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_9229404.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9229404.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9229404.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.83, per 1000 atoms: 0.27 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: 2.708 distance_ideal: 2.720 ideal - model: 0.012 slack: 0.000 delta_slack: 0.012 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: 2.716 distance_ideal: 2.710 ideal - model: -0.006 slack: 0.000 delta_slack: -0.006 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: 0.96 Conformation dependent library (CDL) restraints added in 150.7 milliseconds Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.01: 620 1.01 - 1.24: 2590 1.24 - 1.47: 1461 1.47 - 1.70: 1235 1.70 - 1.93: 28 Bond restraints: 5934 Sorted by residual: bond pdb=" CZ2 TRP B 139 " pdb=" HZ2 TRP B 139 " ideal model delta sigma weight residual 0.930 1.342 -0.412 2.00e-02 2.50e+03 4.24e+02 bond pdb=" CG2 VAL B 69 " pdb="HG22 VAL B 69 " ideal model delta sigma weight residual 0.970 1.372 -0.402 2.00e-02 2.50e+03 4.03e+02 bond pdb=" N ASP B 84 " pdb=" H ASP B 84 " ideal model delta sigma weight residual 0.860 1.243 -0.383 2.00e-02 2.50e+03 3.66e+02 bond pdb=" CG1 ILE A 45 " pdb="HG12 ILE A 45 " ideal model delta sigma weight residual 0.970 1.348 -0.378 2.00e-02 2.50e+03 3.58e+02 bond pdb=" CA ALA A 44 " pdb=" CB ALA A 44 " ideal model delta sigma weight residual 1.526 1.289 0.237 1.26e-02 6.30e+03 3.53e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 5877 4.46 - 8.92: 3551 8.92 - 13.38: 1200 13.38 - 17.85: 175 17.85 - 22.31: 7 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 143 " pdb=" CZ ARG B 143 " pdb=" NH2 ARG B 143 " ideal model delta sigma weight residual 119.20 134.21 -15.01 9.00e-01 1.23e+00 2.78e+02 angle pdb=" O PHE A 127 " pdb=" C PHE A 127 " pdb=" N PRO A 128 " ideal model delta sigma weight residual 121.30 137.47 -16.17 1.03e+00 9.43e-01 2.47e+02 angle pdb=" CA HIS A 179 " pdb=" CB HIS A 179 " pdb=" CG HIS A 179 " ideal model delta sigma weight residual 113.80 98.56 15.24 1.00e+00 1.00e+00 2.32e+02 angle pdb=" O ALA B 63 " pdb=" C ALA B 63 " pdb=" N ASP B 64 " ideal model delta sigma weight residual 122.22 139.02 -16.80 1.17e+00 7.31e-01 2.06e+02 angle pdb=" O ALA B 18 " pdb=" C ALA B 18 " pdb=" N VAL B 19 " ideal model delta sigma weight residual 122.07 136.81 -14.74 1.03e+00 9.43e-01 2.05e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 1849 17.14 - 34.27: 131 34.27 - 51.40: 48 51.40 - 68.54: 16 68.54 - 85.67: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: 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 -145.80 -34.20 0 5.00e+00 4.00e-02 4.68e+01 dihedral pdb=" CB TRP B 139 " pdb=" CG TRP B 139 " pdb=" CD1 TRP B 139 " pdb=" HD1 TRP B 139 " ideal model delta harmonic sigma weight residual 0.00 27.51 -27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -155.92 -24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.236: 216 0.236 - 0.471: 163 0.471 - 0.706: 79 0.706 - 0.941: 27 0.941 - 1.176: 7 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB ILE B 121 " pdb=" CA ILE B 121 " pdb=" CG1 ILE B 121 " pdb=" CG2 ILE B 121 " both_signs ideal model delta sigma weight residual False 2.64 3.82 -1.18 2.00e-01 2.50e+01 3.46e+01 chirality pdb=" CA ILE B 105 " pdb=" N ILE B 105 " pdb=" C ILE B 105 " pdb=" CB ILE B 105 " both_signs ideal model delta sigma weight residual False 2.43 1.36 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CA VAL B 32 " pdb=" N VAL B 32 " pdb=" C VAL B 32 " pdb=" CB VAL B 32 " both_signs ideal model delta sigma weight residual False 2.44 3.47 -1.02 2.00e-01 2.50e+01 2.62e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.023 2.00e-02 2.50e+03 7.18e-02 2.06e+02 pdb=" CG TRP B 146 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.114 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.013 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.062 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.040 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.156 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.065 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.114 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " 0.023 2.00e-02 2.50e+03 6.62e-02 1.75e+02 pdb=" CG TRP B 139 " -0.133 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " 0.100 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.073 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.101 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " 0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.071 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.091 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " -0.035 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.044 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.045 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.032 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 116 " 0.072 2.00e-02 2.50e+03 8.21e-02 1.52e+02 pdb=" CG HIS A 116 " 0.099 2.00e-02 2.50e+03 pdb=" ND1 HIS A 116 " -0.156 2.00e-02 2.50e+03 pdb=" CD2 HIS A 116 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 HIS A 116 " 0.030 2.00e-02 2.50e+03 pdb=" NE2 HIS A 116 " -0.059 2.00e-02 2.50e+03 pdb=" HD2 HIS A 116 " -0.063 2.00e-02 2.50e+03 pdb=" HE1 HIS A 116 " 0.023 2.00e-02 2.50e+03 pdb=" HE2 HIS A 116 " 0.102 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.59: 23 1.59 - 2.34: 2178 2.34 - 3.09: 22084 3.09 - 3.85: 33090 3.85 - 4.60: 52876 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110251 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.837 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.963 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.973 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.146 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.171 2.620 ... (remaining 110246 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_9229404_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= 0.2037 r_free= 0.1987 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.303170 | | target function (ml) not normalized (work): 806039.744435 | | target function (ml) not normalized (free): 16535.545084 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2132 0.1901 6.6948 6.2974| | 2: 2.94 - 2.33 1.00 7339 128 0.1630 0.1632 5.5337 5.5655| | 3: 2.33 - 2.04 0.96 6939 150 0.1635 0.1615 5.1408 5.1586| | 4: 2.04 - 1.85 1.00 7170 155 0.1732 0.1690 4.9539 5.0726| | 5: 1.85 - 1.72 0.99 7113 159 0.1936 0.1624 4.8004 4.7857| | 6: 1.72 - 1.62 0.99 7102 142 0.1996 0.2078 4.6654 4.6919| | 7: 1.62 - 1.54 0.99 7104 148 0.2015 0.2119 4.5673 4.7379| | 8: 1.54 - 1.47 0.96 6798 152 0.2040 0.2164 4.4816 4.5079| | 9: 1.47 - 1.41 0.98 6938 155 0.2128 0.2374 4.4106 4.4986| | 10: 1.41 - 1.36 0.99 7022 150 0.2125 0.1868 4.3163 4.2661| | 11: 1.36 - 1.32 0.99 6997 151 0.2140 0.1994 4.241 4.2072| | 12: 1.32 - 1.28 0.98 6976 149 0.2117 0.1927 4.1912 4.1991| | 13: 1.28 - 1.25 0.98 6907 166 0.2044 0.2177 4.1249 4.2095| | 14: 1.25 - 1.22 0.98 7015 113 0.2096 0.2354 4.0779 4.2642| | 15: 1.22 - 1.19 0.98 6957 137 0.2099 0.1843 4.0397 3.964| | 16: 1.19 - 1.17 0.93 6604 132 0.2117 0.2216 3.9993 4.0255| | 17: 1.17 - 1.14 0.98 6941 135 0.2150 0.1926 3.9505 3.9606| | 18: 1.14 - 1.12 0.98 6875 142 0.2215 0.2108 3.9152 3.8399| | 