Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4021785.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/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.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/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.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_4021785.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4021785.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: 1.99, 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: 2.672 distance_ideal: 2.720 ideal - model: 0.048 slack: 0.000 delta_slack: 0.048 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: 2.739 distance_ideal: 2.710 ideal - model: -0.029 slack: 0.000 delta_slack: -0.029 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 152.3 milliseconds Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.80 - 1.02: 774 1.02 - 1.25: 2479 1.25 - 1.47: 1480 1.47 - 1.70: 1167 1.70 - 1.92: 34 Bond restraints: 5934 Sorted by residual: bond pdb=" C CYS A 8 " pdb=" O CYS A 8 " ideal model delta sigma weight residual 1.234 1.486 -0.252 1.23e-02 6.61e+03 4.19e+02 bond pdb=" CZ2 TRP A 139 " pdb=" HZ2 TRP A 139 " ideal model delta sigma weight residual 0.930 1.323 -0.393 2.00e-02 2.50e+03 3.86e+02 bond pdb=" C VAL B 7 " pdb=" O VAL B 7 " ideal model delta sigma weight residual 1.236 1.452 -0.216 1.12e-02 7.97e+03 3.73e+02 bond pdb=" CA GLN B 94 " pdb=" HA GLN B 94 " ideal model delta sigma weight residual 0.970 1.344 -0.374 2.00e-02 2.50e+03 3.49e+02 bond pdb=" C SER B 36 " pdb=" N VAL B 37 " ideal model delta sigma weight residual 1.332 1.116 0.215 1.16e-02 7.43e+03 3.45e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 5851 4.37 - 8.74: 3526 8.74 - 13.11: 1210 13.11 - 17.49: 209 17.49 - 21.86: 14 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.65 106.34 15.31 7.30e-01 1.88e+00 4.40e+02 angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" O ILE B 134 " ideal model delta sigma weight residual 119.38 105.80 13.58 6.80e-01 2.16e+00 3.99e+02 angle pdb=" CA ALA B 10 " pdb=" C ALA B 10 " pdb=" O ALA B 10 " ideal model delta sigma weight residual 120.34 136.25 -15.91 9.20e-01 1.18e+00 2.99e+02 angle pdb=" NE ARG B 49 " pdb=" CZ ARG B 49 " pdb=" NH1 ARG B 49 " ideal model delta sigma weight residual 121.50 136.97 -15.47 1.00e+00 1.00e+00 2.39e+02 angle pdb=" NE ARG A 149 " pdb=" CZ ARG A 149 " pdb=" NH2 ARG A 149 " ideal model delta sigma weight residual 119.20 106.44 12.76 9.00e-01 1.23e+00 2.01e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.28: 1815 16.28 - 32.56: 163 32.56 - 48.83: 45 48.83 - 65.10: 22 65.10 - 81.37: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+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 -25.21 25.21 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.206: 190 0.206 - 0.412: 150 0.412 - 0.618: 87 0.618 - 0.824: 48 0.824 - 1.029: 17 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB VAL A 102 " pdb=" CA VAL A 102 " pdb=" CG1 VAL A 102 " pdb=" CG2 VAL A 102 " both_signs ideal model delta sigma weight residual False -2.63 -1.60 -1.03 2.00e-01 2.50e+01 2.65e+01 chirality pdb=" CA LEU A 43 " pdb=" N LEU A 43 " pdb=" C LEU A 43 " pdb=" CB LEU A 43 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" CB VAL A 89 " pdb=" CA VAL A 89 " pdb=" CG1 VAL A 89 " pdb=" CG2 VAL A 89 " both_signs ideal model delta sigma weight residual False -2.63 -1.64 -0.99 2.00e-01 2.50e+01 2.43e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.117 2.00e-02 2.50e+03 7.76e-02 1.81e+02 pdb=" CG PHE B 164 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.101 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.124 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.095 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.056 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.115 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.082 2.00e-02 2.50e+03 6.97e-02 1.46e+02 pdb=" CG PHE A 127 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " 0.131 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " 0.045 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " -0.082 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " -0.104 2.00e-02 2.50e+03 pdb=" HD1 PHE A 127 " 0.023 2.00e-02 2.50e+03 pdb=" HD2 PHE A 127 " 0.028 2.00e-02 2.50e+03 pdb=" HE1 PHE A 127 " -0.061 2.00e-02 2.50e+03 pdb=" HE2 PHE A 127 " 0.086 2.00e-02 2.50e+03 pdb=" HZ PHE A 127 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " -0.011 2.00e-02 2.50e+03 6.00e-02 1.44e+02 pdb=" CG TRP A 146 " 0.086 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.141 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.119 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.043 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.030 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.055 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.005 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.014 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.008 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.053 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.031 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.025 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 26 1.61 - 2.35: 2311 2.35 - 3.10: 22267 3.10 - 3.85: 32880 3.85 - 4.60: 52715 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110199 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.857 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.011 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.077 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.081 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.135 2.620 ... (remaining 110194 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_4021785_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2033 r_free= 0.1984 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302262 | | target function (ml) not normalized (work): 805869.632690 | | target function (ml) not normalized (free): 16574.777022 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2141 0.1920 6.6923 6.3185| | 2: 2.94 - 2.33 1.00 7339 128 0.1614 0.1571 5.5415 5.5748| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1619 5.1505 5.151| | 4: 2.04 - 1.85 1.00 7170 155 0.1730 0.1668 4.9636 5.0775| | 5: 1.85 - 1.72 0.99 7113 159 0.1922 0.1652 4.7932 4.8134| | 6: 1.72 - 1.62 0.99 7102 142 0.1957 0.2021 4.6597 4.7412| | 7: 1.62 - 1.54 0.99 7104 148 0.2017 0.1767 4.5599 4.5911| | 8: 1.54 - 1.47 0.96 6798 152 0.2073 0.2104 4.4818 4.4904| | 9: 1.47 - 1.41 0.98 6938 155 0.2102 0.2202 4.3947 4.4604| | 10: 1.41 - 1.36 0.99 7022 150 0.2140 0.2066 4.3219 4.3344| | 11: 1.36 - 1.32 0.99 6997 151 0.2104 0.2333 4.2394 