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_6209618.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_6209618.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_6209618.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 2 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.00, per 1000 atoms: 0.30 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: 2.749 distance_ideal: 2.720 ideal - model: -0.029 slack: 0.000 delta_slack: -0.029 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: 2.632 distance_ideal: 2.710 ideal - model: 0.078 slack: 0.000 delta_slack: 0.078 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: 1.15 Conformation dependent library (CDL) restraints added in 199.6 milliseconds Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.01: 648 1.01 - 1.24: 2509 1.24 - 1.46: 1459 1.46 - 1.69: 1267 1.69 - 1.91: 51 Bond restraints: 5934 Sorted by residual: bond pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta sigma weight residual 1.463 1.694 -0.231 1.11e-02 8.12e+03 4.35e+02 bond pdb=" C VAL B 144 " pdb=" O VAL B 144 " ideal model delta sigma weight residual 1.236 1.040 0.196 1.00e-02 1.00e+04 3.84e+02 bond pdb=" NZ LYS B 52 " pdb=" HZ1 LYS B 52 " ideal model delta sigma weight residual 0.890 1.265 -0.375 2.00e-02 2.50e+03 3.51e+02 bond pdb=" C ASP A 117 " pdb=" N ILE A 118 " ideal model delta sigma weight residual 1.335 1.549 -0.215 1.15e-02 7.56e+03 3.49e+02 bond pdb=" CD1 LEU A 6 " pdb="HD11 LEU A 6 " ideal model delta sigma weight residual 0.970 1.338 -0.368 2.00e-02 2.50e+03 3.38e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.03: 5473 4.03 - 8.05: 3542 8.05 - 12.08: 1468 12.08 - 16.10: 295 16.10 - 20.13: 32 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA LEU A 153 " pdb=" C LEU A 153 " pdb=" O LEU A 153 " ideal model delta sigma weight residual 120.32 137.56 -17.24 1.10e+00 8.26e-01 2.46e+02 angle pdb=" O ILE A 76 " pdb=" C ILE A 76 " pdb=" N LYS A 77 " ideal model delta sigma weight residual 121.87 137.03 -15.16 9.70e-01 1.06e+00 2.44e+02 angle pdb=" CG HIS A 116 " pdb=" CD2 HIS A 116 " pdb=" NE2 HIS A 116 " ideal model delta sigma weight residual 107.20 120.81 -13.61 1.00e+00 1.00e+00 1.85e+02 angle pdb=" CA HIS A 96 " pdb=" CB HIS A 96 " pdb=" CG HIS A 96 " ideal model delta sigma weight residual 113.80 100.50 13.30 1.00e+00 1.00e+00 1.77e+02 angle pdb=" O ARG B 149 " pdb=" C ARG B 149 " pdb=" N VAL B 150 " ideal model delta sigma weight residual 122.27 106.13 16.14 1.23e+00 6.61e-01 1.72e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 1852 17.36 - 34.72: 134 34.72 - 52.07: 44 52.07 - 69.43: 15 69.43 - 86.79: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CG TRP A 146 " pdb=" CD2 TRP A 146 " pdb=" CE3 TRP A 146 " pdb=" HE3 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 -26.94 26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA ILE A 101 " pdb=" C ILE A 101 " pdb=" N VAL A 102 " pdb=" CA VAL A 102 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.219: 209 0.219 - 0.437: 149 0.437 - 0.655: 87 0.655 - 0.873: 34 0.873 - 1.090: 13 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB VAL B 69 " pdb=" CA VAL B 69 " pdb=" CG1 VAL B 69 " pdb=" CG2 VAL B 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.54 -1.09 2.00e-01 2.50e+01 2.97e+01 chirality pdb=" CA GLU B 15 " pdb=" N GLU B 15 " pdb=" C GLU B 15 " pdb=" CB GLU B 15 " both_signs ideal model delta sigma weight residual False 2.51 3.52 -1.01 2.00e-01 2.50e+01 2.53e+01 chirality pdb=" CA ALA B 108 " pdb=" N ALA B 108 " pdb=" C ALA B 108 " pdb=" CB ALA B 108 " both_signs ideal model delta sigma weight residual False 2.48 1.48 1.00 2.00e-01 2.50e+01 2.51e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.020 2.00e-02 2.50e+03 6.80e-02 1.85e+02 pdb=" CG TRP A 146 " 0.092 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.023 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.115 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.050 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.050 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.076 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.074 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.057 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.037 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.051 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.165 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.012 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.022 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 192 " 0.118 2.00e-02 2.50e+03 7.00e-02 1.47e+02 pdb=" CG TYR B 192 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TYR B 192 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 192 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 192 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR B 192 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR B 192 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR B 192 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 TYR B 192 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR B 192 " -0.130 2.00e-02 2.50e+03 pdb=" HE1 TYR B 192 " -0.097 2.00e-02 2.50e+03 pdb=" HE2 TYR B 192 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.078 2.00e-02 2.50e+03 6.74e-02 1.36e+02 pdb=" CG TYR A 194 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.102 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " -0.067 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.063 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " -0.062 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " 0.129 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " -0.011 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.61: 26 1.61 - 2.36: 2402 2.36 - 3.11: 22244 3.11 - 3.85: 33009 3.85 - 4.60: 52588 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110269 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.866 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.935 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 0.984 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.031 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.082 2.620 ... (remaining 110264 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_6209618_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= 0.2031 r_free= 0.2015 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302064 | | target function (ml) not normalized (work): 805832.445341 | | target function (ml) not normalized (free): 16595.488909 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2143 0.1959 6.6872 6.3226| | 2: 2.94 - 2.33 1.00 7339 128 0.1599 0.1621 5.5454 5.5985| | 3: 2.33 - 2.04 0.96 6939 150 0.1637 0.1624 5.1542 5.1851| | 4: 2.04 - 1.85 1.00 7170 155 0.1745 0.1614 4.9681 5.0523| | 5: 1.85 - 1.72 0.99 7113 159 0.1916 0.1795 4.7986 4.8494| | 6: 1.72 - 1.62 0.99 7102 142 0.1980 0.1862 4.6688 4.6631| | 7: 1.62 - 1.54 0.99 7104 148 0.1995 0.1784 4.5546 4.5513| | 8: 1.54 - 1.47 0.96 6798 152 0.2035 0.2296 4.4775 4.5939| | 9: 1.47 - 1.41 0.98 6938 155 0.2120 0.2221 4.4131 4.4652| | 10: 1.41 - 1.36 0.99 7022 150 0.2102 0.2338 4.3123 4.4403| | 11: 1.36 - 1.32 0.99 6997 151 0.2082 0.1980 4.2327 4.2088| | 12: 1.32 - 1.28 0.98 6976 149 0.2098 0.2217 4.1776 4.2633| | 13: 1.28 - 1.25 0.98 6907 166 0.2046 0.2235 4.1382 4.1944| | 14: 1.25 - 1.22 0.98 7015 113 0.2066 0.2581 4.08 4.343| | 