Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6121353.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 { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6121353.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6121353.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" } 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: 2.24, per 1000 atoms: 0.33 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.708 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: 2.596 distance_ideal: 2.710 ideal - model: 0.114 slack: 0.000 delta_slack: 0.114 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 118.6 milliseconds Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.03: 837 1.03 - 1.28: 2584 1.28 - 1.53: 1687 1.53 - 1.77: 812 1.77 - 2.02: 14 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.453 1.268 0.185 8.30e-03 1.45e+04 4.98e+02 bond pdb=" N GLN B 184 " pdb=" CA GLN B 184 " ideal model delta sigma weight residual 1.457 1.748 -0.291 1.33e-02 5.65e+03 4.78e+02 bond pdb=" C THR B 125 " pdb=" N GLY B 126 " ideal model delta sigma weight residual 1.327 1.539 -0.213 1.01e-02 9.80e+03 4.43e+02 bond pdb=" ND1 HIS A 179 " pdb=" CE1 HIS A 179 " ideal model delta sigma weight residual 1.321 1.125 0.196 1.00e-02 1.00e+04 3.86e+02 bond pdb=" CA VAL A 114 " pdb=" CB VAL A 114 " ideal model delta sigma weight residual 1.539 1.644 -0.105 5.40e-03 3.43e+04 3.80e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.22: 5709 4.22 - 8.43: 3520 8.43 - 12.64: 1315 12.64 - 16.86: 241 16.86 - 21.07: 25 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.45 134.50 -12.05 7.20e-01 1.93e+00 2.80e+02 angle pdb=" CA TYR A 195 " pdb=" C TYR A 195 " pdb=" O TYR A 195 " ideal model delta sigma weight residual 121.16 139.43 -18.27 1.12e+00 7.97e-01 2.66e+02 angle pdb=" CA VAL B 7 " pdb=" C VAL B 7 " pdb=" O VAL B 7 " ideal model delta sigma weight residual 120.53 135.02 -14.49 1.07e+00 8.73e-01 1.83e+02 angle pdb=" CA GLY B 165 " pdb=" C GLY B 165 " pdb=" N LEU B 166 " ideal model delta sigma weight residual 117.34 131.00 -13.66 1.01e+00 9.80e-01 1.83e+02 angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" O ILE A 134 " ideal model delta sigma weight residual 119.19 110.42 8.77 6.50e-01 2.37e+00 1.82e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1852 17.85 - 35.69: 136 35.69 - 53.53: 46 53.53 - 71.37: 12 71.37 - 89.22: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -153.65 -26.35 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -156.99 -23.01 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.234: 221 0.234 - 0.468: 168 0.468 - 0.701: 73 0.701 - 0.935: 18 0.935 - 1.168: 12 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA GLN B 184 " pdb=" N GLN B 184 " pdb=" C GLN B 184 " pdb=" CB GLN B 184 " both_signs ideal model delta sigma weight residual False 2.51 3.68 -1.17 2.00e-01 2.50e+01 3.41e+01 chirality pdb=" CA LYS A 167 " pdb=" N LYS A 167 " pdb=" C LYS A 167 " pdb=" CB LYS A 167 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.79e+01 chirality pdb=" CA VAL A 92 " pdb=" N VAL A 92 " pdb=" C VAL A 92 " pdb=" CB VAL A 92 " 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 A 139 " -0.020 2.00e-02 2.50e+03 5.50e-02 1.21e+02 pdb=" CG TRP A 139 " 0.093 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.074 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.037 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.011 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.003 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.042 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.043 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.026 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.149 2.00e-02 2.50e+03 6.32e-02 1.20e+02 pdb=" CG PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.054 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.126 2.00e-02 2.50e+03 6.08e-02 1.11e+02 pdb=" CG PHE B 164 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.082 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.044 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.094 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.063 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.041 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.068 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.78 - 1.55: 19 1.55 - 2.31: 1809 2.31 - 3.07: 21707 3.07 - 3.84: 33221 3.84 - 4.60: 53496 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110252 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.782 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.895 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.010 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.027 2.620 nonbonded pdb="HG22 VAL A 181 " pdb=" O HOH S1566 " model vdw 1.191 2.620 ... (remaining 110247 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_6121353_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2036 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302318 | | target function (ml) not normalized (work): 805880.158526 | | target function (ml) not normalized (free): 16562.564272 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2144 0.1900 6.6905 6.3036| | 2: 2.94 - 2.33 1.00 7339 128 0.1610 0.1506 5.5326 5.5616| | 3: 2.33 - 2.04 0.96 6939 150 0.1633 0.1565 5.1385 5.1047| | 4: 2.04 - 1.85 1.00 7170 155 0.1746 0.1650 4.952 5.0314| | 5: 1.85 - 1.72 0.99 7113 159 0.1912 0.1696 4.7933 4.7993| | 6: 1.72 - 1.62 0.99 7102 142 0.1994 0.1956 4.672 4.72| | 7: 1.62 - 1.54 0.99 7104 148 0.2027 0.1975 4.561 4.6537| | 8: 1.54 - 1.47 0.96 6798 152 0.2043 0.2223 4.4832 4.5222| | 9: 1.47 - 1.41 0.98 6938 155 0.2096 0.2068 4.4068 4.4275| | 10: 1.41 - 1.36 0.99 7022 150 0.2153 0.2152 4.3174 4.3496| | 11: 1.36 - 1.32 0.99 6997 151 0.2098 0.2069 4.2416 4.3028| | 12: 1.32 - 1.28 0.98 6976 149 0.2096 0.2126 4.1839 4.2623| | 13: 1.28 - 1.25 0.98 6907 166 0.2013 0.2063 4.1054 4.1476| | 14: 1.25 - 1.22 0.98 7015 113 0.2063 0.2281 4.0706 4.297| | 15: 1.22 - 1.19 0.98 6957 137 0.2113 0.1907 4.0459 3.9576| | 16: 1.19 - 1.17 0.93 6604 132 0.2109 0.2179 4.0047 4.0594| | 17: 1.17 - 1.14 0.98 6941 135 0.2186 0.2041 3.9754 4.0116| | 18: 1.14 - 1.12 0.98 6875 142 0.2228 0.2450 3.9323 3.9568| | 19: 1.12 - 1.10 0.97 6949 106 0.2249 0.2393 3.8578 3.9348| | 20: 1.10 - 1.08 0.97 6884 147 0.2370 0.2307 3.8368 3.8643| | 21: 1.08 - 1.07 0.97 6852 152 0.2430 0.2652 3.7949 3.8184| | 22: 1.07 - 1.05 0.97 6838 135 0.2563 0.2660 3.7562 3.7785| | 23: 1.05 - 1.03 0.97 6829 159 0.2733 0.2670 3.7389 3.805| | 24: 1.03 - 1.02 0.96 6785 133 0.2885 0.2655 3.7033 3.738| | 25: 1.02 - 1.01 0.93 6552 130 0.3043 0.2955 3.6734 3.7611| | 26: 1.01 - 0.99 0.96 6767 158 0.3229 0.3419 3.6335 3.6555| | 27: 0.99 - 0.98 0.94 6648 131 0.3454 0.3150 3.6491 3.6009| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.43 0.91 0.97 35330.57| | 2: 2.94 - 2.33 7339 128 0.86 20.97 1.08 1.02 14796.02| | 3: 2.33 - 2.04 6939 150 0.93 12.00 1.11 1.06 3854.91| | 4: 2.04 - 1.85 7170 155 0.93 12.95 1.11 1.07 2634.75| | 5: 1.85 - 1.72 7113 159 0.91 15.46 1.11 1.07 2044.09| | 6: 1.72 - 1.62 7102 142 0.90 17.01 1.11 1.08 1690.23| | 7: 1.62 - 1.54 7104 148 0.89 17.94 1.11 1.08 1403.25| | 8: 1.54 - 1.47 6798 152 0.89 18.31 1.10 1.08 1170.67| | 9: 1.47 - 1.41 6938 155 0.88 