4.3601| | 12: 1.32 - 1.28 0.98 6976 149 0.2064 0.2038 4.1834 4.2529| | 13: 1.28 - 1.25 0.98 6907 166 0.1998 0.2284 4.1188 4.2499| | 14: 1.25 - 1.22 0.98 7015 113 0.2058 0.2295 4.072 4.269| | 15: 1.22 - 1.19 0.98 6957 137 0.2116 0.2088 4.0572 4.0482| | 16: 1.19 - 1.17 0.93 6604 132 0.2127 0.2227 4.0107 4.0493| | 17: 1.17 - 1.14 0.98 6941 135 0.2163 0.2118 3.9652 4.0323| | 18: 1.14 - 1.12 0.98 6875 142 0.2241 0.2510 3.9349 3.9462| | 19: 1.12 - 1.10 0.97 6949 106 0.2262 0.2363 3.8616 3.9141| | 20: 1.10 - 1.08 0.97 6884 147 0.2337 0.2063 3.8174 3.7649| | 21: 1.08 - 1.07 0.97 6852 152 0.2454 0.2710 3.7961 3.8048| | 22: 1.07 - 1.05 0.97 6838 135 0.2573 0.2434 3.757 3.7087| | 23: 1.05 - 1.03 0.97 6829 159 0.2732 0.2588 3.7339 3.7905| | 24: 1.03 - 1.02 0.96 6785 133 0.2880 0.2649 3.6982 3.7242| | 25: 1.02 - 1.01 0.93 6552 130 0.3026 0.2959 3.6668 3.7388| | 26: 1.01 - 0.99 0.96 6767 158 0.3199 0.3455 3.623 3.6629| | 27: 0.99 - 0.98 0.94 6648 131 0.3421 0.3071 3.6531 3.6113| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.56 0.91 0.98 36156.19| | 2: 2.94 - 2.33 7339 128 0.85 21.37 1.08 1.02 15304.69| | 3: 2.33 - 2.04 6939 150 0.93 12.62 1.11 1.05 4154.21| | 4: 2.04 - 1.85 7170 155 0.92 13.83 1.11 1.05 2873.51| | 5: 1.85 - 1.72 7113 159 0.90 16.14 1.12 1.06 2133.01| | 6: 1.72 - 1.62 7102 142 0.90 16.94 1.11 1.06 1672.03| | 7: 1.62 - 1.54 7104 148 0.89 17.74 1.11 1.08 1360.47| | 8: 1.54 - 1.47 6798 152 0.88 18.51 1.11 1.07 1160.15| | 9: 1.47 - 1.41 6938 155 0.88 19.46 1.10 1.07 1024.53| | 10: 1.41 - 1.36 7022 150 0.87 20.66 1.09 1.04 904.03| | 11: 1.36 - 1.32 6997 151 0.86 21.26 1.08 1.02 809.84| | 12: 1.32 - 1.28 6976 149 0.86 21.41 1.07 1.01 731.65| | 13: 1.28 - 1.25 6907 166 0.86 21.55 1.07 1.02 685.20| | 14: 1.25 - 1.22 7015 113 0.85 22.35 1.08 1.02 646.27| | 15: 1.22 - 1.19 6957 137 0.85 22.13 1.07 1.03 600.17| | 16: 1.19 - 1.17 6604 132 0.86 21.65 1.08 1.02 538.75| | 17: 1.17 - 1.14 6941 135 0.86 21.84 1.08 1.01 470.17| | 18: 1.14 - 1.12 6875 142 0.86 21.49 1.08 0.99 401.68| | 19: 1.12 - 1.10 6949 106 0.86 21.33 1.07 1.00 353.89| | 20: 1.10 - 1.08 6884 147 0.86 21.46 1.06 0.99 312.03| | 21: 1.08 - 1.07 6852 152 0.85 22.50 1.07 1.00 306.89| | 22: 1.07 - 1.05 6838 135 0.84 24.24 1.06 0.99 304.32| | 23: 1.05 - 1.03 6829 159 0.81 26.75 1.05 0.99 317.98| | 24: 1.03 - 1.02 6785 133 0.78 29.16 1.05 0.98 322.36| | 25: 1.02 - 1.01 6552 130 0.76 31.07 1.03 0.93 316.02| | 26: 1.01 - 0.99 6767 158 0.74 32.83 1.02 0.90 297.15| | 27: 0.99 - 0.98 6648 131 0.75 32.54 1.04 0.86 266.48| |alpha: min = 0.86 max = 1.08 mean = 1.01| |beta: min = 266.48 max = 36156.19 mean = 2886.04| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.90| |phase err.(test): min = 0.00 max = 89.72 mean = 21.90| |-----------------------------------------------------------------------------| ----------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 0.252 2950 Z= 5.483 Angle : 5.271 17.820 4018 Z= 3.748 Chirality : 0.397 1.029 492 Planarity : 0.032 0.156 512 Dihedral : 12.844 81.374 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.44 % Favored : 94.30 % Rotamer: Outliers : 0.97 % Allowed : 4.19 % Favored : 94.84 % Cbeta Deviations : 28.37 % 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: -1.73 (0.40), residues: 386 helix: -1.87 (0.35), residues: 144 sheet: -1.52 (0.50), residues: 86 loop : 0.20 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.023 ARG B 149 TYR 0.140 0.042 TYR B 67 PHE 0.098 0.044 PHE A 164 TRP 0.138 0.045 TRP A 146 HIS 0.109 0.035 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2033 r_free= 0.1984 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.302262 | | target function (ml) not normalized (work): 805869.632690 | | target function (ml) not normalized (free): 16574.777022 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2031 0.2033 0.1984 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2031 0.2033 0.1984 n_refl.: 191155 remove outliers: r(all,work,free)=0.2031 0.2033 0.1984 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2033 0.2035 0.1985 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1802 0.1799 0.1924 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1797 0.1922 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 0.4092 402.814 292.388 0.424 0.933 0.301 13.296-10.522 99.01 99 1 0.2486 528.187 519.495 0.764 0.934 0.255 10.503-8.327 99.45 178 3 0.2486 565.118 556.223 0.947 0.934 0.233 8.318-6.595 100.00 360 8 0.2485 414.736 403.336 0.949 0.934 0.190 6.588-5.215 100.00 711 7 0.2280 381.101 365.561 0.936 0.934 0.170 5.214-4.128 98.38 1367 28 0.1512 557.435 548.704 1.050 0.933 0.055 4.126-3.266 94.74 2603 46 0.1327 508.132 499.479 1.118 0.932 0.018 3.266-2.585 99.86 5447 97 0.1437 342.774 337.781 1.095 0.930 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 254.163 1.105 0.927 0.000 2.046-1.619 99.39 21536 464 0.1607 153.054 149.833 1.128 0.921 0.000 1.619-1.281 98.00 42464 925 0.1924 82.395 80.202 1.123 0.912 0.000 1.281-0.980 96.53 101826 2055 0.2317 44.202 41.657 1.122 0.895 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0175 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1922 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1797 r_free=0.1922 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.096773 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.635078 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 0.1272 0.1506 0.0235 0.040 1.2 10.9 0.0 0.3 0 11.048 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.06 2.35 1.118 13.122 577.635 0.018 12.98 15.74 2.76 1.251 13.363 577.635 0.017 Individual atomic B min max mean iso aniso Overall: 5.22 73.05 15.05 1.41 435 3274 Protein: 5.22 40.35 11.01 1.41 0 2902 Water: 6.39 73.05 29.59 N/A 435 370 Other: 16.07 30.03 23.05 N/A 0 2 Chain A: 5.34 59.74 13.06 N/A 0 1626 Chain B: 5.22 73.05 12.79 N/A 0 1648 Chain S: 11.42 66.23 31.05 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.00 2171 12.00 - 18.79 632 18.79 - 25.57 310 25.57 - 32.35 269 32.35 - 39.14 159 39.14 - 45.92 101 45.92 - 52.70 44 52.70 - 59.49 18 59.49 - 66.27 4 66.27 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1574 r_work=0.1297 r_free=0.1568 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1568 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1558 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015609 | | target function (ls_wunit_k1) not normalized (work): 2923.457106 | | target function (ls_wunit_k1) not normalized (free): 117.803949 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1558 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1635 n_refl.: 191138 remove outliers: r(all,work,free)=0.1470 0.1467 0.1635 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1493 