19: 1.12 - 1.10 0.97 6949 106 0.2250 0.2554 3.8672 4.0263| | 20: 1.10 - 1.08 0.97 6884 147 0.2316 0.2272 3.8203 3.8474| | 21: 1.08 - 1.07 0.97 6852 152 0.2436 0.2755 3.7976 3.8322| | 22: 1.07 - 1.05 0.97 6838 135 0.2548 0.2497 3.7516 3.7557| | 23: 1.05 - 1.03 0.97 6829 159 0.2733 0.2784 3.7411 3.8373| | 24: 1.03 - 1.02 0.96 6785 133 0.2882 0.2997 3.7026 3.8215| | 25: 1.02 - 1.01 0.93 6552 130 0.3076 0.2927 3.6804 3.7403| | 26: 1.01 - 0.99 0.96 6767 158 0.3230 0.3194 3.6436 3.5815| | 27: 0.99 - 0.98 0.94 6648 131 0.3397 0.2863 3.6648 3.5438| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.32 0.91 0.97 34883.36| | 2: 2.94 - 2.33 7339 128 0.86 21.06 1.09 1.03 14865.60| | 3: 2.33 - 2.04 6939 150 0.93 12.26 1.11 1.06 4082.19| | 4: 2.04 - 1.85 7170 155 0.93 13.31 1.11 1.07 2730.78| | 5: 1.85 - 1.72 7113 159 0.91 15.43 1.12 1.08 2080.92| | 6: 1.72 - 1.62 7102 142 0.89 17.41 1.12 1.07 1751.38| | 7: 1.62 - 1.54 7104 148 0.88 19.17 1.11 1.06 1526.68| | 8: 1.54 - 1.47 6798 152 0.88 19.56 1.10 1.05 1285.70| | 9: 1.47 - 1.41 6938 155 0.87 19.84 1.10 1.04 1037.19| | 10: 1.41 - 1.36 7022 150 0.88 19.60 1.09 1.04 820.76| | 11: 1.36 - 1.32 6997 151 0.88 18.97 1.08 1.04 665.39| | 12: 1.32 - 1.28 6976 149 0.88 18.92 1.08 1.05 602.53| | 13: 1.28 - 1.25 6907 166 0.88 19.62 1.08 1.04 593.01| | 14: 1.25 - 1.22 7015 113 0.87 20.74 1.07 1.03 567.12| | 15: 1.22 - 1.19 6957 137 0.87 20.27 1.07 1.03 511.27| | 16: 1.19 - 1.17 6604 132 0.88 19.20 1.07 1.03 439.61| | 17: 1.17 - 1.14 6941 135 0.88 19.81 1.08 1.02 396.11| | 18: 1.14 - 1.12 6875 142 0.87 20.20 1.08 1.00 367.51| | 19: 1.12 - 1.10 6949 106 0.86 21.85 1.07 1.00 372.53| | 20: 1.10 - 1.08 6884 147 0.85 23.02 1.06 0.99 356.44| | 21: 1.08 - 1.07 6852 152 0.83 24.51 1.06 0.97 350.45| | 22: 1.07 - 1.05 6838 135 0.81 26.30 1.05 0.95 339.56| | 23: 1.05 - 1.03 6829 159 0.79 28.71 1.04 0.95 351.18| | 24: 1.03 - 1.02 6785 133 0.77 30.22 1.05 0.97 345.63| | 25: 1.02 - 1.01 6552 130 0.77 30.34 1.02 0.94 308.26| | 26: 1.01 - 0.99 6767 158 0.78 29.72 1.03 0.94 259.91| | 27: 0.99 - 0.98 6648 131 0.81 27.33 1.04 0.96 215.31| |alpha: min = 0.94 max = 1.08 mean = 1.01| |beta: min = 215.31 max = 34883.36 mean = 2796.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.32| |phase err.(test): min = 0.00 max = 89.90 mean = 21.50| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.300 2950 Z= 5.347 Angle : 5.280 17.627 4018 Z= 3.767 Chirality : 0.388 1.176 492 Planarity : 0.033 0.156 512 Dihedral : 12.953 85.674 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.63 % Favored : 95.85 % Rotamer: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Cbeta Deviations : 30.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.38), residues: 386 helix: -2.50 (0.30), residues: 144 sheet: -0.73 (0.60), residues: 66 loop : -0.35 (0.46), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.096 0.021 ARG B 149 TYR 0.107 0.036 TYR A 192 PHE 0.113 0.037 PHE B 119 TRP 0.132 0.043 TRP B 139 HIS 0.123 0.042 HIS A 116 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= 0.2037 r_free= 0.1987 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.303170 | | target function (ml) not normalized (work): 806039.744435 | | target function (ml) not normalized (free): 16535.545084 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2037 0.1987 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2037 0.1987 n_refl.: 191155 remove outliers: r(all,work,free)=0.2036 0.2037 0.1987 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2038 0.2040 0.1988 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1803 0.1907 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1801 0.1907 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 0.4082 402.814 292.149 0.424 0.932 0.297 13.296-10.522 99.01 99 1 0.2496 528.187 519.794 0.769 0.933 0.250 10.503-8.327 98.90 177 3 0.2435 564.205 558.517 0.950 0.933 0.230 8.318-6.595 100.00 360 8 0.2495 414.736 402.077 0.948 0.932 0.179 6.588-5.215 100.00 711 7 0.2249 381.101 364.676 0.935 0.932 0.160 5.214-4.128 98.38 1367 28 0.1501 557.435 549.484 1.045 0.932 0.055 4.126-3.266 94.74 2603 46 0.1347 508.132 498.467 1.119 0.931 0.018 3.266-2.585 99.86 5447 97 0.1453 342.774 337.262 1.097 0.928 0.000 2.585-2.046 97.45 10613 204 0.1396 258.603 254.271 1.106 0.925 0.000 2.046-1.619 99.39 21536 464 0.1607 153.054 149.968 1.130 0.920 0.000 1.619-1.281 98.00 42464 925 0.1934 82.395 80.128 1.123 0.911 0.000 1.281-0.980 96.53 101826 2056 0.2320 44.203 41.690 1.121 0.895 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0224 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1801 r_free=0.1907 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=0.1801 r_free=0.1906 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.444220 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 567.419186 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1267 0.1499 0.0232 0.039 1.1 11.0 0.0 0.3 0 11.222 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.67 14.99 2.32 1.117 13.125 567.419 0.018 12.97 15.71 2.74 1.265 13.406 567.419 0.017 Individual atomic B min max mean iso aniso Overall: 5.15 73.06 15.12 1.41 435 3274 Protein: 5.15 40.55 11.04 1.41 0 2902 Water: 6.32 73.06 29.82 N/A 435 370 Other: 15.91 30.04 22.97 N/A 0 2 Chain A: 5.33 60.10 13.11 N/A 0 1626 Chain B: 5.15 73.06 12.84 N/A 0 1648 Chain S: 11.36 68.40 31.30 N/A 435 0 Histogram: Values Number of atoms 5.15 - 11.94 2161 11.94 - 18.73 630 18.73 - 25.52 320 25.52 - 32.31 257 32.31 - 39.11 162 39.11 - 45.90 107 45.90 - 52.69 47 52.69 - 59.48 18 59.48 - 66.27 5 66.27 - 73.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1571 r_work=0.1296 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 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 = 0.1281 r_free = 0.1555 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.16 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= 0.1281 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015483 | | target function (ls_wunit_k1) not normalized (work): 2899.921265 | | target function (ls_wunit_k1) not normalized (free): 115.943617 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1555 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1471 0.1468 0.1639 n_refl.: 191138 remove outliers: r(all,work,free)=0.1471 0.1468 0.1639 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1494 0.1492 0.1648 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1275 0.1549 n_refl.: 191138 remove outliers: r(all,work,free)=0.1281 0.1275 0.1548 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 0.3607 402.814 382.338 0.472 0.997 0.275 13.296-10.522 99.01 99 1 0.2084 528.187 520.928 0.715 0.999 0.250 10.503-8.327 98.90 177 3 0.1714 564.205 562.041 0.856 0.999 0.203 8.318-6.595 100.00 360 8 0.1707 414.736 412.032 0.877 0.999 0.160 6.588-5.215 100.00 711 7 0.1525 381.101 373.520 0.858 0.999 0.160 5.214-4.128 98.38 1367 28 0.0904 557.435 554.937 0.940 0.999 0.045 4.126-3.266 94.74 2603 46 0.0827 508.132 504.287 1.007 1.000 0.014 3.266-2.585 99.86 5447 97 0.0920 342.774 340.349 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0950 258.603 256.380 1.002 1.000 0.000 2.046-1.619 99.39 21536 464 0.1092 153.054 151.366 1.019 0.999 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.393 1.011 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.167 0.990 