15: 1.22 - 1.19 0.98 6957 137 0.2135 0.2255 4.0711 4.1371| | 16: 1.19 - 1.17 0.93 6604 132 0.2087 0.2368 4.0097 4.1304| | 17: 1.17 - 1.14 0.98 6941 135 0.2160 0.1833 3.9579 3.9539| | 18: 1.14 - 1.12 0.98 6875 142 0.2222 0.2426 3.9211 3.9663| | 19: 1.12 - 1.10 0.97 6949 106 0.2249 0.2602 3.86 4.0004| | 20: 1.10 - 1.08 0.97 6884 147 0.2343 0.2133 3.8307 3.8186| | 21: 1.08 - 1.07 0.97 6852 152 0.2425 0.2604 3.7836 3.7865| | 22: 1.07 - 1.05 0.97 6838 135 0.2507 0.2725 3.733 3.7945| | 23: 1.05 - 1.03 0.97 6829 159 0.2710 0.2414 3.7187 3.7291| | 24: 1.03 - 1.02 0.96 6785 133 0.2891 0.2548 3.7065 3.6677| | 25: 1.02 - 1.01 0.93 6552 130 0.3032 0.3066 3.6651 3.7296| | 26: 1.01 - 0.99 0.96 6767 158 0.3249 0.3449 3.6334 3.6219| | 27: 0.99 - 0.98 0.94 6648 131 0.3419 0.3349 3.6421 3.6187| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.61 0.91 0.98 36135.52| | 2: 2.94 - 2.33 7339 128 0.85 21.32 1.08 1.02 15466.22| | 3: 2.33 - 2.04 6939 150 0.93 12.88 1.11 1.05 4376.41| | 4: 2.04 - 1.85 7170 155 0.92 13.91 1.11 1.05 2873.90| | 5: 1.85 - 1.72 7113 159 0.90 16.07 1.12 1.06 2129.63| | 6: 1.72 - 1.62 7102 142 0.90 16.77 1.11 1.06 1632.19| | 7: 1.62 - 1.54 7104 148 0.89 17.95 1.11 1.06 1373.49| | 8: 1.54 - 1.47 6798 152 0.88 19.22 1.10 1.06 1234.07| | 9: 1.47 - 1.41 6938 155 0.87 19.86 1.10 1.07 1073.85| | 10: 1.41 - 1.36 7022 150 0.87 20.64 1.09 1.06 908.37| | 11: 1.36 - 1.32 6997 151 0.87 20.18 1.08 1.06 759.78| | 12: 1.32 - 1.28 6976 149 0.87 20.60 1.08 1.03 684.87| | 13: 1.28 - 1.25 6907 166 0.86 21.15 1.07 1.03 674.10| | 14: 1.25 - 1.22 7015 113 0.84 22.86 1.07 1.02 670.93| | 15: 1.22 - 1.19 6957 137 0.85 22.78 1.07 1.03 629.27| | 16: 1.19 - 1.17 6604 132 0.86 21.76 1.07 1.03 551.59| | 17: 1.17 - 1.14 6941 135 0.86 21.60 1.08 1.03 467.62| | 18: 1.14 - 1.12 6875 142 0.86 21.47 1.08 1.01 409.38| | 19: 1.12 - 1.10 6949 106 0.86 21.75 1.07 1.00 375.76| | 20: 1.10 - 1.08 6884 147 0.85 22.27 1.06 0.99 339.15| | 21: 1.08 - 1.07 6852 152 0.85 23.21 1.06 0.98 319.31| | 22: 1.07 - 1.05 6838 135 0.83 24.53 1.06 0.98 305.15| | 23: 1.05 - 1.03 6829 159 0.82 25.97 1.06 0.98 295.75| | 24: 1.03 - 1.02 6785 133 0.80 27.44 1.05 1.00 296.97| | 25: 1.02 - 1.01 6552 130 0.78 29.42 1.03 0.95 290.74| | 26: 1.01 - 0.99 6767 158 0.74 32.74 1.03 0.91 296.49| | 27: 0.99 - 0.98 6648 131 0.72 34.61 1.04 0.85 293.10| |alpha: min = 0.85 max = 1.07 mean = 1.01| |beta: min = 290.74 max = 36135.52 mean = 2902.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.90| |phase err.(test): min = 0.00 max = 89.84 mean = 22.23| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.235 2950 Z= 5.464 Angle : 5.212 17.235 4018 Z= 3.717 Chirality : 0.388 1.090 492 Planarity : 0.035 0.148 512 Dihedral : 13.011 86.789 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.63 % Favored : 95.85 % Rotamer: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Cbeta Deviations : 32.87 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.38), residues: 386 helix: -1.82 (0.34), residues: 144 sheet: -0.96 (0.50), residues: 86 loop : -0.49 (0.49), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.079 0.019 ARG A 100 TYR 0.097 0.040 TYR A 67 PHE 0.118 0.030 PHE B 82 TRP 0.108 0.034 TRP B 146 HIS 0.079 0.026 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= 0.2031 r_free= 0.2015 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302064 | | target function (ml) not normalized (work): 805832.445341 | | target function (ml) not normalized (free): 16595.488909 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2029 0.2031 0.2015 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2029 0.2031 0.2015 n_refl.: 191155 remove outliers: r(all,work,free)=0.2029 0.2031 0.2015 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2029 0.2031 0.2015 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1803 0.1799 0.1965 n_refl.: 191145 remove outliers: r(all,work,free)=0.1801 0.1797 0.1964 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4218 400.535 296.475 0.436 0.913 0.299 13.296-10.522 100.00 100 1 0.2553 534.497 522.615 0.790 0.914 0.253 10.503-8.327 98.90 177 3 0.2472 564.205 559.234 0.974 0.914 0.233 8.318-6.595 100.00 360 8 0.2495 414.736 403.926 0.971 0.914 0.174 6.588-5.215 100.00 711 7 0.2254 381.101 365.781 0.956 0.914 0.150 5.214-4.128 98.38 1367 28 0.1487 557.435 549.206 1.074 0.914 0.090 4.126-3.266 94.74 2603 46 0.1355 508.132 499.153 1.145 0.914 0.035 3.266-2.585 99.86 5447 97 0.1445 342.774 338.088 1.119 0.913 0.030 2.585-2.046 97.45 10613 204 0.1394 258.603 254.348 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1618 153.054 149.805 1.142 0.912 0.000 1.619-1.281 98.00 42464 925 0.1912 82.395 80.181 1.128 0.910 0.000 1.281-0.980 96.53 101826 2055 0.2316 44.202 41.678 1.110 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0019 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1964 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1797 r_free=0.1964 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.816435 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 569.447789 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 0.1506 0.0233 0.039 1.1 10.5 0.0 0.3 0 10.908 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.06 2.33 1.118 13.112 569.448 0.018 12.99 15.71 2.72 1.237 13.332 569.448 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.04 15.00 1.40 435 3274 Protein: 5.16 40.32 10.99 1.40 0 2902 Water: 6.31 73.04 29.43 N/A 435 370 Other: 16.10 30.25 23.17 N/A 0 2 Chain A: 5.33 59.88 13.04 N/A 0 1626 Chain B: 5.16 73.04 12.75 N/A 0 1648 Chain S: 11.57 64.06 30.86 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2164 11.95 - 18.74 637 18.74 - 25.53 316 25.53 - 32.31 263 32.31 - 39.10 162 39.10 - 45.89 101 45.89 - 52.68 43 52.68 - 59.47 18 59.47 - 66.26 4 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1572 r_work=0.1299 r_free=0.1567 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1567 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1284 r_free = 0.1555 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1284 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015587 | | target function (ls_wunit_k1) not normalized (work): 2919.325404 | | target function (ls_wunit_k1) not normalized (free): 116.129265 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1284 0.1555 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1473 0.1470 0.1633 n_refl.: 191139 remove outliers: r(all,work,free)=0.1473 0.1470 0.1633 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1496 0.1494 0.1642 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1546 n_refl.: 191139 remove outliers: r(all,work,free)=0.1281 0.1276 0.1546 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 0.3587 402.814 374.451 0.481 0.962 0.275 13.296-10.522 100.00 100 1 0.2102 534.497 531.017 0.748 0.964 0.234 10.503-8.327 98.90 177 3 0.1724 564.205 564.597 0.892 0.964 0.220 8.318-6.595 100.00 360 8 0.1699 414.736 412.753 0.910 0.963 0.155 6.588-5.215 100.00 711 7 0.1528 381.101 373.621 0.888 0.964 0.150 5.214-4.128 98.38 1367 28 0.0900 557.435 555.066 0.978 0.964 0.059 4.126-3.266 94.74 2603 46 0.0827 508.132 504.166 1.045 0.965 0.018 3.266-2.585 99.86 5447 97 0.0922 342.774 340.237 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0954 258.603 256.370 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1093 153.054 151.379 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.418 