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_9682641.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9682641.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9682641.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } 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 =============================================================================== 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: 1.68, per 1000 atoms: 0.25 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: 2.644 distance_ideal: 2.720 ideal - model: 0.076 slack: 0.000 delta_slack: 0.076 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: 2.672 distance_ideal: 2.710 ideal - model: 0.038 slack: 0.000 delta_slack: 0.038 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: 0.74 Conformation dependent library (CDL) restraints added in 188.2 milliseconds Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.04: 954 1.04 - 1.29: 2537 1.29 - 1.54: 1737 1.54 - 1.79: 700 1.79 - 2.03: 6 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL B 114 " pdb=" CB VAL B 114 " ideal model delta sigma weight residual 1.539 1.419 0.120 5.40e-03 3.43e+04 4.96e+02 bond pdb=" N ALA B 5 " pdb=" H ALA B 5 " ideal model delta sigma weight residual 0.860 1.283 -0.423 2.00e-02 2.50e+03 4.47e+02 bond pdb=" N VAL B 92 " pdb=" H VAL B 92 " ideal model delta sigma weight residual 0.860 1.275 -0.415 2.00e-02 2.50e+03 4.31e+02 bond pdb=" NE ARG A 100 " pdb=" HE ARG A 100 " ideal model delta sigma weight residual 0.860 1.265 -0.405 2.00e-02 2.50e+03 4.10e+02 bond pdb=" CA VAL B 37 " pdb=" C VAL B 37 " ideal model delta sigma weight residual 1.523 1.268 0.255 1.27e-02 6.20e+03 4.02e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.98: 5446 3.98 - 7.95: 3579 7.95 - 11.93: 1416 11.93 - 15.91: 341 15.91 - 19.89: 28 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O GLU B 180 " pdb=" C GLU B 180 " pdb=" N VAL B 181 " ideal model delta sigma weight residual 122.07 105.97 16.10 1.03e+00 9.43e-01 2.44e+02 angle pdb=" CA GLY B 165 " pdb=" C GLY B 165 " pdb=" N LEU B 166 " ideal model delta sigma weight residual 117.04 132.23 -15.19 9.90e-01 1.02e+00 2.36e+02 angle pdb=" CA GLY A 78 " pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 121.05 135.96 -14.91 1.03e+00 9.43e-01 2.09e+02 angle pdb=" CA THR B 16 " pdb=" C THR B 16 " pdb=" O THR B 16 " ideal model delta sigma weight residual 120.82 106.09 14.73 1.05e+00 9.07e-01 1.97e+02 angle pdb=" CA VAL B 71 " pdb=" C VAL B 71 " pdb=" O VAL B 71 " ideal model delta sigma weight residual 120.39 135.02 -14.63 1.05e+00 9.07e-01 1.94e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.45: 1826 16.45 - 32.89: 151 32.89 - 49.33: 46 49.33 - 65.77: 23 65.77 - 82.21: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA THR B 33 " pdb=" C THR B 33 " pdb=" N THR B 34 " pdb=" CA THR B 34 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CB TRP A 139 " pdb=" CG TRP A 139 " pdb=" CD1 TRP A 139 " pdb=" HD1 TRP A 139 " ideal model delta harmonic sigma weight residual 0.00 -25.57 25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -157.29 -22.71 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.216: 194 0.216 - 0.428: 152 0.428 - 0.641: 91 0.641 - 0.854: 47 0.854 - 1.066: 8 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA THR B 46 " pdb=" N THR B 46 " pdb=" C THR B 46 " pdb=" CB THR B 46 " both_signs ideal model delta sigma weight residual False 2.53 3.59 -1.07 2.00e-01 2.50e+01 2.84e+01 chirality pdb=" CA VAL B 89 " pdb=" N VAL B 89 " pdb=" C VAL B 89 " pdb=" CB VAL B 89 " both_signs ideal model delta sigma weight residual False 2.44 1.40 1.04 2.00e-01 2.50e+01 2.69e+01 chirality pdb=" CB ILE B 76 " pdb=" CA ILE B 76 " pdb=" CG1 ILE B 76 " pdb=" CG2 ILE B 76 " both_signs ideal model delta sigma weight residual False 2.64 3.57 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.086 2.00e-02 2.50e+03 8.15e-02 1.99e+02 pdb=" CG TYR A 194 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " -0.084 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " 0.079 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.098 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.114 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " -0.108 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " 0.130 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.160 2.00e-02 2.50e+03 7.10e-02 1.51e+02 pdb=" CG PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.105 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.039 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.038 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.078 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.094 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.086 2.00e-02 2.50e+03 6.12e-02 1.50e+02 pdb=" CG TRP A 139 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.081 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.112 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.046 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.079 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.046 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.041 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.090 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.063 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.074 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.55: 20 1.55 - 2.31: 1850 2.31 - 3.07: 21751 3.07 - 3.84: 33107 3.84 - 4.60: 53626 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110354 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.784 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.034 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.035 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.153 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.168 2.620 ... (remaining 110349 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_9682641_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= 0.2036 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298484 | | target function (ml) not normalized (work): 805162.025837 | | target function (ml) not normalized (free): 16558.751222 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2134 0.1993 6.6834 6.3158| | 2: 2.94 - 2.33 1.00 7339 128 0.1634 0.1456 5.5451 5.5638| | 3: 2.33 - 2.04 0.96 6939 150 0.1642 0.1458 5.139 5.109| | 4: 2.04 - 1.85 1.00 7170 155 0.1757 0.1748 4.9695 5.1212| | 5: 1.85 - 1.72 0.99 7113 159 0.1935 0.1752 4.8038 4.8252| | 6: 1.72 - 1.62 0.99 7102 142 0.2009 0.1889 4.6758 4.74| | 7: 1.62 - 1.54 0.99 7104 148 0.2022 0.1685 4.5682 4.5385| | 8: 1.54 - 1.47 0.96 6798 152 0.2060 0.2397 4.4734 4.5913| | 9: 1.47 - 1.41 0.98 6938 155 0.2084 0.2246 4.396 4.4797| | 10: 1.41 - 1.36 0.99 7022 150 0.2081 0.2174 4.3044 4.3126| | 11: 1.36 - 1.32 0.99 6997 151 0.2074 0.2151 4.229 4.2647| | 12: 1.32 - 1.28 0.98 6976 149 0.2063 0.2119 4.1644 4.2517| | 13: 1.28 - 1.25 0.98 6907 166 0.2047 0.2003 4.1155 4.1306| | 14: 1.25 - 1.22 0.98 7015 113 0.2039 0.2148 4.055 4.1559| | 15: 1.22 - 1.19 0.98 6957 137 0.2095 0.1851 4.0264 3.9406| | 16: 1.19 - 1.17 0.93 6604 132 0.2119 0.2009 4 4.0098| | 17: 1.17 - 1.14 0.98 6941 135 0.2158 0.1951 3.9584 3.9819| | 18: 1.14 - 1.12 0.98 6875 142 0.2197 0.2398 3.9103 3.9222| | 19: 1.12 - 1.10 0.97 6949 106 0.2285 0.2780 3.8827 