18.78 1.10 1.07 977.33| | 10: 1.41 - 1.36 7022 150 0.87 20.24 1.10 1.06 872.05| | 11: 1.36 - 1.32 6997 151 0.87 20.55 1.08 1.05 776.61| | 12: 1.32 - 1.28 6976 149 0.87 20.66 1.08 1.02 689.02| | 13: 1.28 - 1.25 6907 166 0.87 20.41 1.07 1.02 613.04| | 14: 1.25 - 1.22 7015 113 0.87 20.62 1.07 1.03 570.02| | 15: 1.22 - 1.19 6957 137 0.87 20.44 1.07 1.04 523.39| | 16: 1.19 - 1.17 6604 132 0.87 20.36 1.08 1.02 482.25| | 17: 1.17 - 1.14 6941 135 0.86 21.19 1.08 0.99 437.28| | 18: 1.14 - 1.12 6875 142 0.86 21.70 1.08 0.99 414.80| | 19: 1.12 - 1.10 6949 106 0.85 22.51 1.07 0.99 387.66| | 20: 1.10 - 1.08 6884 147 0.84 23.18 1.06 0.99 362.22| | 21: 1.08 - 1.07 6852 152 0.84 24.08 1.05 0.98 343.83| | 22: 1.07 - 1.05 6838 135 0.82 25.83 1.04 0.97 333.54| | 23: 1.05 - 1.03 6829 159 0.80 27.65 1.05 0.97 333.52| | 24: 1.03 - 1.02 6785 133 0.78 29.39 1.05 0.97 329.99| | 25: 1.02 - 1.01 6552 130 0.77 30.84 1.03 0.94 319.22| | 26: 1.01 - 0.99 6767 158 0.74 32.86 1.03 0.91 302.69| | 27: 0.99 - 0.98 6648 131 0.74 33.49 1.04 0.88 284.86| |alpha: min = 0.88 max = 1.08 mean = 1.01| |beta: min = 284.86 max = 35330.57 mean = 2802.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.76| |phase err.(test): min = 0.00 max = 88.94 mean = 21.89| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.291 2950 Z= 5.428 Angle : 5.105 18.275 4018 Z= 3.629 Chirality : 0.380 1.168 492 Planarity : 0.032 0.130 512 Dihedral : 13.070 89.216 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.78 % Allowed : 3.63 % Favored : 95.60 % Rotamer: Outliers : 1.61 % Allowed : 2.90 % Favored : 95.48 % Cbeta Deviations : 33.99 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.39), residues: 386 helix: -2.70 (0.31), residues: 142 sheet: -0.80 (0.54), residues: 86 loop : 0.05 (0.49), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.116 0.020 ARG B 175 TYR 0.102 0.033 TYR A 67 PHE 0.120 0.032 PHE B 82 TRP 0.074 0.035 TRP B 146 HIS 0.092 0.031 HIS B 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= 0.2036 r_free= 0.1970 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302318 | | target function (ml) not normalized (work): 805880.158526 | | target function (ml) not normalized (free): 16562.564272 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2036 0.1970 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2036 0.1970 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2037 0.1970 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2035 0.2037 0.1970 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1806 0.1908 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1804 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 0.4077 402.814 292.641 0.436 0.912 0.301 13.296-10.522 99.01 99 1 0.2484 528.187 520.308 0.789 0.913 0.260 10.503-8.327 99.45 178 3 0.2524 565.118 556.555 0.972 0.913 0.243 8.318-6.595 100.00 360 8 0.2509 414.736 402.829 0.977 0.913 0.179 6.588-5.215 100.00 711 7 0.2276 381.101 365.705 0.953 0.913 0.109 5.214-4.128 98.38 1367 28 0.1502 557.435 549.298 1.073 0.913 0.080 4.126-3.266 94.74 2603 46 0.1364 508.132 499.053 1.145 0.913 0.023 3.266-2.585 99.86 5447 97 0.1446 342.774 337.253 1.121 0.913 0.000 2.585-2.046 97.45 10613 204 0.1394 258.603 254.332 1.123 0.912 0.000 2.046-1.619 99.39 21536 464 0.1618 153.054 149.863 1.143 0.911 0.000 1.619-1.281 98.00 42464 925 0.1930 82.395 80.232 1.129 0.909 0.000 1.281-0.980 96.53 101826 2055 0.2323 44.202 41.673 1.110 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0068 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1804 r_free=0.1907 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1804 r_free=0.1907 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.342527 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.866395 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 0.1273 0.1482 0.0209 0.035 1.2 12.1 0.0 0.3 0 11.171 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 14.82 2.09 1.118 13.115 571.866 0.019 13.02 15.52 2.50 1.247 13.341 571.866 0.018 Individual atomic B min max mean iso aniso Overall: 5.19 73.05 15.01 1.41 435 3274 Protein: 5.19 40.47 10.99 1.41 0 2902 Water: 6.25 73.05 29.48 N/A 435 370 Other: 15.95 31.15 23.55 N/A 0 2 Chain A: 5.30 60.86 13.05 N/A 0 1626 Chain B: 5.19 73.05 12.78 N/A 0 1648 Chain S: 11.66 62.66 30.83 N/A 435 0 Histogram: Values Number of atoms 5.19 - 11.98 2168 11.98 - 18.76 634 18.76 - 25.55 312 25.55 - 32.33 268 32.33 - 39.12 156 39.12 - 45.91 104 45.91 - 52.69 46 52.69 - 59.48 17 59.48 - 66.26 3 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1302 r_free=0.1552 r_work=0.1301 r_free=0.1548 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1301 r_free = 0.1548 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1287 r_free = 0.1535 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1287 r_free= 0.1535 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015839 | | target function (ls_wunit_k1) not normalized (work): 2966.539773 | | target function (ls_wunit_k1) not normalized (free): 113.219465 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1287 0.1535 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1472 0.1470 0.1607 n_refl.: 191138 remove outliers: r(all,work,free)=0.1472 0.1470 0.1607 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1497 0.1495 0.1619 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1284 0.1279 0.1529 n_refl.: 191138 remove outliers: r(all,work,free)=0.1284 0.1279 0.1529 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 0.3646 402.814 375.487 0.467 1.002 0.287 13.296-10.522 99.01 99 1 0.2112 528.187 522.971 0.716 1.003 0.265 10.503-8.327 99.45 178 3 0.1761 565.118 560.625 0.852 1.003 0.213 8.318-6.595 100.00 360 8 0.1756 414.736 411.830 0.875 1.003 0.154 6.588-5.215 100.00 711 7 0.1590 381.101 374.129 0.851 1.003 0.109 5.214-4.128 98.38 1367 28 0.0928 557.435 553.947 0.938 1.004 0.080 4.126-3.266 94.74 2603 46 0.0857 508.132 504.117 1.004 1.004 0.014 3.266-2.585 99.86 5447 97 0.0930 342.774 340.269 0.987 1.004 0.000 2.585-2.046 97.45 10613 204 0.0947 258.603 256.377 0.997 1.004 0.000 2.046-1.619 99.39 21536 464 0.1081 153.054 151.363 1.015 1.004 0.000 1.619-1.281 98.00 42464 925 0.1280 82.395 81.407 1.007 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1880 44.202 42.151 0.985 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0392 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1279 r_free=0.1529 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1279 r_free=0.1529 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1529 | n_water=805 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1282 r_free=0.1531 | n_water=797 | time (s): 98.550 (total time: 100.810) Filter (q & B) r_work=0.1283 r_free=0.1532 | n_water=789 | time (s): 4.250 (total time: 105.060) Compute maps r_work=0.1283 r_free=0.1532 | n_water=789 | time (s): 1.840 (total time: 106.900) Filter (map) r_work=0.1306 r_free=0.1534 | n_water=662 | time (s): 4.020 (total time: 110.920) Find peaks r_work=0.1306 r_free=0.1534 | n_water=662 | time (s): 0.610 (total time: 111.530) Add new water r_work=0.1330 r_free=0.1568 | n_water=976 | time (s): 4.200 (total time: 115.730) Refine new water occ: r_work=0.1286 r_free=0.1504 adp: r_work=0.1273 r_free=0.1504 occ: r_work=0.1276 r_free=0.1495 adp: r_work=0.1269 r_free=0.1497 occ: r_work=0.1270 r_free=0.1492 adp: r_work=0.1267 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1493 r_work=0.1267 r_free=0.1493 | n_water=976 | time (s): 91.120 (total time: 206.850) Filter (q & B) r_work=0.1271 r_free=0.1499 | n_water=902 | time (s): 4.570 (total time: 211.420) Filter (dist only) r_work=0.1272 r_free=0.1499 | n_water=900 | time (s): 115.480 (total time: 326.