0.1491 0.1646 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1282 0.1277 0.1550 n_refl.: 191138 remove outliers: r(all,work,free)=0.1282 0.1277 0.1550 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 402.814 384.143 0.489 0.963 0.269 13.296-10.522 99.01 99 1 0.2105 528.187 519.770 0.736 0.965 0.240 10.503-8.327 99.45 178 3 0.1766 565.118 561.971 0.889 0.965 0.198 8.318-6.595 100.00 360 8 0.1710 414.736 412.011 0.909 0.965 0.160 6.588-5.215 100.00 711 7 0.1534 381.101 373.544 0.888 0.965 0.160 5.214-4.128 98.38 1367 28 0.0897 557.435 555.098 0.976 0.965 0.049 4.126-3.266 94.74 2603 46 0.0833 508.132 504.244 1.043 0.966 0.014 3.266-2.585 99.86 5447 97 0.0924 342.774 340.295 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.340 1.037 0.966 0.000 2.046-1.619 99.39 21536 464 0.1092 153.054 151.371 1.054 0.966 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.411 1.047 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.174 1.024 0.965 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0362 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1550 | n_water=805 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1281 r_free=0.1555 | n_water=795 | time (s): 98.940 (total time: 101.710) Filter (q & B) r_work=0.1281 r_free=0.1554 | n_water=790 | time (s): 4.770 (total time: 106.480) Compute maps r_work=0.1281 r_free=0.1554 | n_water=790 | time (s): 1.650 (total time: 108.130) Filter (map) r_work=0.1308 r_free=0.1534 | n_water=649 | time (s): 5.220 (total time: 113.350) Find peaks r_work=0.1308 r_free=0.1534 | n_water=649 | time (s): 0.630 (total time: 113.980) Add new water r_work=0.1331 r_free=0.1564 | n_water=948 | time (s): 4.210 (total time: 118.190) Refine new water occ: r_work=0.1289 r_free=0.1522 adp: r_work=0.1277 r_free=0.1516 occ: r_work=0.1278 r_free=0.1515 adp: r_work=0.1272 r_free=0.1514 occ: r_work=0.1273 r_free=0.1513 adp: r_work=0.1271 r_free=0.1513 ADP+occupancy (water only), MIN, final r_work=0.1271 r_free=0.1513 r_work=0.1271 r_free=0.1513 | n_water=948 | time (s): 84.070 (total time: 202.260) Filter (q & B) r_work=0.1274 r_free=0.1515 | n_water=884 | time (s): 4.540 (total time: 206.800) Filter (dist only) r_work=0.1275 r_free=0.1515 | n_water=883 | time (s): 111.770 (total time: 318.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.610921 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 598.681586 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1257 0.1529 0.0272 0.041 1.1 16.5 0.0 0.3 0 11.305 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.29 2.72 2.047 15.201 598.682 0.015 12.35 15.23 2.88 2.424 15.253 598.682 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 68.21 16.36 1.21 515 3272 Protein: 5.40 40.44 10.99 1.21 0 2902 Water: 6.67 68.21 33.98 N/A 515 368 Other: 16.53 33.63 25.08 N/A 0 2 Chain A: 5.55 56.23 13.01 N/A 0 1624 Chain B: 5.40 68.21 12.84 N/A 0 1648 Chain S: 12.53 67.89 38.17 N/A 515 0 Histogram: Values Number of atoms 5.40 - 11.68 2063 11.68 - 17.96 705 17.96 - 24.24 255 24.24 - 30.52 209 30.52 - 36.81 185 36.81 - 43.09 160 43.09 - 49.37 111 49.37 - 55.65 50 55.65 - 61.93 38 61.93 - 68.21 11 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1523 r_work=0.1236 r_free=0.1524 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1524 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1517 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013503 | | target function (ls_wunit_k1) not normalized (work): 2529.061431 | | target function (ls_wunit_k1) not normalized (free): 102.099538 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1229 0.1517 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1625 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1436 0.1625 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1436 0.1433 0.1624 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1235 0.1526 n_refl.: 191138 remove outliers: r(all,work,free)=0.1241 0.1235 0.1526 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 0.3281 402.814 378.145 0.493 0.962 0.271 13.296-10.522 99.01 99 1 0.1920 528.187 520.231 0.755 0.963 0.218 10.503-8.327 99.45 178 3 0.1398 565.118 567.446 0.923 0.963 0.169 8.318-6.595 100.00 360 8 0.1550 414.736 414.368 0.935 0.963 0.150 6.588-5.215 100.00 711 7 0.1346 381.101 376.744 0.911 0.963 0.150 5.214-4.128 98.38 1367 28 0.0830 557.435 556.062 0.994 0.963 0.070 4.126-3.266 94.74 2603 46 0.0766 508.132 505.712 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0860 342.774 341.285 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0901 258.603 256.766 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.610 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1259 82.395 81.344 1.073 0.955 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.212 1.059 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0462 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1235 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1235 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1235 r_free=0.1526 | n_water=883 | time (s): 3.080 (total time: 3.080) Filter (dist) r_work=0.1237 r_free=0.1527 | n_water=877 | time (s): 115.560 (total time: 118.640) Filter (q & B) r_work=0.1238 r_free=0.1528 | n_water=873 | time (s): 4.760 (total time: 123.400) Compute maps r_work=0.1238 r_free=0.1528 | n_water=873 | time (s): 1.780 (total time: 125.180) Filter (map) r_work=0.1276 r_free=0.1524 | n_water=688 | time (s): 4.640 (total time: 129.820) Find peaks r_work=0.1276 r_free=0.1524 | n_water=688 | time (s): 0.600 (total time: 130.420) Add new water r_work=0.1298 r_free=0.1557 | n_water=1001 | time (s): 3.980 (total time: 134.400) Refine new water occ: r_work=0.1254 r_free=0.1514 adp: r_work=0.1254 r_free=0.1514 occ: r_work=0.1250 r_free=0.1511 adp: r_work=0.1249 r_free=0.1511 occ: r_work=0.1247 r_free=0.1508 adp: r_work=0.1247 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1247 r_free=0.1508 r_work=0.1247 r_free=0.1508 | n_water=1001 | time (s): 244.830 (total time: 379.230) Filter (q & B) r_work=0.1251 r_free=0.1516 | n_water=869 | time (s): 5.000 (total time: 384.230) Filter (dist only) r_work=0.1251 r_free=0.1516 | n_water=868 | time (s): 127.380 (total time: 511.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.703400 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.529758 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1238 0.1435 0.0197 0.035 1.1 6.8 0.0 0.0 0 0.852 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.35 1.97 1.935 14.517 16.530 3.940 12.31 13.93 1.62 2.201 14.434 16.530 3.897 Individual atomic B min max mean iso aniso Overall: 5.52 67.88 15.16 1.07 501 3271 Protein: 5.52 37.04 10.77 1.07 0 2902 Water: 6.71 67.88 29.83 N/A 501 367 Other: 14.21 29.37 21.79 N/A 0 2 Chain A: 5.52 55.51 12.80 N/A 0 1624 Chain B: 5.55 67.88 12.57 N/A 0 1647 Chain S: 14.58 63.08 31.33 N/A 501 0 Histogram: Values Number of atoms 5.52 - 11.76 2134 11.76 - 17.99 676 17.99 - 24.23 302 24.23 - 30.47 263 30.47 - 36.70 168 36.70 - 42.94 122 42.94 - 49.17 75 49.17 - 55.41 22 55.41 - 61.64 8 61.64 - 67.