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0364 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1548 | n_water=805 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1280 r_free=0.1554 | n_water=795 | time (s): 95.690 (total time: 98.380) Filter (q & B) r_work=0.1280 r_free=0.1553 | n_water=791 | time (s): 4.630 (total time: 103.010) Compute maps r_work=0.1280 r_free=0.1553 | n_water=791 | time (s): 1.740 (total time: 104.750) Filter (map) r_work=0.1307 r_free=0.1536 | n_water=653 | time (s): 4.380 (total time: 109.130) Find peaks r_work=0.1307 r_free=0.1536 | n_water=653 | time (s): 0.770 (total time: 109.900) Add new water r_work=0.1329 r_free=0.1557 | n_water=962 | time (s): 4.780 (total time: 114.680) Refine new water occ: r_work=0.1286 r_free=0.1519 adp: r_work=0.1273 r_free=0.1513 occ: r_work=0.1275 r_free=0.1514 adp: r_work=0.1269 r_free=0.1513 occ: r_work=0.1270 r_free=0.1513 adp: r_work=0.1269 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1269 r_free=0.1512 r_work=0.1269 r_free=0.1512 | n_water=962 | time (s): 85.890 (total time: 200.570) Filter (q & B) r_work=0.1273 r_free=0.1513 | n_water=888 | time (s): 5.640 (total time: 206.210) Filter (dist only) r_work=0.1273 r_free=0.1511 | n_water=885 | time (s): 108.750 (total time: 314.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.797832 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 582.600750 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 0.1257 0.1532 0.0274 0.041 1.1 17.8 0.0 0.3 0 11.399 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.32 2.74 2.052 15.186 582.601 0.014 12.35 15.13 2.78 2.443 15.229 582.601 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 68.22 16.28 1.20 517 3272 Protein: 5.39 40.45 11.00 1.20 0 2902 Water: 6.58 68.22 33.60 N/A 517 368 Other: 16.38 32.46 24.42 N/A 0 2 Chain A: 5.56 56.09 13.02 N/A 0 1624 Chain B: 5.39 68.22 12.85 N/A 0 1648 Chain S: 9.28 65.80 37.46 N/A 517 0 Histogram: Values Number of atoms 5.39 - 11.68 2052 11.68 - 17.96 720 17.96 - 24.24 264 24.24 - 30.52 213 30.52 - 36.81 172 36.81 - 43.09 174 43.09 - 49.37 103 49.37 - 55.65 44 55.65 - 61.94 36 61.94 - 68.22 11 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1513 r_work=0.1236 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1515 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 = 0.1229 r_free = 0.1510 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 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= 0.1229 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013453 | | target function (ls_wunit_k1) not normalized (work): 2519.730449 | | target function (ls_wunit_k1) not normalized (free): 98.455602 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1510 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1443 0.1440 0.1612 n_refl.: 191137 remove outliers: r(all,work,free)=0.1443 0.1440 0.1612 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1439 0.1436 0.1610 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1237 0.1518 n_refl.: 191137 remove outliers: r(all,work,free)=0.1242 0.1237 0.1518 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 0.3238 402.814 388.155 0.507 0.961 0.277 13.296-10.522 99.01 99 1 0.1897 528.187 528.096 0.770 0.962 0.233 10.503-8.327 98.90 177 3 0.1403 564.205 565.863 0.918 0.962 0.184 8.318-6.595 100.00 360 8 0.1572 414.736 414.069 0.940 0.961 0.160 6.588-5.215 100.00 711 7 0.1341 381.101 376.416 0.916 0.962 0.160 5.214-4.128 98.38 1367 28 0.0824 557.435 555.799 0.994 0.962 0.070 4.126-3.266 94.74 2603 46 0.0764 508.132 505.733 1.063 0.962 0.019 3.266-2.585 99.86 5447 97 0.0858 342.774 341.233 1.048 0.961 0.000 2.585-2.046 97.45 10613 204 0.0900 258.603 256.765 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1050 153.054 151.571 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1263 82.395 81.410 1.072 0.958 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.217 1.055 0.955 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0589 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1237 r_free=0.1517 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1237 r_free=0.1517 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1237 r_free=0.1517 | n_water=885 | time (s): 3.350 (total time: 3.350) Filter (dist) r_work=0.1239 r_free=0.1520 | n_water=878 | time (s): 110.850 (total time: 114.200) Filter (q & B) r_work=0.1239 r_free=0.1520 | n_water=877 | time (s): 4.910 (total time: 119.110) Compute maps r_work=0.1239 r_free=0.1520 | n_water=877 | time (s): 1.980 (total time: 121.090) Filter (map) r_work=0.1278 r_free=0.1515 | n_water=687 | time (s): 4.970 (total time: 126.060) Find peaks r_work=0.1278 r_free=0.1515 | n_water=687 | time (s): 0.610 (total time: 126.670) Add new water r_work=0.1302 r_free=0.1545 | n_water=1009 | time (s): 4.380 (total time: 131.050) Refine new water occ: r_work=0.1257 r_free=0.1509 adp: r_work=0.1258 r_free=0.1511 occ: r_work=0.1253 r_free=0.1505 adp: r_work=0.1253 r_free=0.1507 occ: r_work=0.1250 r_free=0.1503 adp: r_work=0.1250 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1250 r_free=0.1505 r_work=0.1250 r_free=0.1505 | n_water=1009 | time (s): 276.740 (total time: 407.790) Filter (q & B) r_work=0.1254 r_free=0.1506 | n_water=881 | time (s): 5.820 (total time: 413.610) Filter (dist only) r_work=0.1255 r_free=0.1506 | n_water=880 | time (s): 122.910 (total time: 536.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.689052 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.634938 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 0.1242 0.1435 0.0193 0.035 1.1 8.8 0.0 0.0 0 0.845 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.42 14.35 1.93 1.934 14.622 16.635 3.941 12.33 13.93 1.59 2.208 14.536 16.635 3.896 Individual atomic B min max mean iso aniso Overall: 5.54 67.88 15.34 1.07 514 3270 Protein: 5.54 37.02 10.77 1.07 0 2902 Water: 6.69 67.88 30.37 N/A 514 366 Other: 14.02 28.42 21.22 N/A 0 2 Chain A: 5.54 55.28 12.78 N/A 0 1623 Chain B: 5.56 67.88 12.58 N/A 0 1647 Chain S: 13.12 65.15 32.21 N/A 514 0 Histogram: Values Number of atoms 5.54 - 11.78 2131 11.78 - 18.01 684 18.01 - 24.25 294 24.25 - 30.48 253 30.48 - 36.71 162 36.71 - 42.95 148 42.95 - 49.18 81 49.18 - 55.42 20 55.42 - 61.65 8 61.65 - 67.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1393 r_work=0.1234 r_free=0.1394 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1394 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1388 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891060 | | target function (ml) not normalized (work): 728780.031383 | | target function (ml) not normalized (free): 15215.797046 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1388 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1445 0.1445 0.1482 n_refl.: 191137 remove outliers: r(all,work,free)=0.1445 0.1445 0.1482 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1439 0.1439 0.1478 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1381 n_refl.: 191137 remove outliers: r(all,work,free)=0.1227 0.1224 0.1381 n_refl.: 191135 ======================== 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 0.3825 398.008 359.077 0.418 0.947 0.241 13.296-10.522 99.01 99 1 0.2382 528.187 509.658 0.708 0.948 0.215 10.503-8.327 98.35 176 3 0.1928 556.299 558.695 0.878 0.948 0.210 8.318-6.595 100.00 360 8 0.2060 414.736 410.928 0.897 