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.836444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.981976 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1254 0.1515 0.0261 0.039 1.1 16.1 0.0 0.3 0 11.918 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.15 2.61 2.043 15.294 573.982 0.014 12.31 15.03 2.71 2.423 15.348 573.982 0.014 Individual atomic B min max mean iso aniso Overall: 5.36 68.22 16.53 1.20 531 3273 Protein: 5.36 40.61 10.98 1.20 0 2902 Water: 6.59 68.22 34.42 N/A 531 369 Other: 16.26 31.53 23.90 N/A 0 2 Chain A: 5.46 56.84 13.02 N/A 0 1625 Chain B: 5.36 68.22 12.83 N/A 0 1648 Chain S: 13.11 66.25 38.76 N/A 531 0 Histogram: Values Number of atoms 5.36 - 11.64 2042 11.64 - 17.93 725 17.93 - 24.22 270 24.22 - 30.50 204 30.50 - 36.79 185 36.79 - 43.07 148 43.07 - 49.36 104 49.36 - 55.65 53 55.65 - 61.93 57 61.93 - 68.22 16 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1503 r_work=0.1232 r_free=0.1504 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1504 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1500 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1500 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013389 | | target function (ls_wunit_k1) not normalized (work): 2507.766053 | | target function (ls_wunit_k1) not normalized (free): 97.320167 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1225 0.1500 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1431 0.1428 0.1597 n_refl.: 191138 remove outliers: r(all,work,free)=0.1431 0.1428 0.1597 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1428 0.1425 0.1595 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1507 n_refl.: 191138 remove outliers: r(all,work,free)=0.1237 0.1231 0.1507 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3158 398.008 379.611 0.499 0.963 0.283 13.296-10.522 99.01 99 1 0.1867 528.187 518.339 0.754 0.964 0.233 10.503-8.327 99.45 178 3 0.1419 565.118 565.854 0.922 0.964 0.174 8.318-6.595 100.00 360 8 0.1548 414.736 413.259 0.933 0.963 0.135 6.588-5.215 100.00 711 7 0.1377 381.101 376.055 0.909 0.963 0.110 5.214-4.128 98.38 1367 28 0.0828 557.435 555.924 0.995 0.963 0.100 4.126-3.266 94.74 2603 46 0.0754 508.132 505.480 1.059 0.963 0.019 3.266-2.585 99.86 5447 97 0.0861 342.774 341.217 1.045 0.962 0.010 2.585-2.046 97.45 10613 204 0.0895 258.603 256.744 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1039 153.054 151.640 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.356 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.217 1.059 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0482 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1507 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1507 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1507 | n_water=900 | time (s): 3.360 (total time: 3.360) Filter (dist) r_work=0.1233 r_free=0.1508 | n_water=897 | time (s): 116.970 (total time: 120.330) Filter (q & B) r_work=0.1233 r_free=0.1509 | n_water=893 | time (s): 4.330 (total time: 124.660) Compute maps r_work=0.1233 r_free=0.1509 | n_water=893 | time (s): 1.600 (total time: 126.260) Filter (map) r_work=0.1275 r_free=0.1513 | n_water=690 | time (s): 4.470 (total time: 130.730) Find peaks r_work=0.1275 r_free=0.1513 | n_water=690 | time (s): 0.760 (total time: 131.490) Add new water r_work=0.1297 r_free=0.1548 | n_water=998 | time (s): 4.980 (total time: 136.470) Refine new water occ: r_work=0.1254 r_free=0.1495 adp: r_work=0.1254 r_free=0.1495 occ: r_work=0.1249 r_free=0.1493 adp: r_work=0.1249 r_free=0.1494 occ: r_work=0.1246 r_free=0.1492 adp: r_work=0.1245 r_free=0.1493 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1493 r_work=0.1245 r_free=0.1493 | n_water=998 | time (s): 244.280 (total time: 380.750) Filter (q & B) r_work=0.1250 r_free=0.1506 | n_water=862 | time (s): 6.310 (total time: 387.060) Filter (dist only) r_work=0.1250 r_free=0.1506 | n_water=861 | time (s): 119.810 (total time: 506.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.717345 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.543077 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1240 0.1431 0.0191 0.035 1.1 8.5 0.0 0.0 0 0.859 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.31 1.91 1.929 14.578 15.543 3.940 12.33 13.90 1.57 2.181 14.492 15.543 3.898 Individual atomic B min max mean iso aniso Overall: 5.51 67.85 15.28 1.06 493 3272 Protein: 5.51 37.13 10.77 1.06 0 2902 Water: 6.65 67.85 30.45 N/A 493 368 Other: 14.21 27.98 21.10 N/A 0 2 Chain A: 5.53 56.08 12.81 N/A 0 1624 Chain B: 5.51 67.85 12.60 N/A 0 1648 Chain S: 14.15 59.94 32.37 N/A 493 0 Histogram: Values Number of atoms 5.51 - 11.74 2120 11.74 - 17.97 682 17.97 - 24.21 297 24.21 - 30.44 231 30.44 - 36.68 184 36.68 - 42.91 137 42.91 - 49.15 75 49.15 - 55.38 30 55.38 - 61.62 8 61.62 - 67.85 1 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1391 r_work=0.1234 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1391 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1385 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1385 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892795 | | target function (ml) not normalized (work): 729104.988346 | | target function (ml) not normalized (free): 15221.650452 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1385 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1443 0.1443 0.1492 n_refl.: 191137 remove outliers: r(all,work,free)=0.1443 0.1443 0.1492 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1437 0.1488 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1379 n_refl.: 191137 remove outliers: r(all,work,free)=0.1228 0.1225 0.1379 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3810 398.895 352.249 0.414 0.947 0.243 13.296-10.522 98.02 98 1 0.2347 528.900 502.670 0.705 0.948 0.208 10.503-8.327 98.35 176 3 0.2017 555.265 556.438 0.888 0.948 0.159 8.318-6.595 100.00 360 8 0.2104 414.736 409.005 0.896 0.947 0.120 6.588-5.215 100.00 711 7 0.1847 381.101 370.340 0.883 0.948 0.105 5.214-4.128 98.38 1367 28 0.1170 557.435 551.764 0.972 0.948 0.100 4.126-3.266 94.74 2603 46 0.1095 508.132 501.259 1.032 0.948 0.009 3.266-2.585 99.86 5447 97 0.1079 342.774 339.248 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0959 258.603 255.785 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0970 153.054 151.458 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1055 82.395 81.491 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1693 44.202 42.321 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0984 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1379 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1379 | n_water=861 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1226 r_free=0.1382 | n_water=860 | time (s): 104.420 (total time: 106.970) Filter (q & B) r_work=0.1226 r_free=0.1381 | n_water=850 | time (s): 4.500 (total time: 111.470) Compute maps r_work=0.1226 r_free=0.1381 | n_water=850 | time (s): 2.020 (total time: 113.490) Filter (map) r_work=0.1245 r_free=0.1381 | n_water=721 | time (s): 4.340 (total time: 117.830) Find peaks r_work=0.1245 r_free=0.1381 | n_water=721 | time (s): 0.750 (total time: 118.580) Add new water r_work=0.1259 r_free=0.1396 | n_water=948 | time (s): 5.330 (total time: 123.910) Refine new water occ: r_work=0.1225 r_free=0.1360 adp: r_work=0.1225 r_free=0.1359 occ: r_work=0.1223 r_free=0.1359 adp: r_work=0.1223 r_free=0.1359 occ: r_work=0.1221 r_free=0.1359 adp: r_work=0.1220 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1220 r_free=0.1359 r_work=0.1220 r_free=0.1359 | n_water=948 | time (s): 288.230 (total time: 412.140) Filter (q & B) r_work=0.1224 r_free=0.1366 | n_water=868 | time (s): 4.250 (total time: 416.390) Filter (dist only) r_work=0.1225 r_free=0.1365 | n_water=867 | time (s): 110.130 (total time: 526.