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1393 r_work=0.1231 r_free=0.1394 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1394 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1383 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891389 | | target function (ml) not normalized (work): 728845.503957 | | target function (ml) not normalized (free): 15219.109157 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1227 0.1383 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1442 0.1476 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1442 0.1476 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1436 0.1473 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1226 0.1223 0.1380 n_refl.: 191138 remove outliers: r(all,work,free)=0.1225 0.1222 0.1380 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3685 393.525 364.448 0.418 0.946 0.240 13.296-10.522 99.01 99 1 0.2436 528.187 506.795 0.702 0.947 0.207 10.503-8.327 98.35 176 3 0.2025 555.265 556.956 0.883 0.947 0.177 8.318-6.595 100.00 360 8 0.2156 414.736 409.919 0.897 0.947 0.127 6.588-5.215 100.00 711 7 0.1834 381.101 370.276 0.883 0.947 0.103 5.214-4.128 98.38 1367 28 0.1163 557.435 551.841 0.971 0.947 0.060 4.126-3.266 94.74 2603 46 0.1081 508.132 501.671 1.033 0.947 0.009 3.266-2.585 99.86 5447 97 0.1073 342.774 339.324 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0958 258.603 255.747 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.403 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.485 1.053 0.942 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.319 1.039 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0968 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1380 | n_water=868 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1222 r_free=0.1378 | n_water=865 | time (s): 103.970 (total time: 106.340) Filter (q & B) r_work=0.1223 r_free=0.1379 | n_water=853 | time (s): 4.910 (total time: 111.250) Compute maps r_work=0.1223 r_free=0.1379 | n_water=853 | time (s): 1.710 (total time: 112.960) Filter (map) r_work=0.1245 r_free=0.1388 | n_water=716 | time (s): 4.890 (total time: 117.850) Find peaks r_work=0.1245 r_free=0.1388 | n_water=716 | time (s): 0.660 (total time: 118.510) Add new water r_work=0.1257 r_free=0.1407 | n_water=964 | time (s): 4.730 (total time: 123.240) Refine new water occ: r_work=0.1211 r_free=0.1361 adp: r_work=0.1204 r_free=0.1357 occ: r_work=0.1202 r_free=0.1356 adp: r_work=0.1202 r_free=0.1356 occ: r_work=0.1202 r_free=0.1356 adp: r_work=0.1202 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1356 r_work=0.1202 r_free=0.1356 | n_water=964 | time (s): 179.960 (total time: 303.200) Filter (q & B) r_work=0.1208 r_free=0.1365 | n_water=830 | time (s): 4.700 (total time: 307.900) Filter (dist only) r_work=0.1208 r_free=0.1364 | n_water=829 | time (s): 107.260 (total time: 415.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.594919 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.220302 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 0.1364 0.0157 0.035 1.1 6.1 0.0 0.0 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.64 1.57 1.842 14.120 15.220 3.875 12.03 13.61 1.58 1.965 14.076 15.220 3.868 Individual atomic B min max mean iso aniso Overall: 5.51 67.45 14.79 1.00 462 3271 Protein: 5.51 33.74 10.67 1.00 0 2902 Water: 5.81 67.45 29.18 N/A 462 367 Other: 13.95 28.32 21.13 N/A 0 2 Chain A: 5.55 54.49 12.65 N/A 0 1624 Chain B: 5.51 67.45 12.47 N/A 0 1647 Chain S: 5.81 61.13 30.58 N/A 462 0 Histogram: Values Number of atoms 5.51 - 11.70 2123 11.70 - 17.90 719 17.90 - 24.09 291 24.09 - 30.28 239 30.28 - 36.48 147 36.48 - 42.67 114 42.67 - 48.87 69 48.87 - 55.06 23 55.06 - 61.25 7 61.25 - 67.45 1 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1362 r_work=0.1204 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1362 target_work(ml) = 3.868 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1359 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865808 | | target function (ml) not normalized (work): 724038.787576 | | target function (ml) not normalized (free): 15135.420263 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1359 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1433 0.1433 0.1458 n_refl.: 191134 remove outliers: r(all,work,free)=0.1433 0.1433 0.1458 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1426 0.1426 0.1454 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1359 n_refl.: 191134 remove outliers: r(all,work,free)=0.1203 0.1199 0.1359 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3759 356.185 322.757 0.412 0.945 0.245 13.296-10.522 98.02 98 1 0.2446 478.714 455.486 0.699 0.946 0.200 10.503-8.327 98.35 176 3 0.2131 502.578 494.256 0.865 0.947 0.177 8.318-6.595 100.00 360 8 0.2230 375.383 369.051 0.897 0.946 0.129 6.588-5.215 100.00 711 7 0.1899 344.940 334.540 0.884 0.946 0.107 5.214-4.128 98.38 1367 28 0.1213 504.542 498.852 0.975 0.947 0.080 4.126-3.266 94.74 2603 46 0.1114 459.917 453.553 1.035 0.947 0.000 3.266-2.585 99.86 5447 97 0.1080 310.249 307.065 1.023 0.946 0.000 2.585-2.046 97.45 10613 204 0.0938 234.065 231.581 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0920 138.531 137.237 1.058 0.945 0.000 1.619-1.281 98.00 42464 925 0.0992 74.577 73.865 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1664 40.007 38.347 1.040 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1359 | n_water=829 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1200 r_free=0.1359 | n_water=829 | time (s): 104.870 (total time: 107.350) Filter (q & B) r_work=0.1200 r_free=0.1359 | n_water=821 | time (s): 5.520 (total time: 112.870) Compute maps r_work=0.1200 r_free=0.1359 | n_water=821 | time (s): 2.160 (total time: 115.030) Filter (map) r_work=0.1220 r_free=0.1376 | n_water=710 | time (s): 4.220 (total time: 119.250) Find peaks r_work=0.1220 r_free=0.1376 | n_water=710 | time (s): 0.770 (total time: 120.020) Add new water r_work=0.1234 r_free=0.1396 | n_water=945 | time (s): 4.950 (total time: 124.970) Refine new water occ: r_work=0.1197 r_free=0.1355 adp: r_work=0.1197 r_free=0.1355 occ: r_work=0.1194 r_free=0.1353 adp: r_work=0.1194 r_free=0.1353 occ: r_work=0.1192 r_free=0.1352 adp: r_work=0.1192 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1352 r_work=0.1192 r_free=0.1352 | n_water=945 | time (s): 231.200 (total time: 356.170) Filter (q & B) r_work=0.1195 r_free=0.1358 | n_water=871 | time (s): 4.750 (total time: 360.920) Filter (dist only) r_work=0.1196 r_free=0.1358 | n_water=870 | time (s): 111.710 (total time: 472.