4.1172| | 20: 1.10 - 1.08 0.97 6884 147 0.2290 0.2312 3.8222 3.8762| | 21: 1.08 - 1.07 0.97 6852 152 0.2439 0.2683 3.797 3.8572| | 22: 1.07 - 1.05 0.97 6838 135 0.2551 0.2369 3.7515 3.6991| | 23: 1.05 - 1.03 0.97 6829 159 0.2706 0.2738 3.7294 3.8311| | 24: 1.03 - 1.02 0.96 6785 133 0.2881 0.2972 3.6975 3.8012| | 25: 1.02 - 1.01 0.93 6552 130 0.3085 0.2995 3.6764 3.7178| | 26: 1.01 - 0.99 0.96 6767 158 0.3213 0.3235 3.6293 3.6164| | 27: 0.99 - 0.98 0.94 6648 131 0.3463 0.3244 3.6417 3.6296| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.73 0.91 0.98 36458.10| | 2: 2.94 - 2.33 7339 128 0.85 21.34 1.09 1.02 15274.55| | 3: 2.33 - 2.04 6939 150 0.93 12.28 1.11 1.05 4027.76| | 4: 2.04 - 1.85 7170 155 0.92 13.64 1.11 1.07 2827.50| | 5: 1.85 - 1.72 7113 159 0.91 15.91 1.12 1.07 2143.47| | 6: 1.72 - 1.62 7102 142 0.90 17.08 1.12 1.07 1699.53| | 7: 1.62 - 1.54 7104 148 0.89 17.73 1.11 1.07 1373.90| | 8: 1.54 - 1.47 6798 152 0.88 19.12 1.11 1.07 1221.81| | 9: 1.47 - 1.41 6938 155 0.88 19.32 1.10 1.07 1027.55| | 10: 1.41 - 1.36 7022 150 0.87 20.21 1.09 1.07 878.49| | 11: 1.36 - 1.32 6997 151 0.88 19.42 1.09 1.06 709.80| | 12: 1.32 - 1.28 6976 149 0.88 19.34 1.08 1.05 635.54| | 13: 1.28 - 1.25 6907 166 0.88 19.15 1.07 1.04 559.91| | 14: 1.25 - 1.22 7015 113 0.88 19.65 1.08 1.04 524.67| | 15: 1.22 - 1.19 6957 137 0.88 19.36 1.08 1.04 477.18| | 16: 1.19 - 1.17 6604 132 0.88 19.18 1.08 1.03 439.11| | 17: 1.17 - 1.14 6941 135 0.87 20.33 1.08 1.02 419.20| | 18: 1.14 - 1.12 6875 142 0.86 21.65 1.08 0.99 407.41| | 19: 1.12 - 1.10 6949 106 0.84 23.55 1.07 0.99 420.39| | 20: 1.10 - 1.08 6884 147 0.83 24.09 1.06 0.97 383.10| | 21: 1.08 - 1.07 6852 152 0.83 24.79 1.06 0.97 358.58| | 22: 1.07 - 1.05 6838 135 0.82 25.44 1.05 0.96 323.01| | 23: 1.05 - 1.03 6829 159 0.80 27.68 1.05 0.96 329.85| | 24: 1.03 - 1.02 6785 133 0.77 29.89 1.05 0.96 332.66| | 25: 1.02 - 1.01 6552 130 0.76 31.19 1.03 0.93 319.46| | 26: 1.01 - 0.99 6767 158 0.74 32.79 1.03 0.93 304.82| | 27: 0.99 - 0.98 6648 131 0.74 33.21 1.03 0.93 295.30| |alpha: min = 0.93 max = 1.07 mean = 1.02| |beta: min = 295.30 max = 36458.10 mean = 2877.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.70| |phase err.(test): min = 0.00 max = 89.49 mean = 21.81| |-----------------------------------------------------------------------------| ----------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 0.255 2950 Z= 5.466 Angle : 5.218 16.102 4018 Z= 3.748 Chirality : 0.392 1.066 492 Planarity : 0.032 0.135 512 Dihedral : 12.472 82.207 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.60 % Rotamer: Outliers : 0.65 % Allowed : 3.87 % Favored : 95.48 % Cbeta Deviations : 29.78 % 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: -1.18 (0.40), residues: 386 helix: -1.88 (0.35), residues: 144 sheet: -0.41 (0.54), residues: 82 loop : 0.45 (0.49), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.073 0.015 ARG A 49 TYR 0.103 0.043 TYR B 195 PHE 0.102 0.032 PHE A 164 TRP 0.114 0.043 TRP A 139 HIS 0.080 0.040 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= 0.2036 r_free= 0.1975 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298484 | | target function (ml) not normalized (work): 805162.025837 | | target function (ml) not normalized (free): 16558.751222 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2036 0.1975 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2036 0.1975 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2036 0.1975 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2036 0.2038 0.1976 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1804 0.1801 0.1917 n_refl.: 191145 remove outliers: r(all,work,free)=0.1801 0.1799 0.1917 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 0.4065 402.814 291.795 0.424 0.933 0.303 13.296-10.522 99.01 99 1 0.2520 528.187 518.003 0.768 0.934 0.253 10.503-8.327 98.90 177 3 0.2472 564.205 560.057 0.949 0.934 0.227 8.318-6.595 100.00 360 8 0.2459 414.736 404.104 0.942 0.933 0.155 6.588-5.215 100.00 711 7 0.2275 381.101 365.747 0.936 0.933 0.150 5.214-4.128 98.38 1367 28 0.1484 557.435 549.595 1.046 0.933 0.080 4.126-3.266 94.74 2603 46 0.1350 508.132 498.304 1.117 0.932 0.018 3.266-2.585 99.86 5447 97 0.1451 342.774 337.220 1.095 0.929 0.000 2.585-2.046 97.45 10613 204 0.1407 258.603 254.213 1.104 0.926 0.000 2.046-1.619 99.39 21536 464 0.1631 153.054 149.695 1.128 0.920 0.000 1.619-1.281 98.00 42464 925 0.1904 82.395 80.277 1.124 0.911 0.000 1.281-0.980 96.53 101826 2056 0.2313 44.203 41.686 1.121 0.894 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0234 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1799 r_free=0.1917 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1800 r_free=0.1915 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.800359 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.935147 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 0.1268 0.1496 0.0229 0.038 1.2 10.5 0.0 0.3 0 11.900 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.68 14.96 2.29 1.117 13.126 570.935 0.018 12.99 15.69 2.70 1.250 13.360 570.935 0.017 Individual atomic B min max mean iso aniso Overall: 5.15 73.06 15.04 1.40 435 3274 Protein: 5.15 40.33 11.02 1.40 0 2902 Water: 6.32 73.06 29.52 N/A 435 370 Other: 16.13 31.17 23.65 N/A 0 2 Chain A: 5.36 60.34 13.06 N/A 0 1626 Chain B: 5.15 73.06 12.78 N/A 0 1648 Chain S: 11.61 66.26 30.99 N/A 435 0 Histogram: Values Number of atoms 5.15 - 11.94 2161 11.94 - 18.73 645 18.73 - 25.52 310 25.52 - 32.31 266 32.31 - 39.10 154 39.10 - 45.89 108 45.89 - 52.69 41 52.69 - 59.48 18 59.48 - 66.27 5 66.27 - 73.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1569 r_work=0.1298 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1566 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1553 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015553 | | target function (ls_wunit_k1) not normalized (work): 2913.039005 | | target function (ls_wunit_k1) not normalized (free): 117.162248 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1553 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1473 0.1470 0.1632 n_refl.: 191138 remove outliers: r(all,work,free)=0.1473 0.1470 0.1632 n_refl.: 191138 overall B=0.15 to atoms: r(all,work,free)=0.1494 0.1492 0.1641 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1278 0.1547 n_refl.: 191138 remove outliers: r(all,work,free)=0.1283 0.1278 0.1546 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3648 402.814 367.946 0.477 0.963 0.287 13.296-10.522 99.01 99 1 0.2059 528.187 519.740 0.734 0.964 0.240 10.503-8.327 98.90 177 3 0.1739 564.205 564.109 0.890 0.965 0.215 8.318-6.595 100.00 360 8 0.1697 414.736 412.374 0.905 0.964 0.145 6.588-5.215 100.00 711 7 0.1530 381.101 374.285 0.890 0.965 0.140 5.214-4.128 98.38 1367 28 0.0907 557.435 554.451 0.975 0.965 0.070 4.126-3.266 94.74 2603 46 0.0830 508.132 504.118 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0918 342.774 340.456 1.026 0.965 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.366 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1091 153.054 151.425 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1287 82.395 81.371 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1883 44.202 42.215 1.025 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0341 