513 adp: r_work=0.1263 r_free=0.1513 ADP+occupancy (water only), MIN, final r_work=0.1263 r_free=0.1513 r_work=0.1263 r_free=0.1513 | n_water=955 | time (s): 94.640 (total time: 211.570) Filter (q & B) r_work=0.1267 r_free=0.1515 | n_water=885 | time (s): 5.420 (total time: 216.990) Filter (dist only) r_work=0.1268 r_free=0.1511 | n_water=883 | time (s): 111.980 (total time: 328.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.428172 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 596.705688 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 0.1253 0.1516 0.0264 0.042 1.1 17.8 0.0 0.0 0 11.714 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.16 2.64 2.031 15.120 596.706 0.015 12.33 15.07 2.74 2.376 15.180 596.706 0.014 Individual atomic B min max mean iso aniso Overall: 5.43 68.22 16.27 1.20 515 3272 Protein: 5.43 40.43 10.98 1.20 0 2902 Water: 6.62 68.22 33.66 N/A 515 368 Other: 16.46 33.20 24.83 N/A 0 2 Chain A: 5.55 56.91 12.98 N/A 0 1624 Chain B: 5.43 68.22 12.80 N/A 0 1648 Chain S: 13.17 67.44 37.78 N/A 515 0 Histogram: Values Number of atoms 5.43 - 11.71 2064 11.71 - 17.99 708 17.99 - 24.27 264 24.27 - 30.55 215 30.55 - 36.82 177 36.82 - 43.10 163 43.10 - 49.38 97 49.38 - 55.66 51 55.66 - 61.94 36 61.94 - 68.22 12 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1507 r_work=0.1234 r_free=0.1508 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1508 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1505 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013455 | | target function (ls_wunit_k1) not normalized (work): 2520.009853 | | target function (ls_wunit_k1) not normalized (free): 100.051351 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1505 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1437 0.1592 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1437 0.1592 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1436 0.1434 0.1591 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1510 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1233 0.1510 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3308 402.814 379.204 0.486 0.962 0.267 13.296-10.522 100.00 100 1 0.1920 534.497 527.708 0.761 0.963 0.223 10.503-8.327 98.90 177 3 0.1449 564.205 566.219 0.917 0.963 0.179 8.318-6.595 100.00 360 8 0.1571 414.736 413.825 0.936 0.963 0.160 6.588-5.215 100.00 711 7 0.1340 381.101 376.359 0.914 0.963 0.160 5.214-4.128 98.38 1367 28 0.0835 557.435 556.198 0.995 0.963 0.090 4.126-3.266 94.74 2603 46 0.0761 508.132 505.494 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0855 342.774 341.482 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.737 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.625 1.081 0.958 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.352 1.074 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.225 1.060 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0486 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1510 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1510 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1510 | n_water=883 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1236 r_free=0.1509 | n_water=875 | time (s): 124.760 (total time: 127.390) Filter (q & B) r_work=0.1236 r_free=0.1509 | n_water=872 | time (s): 4.430 (total time: 131.820) Compute maps r_work=0.1236 r_free=0.1509 | n_water=872 | time (s): 1.760 (total time: 133.580) Filter (map) r_work=0.1276 r_free=0.1519 | n_water=679 | time (s): 4.400 (total time: 137.980) Find peaks r_work=0.1276 r_free=0.1519 | n_water=679 | time (s): 0.730 (total time: 138.710) Add new water r_work=0.1302 r_free=0.1549 | n_water=1015 | time (s): 4.810 (total time: 143.520) Refine new water occ: r_work=0.1252 r_free=0.1502 adp: r_work=0.1253 r_free=0.1502 occ: r_work=0.1249 r_free=0.1499 adp: r_work=0.1248 r_free=0.1500 occ: r_work=0.1246 r_free=0.1496 adp: r_work=0.1245 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1497 r_work=0.1245 r_free=0.1497 | n_water=1015 | time (s): 273.540 (total time: 417.060) Filter (q & B) r_work=0.1250 r_free=0.1497 | n_water=872 | time (s): 4.230 (total time: 421.290) Filter (dist only) r_work=0.1250 r_free=0.1497 | n_water=871 | time (s): 109.560 (total time: 530.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.675651 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.508478 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 0.1238 0.1434 0.0195 0.035 1.1 7.5 0.0 0.0 0 0.838 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.34 1.95 1.928 14.523 16.508 3.940 12.31 13.90 1.59 2.203 14.431 16.508 3.897 Individual atomic B min max mean iso aniso Overall: 5.54 67.83 15.17 1.06 504 3271 Protein: 5.54 36.82 10.75 1.06 0 2902 Water: 6.68 67.83 29.87 N/A 504 367 Other: 14.18 29.01 21.59 N/A 0 2 Chain A: 5.54 56.04 12.76 N/A 0 1624 Chain B: 5.55 67.83 12.53 N/A 0 1647 Chain S: 14.74 64.63 31.56 N/A 504 0 Histogram: Values Number of atoms 5.54 - 11.77 2132 11.77 - 18.00 681 18.00 - 24.23 307 24.23 - 30.46 253 30.46 - 36.69 162 36.69 - 42.92 145 42.92 - 49.15 64 49.15 - 55.38 22 55.38 - 61.60 7 61.60 - 67.