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544019 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.545922 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1358 0.0159 0.036 1.1 7.8 0.0 0.0 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.58 1.59 1.795 14.113 14.546 3.766 12.05 13.65 1.60 1.899 14.074 14.546 3.764 Individual atomic B min max mean iso aniso Overall: 5.56 66.97 14.89 0.94 505 3269 Protein: 5.56 31.77 10.58 0.94 0 2902 Water: 6.04 66.97 29.23 N/A 505 365 Other: 13.80 26.72 20.26 N/A 0 2 Chain A: 5.56 53.36 12.51 N/A 0 1623 Chain B: 5.58 66.97 12.34 N/A 0 1646 Chain S: 6.04 61.22 30.84 N/A 505 0 Histogram: Values Number of atoms 5.56 - 11.70 2139 11.70 - 17.84 718 17.84 - 23.98 287 23.98 - 30.12 235 30.12 - 36.27 176 36.27 - 42.41 117 42.41 - 48.55 71 48.55 - 54.69 22 54.69 - 60.83 7 60.83 - 66.97 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1365 r_work=0.1205 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1365 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762883 | | target function (ml) not normalized (work): 704757.850126 | | target function (ml) not normalized (free): 14745.876546 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1366 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1428 0.1427 0.1471 n_refl.: 191133 remove outliers: r(all,work,free)=0.1428 0.1427 0.1471 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1420 0.1419 0.1466 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1363 n_refl.: 191133 remove outliers: r(all,work,free)=0.1204 0.1201 0.1363 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3735 356.953 315.586 0.393 0.947 0.223 13.296-10.522 97.03 97 1 0.2403 480.987 457.041 0.695 0.949 0.180 10.503-8.327 98.35 176 3 0.2125 502.578 494.325 0.864 0.949 0.160 8.318-6.595 100.00 360 8 0.2196 375.383 368.789 0.892 0.949 0.120 6.588-5.215 100.00 711 7 0.1905 344.940 334.409 0.884 0.949 0.094 5.214-4.128 98.38 1367 28 0.1200 504.542 499.013 0.972 0.949 0.050 4.126-3.266 94.74 2603 46 0.1140 459.917 453.519 1.036 0.949 0.014 3.266-2.585 99.86 5447 97 0.1099 310.249 307.126 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0949 234.065 231.563 1.034 0.948 0.000 2.046-1.619 99.39 21536 464 0.0925 138.531 137.225 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0984 74.577 73.863 1.055 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1655 40.007 38.343 1.043 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1293 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1363 | n_water=870 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1201 r_free=0.1363 | n_water=870 | time (s): 113.470 (total time: 116.000) Filter (q & B) r_work=0.1201 r_free=0.1364 | n_water=861 | time (s): 5.100 (total time: 121.100) Compute maps r_work=0.1201 r_free=0.1364 | n_water=861 | time (s): 1.950 (total time: 123.050) Filter (map) r_work=0.1223 r_free=0.1373 | n_water=737 | time (s): 4.320 (total time: 127.370) Find peaks r_work=0.1223 r_free=0.1373 | n_water=737 | time (s): 0.660 (total time: 128.030) Add new water r_work=0.1233 r_free=0.1383 | n_water=940 | time (s): 4.040 (total time: 132.070) Refine new water occ: r_work=0.1199 r_free=0.1349 adp: r_work=0.1199 r_free=0.1348 occ: r_work=0.1197 r_free=0.1348 adp: r_work=0.1197 r_free=0.1347 occ: r_work=0.1195 r_free=0.1347 adp: r_work=0.1195 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1347 r_work=0.1195 r_free=0.1347 | n_water=940 | time (s): 196.770 (total time: 328.840) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=876 | time (s): 4.670 (total time: 333.510) Filter (dist only) r_work=0.1199 r_free=0.1356 | n_water=875 | time (s): 112.680 (total time: 446.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570935 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.708398 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1361 0.0159 0.037 1.1 6.5 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.61 1.59 1.755 13.992 14.708 3.763 12.02 13.63 1.62 1.870 13.950 14.708 3.759 Individual atomic B min max mean iso aniso Overall: 5.57 65.92 14.78 0.90 510 3269 Protein: 5.57 29.36 10.48 0.90 0 2902 Water: 6.00 65.92 29.01 N/A 510 365 Other: 13.84 23.91 18.88 N/A 0 2 Chain A: 5.64 51.09 12.37 N/A 0 1623 Chain B: 5.57 65.92 12.21 N/A 0 1646 Chain S: 6.00 61.53 30.73 N/A 510 0 Histogram: Values Number of atoms 5.57 - 11.60 2117 11.60 - 17.64 770 17.64 - 23.67 273 23.67 - 29.71 224 29.71 - 35.74 159 35.74 - 41.78 132 41.78 - 47.81 69 47.81 - 53.85 26 53.85 - 59.88 6 59.88 - 65.92 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1363 r_work=0.1202 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1364 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1364 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757996 | | target function (ml) not normalized (work): 703835.037379 | | target function (ml) not normalized (free): 14732.984274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1364 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1487 n_refl.: 191131 remove outliers: r(all,work,free)=0.1407 0.1405 0.1487 n_refl.: 191131 overall B=-0.22 to atoms: r(all,work,free)=0.1370 0.1368 0.1465 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1366 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1366 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3743 356.953 319.594 0.405 0.950 0.217 13.296-10.522 97.03 97 1 0.2366 480.987 461.241 0.713 0.952 0.163 10.503-8.327 98.35 176 3 0.2173 502.578 493.959 0.883 0.952 0.137 8.318-6.595 100.00 360 8 0.2200 375.383 369.060 0.909 0.952 0.110 6.588-5.215 100.00 711 7 0.1911 344.940 334.816 0.905 0.952 0.092 5.214-4.128 98.38 1367 28 0.1218 504.542 498.535 0.996 0.952 0.090 4.126-3.266 94.74 2603 46 0.1157 459.917 453.047 1.058 0.952 0.005 3.266-2.585 99.86 5447 97 0.1109 310.249 306.908 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0950 234.065 231.535 1.048 0.951 0.000 2.046-1.619 99.39 21536 464 0.0915 138.531 137.228 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0972 74.577 73.877 1.055 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.007 38.341 1.027 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0491 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1366 | n_water=875 | time (s): 3.110 (total time: 3.110) Filter (dist) r_work=0.1199 r_free=0.1366 | n_water=875 | time (s): 104.160 (total time: 107.270) Filter (q & B) r_work=0.1199 r_free=0.1366 | n_water=867 | time (s): 4.820 (total time: 