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.607161 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.656059 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 0.1224 0.1367 0.0143 0.035 1.1 6.5 0.0 0.0 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.24 13.67 1.43 1.839 14.297 15.656 3.888 12.19 13.62 1.43 1.976 14.243 15.656 3.879 Individual atomic B min max mean iso aniso Overall: 5.47 67.45 15.08 1.00 500 3271 Protein: 5.47 33.76 10.67 1.00 0 2902 Water: 6.65 67.45 29.84 N/A 500 367 Other: 14.01 26.90 20.46 N/A 0 2 Chain A: 5.53 54.95 12.63 N/A 0 1623 Chain B: 5.47 67.45 12.48 N/A 0 1648 Chain S: 13.68 59.94 31.60 N/A 500 0 Histogram: Values Number of atoms 5.47 - 11.67 2108 11.67 - 17.87 725 17.87 - 24.07 296 24.07 - 30.26 226 30.26 - 36.46 180 36.46 - 42.66 125 42.66 - 48.85 78 48.85 - 55.05 25 55.05 - 61.25 7 61.25 - 67.45 1 =========================== Idealize ADP of riding H ========================== r_work=0.1219 r_free=0.1363 r_work=0.1219 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1219 r_free = 0.1363 target_work(ml) = 3.879 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1217 r_free = 0.1360 target_work(ml) = 3.877 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1217 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.876901 | | target function (ml) not normalized (work): 726112.471106 | | target function (ml) not normalized (free): 15163.174314 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1217 0.1360 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1423 0.1422 0.1481 n_refl.: 191133 remove outliers: r(all,work,free)=0.1423 0.1422 0.1481 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1416 0.1415 0.1476 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1218 0.1215 0.1357 n_refl.: 191133 remove outliers: r(all,work,free)=0.1218 0.1215 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3632 360.611 316.645 0.414 0.950 0.241 13.296-10.522 97.03 97 1 0.2407 477.763 451.810 0.703 0.951 0.201 10.503-8.327 98.35 176 3 0.2055 502.396 495.483 0.868 0.951 0.166 8.318-6.595 100.00 360 8 0.2173 375.247 369.655 0.894 0.951 0.135 6.588-5.215 100.00 711 7 0.1923 344.815 334.388 0.881 0.951 0.108 5.214-4.128 98.38 1367 28 0.1205 504.359 499.279 0.970 0.951 0.100 4.126-3.266 94.74 2603 46 0.1121 459.751 453.439 1.030 0.952 0.005 3.266-2.585 99.86 5447 97 0.1107 310.137 306.938 1.017 0.951 0.000 2.585-2.046 97.45 10613 204 0.0949 233.980 231.679 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0945 138.481 137.148 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.1017 74.550 73.834 1.050 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1675 39.993 38.333 1.036 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1220 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1215 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1215 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1215 r_free=0.1357 | n_water=867 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1215 r_free=0.1357 | n_water=866 | time (s): 106.490 (total time: 109.010) Filter (q & B) r_work=0.1215 r_free=0.1356 | n_water=858 | time (s): 4.830 (total time: 113.840) Compute maps r_work=0.1215 r_free=0.1356 | n_water=858 | time (s): 1.730 (total time: 115.570) Filter (map) r_work=0.1233 r_free=0.1352 | n_water=751 | time (s): 4.530 (total time: 120.100) Find peaks r_work=0.1233 r_free=0.1352 | n_water=751 | time (s): 0.850 (total time: 120.950) Add new water r_work=0.1246 r_free=0.1371 | n_water=971 | time (s): 4.920 (total time: 125.870) Refine new water occ: r_work=0.1213 r_free=0.1349 adp: r_work=0.1213 r_free=0.1349 occ: r_work=0.1211 r_free=0.1349 adp: r_work=0.1211 r_free=0.1349 occ: r_work=0.1209 r_free=0.1350 adp: r_work=0.1209 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1209 r_free=0.1350 r_work=0.1209 r_free=0.1350 | n_water=971 | time (s): 290.870 (total time: 416.740) Filter (q & B) r_work=0.1214 r_free=0.1356 | n_water=887 | time (s): 5.560 (total time: 422.300) Filter (dist only) r_work=0.1214 r_free=0.1355 | n_water=886 | time (s): 115.650 (total time: 537.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.594197 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.565757 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 0.1216 0.1359 0.0143 0.037 1.1 6.3 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.16 13.59 1.43 1.793 14.193 14.566 3.777 12.21 13.62 1.42 1.828 14.179 14.566 3.775 Individual atomic B min max mean iso aniso Overall: 5.56 67.26 15.08 0.96 519 3271 Protein: 5.56 32.88 10.62 0.96 0 2902 Water: 6.69 67.26 29.68 N/A 519 367 Other: 13.81 26.31 20.06 N/A 0 2 Chain A: 5.63 54.50 12.56 N/A 0 1623 Chain B: 5.56 67.26 12.42 N/A 0 1648 Chain S: 13.28 59.89 31.39 N/A 519 0 Histogram: Values Number of atoms 5.56 - 11.73 2145 11.73 - 17.90 702 17.90 - 24.07 300 24.07 - 30.24 222 30.24 - 36.41 186 36.41 - 42.58 123 42.58 - 48.75 79 48.75 - 54.92 25 54.92 - 61.09 7 61.09 - 67.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.1221 r_free=0.1362 r_work=0.1221 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1221 r_free = 0.1363 target_work(ml) = 3.775 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1219 r_free = 0.1366 target_work(ml) = 3.775 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1219 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.774616 | | target function (ml) not normalized (work): 706947.748022 | | target function (ml) not normalized (free): 14782.011316 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1219 0.1366 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1416 0.1415 0.1498 n_refl.: 191131 remove outliers: r(all,work,free)=0.1416 0.1415 0.1498 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1408 0.1407 0.1492 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1221 0.1218 0.1365 n_refl.: 191131 remove outliers: r(all,work,free)=0.1221 0.1218 0.1365 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3640 360.611 333.754 0.430 0.950 0.235 13.296-10.522 96.04 96 1 0.2320 480.051 457.225 0.706 0.952 0.194 10.503-8.327 98.35 176 3 0.2106 502.396 495.168 0.867 0.952 0.149 8.318-6.595 100.00 360 8 0.2175 375.247 369.475 0.890 0.952 0.120 6.588-5.215 100.00 711 7 0.1946 344.815 333.987 0.881 0.952 0.110 5.214-4.128 98.38 1367 28 0.1219 504.359 499.018 0.970 0.952 0.100 4.126-3.266 