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1278 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1546 | n_water=805 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1282 r_free=0.1548 | n_water=793 | time (s): 107.570 (total time: 110.060) Filter (q & B) r_work=0.1283 r_free=0.1549 | n_water=788 | time (s): 4.710 (total time: 114.770) Compute maps r_work=0.1283 r_free=0.1549 | n_water=788 | time (s): 2.110 (total time: 116.880) Filter (map) r_work=0.1309 r_free=0.1534 | n_water=650 | time (s): 4.360 (total time: 121.240) Find peaks r_work=0.1309 r_free=0.1534 | n_water=650 | time (s): 0.760 (total time: 122.000) Add new water r_work=0.1330 r_free=0.1565 | n_water=944 | time (s): 4.520 (total time: 126.520) Refine new water occ: r_work=0.1288 r_free=0.1522 adp: r_work=0.1276 r_free=0.1516 occ: r_work=0.1278 r_free=0.1518 adp: r_work=0.1272 r_free=0.1514 occ: r_work=0.1273 r_free=0.1514 adp: r_work=0.1271 r_free=0.1513 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1513 r_work=0.1271 r_free=0.1513 | n_water=944 | time (s): 79.480 (total time: 206.000) Filter (q & B) r_work=0.1274 r_free=0.1516 | n_water=878 | time (s): 5.110 (total time: 211.110) Filter (dist only) r_work=0.1275 r_free=0.1516 | n_water=877 | time (s): 112.210 (total time: 323.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.516577 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 589.280183 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 0.1258 0.1529 0.0271 0.041 1.2 19.0 0.0 0.0 0 11.758 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.58 15.29 2.71 2.042 15.095 589.280 0.014 12.31 15.08 2.77 2.405 15.163 589.280 0.014 Individual atomic B min max mean iso aniso Overall: 5.41 68.21 16.20 1.21 509 3272 Protein: 5.41 40.63 10.98 1.21 0 2902 Water: 6.64 68.21 33.44 N/A 509 368 Other: 16.36 33.98 25.17 N/A 0 2 Chain A: 5.53 56.67 13.01 N/A 0 1624 Chain B: 5.41 68.21 12.81 N/A 0 1648 Chain S: 13.45 66.67 37.34 N/A 509 0 Histogram: Values Number of atoms 5.41 - 11.69 2064 11.69 - 17.97 712 17.97 - 24.25 266 24.25 - 30.53 203 30.53 - 36.81 178 36.81 - 43.09 164 43.09 - 49.37 108 49.37 - 55.65 47 55.65 - 61.93 27 61.93 - 68.21 12 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1509 r_work=0.1232 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1510 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 = 0.1226 r_free = 0.1511 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1511 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013438 | | target function (ls_wunit_k1) not normalized (work): 2516.955330 | | target function (ls_wunit_k1) not normalized (free): 100.764187 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1511 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1606 n_refl.: 191137 remove outliers: r(all,work,free)=0.1435 0.1432 0.1606 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1604 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1515 n_refl.: 191137 remove outliers: r(all,work,free)=0.1239 0.1233 0.1515 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3300 402.814 379.484 0.490 0.963 0.275 13.296-10.522 99.01 99 1 0.1877 528.187 519.999 0.754 0.964 0.221 10.503-8.327 98.90 177 3 0.1465 564.205 565.797 0.921 0.964 0.190 8.318-6.595 100.00 360 8 0.1531 414.736 414.277 0.936 0.963 0.150 6.588-5.215 100.00 711 7 0.1324 381.101 376.941 0.916 0.963 0.140 5.214-4.128 98.38 1367 28 0.0823 557.435 556.026 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0768 508.132 505.604 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0864 342.774 341.401 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.768 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.625 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.354 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.216 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0555 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1515 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1515 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1515 | n_water=877 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1235 r_free=0.1519 | n_water=869 | time (s): 123.390 (total time: 125.690) Filter (q & B) r_work=0.1235 r_free=0.1519 | n_water=869 | time (s): 1.810 (total time: 127.500) Compute maps r_work=0.1235 r_free=0.1519 | n_water=869 | time (s): 2.280 (total time: 129.780) Filter (map) r_work=0.1274 r_free=0.1518 | n_water=685 | time (s): 4.530 (total time: 134.310) Find peaks r_work=0.1274 r_free=0.1518 | n_water=685 | time (s): 0.660 (total time: 134.970) Add new water r_work=0.1297 r_free=0.1554 | n_water=1009 | time (s): 4.320 (total time: 139.290) Refine new water occ: r_work=0.1251 r_free=0.1520 adp: r_work=0.1252 r_free=0.1520 occ: r_work=0.1248 r_free=0.1518 adp: r_work=0.1248 r_free=0.1518 occ: r_work=0.1245 r_free=0.1517 adp: r_work=0.1244 r_free=0.1516 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1516 r_work=0.1244 r_free=0.1516 | n_water=1009 | time (s): 349.980 (total time: 489.270) Filter (q & B) r_work=0.1250 r_free=0.1516 | n_water=861 | time (s): 4.370 (total time: 493.640) Filter (dist only) r_work=0.1251 r_free=0.1517 | n_water=860 | time (s): 113.600 (total time: 607.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.669045 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.312125 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1240 0.1439 0.0199 0.035 1.1 6.5 0.0 0.0 0 0.835 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.39 1.99 1.934 14.552 16.312 3.938 12.36 14.04 1.68 2.224 14.457 16.312 3.898 Individual atomic B min max mean iso aniso Overall: 5.53 67.78 15.20 1.06 493 3271 Protein: 5.53 36.77 10.75 1.06 0 2902 Water: 6.68 67.78 30.21 N/A 493 367 Other: 14.16 29.29 21.73 N/A 0 2 Chain A: 5.56 55.79 12.78 N/A 0 1624 Chain B: 5.53 67.78 12.54 N/A 0 1647 Chain S: 14.20 63.54 32.09 N/A 493 0 Histogram: Values Number of atoms 5.53 - 11.76 2131 11.76 - 17.98 687 17.98 - 24.21 292 24.21 - 30.43 231 30.43 - 36.66 173 36.66 - 42.88 143 42.88 - 49.11 72 49.11 - 55.33 23 55.33 - 61.55 8 61.55 - 67.78 4 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1405 r_work=0.1236 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1406 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1395 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891740 | | target function (ml) not normalized (work): 728907.243936 | | target function (ml) not normalized (free): 15224.076895 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1394 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1448 0.1447 0.1485 n_refl.: 191137 remove outliers: r(all,work,free)=0.1448 0.1447 0.1485 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1442 0.1441 0.1482 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1228 0.1389 n_refl.: 191137 remove outliers: r(all,work,free)=0.1230 0.1227 0.1389 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3808 398.008 363.361 0.417 0.946 0.241 13.296-10.522 99.01 99 1 0.2563 528.187 505.992 0.704 0.947 0.215 10.503-8.327 97.80 175 3 0.2056 554.286 557.231 0.884 0.947 0.168 8.318-6.595 100.00 360 8 0.2122 414.736 410.482 0.896 0.947 0.130 6.588-5.215 100.00 711 7 0.1827 381.101 371.122 0.889 0.947 0.130 5.214-4.128 98.38 1367 28 0.1175 557.435 552.326 0.972 0.947 0.090 4.126-3.266 94.74 2603 46 0.1109 508.132 500.882 