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.179 1.023 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0377 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1546 | n_water=805 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1280 r_free=0.1551 | n_water=794 | time (s): 97.030 (total time: 99.500) Filter (q & B) r_work=0.1280 r_free=0.1550 | n_water=791 | time (s): 4.360 (total time: 103.860) Compute maps r_work=0.1280 r_free=0.1550 | n_water=791 | time (s): 2.100 (total time: 105.960) Filter (map) r_work=0.1305 r_free=0.1525 | n_water=652 | time (s): 4.350 (total time: 110.310) Find peaks r_work=0.1305 r_free=0.1525 | n_water=652 | time (s): 0.760 (total time: 111.070) Add new water r_work=0.1328 r_free=0.1551 | n_water=955 | time (s): 4.290 (total time: 115.360) Refine new water occ: r_work=0.1285 r_free=0.1511 adp: r_work=0.1273 r_free=0.1508 occ: r_work=0.1275 r_free=0.1509 adp: r_work=0.1268 r_free=0.1509 occ: r_work=0.1270 r_free=0.1508 adp: r_work=0.1267 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1508 r_work=0.1267 r_free=0.1508 | n_water=955 | time (s): 84.710 (total time: 200.070) Filter (q & B) r_work=0.1271 r_free=0.1510 | n_water=881 | time (s): 5.210 (total time: 205.280) Filter (dist only) r_work=0.1271 r_free=0.1510 | n_water=880 | time (s): 107.750 (total time: 313.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.406439 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 589.031888 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1253 0.1532 0.0279 0.041 1.1 17.3 0.0 0.3 0 12.203 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.32 2.79 2.039 15.045 589.032 0.014 12.32 15.17 2.85 2.403 15.109 589.032 0.014 Individual atomic B min max mean iso aniso Overall: 5.44 68.71 16.11 1.20 512 3272 Protein: 5.44 40.00 10.98 1.20 0 2902 Water: 6.55 68.71 33.04 N/A 512 368 Other: 16.25 31.92 24.09 N/A 0 2 Chain A: 5.52 56.62 12.97 N/A 0 1624 Chain B: 5.44 68.71 12.81 N/A 0 1648 Chain S: 11.16 65.02 36.73 N/A 512 0 Histogram: Values Number of atoms 5.44 - 11.77 2080 11.77 - 18.09 693 18.09 - 24.42 270 24.42 - 30.75 224 30.75 - 37.07 180 37.07 - 43.40 164 43.40 - 49.73 95 49.73 - 56.05 47 56.05 - 62.38 24 62.38 - 68.71 7 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1517 r_work=0.1233 r_free=0.1519 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1519 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1517 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013460 | | target function (ls_wunit_k1) not normalized (work): 2521.047829 | | target function (ls_wunit_k1) not normalized (free): 102.832599 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1517 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1437 0.1434 0.1611 n_refl.: 191138 remove outliers: r(all,work,free)=0.1437 0.1434 0.1611 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1434 0.1431 0.1609 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1525 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1234 0.1525 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 0.3291 402.814 376.880 0.485 0.963 0.261 13.296-10.522 100.00 100 1 0.1940 534.497 526.808 0.764 0.964 0.224 10.503-8.327 98.90 177 3 0.1415 564.205 566.989 0.918 0.964 0.210 8.318-6.595 100.00 360 8 0.1538 414.736 415.064 0.936 0.963 0.150 6.588-5.215 100.00 711 7 0.1356 381.101 376.640 0.914 0.963 0.150 5.214-4.128 98.38 1367 28 0.0821 557.435 556.016 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0759 508.132 505.497 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0854 342.774 341.447 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0903 258.603 256.806 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.628 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.362 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.220 1.058 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0491 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1525 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1525 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1525 | n_water=880 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1236 r_free=0.1525 | n_water=874 | time (s): 110.360 (total time: 112.840) Filter (q & B) r_work=0.1236 r_free=0.1524 | n_water=873 | time (s): 4.290 (total time: 117.130) Compute maps r_work=0.1236 r_free=0.1524 | n_water=873 | time (s): 1.950 (total time: 119.080) Filter (map) r_work=0.1275 r_free=0.1511 | n_water=698 | time (s): 4.090 (total time: 123.170) Find peaks r_work=0.1275 r_free=0.1511 | n_water=698 | time (s): 0.760 (total time: 123.930) Add new water r_work=0.1297 r_free=0.1542 | n_water=1005 | time (s): 3.980 (total time: 127.910) Refine new water occ: r_work=0.1252 r_free=0.1507 adp: r_work=0.1253 r_free=0.1507 occ: r_work=0.1248 r_free=0.1505 adp: r_work=0.1248 r_free=0.1505 occ: r_work=0.1245 r_free=0.1503 adp: r_work=0.1244 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1503 r_work=0.1244 r_free=0.1503 | n_water=1005 | time (s): 211.550 (total time: 339.460) Filter (q & B) r_work=0.1248 r_free=0.1511 | n_water=883 | time (s): 5.870 (total time: 345.330) Filter (dist only) r_work=0.1249 r_free=0.1511 | n_water=882 | time (s): 120.360 (total time: 465.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.717620 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.936834 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 0.1239 0.1437 0.0198 0.035 1.1 7.1 0.0 0.0 0 0.859 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.37 1.98 1.930 14.571 16.937 3.940 12.30 13.98 1.69 2.211 14.479 16.937 3.895 Individual atomic B min max mean iso aniso Overall: 5.53 68.31 15.25 1.07 515 3271 Protein: 5.53 36.58 10.74 1.07 0 2902 Water: 6.66 68.31 30.05 N/A 515 367 Other: 14.05 27.71 20.88 N/A 0 2 Chain A: 5.53 55.75 12.75 N/A 0 1624 Chain B: 5.55 68.31 12.53 N/A 0 1647 Chain S: 13.95 61.54 31.83 N/A 515 0 Histogram: Values Number of atoms 5.53 - 11.80 2142 11.80 - 18.08 680 18.08 - 24.36 302 24.36 - 30.64 239 30.64 - 36.92 182 36.92 - 43.20 149 43.20 - 49.48 62 49.48 - 55.75 25 55.75 - 62.03 4 62.03 - 68.31 1 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1399 r_work=0.1230 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1399 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1390 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889691 | | target function (ml) not normalized (work): 728527.458684 | | target function (ml) not normalized (free): 15217.886196 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1228 0.1225 0.1389 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1437 0.1436 0.1498 n_refl.: 191138 remove outliers: r(all,work,free)=0.1437 0.1436 0.1498 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1431 0.1430 0.1494 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1221 0.1383 n_refl.: 191138 remove outliers: r(all,work,free)=0.1224 0.1221 0.1383 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3849 398.008 362.078 0.424 0.947 0.250 13.296-10.522 99.01 99 1 0.2451 528.187 513.640 0.710 0.948 0.209 10.503-8.327 97.80 175 3 0.1971 554.286 557.353 0.885 0.948 0.188 8.318-6.595 100.00 360 8 0.2053 414.736 411.261 0.895 0.948 0.125 6.588-5.215 100.00 711 7 0.1839 381.101 370.735 0.888 0.948 0.120 5.214-4.128 98.38 1367 28 0.1161 557.435 552.099 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1097 508.132 501.025 