94.74 2603 46 0.1142 459.751 453.164 1.032 0.953 0.009 3.266-2.585 99.86 5447 97 0.1121 310.137 306.829 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0958 233.980 231.565 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0950 138.481 137.123 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.1011 74.550 73.817 1.047 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1667 39.993 38.330 1.033 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1400 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1218 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1218 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1218 r_free=0.1365 | n_water=886 | time (s): 3.280 (total time: 3.280) Filter (dist) r_work=0.1218 r_free=0.1367 | n_water=885 | time (s): 109.120 (total time: 112.400) Filter (q & B) r_work=0.1218 r_free=0.1366 | n_water=876 | time (s): 4.200 (total time: 116.600) Compute maps r_work=0.1218 r_free=0.1366 | n_water=876 | time (s): 1.660 (total time: 118.260) Filter (map) r_work=0.1234 r_free=0.1362 | n_water=769 | time (s): 4.820 (total time: 123.080) Find peaks r_work=0.1234 r_free=0.1362 | n_water=769 | time (s): 0.680 (total time: 123.760) Add new water r_work=0.1247 r_free=0.1372 | n_water=966 | time (s): 4.910 (total time: 128.670) Refine new water occ: r_work=0.1206 r_free=0.1341 adp: r_work=0.1198 r_free=0.1336 occ: r_work=0.1196 r_free=0.1335 adp: r_work=0.1196 r_free=0.1335 occ: r_work=0.1194 r_free=0.1336 adp: r_work=0.1194 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1336 r_work=0.1194 r_free=0.1336 | n_water=966 | time (s): 329.620 (total time: 458.290) Filter (q & B) r_work=0.1199 r_free=0.1344 | n_water=885 | time (s): 5.620 (total time: 463.910) Filter (dist only) r_work=0.1199 r_free=0.1344 | n_water=884 | time (s): 112.820 (total time: 576.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.573706 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.738250 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1349 0.0149 0.036 1.1 7.2 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.49 1.49 1.770 14.104 15.738 3.763 11.98 13.50 1.52 1.851 14.082 15.738 3.757 Individual atomic B min max mean iso aniso Overall: 5.55 66.57 14.97 0.94 517 3271 Protein: 5.55 30.69 10.55 0.94 0 2902 Water: 6.01 66.57 29.46 N/A 517 367 Other: 13.85 24.69 19.27 N/A 0 2 Chain A: 5.62 52.70 12.46 N/A 0 1623 Chain B: 5.55 66.57 12.33 N/A 0 1648 Chain S: 6.01 59.84 31.28 N/A 517 0 Histogram: Values Number of atoms 5.55 - 11.66 2124 11.66 - 17.76 740 17.76 - 23.86 282 23.86 - 29.96 223 29.96 - 36.06 193 36.06 - 42.16 116 42.16 - 48.26 76 48.26 - 54.36 26 54.36 - 60.47 7 60.47 - 66.57 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1350 r_work=0.1198 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1350 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1349 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756059 | | target function (ml) not normalized (work): 703468.510206 | | target function (ml) not normalized (free): 14723.078627 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1350 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1498 n_refl.: 191130 remove outliers: r(all,work,free)=0.1395 0.1393 0.1498 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1359 0.1357 0.1471 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1348 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1348 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3593 360.611 334.673 0.447 0.952 0.242 13.296-10.522 96.04 96 1 0.2347 480.051 459.025 0.723 0.953 0.172 10.503-8.327 98.35 176 3 0.2159 502.396 494.681 0.885 0.954 0.143 8.318-6.595 100.00 360 8 0.2166 375.247 369.398 0.911 0.953 0.111 6.588-5.215 100.00 711 7 0.1928 344.815 334.042 0.901 0.953 0.097 5.214-4.128 98.38 1367 28 0.1206 504.359 499.083 0.994 0.954 0.080 4.126-3.266 94.74 2603 46 0.1141 459.751 452.799 1.054 0.954 0.000 3.266-2.585 99.86 5447 97 0.1105 310.137 306.842 1.038 0.953 0.000 2.585-2.046 97.45 10613 204 0.0941 233.980 231.548 1.046 0.953 0.000 2.046-1.619 99.39 21536 464 0.0915 138.481 137.171 1.064 0.953 0.000 1.619-1.281 98.00 42464 925 0.0971 74.550 73.848 1.052 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1648 39.993 38.340 1.023 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0510 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1348 | n_water=884 | time (s): 3.070 (total time: 3.070) Filter (dist) r_work=0.1195 r_free=0.1348 | n_water=884 | time (s): 102.140 (total time: 105.210) Filter (q & B) r_work=0.1195 r_free=0.1348 | n_water=879 | time (s): 5.220 (total time: 110.430) Compute maps r_work=0.1195 r_free=0.1348 | n_water=879 | time (s): 1.610 (total time: 112.040) Filter (map) r_work=0.1214 r_free=0.1350 | n_water=772 | time (s): 4.170 (total time: 116.210) Find peaks r_work=0.1214 r_free=0.1350 | n_water=772 | time (s): 0.620 (total time: 116.830) Add new water r_work=0.1224 r_free=0.1361 | n_water=977 | time (s): 4.690 (total time: 121.520) Refine new water occ: r_work=0.1193 r_free=0.1337 adp: r_work=0.1193 r_free=0.1338 occ: r_work=0.1191 r_free=0.1337 adp: r_work=0.1191 r_free=0.1338 occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1189 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1338 r_work=0.1189 r_free=0.1338 | n_water=977 | time (s): 219.320 (total time: 340.840) Filter (q & B) r_work=0.1193 r_free=0.1344 | n_water=908 | time (s): 5.250 (total time: 346.090) Filter (dist only) r_work=0.1193 r_free=0.1343 | n_water=907 | time (s): 114.150 (total time: 460.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.481451 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.804602 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1351 0.0154 0.037 1.1 7.3 0.0 0.3 0 0.741 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.51 1.54 1.745 13.893 14.805 3.758 12.00 13.57 1.56 1.823 13.863 14.805 3.757 Individual atomic B min max mean iso aniso Overall: 5.40 65.43 14.80 0.90 540 3271 Protein: 5.40 29.06 10.28 0.90 0 2902 Water: 5.84 65.43 29.22 N/A 540 367 Other: 13.68 22.83 18.25 N/A 0 2 Chain A: 5.44 51.37 12.16 N/A 0 1623 Chain B: 5.40 65.43 12.03 N/A 0 1648 Chain S: 5.84 59.58 31.16 N/A 540 0 Histogram: Values Number of atoms 5.40 - 11.40 2114 11.40 - 17.41 768 17.41 - 23.41 274 23.41 - 29.41 209 29.41 - 35.41 192 35.41 - 41.42 130 41.42 - 47.42 85 47.42 - 53.42 29 53.42 - 59.42 8 59.42 - 65.