0.947 0.129 6.588-5.215 100.00 711 7 0.1826 381.101 371.131 0.884 0.948 0.107 5.214-4.128 98.38 1367 28 0.1177 557.435 551.991 0.969 0.948 0.050 4.126-3.266 94.74 2603 46 0.1090 508.132 501.316 1.034 0.948 0.014 3.266-2.585 99.86 5447 97 0.1085 342.774 339.007 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0965 258.603 255.809 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0976 153.054 151.405 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.489 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.317 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1026 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1381 | n_water=880 | time (s): 2.700 (total time: 2.700) Filter (dist) r_work=0.1224 r_free=0.1381 | n_water=880 | time (s): 104.500 (total time: 107.200) Filter (q & B) r_work=0.1225 r_free=0.1381 | n_water=865 | time (s): 5.140 (total time: 112.340) Compute maps r_work=0.1225 r_free=0.1381 | n_water=865 | time (s): 2.270 (total time: 114.610) Filter (map) r_work=0.1249 r_free=0.1388 | n_water=716 | time (s): 4.310 (total time: 118.920) Find peaks r_work=0.1249 r_free=0.1388 | n_water=716 | time (s): 0.550 (total time: 119.470) Add new water r_work=0.1262 r_free=0.1396 | n_water=965 | time (s): 4.850 (total time: 124.320) Refine new water occ: r_work=0.1212 r_free=0.1366 adp: r_work=0.1204 r_free=0.1359 occ: r_work=0.1202 r_free=0.1362 adp: r_work=0.1202 r_free=0.1361 occ: r_work=0.1201 r_free=0.1364 adp: r_work=0.1200 r_free=0.1362 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1362 r_work=0.1200 r_free=0.1362 | n_water=965 | time (s): 326.760 (total time: 451.080) Filter (q & B) r_work=0.1206 r_free=0.1370 | n_water=867 | time (s): 5.130 (total time: 456.210) Filter (dist only) r_work=0.1206 r_free=0.1369 | n_water=866 | time (s): 118.120 (total time: 574.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.612906 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.525437 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 0.1373 0.0168 0.036 1.1 6.6 0.0 0.0 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.73 1.68 1.843 14.262 16.525 3.874 11.97 13.66 1.69 1.993 14.208 16.525 3.864 Individual atomic B min max mean iso aniso Overall: 5.49 67.36 15.01 1.01 500 3270 Protein: 5.49 33.49 10.66 1.01 0 2902 Water: 5.85 67.36 29.58 N/A 500 366 Other: 13.98 26.98 20.48 N/A 0 2 Chain A: 5.56 53.86 12.62 N/A 0 1623 Chain B: 5.49 67.36 12.46 N/A 0 1647 Chain S: 5.85 61.79 31.23 N/A 500 0 Histogram: Values Number of atoms 5.49 - 11.68 2113 11.68 - 17.87 731 17.87 - 24.05 284 24.05 - 30.24 243 30.24 - 36.43 169 36.43 - 42.62 124 42.62 - 48.80 80 48.80 - 54.99 18 54.99 - 61.18 5 61.18 - 67.36 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1366 r_work=0.1197 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1367 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1363 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862349 | | target function (ml) not normalized (work): 723394.819106 | | target function (ml) not normalized (free): 15124.232370 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1363 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1423 0.1423 0.1471 n_refl.: 191135 remove outliers: r(all,work,free)=0.1423 0.1423 0.1471 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1416 0.1415 0.1467 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1363 n_refl.: 191135 remove outliers: r(all,work,free)=0.1197 0.1194 0.1363 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 0.3780 356.981 317.756 0.404 0.946 0.235 13.296-10.522 98.02 98 1 0.2394 478.751 457.191 0.694 0.948 0.190 10.503-8.327 97.80 175 3 0.2081 501.731 498.044 0.869 0.948 0.167 8.318-6.595 100.00 360 8 0.2141 375.413 370.443 0.890 0.948 0.105 6.588-5.215 100.00 711 7 0.1896 344.966 334.821 0.883 0.948 0.100 5.214-4.128 98.38 1367 28 0.1180 504.581 499.761 0.971 0.948 0.040 4.126-3.266 94.74 2603 46 0.1116 459.953 453.517 1.034 0.948 0.009 3.266-2.585 99.86 5447 97 0.1087 310.273 307.029 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0934 234.083 231.669 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0912 138.542 137.258 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0986 74.583 73.875 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.011 38.352 1.039 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1184 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1363 | n_water=866 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1194 r_free=0.1363 | n_water=866 | time (s): 101.960 (total time: 104.380) Filter (q & B) r_work=0.1194 r_free=0.1362 | n_water=858 | time (s): 5.910 (total time: 110.290) Compute maps r_work=0.1194 r_free=0.1362 | n_water=858 | time (s): 1.910 (total time: 112.200) Filter (map) r_work=0.1216 r_free=0.1372 | n_water=738 | time (s): 4.610 (total time: 116.810) Find peaks r_work=0.1216 r_free=0.1372 | n_water=738 | time (s): 0.850 (total time: 117.660) Add new water r_work=0.1227 r_free=0.1389 | n_water=950 | time (s): 4.930 (total time: 122.590) Refine new water occ: r_work=0.1193 r_free=0.1353 adp: r_work=0.1193 r_free=0.1353 occ: r_work=0.1190 r_free=0.1352 adp: r_work=0.1190 r_free=0.1352 occ: r_work=0.1188 r_free=0.1352 adp: r_work=0.1188 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1352 r_work=0.1188 r_free=0.1352 | n_water=950 | time (s): 274.810 (total time: 397.400) Filter (q & B) r_work=0.1193 r_free=0.1358 | n_water=873 | time (s): 5.470 (total time: 402.870) Filter (dist only) r_work=0.1193 r_free=0.1357 | n_water=872 | time (s): 110.750 (total time: 513.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.611073 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.579589 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1362 0.0166 0.036 1.1 5.8 0.0 0.3 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.62 1.66 1.794 14.124 15.580 3.762 12.00 13.66 1.66 1.844 14.102 15.580 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 67.06 14.94 0.96 507 3269 Protein: 5.58 32.29 10.60 0.96 0 2902 Water: 5.93 67.06 29.38 N/A 507 365 Other: 13.81 26.00 19.91 N/A 0 2 Chain A: 5.58 53.15 12.53 N/A 0 1623 Chain B: 5.60 67.06 12.36 N/A 0 1646 Chain S: 5.93 61.68 31.05 N/A 507 0 Histogram: Values Number of atoms 5.58 - 11.72 2142 11.72 - 17.87 721 17.87 - 24.02 288 24.02 - 30.17 229 30.17 - 36.32 161 36.32 - 42.47 127 42.47 - 48.61 79 48.61 - 54.76 22 54.76 - 60.91 3 60.91 - 67.06 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1366 r_work=0.1200 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1367 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759198 | | target function (ml) not normalized (work): 704060.136686 | | target function (ml) not normalized (free): 14737.509872 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1365 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1410 0.1409 0.1485 n_refl.: 191131 remove outliers: r(all,work,free)=0.1410 0.1409 0.1485 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1402 0.1401 0.1480 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1364 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1196 0.1364 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3691 356.629 310.044 0.393 0.951 0.221 13.296-10.522 98.02 98 1 0.2421 478.751 462.123 0.692 0.953 0.178 10.503-8.327 97.80 175 3 0.2106 501.731 496.351 0.857 0.953 0.153 8.318-6.595 