1.033 0.948 0.019 3.266-2.585 99.86 5447 97 0.1078 342.774 339.142 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0959 258.603 255.752 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0968 153.054 151.407 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1049 82.395 81.484 1.051 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.311 1.036 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0919 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1221 r_free=0.1383 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1221 r_free=0.1383 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1383 | n_water=882 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1221 r_free=0.1383 | n_water=881 | time (s): 108.720 (total time: 111.610) Filter (q & B) r_work=0.1222 r_free=0.1381 | n_water=870 | time (s): 4.270 (total time: 115.880) Compute maps r_work=0.1222 r_free=0.1381 | n_water=870 | time (s): 1.800 (total time: 117.680) Filter (map) r_work=0.1245 r_free=0.1385 | n_water=725 | time (s): 4.620 (total time: 122.300) Find peaks r_work=0.1245 r_free=0.1385 | n_water=725 | time (s): 0.870 (total time: 123.170) Add new water r_work=0.1261 r_free=0.1405 | n_water=965 | time (s): 4.060 (total time: 127.230) Refine new water occ: r_work=0.1211 r_free=0.1363 adp: r_work=0.1204 r_free=0.1360 occ: r_work=0.1201 r_free=0.1360 adp: r_work=0.1201 r_free=0.1360 occ: r_work=0.1201 r_free=0.1360 adp: r_work=0.1201 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1360 r_work=0.1201 r_free=0.1360 | n_water=965 | time (s): 240.290 (total time: 367.520) Filter (q & B) r_work=0.1206 r_free=0.1370 | n_water=863 | time (s): 4.590 (total time: 372.110) Filter (dist only) r_work=0.1206 r_free=0.1369 | n_water=862 | time (s): 113.170 (total time: 485.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.537895 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.216241 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 0.1207 0.1373 0.0167 0.033 1.1 5.8 0.0 0.0 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.73 1.67 1.838 14.111 16.216 3.874 12.01 13.71 1.70 1.954 14.071 16.216 3.866 Individual atomic B min max mean iso aniso Overall: 5.50 67.85 14.79 1.01 495 3271 Protein: 5.50 33.37 10.66 1.01 0 2902 Water: 5.88 67.85 28.70 N/A 495 367 Other: 14.01 26.84 20.43 N/A 0 2 Chain A: 5.53 54.61 12.61 N/A 0 1624 Chain B: 5.50 67.85 12.42 N/A 0 1647 Chain S: 5.88 61.52 29.82 N/A 495 0 Histogram: Values Number of atoms 5.50 - 11.74 2126 11.74 - 17.97 721 17.97 - 24.21 334 24.21 - 30.44 233 30.44 - 36.68 142 36.68 - 42.91 128 42.91 - 49.15 56 49.15 - 55.38 21 55.38 - 61.62 4 61.62 - 67.85 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1371 r_work=0.1201 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1371 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1366 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863733 | | target function (ml) not normalized (work): 723650.163395 | | target function (ml) not normalized (free): 15137.577070 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1367 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1429 0.1428 0.1490 n_refl.: 191134 remove outliers: r(all,work,free)=0.1429 0.1428 0.1490 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1422 0.1421 0.1485 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1197 0.1365 n_refl.: 191134 remove outliers: r(all,work,free)=0.1200 0.1196 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 93.07 91 3 0.3672 360.246 315.453 0.411 0.945 0.245 13.296-10.522 96.04 96 1 0.2342 480.643 449.818 0.694 0.947 0.191 10.503-8.327 97.80 175 3 0.2140 502.128 495.380 0.862 0.947 0.167 8.318-6.595 100.00 360 8 0.2214 375.710 370.706 0.888 0.946 0.120 6.588-5.215 100.00 711 7 0.1931 345.240 335.617 0.883 0.947 0.084 5.214-4.128 98.38 1367 28 0.1215 504.981 500.109 0.974 0.947 0.070 4.126-3.266 94.74 2603 46 0.1127 460.318 454.024 1.036 0.947 0.005 3.266-2.585 99.86 5447 97 0.1086 310.519 307.404 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0931 234.269 231.906 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0910 138.652 137.401 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0987 74.642 73.948 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.042 38.393 1.038 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1135 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1365 | n_water=862 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1197 r_free=0.1368 | n_water=861 | time (s): 101.290 (total time: 104.430) Filter (q & B) r_work=0.1198 r_free=0.1366 | n_water=850 | time (s): 5.110 (total time: 109.540) Compute maps r_work=0.1198 r_free=0.1366 | n_water=850 | time (s): 1.670 (total time: 111.210) Filter (map) r_work=0.1220 r_free=0.1364 | n_water=729 | time (s): 4.040 (total time: 115.250) Find peaks r_work=0.1220 r_free=0.1364 | n_water=729 | time (s): 0.580 (total time: 115.830) Add new water r_work=0.1232 r_free=0.1382 | n_water=956 | time (s): 5.150 (total time: 120.980) Refine new water occ: r_work=0.1194 r_free=0.1348 adp: r_work=0.1194 r_free=0.1348 occ: r_work=0.1191 r_free=0.1346 adp: r_work=0.1191 r_free=0.1346 occ: r_work=0.1189 r_free=0.1345 adp: r_work=0.1189 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1345 r_work=0.1189 r_free=0.1345 | n_water=956 | time (s): 235.020 (total time: 356.000) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=884 | time (s): 5.270 (total time: 361.270) Filter (dist only) r_work=0.1193 r_free=0.1348 | n_water=883 | time (s): 110.950 (total time: 472.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.562768 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.837175 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1350 0.0154 0.034 1.1 7.2 0.0 0.0 0 0.781 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.50 1.54 1.795 14.089 14.837 3.764 12.00 13.56 1.56 1.840 14.072 14.837 3.762 Individual atomic B min max mean iso aniso Overall: 5.56 67.61 14.89 0.97 517 3270 Protein: 5.56 32.39 10.60 0.97 0 2902 Water: 5.97 67.61 28.96 N/A 517 366 Other: 13.80 25.98 19.89 N/A 0 2 Chain A: 5.59 54.06 12.54 N/A 0 1624 Chain B: 5.56 67.61 12.34 N/A 0 1646 Chain S: 5.97 61.48 30.39 N/A 517 0 Histogram: Values Number of atoms 5.56 - 11.76 2154 11.76 - 17.97 713 17.97 - 24.18 305 24.18 - 30.38 233 30.38 - 36.59 166 36.59 - 42.79 136 42.79 - 49.00 55 49.00 - 55.20 20 55.20 - 61.41 3 61.41 - 67.