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1357 r_work=0.1201 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1357 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756609 | | target function (ml) not normalized (work): 703571.538531 | | target function (ml) not normalized (free): 14731.639848 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1368 0.1366 0.1483 n_refl.: 191130 remove outliers: r(all,work,free)=0.1368 0.1366 0.1483 n_refl.: 191130 overall B=0.06 to atoms: r(all,work,free)=0.1375 0.1373 0.1489 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191130 remove outliers: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3512 360.611 334.878 0.468 0.909 0.238 13.296-10.522 96.04 96 1 0.2381 480.051 458.440 0.758 0.910 0.162 10.503-8.327 98.35 176 3 0.2183 502.396 493.474 0.936 0.911 0.130 8.318-6.595 100.00 360 8 0.2175 375.247 368.944 0.959 0.911 0.104 6.588-5.215 100.00 711 7 0.1938 344.815 334.209 0.952 0.911 0.087 5.214-4.128 98.38 1367 28 0.1231 504.359 498.271 1.051 0.912 0.080 4.126-3.266 94.74 2603 46 0.1150 459.751 452.165 1.115 0.913 0.000 3.266-2.585 99.86 5447 97 0.1117 310.137 306.576 1.097 0.913 0.000 2.585-2.046 97.45 10613 204 0.0950 233.980 231.422 1.106 0.915 0.000 2.046-1.619 99.39 21536 464 0.0911 138.481 137.100 1.123 0.917 0.000 1.619-1.281 98.00 42464 925 0.0953 74.550 73.885 1.111 0.921 0.000 1.281-0.980 96.53 101826 2055 0.1630 39.993 38.309 1.075 0.928 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0609 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1348 | n_water=907 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1190 r_free=0.1348 | n_water=907 | time (s): 115.710 (total time: 118.100) Filter (q & B) r_work=0.1191 r_free=0.1348 | n_water=897 | time (s): 4.240 (total time: 122.340) Compute maps r_work=0.1191 r_free=0.1348 | n_water=897 | time (s): 2.520 (total time: 124.860) Filter (map) r_work=0.1210 r_free=0.1347 | n_water=780 | time (s): 4.750 (total time: 129.610) Find peaks r_work=0.1210 r_free=0.1347 | n_water=780 | time (s): 0.800 (total time: 130.410) Add new water r_work=0.1219 r_free=0.1359 | n_water=989 | time (s): 5.140 (total time: 135.550) Refine new water occ: r_work=0.1187 r_free=0.1336 adp: r_work=0.1187 r_free=0.1337 occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1185 r_free=0.1336 occ: r_work=0.1184 r_free=0.1334 adp: r_work=0.1184 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1334 r_work=0.1184 r_free=0.1334 | n_water=989 | time (s): 226.530 (total time: 362.080) Filter (q & B) r_work=0.1189 r_free=0.1341 | n_water=916 | time (s): 4.190 (total time: 366.270) Filter (dist only) r_work=0.1189 r_free=0.1339 | n_water=913 | time (s): 117.470 (total time: 483.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567182 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.243680 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1348 0.0157 0.038 1.1 6.3 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.48 1.57 1.691 13.812 14.244 3.755 11.94 13.52 1.58 1.735 13.796 14.244 3.754 Individual atomic B min max mean iso aniso Overall: 5.50 64.46 14.72 0.88 546 3271 Protein: 5.50 28.28 10.33 0.88 0 2902 Water: 5.90 64.46 28.68 N/A 546 367 Other: 13.78 22.07 17.92 N/A 0 2 Chain A: 5.54 51.09 12.16 N/A 0 1623 Chain B: 5.50 64.46 12.05 N/A 0 1648 Chain S: 5.90 59.56 30.40 N/A 546 0 Histogram: Values Number of atoms 5.50 - 11.39 2084 11.39 - 17.29 799 17.29 - 23.19 272 23.19 - 29.08 231 29.08 - 34.98 194 34.98 - 40.87 105 40.87 - 46.77 89 46.77 - 52.66 30 52.66 - 58.56 10 58.56 - 64.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1353 r_work=0.1194 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753501 | | target function (ml) not normalized (work): 702989.431515 | | target function (ml) not normalized (free): 14727.438047 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1353 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1386 0.1384 0.1501 n_refl.: 191130 remove outliers: r(all,work,free)=0.1386 0.1384 0.1501 n_refl.: 191130 overall B=0.01 to atoms: r(all,work,free)=0.1388 0.1385 0.1503 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1351 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1192 0.1351 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3645 360.611 331.930 0.418 0.973 0.219 13.296-10.522 96.04 96 1 0.2416 480.051 457.694 0.704 0.975 0.155 10.503-8.327 98.35 176 3 0.2236 502.396 493.242 0.868 0.975 0.127 8.318-6.595 100.00 360 8 0.2202 375.247 369.026 0.892 0.975 0.096 6.588-5.215 100.00 711 7 0.1979 344.815 333.923 0.887 0.975 0.080 5.214-4.128 98.38 1367 28 0.1238 504.359 498.111 0.981 0.976 0.080 4.126-3.266 94.74 2603 46 0.1171 459.751 451.922 1.041 0.977 0.000 3.266-2.585 99.86 5447 97 0.1127 310.137 306.534 1.025 0.978 0.000 2.585-2.046 97.45 10613 204 0.0951 233.980 231.370 1.033 0.980 0.000 2.046-1.619 99.39 21536 464 0.0908 138.481 137.122 1.050 0.984 0.000 1.619-1.281 98.00 42464 925 0.0947 74.550 73.895 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1625 39.993 38.297 1.009 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0164 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1351 | n_water=913 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1192 r_free=0.1351 | n_water=913 | time (s): 109.450 (total time: 112.510) Filter (q & B) r_work=0.1193 r_free=0.1351 | n_water=903 | time (s): 5.190 (total time: 117.700) Compute maps r_work=0.1193 r_free=0.1351 | n_water=903 | time (s): 2.000 (total time: 119.700) Filter (map) r_work=0.1210 r_free=0.1352 | n_water=793 | time (s): 5.370 (total time: 125.070) Find peaks r_work=0.1210 r_free=0.1352 | n_water=793 | time (s): 0.530 (total time: 125.600) Add new water r_work=0.1218 r_free=0.1366 | n_water=980 | time (s): 4.090 (total time: 129.690) Refine new water occ: r_work=0.1190 r_free=0.1340 adp: r_work=0.1190 r_free=0.1341 occ: r_work=0.1188 r_free=0.1340 adp: r_work=0.1188 r_free=0.1341 occ: r_work=0.1187 r_free=0.1340 adp: r_work=0.1187 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1341 r_work=0.1187 r_free=0.1341 | n_water=980 | time (s): 181.190 (total time: 310.880) Filter (q & B) r_work=0.1190 r_free=0.1348 | n_water=907 | time (s): 4.420 (total time: 315.300) Filter (dist only) r_work=0.1191 r_free=0.1346 | n_water=904 | time (s): 115.250 (total time: 430.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.577648 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.469621 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 0.1193 0.1349 0.0156 0.038 1.1 4.9 0.0 0.3 0 0.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.49 1.56 1.683 13.789 14.470 3.754 11.94 13.54 1.60 1.699 13.781 14.470 3.753 Individual atomic B min max mean iso aniso Overall: 5.56 63.40 14.70 0.87 537 3271 Protein: 5.56 28.22 10.35 0.87 0 2902 Water: 6.00 63.40 28.68 N/A 537 367 Other: 13.80 22.14 17.97 N/A 0 2 Chain A: 5.61 50.74 12.15 N/A 0 1623 Chain B: 5.56 63.40 12.04 N/A 0 1648 Chain S: 6.00 59.47 30.59 N/A 537 0 Histogram: Values Number of atoms 5.56 - 11.35 2065 11.35 - 17.13 816 17.13 - 22.91 265 22.91 - 28.70 224 28.70 - 34.48 186 34.48 - 40.27 119 40.27 - 46.05 81 46.05 - 51.84 35 51.84 - 57.62 14 57.62 - 63.40 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1354 r_work=0.1194 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1354 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1352 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752382 | | target function (ml) not normalized (work): 702779.889005 | | target function (ml) not normalized (free): 14726.116839 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1352 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1396 0.1394 0.1502 n_refl.: 191130 remove outliers: r(all,work,free)=0.1396 0.1394 0.1502 n_refl.: 191130 overall B=-0.00 to atoms: r(all,work,free)=0.1395 0.1393 0.1502 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1348 n_refl.: 191130 remove outliers: r(all,work,free)=0.1194 0.1191 0.1348 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3601 360.611 331.816 0.412 0.994 0.223 13.296-10.522 96.04 96 1 0.2413 480.051 457.682 0.687 0.996 0.155 10.503-8.327 98.35 176 3 0.2232 502.396 493.533 