100.00 360 8 0.2168 375.413 370.179 0.882 0.952 0.106 6.588-5.215 100.00 711 7 0.1899 344.966 335.406 0.879 0.953 0.087 5.214-4.128 98.38 1367 28 0.1208 504.581 499.605 0.968 0.953 0.044 4.126-3.266 94.74 2603 46 0.1135 459.953 453.449 1.030 0.953 0.005 3.266-2.585 99.86 5447 97 0.1108 310.273 307.049 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0946 234.083 231.679 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0914 138.542 137.252 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0975 74.583 73.885 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.011 38.348 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1291 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1364 | n_water=872 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1197 r_free=0.1364 | n_water=872 | time (s): 103.210 (total time: 105.600) Filter (q & B) r_work=0.1197 r_free=0.1365 | n_water=863 | time (s): 4.160 (total time: 109.760) Compute maps r_work=0.1197 r_free=0.1365 | n_water=863 | time (s): 1.790 (total time: 111.550) Filter (map) r_work=0.1219 r_free=0.1365 | n_water=752 | time (s): 5.560 (total time: 117.110) Find peaks r_work=0.1219 r_free=0.1365 | n_water=752 | time (s): 0.720 (total time: 117.830) Add new water r_work=0.1227 r_free=0.1375 | n_water=952 | time (s): 5.010 (total time: 122.840) Refine new water occ: r_work=0.1193 r_free=0.1353 adp: r_work=0.1193 r_free=0.1352 occ: r_work=0.1191 r_free=0.1355 adp: r_work=0.1191 r_free=0.1354 occ: r_work=0.1190 r_free=0.1356 adp: r_work=0.1190 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1355 r_work=0.1190 r_free=0.1355 | n_water=952 | time (s): 273.270 (total time: 396.110) Filter (q & B) r_work=0.1194 r_free=0.1361 | n_water=880 | time (s): 4.940 (total time: 401.050) Filter (dist only) r_work=0.1194 r_free=0.1361 | n_water=878 | time (s): 110.220 (total time: 511.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.518914 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.462138 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 0.1369 0.0170 0.037 1.1 7.3 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.69 1.70 1.767 14.040 14.462 3.761 12.03 13.71 1.68 1.914 13.992 14.462 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 65.88 14.82 0.90 513 3269 Protein: 5.58 29.29 10.49 0.90 0 2902 Water: 5.92 65.88 29.14 N/A 513 365 Other: 13.83 23.13 18.48 N/A 0 2 Chain A: 5.61 52.62 12.38 N/A 0 1623 Chain B: 5.58 65.88 12.22 N/A 0 1646 Chain S: 5.92 61.84 30.90 N/A 513 0 Histogram: Values Number of atoms 5.58 - 11.61 2120 11.61 - 17.64 765 17.64 - 23.67 275 23.67 - 29.70 216 29.70 - 35.73 164 35.73 - 41.76 127 41.76 - 47.79 80 47.79 - 53.82 27 53.82 - 59.85 4 59.85 - 65.88 4 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1371 r_work=0.1204 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1372 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1372 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759173 | | target function (ml) not normalized (work): 704051.705252 | | target function (ml) not normalized (free): 14738.873401 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1372 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1405 0.1404 0.1501 n_refl.: 191130 remove outliers: r(all,work,free)=0.1405 0.1404 0.1501 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1398 0.1396 0.1495 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1371 n_refl.: 191130 remove outliers: r(all,work,free)=0.1204 0.1201 0.1371 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3615 356.629 329.441 0.419 0.952 0.227 13.296-10.522 98.02 98 1 0.2431 478.751 460.527 0.691 0.954 0.173 10.503-8.327 97.80 175 3 0.2129 501.731 495.772 0.855 0.954 0.147 8.318-6.595 100.00 360 8 0.2142 375.413 370.353 0.880 0.954 0.103 6.588-5.215 100.00 711 7 0.1920 344.966 335.119 0.877 0.954 0.083 5.214-4.128 98.38 1367 28 0.1234 504.581 499.346 0.969 0.954 0.060 4.126-3.266 94.74 2603 46 0.1154 459.953 453.103 1.030 0.954 0.000 3.266-2.585 99.86 5447 97 0.1123 310.273 306.973 1.016 0.954 0.000 2.585-2.046 97.45 10613 204 0.0953 234.083 231.592 1.028 0.953 0.000 2.046-1.619 99.39 21536 464 0.0914 138.542 137.219 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0973 74.583 73.876 1.049 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.011 38.347 1.037 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1370 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1371 | n_water=878 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1201 r_free=0.1371 | n_water=878 | time (s): 116.010 (total time: 118.210) Filter (q & B) r_work=0.1202 r_free=0.1371 | n_water=868 | time (s): 5.240 (total time: 123.450) Compute maps r_work=0.1202 r_free=0.1371 | n_water=868 | time (s): 1.810 (total time: 125.260) Filter (map) r_work=0.1223 r_free=0.1372 | n_water=751 | time (s): 4.930 (total time: 130.190) Find peaks r_work=0.1223 r_free=0.1372 | n_water=751 | time (s): 0.570 (total time: 130.760) Add new water r_work=0.1233 r_free=0.1388 | n_water=963 | time (s): 3.970 (total time: 134.730) Refine new water occ: r_work=0.1198 r_free=0.1356 adp: r_work=0.1198 r_free=0.1357 occ: r_work=0.1196 r_free=0.1354 adp: r_work=0.1196 r_free=0.1355 occ: r_work=0.1195 r_free=0.1352 adp: r_work=0.1195 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1353 r_work=0.1195 r_free=0.1353 | n_water=963 | time (s): 248.010 (total time: 382.740) Filter (q & B) r_work=0.1199 r_free=0.1357 | n_water=888 | time (s): 4.230 (total time: 386.970) Filter (dist only) r_work=0.1199 r_free=0.1357 | n_water=887 | time (s): 110.900 (total time: 497.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.583875 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.672635 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1362 0.0159 0.038 1.1 6.3 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.62 1.59 1.719 13.904 13.673 3.759 12.04 13.65 1.61 1.771 13.884 13.673 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 64.84 14.77 0.87 522 3269 Protein: 5.59 28.50 10.43 0.87 0 2902 Water: 5.98 64.84 28.95 N/A 522 365 Other: 13.87 22.23 18.05 N/A 0 2 Chain A: 5.64 52.24 12.28 N/A 0 1623 Chain B: 5.59 64.84 12.14 N/A 0 1646 Chain S: 5.98 61.99 30.77 N/A 522 0 Histogram: Values Number of atoms 5.59 - 11.52 2100 11.52 - 17.44 782 17.44 - 23.37 280 23.37 - 29.29 212 29.29 - 35.22 168 35.22 - 41.14 122 41.14 - 47.07 87 47.07 - 52.99 30 52.99 - 58.92 6 58.92 - 64.84 4 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1365 r_work=0.1204 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757545 | | target function (ml) not normalized (work): 703746.842321 | | target function (ml) not normalized (free): 14731.321038 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1491 n_refl.: 191130 remove outliers: r(all,work,free)=0.1406 0.1404 0.1491 n_refl.: 191130 overall B=-0.24 to atoms: r(all,work,free)=0.1370 0.1368 0.1466 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1203 0.1364 n_refl.: 191130 remove outliers: r(all,work,free)=0.1206 0.1203 0.1364 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3690 356.629 327.369 0.419 0.951 0.207 13.296-10.522 98.02 98 1 0.2484 478.751 462.338 0.707 0.952 0.155 10.503-8.327 97.80 175 3 0.2148 501.731 494.964 0.885 0.953 0.130 8.318-6.595 100.00 360 8 0.2170 375.413 370.365 0.911 0.952 0.100 6.588-5.215 100.00 711 7 0.1923 344.966 