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1356 r_work=0.1200 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1357 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1357 target_work(ml) = 3.761 | | 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761459 | | target function (ml) not normalized (work): 704479.932930 | | target function (ml) not normalized (free): 14744.850367 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1356 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1417 0.1416 0.1484 n_refl.: 191130 remove outliers: r(all,work,free)=0.1417 0.1416 0.1484 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1409 0.1408 0.1479 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1358 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 93.07 91 3 0.3648 360.246 332.537 0.433 0.949 0.247 13.296-10.522 96.04 96 1 0.2371 480.643 463.753 0.711 0.950 0.190 10.503-8.327 97.80 175 3 0.2138 502.128 495.118 0.859 0.951 0.163 8.318-6.595 100.00 360 8 0.2191 375.710 371.468 0.880 0.950 0.095 6.588-5.215 100.00 711 7 0.1913 345.240 335.672 0.881 0.950 0.085 5.214-4.128 98.38 1367 28 0.1223 504.981 499.393 0.972 0.951 0.080 4.126-3.266 94.74 2603 46 0.1132 460.318 453.581 1.033 0.951 0.000 3.266-2.585 99.86 5447 97 0.1091 310.519 307.236 1.019 0.950 0.000 2.585-2.046 97.45 10613 204 0.0946 234.269 231.815 1.031 0.949 0.000 2.046-1.619 99.39 21536 464 0.0915 138.652 137.318 1.054 0.948 0.000 1.619-1.281 98.00 42464 925 0.0979 74.642 73.922 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.042 38.378 1.040 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1242 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1357 | n_water=883 | time (s): 2.780 (total time: 2.780) Filter (dist) r_work=0.1197 r_free=0.1357 | n_water=883 | time (s): 105.280 (total time: 108.060) Filter (q & B) r_work=0.1197 r_free=0.1356 | n_water=872 | time (s): 4.200 (total time: 112.260) Compute maps r_work=0.1197 r_free=0.1356 | n_water=872 | time (s): 1.960 (total time: 114.220) Filter (map) r_work=0.1217 r_free=0.1369 | n_water=759 | time (s): 5.470 (total time: 119.690) Find peaks r_work=0.1217 r_free=0.1369 | n_water=759 | time (s): 0.620 (total time: 120.310) Add new water r_work=0.1229 r_free=0.1388 | n_water=973 | time (s): 5.290 (total time: 125.600) Refine new water occ: r_work=0.1194 r_free=0.1354 adp: r_work=0.1194 r_free=0.1355 occ: r_work=0.1192 r_free=0.1352 adp: r_work=0.1192 r_free=0.1353 occ: r_work=0.1191 r_free=0.1350 adp: r_work=0.1190 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1351 r_work=0.1190 r_free=0.1351 | n_water=973 | time (s): 283.980 (total time: 409.580) Filter (q & B) r_work=0.1194 r_free=0.1352 | n_water=892 | time (s): 5.170 (total time: 414.750) Filter (dist only) r_work=0.1194 r_free=0.1351 | n_water=891 | time (s): 114.690 (total time: 529.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.546599 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.802722 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1357 0.0159 0.036 1.1 5.6 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.57 1.59 1.769 14.023 14.803 3.762 12.01 13.59 1.58 1.924 13.972 14.803 3.760 Individual atomic B min max mean iso aniso Overall: 5.57 66.48 14.78 0.91 525 3270 Protein: 5.57 29.54 10.49 0.91 0 2902 Water: 6.01 66.48 28.74 N/A 525 366 Other: 13.85 23.04 18.44 N/A 0 2 Chain A: 5.62 52.93 12.39 N/A 0 1624 Chain B: 5.57 66.48 12.21 N/A 0 1646 Chain S: 6.01 61.33 30.25 N/A 525 0 Histogram: Values Number of atoms 5.57 - 11.67 2130 11.67 - 17.76 768 17.76 - 23.85 279 23.85 - 29.94 227 29.94 - 36.03 171 36.03 - 42.12 133 42.12 - 48.21 57 48.21 - 54.30 24 54.30 - 60.39 4 60.39 - 66.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1360 r_work=0.1202 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1360 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1358 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758662 | | target function (ml) not normalized (work): 703956.119847 | | target function (ml) not normalized (free): 14736.692535 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1199 0.1358 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1417 0.1416 0.1479 n_refl.: 191130 remove outliers: r(all,work,free)=0.1417 0.1416 0.1479 n_refl.: 191130 overall B=-0.22 to atoms: r(all,work,free)=0.1379 0.1378 0.1456 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1354 n_refl.: 191130 remove outliers: r(all,work,free)=0.1201 0.1198 0.1354 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3612 361.056 328.755 0.435 0.949 0.239 13.296-10.522 96.04 96 1 0.2338 480.643 463.753 0.728 0.950 0.184 10.503-8.327 97.80 175 3 0.2155 502.128 495.515 0.881 0.950 0.157 8.318-6.595 100.00 360 8 0.2212 375.710 371.025 0.906 0.950 0.106 6.588-5.215 100.00 711 7 0.1927 345.240 335.211 0.905 0.950 0.083 5.214-4.128 98.38 1367 28 0.1222 504.981 499.682 0.996 0.950 0.039 4.126-3.266 94.74 2603 46 0.1153 460.318 453.382 1.059 0.950 0.000 3.266-2.585 99.86 5447 97 0.1111 310.519 307.179 1.042 0.950 0.000 2.585-2.046 97.45 10613 204 0.0952 234.269 231.790 1.050 0.950 0.000 2.046-1.619 99.39 21536 464 0.0911 138.652 137.345 1.068 0.949 0.000 1.619-1.281 98.00 42464 925 0.0971 74.642 73.937 1.056 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.042 38.379 1.027 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0492 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1354 | n_water=891 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1199 r_free=0.1354 | n_water=890 | time (s): 112.080 (total time: 114.850) Filter (q & B) r_work=0.1200 r_free=0.1353 | n_water=881 | time (s): 5.680 (total time: 120.530) Compute maps r_work=0.1200 r_free=0.1353 | n_water=881 | time (s): 2.130 (total time: 122.660) Filter (map) r_work=0.1223 r_free=0.1365 | n_water=769 | time (s): 4.860 (total time: 127.520) Find peaks r_work=0.1223 r_free=0.1365 | n_water=769 | time (s): 0.650 (total time: 128.170) Add new water r_work=0.1231 r_free=0.1376 | n_water=972 | time (s): 3.870 (total time: 132.040) Refine new water occ: r_work=0.1198 r_free=0.1344 adp: r_work=0.1198 r_free=0.1345 occ: r_work=0.1196 r_free=0.1342 adp: r_work=0.1196 r_free=0.1343 occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1194 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1343 r_work=0.1194 r_free=0.1343 | n_water=972 | time (s): 218.620 (total time: 350.660) Filter (q & B) r_work=0.1198 r_free=0.1350 | n_water=901 | time (s): 4.680 (total time: 355.340) Filter (dist only) r_work=0.1198 r_free=0.1349 | n_water=900 | time (s): 119.200 (total time: 474.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.569740 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.609270 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 0.1352 0.0151 0.036 1.1 6.3 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.52 1.51 1.722 13.713 15.609 3.760 11.99 13.51 1.52 1.762 13.699 15.609 3.755 Individual atomic B min max mean iso aniso Overall: 5.38 65.08 14.57 0.90 534 3270 Protein: 5.38 28.97 10.26 0.90 0 2902 Water: 5.83 65.08 28.46 N/A 534 366 Other: 13.69 21.80 17.74 N/A 0 2 Chain A: 5.44 52.28 12.11 N/A 0 1624 Chain B: 5.38 65.08 11.95 N/A 0 1646 Chain S: 5.83 61.07 30.11 N/A 534 0 Histogram: Values Number of atoms 5.38 - 11.35 2098 11.35 - 17.32 792 17.32 - 23.29 275 23.29 - 29.26 223 29.26 - 35.23 181 35.23 - 41.20 131 41.20 - 47.17 69 47.17 - 53.14 28 53.14 - 59.11 5 59.11 - 65.