0.848 0.996 0.127 8.318-6.595 100.00 360 8 0.2199 375.247 368.915 0.872 0.996 0.100 6.588-5.215 100.00 711 7 0.1968 344.815 333.947 0.867 0.997 0.083 5.214-4.128 98.38 1367 28 0.1245 504.359 498.000 0.957 0.998 0.034 4.126-3.266 94.74 2603 46 0.1180 459.751 451.860 1.020 0.999 0.000 3.266-2.585 99.86 5447 97 0.1128 310.137 306.540 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0952 233.980 231.351 1.012 1.002 0.000 2.046-1.619 99.39 21536 464 0.0906 138.481 137.123 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0942 74.550 73.898 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1624 39.993 38.288 0.989 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0125 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1348 After: r_work=0.1192 r_free=0.1348 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1348 | n_water=904 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1192 r_free=0.1348 | n_water=904 | time (s): 112.570 (total time: 115.300) Filter (q & B) r_work=0.1193 r_free=0.1348 | n_water=897 | time (s): 4.230 (total time: 119.530) Compute maps r_work=0.1193 r_free=0.1348 | n_water=897 | time (s): 2.100 (total time: 121.630) Filter (map) r_work=0.1211 r_free=0.1353 | n_water=795 | time (s): 4.280 (total time: 125.910) Find peaks r_work=0.1211 r_free=0.1353 | n_water=795 | time (s): 0.540 (total time: 126.450) Add new water r_work=0.1218 r_free=0.1366 | n_water=990 | time (s): 4.440 (total time: 130.890) Refine new water occ: r_work=0.1189 r_free=0.1341 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1187 r_free=0.1340 occ: r_work=0.1186 r_free=0.1339 adp: r_work=0.1186 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1340 r_work=0.1186 r_free=0.1340 | n_water=990 | time (s): 223.690 (total time: 354.580) Filter (q & B) r_work=0.1190 r_free=0.1347 | n_water=917 | time (s): 5.520 (total time: 360.100) Filter (dist only) r_work=0.1191 r_free=0.1345 | n_water=914 | time (s): 121.170 (total time: 481.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.560115 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.868546 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1346 0.0154 0.038 1.1 7.0 0.0 0.3 0 0.780 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.46 1.54 1.681 13.795 13.869 3.754 11.94 13.49 1.55 1.675 13.796 13.869 3.753 Individual atomic B min max mean iso aniso Overall: 5.57 63.18 14.73 0.86 548 3270 Protein: 5.57 28.09 10.36 0.86 0 2902 Water: 6.03 63.18 28.58 N/A 548 366 Other: 13.85 22.14 17.99 N/A 0 2 Chain A: 5.63 50.67 12.14 N/A 0 1623 Chain B: 5.57 63.18 12.03 N/A 0 1647 Chain S: 6.03 59.45 30.51 N/A 548 0 Histogram: Values Number of atoms 5.57 - 11.33 2057 11.33 - 17.09 826 17.09 - 22.85 274 22.85 - 28.61 223 28.61 - 34.37 186 34.37 - 40.13 118 40.13 - 45.89 82 45.89 - 51.66 35 51.66 - 57.42 13 57.42 - 63.18 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1349 r_work=0.1194 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1349 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1349 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753035 | | target function (ml) not normalized (work): 702902.095219 | | target function (ml) not normalized (free): 14723.321710 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1368 0.1462 5.6928 5.7821| | 2: 2.94 - 2.33 1.00 7339 128 0.1072 0.1300 5.0802 5.168| | 3: 2.33 - 2.04 0.96 6939 150 0.0892 0.1170 4.6433 4.7266| | 4: 2.04 - 1.85 1.00 7170 155 0.0900 0.1051 4.3899 4.5743| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0986 4.1497 4.2392| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1108 3.9491 4.0937| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0965 3.798 3.9257| | 8: 1.54 - 1.47 0.96 6798 152 0.0891 0.1301 3.699 3.8939| | 9: 1.47 - 1.41 0.98 6938 155 0.0924 0.1133 3.6195 3.7594| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1201 3.5554 3.6737| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1137 3.4853 3.5845| | 12: 1.32 - 1.28 0.98 6975 149 0.1034 0.1125 3.4595 3.5852| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1240 3.4349 3.5553| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1577 3.4303 3.6692| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1261 3.4468 3.493| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1560 3.4635 3.6636| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1229 3.432 3.4406| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1697 3.4373 3.5294| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1743 3.4183 3.5917| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1571 3.4094 3.4354| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2135 3.4169 3.5027| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1929 3.4118 3.4097| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2023 3.4323 3.4856| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2257 3.4345 3.509| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2515 3.4481 3.5242| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2853 3.4149 3.4237| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2805 3.4674 3.3945| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 11.99 1.00 0.95 11523.30| | 2: 2.94 - 2.33 7339 128 0.92 12.92 0.99 0.95 5184.22| | 3: 2.33 - 2.04 6939 150 0.96 7.47 1.01 0.95 1642.07| | 4: 2.04 - 1.85 7170 155 0.96 7.58 1.00 0.95 995.36| | 5: 1.85 - 1.72 7113 159 0.96 8.08 1.00 0.96 633.51| | 6: 1.72 - 1.62 7102 142 0.96 8.10 1.00 0.96 448.85| | 7: 1.62 - 1.54 7104 148 0.96 8.18 1.01 0.97 337.90| | 8: 1.54 - 1.47 6798 152 0.96 8.33 1.01 0.97 279.76| | 9: 1.47 - 1.41 6938 155 0.96 8.47 1.00 0.98 230.70| | 10: 1.41 - 1.36 7022 150 0.96 8.92 1.00 0.97 202.44| | 11: 1.36 - 1.32 6997 151 0.96 8.93 0.99 0.96 174.97| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.98 0.95 160.32| | 13: 1.28 - 1.25 6907 166 0.96 9.49 1.01 0.96 157.21| | 14: 1.25 - 1.22 7015 112 0.95 10.63 1.01 0.97 161.48| | 15: 1.22 - 1.19 6956 137 0.95 11.19 1.01 0.98 165.50| | 16: 1.19 - 1.17 6604 132 0.95 11.41 1.01 0.96 159.79| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.96 153.65| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.95 147.00| | 19: 1.12 - 1.10 6948 106 0.93 14.11 1.00 0.95 150.50| | 20: 1.10 - 1.08 6884 147 0.92 15.20 1.00 0.94 149.74| | 21: 1.08 - 1.07 6852 152 0.91 16.63 1.00 0.93 152.87| | 22: 1.07 - 1.05 6836 135 0.89 18.25 0.99 0.93 154.12| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.92 164.16| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.93 178.63| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.98 0.90 181.93| | 26: 1.01 - 0.99 6767 158 0.81 26.63 0.98 0.88 176.44| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.99 0.87 160.95| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.00 max = 11523.30 mean = 937.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.29| |phase err.