335.264 0.907 0.953 0.083 5.214-4.128 98.38 1367 28 0.1239 504.581 499.134 1.003 0.953 0.070 4.126-3.266 94.74 2603 46 0.1163 459.953 453.026 1.065 0.954 0.005 3.266-2.585 99.86 5447 97 0.1132 310.273 306.972 1.047 0.953 0.000 2.585-2.046 97.45 10613 204 0.0955 234.083 231.594 1.053 0.954 0.000 2.046-1.619 99.39 21536 464 0.0910 138.542 137.254 1.069 0.955 0.000 1.619-1.281 98.00 42464 925 0.0970 74.583 73.881 1.055 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.011 38.338 1.022 0.958 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0504 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1203 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1203 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1364 | n_water=887 | time (s): 3.250 (total time: 3.250) Filter (dist) r_work=0.1203 r_free=0.1364 | n_water=886 | time (s): 108.170 (total time: 111.420) Filter (q & B) r_work=0.1204 r_free=0.1365 | n_water=878 | time (s): 5.700 (total time: 117.120) Compute maps r_work=0.1204 r_free=0.1365 | n_water=878 | time (s): 2.370 (total time: 119.490) Filter (map) r_work=0.1225 r_free=0.1373 | n_water=766 | time (s): 5.010 (total time: 124.500) Find peaks r_work=0.1225 r_free=0.1373 | n_water=766 | time (s): 0.840 (total time: 125.340) Add new water r_work=0.1236 r_free=0.1382 | n_water=976 | time (s): 4.600 (total time: 129.940) Refine new water occ: r_work=0.1201 r_free=0.1350 adp: r_work=0.1201 r_free=0.1350 occ: r_work=0.1199 r_free=0.1350 adp: r_work=0.1199 r_free=0.1350 occ: r_work=0.1197 r_free=0.1351 adp: r_work=0.1197 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1351 r_work=0.1197 r_free=0.1351 | n_water=976 | time (s): 230.160 (total time: 360.100) Filter (q & B) r_work=0.1201 r_free=0.1354 | n_water=893 | time (s): 5.080 (total time: 365.180) Filter (dist only) r_work=0.1201 r_free=0.1354 | n_water=891 | time (s): 111.860 (total time: 477.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533226 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.411733 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 0.1362 0.0157 0.038 1.1 6.0 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.62 1.57 1.697 13.599 13.412 3.759 12.07 13.66 1.59 1.721 13.591 13.412 3.759 Individual atomic B min max mean iso aniso Overall: 5.37 63.69 14.47 0.86 526 3269 Protein: 5.37 27.86 10.19 0.86 0 2902 Water: 5.77 63.69 28.40 N/A 526 365 Other: 13.67 21.99 17.83 N/A 0 2 Chain A: 5.45 51.73 12.00 N/A 0 1623 Chain B: 5.37 63.69 11.87 N/A 0 1646 Chain S: 5.77 61.95 30.22 N/A 526 0 Histogram: Values Number of atoms 5.37 - 11.20 2072 11.20 - 17.03 811 17.03 - 22.87 275 22.87 - 28.70 215 28.70 - 34.53 181 34.53 - 40.36 115 40.36 - 46.20 79 46.20 - 52.03 35 52.03 - 57.86 7 57.86 - 63.69 5 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1366 r_work=0.1207 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1367 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758205 | | target function (ml) not normalized (work): 703870.431980 | | target function (ml) not normalized (free): 14733.807903 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1209 0.1206 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1377 0.1375 0.1473 n_refl.: 191130 remove outliers: r(all,work,free)=0.1377 0.1375 0.1473 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1377 0.1375 0.1473 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1354 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1354 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3674 356.629 327.726 0.434 0.908 0.213 13.296-10.522 98.02 98 1 0.2468 478.751 460.906 0.723 0.909 0.146 10.503-8.327 97.80 175 3 0.2198 501.731 493.951 0.908 0.910 0.117 8.315-6.595 100.00 359 8 0.2157 374.467 369.882 0.938 0.909 0.100 6.588-5.215 100.00 711 7 0.1934 344.966 335.094 0.936 0.910 0.083 5.214-4.128 98.38 1367 28 0.1252 504.581 498.970 1.033 0.911 0.034 4.126-3.266 94.74 2603 46 0.1166 459.953 452.539 1.098 0.912 0.000 3.266-2.585 99.86 5447 97 0.1133 310.273 306.691 1.080 0.912 0.000 2.585-2.046 97.45 10613 204 0.0960 234.083 231.485 1.086 0.914 0.000 2.046-1.619 99.39 21536 464 0.0911 138.542 137.148 1.099 0.917 0.000 1.619-1.281 98.00 42464 925 0.0952 74.583 73.916 1.083 0.922 0.000 1.281-0.980 96.53 101826 2055 0.1632 40.011 38.317 1.041 0.930 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1229 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1354 | n_water=891 | time (s): 2.700 (total time: 2.700) Filter (dist) r_work=0.1196 r_free=0.1354 | n_water=891 | time (s): 113.520 (total time: 116.220) Filter (q & B) r_work=0.1196 r_free=0.1355 | n_water=881 | time (s): 4.830 (total time: 121.050) Compute maps r_work=0.1196 r_free=0.1355 | n_water=881 | time (s): 1.690 (total time: 122.740) Filter (map) r_work=0.1219 r_free=0.1364 | n_water=768 | time (s): 4.460 (total time: 127.200) Find peaks r_work=0.1219 r_free=0.1364 | n_water=768 | time (s): 0.650 (total time: 127.850) Add new water r_work=0.1227 r_free=0.1374 | n_water=973 | time (s): 3.990 (total time: 131.840) Refine new water occ: r_work=0.1193 r_free=0.1342 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1340 adp: r_work=0.1192 r_free=0.1341 occ: r_work=0.1190 r_free=0.1340 adp: r_work=0.1190 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1341 r_work=0.1190 r_free=0.1341 | n_water=973 | time (s): 210.310 (total time: 342.150) Filter (q & B) r_work=0.1194 r_free=0.1351 | n_water=890 | time (s): 4.100 (total time: 346.250) Filter (dist only) r_work=0.1195 r_free=0.1350 | n_water=888 | time (s): 112.490 (total time: 458.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565012 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.269559 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 0.1356 0.0158 0.038 1.1 6.1 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.56 1.58 1.658 13.576 14.270 3.757 11.97 13.57 1.60 1.661 13.574 14.270 3.753 Individual atomic B min max mean iso aniso Overall: 5.41 62.59 14.48 0.86 523 3269 Protein: 5.41 27.83 10.21 0.86 0 2902 Water: 5.76 62.59 28.45 N/A 523 365 Other: 13.68 22.01 17.84 N/A 0 2 Chain A: 5.51 51.36 11.99 N/A 0 1623 Chain B: 5.41 62.59 11.86 N/A 0 1646 Chain S: 5.76 62.14 30.47 N/A 523 0 Histogram: Values Number of atoms 5.41 - 11.13 2044 11.13 - 16.85 831 16.85 - 22.57 273 22.57 - 28.28 201 28.28 - 34.00 182 34.00 - 39.72 120 39.72 - 45.44 86 45.44 - 51.15 40 51.15 - 56.87 9 56.87 - 62.59 6 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1357 r_work=0.1197 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1358 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753027 | | target function (ml) not normalized (work): 702896.830208 | | target function (ml) not normalized (free): 14722.280526 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1358 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1384 0.1382 0.1479 n_refl.: 191129 remove outliers: r(all,work,free)=0.1384 0.1382 0.1479 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1384 0.1382 0.1479 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1194 0.1356 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3694 356.629 326.144 0.390 0.975 0.191 13.296-10.522 97.03 97 1 0.2412 481.024 460.302 0.670 0.977 0.143 10.503-8.327 97.80 175 3 0.2202 501.731 494.329 0.845 0.977 0.120 8.315-6.595 100.00 359 8 0.2149 374.467 369.180 0.871 0.977 0.096 