1.033 0.947 0.015 3.266-2.585 99.86 5447 97 0.1092 342.774 339.077 1.020 0.946 0.005 2.585-2.046 97.45 10613 204 0.0968 258.603 255.715 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0971 153.054 151.418 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1049 82.395 81.492 1.054 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.314 1.039 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0976 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1389 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1389 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1389 | n_water=860 | time (s): 3.280 (total time: 3.280) Filter (dist) r_work=0.1227 r_free=0.1391 | n_water=859 | time (s): 104.830 (total time: 108.110) Filter (q & B) r_work=0.1227 r_free=0.1389 | n_water=853 | time (s): 5.470 (total time: 113.580) Compute maps r_work=0.1227 r_free=0.1389 | n_water=853 | time (s): 1.650 (total time: 115.230) Filter (map) r_work=0.1250 r_free=0.1400 | n_water=712 | time (s): 4.500 (total time: 119.730) Find peaks r_work=0.1250 r_free=0.1400 | n_water=712 | time (s): 0.750 (total time: 120.480) Add new water r_work=0.1266 r_free=0.1418 | n_water=951 | time (s): 5.030 (total time: 125.510) Refine new water occ: r_work=0.1217 r_free=0.1367 adp: r_work=0.1209 r_free=0.1364 occ: r_work=0.1207 r_free=0.1363 adp: r_work=0.1207 r_free=0.1363 occ: r_work=0.1206 r_free=0.1362 adp: r_work=0.1205 r_free=0.1362 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1362 r_work=0.1205 r_free=0.1362 | n_water=951 | time (s): 328.020 (total time: 453.530) Filter (q & B) r_work=0.1210 r_free=0.1374 | n_water=848 | time (s): 4.410 (total time: 457.940) Filter (dist only) r_work=0.1211 r_free=0.1373 | n_water=847 | time (s): 107.830 (total time: 565.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.537309 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.886538 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 0.1209 0.1376 0.0166 0.036 1.1 6.1 0.0 0.0 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.09 13.76 1.66 1.833 14.161 15.887 3.875 12.03 13.72 1.69 1.964 14.111 15.887 3.866 Individual atomic B min max mean iso aniso Overall: 5.50 67.21 14.87 1.00 480 3271 Protein: 5.50 33.34 10.65 1.00 0 2902 Water: 5.95 67.21 29.31 N/A 480 367 Other: 13.99 27.90 20.95 N/A 0 2 Chain A: 5.56 54.47 12.62 N/A 0 1624 Chain B: 5.50 67.21 12.42 N/A 0 1647 Chain S: 5.95 63.46 30.88 N/A 480 0 Histogram: Values Number of atoms 5.50 - 11.67 2112 11.67 - 17.85 732 17.85 - 24.02 295 24.02 - 30.19 224 30.19 - 36.36 162 36.36 - 42.53 133 42.53 - 48.70 61 48.70 - 54.87 21 54.87 - 61.04 7 61.04 - 67.21 4 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1372 r_work=0.1203 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1372 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1369 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863789 | | target function (ml) not normalized (work): 723660.541450 | | target function (ml) not normalized (free): 15131.497735 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1370 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1429 0.1429 0.1476 n_refl.: 191134 remove outliers: r(all,work,free)=0.1429 0.1429 0.1476 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1422 0.1421 0.1472 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1370 n_refl.: 191134 remove outliers: r(all,work,free)=0.1202 0.1199 0.1370 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3945 360.307 324.374 0.406 0.946 0.236 13.296-10.522 98.02 98 1 0.2546 478.800 453.398 0.702 0.948 0.210 10.503-8.327 97.80 175 3 0.2137 501.782 497.988 0.864 0.948 0.163 8.318-6.595 100.00 360 8 0.2178 375.451 371.463 0.890 0.947 0.105 6.588-5.215 100.00 711 7 0.1899 345.002 335.470 0.883 0.947 0.085 5.214-4.128 98.38 1367 28 0.1208 504.632 499.673 0.973 0.948 0.080 4.126-3.266 94.74 2603 46 0.1130 460.000 453.273 1.035 0.948 0.009 3.266-2.585 99.86 5447 97 0.1089 310.305 307.077 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0940 234.107 231.653 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0911 138.556 137.266 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0986 74.591 73.882 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.015 38.353 1.038 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1370 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1370 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1370 | n_water=847 | time (s): 3.040 (total time: 3.040) Filter (dist) r_work=0.1200 r_free=0.1370 | n_water=845 | time (s): 108.380 (total time: 111.420) Filter (q & B) r_work=0.1200 r_free=0.1369 | n_water=837 | time (s): 4.940 (total time: 116.360) Compute maps r_work=0.1200 r_free=0.1369 | n_water=837 | time (s): 1.840 (total time: 118.200) Filter (map) r_work=0.1223 r_free=0.1366 | n_water=709 | time (s): 5.190 (total time: 123.390) Find peaks r_work=0.1223 r_free=0.1366 | n_water=709 | time (s): 0.570 (total time: 123.960) Add new water r_work=0.1236 r_free=0.1386 | n_water=940 | time (s): 4.380 (total time: 128.340) Refine new water occ: r_work=0.1198 r_free=0.1353 adp: r_work=0.1198 r_free=0.1354 occ: r_work=0.1195 r_free=0.1352 adp: r_work=0.1195 r_free=0.1352 occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1193 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1351 r_work=0.1193 r_free=0.1351 | n_water=940 | time (s): 206.860 (total time: 335.200) Filter (q & B) r_work=0.1196 r_free=0.1361 | n_water=871 | time (s): 4.290 (total time: 339.490) Filter (dist only) r_work=0.1196 r_free=0.1360 | n_water=870 | time (s): 112.980 (total time: 452.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560274 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.367819 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1365 0.0166 0.036 1.1 6.5 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.65 1.66 1.789 14.082 15.368 3.764 12.05 13.70 1.65 1.854 14.054 15.368 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 66.85 14.87 0.95 504 3270 Protein: 5.58 31.90 10.58 0.95 0 2902 Water: 6.03 66.85 29.15 N/A 504 366 Other: 13.79 26.71 20.25 N/A 0 2 Chain A: 5.58 53.64 12.53 N/A 0 1624 Chain B: 5.59 66.85 12.32 N/A 0 1646 Chain S: 6.03 63.39 30.74 N/A 504 0 Histogram: Values Number of atoms 5.58 - 11.70 2142 11.70 - 17.83 717 17.83 - 23.96 306 23.96 - 30.09 210 30.09 - 36.21 170 36.21 - 42.34 134 42.34 - 48.47 67 48.47 - 54.60 19 54.60 - 60.73 5 60.73 - 66.85 4 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1370 r_work=0.1205 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1370 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1369 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761045 | | target function (ml) not normalized (work): 704413.714177 | | target function (ml) not normalized (free): 14747.317933 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1368 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1430 0.1429 0.1484 n_refl.: 191133 remove outliers: r(all,work,free)=0.1430 0.1429 0.1484 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1424 0.1423 0.1480 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1362 n_refl.: 191133 remove outliers: r(all,work,free)=0.1201 0.1197 0.1362 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3613 360.806 310.479 0.387 0.971 0.233 13.296-10.522 98.02 