(test): min = 0.00 max = 89.48 mean = 13.43| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1349 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1510 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1401 0.1510 n_refl.: 191130 overall B=-0.06 to atoms: r(all,work,free)=0.1393 0.1391 0.1502 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3557 360.611 332.519 0.415 0.972 0.232 13.296-10.522 96.04 96 1 0.2425 480.051 458.564 0.681 0.974 0.153 10.503-8.327 98.35 176 3 0.2251 502.396 493.496 0.844 0.974 0.117 8.318-6.595 100.00 360 8 0.2193 375.247 369.240 0.869 0.974 0.093 6.588-5.215 100.00 711 7 0.1973 344.815 333.949 0.865 0.975 0.082 5.214-4.128 98.38 1367 28 0.1249 504.359 498.059 0.956 0.976 0.046 4.126-3.266 94.74 2603 46 0.1176 459.751 451.754 1.018 0.977 0.000 3.266-2.585 99.86 5447 97 0.1122 310.137 306.585 1.001 0.979 0.000 2.585-2.046 97.45 10613 204 0.0956 233.980 231.351 1.008 0.981 0.000 2.046-1.619 99.39 21536 464 0.0910 138.481 137.130 1.023 0.986 0.000 1.619-1.281 98.00 42464 925 0.0945 74.550 73.895 1.012 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1624 39.993 38.279 0.979 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0141 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2036 0.1970 0.081 5.105 5.2 78.0 14.6 805 0.000 1_bss: 0.1804 0.1907 0.081 5.105 5.2 78.0 14.6 805 0.000 1_settarget: 0.1804 0.1907 0.081 5.105 5.2 78.0 14.6 805 0.000 1_nqh: 0.1804 0.1907 0.081 5.105 5.2 78.0 14.6 805 0.000 1_weight: 0.1804 0.1907 0.081 5.105 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1273 0.1482 0.035 1.169 5.2 78.0 14.6 805 0.143 1_adp: 0.1302 0.1552 0.035 1.169 5.2 73.0 15.0 805 0.143 1_regHadp: 0.1301 0.1548 0.035 1.169 5.2 73.0 15.0 805 0.143 1_occ: 0.1287 0.1535 0.035 1.169 5.2 73.0 15.0 805 0.143 2_bss: 0.1279 0.1529 0.035 1.169 5.4 73.2 15.2 805 0.143 2_settarget: 0.1279 0.1529 0.035 1.169 5.4 73.2 15.2 805 0.143 2_updatecdl: 0.1279 0.1529 0.035 1.181 5.4 73.2 15.2 805 0.143 2_nqh: 0.1279 0.1529 0.035 1.181 5.4 73.2 15.2 805 0.143 2_sol: 0.1272 0.1499 0.035 1.181 5.4 73.2 16.4 900 n/a 2_weight: 0.1272 0.1499 0.035 1.181 5.4 73.2 16.4 900 n/a 2_xyzrec: 0.1254 0.1515 0.039 1.148 5.4 73.2 16.4 900 n/a 2_adp: 0.1232 0.1503 0.039 1.148 5.4 68.2 16.5 900 n/a 2_regHadp: 0.1232 0.1504 0.039 1.148 5.4 68.2 16.5 900 n/a 2_occ: 0.1225 0.1500 0.039 1.148 5.4 68.2 16.5 900 n/a 3_bss: 0.1231 0.1507 0.039 1.148 5.3 68.2 16.5 900 n/a 3_settarget: 0.1231 0.1507 0.039 1.148 5.3 68.2 16.5 900 n/a 3_updatecdl: 0.1231 0.1507 0.039 1.157 5.3 68.2 16.5 900 n/a 3_nqh: 0.1231 0.1507 0.039 1.157 5.3 68.2 16.5 900 n/a 3_sol: 0.1250 0.1506 0.039 1.157 5.3 68.2 15.4 861 n/a 3_weight: 0.1250 0.1506 0.039 1.157 5.3 68.2 15.4 861 n/a 3_xyzrec: 0.1240 0.1431 0.035 1.096 5.3 68.2 15.4 861 n/a 3_adp: 0.1233 0.1391 0.035 1.096 5.5 67.9 15.3 861 n/a 3_regHadp: 0.1234 0.1391 0.035 1.096 5.5 67.9 15.3 861 n/a 3_occ: 0.1229 0.1385 0.035 1.096 5.5 67.9 15.3 861 n/a 4_bss: 0.1225 0.1379 0.035 1.096 5.5 67.8 15.2 861 n/a 4_settarget: 0.1225 0.1379 0.035 1.096 5.5 67.8 15.2 861 n/a 4_updatecdl: 0.1225 0.1379 0.035 1.096 5.5 67.8 15.2 861 n/a 4_nqh: 0.1225 0.1379 0.035 1.096 5.5 67.8 15.2 861 n/a 4_sol: 0.1225 0.1365 0.035 1.096 5.5 67.8 15.2 867 n/a 4_weight: 0.1225 0.1365 0.035 1.096 5.5 67.8 15.2 867 n/a 4_xyzrec: 0.1224 0.1367 0.035 1.120 5.5 67.8 15.2 867 n/a 4_adp: 0.1219 0.1363 0.035 1.120 5.5 67.4 15.1 867 n/a 4_regHadp: 0.1219 0.1363 0.035 1.120 5.5 67.4 15.1 867 n/a 4_occ: 0.1217 0.1360 0.035 1.120 5.5 67.4 15.1 867 n/a 5_bss: 0.1215 0.1357 0.035 1.120 5.4 67.4 15.0 867 n/a 5_settarget: 0.1215 0.1357 0.035 1.120 5.4 67.4 15.0 867 n/a 5_updatecdl: 0.1215 0.1357 0.035 1.120 5.4 67.4 15.0 867 n/a 5_nqh: 0.1215 0.1357 0.035 1.120 5.4 67.4 15.0 867 n/a 5_sol: 0.1214 0.1355 0.035 1.120 5.4 67.4 15.1 886 n/a 5_weight: 0.1214 0.1355 0.035 1.120 5.4 67.4 15.1 886 n/a 5_xyzrec: 0.1216 0.1359 0.037 1.114 5.4 67.4 15.1 886 n/a 5_adp: 0.1221 0.1362 0.037 1.114 5.6 67.3 15.1 886 n/a 5_regHadp: 0.1221 0.1363 0.037 1.114 5.6 67.3 15.1 886 n/a 5_occ: 0.1219 0.1366 0.037 1.114 5.6 67.3 15.1 886 n/a 6_bss: 0.1218 0.1365 0.037 1.114 5.5 67.2 15.0 886 n/a 6_settarget: 0.1218 0.1365 0.037 1.114 5.5 67.2 15.0 886 n/a 6_updatecdl: 0.1218 0.1365 0.037 1.114 5.5 67.2 15.0 886 n/a 6_nqh: 0.1218 0.1365 0.037 1.114 5.5 67.2 15.0 886 n/a 6_sol: 0.1199 0.1344 0.037 1.114 5.5 67.2 15.0 884 n/a 6_weight: 0.1199 0.1344 0.037 1.114 5.5 67.2 15.0 884 n/a 6_xyzrec: 0.1201 0.1349 0.036 1.126 5.5 67.2 15.0 884 n/a 6_adp: 0.1198 0.1350 0.036 1.126 5.6 66.6 15.0 884 n/a 6_regHadp: 0.1198 0.1350 0.036 1.126 5.6 66.6 15.0 884 n/a 6_occ: 0.1196 0.1349 0.036 1.126 5.6 66.6 15.0 884 n/a 7_bss: 0.1195 0.1348 0.036 1.126 5.3 66.3 14.7 884 n/a 7_settarget: 0.1195 0.1348 0.036 1.126 5.3 66.3 14.7 884 n/a 7_updatecdl: 0.1195 0.1348 0.036 1.127 5.3 66.3 14.7 884 n/a 7_nqh: 0.1195 0.1348 0.036 1.127 5.3 66.3 14.7 884 n/a 7_sol: 0.1193 0.1343 0.036 1.127 5.3 66.3 14.8 907 n/a 7_weight: 0.1193 0.1343 0.036 1.127 5.3 66.3 14.8 907 n/a 7_xyzrec: 0.1197 0.1351 0.037 1.118 5.3 66.3 14.8 907 n/a 7_adp: 0.1201 0.1357 0.037 1.118 5.4 65.4 14.8 907 n/a 7_regHadp: 0.1201 0.1357 0.037 1.118 5.4 65.4 14.8 907 n/a 7_occ: 0.1199 0.1358 0.037 1.118 5.4 65.4 14.8 907 n/a 8_bss: 0.1190 0.1348 0.037 1.118 5.5 65.5 14.9 907 n/a 8_settarget: 0.1190 0.1348 0.037 1.118 5.5 65.5 14.9 907 n/a 8_updatecdl: 0.1190 0.1348 0.037 1.118 5.5 65.5 14.9 907 n/a 8_nqh: 0.1190 0.1348 0.037 1.118 5.5 65.5 14.9 907 n/a 8_sol: 0.1189 0.1339 0.037 1.118 5.5 65.5 14.8 913 n/a 8_weight: 0.1189 0.1339 0.037 1.118 5.5 65.5 14.8 913 n/a 8_xyzrec: 0.1191 0.1348 0.038 1.119 5.5 65.5 14.8 913 n/a 8_adp: 0.1194 0.1353 0.038 1.119 5.5 64.5 14.7 913 n/a 8_regHadp: 0.1194 0.1353 0.038 1.119 5.5 64.5 14.7 913 n/a 8_occ: 0.1193 0.1353 0.038 1.119 5.5 64.5 14.7 913 n/a 9_bss: 0.1192 0.1351 0.038 1.119 5.5 64.5 14.7 913 n/a 9_settarget: 0.1192 0.1351 0.038 1.119 5.5 64.5 14.7 913 n/a 9_updatecdl: 0.1192 0.1351 0.038 1.119 5.5 64.5 14.7 913 n/a 9_nqh: 0.1192 0.1351 0.038 1.119 5.5 64.5 14.7 913 n/a 9_sol: 0.1191 0.1346 0.038 1.119 5.5 64.5 14.7 904 n/a 9_weight: 0.1191 0.1346 0.038 1.119 5.5 64.5 14.7 904 n/a 9_xyzrec: 0.1193 0.1349 0.038 1.120 5.5 64.5 14.7 904 n/a 9_adp: 0.1194 0.1354 0.038 1.120 5.6 63.4 14.7 904 n/a 9_regHadp: 0.1194 0.1354 0.038 1.120 5.6 63.4 14.7 904 n/a 9_occ: 0.1192 0.1352 0.038 1.120 5.6 63.4 14.7 904 n/a 10_bss: 0.1191 0.1348 0.038 1.120 5.6 63.4 14.7 904 n/a 10_settarget: 0.1191 0.1348 0.038 1.120 5.6 63.4 14.7 904 n/a 10_updatecdl: 0.1191 0.1348 0.038 1.120 5.6 63.4 14.7 904 n/a 10_setrh: 0.1192 0.1348 0.038 1.120 5.6 63.4 14.7 904 n/a 10_nqh: 0.1192 0.1348 0.038 1.120 5.6 63.4 14.7 904 n/a 10_sol: 0.1191 0.1345 0.038 1.120 5.6 63.4 14.7 914 n/a 10_weight: 0.1191 0.1345 0.038 1.120 5.6 63.4 14.7 914 n/a 10_xyzrec: 0.1192 0.1346 0.038 1.150 5.6 63.4 14.7 914 n/a 10_adp: 0.1194 0.1349 0.038 1.150 5.6 63.2 14.7 914 n/a 10_regHadp: 0.1194 0.1349 0.038 1.150 5.6 63.2 14.7 914 n/a 10_occ: 0.1193 0.1349 0.038 1.150 5.6 63.2 14.7 914 n/a end: 0.1192 0.1348 0.038 1.150 5.5 63.1 14.7 914 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6121353_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6121353_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1200 Refinement macro-cycles (run) : 12111.7500 Write final files (write_after_run_outputs) : 155.9800 Total : 12274.8500 Total CPU time: 3.42 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:53 PST -0800 (1736736113.28 s) Start R-work = 0.1804, R-free = 0.1907 Final R-work = 0.1192, R-free = 0.1348 =============================================================================== Job complete usr+sys time: 12545.38 seconds wall clock time: 210 minutes 8.45 seconds (12608.45 seconds total)