6.588-5.215 100.00 711 7 0.1948 344.966 334.869 0.871 0.978 0.083 5.214-4.128 98.38 1367 28 0.1270 504.581 498.805 0.961 0.979 0.039 4.126-3.266 94.74 2603 46 0.1176 459.953 452.328 1.023 0.980 0.000 3.266-2.585 99.86 5447 97 0.1140 310.273 306.689 1.005 0.981 0.000 2.585-2.046 97.45 10613 204 0.0959 234.083 231.487 1.011 0.983 0.000 2.046-1.619 99.39 21536 464 0.0907 138.542 137.187 1.025 0.986 0.000 1.619-1.281 98.00 42464 925 0.0943 74.583 73.935 1.011 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.011 38.309 0.974 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0859 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1194 r_free=0.1356 After: r_work=0.1195 r_free=0.1356 ================================== NQH flips ================================== r_work=0.1195 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1356 | n_water=888 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1195 r_free=0.1356 | n_water=888 | time (s): 108.330 (total time: 110.750) Filter (q & B) r_work=0.1196 r_free=0.1354 | n_water=878 | time (s): 4.860 (total time: 115.610) Compute maps r_work=0.1196 r_free=0.1354 | n_water=878 | time (s): 2.200 (total time: 117.810) Filter (map) r_work=0.1219 r_free=0.1362 | n_water=765 | time (s): 5.690 (total time: 123.500) Find peaks r_work=0.1219 r_free=0.1362 | n_water=765 | time (s): 0.870 (total time: 124.370) Add new water r_work=0.1226 r_free=0.1373 | n_water=971 | time (s): 4.820 (total time: 129.190) Refine new water occ: r_work=0.1193 r_free=0.1343 adp: r_work=0.1193 r_free=0.1343 occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1343 occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1190 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1343 r_work=0.1190 r_free=0.1343 | n_water=971 | time (s): 323.310 (total time: 452.500) Filter (q & B) r_work=0.1193 r_free=0.1356 | n_water=892 | time (s): 4.270 (total time: 456.770) Filter (dist only) r_work=0.1193 r_free=0.1356 | n_water=890 | time (s): 117.410 (total time: 574.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.587984 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.276618 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1357 0.0163 0.038 1.1 7.5 0.0 0.3 0 0.794 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.57 1.63 1.660 13.575 14.277 3.754 11.95 13.59 1.65 1.652 13.576 14.277 3.753 Individual atomic B min max mean iso aniso Overall: 5.43 62.27 14.47 0.86 525 3269 Protein: 5.43 27.82 10.23 0.86 0 2902 Water: 5.87 62.27 28.28 N/A 525 365 Other: 13.73 21.98 17.86 N/A 0 2 Chain A: 5.53 51.25 11.99 N/A 0 1623 Chain B: 5.43 62.27 11.87 N/A 0 1646 Chain S: 5.87 62.19 30.30 N/A 525 0 Histogram: Values Number of atoms 5.43 - 11.12 2037 11.12 - 16.80 840 16.80 - 22.48 275 22.48 - 28.17 203 28.17 - 33.85 183 33.85 - 39.53 117 39.53 - 45.22 86 45.22 - 50.90 38 50.90 - 56.58 9 56.58 - 62.27 6 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1360 r_work=0.1195 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1360 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1360 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752857 | | target function (ml) not normalized (work): 702861.343192 | | target function (ml) not normalized (free): 14720.248594 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1370 0.1525 5.6959 5.7819| | 2: 2.94 - 2.33 1.00 7339 128 0.1073 0.1308 5.0857 5.1627| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1197 4.6506 4.7642| | 4: 2.04 - 1.85 1.00 7170 155 0.0896 0.1031 4.3864 4.5398| | 5: 1.85 - 1.72 0.99 7113 159 0.0933 0.0998 4.1518 4.2464| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1062 3.9454 4.0705| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0979 3.7965 3.9321| | 8: 1.54 - 1.47 0.96 6798 152 0.0887 0.1302 3.6937 3.8889| | 9: 1.47 - 1.41 0.98 6938 155 0.0921 0.1127 3.6161 3.7463| | 10: 1.41 - 1.36 0.99 7022 150 0.0970 0.1172 3.5515 3.6691| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1115 3.4807 3.5849| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1137 3.4589 3.5861| | 13: 1.28 - 1.25 0.98 6907 166 0.1046 0.1253 3.4378 3.57| | 14: 1.25 - 1.22 0.98 7015 112 0.1111 0.1593 3.4322 3.6779| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1249 3.4468 3.4891| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1552 3.4635 3.6593| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1230 3.4319 3.4406| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1706 3.4369 3.5308| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1739 3.4179 3.5926| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1576 3.4084 3.4318| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2128 3.4169 3.5014| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1955 3.4122 3.4139| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2023 3.4322 3.4827| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2259 3.4343 3.5104| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2507 3.448 3.5236| | 26: 1.01 - 0.99 0.96 6767 158 0.2760 0.2871 3.415 3.4226| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2805 3.4682 3.3941| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 12.00 1.00 0.97 11670.35| | 2: 2.94 - 2.33 7339 128 0.92 12.97 0.99 0.97 5251.58| | 3: 2.33 - 2.04 6939 150 0.96 7.52 1.01 0.97 1666.92| | 4: 2.04 - 1.85 7170 155 0.96 7.51 1.00 0.97 984.03| | 5: 1.85 - 1.72 7113 159 0.96 8.07 1.00 0.97 634.00| | 6: 1.72 - 1.62 7102 142 0.96 8.01 1.00 0.98 441.14| | 7: 1.62 - 1.54 7104 148 0.96 8.12 1.01 0.99 334.93| | 8: 1.54 - 1.47 6798 152 0.96 8.18 1.01 0.99 275.89| | 9: 1.47 - 1.41 6938 155 0.96 8.38 1.01 0.99 227.77| | 10: 1.41 - 1.36 7022 150 0.96 8.87 1.00 0.99 200.79| | 11: 1.36 - 1.32 6997 151 0.96 8.90 0.99 0.97 174.09| | 12: 1.32 - 1.28 6975 149 0.96 9.00 0.98 0.96 160.81| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.98 158.52| | 14: 1.25 - 1.22 7015 112 0.95 10.74 1.02 0.98 163.26| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 0.99 166.48| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.98 160.07| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.98 153.81| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.96 147.48| | 19: 1.12 - 1.10 6948 106 0.93 14.11 1.00 0.96 150.54| | 20: 1.10 - 1.08 6884 147 0.92 15.18 1.00 0.95 149.65| | 21: 1.08 - 1.07 6852 152 0.91 16.61 1.00 0.94 152.63| | 22: 1.07 - 1.05 6836 135 0.89 18.26 0.99 0.94 154.41| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.93 164.24| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.94 178.75| | 25: 1.02 - 1.01 6552 130 0.83 25.13 0.97 0.91 181.75| | 26: 1.01 - 0.99 6767 158 0.81 26.61 0.98 0.89 176.19| | 27: 0.99 - 0.98 6647 131 0.82 26.25 0.98 0.88 160.43| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 147.48 max = 11670.35 mean = 946.15| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.28| |phase err.