98 1 0.2481 478.800 460.250 0.677 0.973 0.186 10.503-8.327 97.80 175 3 0.2194 501.782 497.270 0.836 0.973 0.163 8.318-6.595 100.00 360 8 0.2179 375.451 371.397 0.862 0.972 0.105 6.588-5.215 100.00 711 7 0.1915 345.002 334.980 0.860 0.972 0.090 5.214-4.128 98.38 1367 28 0.1220 504.632 499.549 0.947 0.971 0.080 4.126-3.266 94.74 2603 46 0.1155 460.000 452.913 1.008 0.970 0.000 3.266-2.585 99.86 5447 97 0.1110 310.305 307.000 0.997 0.967 0.000 2.585-2.046 97.45 10613 204 0.0952 234.107 231.648 1.013 0.963 0.000 2.046-1.619 99.39 21536 464 0.0914 138.556 137.252 1.042 0.956 0.000 1.619-1.281 98.00 42464 925 0.0971 74.591 73.902 1.050 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1643 40.015 38.347 1.054 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1011 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1362 | n_water=870 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1197 r_free=0.1362 | n_water=870 | time (s): 103.420 (total time: 106.080) Filter (q & B) r_work=0.1198 r_free=0.1362 | n_water=857 | time (s): 4.790 (total time: 110.870) Compute maps r_work=0.1198 r_free=0.1362 | n_water=857 | time (s): 2.240 (total time: 113.110) Filter (map) r_work=0.1220 r_free=0.1364 | n_water=736 | time (s): 4.790 (total time: 117.900) Find peaks r_work=0.1220 r_free=0.1364 | n_water=736 | time (s): 0.880 (total time: 118.780) Add new water r_work=0.1231 r_free=0.1384 | n_water=952 | time (s): 5.100 (total time: 123.880) Refine new water occ: r_work=0.1195 r_free=0.1344 adp: r_work=0.1196 r_free=0.1344 occ: r_work=0.1193 r_free=0.1343 adp: r_work=0.1193 r_free=0.1344 occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1343 r_work=0.1191 r_free=0.1343 | n_water=952 | time (s): 329.700 (total time: 453.580) Filter (q & B) r_work=0.1195 r_free=0.1351 | n_water=877 | time (s): 4.860 (total time: 458.440) Filter (dist only) r_work=0.1195 r_free=0.1351 | n_water=875 | time (s): 113.770 (total time: 572.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.521409 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.768890 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1361 0.0162 0.037 1.1 7.3 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.61 1.62 1.759 14.011 14.769 3.761 12.02 13.64 1.62 1.894 13.964 14.769 3.759 Individual atomic B min max mean iso aniso Overall: 5.59 65.62 14.79 0.90 509 3270 Protein: 5.59 29.27 10.48 0.90 0 2902 Water: 5.94 65.62 29.06 N/A 509 366 Other: 13.82 23.60 18.71 N/A 0 2 Chain A: 5.64 52.47 12.39 N/A 0 1624 Chain B: 5.59 65.62 12.20 N/A 0 1646 Chain S: 5.94 63.32 30.83 N/A 509 0 Histogram: Values Number of atoms 5.59 - 11.59 2112 11.59 - 17.59 775 17.59 - 23.60 283 23.60 - 29.60 196 29.60 - 35.60 172 35.60 - 41.61 127 41.61 - 47.61 77 47.61 - 53.61 28 53.61 - 59.62 5 59.62 - 65.62 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1364 r_work=0.1202 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1365 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1365 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757927 | | target function (ml) not normalized (work): 703822.172630 | | target function (ml) not normalized (free): 14736.000361 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1199 0.1365 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1483 n_refl.: 191131 remove outliers: r(all,work,free)=0.1404 0.1403 0.1483 n_refl.: 191131 overall B=-0.23 to atoms: r(all,work,free)=0.1367 0.1365 0.1462 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1367 n_refl.: 191131 remove outliers: r(all,work,free)=0.1206 0.1203 0.1367 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3624 360.806 334.562 0.434 0.952 0.225 13.296-10.522 98.02 98 1 0.2476 478.800 460.973 0.706 0.953 0.171 10.503-8.327 97.80 175 3 0.2190 501.782 497.203 0.881 0.953 0.147 8.318-6.595 100.00 360 8 0.2175 375.451 371.782 0.906 0.953 0.100 6.588-5.215 100.00 711 7 0.1935 345.002 334.991 0.904 0.953 0.090 5.214-4.128 98.38 1367 28 0.1231 504.632 499.471 0.993 0.954 0.080 4.126-3.266 94.74 2603 46 0.1165 460.000 453.053 1.056 0.954 0.005 3.266-2.585 99.86 5447 97 0.1122 310.305 306.999 1.039 0.954 0.000 2.585-2.046 97.45 10613 204 0.0957 234.107 231.643 1.046 0.954 0.000 2.046-1.619 99.39 21536 464 0.0912 138.556 137.256 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0973 74.591 73.886 1.049 0.954 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.015 38.348 1.018 0.954 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0514 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1367 | n_water=875 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1203 r_free=0.1368 | n_water=873 | time (s): 107.460 (total time: 110.600) Filter (q & B) r_work=0.1204 r_free=0.1367 | n_water=861 | time (s): 4.810 (total time: 115.410) Compute maps r_work=0.1204 r_free=0.1367 | n_water=861 | time (s): 2.410 (total time: 117.820) Filter (map) r_work=0.1225 r_free=0.1376 | n_water=742 | time (s): 5.540 (total time: 123.360) Find peaks r_work=0.1225 r_free=0.1376 | n_water=742 | time (s): 0.750 (total time: 124.110) Add new water r_work=0.1237 r_free=0.1393 | n_water=957 | time (s): 4.920 (total time: 129.030) Refine new water occ: r_work=0.1201 r_free=0.1346 adp: r_work=0.1201 r_free=0.1347 occ: r_work=0.1199 r_free=0.1345 adp: r_work=0.1199 r_free=0.1346 occ: r_work=0.1198 r_free=0.1344 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=957 | time (s): 197.390 (total time: 326.420) Filter (q & B) r_work=0.1201 r_free=0.1358 | n_water=886 | time (s): 4.440 (total time: 330.860) Filter (dist only) r_work=0.1201 r_free=0.1357 | n_water=885 | time (s): 115.540 (total time: 446.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.509569 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.580456 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 0.1366 0.0161 0.037 1.1 6.3 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.66 1.61 1.718 13.675 13.580 3.760 12.09 13.69 1.60 1.777 13.645 13.580 3.760 Individual atomic B min max mean iso aniso Overall: 5.40 64.31 14.49 0.87 519 3270 Protein: 5.40 28.19 10.22 0.87 0 2902 Water: 5.75 64.31 28.49 N/A 519 366 Other: 13.63 21.99 17.81 N/A 0 2 Chain A: 5.46 51.91 12.09 N/A 0 1624 Chain B: 5.40 64.31 11.91 N/A 0 1646 Chain S: 5.75 63.11 30.22 N/A 519 0 Histogram: Values Number of atoms 5.40 - 11.29 2088 11.29 - 17.18 795 17.18 - 23.07 291 23.07 - 28.96 200 28.96 - 34.86 171 34.86 - 40.75 122 40.75 - 46.64 79 46.64 - 52.53 35 52.53 - 58.42 4 58.42 - 64.31 4 =========================== Idealize ADP of riding H ========================== r_work=0.1209 r_free=0.1369 r_work=0.1209 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1370 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1207 r_free = 0.1370 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1207 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759516 | | target function (ml) not normalized (work): 704119.685723 | | target function (ml) not normalized (free): 14743.018351 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1211 0.1208 0.1370 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1376 0.1375 0.1465 n_refl.: 191131 remove outliers: r(all,work,free)=0.1376 0.1375 0.1465 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1384 0.1383 0.1470 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3685 360.806 