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1351 r_work=0.1200 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1352 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1352 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.753954 | | target function (ml) not normalized (work): 703070.488640 | | target function (ml) not normalized (free): 14718.474125 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1352 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1370 0.1368 0.1457 n_refl.: 191129 remove outliers: r(all,work,free)=0.1370 0.1368 0.1457 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1377 0.1376 0.1461 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1339 n_refl.: 191129 remove outliers: r(all,work,free)=0.1191 0.1188 0.1339 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3601 361.056 333.897 0.429 0.972 0.229 13.296-10.522 96.04 96 1 0.2345 480.643 463.405 0.709 0.974 0.167 10.503-8.327 97.80 175 3 0.2193 502.128 495.038 0.865 0.974 0.140 8.318-6.595 100.00 360 8 0.2189 375.710 370.591 0.888 0.974 0.090 6.588-5.215 100.00 711 7 0.1955 345.240 334.762 0.890 0.975 0.090 5.214-4.128 98.38 1367 28 0.1252 504.981 498.799 0.981 0.976 0.039 4.126-3.266 94.74 2603 46 0.1160 460.318 452.781 1.044 0.977 0.005 3.266-2.585 99.86 5447 97 0.1109 310.519 306.979 1.026 0.977 0.000 2.585-2.046 97.45 10613 204 0.0954 234.269 231.662 1.034 0.979 0.000 2.046-1.619 99.39 21536 464 0.0902 138.652 137.269 1.049 0.982 0.000 1.619-1.281 98.00 42464 925 0.0945 74.642 73.981 1.037 0.986 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.042 38.356 1.003 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0625 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1339 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1339 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1339 | n_water=900 | time (s): 3.400 (total time: 3.400) Filter (dist) r_work=0.1188 r_free=0.1339 | n_water=900 | time (s): 117.460 (total time: 120.860) Filter (q & B) r_work=0.1189 r_free=0.1338 | n_water=888 | time (s): 5.350 (total time: 126.210) Compute maps r_work=0.1189 r_free=0.1338 | n_water=888 | time (s): 1.860 (total time: 128.070) Filter (map) r_work=0.1212 r_free=0.1346 | n_water=773 | time (s): 5.050 (total time: 133.120) Find peaks r_work=0.1212 r_free=0.1346 | n_water=773 | time (s): 0.690 (total time: 133.810) Add new water r_work=0.1220 r_free=0.1357 | n_water=983 | time (s): 4.290 (total time: 138.100) Refine new water occ: r_work=0.1185 r_free=0.1328 adp: r_work=0.1185 r_free=0.1327 occ: r_work=0.1183 r_free=0.1327 adp: r_work=0.1183 r_free=0.1327 occ: r_work=0.1182 r_free=0.1327 adp: r_work=0.1182 r_free=0.1327 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1327 r_work=0.1182 r_free=0.1327 | n_water=983 | time (s): 245.560 (total time: 383.660) Filter (q & B) r_work=0.1185 r_free=0.1334 | n_water=911 | time (s): 5.000 (total time: 388.660) Filter (dist only) r_work=0.1186 r_free=0.1334 | n_water=910 | time (s): 117.220 (total time: 505.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.535020 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.583249 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1345 0.0156 0.037 1.1 4.9 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.45 1.56 1.687 13.726 13.583 3.753 11.92 13.47 1.55 1.678 13.733 13.583 3.754 Individual atomic B min max mean iso aniso Overall: 5.48 65.10 14.63 0.88 544 3270 Protein: 5.48 28.94 10.34 0.88 0 2902 Water: 5.94 65.10 28.30 N/A 544 366 Other: 13.76 21.90 17.83 N/A 0 2 Chain A: 5.58 52.32 12.18 N/A 0 1624 Chain B: 5.48 65.10 12.03 N/A 0 1646 Chain S: 5.94 58.50 29.82 N/A 544 0 Histogram: Values Number of atoms 5.48 - 11.44 2108 11.44 - 17.40 788 17.40 - 23.36 274 23.36 - 29.33 232 29.33 - 35.29 185 35.29 - 41.25 129 41.25 - 47.21 66 47.21 - 53.17 26 53.17 - 59.13 5 59.13 - 65.10 1 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1347 r_work=0.1192 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1347 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1348 target_work(ml) = 3.753 | | 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.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753181 | | target function (ml) not normalized (work): 702925.814756 | | target function (ml) not normalized (free): 14723.133056 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1385 0.1383 0.1473 n_refl.: 191129 remove outliers: r(all,work,free)=0.1385 0.1383 0.1473 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1386 0.1385 0.1474 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1347 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1347 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3692 361.056 330.219 0.414 0.973 0.213 13.296-10.522 96.04 96 1 0.2353 480.643 463.733 0.703 0.975 0.156 10.503-8.327 97.80 175 3 0.2225 502.128 493.470 0.864 0.975 0.121 8.318-6.595 100.00 360 8 0.2196 375.710 370.167 0.887 0.975 0.095 6.588-5.215 100.00 711 7 0.1964 345.240 334.864 0.889 0.976 0.077 5.214-4.128 98.38 1367 28 0.1241 504.981 499.052 0.979 0.976 0.029 4.126-3.266 94.74 2603 46 0.1168 460.318 452.700 1.042 0.978 0.000 3.266-2.585 99.86 5447 97 0.1116 310.519 306.968 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0953 234.269 231.634 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0901 138.652 137.290 1.050 0.984 0.000 1.619-1.281 98.00 42464 925 0.0945 74.642 73.986 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.042 38.338 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0157 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1347 | n_water=910 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1189 r_free=0.1347 | n_water=910 | time (s): 117.120 (total time: 119.780) Filter (q & B) r_work=0.1189 r_free=0.1348 | n_water=900 | time (s): 4.550 (total time: 124.330) Compute maps r_work=0.1189 r_free=0.1348 | n_water=900 | time (s): 2.460 (total time: 126.790) Filter (map) r_work=0.1211 r_free=0.1350 | n_water=786 | time (s): 5.310 (total time: 132.100) Find peaks r_work=0.1211 r_free=0.1350 | n_water=786 | time (s): 0.670 (total time: 132.770) Add new water r_work=0.1218 r_free=0.1364 | n_water=997 | time (s): 4.090 (total time: 136.860) Refine new water occ: r_work=0.1185 r_free=0.1333 adp: r_work=0.1186 r_free=0.1333 occ: r_work=0.1184 r_free=0.1334 adp: r_work=0.1184 r_free=0.1334 occ: r_work=0.1183 r_free=0.1334 adp: r_work=0.1182 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1334 r_work=0.1182 r_free=0.1334 | n_water=997 | time (s): 258.070 (total time: 394.930) Filter (q & B) r_work=0.1187 r_free=0.1345 | n_water=910 | time (s): 5.580 (total time: 400.510) Filter (dist only) r_work=0.1187 r_free=0.1344 | n_water=908 | time (s): 113.720 (total time: 514.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.483164 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.772988 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 0.1345 0.0153 0.037 1.1 5.6 0.0 0.3 0 0.742 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.45 1.53 1.689 13.754 14.773 3.755 11.92 13.48 1.56 1.696 13.754 14.773 3.752 Individual atomic B min max mean iso aniso Overall: 5.52 64.61 14.64 0.88 542 3270 Protein: 5.52 28.59 10.37 0.88 0 2902 Water: 5.95 64.61 28.27 N/A 542 366 Other: 13.82 22.00 17.91 N/A 0 2 Chain A: 5.63 52.10 12.18 N/A 0 1624 Chain B: 5.52 64.61 12.03 N/A 0 1646 Chain S: 5.95 58.54 29.90 N/A 542 0 Histogram: Values Number of atoms 5.52 - 11.43 2084 11.43 - 17.34 812 17.34 - 23.25 272 23.25 - 29.16 234 29.16 - 35.06 178 35.06 - 40.97 128 40.97 - 46.88 71 46.88 - 52.79 27 52.79 - 58.70 5 58.70 - 64.61 1 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1348 r_work=0.1192 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1348 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1347 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751538 | | target function (ml) not normalized (work): 702618.011439 | | target function (ml) not normalized (free): 14717.199793 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1347 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1395 0.1394 0.1476 n_refl.: 191129 remove outliers: r(all,work,free)=0.1395 0.1394 0.1476 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1394 0.1393 0.1476 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1346 