(test): min = 0.00 max = 89.14 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1390 0.1389 0.1495 n_refl.: 191128 remove outliers: r(all,work,free)=0.1390 0.1389 0.1495 n_refl.: 191128 overall B=0.00 to atoms: r(all,work,free)=0.1390 0.1389 0.1495 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1361 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1361 n_refl.: 191127 ======================== 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 90.10 88 3 0.3551 347.962 326.362 0.389 0.995 0.207 13.296-10.522 97.03 97 1 0.2397 481.024 463.736 0.657 0.996 0.144 10.503-8.327 97.80 175 3 0.2192 501.731 494.200 0.821 0.996 0.111 8.315-6.595 100.00 359 8 0.2158 374.467 369.078 0.847 0.996 0.091 6.588-5.215 100.00 711 7 0.1934 344.966 335.075 0.848 0.997 0.077 5.214-4.128 98.38 1367 28 0.1261 504.581 498.845 0.936 0.998 0.034 4.126-3.266 94.74 2603 46 0.1175 459.953 452.412 0.997 0.999 0.000 3.266-2.585 99.86 5447 97 0.1135 310.273 306.720 0.980 1.001 0.000 2.585-2.046 97.45 10613 204 0.0960 234.083 231.468 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0908 138.542 137.168 0.999 1.007 0.000 1.619-1.281 98.00 42464 925 0.0943 74.583 73.930 0.987 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.011 38.302 0.952 1.027 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0480 ================= 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 : 0.2037 0.1987 0.080 5.280 5.2 78.0 14.6 805 0.000 1_bss: 0.1801 0.1907 0.080 5.280 5.2 78.1 14.6 805 0.000 1_settarget: 0.1801 0.1907 0.080 5.280 5.2 78.1 14.6 805 0.000 1_nqh: 0.1801 0.1906 0.080 5.280 5.2 78.1 14.6 805 0.002 1_weight: 0.1801 0.1906 0.080 5.280 5.2 78.1 14.6 805 0.002 1_xyzrec: 0.1267 0.1499 0.039 1.146 5.2 78.1 14.6 805 0.159 1_adp: 0.1297 0.1571 0.039 1.146 5.2 73.1 15.1 805 0.159 1_regHadp: 0.1296 0.1566 0.039 1.146 5.2 73.1 15.1 805 0.159 1_occ: 0.1281 0.1555 0.039 1.146 5.2 73.1 15.1 805 0.159 2_bss: 0.1275 0.1548 0.039 1.146 5.3 73.2 15.3 805 0.159 2_settarget: 0.1275 0.1548 0.039 1.146 5.3 73.2 15.3 805 0.159 2_updatecdl: 0.1275 0.1548 0.039 1.170 5.3 73.2 15.3 805 0.159 2_nqh: 0.1275 0.1548 0.039 1.170 5.3 73.2 15.3 805 0.159 2_sol: 0.1273 0.1511 0.039 1.170 5.3 73.2 16.2 885 n/a 2_weight: 0.1273 0.1511 0.039 1.170 5.3 73.2 16.2 885 n/a 2_xyzrec: 0.1257 0.1532 0.041 1.131 5.3 73.2 16.2 885 n/a 2_adp: 0.1235 0.1513 0.041 1.131 5.4 68.2 16.3 885 n/a 2_regHadp: 0.1236 0.1515 0.041 1.131 5.4 68.2 16.3 885 n/a 2_occ: 0.1229 0.1510 0.041 1.131 5.4 68.2 16.3 885 n/a 3_bss: 0.1237 0.1517 0.041 1.131 5.4 68.2 16.3 885 n/a 3_settarget: 0.1237 0.1517 0.041 1.131 5.4 68.2 16.3 885 n/a 3_updatecdl: 0.1237 0.1517 0.041 1.136 5.4 68.2 16.3 885 n/a 3_nqh: 0.1237 0.1517 0.041 1.136 5.4 68.2 16.3 885 n/a 3_sol: 0.1255 0.1506 0.041 1.136 5.4 68.2 15.5 880 n/a 3_weight: 0.1255 0.1506 0.041 1.136 5.4 68.2 15.5 880 n/a 3_xyzrec: 0.1242 0.1435 0.035 1.099 5.4 68.2 15.5 880 n/a 3_adp: 0.1233 0.1393 0.035 1.099 5.5 67.9 15.3 880 n/a 3_regHadp: 0.1234 0.1394 0.035 1.099 5.5 67.9 15.3 880 n/a 3_occ: 0.1229 0.1388 0.035 1.099 5.5 67.9 15.3 880 n/a 4_bss: 0.1224 0.1381 0.035 1.099 5.5 67.9 15.3 880 n/a 4_settarget: 0.1224 0.1381 0.035 1.099 5.5 67.9 15.3 880 n/a 4_updatecdl: 0.1224 0.1381 0.035 1.102 5.5 67.9 15.3 880 n/a 4_nqh: 0.1224 0.1381 0.035 1.102 5.5 67.9 15.3 880 n/a 4_sol: 0.1206 0.1369 0.035 1.102 5.5 67.9 15.1 866 n/a 4_weight: 0.1206 0.1369 0.035 1.102 5.5 67.9 15.1 866 n/a 4_xyzrec: 0.1205 0.1373 0.036 1.127 5.5 67.9 15.1 866 n/a 4_adp: 0.1197 0.1366 0.036 1.127 5.5 67.4 15.0 866 n/a 4_regHadp: 0.1197 0.1367 0.036 1.127 5.5 67.4 15.0 866 n/a 4_occ: 0.1196 0.1363 0.036 1.127 5.5 67.4 15.0 866 n/a 5_bss: 0.1194 0.1363 0.036 1.127 5.5 67.3 15.0 866 n/a 5_settarget: 0.1194 0.1363 0.036 1.127 5.5 67.3 15.0 866 n/a 5_updatecdl: 0.1194 0.1363 0.036 1.127 5.5 67.3 15.0 866 n/a 5_nqh: 0.1194 0.1363 0.036 1.127 5.5 67.3 15.0 866 n/a 5_sol: 0.1193 0.1357 0.036 1.127 5.5 67.3 15.0 872 n/a 5_weight: 0.1193 0.1357 0.036 1.127 5.5 67.3 15.0 872 n/a 5_xyzrec: 0.1196 0.1362 0.036 1.132 5.5 67.3 15.0 872 n/a 5_adp: 0.1200 0.1366 0.036 1.132 5.6 67.1 14.9 872 n/a 5_regHadp: 0.1200 0.1367 0.036 1.132 5.6 67.1 14.9 872 n/a 5_occ: 0.1198 0.1365 0.036 1.132 5.6 67.1 14.9 872 n/a 6_bss: 0.1197 0.1364 0.036 1.132 5.5 67.0 14.9 872 n/a 6_settarget: 0.1197 0.1364 0.036 1.132 5.5 67.0 14.9 872 n/a 6_updatecdl: 0.1197 0.1364 0.036 1.131 5.5 67.0 14.9 872 n/a 6_nqh: 0.1197 0.1364 0.036 1.131 5.5 67.0 14.9 872 n/a 6_sol: 0.1194 0.1361 0.036 1.131 5.5 67.0 14.9 878 n/a 6_weight: 0.1194 0.1361 0.036 1.131 5.5 67.0 14.9 878 n/a 6_xyzrec: 0.1199 0.1369 0.037 1.117 5.5 67.0 14.9 878 n/a 6_adp: 0.1203 0.1371 0.037 1.117 5.6 65.9 14.8 878 n/a 6_regHadp: 0.1204 0.1372 0.037 1.117 5.6 65.9 14.8 878 n/a 6_occ: 0.1202 0.1372 0.037 1.117 5.6 65.9 14.8 878 n/a 7_bss: 0.1201 0.1371 0.037 1.117 5.5 65.8 14.8 878 n/a 7_settarget: 0.1201 0.1371 0.037 1.117 5.5 65.8 14.8 878 n/a 7_updatecdl: 0.1201 0.1371 0.037 1.118 5.5 65.8 14.8 878 n/a 7_nqh: 0.1201 0.1371 0.037 1.118 5.5 65.8 14.8 878 n/a 7_sol: 0.1199 0.1357 0.037 1.118 5.5 65.8 14.8 887 n/a 7_weight: 0.1199 0.1357 0.037 1.118 5.5 65.8 14.8 887 n/a 7_xyzrec: 0.1202 0.1362 0.038 1.133 5.5 65.8 14.8 887 n/a 7_adp: 0.1204 0.1365 0.038 1.133 5.6 64.8 14.8 887 n/a 7_regHadp: 0.1204 0.1366 0.038 1.133 5.6 64.8 14.8 887 n/a 7_occ: 0.1203 0.1366 0.038 1.133 5.6 64.8 14.8 887 n/a 8_bss: 0.1203 0.1364 0.038 1.133 5.4 64.6 14.5 887 n/a 8_settarget: 0.1203 0.1364 0.038 1.133 5.4 64.6 14.5 887 n/a 8_updatecdl: 0.1203 0.1364 0.038 1.133 5.4 64.6 14.5 887 n/a 8_nqh: 0.1203 0.1364 0.038 1.133 5.4 64.6 14.5 887 n/a 8_sol: 0.1201 0.1354 0.038 1.133 5.4 64.6 14.5 891 n/a 8_weight: 0.1201 0.1354 0.038 1.133 5.4 64.6 14.5 891 n/a 8_xyzrec: 0.1205 0.1362 0.038 1.128 5.4 64.6 14.5 891 n/a 8_adp: 0.1207 0.1366 0.038 1.128 5.4 63.7 14.5 891 n/a 8_regHadp: 0.1207 0.1367 0.038 1.128 5.4 63.7 14.5 891 n/a 8_occ: 0.1206 0.1366 0.038 1.128 5.4 63.7 14.5 891 n/a 9_bss: 0.1196 0.1354 0.038 1.128 5.4 63.7 14.5 891 n/a 9_settarget: 0.1196 0.1354 0.038 1.128 5.4 63.7 14.5 891 n/a 9_updatecdl: 0.1196 0.1354 0.038 1.128 5.4 63.7 14.5 891 n/a 9_nqh: 0.1196 0.1354 0.038 1.128 5.4 63.7 14.5 891 n/a 9_sol: 0.1195 0.1350 0.038 1.128 5.4 63.7 14.5 888 n/a 9_weight: 0.1195 0.1350 0.038 1.128 5.4 63.7 14.5 888 n/a 9_xyzrec: 0.1199 0.1356 0.038 1.119 5.4 63.7 14.5 888 n/a 9_adp: 0.1197 0.1357 0.038 1.119 5.4 62.6 14.5 888 n/a 9_regHadp: 0.1197 0.1357 0.038 1.119 5.4 62.6 14.5 888 n/a 9_occ: 0.1195 0.1358 0.038 1.119 5.4 62.6 14.5 888 n/a 10_bss: 0.1194 0.1356 0.038 1.119 5.4 62.6 14.5 888 n/a 10_settarget: 0.1194 0.1356 0.038 1.119 5.4 62.6 14.5 888 n/a 10_updatecdl: 0.1194 0.1356 0.038 1.119 5.4 62.6 14.5 888 n/a 10_setrh: 0.1195 0.1356 0.038 1.119 5.4 62.6 14.5 888 n/a 10_nqh: 0.1195 0.1356 0.038 1.119 5.4 62.6 14.5 888 n/a 10_sol: 0.1193 0.1356 0.038 1.119 5.4 62.6 14.5 890 n/a 10_weight: 0.1193 0.1356 0.038 1.119 5.4 62.6 14.5 890 n/a 10_xyzrec: 0.1194 0.1357 0.038 1.150 5.4 62.6 14.5 890 n/a 10_adp: 0.1195 0.1360 0.038 1.150 5.4 62.3 14.5 890 n/a 10_regHadp: 0.1195 0.1360 0.038 1.150 5.4 62.3 14.5 890 n/a 10_occ: 0.1194 0.1360 0.038 1.150 5.4 62.3 14.5 890 n/a end: 0.1193 0.1361 0.038 1.150 5.4 62.3 14.5 890 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9229404_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9229404_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.7800 Refinement macro-cycles (run) : 12071.4900 Write final files (write_after_run_outputs) : 159.3400 Total : 12237.6100 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:05 PST -0800 (1736736065.91 s) Start R-work = 0.1801, R-free = 0.1907 Final R-work = 0.1193, R-free = 0.1361 =============================================================================== Job complete usr+sys time: 12510.94 seconds wall clock time: 209 minutes 28.17 seconds (12568.17 seconds total)