333.218 0.408 0.995 0.217 13.296-10.522 98.02 98 1 0.2487 478.800 459.149 0.678 0.997 0.163 10.503-8.327 97.80 175 3 0.2214 501.782 495.791 0.845 0.997 0.137 8.318-6.595 100.00 360 8 0.2193 375.451 370.552 0.872 0.997 0.104 6.588-5.215 100.00 711 7 0.1970 345.002 334.307 0.870 0.998 0.087 5.214-4.128 98.38 1367 28 0.1246 504.632 499.009 0.957 0.998 0.044 4.126-3.266 94.74 2603 46 0.1179 460.000 452.564 1.020 1.000 0.005 3.266-2.585 99.86 5447 97 0.1132 310.305 306.635 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0963 234.107 231.502 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.556 137.164 1.026 1.004 0.000 1.619-1.281 98.00 42464 925 0.0954 74.591 73.927 1.015 1.008 0.000 1.281-0.980 96.53 101826 2055 0.1631 40.015 38.325 0.982 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0590 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1357 | n_water=885 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1198 r_free=0.1356 | n_water=884 | time (s): 110.140 (total time: 112.510) Filter (q & B) r_work=0.1199 r_free=0.1356 | n_water=870 | time (s): 5.220 (total time: 117.730) Compute maps r_work=0.1199 r_free=0.1356 | n_water=870 | time (s): 1.910 (total time: 119.640) Filter (map) r_work=0.1220 r_free=0.1361 | n_water=747 | time (s): 4.410 (total time: 124.050) Find peaks r_work=0.1220 r_free=0.1361 | n_water=747 | time (s): 0.690 (total time: 124.740) Add new water r_work=0.1229 r_free=0.1375 | n_water=972 | time (s): 4.180 (total time: 128.920) Refine new water occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1196 r_free=0.1341 occ: r_work=0.1193 r_free=0.1340 adp: r_work=0.1193 r_free=0.1341 occ: r_work=0.1192 r_free=0.1340 adp: r_work=0.1192 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1341 r_work=0.1192 r_free=0.1341 | n_water=972 | time (s): 168.860 (total time: 297.780) Filter (q & B) r_work=0.1195 r_free=0.1355 | n_water=894 | time (s): 4.290 (total time: 302.070) Filter (dist only) r_work=0.1196 r_free=0.1354 | n_water=893 | time (s): 117.970 (total time: 420.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.510444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.838296 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1359 0.0160 0.038 1.1 7.8 0.0 0.3 0 0.755 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.59 1.60 1.669 13.683 13.838 3.758 11.98 13.60 1.62 1.690 13.670 13.838 3.755 Individual atomic B min max mean iso aniso Overall: 5.50 63.29 14.56 0.86 527 3270 Protein: 5.50 28.03 10.29 0.86 0 2902 Water: 5.93 63.29 28.44 N/A 527 366 Other: 13.74 22.00 17.87 N/A 0 2 Chain A: 5.57 51.60 12.12 N/A 0 1624 Chain B: 5.50 63.15 11.95 N/A 0 1646 Chain S: 5.93 63.29 30.27 N/A 527 0 Histogram: Values Number of atoms 5.50 - 11.28 2061 11.28 - 17.06 825 17.06 - 22.83 273 22.83 - 28.61 196 28.61 - 34.39 186 34.39 - 40.17 127 40.17 - 45.95 84 45.95 - 51.73 35 51.73 - 57.51 4 57.51 - 63.29 6 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1360 r_work=0.1198 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1360 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754322 | | target function (ml) not normalized (work): 703147.030359 | | target function (ml) not normalized (free): 14728.664067 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1389 0.1388 0.1472 n_refl.: 191131 remove outliers: r(all,work,free)=0.1389 0.1388 0.1472 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1392 0.1390 0.1473 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191131 remove outliers: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3664 360.806 333.201 0.409 0.974 0.205 13.296-10.522 98.02 98 1 0.2461 478.800 459.690 0.687 0.976 0.151 10.503-8.327 97.80 175 3 0.2219 501.782 495.383 0.861 0.976 0.127 8.318-6.595 100.00 360 8 0.2198 375.451 370.673 0.888 0.976 0.101 6.588-5.215 100.00 711 7 0.1973 345.002 334.194 0.887 0.977 0.083 5.214-4.128 98.38 1367 28 0.1238 504.632 499.049 0.976 0.977 0.034 4.126-3.266 94.74 2603 46 0.1185 460.000 452.390 1.042 0.979 0.005 3.266-2.585 99.86 5447 97 0.1134 310.305 306.674 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0961 234.107 231.484 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0906 138.556 137.183 1.049 0.984 0.000 1.619-1.281 98.00 42464 925 0.0946 74.591 73.940 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.015 38.310 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0203 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1195 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1359 | n_water=893 | time (s): 3.260 (total time: 3.260) Filter (dist) r_work=0.1195 r_free=0.1358 | n_water=892 | time (s): 118.200 (total time: 121.460) Filter (q & B) r_work=0.1197 r_free=0.1361 | n_water=875 | time (s): 4.710 (total time: 126.170) Compute maps r_work=0.1197 r_free=0.1361 | n_water=875 | time (s): 2.350 (total time: 128.520) Filter (map) r_work=0.1222 r_free=0.1363 | n_water=753 | time (s): 4.520 (total time: 133.040) Find peaks r_work=0.1222 r_free=0.1363 | n_water=753 | time (s): 0.630 (total time: 133.670) Add new water r_work=0.1230 r_free=0.1377 | n_water=974 | time (s): 4.040 (total time: 137.710) Refine new water occ: r_work=0.1195 r_free=0.1345 adp: r_work=0.1195 r_free=0.1345 occ: r_work=0.1193 r_free=0.1344 adp: r_work=0.1193 r_free=0.1344 occ: r_work=0.1192 r_free=0.1344 adp: r_work=0.1192 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1344 r_work=0.1192 r_free=0.1344 | n_water=974 | time (s): 174.430 (total time: 312.140) Filter (q & B) r_work=0.1195 r_free=0.1354 | n_water=892 | time (s): 4.460 (total time: 316.600) Filter (dist only) r_work=0.1195 r_free=0.1353 | n_water=891 | time (s): 114.410 (total time: 431.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.542077 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.670308 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1358 0.0160 0.039 1.1 6.1 0.0 0.3 0 0.771 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.58 1.60 1.672 13.650 13.670 3.756 11.99 13.62 1.63 1.673 13.648 13.670 3.755 Individual atomic B min max mean iso aniso Overall: 5.51 63.31 14.51 0.85 525 3270 Protein: 5.51 27.90 10.32 0.85 0 2902 Water: 5.96 63.31 28.12 N/A 525 366 Other: 13.79 22.05 17.92 N/A 0 2 Chain A: 5.61 51.49 12.12 N/A 0 1624 Chain B: 5.51 62.79 11.96 N/A 0 1646 Chain S: 5.96 63.31 29.87 N/A 525 0 Histogram: Values Number of atoms 5.51 - 11.29 2062 11.29 - 17.07 826 17.07 - 22.85 286 22.85 - 28.63 202 28.63 - 34.41 182 34.41 - 40.19 113 40.19 - 45.97 81 45.97 - 51.75 33 51.75 - 57.53 4 57.53 - 63.31 6 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1362 r_work=0.1199 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1362 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1363 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754503 | | target function (ml) not normalized (work): 703180.792505 | | target function (ml) not normalized (free): 14730.548944 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1497 n_refl.: 191131 remove outliers: r(all,work,free)=0.1403 0.1401 0.1497 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1402 0.1401 0.1497 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3694 360.806 332.585 0.407 0.974 0.206 13.296-10.522 98.02 98 1 0.2516 478.800 459.171 0.684 0.976 0.154 10.503-8.327 97.80 175 3 0.2269 501.782 494.384 0.859 