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1390 r_work=0.1231 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1391 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1384 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891144 | | target function (ml) not normalized (work): 728799.631377 | | target function (ml) not normalized (free): 15217.736905 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1226 0.1384 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1444 0.1444 0.1471 n_refl.: 191138 remove outliers: r(all,work,free)=0.1444 0.1444 0.1471 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1438 0.1438 0.1468 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1378 n_refl.: 191138 remove outliers: r(all,work,free)=0.1225 0.1222 0.1378 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3879 398.895 355.841 0.415 0.946 0.245 13.296-10.522 100.00 100 1 0.2454 534.497 516.076 0.712 0.948 0.208 10.503-8.327 97.80 175 3 0.2059 554.286 557.197 0.877 0.948 0.187 8.318-6.595 100.00 360 8 0.2062 414.736 409.672 0.898 0.947 0.138 6.588-5.215 100.00 711 7 0.1838 381.101 370.536 0.884 0.947 0.113 5.214-4.128 98.38 1367 28 0.1167 557.435 551.641 0.970 0.947 0.060 4.126-3.266 94.74 2603 46 0.1090 508.132 501.430 1.034 0.948 0.019 3.266-2.585 99.86 5447 97 0.1082 342.774 339.351 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0957 258.603 255.821 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0966 153.054 151.442 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.491 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.313 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0949 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1378 | n_water=871 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1222 r_free=0.1378 | n_water=870 | time (s): 106.990 (total time: 109.330) Filter (q & B) r_work=0.1223 r_free=0.1377 | n_water=861 | time (s): 5.490 (total time: 114.820) Compute maps r_work=0.1223 r_free=0.1377 | n_water=861 | time (s): 2.540 (total time: 117.360) Filter (map) r_work=0.1246 r_free=0.1384 | n_water=724 | time (s): 4.300 (total time: 121.660) Find peaks r_work=0.1246 r_free=0.1384 | n_water=724 | time (s): 0.720 (total time: 122.380) Add new water r_work=0.1260 r_free=0.1398 | n_water=958 | time (s): 4.360 (total time: 126.740) Refine new water occ: r_work=0.1212 r_free=0.1355 adp: r_work=0.1204 r_free=0.1350 occ: r_work=0.1202 r_free=0.1350 adp: r_work=0.1202 r_free=0.1349 occ: r_work=0.1200 r_free=0.1350 adp: r_work=0.1200 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1350 r_work=0.1200 r_free=0.1350 | n_water=958 | time (s): 259.280 (total time: 386.020) Filter (q & B) r_work=0.1206 r_free=0.1354 | n_water=852 | time (s): 5.210 (total time: 391.230) Filter (dist only) r_work=0.1206 r_free=0.1353 | n_water=851 | time (s): 111.430 (total time: 502.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.580145 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.899113 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1354 0.0149 0.035 1.1 5.3 0.0 0.0 0 0.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.54 1.49 1.835 14.118 15.899 3.873 12.00 13.52 1.52 1.949 14.077 15.899 3.865 Individual atomic B min max mean iso aniso Overall: 5.50 67.42 14.81 1.01 484 3271 Protein: 5.50 33.55 10.66 1.01 0 2902 Water: 6.00 67.42 28.93 N/A 484 367 Other: 14.04 27.93 20.98 N/A 0 2 Chain A: 5.53 54.97 12.62 N/A 0 1624 Chain B: 5.50 67.42 12.43 N/A 0 1647 Chain S: 6.00 64.68 30.25 N/A 484 0 Histogram: Values Number of atoms 5.50 - 11.69 2113 11.69 - 17.88 732 17.88 - 24.08 318 24.08 - 30.27 240 30.27 - 36.46 137 36.46 - 42.65 129 42.65 - 48.84 56 48.84 - 55.04 22 55.04 - 61.23 6 61.23 - 67.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1352 r_work=0.1200 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1352 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1350 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863252 | | target function (ml) not normalized (work): 723559.977209 | | target function (ml) not normalized (free): 15130.058854 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1350 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1412 0.1412 0.1453 n_refl.: 191134 remove outliers: r(all,work,free)=0.1412 0.1412 0.1453 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1405 0.1405 0.1449 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1349 n_refl.: 191134 remove outliers: r(all,work,free)=0.1199 0.1196 0.1349 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3666 360.896 315.215 0.406 0.949 0.237 13.296-10.522 97.03 97 1 0.2353 486.296 457.119 0.701 0.951 0.196 10.503-8.327 97.80 175 3 0.2155 501.907 495.739 0.856 0.951 0.177 8.318-6.595 100.00 360 8 0.2191 375.544 369.771 0.890 0.950 0.120 6.588-5.215 100.00 711 7 0.1930 345.087 335.077 0.878 0.951 0.089 5.214-4.128 98.38 1367 28 0.1214 504.758 499.712 0.969 0.951 0.070 4.126-3.266 94.74 2603 46 0.1116 460.114 453.892 1.031 0.951 0.000 3.266-2.585 99.86 5447 97 0.1085 310.382 307.328 1.018 0.951 0.000 2.585-2.046 97.45 10613 204 0.0931 234.165 231.825 1.029 0.950 0.000 2.046-1.619 99.39 21536 464 0.0912 138.591 137.366 1.053 0.949 0.000 1.619-1.281 98.00 42464 925 0.0986 74.609 73.921 1.049 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.025 38.376 1.035 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1131 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1349 | n_water=851 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1196 r_free=0.1349 | n_water=851 | time (s): 99.400 (total time: 101.990) Filter (q & B) r_work=0.1196 r_free=0.1350 | n_water=845 | time (s): 4.340 (total time: 106.330) Compute maps r_work=0.1196 r_free=0.1350 | n_water=845 | time (s): 1.830 (total time: 108.160) Filter (map) r_work=0.1220 r_free=0.1359 | n_water=729 | time (s): 4.850 (total time: 113.010) Find peaks r_work=0.1220 r_free=0.1359 | n_water=729 | time (s): 0.790 (total time: 113.800) Add new water r_work=0.1231 r_free=0.1370 | n_water=950 | time (s): 4.730 (total time: 118.530) Refine new water occ: r_work=0.1194 r_free=0.1337 adp: r_work=0.1195 r_free=0.1338 occ: r_work=0.1192 r_free=0.1336 adp: r_work=0.1192 r_free=0.1336 occ: r_work=0.1190 r_free=0.1335 adp: r_work=0.1190 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1335 r_work=0.1190 r_free=0.1335 | n_water=950 | time (s): 199.340 (total time: 317.870) Filter (q & B) r_work=0.1194 r_free=0.1341 | n_water=871 | time (s): 4.340 (total time: 322.210) Filter (dist only) r_work=0.1194 r_free=0.1340 | n_water=869 | time (s): 114.180 (total time: 436.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544274 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.308353 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 0.1348 0.0150 0.036 1.1 5.8 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.48 1.50 1.794 14.050 15.308 3.764 12.02 13.51 1.49 1.853 14.025 15.308 3.761 Individual atomic B min max mean iso aniso Overall: 5.57 67.12 14.81 0.96 502 3271 Protein: 5.57 32.40 10.60 0.96 0 2902 Water: 6.04 67.12 28.87 N/A 502 367 Other: 13.78 26.88 20.33 N/A 0 2 Chain A: 5.58 54.24 12.53 N/A 0 1624 Chain B: 5.57 67.12 12.34 N/A 0 1647 Chain S: 6.04 64.68 30.27 N/A 502 0 Histogram: Values Number of atoms 5.57 - 11.72 2140 11.72 - 17.88 720 17.88 - 24.03 313 24.03 - 30.19 228 30.19 - 36.34 158 36.34 - 42.50 133 42.50 - 48.65 56 48.65 - 54.81 17 54.81 - 60.97 6 60.97 - 67.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1351 r_work=0.1202 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1351 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1352 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760548 | | target function (ml) not normalized (work): 704309.301245 | | target function (ml) not normalized (free): 14739.582594 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1353 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1466 n_refl.: 191130 remove outliers: r(all,work,free)=0.1401 0.1400 0.1466 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1393 0.1392 0.1461 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1353 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1199 0.1353 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3670 360.896 332.670 0.430 0.951 0.241 13.296-10.522 97.03 97 1 0.2407 486.296 469.118 0.714 0.952 0.194 10.503-8.327 97.80 175 3 0.2227 501.907 493.928 0.854 0.953 0.173 8.318-6.595 100.00 360 8 0.2174 375.544 369.690 0.886 0.952 0.109 6.588-5.215 100.00 711 7 0.1933 345.087 335.100 0.877 0.953 0.080 5.214-4.128 98.38 1367 28 0.1227 504.758 499.177 0.969 0.953 0.070 4.126-3.266 94.74 2603 46 0.1148 460.114 453.128 1.031 0.953 0.000 3.266-2.585 99.86 5447 97 0.1108 310.382 307.122 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0940 234.165 231.694 1.028 0.953 0.000 2.046-1.619 99.39 21536 464 0.0913 138.591 137.291 1.050 0.952 0.000 1.619-1.281 98.00 42464 925 0.0977 74.609 73.895 1.047 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.025 38.359 1.032 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1287 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1353 | n_water=869 | time (s): 3.260 (total time: 3.260) Filter (dist) r_work=0.1199 r_free=0.1353 | n_water=869 | time (s): 103.610 (total time: 106.870) Filter (q & B) r_work=0.1200 r_free=0.1351 | n_water=858 | time (s): 4.250 (total time: 111.120) Compute maps r_work=0.1200 r_free=0.1351 | n_water=858 | time (s): 1.870 (total time: 112.990) Filter (map) r_work=0.1222 r_free=0.1362 | n_water=739 | time (s): 4.070 (total time: 117.060) Find peaks r_work=0.1222 r_free=0.1362 | n_water=739 | time (s): 0.570 (total time: 117.630) Add new water r_work=0.1234 r_free=0.1375 | n_water=963 | time (s): 3.840 (total time: 121.470) Refine new water occ: r_work=0.1197 r_free=0.1346 adp: r_work=0.1197 r_free=0.1346 occ: r_work=0.1195 r_free=0.1343 adp: r_work=0.1195 r_free=0.1344 occ: r_work=0.1194 r_free=0.1341 adp: r_work=0.1194 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1342 r_work=0.1194 r_free=0.1342 | n_water=963 | time (s): 239.860 (total time: 361.330) Filter (q & B) r_work=0.1198 r_free=0.1344 | n_water=877 | time (s): 4.960 (total time: 366.290) Filter (dist only) r_work=0.1198 r_free=0.1343 | n_water=876 | time (s): 111.340 (total time: 477.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.541440 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.293979 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1351 0.0150 0.037 1.1 5.3 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.51 1.50 1.765 13.969 14.294 3.762 12.06 13.55 1.49 1.933 13.913 14.294 3.761 Individual atomic B min max mean iso aniso Overall: 5.60 65.96 14.69 0.89 509 3271 Protein: 5.60 29.19 10.47 0.89 0 2902 Water: 6.02 65.96 28.66 N/A 509 367 Other: 13.81 23.76 18.79 N/A 0 2 Chain A: 5.62 52.25 12.37 N/A 0 1624 Chain B: 5.60 65.96 12.20 N/A 0 1647 Chain S: 6.02 64.73 30.16 N/A 509 0 Histogram: Values Number of atoms 5.60 - 11.63 2121 11.63 - 17.67 772 17.67 - 23.71 284 23.71 - 29.74 223 29.74 - 35.78 160 35.78 - 41.81 127 41.81 - 47.85 62 47.85 - 53.89 22 53.89 - 59.92 7 59.92 - 65.