112.090) Compute maps r_work=0.1199 r_free=0.1366 | n_water=867 | time (s): 1.770 (total time: 113.860) Filter (map) r_work=0.1220 r_free=0.1369 | n_water=754 | time (s): 4.180 (total time: 118.040) Find peaks r_work=0.1220 r_free=0.1369 | n_water=754 | time (s): 0.750 (total time: 118.790) Add new water r_work=0.1231 r_free=0.1383 | n_water=971 | time (s): 4.240 (total time: 123.030) Refine new water occ: r_work=0.1196 r_free=0.1355 adp: r_work=0.1196 r_free=0.1356 occ: r_work=0.1194 r_free=0.1354 adp: r_work=0.1194 r_free=0.1354 occ: r_work=0.1192 r_free=0.1353 adp: r_work=0.1192 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1353 r_work=0.1192 r_free=0.1353 | n_water=971 | time (s): 201.210 (total time: 324.240) Filter (q & B) r_work=0.1196 r_free=0.1358 | n_water=896 | time (s): 4.680 (total time: 328.920) Filter (dist only) r_work=0.1196 r_free=0.1358 | n_water=895 | time (s): 111.730 (total time: 440.650) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.518629 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.774017 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 0.1367 0.0166 0.038 1.1 8.4 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.67 1.66 1.719 13.722 14.774 3.760 12.02 13.68 1.65 1.772 13.701 14.774 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 64.56 14.58 0.88 530 3269 Protein: 5.39 28.45 10.24 0.88 0 2902 Water: 5.77 64.56 28.64 N/A 530 365 Other: 13.67 22.09 17.88 N/A 0 2 Chain A: 5.43 50.49 12.09 N/A 0 1623 Chain B: 5.39 64.56 11.94 N/A 0 1646 Chain S: 5.77 61.61 30.41 N/A 530 0 Histogram: Values Number of atoms 5.39 - 11.31 2093 11.31 - 17.23 790 17.23 - 23.14 274 23.14 - 29.06 218 29.06 - 34.98 178 34.98 - 40.90 134 40.90 - 46.81 74 46.81 - 52.73 27 52.73 - 58.65 7 58.65 - 64.56 4 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1368 r_work=0.1203 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1368 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1369 target_work(ml) = 3.757 | | 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.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756512 | | target function (ml) not normalized (work): 703557.069602 | | target function (ml) not normalized (free): 14733.363213 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1201 0.1369 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1375 0.1374 0.1471 n_refl.: 191131 remove outliers: r(all,work,free)=0.1375 0.1374 0.1471 n_refl.: 191131 overall B=0.06 to atoms: r(all,work,free)=0.1383 0.1381 0.1475 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3835 356.953 318.162 0.383 0.975 0.202 13.296-10.522 97.03 97 1 0.2388 480.987 461.522 0.694 0.977 0.151 10.503-8.327 98.35 176 3 0.2180 502.578 493.302 0.867 0.977 0.120 8.318-6.595 100.00 360 8 0.2198 375.383 368.642 0.892 0.977 0.097 6.588-5.215 100.00 711 7 0.1943 344.940 334.471 0.889 0.977 0.080 5.214-4.128 98.38 1367 28 0.1231 504.542 497.989 0.978 0.978 0.049 4.126-3.266 94.74 2603 46 0.1174 459.917 452.224 1.041 0.979 0.009 3.266-2.585 99.86 5447 97 0.1122 310.249 306.524 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0956 234.065 231.423 1.031 0.981 0.000 2.046-1.619 99.39 21536 464 0.0908 138.531 137.156 1.048 0.983 0.000 1.619-1.281 98.00 42464 925 0.0949 74.577 73.919 1.037 0.987 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.007 38.315 1.003 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0614 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1358 | n_water=895 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1193 r_free=0.1357 | n_water=894 | time (s): 110.790 (total time: 113.940) Filter (q & B) r_work=0.1193 r_free=0.1359 | n_water=880 | time (s): 4.240 (total time: 118.180) Compute maps r_work=0.1193 r_free=0.1359 | n_water=880 | time (s): 1.730 (total time: 119.910) Filter (map) r_work=0.1215 r_free=0.1359 | n_water=759 | time (s): 4.460 (total time: 124.370) Find peaks r_work=0.1215 r_free=0.1359 | n_water=759 | time (s): 0.530 (total time: 124.900) Add new water r_work=0.1224 r_free=0.1374 | n_water=986 | time (s): 4.150 (total time: 129.050) Refine new water occ: r_work=0.1190 r_free=0.1348 adp: r_work=0.1191 r_free=0.1348 occ: r_work=0.1188 r_free=0.1348 adp: r_work=0.1188 r_free=0.1347 occ: r_work=0.1186 r_free=0.1347 adp: r_work=0.1186 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1347 r_work=0.1186 r_free=0.1347 | n_water=986 | time (s): 246.810 (total time: 375.860) Filter (q & B) r_work=0.1191 r_free=0.1354 | n_water=902 | time (s): 4.810 (total time: 380.670) Filter (dist only) r_work=0.1191 r_free=0.1354 | n_water=900 | time (s): 114.300 (total time: 494.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.506764 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.137941 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 0.1195 0.1359 0.0164 0.038 1.1 7.0 0.0 0.3 0 0.753 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.59 1.64 1.677 13.716 14.138 3.755 11.96 13.62 1.66 1.690 13.705 14.138 3.755 Individual atomic B min max mean iso aniso Overall: 5.48 64.08 14.61 0.87 535 3269 Protein: 5.48 28.17 10.31 0.87 0 2902 Water: 5.90 64.08 28.47 N/A 535 365 Other: 13.72 22.09 17.91 N/A 0 2 Chain A: 5.56 50.30 12.12 N/A 0 1623 Chain B: 5.48 64.08 11.98 N/A 0 1646 Chain S: 5.90 61.81 30.24 N/A 535 0 Histogram: Values Number of atoms 5.48 - 11.34 2080 11.34 - 17.20 808 17.20 - 23.06 271 23.06 - 28.92 215 28.92 - 34.78 183 34.78 - 40.64 133 40.64 - 46.50 77 46.50 - 52.36 25 52.36 - 58.22 8 58.22 - 64.08 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1362 r_work=0.1196 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1362 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1365 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754169 | | target function (ml) not normalized (work): 703118.377310 | | target function (ml) not normalized (free): 14727.570603 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1364 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1392 0.1391 0.1483 n_refl.: 191131 remove outliers: r(all,work,free)=0.1392 0.1391 0.1483 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1394 0.1393 0.1484 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1363 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1194 0.1363 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3841 356.953 317.587 0.404 0.911 0.195 13.296-10.522 97.03 97 1 0.2391 480.987 461.251 0.737 0.913 0.137 10.503-8.327 98.35 176 3 0.2206 502.578 492.774 0.924 0.913 0.110 8.318-6.595 100.00 360 8 0.2215 375.383 367.830 0.950 0.913 0.090 6.588-5.215 100.00 711 7 0.1979 344.940 334.145 0.948 0.913 0.073 5.214-4.128 98.38 1367 28 0.1244 504.542 497.662 1.047 0.914 0.044 4.126-3.266 94.74 