0.976 0.122 8.318-6.595 100.00 360 8 0.2233 375.451 370.181 0.887 0.976 0.097 6.588-5.215 100.00 711 7 0.1999 345.002 333.743 0.886 0.976 0.087 5.214-4.128 98.38 1367 28 0.1262 504.632 498.825 0.977 0.977 0.039 4.126-3.266 94.74 2603 46 0.1191 460.000 452.180 1.043 0.978 0.005 3.266-2.585 99.86 5447 97 0.1140 310.305 306.588 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0963 234.107 231.450 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0907 138.556 137.179 1.051 0.985 0.000 1.619-1.281 98.00 42464 925 0.0943 74.591 73.943 1.042 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.015 38.301 1.013 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0120 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1197 r_free=0.1362 After: r_work=0.1198 r_free=0.1362 ================================== NQH flips ================================== r_work=0.1198 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1362 | n_water=891 | time (s): 2.720 (total time: 2.720) Filter (dist) r_work=0.1198 r_free=0.1362 | n_water=890 | time (s): 124.670 (total time: 127.390) Filter (q & B) r_work=0.1199 r_free=0.1362 | n_water=880 | time (s): 4.580 (total time: 131.970) Compute maps r_work=0.1199 r_free=0.1362 | n_water=880 | time (s): 2.310 (total time: 134.280) Filter (map) r_work=0.1221 r_free=0.1359 | n_water=757 | time (s): 5.480 (total time: 139.760) Find peaks r_work=0.1221 r_free=0.1359 | n_water=757 | time (s): 0.650 (total time: 140.410) Add new water r_work=0.1229 r_free=0.1375 | n_water=963 | time (s): 5.060 (total time: 145.470) Refine new water occ: r_work=0.1195 r_free=0.1343 adp: r_work=0.1195 r_free=0.1344 occ: r_work=0.1193 r_free=0.1343 adp: r_work=0.1193 r_free=0.1343 occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1343 r_work=0.1192 r_free=0.1343 | n_water=963 | time (s): 196.580 (total time: 342.050) Filter (q & B) r_work=0.1195 r_free=0.1355 | n_water=896 | time (s): 4.420 (total time: 346.470) Filter (dist only) r_work=0.1196 r_free=0.1354 | n_water=894 | time (s): 118.530 (total time: 465.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540896 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.071955 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 0.1363 0.0158 0.039 1.2 9.4 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.63 1.58 1.671 13.664 14.072 3.761 12.04 13.65 1.61 1.667 13.669 14.072 3.759 Individual atomic B min max mean iso aniso Overall: 5.56 63.42 14.53 0.86 529 3269 Protein: 5.56 27.93 10.34 0.86 0 2902 Water: 6.00 63.42 28.13 N/A 529 365 Other: 13.82 22.06 17.94 N/A 0 2 Chain A: 5.63 51.20 12.10 N/A 0 1623 Chain B: 5.56 61.74 11.96 N/A 0 1646 Chain S: 6.00 63.42 30.01 N/A 529 0 Histogram: Values Number of atoms 5.56 - 11.35 2065 11.35 - 17.13 835 17.13 - 22.92 278 22.92 - 28.70 198 28.70 - 34.49 181 34.49 - 40.27 121 40.27 - 46.06 78 46.06 - 51.85 33 51.85 - 57.63 3 57.63 - 63.42 6 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1365 r_work=0.1204 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1365 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1362 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.758709 | | target function (ml) not normalized (work): 703968.653857 | | target function (ml) not normalized (free): 14743.613011 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1384 0.1465 5.7062 5.7802| | 2: 2.94 - 2.33 1.00 7339 128 0.1084 0.1365 5.0932 5.1932| | 3: 2.33 - 2.04 0.96 6939 150 0.0913 0.1222 4.6623 4.7574| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1045 4.3936 4.5648| | 5: 1.85 - 1.72 0.99 7113 159 0.0939 0.0985 4.1548 4.2321| | 6: 1.72 - 1.62 0.99 7102 142 0.0901 0.1080 3.9491 4.0781| | 7: 1.62 - 1.54 0.99 7104 148 0.0898 0.0977 3.8059 3.9366| | 8: 1.54 - 1.47 0.96 6798 152 0.0903 0.1334 3.7115 3.9195| | 9: 1.47 - 1.41 0.98 6938 155 0.0934 0.1135 3.6299 3.7649| | 10: 1.41 - 1.36 0.99 7022 150 0.0982 0.1193 3.5635 3.6845| | 11: 1.36 - 1.32 0.99 6997 151 0.1000 0.1114 3.4909 3.5867| | 12: 1.32 - 1.28 0.98 6975 149 0.1038 0.1127 3.4639 3.5861| | 13: 1.28 - 1.25 0.98 6907 166 0.1048 0.1252 3.4419 3.5766| | 14: 1.25 - 1.22 0.98 7015 112 0.1110 0.1583 3.4365 3.6819| | 15: 1.22 - 1.19 0.98 6956 137 0.1173 0.1245 3.4519 3.4932| | 16: 1.19 - 1.17 0.93 6604 132 0.1254 0.1531 3.467 3.643| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1226 3.4345 3.4465| | 18: 1.14 - 1.12 0.98 6875 142 0.1391 0.1730 3.4416 3.5391| | 19: 1.12 - 1.10 0.97 6948 106 0.1474 0.1795 3.4221 3.603| | 20: 1.10 - 1.08 0.97 6884 147 0.1586 0.1604 3.412 3.4412| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2153 3.419 3.5046| | 22: 1.07 - 1.05 0.97 6836 135 0.1907 0.1947 3.4144 3.4162| | 23: 1.05 - 1.03 0.97 6827 159 0.2122 0.2031 3.434 3.4907| | 24: 1.03 - 1.02 0.96 6784 133 0.2336 0.2269 3.4365 3.5142| | 25: 1.02 - 1.01 0.93 6552 130 0.2619 0.2517 3.4502 3.5229| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2865 3.4155 3.4228| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2786 3.4696 3.396| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7399 127 0.93 11.91 1.00 0.96 11621.70| | 2: 2.94 - 2.33 7339 128 0.92 13.00 0.99 0.96 5282.18| | 3: 2.33 - 2.04 6939 150 0.96 7.66 1.01 0.95 1707.33| | 4: 2.04 - 1.85 7170 155 0.96 7.59 1.00 0.95 994.50| | 5: 1.85 - 1.72 7113 159 0.96 8.00 1.00 0.96 627.22| | 6: 1.72 - 1.62 7102 142 0.96 8.05 1.00 0.96 443.34| | 7: 1.62 - 1.54 7104 148 0.96 8.20 1.01 0.97 340.31| | 8: 1.54 - 1.47 6798 152 0.96 8.40 1.01 0.97 285.01| | 9: 1.47 - 1.41 6938 155 0.96 8.62 1.00 0.98 236.13| | 10: 1.41 - 1.36 7022 150 0.96 9.06 1.00 0.97 206.68| | 11: 1.36 - 1.32 6997 151 0.96 9.04 0.99 0.96 177.27| | 12: 1.32 - 1.28 6975 149 0.96 9.07 0.98 0.95 162.47| | 13: 1.28 - 1.25 6907 166 0.96 9.61 1.01 0.96 159.59| | 14: 1.25 - 1.22 7015 112 0.95 10.77 1.01 0.96 164.31| | 15: 1.22 - 1.19 6956 137 0.95 11.28 1.01 0.98 167.07| | 16: 1.19 - 1.17 6604 132 0.95 11.45 1.01 0.96 160.34| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.96 154.29| | 18: 1.14 - 1.12 6875 142 0.94 12.86 1.01 0.95 149.30| | 19: 1.12 - 1.10 6948 106 0.93 14.29 1.00 0.94 153.35| | 20: 1.10 - 1.08 6884 147 0.92 15.37 1.00 0.94 152.35| | 21: 1.08 - 1.07 6852 152 0.91 16.75 1.00 0.93 154.73| | 22: 1.07 - 1.05 6836 135 0.89 18.39 0.99 0.93 156.02| | 23: 1.05 - 1.03 6827 159 0.87 20.59 0.99 0.92 165.86| | 24: 1.03 - 1.02 6784 133 0.85 23.24 0.99 0.93 179.89| | 25: 1.02 - 1.01 6552 130 0.83 25.20 0.98 0.90 182.37| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.88 176.26| | 27: 0.99 - 0.98 6647 131 0.82 26.22 0.99 0.87 160.28| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 149.30 max = 11621.70 mean = 949.23| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.37| |phase err.