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1356 r_work=0.1207 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1356 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1354 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759767 | | target function (ml) not normalized (work): 704163.005488 | | target function (ml) not normalized (free): 14739.921177 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1354 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1405 0.1403 0.1472 n_refl.: 191130 remove outliers: r(all,work,free)=0.1405 0.1403 0.1472 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1397 0.1396 0.1467 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1352 n_refl.: 191130 remove outliers: r(all,work,free)=0.1205 0.1202 0.1352 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3619 360.896 332.347 0.428 0.952 0.239 13.296-10.522 97.03 97 1 0.2406 486.296 469.239 0.712 0.954 0.189 10.503-8.327 97.80 175 3 0.2220 501.907 494.438 0.852 0.954 0.167 8.315-6.595 100.00 359 8 0.2147 374.598 370.539 0.885 0.954 0.110 6.588-5.215 100.00 711 7 0.1962 345.087 334.890 0.877 0.954 0.090 5.214-4.128 98.38 1367 28 0.1248 504.758 499.089 0.969 0.954 0.080 4.126-3.266 94.74 2603 46 0.1161 460.114 453.054 1.031 0.954 0.000 3.266-2.585 99.86 5447 97 0.1121 310.382 307.055 1.016 0.954 0.000 2.585-2.046 97.45 10613 204 0.0952 234.165 231.646 1.027 0.953 0.000 2.046-1.619 99.39 21536 464 0.0914 138.591 137.293 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0972 74.609 73.903 1.048 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.025 38.363 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=-0.1356 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1352 | n_water=876 | time (s): 3.260 (total time: 3.260) Filter (dist) r_work=0.1202 r_free=0.1353 | n_water=875 | time (s): 112.170 (total time: 115.430) Filter (q & B) r_work=0.1203 r_free=0.1353 | n_water=867 | time (s): 5.140 (total time: 120.570) Compute maps r_work=0.1203 r_free=0.1353 | n_water=867 | time (s): 1.730 (total time: 122.300) Filter (map) r_work=0.1226 r_free=0.1358 | n_water=750 | time (s): 5.020 (total time: 127.320) Find peaks r_work=0.1226 r_free=0.1358 | n_water=750 | time (s): 0.660 (total time: 127.980) Add new water r_work=0.1238 r_free=0.1373 | n_water=967 | time (s): 4.910 (total time: 132.890) Refine new water occ: r_work=0.1201 r_free=0.1348 adp: r_work=0.1202 r_free=0.1347 occ: r_work=0.1199 r_free=0.1346 adp: r_work=0.1199 r_free=0.1346 occ: r_work=0.1198 r_free=0.1345 adp: r_work=0.1198 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1345 r_work=0.1198 r_free=0.1345 | n_water=967 | time (s): 205.550 (total time: 338.440) Filter (q & B) r_work=0.1202 r_free=0.1350 | n_water=887 | time (s): 4.770 (total time: 343.210) Filter (dist only) r_work=0.1202 r_free=0.1350 | n_water=886 | time (s): 113.560 (total time: 456.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.539965 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.293810 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1356 0.0151 0.038 1.1 6.5 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.56 1.51 1.713 13.828 14.294 3.761 12.05 13.57 1.53 1.756 13.810 14.294 3.757 Individual atomic B min max mean iso aniso Overall: 5.60 64.80 14.65 0.88 519 3271 Protein: 5.60 28.62 10.42 0.88 0 2902 Water: 5.94 64.80 28.50 N/A 519 367 Other: 13.84 22.14 17.99 N/A 0 2 Chain A: 5.63 51.71 12.28 N/A 0 1624 Chain B: 5.60 64.80 12.12 N/A 0 1647 Chain S: 5.94 64.79 30.11 N/A 519 0 Histogram: Values Number of atoms 5.60 - 11.52 2103 11.52 - 17.44 785 17.44 - 23.36 283 23.36 - 29.28 220 29.28 - 35.20 173 35.20 - 41.12 113 41.12 - 47.04 77 47.04 - 52.96 26 52.96 - 58.88 8 58.88 - 64.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1358 r_work=0.1205 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1359 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756713 | | target function (ml) not normalized (work): 703587.339758 | | target function (ml) not normalized (free): 14729.422645 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1359 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1487 n_refl.: 191129 remove outliers: r(all,work,free)=0.1402 0.1401 0.1487 n_refl.: 191129 overall B=-0.24 to atoms: r(all,work,free)=0.1367 0.1365 0.1465 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1360 n_refl.: 191129 remove outliers: r(all,work,free)=0.1206 0.1203 0.1360 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3671 360.896 331.217 0.429 0.950 0.225 13.296-10.522 97.03 97 1 0.2449 486.296 468.956 0.728 0.951 0.172 10.503-8.327 97.80 175 3 0.2259 501.907 493.747 0.877 0.952 0.129 8.315-6.595 100.00 359 8 0.2146 374.598 370.117 0.906 0.952 0.100 6.588-5.215 100.00 711 7 0.1952 345.087 335.081 0.902 0.952 0.085 5.214-4.128 98.38 1367 28 0.1275 504.758 498.769 0.997 0.952 0.080 4.126-3.266 94.74 2603 46 0.1167 460.114 452.815 1.059 0.953 0.005 3.266-2.585 99.86 5447 97 0.1128 310.382 307.101 1.040 0.953 0.000 2.585-2.046 97.45 10613 204 0.0955 234.165 231.654 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0909 138.591 137.325 1.062 0.954 0.000 1.619-1.281 98.00 42464 925 0.0965 74.609 73.918 1.048 