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1346 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3665 361.056 330.736 0.402 0.994 0.211 13.296-10.522 96.04 96 1 0.2357 480.643 464.347 0.685 0.996 0.150 10.503-8.327 97.80 175 3 0.2234 502.128 493.766 0.842 0.996 0.116 8.318-6.595 100.00 360 8 0.2210 375.710 369.980 0.867 0.996 0.091 6.588-5.215 100.00 711 7 0.1977 345.240 334.842 0.869 0.997 0.073 5.214-4.128 98.38 1367 28 0.1251 504.981 498.960 0.957 0.998 0.034 4.126-3.266 94.74 2603 46 0.1172 460.318 452.726 1.020 0.999 0.005 3.266-2.585 99.86 5447 97 0.1120 310.519 306.917 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0956 234.269 231.625 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0901 138.652 137.295 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0941 74.642 73.991 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.042 38.332 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=-0.0130 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1346 After: r_work=0.1190 r_free=0.1347 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1347 | n_water=908 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1190 r_free=0.1347 | n_water=908 | time (s): 114.580 (total time: 117.060) Filter (q & B) r_work=0.1191 r_free=0.1345 | n_water=896 | time (s): 4.890 (total time: 121.950) Compute maps r_work=0.1191 r_free=0.1345 | n_water=896 | time (s): 1.840 (total time: 123.790) Filter (map) r_work=0.1212 r_free=0.1353 | n_water=791 | time (s): 4.300 (total time: 128.090) Find peaks r_work=0.1212 r_free=0.1353 | n_water=791 | time (s): 0.790 (total time: 128.880) Add new water r_work=0.1217 r_free=0.1363 | n_water=986 | time (s): 4.220 (total time: 133.100) Refine new water occ: r_work=0.1186 r_free=0.1332 adp: r_work=0.1186 r_free=0.1331 occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1185 r_free=0.1331 occ: r_work=0.1184 r_free=0.1331 adp: r_work=0.1184 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1331 r_work=0.1184 r_free=0.1331 | n_water=986 | time (s): 228.110 (total time: 361.210) Filter (q & B) r_work=0.1188 r_free=0.1342 | n_water=903 | time (s): 4.820 (total time: 366.030) Filter (dist only) r_work=0.1189 r_free=0.1341 | n_water=902 | time (s): 119.800 (total time: 485.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.487781 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.679691 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1347 0.0155 0.037 1.2 7.8 0.0 0.3 0 0.744 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.47 1.55 1.689 13.736 14.680 3.754 11.92 13.50 1.58 1.695 13.733 14.680 3.753 Individual atomic B min max mean iso aniso Overall: 5.57 63.77 14.59 0.87 536 3270 Protein: 5.57 28.39 10.38 0.87 0 2902 Water: 6.02 63.77 28.12 N/A 536 366 Other: 13.88 21.95 17.92 N/A 0 2 Chain A: 5.65 51.79 12.16 N/A 0 1624 Chain B: 5.57 63.77 12.03 N/A 0 1646 Chain S: 6.02 58.51 29.80 N/A 536 0 Histogram: Values Number of atoms 5.57 - 11.39 2066 11.39 - 17.21 831 17.21 - 23.03 272 23.03 - 28.85 224 28.85 - 34.67 177 34.67 - 40.49 124 40.49 - 46.31 75 46.31 - 52.13 29 52.13 - 57.95 6 57.95 - 63.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1350 r_work=0.1193 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752749 | | target function (ml) not normalized (work): 702844.943129 | | target function (ml) not normalized (free): 14720.040112 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1365 0.1474 5.6913 5.7648| | 2: 2.94 - 2.33 1.00 7339 128 0.1069 0.1284 5.0759 5.1461| | 3: 2.33 - 2.04 0.96 6939 150 0.0897 0.1200 4.6473 4.7524| | 4: 2.04 - 1.85 1.00 7170 155 0.0893 0.1039 4.3856 4.5542| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.1001 4.1467 4.2482| | 6: 1.72 - 1.62 0.99 7102 142 0.0892 0.1064 3.9398 4.0604| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0965 3.793 3.9201| | 8: 1.54 - 1.47 0.96 6798 152 0.0887 0.1301 3.6948 3.8976| | 9: 1.47 - 1.41 0.98 6938 155 0.0925 0.1123 3.6194 3.7539| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1189 3.5554 3.6773| | 11: 1.36 - 1.32 0.99 6997 151 0.0995 0.1133 3.4867 3.5939| | 12: 1.32 - 1.28 0.98 6975 149 0.1033 0.1121 3.4594 3.5795| | 13: 1.28 - 1.25 0.98 6907 166 0.1039 0.1243 3.4354 3.5613| | 14: 1.25 - 1.22 0.98 7015 112 0.1102 0.1587 3.43 3.6756| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1249 3.4481 3.4931| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1548 3.4653 3.6541| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1228 3.434 3.4451| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1716 3.4392 3.537| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1777 3.4211 3.599| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1578 3.4108 3.4366| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2139 3.418 3.5046| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1959 3.4132 3.4177| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2013 3.4333 3.4852| | 24: 1.03 - 1.02 0.96 6784 133 0.2330 0.2249 3.4354 3.5098| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2512 3.4497 3.5239| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2842 3.4159 3.4203| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2803 3.4689 3.3971| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7397 127 0.93 11.62 1.00 0.95 11100.85| | 2: 2.94 - 2.33 7339 128 0.93 12.63 0.99 0.95 5054.08| | 3: 2.33 - 2.04 6939 150 0.96 7.50 1.01 0.95 1660.18| | 4: 2.04 - 1.85 7170 155 0.96 7.58 1.00 0.95 991.38| | 5: 1.85 - 1.72 7113 159 0.96 8.05 1.00 0.96 630.56| | 6: 1.72 - 1.62 7102 142 0.96 7.90 1.00 0.96 434.96| | 7: 1.62 - 1.54 7104 148 0.96 8.01 1.01 0.97 329.99| | 8: 1.54 - 1.47 6798 152 0.96 8.17 1.01 0.97 275.46| | 9: 1.47 - 1.41 6938 155 0.96 8.44 1.00 0.98 230.09| | 10: 1.41 - 1.36 7022 150 0.96 8.94 1.00 0.97 203.17| | 11: 1.36 - 1.32 6997 151 0.96 8.97 0.99 0.96 175.61| | 12: 1.32 - 1.28 6975 149 0.96 8.99 0.98 0.95 160.89| | 13: 1.28 - 1.25 6907 166 0.96 9.49 1.01 0.96 157.46| | 14: 1.25 - 1.22 7015 112 0.95 10.64 1.01 0.97 162.26| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 0.98 166.06| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.01 0.96 160.59| | 17: 1.17 - 1.14 6940 135 0.94 12.28 1.01 0.96 154.59| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.95 148.73| | 19: 1.12 - 1.10 6948 106 0.93 14.19 1.00 0.95 151.85| | 20: 1.10 - 1.08 6884 147 0.92 15.26 1.00 0.94 150.87| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.93 153.49| | 22: 1.07 - 1.05 6836 135 0.89 18.28 0.99 0.93 154.98| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.92 164.57| | 24: 1.03 - 1.02 6784 133 0.85 23.11 0.99 0.93 178.67| | 25: 1.02 - 1.01 6552 130 0.83 25.10 0.98 0.90 181.66| | 26: 1.01 - 0.99 6767 158 0.81 26.60 0.98 0.88 176.48| | 27: 0.99 - 0.98 6647 131 0.82 26.34 0.99 0.87 161.63| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.73 max = 11100.85 mean = 915.88| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.85 mean = 13.26| |phase err.