(test): min = 0.00 max = 88.17 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1362 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1414 0.1412 0.1502 n_refl.: 191131 remove outliers: r(all,work,free)=0.1414 0.1412 0.1502 n_refl.: 191131 overall B=-0.06 to atoms: r(all,work,free)=0.1405 0.1404 0.1496 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1202 0.1360 n_refl.: 191131 remove outliers: r(all,work,free)=0.1205 0.1202 0.1360 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3638 360.806 333.519 0.390 0.974 0.195 13.296-10.522 98.02 98 1 0.2515 478.800 458.598 0.662 0.976 0.144 10.503-8.327 97.80 175 3 0.2240 501.782 494.871 0.837 0.976 0.113 8.318-6.595 100.00 360 8 0.2213 375.451 370.498 0.863 0.976 0.090 6.588-5.215 100.00 711 7 0.1971 345.002 334.103 0.865 0.977 0.080 5.214-4.128 98.38 1367 28 0.1258 504.632 498.818 0.951 0.978 0.029 4.126-3.266 94.74 2603 46 0.1195 460.000 451.978 1.017 0.979 0.000 3.266-2.585 99.86 5447 97 0.1138 310.305 306.651 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0971 234.107 231.445 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0915 138.556 137.174 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0954 74.591 73.934 1.012 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.015 38.292 0.980 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0122 ================= 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 : 0.2036 0.1975 0.081 5.218 5.2 78.0 14.6 805 0.000 1_bss: 0.1799 0.1917 0.081 5.218 5.2 78.1 14.6 805 0.000 1_settarget: 0.1799 0.1917 0.081 5.218 5.2 78.1 14.6 805 0.000 1_nqh: 0.1800 0.1915 0.081 5.218 5.2 78.1 14.6 805 0.002 1_weight: 0.1800 0.1915 0.081 5.218 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1268 0.1496 0.038 1.185 5.2 78.1 14.6 805 0.154 1_adp: 0.1299 0.1569 0.038 1.185 5.1 73.1 15.0 805 0.154 1_regHadp: 0.1298 0.1566 0.038 1.185 5.1 73.1 15.0 805 0.154 1_occ: 0.1283 0.1553 0.038 1.185 5.1 73.1 15.0 805 0.154 2_bss: 0.1278 0.1546 0.038 1.185 5.3 73.2 15.2 805 0.154 2_settarget: 0.1278 0.1546 0.038 1.185 5.3 73.2 15.2 805 0.154 2_updatecdl: 0.1278 0.1546 0.038 1.208 5.3 73.2 15.2 805 0.154 2_nqh: 0.1278 0.1546 0.038 1.208 5.3 73.2 15.2 805 0.154 2_sol: 0.1275 0.1516 0.038 1.208 5.3 73.2 16.1 877 n/a 2_weight: 0.1275 0.1516 0.038 1.208 5.3 73.2 16.1 877 n/a 2_xyzrec: 0.1258 0.1529 0.041 1.153 5.3 73.2 16.1 877 n/a 2_adp: 0.1231 0.1509 0.041 1.153 5.4 68.2 16.2 877 n/a 2_regHadp: 0.1232 0.1510 0.041 1.153 5.4 68.2 16.2 877 n/a 2_occ: 0.1226 0.1511 0.041 1.153 5.4 68.2 16.2 877 n/a 3_bss: 0.1233 0.1515 0.041 1.153 5.4 68.2 16.2 877 n/a 3_settarget: 0.1233 0.1515 0.041 1.153 5.4 68.2 16.2 877 n/a 3_updatecdl: 0.1233 0.1515 0.041 1.156 5.4 68.2 16.2 877 n/a 3_nqh: 0.1233 0.1515 0.041 1.156 5.4 68.2 16.2 877 n/a 3_sol: 0.1251 0.1517 0.041 1.156 5.4 68.2 15.4 860 n/a 3_weight: 0.1251 0.1517 0.041 1.156 5.4 68.2 15.4 860 n/a 3_xyzrec: 0.1240 0.1439 0.035 1.102 5.4 68.2 15.4 860 n/a 3_adp: 0.1236 0.1405 0.035 1.102 5.5 67.8 15.2 860 n/a 3_regHadp: 0.1236 0.1406 0.035 1.102 5.5 67.8 15.2 860 n/a 3_occ: 0.1231 0.1395 0.035 1.102 5.5 67.8 15.2 860 n/a 4_bss: 0.1227 0.1389 0.035 1.102 5.5 67.8 15.2 860 n/a 4_settarget: 0.1227 0.1389 0.035 1.102 5.5 67.8 15.2 860 n/a 4_updatecdl: 0.1227 0.1389 0.035 1.103 5.5 67.8 15.2 860 n/a 4_nqh: 0.1227 0.1389 0.035 1.103 5.5 67.8 15.2 860 n/a 4_sol: 0.1211 0.1373 0.035 1.103 5.5 67.8 15.0 847 n/a 4_weight: 0.1211 0.1373 0.035 1.103 5.5 67.8 15.0 847 n/a 4_xyzrec: 0.1209 0.1376 0.036 1.122 5.5 67.8 15.0 847 n/a 4_adp: 0.1203 0.1372 0.036 1.122 5.5 67.2 14.9 847 n/a 4_regHadp: 0.1203 0.1372 0.036 1.122 5.5 67.2 14.9 847 n/a 4_occ: 0.1201 0.1369 0.036 1.122 5.5 67.2 14.9 847 n/a 5_bss: 0.1199 0.1370 0.036 1.122 5.5 67.2 14.8 847 n/a 5_settarget: 0.1199 0.1370 0.036 1.122 5.5 67.2 14.8 847 n/a 5_updatecdl: 0.1199 0.1370 0.036 1.122 5.5 67.2 14.8 847 n/a 5_nqh: 0.1199 0.1370 0.036 1.122 5.5 67.2 14.8 847 n/a 5_sol: 0.1196 0.1360 0.036 1.122 5.5 67.2 14.9 870 n/a 5_weight: 0.1196 0.1360 0.036 1.122 5.5 67.2 14.9 870 n/a 5_xyzrec: 0.1199 0.1365 0.036 1.128 5.5 67.2 14.9 870 n/a 5_adp: 0.1205 0.1370 0.036 1.128 5.6 66.9 14.9 870 n/a 5_regHadp: 0.1205 0.1370 0.036 1.128 5.6 66.9 14.9 870 n/a 5_occ: 0.1202 0.1369 0.036 1.128 5.6 66.9 14.9 870 n/a 6_bss: 0.1197 0.1362 0.036 1.128 5.5 66.8 14.8 870 n/a 6_settarget: 0.1197 0.1362 0.036 1.128 5.5 66.8 14.8 870 n/a 6_updatecdl: 0.1197 0.1362 0.036 1.128 5.5 66.8 14.8 870 n/a 6_nqh: 0.1197 0.1362 0.036 1.128 5.5 66.8 14.8 870 n/a 6_sol: 0.1195 0.1351 0.036 1.128 5.5 66.8 14.9 875 n/a 6_weight: 0.1195 0.1351 0.036 1.128 5.5 66.8 14.9 875 n/a 6_xyzrec: 0.1199 0.1361 0.037 1.124 5.5 66.8 14.9 875 n/a 6_adp: 0.1202 0.1364 0.037 1.124 5.6 65.6 14.8 875 n/a 6_regHadp: 0.1202 0.1365 0.037 1.124 5.6 65.6 14.8 875 n/a 6_occ: 0.1199 0.1365 0.037 1.124 5.6 65.6 14.8 875 n/a 7_bss: 0.1203 0.1367 0.037 1.124 5.4 65.4 14.6 875 n/a 7_settarget: 0.1203 0.1367 0.037 1.124 5.4 65.4 14.6 875 n/a 7_updatecdl: 0.1203 0.1367 0.037 1.124 5.4 65.4 14.6 875 n/a 7_nqh: 0.1203 0.1367 0.037 1.124 5.4 65.4 14.6 875 n/a 7_sol: 0.1201 0.1357 0.037 1.124 5.4 65.4 14.5 885 n/a 7_weight: 0.1201 0.1357 0.037 1.124 5.4 65.4 14.5 885 n/a 7_xyzrec: 0.1205 0.1366 0.037 1.126 5.4 65.4 14.5 885 n/a 7_adp: 0.1209 0.1369 0.037 1.126 5.4 64.3 14.5 885 n/a 7_regHadp: 0.1209 0.1370 0.037 1.126 5.4 64.3 14.5 885 n/a 7_occ: 0.1207 0.1370 0.037 1.126 5.4 64.3 14.5 885 n/a 8_bss: 0.1198 0.1357 0.037 1.126 5.5 64.4 14.6 885 n/a 8_settarget: 0.1198 0.1357 0.037 1.126 5.5 64.4 14.6 885 n/a 8_updatecdl: 0.1198 0.1357 0.037 1.126 5.5 64.4 14.6 885 n/a 8_nqh: 0.1198 0.1357 0.037 1.126 5.5 64.4 14.6 885 n/a 8_sol: 0.1196 0.1354 0.037 1.126 5.5 64.4 14.6 893 n/a 8_weight: 0.1196 0.1354 0.037 1.126 5.5 64.4 14.6 893 n/a 8_xyzrec: 0.1199 0.1359 0.038 1.119 5.5 64.4 14.6 893 n/a 8_adp: 0.1198 0.1360 0.038 1.119 5.5 63.3 14.6 893 n/a 8_regHadp: 0.1198 0.1360 0.038 1.119 5.5 63.3 14.6 893 n/a 8_occ: 0.1196 0.1359 0.038 1.119 5.5 63.3 14.6 893 n/a 9_bss: 0.1195 0.1356 0.038 1.119 5.5 63.3 14.6 893 n/a 9_settarget: 0.1195 0.1356 0.038 1.119 5.5 63.3 14.6 893 n/a 9_updatecdl: 0.1195 0.1356 0.038 1.119 5.5 63.3 14.6 893 n/a 9_nqh: 0.1195 0.1359 0.038 1.119 5.5 63.3 14.6 893 n/a 9_sol: 0.1195 0.1353 0.038 1.119 5.5 63.3 14.5 891 n/a 9_weight: 0.1195 0.1353 0.038 1.119 5.5 63.3 14.5 891 n/a 9_xyzrec: 0.1199 0.1358 0.039 1.121 5.5 63.3 14.5 891 n/a 9_adp: 0.1199 0.1362 0.039 1.121 5.5 63.3 14.5 891 n/a 9_regHadp: 0.1199 0.1362 0.039 1.121 5.5 63.3 14.5 891 n/a 9_occ: 0.1199 0.1363 0.039 1.121 5.5 63.3 14.5 891 n/a 10_bss: 0.1197 0.1362 0.039 1.121 5.5 63.3 14.5 891 n/a 10_settarget: 0.1197 0.1362 0.039 1.121 5.5 63.3 14.5 891 n/a 10_updatecdl: 0.1197 0.1362 0.039 1.122 5.5 63.3 14.5 891 n/a 10_setrh: 0.1198 0.1362 0.039 1.122 5.5 63.3 14.5 891 n/a 10_nqh: 0.1198 0.1362 0.039 1.122 5.5 63.3 14.5 891 n/a 10_sol: 0.1196 0.1354 0.039 1.122 5.5 63.3 14.5 894 n/a 10_weight: 0.1196 0.1354 0.039 1.122 5.5 63.3 14.5 894 n/a 10_xyzrec: 0.1204 0.1363 0.039 1.189 5.5 63.3 14.5 894 n/a 10_adp: 0.1204 0.1365 0.039 1.189 5.6 63.4 14.5 894 n/a 10_regHadp: 0.1204 0.1365 0.039 1.189 5.6 63.4 14.5 894 n/a 10_occ: 0.1203 0.1362 0.039 1.189 5.6 63.4 14.5 894 n/a end: 0.1202 0.1360 0.039 1.189 5.5 63.4 14.5 894 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9682641_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9682641_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.8400 Refinement macro-cycles (run) : 12039.5000 Write final files (write_after_run_outputs) : 162.1000 Total : 12207.4400 Total CPU time: 3.40 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:39 PST -0800 (1736736039.09 s) Start R-work = 0.1799, R-free = 0.1917 Final R-work = 0.1202, R-free = 0.1360 =============================================================================== Job complete usr+sys time: 12494.36 seconds wall clock time: 209 minutes 15.01 seconds (12555.01 seconds total)