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.025 38.358 1.015 0.958 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0525 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1360 | n_water=886 | time (s): 2.460 (total time: 2.460) Filter (dist) r_work=0.1203 r_free=0.1360 | n_water=886 | time (s): 111.440 (total time: 113.900) Filter (q & B) r_work=0.1204 r_free=0.1359 | n_water=878 | time (s): 5.310 (total time: 119.210) Compute maps r_work=0.1204 r_free=0.1359 | n_water=878 | time (s): 2.150 (total time: 121.360) Filter (map) r_work=0.1228 r_free=0.1361 | n_water=750 | time (s): 4.820 (total time: 126.180) Find peaks r_work=0.1228 r_free=0.1361 | n_water=750 | time (s): 0.790 (total time: 126.970) Add new water r_work=0.1239 r_free=0.1378 | n_water=988 | time (s): 3.990 (total time: 130.960) Refine new water occ: r_work=0.1200 r_free=0.1344 adp: r_work=0.1200 r_free=0.1344 occ: r_work=0.1197 r_free=0.1343 adp: r_work=0.1198 r_free=0.1343 occ: r_work=0.1196 r_free=0.1342 adp: r_work=0.1196 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1342 r_work=0.1196 r_free=0.1342 | n_water=988 | time (s): 230.250 (total time: 361.210) Filter (q & B) r_work=0.1201 r_free=0.1351 | n_water=897 | time (s): 5.090 (total time: 366.300) Filter (dist only) r_work=0.1201 r_free=0.1350 | n_water=895 | time (s): 114.740 (total time: 481.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.548811 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.194022 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 0.1204 0.1357 0.0153 0.038 1.1 6.1 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.57 1.53 1.697 13.568 14.194 3.758 12.06 13.61 1.55 1.720 13.557 14.194 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 64.63 14.41 0.87 528 3271 Protein: 5.39 27.86 10.18 0.87 0 2902 Water: 5.84 64.63 28.12 N/A 528 367 Other: 13.62 22.07 17.84 N/A 0 2 Chain A: 5.44 51.07 12.00 N/A 0 1624 Chain B: 5.39 63.47 11.86 N/A 0 1647 Chain S: 5.84 64.63 29.79 N/A 528 0 Histogram: Values Number of atoms 5.39 - 11.31 2104 11.31 - 17.24 798 17.24 - 23.16 277 23.16 - 29.09 223 29.09 - 35.01 174 35.01 - 40.93 117 40.93 - 46.86 73 46.86 - 52.78 24 52.78 - 58.71 7 58.71 - 64.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1361 r_work=0.1206 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1361 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1361 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756418 | | target function (ml) not normalized (work): 703532.092898 | | target function (ml) not normalized (free): 14731.700845 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1373 0.1371 0.1475 n_refl.: 191129 remove outliers: r(all,work,free)=0.1373 0.1371 0.1475 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1373 0.1371 0.1475 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1350 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3720 360.896 330.796 0.431 0.907 0.211 13.296-10.522 96.04 96 1 0.2400 480.430 466.069 0.750 0.909 0.163 10.503-8.327 97.80 175 3 0.2250 501.907 493.691 0.909 0.910 0.114 8.315-6.595 100.00 359 8 0.2168 374.598 369.220 0.937 0.910 0.090 6.588-5.215 100.00 711 7 0.1962 345.087 334.633 0.936 0.910 0.090 5.214-4.128 98.38 1367 28 0.1278 504.758 498.038 1.035 0.911 0.080 4.126-3.266 94.74 2603 46 0.1172 460.114 452.279 1.099 0.912 0.000 3.266-2.585 99.86 5447 97 0.1127 310.382 306.806 1.079 0.913 0.000 2.585-2.046 97.45 10613 204 0.0958 234.165 231.542 1.085 0.914 0.000 2.046-1.619 99.39 21536 464 0.0906 138.591 137.221 1.099 0.917 0.000 1.619-1.281 98.00 42464 925 0.0946 74.609 73.950 1.083 0.922 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.025 38.333 1.040 0.930 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1245 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1350 | n_water=895 | time (s): 3.210 (total time: 3.210) Filter (dist) r_work=0.1195 r_free=0.1349 | n_water=894 | time (s): 123.430 (total time: 126.640) Filter (q & B) r_work=0.1195 r_free=0.1348 | n_water=887 | time (s): 5.000 (total time: 131.640) Compute maps r_work=0.1195 r_free=0.1348 | n_water=887 | time (s): 1.690 (total time: 133.330) Filter (map) r_work=0.1220 r_free=0.1354 | n_water=761 | time (s): 4.090 (total time: 137.420) Find peaks r_work=0.1220 r_free=0.1354 | n_water=761 | time (s): 0.590 (total time: 138.010) Add new water r_work=0.1230 r_free=0.1368 | n_water=979 | time (s): 4.890 (total time: 142.900) Refine new water occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1193 r_free=0.1339 occ: r_work=0.1191 r_free=0.1338 adp: r_work=0.1191 r_free=0.1337 occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1189 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1336 r_work=0.1189 r_free=0.1336 | n_water=979 | time (s): 300.580 (total time: 443.480) Filter (q & B) r_work=0.1194 r_free=0.1344 | n_water=890 | time (s): 4.600 (total time: 448.080) Filter (dist only) r_work=0.1194 r_free=0.1344 | n_water=888 | time (s): 113.690 (total time: 561.