2603 46 0.1176 459.917 452.261 1.114 0.915 0.009 3.266-2.585 99.86 5447 97 0.1131 310.249 306.545 1.095 0.916 0.000 2.585-2.046 97.45 10613 204 0.0957 234.065 231.396 1.104 0.917 0.000 2.046-1.619 99.39 21536 464 0.0909 138.531 137.165 1.122 0.920 0.000 1.619-1.281 98.00 42464 925 0.0944 74.577 73.928 1.112 0.924 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.007 38.300 1.079 0.932 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0214 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1363 | n_water=900 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1194 r_free=0.1363 | n_water=900 | time (s): 107.740 (total time: 110.430) Filter (q & B) r_work=0.1194 r_free=0.1362 | n_water=889 | time (s): 4.460 (total time: 114.890) Compute maps r_work=0.1194 r_free=0.1362 | n_water=889 | time (s): 2.290 (total time: 117.180) Filter (map) r_work=0.1218 r_free=0.1366 | n_water=774 | time (s): 4.660 (total time: 121.840) Find peaks r_work=0.1218 r_free=0.1366 | n_water=774 | time (s): 0.880 (total time: 122.720) Add new water r_work=0.1226 r_free=0.1378 | n_water=996 | time (s): 4.260 (total time: 126.980) Refine new water occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1191 r_free=0.1347 occ: r_work=0.1189 r_free=0.1345 adp: r_work=0.1189 r_free=0.1346 occ: r_work=0.1187 r_free=0.1344 adp: r_work=0.1187 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1345 r_work=0.1187 r_free=0.1345 | n_water=996 | time (s): 222.660 (total time: 349.640) Filter (q & B) r_work=0.1192 r_free=0.1355 | n_water=902 | time (s): 4.650 (total time: 354.290) Filter (dist only) r_work=0.1192 r_free=0.1355 | n_water=900 | time (s): 117.120 (total time: 471.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.471444 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.295831 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 0.1359 0.0163 0.038 1.1 8.4 0.0 0.3 0 0.736 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.59 1.63 1.677 13.718 14.296 3.755 11.96 13.59 1.63 1.691 13.714 14.296 3.753 Individual atomic B min max mean iso aniso Overall: 5.54 63.06 14.60 0.86 535 3269 Protein: 5.54 27.99 10.33 0.86 0 2902 Water: 5.99 63.06 28.38 N/A 535 365 Other: 13.77 22.02 17.89 N/A 0 2 Chain A: 5.59 49.86 12.11 N/A 0 1623 Chain B: 5.54 63.06 11.98 N/A 0 1646 Chain S: 5.99 62.09 30.23 N/A 535 0 Histogram: Values Number of atoms 5.54 - 11.29 2061 11.29 - 17.04 826 17.04 - 22.80 273 22.80 - 28.55 204 28.55 - 34.30 182 34.30 - 40.05 135 40.05 - 45.80 78 45.80 - 51.56 32 51.56 - 57.31 9 57.31 - 63.06 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1359 r_work=0.1196 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1360 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752855 | | target function (ml) not normalized (work): 702872.165175 | | target function (ml) not normalized (free): 14721.238083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1194 0.1360 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1486 n_refl.: 191131 remove outliers: r(all,work,free)=0.1402 0.1401 0.1486 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1402 0.1401 0.1486 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3851 356.953 315.897 0.401 0.913 0.197 13.296-10.522 97.03 97 1 0.2379 480.987 461.698 0.736 0.914 0.142 10.503-8.327 98.35 176 3 0.2225 502.578 493.038 0.919 0.915 0.111 8.318-6.595 100.00 360 8 0.2204 375.383 367.924 0.948 0.915 0.093 6.588-5.215 100.00 711 7 0.1971 344.940 334.362 0.945 0.915 0.080 5.214-4.128 98.38 1367 28 0.1251 504.542 497.715 1.044 0.916 0.044 4.126-3.266 94.74 2603 46 0.1179 459.917 452.322 1.112 0.917 0.005 3.266-2.585 99.86 5447 97 0.1131 310.249 306.549 1.093 0.918 0.000 2.585-2.046 97.45 10613 204 0.0961 234.065 231.406 1.102 0.920 0.000 2.046-1.619 99.39 21536 464 0.0909 138.531 137.167 1.121 0.923 0.000 1.619-1.281 98.00 42464 925 0.0940 74.577 73.929 1.112 0.928 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.007 38.288 1.080 0.937 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0052 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1194 r_free=0.1359 After: r_work=0.1194 r_free=0.1360 ================================== NQH flips ================================== r_work=0.1194 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1360 | n_water=900 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1194 r_free=0.1360 | n_water=900 | time (s): 108.820 (total time: 111.390) Filter (q & B) r_work=0.1196 r_free=0.1359 | n_water=885 | time (s): 3.930 (total time: 115.320) Compute maps r_work=0.1196 r_free=0.1359 | n_water=885 | time (s): 1.820 (total time: 117.140) Filter (map) r_work=0.1218 r_free=0.1365 | n_water=775 | time (s): 4.430 (total time: 121.570) Find peaks r_work=0.1218 r_free=0.1365 | n_water=775 | time (s): 0.550 (total time: 122.120) Add new water r_work=0.1226 r_free=0.1379 | n_water=1003 | time (s): 4.730 (total time: 126.850) Refine new water occ: r_work=0.1192 r_free=0.1349 adp: r_work=0.1192 r_free=0.1350 occ: r_work=0.1190 r_free=0.1348 adp: r_work=0.1190 r_free=0.1348 occ: r_work=0.1189 r_free=0.1347 adp: r_work=0.1189 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1347 r_work=0.1189 r_free=0.1347 | n_water=1003 | time (s): 245.990 (total time: 372.840) Filter (q & B) r_work=0.1193 r_free=0.1353 | n_water=903 | time (s): 4.790 (total time: 377.630) Filter (dist only) r_work=0.1193 r_free=0.1353 | n_water=901 | time (s): 115.890 (total time: 493.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.503040 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.555886 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 0.1358 0.0162 0.038 1.2 10.9 0.0 0.3 0 0.752 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.58 1.62 1.675 13.699 14.556 3.755 11.95 13.60 1.65 1.668 13.700 14.556 3.753 Individual atomic B min max mean iso aniso Overall: 5.54 62.64 14.58 0.86 536 3269 Protein: 5.54 28.03 10.35 0.86 0 2902 Water: 6.00 62.64 28.19 N/A 536 365 Other: 13.81 22.01 17.91 N/A 0 2 Chain A: 5.66 49.71 12.11 N/A 0 1623 Chain B: 5.54 62.64 11.98 N/A 0 1646 Chain S: 6.00 62.16 30.03 N/A 536 0 Histogram: Values Number of atoms 5.54 - 11.25 2043 11.25 - 16.96 842 16.96 - 22.67 277 22.67 - 28.38 203 28.38 - 34.09 192 34.09 - 39.80 124 39.80 - 45.51 78 45.51 - 51.22 32 51.22 - 56.93 10 56.93 - 62.64 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1360 r_work=0.1195 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1360 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1360 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753215 | | target function (ml) not normalized (work): 702939.723337 | | target function (ml) not normalized (free): 14723.256885 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7399 