(test): min = 0.00 max = 89.98 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1487 n_refl.: 191129 remove outliers: r(all,work,free)=0.1404 0.1403 0.1487 n_refl.: 191129 overall B=-0.06 to atoms: r(all,work,free)=0.1395 0.1393 0.1481 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1348 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1348 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3622 361.056 331.576 0.429 0.916 0.216 13.296-10.522 96.04 96 1 0.2360 480.643 464.192 0.725 0.917 0.151 10.503-8.327 97.80 175 3 0.2211 502.128 494.606 0.892 0.918 0.119 8.318-6.595 100.00 360 8 0.2208 375.710 370.639 0.919 0.917 0.097 6.588-5.215 100.00 711 7 0.1959 345.240 334.893 0.921 0.918 0.080 5.214-4.128 98.38 1367 28 0.1242 504.981 499.064 1.014 0.919 0.034 4.126-3.266 94.74 2603 46 0.1176 460.318 452.702 1.081 0.920 0.000 3.266-2.585 99.86 5447 97 0.1118 310.519 307.006 1.063 0.922 0.000 2.585-2.046 97.45 10613 204 0.0959 234.269 231.631 1.070 0.924 0.000 2.046-1.619 99.39 21536 464 0.0905 138.652 137.279 1.086 0.928 0.000 1.619-1.281 98.00 42464 925 0.0944 74.642 73.988 1.075 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.042 38.325 1.040 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0130 ================= 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 : 0.2031 0.2015 0.082 5.212 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1964 0.082 5.212 5.2 78.0 14.6 805 0.000 1_settarget: 0.1797 0.1964 0.082 5.212 5.2 78.0 14.6 805 0.000 1_nqh: 0.1797 0.1964 0.082 5.212 5.2 78.0 14.6 805 0.000 1_weight: 0.1797 0.1964 0.082 5.212 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1273 0.1506 0.039 1.144 5.2 78.0 14.6 805 0.157 1_adp: 0.1300 0.1572 0.039 1.144 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1299 0.1567 0.039 1.144 5.2 73.0 15.0 805 0.157 1_occ: 0.1284 0.1555 0.039 1.144 5.2 73.0 15.0 805 0.157 2_bss: 0.1276 0.1546 0.039 1.144 5.3 73.2 15.2 805 0.157 2_settarget: 0.1276 0.1546 0.039 1.144 5.3 73.2 15.2 805 0.157 2_updatecdl: 0.1276 0.1546 0.039 1.162 5.3 73.2 15.2 805 0.157 2_nqh: 0.1276 0.1546 0.039 1.162 5.3 73.2 15.2 805 0.157 2_sol: 0.1271 0.1510 0.039 1.162 5.3 73.2 16.0 880 n/a 2_weight: 0.1271 0.1510 0.039 1.162 5.3 73.2 16.0 880 n/a 2_xyzrec: 0.1253 0.1532 0.041 1.139 5.3 73.2 16.0 880 n/a 2_adp: 0.1232 0.1517 0.041 1.139 5.4 68.7 16.1 880 n/a 2_regHadp: 0.1233 0.1519 0.041 1.139 5.4 68.7 16.1 880 n/a 2_occ: 0.1227 0.1517 0.041 1.139 5.4 68.7 16.1 880 n/a 3_bss: 0.1234 0.1525 0.041 1.139 5.4 68.7 16.1 880 n/a 3_settarget: 0.1234 0.1525 0.041 1.139 5.4 68.7 16.1 880 n/a 3_updatecdl: 0.1234 0.1525 0.041 1.150 5.4 68.7 16.1 880 n/a 3_nqh: 0.1234 0.1525 0.041 1.150 5.4 68.7 16.1 880 n/a 3_sol: 0.1249 0.1511 0.041 1.150 5.4 68.7 15.4 882 n/a 3_weight: 0.1249 0.1511 0.041 1.150 5.4 68.7 15.4 882 n/a 3_xyzrec: 0.1239 0.1437 0.035 1.108 5.4 68.7 15.4 882 n/a 3_adp: 0.1230 0.1399 0.035 1.108 5.5 68.3 15.2 882 n/a 3_regHadp: 0.1230 0.1399 0.035 1.108 5.5 68.3 15.2 882 n/a 3_occ: 0.1225 0.1390 0.035 1.108 5.5 68.3 15.2 882 n/a 4_bss: 0.1221 0.1383 0.035 1.108 5.5 68.3 15.2 882 n/a 4_settarget: 0.1221 0.1383 0.035 1.108 5.5 68.3 15.2 882 n/a 4_updatecdl: 0.1221 0.1383 0.035 1.106 5.5 68.3 15.2 882 n/a 4_nqh: 0.1221 0.1383 0.035 1.106 5.5 68.3 15.2 882 n/a 4_sol: 0.1206 0.1369 0.035 1.106 5.5 68.3 14.9 862 n/a 4_weight: 0.1206 0.1369 0.035 1.106 5.5 68.3 14.9 862 n/a 4_xyzrec: 0.1207 0.1373 0.033 1.107 5.5 68.3 14.9 862 n/a 4_adp: 0.1201 0.1371 0.033 1.107 5.5 67.9 14.8 862 n/a 4_regHadp: 0.1201 0.1371 0.033 1.107 5.5 67.9 14.8 862 n/a 4_occ: 0.1199 0.1366 0.033 1.107 5.5 67.9 14.8 862 n/a 5_bss: 0.1196 0.1365 0.033 1.107 5.5 67.8 14.8 862 n/a 5_settarget: 0.1196 0.1365 0.033 1.107 5.5 67.8 14.8 862 n/a 5_updatecdl: 0.1196 0.1365 0.033 1.107 5.5 67.8 14.8 862 n/a 5_nqh: 0.1196 0.1365 0.033 1.107 5.5 67.8 14.8 862 n/a 5_sol: 0.1193 0.1348 0.033 1.107 5.5 67.8 14.9 883 n/a 5_weight: 0.1193 0.1348 0.033 1.107 5.5 67.8 14.9 883 n/a 5_xyzrec: 0.1196 0.1350 0.034 1.127 5.5 67.8 14.9 883 n/a 5_adp: 0.1200 0.1356 0.034 1.127 5.6 67.6 14.9 883 n/a 5_regHadp: 0.1200 0.1357 0.034 1.127 5.6 67.6 14.9 883 n/a 5_occ: 0.1198 0.1357 0.034 1.127 5.6 67.6 14.9 883 n/a 6_bss: 0.1197 0.1357 0.034 1.127 5.5 67.6 14.9 883 n/a 6_settarget: 0.1197 0.1357 0.034 1.127 5.5 67.6 14.9 883 n/a 6_updatecdl: 0.1197 0.1357 0.034 1.127 5.5 67.6 14.9 883 n/a 6_nqh: 0.1197 0.1357 0.034 1.127 5.5 67.6 14.9 883 n/a 6_sol: 0.1194 0.1351 0.034 1.127 5.5 67.6 14.9 891 n/a 6_weight: 0.1194 0.1351 0.034 1.127 5.5 67.6 14.9 891 n/a 6_xyzrec: 0.1198 0.1357 0.036 1.121 5.5 67.6 14.9 891 n/a 6_adp: 0.1201 0.1360 0.036 1.121 5.6 66.5 14.8 891 n/a 6_regHadp: 0.1202 0.1360 0.036 1.121 5.6 66.5 14.8 891 n/a 6_occ: 0.1199 0.1358 0.036 1.121 5.6 66.5 14.8 891 n/a 7_bss: 0.1199 0.1354 0.036 1.121 5.4 66.3 14.6 891 n/a 7_settarget: 0.1199 0.1354 0.036 1.121 5.4 66.3 14.6 891 n/a 7_updatecdl: 0.1199 0.1354 0.036 1.121 5.4 66.3 14.6 891 n/a 7_nqh: 0.1199 0.1354 0.036 1.121 5.4 66.3 14.6 891 n/a 7_sol: 0.1198 0.1349 0.036 1.121 5.4 66.3 14.6 900 n/a 7_weight: 0.1198 0.1349 0.036 1.121 5.4 66.3 14.6 900 n/a 7_xyzrec: 0.1201 0.1352 0.036 1.132 5.4 66.3 14.6 900 n/a 7_adp: 0.1199 0.1351 0.036 1.132 5.4 65.1 14.6 900 n/a 7_regHadp: 0.1200 0.1352 0.036 1.132 5.4 65.1 14.6 900 n/a 7_occ: 0.1197 0.1352 0.036 1.132 5.4 65.1 14.6 900 n/a 8_bss: 0.1188 0.1339 0.036 1.132 5.4 65.1 14.6 900 n/a 8_settarget: 0.1188 0.1339 0.036 1.132 5.4 65.1 14.6 900 n/a 8_updatecdl: 0.1188 0.1339 0.036 1.132 5.4 65.1 14.6 900 n/a 8_nqh: 0.1188 0.1339 0.036 1.132 5.4 65.1 14.6 900 n/a 8_sol: 0.1186 0.1334 0.036 1.132 5.4 65.1 14.6 910 n/a 8_weight: 0.1186 0.1334 0.036 1.132 5.4 65.1 14.6 910 n/a 8_xyzrec: 0.1189 0.1345 0.037 1.116 5.4 65.1 14.6 910 n/a 8_adp: 0.1192 0.1347 0.037 1.116 5.5 65.1 14.6 910 n/a 8_regHadp: 0.1192 0.1347 0.037 1.116 5.5 65.1 14.6 910 n/a 8_occ: 0.1190 0.1348 0.037 1.116 5.5 65.1 14.6 910 n/a 9_bss: 0.1189 0.1347 0.037 1.116 5.5 65.1 14.6 910 n/a 9_settarget: 0.1189 0.1347 0.037 1.116 5.5 65.1 14.6 910 n/a 9_updatecdl: 0.1189 0.1347 0.037 1.116 5.5 65.1 14.6 910 n/a 9_nqh: 0.1189 0.1347 0.037 1.116 5.5 65.1 14.6 910 n/a 9_sol: 0.1187 0.1344 0.037 1.116 5.5 65.1 14.6 908 n/a 9_weight: 0.1187 0.1344 0.037 1.116 5.5 65.1 14.6 908 n/a 9_xyzrec: 0.1192 0.1345 0.037 1.113 5.5 65.1 14.6 908 n/a 9_adp: 0.1192 0.1348 0.037 1.113 5.5 64.6 14.6 908 n/a 9_regHadp: 0.1192 0.1348 0.037 1.113 5.5 64.6 14.6 908 n/a 9_occ: 0.1191 0.1347 0.037 1.113 5.5 64.6 14.6 908 n/a 10_bss: 0.1189 0.1346 0.037 1.113 5.5 64.6 14.6 908 n/a 10_settarget: 0.1189 0.1346 0.037 1.113 5.5 64.6 14.6 908 n/a 10_updatecdl: 0.1189 0.1346 0.037 1.113 5.5 64.6 14.6 908 n/a 10_setrh: 0.1190 0.1347 0.037 1.113 5.5 64.6 14.6 908 n/a 10_nqh: 0.1190 0.1347 0.037 1.113 5.5 64.6 14.6 908 n/a 10_sol: 0.1189 0.1341 0.037 1.113 5.5 64.6 14.6 902 n/a 10_weight: 0.1189 0.1341 0.037 1.113 5.5 64.6 14.6 902 n/a 10_xyzrec: 0.1191 0.1347 0.037 1.159 5.5 64.6 14.6 902 n/a 10_adp: 0.1192 0.1350 0.037 1.159 5.6 63.8 14.6 902 n/a 10_regHadp: 0.1193 0.1350 0.037 1.159 5.6 63.8 14.6 902 n/a 10_occ: 0.1191 0.1350 0.037 1.159 5.6 63.8 14.6 902 n/a end: 0.1191 0.1348 0.037 1.159 5.5 63.7 14.5 902 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6209618_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_6209618_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2500 Refinement macro-cycles (run) : 12082.4700 Write final files (write_after_run_outputs) : 159.9100 Total : 12248.6300 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:25 PST -0800 (1736736085.34 s) Start R-work = 0.1797, R-free = 0.1964 Final R-work = 0.1191, R-free = 0.1348 =============================================================================== Job complete usr+sys time: 12533.95 seconds wall clock time: 209 minutes 55.22 seconds (12595.22 seconds total)