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.538003 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.293790 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1349 0.0152 0.038 1.1 4.6 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.49 1.52 1.659 13.508 14.294 3.755 11.96 13.52 1.55 1.655 13.505 14.294 3.753 Individual atomic B min max mean iso aniso Overall: 5.39 64.65 14.36 0.86 521 3271 Protein: 5.39 27.88 10.20 0.86 0 2902 Water: 5.83 64.65 27.95 N/A 521 367 Other: 13.63 22.01 17.82 N/A 0 2 Chain A: 5.48 50.91 11.99 N/A 0 1624 Chain B: 5.39 63.02 11.86 N/A 0 1647 Chain S: 5.83 64.65 29.68 N/A 521 0 Histogram: Values Number of atoms 5.39 - 11.32 2097 11.32 - 17.24 811 17.24 - 23.17 275 23.17 - 29.10 228 29.10 - 35.02 166 35.02 - 40.95 110 40.95 - 46.87 73 46.87 - 52.80 24 52.80 - 58.72 6 58.72 - 64.65 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1352 r_work=0.1197 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1352 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1352 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.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753038 | | target function (ml) not normalized (work): 702895.136402 | | target function (ml) not normalized (free): 14723.135077 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1352 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1381 0.1380 0.1479 n_refl.: 191128 remove outliers: r(all,work,free)=0.1381 0.1380 0.1479 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1381 0.1380 0.1479 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3762 360.896 329.039 0.405 0.973 0.216 13.296-10.522 96.04 96 1 0.2391 480.430 462.043 0.694 0.975 0.163 10.503-8.327 97.80 175 3 0.2250 501.907 493.024 0.844 0.975 0.114 8.315-6.595 100.00 359 8 0.2164 374.598 369.838 0.873 0.975 0.090 6.588-5.215 100.00 711 7 0.1977 345.087 334.400 0.873 0.976 0.090 5.214-4.128 98.38 1367 28 0.1279 504.758 498.056 0.965 0.977 0.080 4.126-3.266 94.74 2603 46 0.1183 460.114 452.328 1.026 0.978 0.005 3.266-2.585 99.86 5447 97 0.1132 310.382 306.836 1.007 0.979 0.000 2.585-2.046 97.45 10613 204 0.0957 234.165 231.553 1.013 0.981 0.000 2.046-1.619 99.39 21536 464 0.0907 138.591 137.250 1.027 0.984 0.000 1.619-1.281 98.00 42464 925 0.0941 74.609 73.965 1.013 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.025 38.329 0.976 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0894 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1194 r_free=0.1351 After: r_work=0.1195 r_free=0.1352 ================================== NQH flips ================================== r_work=0.1195 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1352 | n_water=888 | time (s): 3.220 (total time: 3.220) Filter (dist) r_work=0.1195 r_free=0.1352 | n_water=888 | time (s): 111.850 (total time: 115.070) Filter (q & B) r_work=0.1195 r_free=0.1352 | n_water=882 | time (s): 5.550 (total time: 120.620) Compute maps r_work=0.1195 r_free=0.1352 | n_water=882 | time (s): 1.840 (total time: 122.460) Filter (map) r_work=0.1217 r_free=0.1351 | n_water=769 | time (s): 4.210 (total time: 126.670) Find peaks r_work=0.1217 r_free=0.1351 | n_water=769 | time (s): 0.560 (total time: 127.230) Add new water r_work=0.1226 r_free=0.1370 | n_water=984 | time (s): 4.390 (total time: 131.620) Refine new water occ: r_work=0.1193 r_free=0.1342 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1191 r_free=0.1340 adp: r_work=0.1191 r_free=0.1340 occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1190 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1338 r_work=0.1190 r_free=0.1338 | n_water=984 | time (s): 317.130 (total time: 448.750) Filter (q & B) r_work=0.1195 r_free=0.1345 | n_water=891 | time (s): 4.140 (total time: 452.890) Filter (dist only) r_work=0.1195 r_free=0.1344 | n_water=889 | time (s): 117.840 (total time: 570.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.488018 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.367119 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1348 0.0151 0.039 1.1 7.5 0.0 0.3 0 0.744 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.48 1.51 1.660 13.511 14.367 3.755 11.98 13.49 1.51 1.657 13.510 14.367 3.754 Individual atomic B min max mean iso aniso Overall: 5.45 64.63 14.35 0.86 522 3271 Protein: 5.45 27.86 10.22 0.86 0 2902 Water: 5.89 64.63 27.83 N/A 522 367 Other: 13.69 21.98 17.84 N/A 0 2 Chain A: 5.56 50.62 11.99 N/A 0 1624 Chain B: 5.45 62.12 11.86 N/A 0 1647 Chain S: 5.89 64.63 29.60 N/A 522 0 Histogram: Values Number of atoms 5.45 - 11.37 2102 11.37 - 17.29 817 17.29 - 23.21 268 23.21 - 29.12 233 29.12 - 35.04 160 35.04 - 40.96 109 40.96 - 46.88 69 46.88 - 52.79 27 52.79 - 58.71 6 58.71 - 64.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1349 r_work=0.1198 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1349 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1347 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754025 | | target function (ml) not normalized (work): 703080.019440 | | target function (ml) not normalized (free): 14718.207730 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1381 0.1472 5.7046 5.7792| | 2: 2.94 - 2.33 1.00 7339 128 0.1076 0.1288 5.0843 5.1632| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1157 4.6485 4.724| | 4: 2.04 - 1.85 1.00 7170 155 0.0898 0.1047 4.3889 4.5584| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.1002 4.1521 4.2556| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1079 3.9478 4.0731| | 7: 1.62 - 1.54 0.99 7104 148 0.0891 0.0970 3.799 3.9333| | 8: 1.54 - 1.47 0.96 6798 152 0.0890 0.1320 3.6991 3.9086| | 9: 1.47 - 1.41 0.98 6938 155 0.0927 0.1126 3.6203 3.7451| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1173 3.5514 3.6593| | 11: 1.36 - 1.32 0.99 6997 151 0.0990 0.1110 3.48 3.5752| | 12: 1.32 - 1.28 0.98 6975 149 0.1034 0.1114 3.4572 3.574| | 13: 1.28 - 1.25 0.98 6907 166 0.1046 0.1255 3.4374 3.5699| | 14: 1.25 - 1.22 0.98 7015 112 0.1110 0.1604 3.4327 3.6836| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1226 3.4486 3.4844| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1548 3.464 3.6565| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1227 3.4325 3.4422| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1704 3.4379 3.5308| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1756 3.4194 3.6003| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1577 3.4099 3.4302| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2140 3.4182 3.5028| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1963 3.4127 3.4164| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2028 3.4324 3.4867| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2251 3.435 3.5086| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2501 3.4489 3.5224| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2871 3.415 3.4232| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2801 3.4687 3.3942| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7396 127 0.93 11.97 1.00 0.96 11551.12| | 2: 2.94 - 2.33 7339 128 0.93 12.89 0.99 0.97 5189.70| | 3: 2.33 - 2.04 6939 150 0.96 7.43 1.01 0.97 1643.99| | 4: 2.04 - 1.85 7170 155 0.96 7.56 1.00 0.97 988.79| | 5: 1.85 - 1.72 7113 159 0.96 8.09 1.00 0.97 635.32| | 6: 1.72 - 1.62 7102 142 0.96 8.03 1.00 0.98 444.66| | 7: 1.62 - 1.54 7104 148 0.96 8.14 1.01 0.99 337.32| | 8: 1.54 - 1.47 6798 152 0.96 8.24 1.01 0.99 278.75| | 9: 1.47 - 1.41 6938 155 0.96 8.40 1.00 0.99 228.44| | 10: 1.41 - 1.36 7022 150 0.96 8.80 1.00 0.99 198.85| | 11: 1.36 - 1.32 6997 151 0.96 8.77 0.99 0.97 170.97| | 12: 1.32 - 1.28 6975 149 0.96 8.86 0.98 0.96 157.92| | 13: 1.28 - 1.25 6907 166 0.96 9.48 1.01 0.98 156.98| | 14: 1.25 - 1.22 7015 112 0.95 10.70 1.02 0.98 163.00| | 15: 1.22 - 1.19 6956 137 0.95 11.24 1.01 0.99 166.56| | 16: 1.19 - 1.17 6604 132 0.95 11.40 1.01 0.98 159.92| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.98 153.40| | 18: 1.14 - 1.12 6875 142 0.94 12.71 1.01 0.96 147.21| | 19: 1.12 - 1.10 6948 106 0.93 14.12 1.00 0.96 150.74| | 20: 1.10 - 1.08 6884 147 0.92 15.19 1.00 0.95 149.80| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.94 153.18| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.94 154.89| | 23: 1.05 - 1.03 6827 159 0.87 20.48 0.99 0.93 164.80| | 24: 1.03 - 1.02 6784 133 0.85 23.13 0.99 0.94 178.75| | 25: 1.02 - 1.01 6552 130 0.83 25.10 0.97 0.91 181.63| | 26: 1.01 - 0.99 6767 158 0.81 26.54 0.98 0.89 175.88| | 27: 0.99 - 0.98 6647 131 0.82 26.18 0.98 0.88 160.08| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 147.21 max = 11551.12 mean = 938.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.26| |phase err.(test): min = 0.00 max = 87.41 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1347 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1473 n_refl.: 191128 remove outliers: r(all,work,free)=0.1391 0.1390 0.1473 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1391 0.1390 0.1473 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1343 n_refl.: 191128 remove outliers: r(all,work,free)=0.1199 0.1196 0.1343 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3776 360.896 328.618 0.403 0.973 0.215 13.296-10.522 96.04 96 1 0.2391 480.430 462.229 0.692 0.974 0.161 10.503-8.327 97.80 175 3 0.2253 501.907 493.681 0.842 0.975 0.112 8.315-6.595 100.00 359 8 0.2155 374.598 369.923 0.872 0.975 0.090 6.588-5.215 100.00 711 7 0.1973 345.087 334.244 0.871 0.975 0.085 5.214-4.128 98.38 1367 28 0.1285 504.758 498.064 0.962 0.976 0.044 4.126-3.266 94.74 2603 46 0.1183 460.114 452.333 1.027 0.978 0.005 3.266-2.585 99.86 5447 97 0.1129 310.382 306.847 1.008 0.979 0.000 2.585-2.046 97.45 10613 204 0.0961 234.165 231.568 1.014 0.981 0.000 2.046-1.619 99.39 21536 464 0.0911 138.591 137.247 1.028 0.985 0.000 1.619-1.281 98.00 42464 925 0.0945 74.609 73.962 1.015 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.025 38.323 0.979 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0557 ================= 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 : 0.2033 0.1974 0.081 5.167 5.2 78.0 14.6 805 0.000 1_bss: 0.1801 0.1902 0.081 5.167 5.2 78.1 14.6 805 0.000 1_settarget: 0.1801 0.1902 0.081 5.167 5.2 78.1 14.6 805 0.000 1_nqh: 0.1806 0.1901 0.081 5.167 5.2 78.1 14.6 805 0.002 1_weight: 0.1806 0.1901 0.081 5.167 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1270 0.1497 0.037 1.163 5.2 78.1 14.6 805 0.156 1_adp: 0.1293 0.1563 0.037 1.163 5.1 73.1 14.9 805 0.156 1_regHadp: 0.1292 0.1559 0.037 1.163 5.1 73.1 14.9 805 0.156 1_occ: 0.1278 0.1547 0.037 1.163 5.1 73.1 14.9 805 0.156 2_bss: 0.1270 0.1539 0.037 1.163 5.3 73.2 15.1 805 0.156 2_settarget: 0.1270 0.1539 0.037 1.163 5.3 73.2 15.1 805 0.156 2_updatecdl: 0.1270 0.1539 0.037 1.170 5.3 73.2 15.1 805 0.156 2_nqh: 0.1271 0.1541 0.037 1.170 5.3 73.2 15.1 805 0.155 2_sol: 0.1268 0.1511 0.037 1.170 5.3 73.2 16.2 883 n/a 2_weight: 0.1268 0.1511 0.037 1.170 5.3 73.2 16.2 883 n/a 2_xyzrec: 0.1253 0.1516 0.042 1.146 5.3 73.2 16.2 883 n/a 2_adp: 0.1233 0.1507 0.042 1.146 5.4 68.2 16.3 883 n/a 2_regHadp: 0.1234 0.1508 0.042 1.146 5.4 68.2 16.3 883 n/a 2_occ: 0.1227 0.1505 0.042 1.146 5.4 68.2 16.3 883 n/a 3_bss: 0.1233 0.1510 0.042 1.146 5.4 68.2 16.3 883 n/a 3_settarget: 0.1233 0.1510 0.042 1.146 5.4 68.2 16.3 883 n/a 3_updatecdl: 0.1233 0.1510 0.042 1.149 5.4 68.2 16.3 883 n/a 3_nqh: 0.1233 0.1510 0.042 1.149 5.4 68.2 16.3 883 n/a 3_sol: 0.1250 0.1497 0.042 1.149 5.4 68.2 15.3 871 n/a 3_weight: 0.1250 0.1497 0.042 1.149 5.4 68.2 15.3 871 n/a 3_xyzrec: 0.1238 0.1434 0.035 1.102 5.4 68.2 15.3 871 n/a 3_adp: 0.1231 0.1390 0.035 1.102 5.5 67.8 15.2 871 n/a 3_regHadp: 0.1231 0.1391 0.035 1.102 5.5 67.8 15.2 871 n/a 3_occ: 0.1226 0.1384 0.035 1.102 5.5 67.8 15.2 871 n/a 4_bss: 0.1222 0.1378 0.035 1.102 5.5 67.8 15.1 871 n/a 4_settarget: 0.1222 0.1378 0.035 1.102 5.5 67.8 15.1 871 n/a 4_updatecdl: 0.1222 0.1378 0.035 1.103 5.5 67.8 15.1 871 n/a 4_nqh: 0.1222 0.1378 0.035 1.103 5.5 67.8 15.1 871 n/a 4_sol: 0.1206 0.1353 0.035 1.103 5.5 67.8 14.9 851 n/a 4_weight: 0.1206 0.1353 0.035 1.103 5.5 67.8 14.9 851 n/a 4_xyzrec: 0.1205 0.1354 0.035 1.122 5.5 67.8 14.9 851 n/a 4_adp: 0.1200 0.1352 0.035 1.122 5.5 67.4 14.8 851 n/a 4_regHadp: 0.1200 0.1352 0.035 1.122 5.5 67.4 14.8 851 n/a 4_occ: 0.1198 0.1350 0.035 1.122 5.5 67.4 14.8 851 n/a 5_bss: 0.1196 0.1349 0.035 1.122 5.5 67.4 14.8 851 n/a 5_settarget: 0.1196 0.1349 0.035 1.122 5.5 67.4 14.8 851 n/a 5_updatecdl: 0.1196 0.1349 0.035 1.123 5.5 67.4 14.8 851 n/a 5_nqh: 0.1196 0.1349 0.035 1.123 5.5 67.4 14.8 851 n/a 5_sol: 0.1194 0.1340 0.035 1.123 5.5 67.4 14.9 869 n/a 5_weight: 0.1194 0.1340 0.035 1.123 5.5 67.4 14.9 869 n/a 5_xyzrec: 0.1198 0.1348 0.036 1.128 5.5 67.4 14.9 869 n/a 5_adp: 0.1202 0.1351 0.036 1.128 5.6 67.1 14.8 869 n/a 5_regHadp: 0.1202 0.1351 0.036 1.128 5.6 67.1 14.8 869 n/a 5_occ: 0.1200 0.1352 0.036 1.128 5.6 67.1 14.8 869 n/a 6_bss: 0.1199 0.1353 0.036 1.128 5.5 67.1 14.8 869 n/a 6_settarget: 0.1199 0.1353 0.036 1.128 5.5 67.1 14.8 869 n/a 6_updatecdl: 0.1199 0.1353 0.036 1.128 5.5 67.1 14.8 869 n/a 6_nqh: 0.1199 0.1353 0.036 1.128 5.5 67.1 14.8 869 n/a 6_sol: 0.1198 0.1343 0.036 1.128 5.5 67.1 14.8 876 n/a 6_weight: 0.1198 0.1343 0.036 1.128 5.5 67.1 14.8 876 n/a 6_xyzrec: 0.1201 0.1351 0.037 1.124 5.5 67.1 14.8 876 n/a 6_adp: 0.1206 0.1356 0.037 1.124 5.6 66.0 14.7 876 n/a 6_regHadp: 0.1207 0.1356 0.037 1.124 5.6 66.0 14.7 876 n/a 6_occ: 0.1204 0.1354 0.037 1.124 5.6 66.0 14.7 876 n/a 7_bss: 0.1202 0.1352 0.037 1.124 5.6 65.9 14.7 876 n/a 7_settarget: 0.1202 0.1352 0.037 1.124 5.6 65.9 14.7 876 n/a 7_updatecdl: 0.1202 0.1352 0.037 1.124 5.6 65.9 14.7 876 n/a 7_nqh: 0.1202 0.1352 0.037 1.124 5.6 65.9 14.7 876 n/a 7_sol: 0.1202 0.1350 0.037 1.124 5.6 65.9 14.7 886 n/a 7_weight: 0.1202 0.1350 0.037 1.124 5.6 65.9 14.7 886 n/a 7_xyzrec: 0.1205 0.1356 0.038 1.124 5.6 65.9 14.7 886 n/a 7_adp: 0.1205 0.1358 0.038 1.124 5.6 64.8 14.7 886 n/a 7_regHadp: 0.1205 0.1358 0.038 1.124 5.6 64.8 14.7 886 n/a 7_occ: 0.1203 0.1359 0.038 1.124 5.6 64.8 14.7 886 n/a 8_bss: 0.1203 0.1360 0.038 1.124 5.4 64.6 14.4 886 n/a 8_settarget: 0.1203 0.1360 0.038 1.124 5.4 64.6 14.4 886 n/a 8_updatecdl: 0.1203 0.1360 0.038 1.125 5.4 64.6 14.4 886 n/a 8_nqh: 0.1203 0.1360 0.038 1.125 5.4 64.6 14.4 886 n/a 8_sol: 0.1201 0.1350 0.038 1.125 5.4 64.6 14.4 895 n/a 8_weight: 0.1201 0.1350 0.038 1.125 5.4 64.6 14.4 895 n/a 8_xyzrec: 0.1204 0.1357 0.038 1.120 5.4 64.6 14.4 895 n/a 8_adp: 0.1206 0.1361 0.038 1.120 5.4 64.6 14.4 895 n/a 8_regHadp: 0.1206 0.1361 0.038 1.120 5.4 64.6 14.4 895 n/a 8_occ: 0.1204 0.1361 0.038 1.120 5.4 64.6 14.4 895 n/a 9_bss: 0.1194 0.1350 0.038 1.120 5.4 64.6 14.4 895 n/a 9_settarget: 0.1194 0.1350 0.038 1.120 5.4 64.6 14.4 895 n/a 9_updatecdl: 0.1194 0.1350 0.038 1.120 5.4 64.6 14.4 895 n/a 9_nqh: 0.1194 0.1350 0.038 1.120 5.4 64.6 14.4 895 n/a 9_sol: 0.1194 0.1344 0.038 1.120 5.4 64.6 14.4 888 n/a 9_weight: 0.1194 0.1344 0.038 1.120 5.4 64.6 14.4 888 n/a 9_xyzrec: 0.1197 0.1349 0.038 1.112 5.4 64.6 14.4 888 n/a 9_adp: 0.1197 0.1352 0.038 1.112 5.4 64.6 14.4 888 n/a 9_regHadp: 0.1197 0.1352 0.038 1.112 5.4 64.6 14.4 888 n/a 9_occ: 0.1195 0.1352 0.038 1.112 5.4 64.6 14.4 888 n/a 10_bss: 0.1194 0.1351 0.038 1.112 5.4 64.6 14.4 888 n/a 10_settarget: 0.1194 0.1351 0.038 1.112 5.4 64.6 14.4 888 n/a 10_updatecdl: 0.1194 0.1351 0.038 1.112 5.4 64.6 14.4 888 n/a 10_setrh: 0.1195 0.1352 0.038 1.112 5.4 64.6 14.4 888 n/a 10_nqh: 0.1195 0.1352 0.038 1.112 5.4 64.6 14.4 888 n/a 10_sol: 0.1195 0.1344 0.038 1.112 5.4 64.6 14.4 889 n/a 10_weight: 0.1195 0.1344 0.038 1.112 5.4 64.6 14.4 889 n/a 10_xyzrec: 0.1197 0.1348 0.039 1.148 5.4 64.6 14.4 889 n/a 10_adp: 0.1198 0.1349 0.039 1.148 5.5 64.6 14.4 889 n/a 10_regHadp: 0.1198 0.1349 0.039 1.148 5.5 64.6 14.4 889 n/a 10_occ: 0.1197 0.1347 0.039 1.148 5.5 64.6 14.4 889 n/a end: 0.1196 0.1343 0.039 1.148 5.5 64.6 14.4 889 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6195814_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6195814_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.9700 Refinement macro-cycles (run) : 12244.0700 Write final files (write_after_run_outputs) : 148.1800 Total : 12399.2200 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:51 PST -0800 (1736736231.73 s) Start R-work = 0.1801, R-free = 0.1902 Final R-work = 0.1196, R-free = 0.1343 =============================================================================== Job complete usr+sys time: 12659.66 seconds wall clock time: 212 minutes 1.44 seconds (12721.44 seconds total)