127 0.1374 0.1507 5.7036 5.8032| | 2: 2.94 - 2.33 1.00 7339 128 0.1074 0.1376 5.0943 5.1943| | 3: 2.33 - 2.04 0.96 6939 150 0.0903 0.1169 4.6553 4.7358| | 4: 2.04 - 1.85 1.00 7170 155 0.0897 0.1039 4.3866 4.5431| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0990 4.1481 4.2464| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1080 3.9436 4.0735| | 7: 1.62 - 1.54 0.99 7104 148 0.0890 0.0960 3.7958 3.929| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1297 3.6933 3.893| | 9: 1.47 - 1.41 0.98 6938 155 0.0918 0.1104 3.6118 3.7357| | 10: 1.41 - 1.36 0.99 7022 150 0.0971 0.1161 3.5493 3.6593| | 11: 1.36 - 1.32 0.99 6997 151 0.0990 0.1136 3.4826 3.6002| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1128 3.4581 3.5816| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1255 3.4365 3.5724| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1580 3.4318 3.6801| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1231 3.4456 3.4847| | 16: 1.19 - 1.17 0.93 6604 132 0.1248 0.1526 3.4622 3.6456| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1217 3.4308 3.4361| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1702 3.4365 3.5335| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1770 3.419 3.6009| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1589 3.4093 3.4376| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2141 3.4177 3.5054| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1956 3.4121 3.4124| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2021 3.4325 3.4861| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2258 3.4351 3.5107| | 25: 1.02 - 1.01 0.93 6552 130 0.2610 0.2514 3.4485 3.5226| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2869 3.4152 3.4234| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2794 3.468 3.395| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7399 127 0.93 12.22 1.00 0.96 12076.42| | 2: 2.94 - 2.33 7339 128 0.92 13.21 0.99 0.95 5406.45| | 3: 2.33 - 2.04 6939 150 0.96 7.57 1.01 0.95 1681.06| | 4: 2.04 - 1.85 7170 155 0.96 7.53 1.00 0.95 986.47| | 5: 1.85 - 1.72 7113 159 0.96 8.03 1.00 0.96 628.26| | 6: 1.72 - 1.62 7102 142 0.96 8.02 1.00 0.96 440.62| | 7: 1.62 - 1.54 7104 148 0.96 8.09 1.01 0.97 333.28| | 8: 1.54 - 1.47 6798 152 0.96 8.14 1.01 0.97 273.58| | 9: 1.47 - 1.41 6938 155 0.96 8.30 1.00 0.98 225.25| | 10: 1.41 - 1.36 7022 150 0.96 8.81 1.00 0.97 199.33| | 11: 1.36 - 1.32 6997 151 0.96 8.92 0.99 0.96 174.64| | 12: 1.32 - 1.28 6975 149 0.96 9.04 0.98 0.95 161.84| | 13: 1.28 - 1.25 6907 166 0.96 9.59 1.01 0.96 159.16| | 14: 1.25 - 1.22 7015 112 0.95 10.72 1.01 0.97 163.07| | 15: 1.22 - 1.19 6956 137 0.95 11.18 1.01 0.98 165.45| | 16: 1.19 - 1.17 6604 132 0.95 11.35 1.01 0.96 158.62| | 17: 1.17 - 1.14 6940 135 0.94 12.19 1.01 0.96 152.74| | 18: 1.14 - 1.12 6875 142 0.94 12.75 1.01 0.95 147.56| | 19: 1.12 - 1.10 6948 106 0.93 14.19 1.00 0.95 151.65| | 20: 1.10 - 1.08 6884 147 0.92 15.26 1.00 0.94 150.83| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.55| | 22: 1.07 - 1.05 6836 135 0.89 18.32 0.99 0.93 154.91| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 164.68| | 24: 1.03 - 1.02 6784 133 0.85 23.21 0.99 0.93 179.17| | 25: 1.02 - 1.01 6552 130 0.83 25.19 0.98 0.90 182.24| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.89 176.63| | 27: 0.99 - 0.98 6647 131 0.82 26.28 0.99 0.87 160.67| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.56 max = 12076.42 mean = 968.68| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.31| |phase err.(test): min = 0.00 max = 88.93 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1493 n_refl.: 191131 remove outliers: r(all,work,free)=0.1411 0.1410 0.1493 n_refl.: 191131 overall B=-0.05 to atoms: r(all,work,free)=0.1403 0.1402 0.1488 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191131 remove outliers: r(all,work,free)=0.1197 0.1194 0.1358 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3874 356.953 315.249 0.359 0.995 0.201 13.296-10.522 97.03 97 1 0.2408 480.987 461.105 0.659 0.996 0.149 10.503-8.327 98.35 176 3 0.2192 502.578 493.171 0.823 0.997 0.116 8.318-6.595 100.00 360 8 0.2173 375.383 367.957 0.847 0.996 0.093 6.588-5.215 100.00 711 7 0.1972 344.940 334.011 0.846 0.997 0.077 5.214-4.128 98.38 1367 28 0.1260 504.542 497.930 0.934 0.998 0.034 4.126-3.266 94.74 2603 46 0.1182 459.917 452.305 0.996 0.999 0.000 3.266-2.585 99.86 5447 97 0.1126 310.249 306.598 0.979 1.000 0.000 2.585-2.046 97.45 10613 204 0.0962 234.065 231.433 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0908 138.531 137.162 1.002 1.007 0.000 1.619-1.281 98.00 42464 925 0.0942 74.577 73.932 0.993 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.007 38.284 0.962 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0108 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2033 0.1984 0.082 5.271 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1922 0.082 5.271 5.2 78.1 14.6 805 0.000 1_settarget: 0.1797 0.1922 0.082 5.271 5.2 78.1 14.6 805 0.000 1_nqh: 0.1797 0.1922 0.082 5.271 5.2 78.1 14.6 805 0.000 1_weight: 0.1797 0.1922 0.082 5.271 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1272 0.1506 0.040 1.159 5.2 78.1 14.6 805 0.158 1_adp: 0.1298 0.1574 0.040 1.159 5.2 73.1 15.0 805 0.158 1_regHadp: 0.1297 0.1568 0.040 1.159 5.2 73.1 15.0 805 0.158 1_occ: 0.1283 0.1558 0.040 1.159 5.2 73.1 15.0 805 0.158 2_bss: 0.1277 0.1550 0.040 1.159 5.4 73.2 15.2 805 0.158 2_settarget: 0.1277 0.1550 0.040 1.159 5.4 73.2 15.2 805 0.158 2_updatecdl: 0.1277 0.1550 0.040 1.170 5.4 73.2 15.2 805 0.158 2_nqh: 0.1277 0.1550 0.040 1.170 5.4 73.2 15.2 805 0.158 2_sol: 0.1275 0.1515 0.040 1.170 5.4 73.2 16.3 883 n/a 2_weight: 0.1275 0.1515 0.040 1.170 5.4 73.2 16.3 883 n/a 2_xyzrec: 0.1257 0.1529 0.041 1.124 5.4 73.2 16.3 883 n/a 2_adp: 0.1235 0.1523 0.041 1.124 5.4 68.2 16.4 883 n/a 2_regHadp: 0.1236 0.1524 0.041 1.124 5.4 68.2 16.4 883 n/a 2_occ: 0.1229 0.1517 0.041 1.124 5.4 68.2 16.4 883 n/a 3_bss: 0.1235 0.1526 0.041 1.124 5.4 68.2 16.3 883 n/a 3_settarget: 0.1235 0.1526 0.041 1.124 5.4 68.2 16.3 883 n/a 3_updatecdl: 0.1235 0.1526 0.041 1.129 5.4 68.2 16.3 883 n/a 3_nqh: 0.1235 0.1526 0.041 1.129 5.4 68.2 16.3 883 n/a 3_sol: 0.1251 0.1516 0.041 1.129 5.4 68.2 15.3 868 n/a 3_weight: 0.1251 0.1516 0.041 1.129 5.4 68.2 15.3 868 n/a 3_xyzrec: 0.1238 0.1435 0.035 1.105 5.4 68.2 15.3 868 n/a 3_adp: 0.1231 0.1393 0.035 1.105 5.5 67.9 15.2 868 n/a 3_regHadp: 0.1231 0.1394 0.035 1.105 5.5 67.9 15.2 868 n/a 3_occ: 0.1227 0.1383 0.035 1.105 5.5 67.9 15.2 868 n/a 4_bss: 0.1222 0.1380 0.035 1.105 5.5 67.9 15.1 868 n/a 4_settarget: 0.1222 0.1380 0.035 1.105 5.5 67.9 15.1 868 n/a 4_updatecdl: 0.1222 0.1380 0.035 1.106 5.5 67.9 15.1 868 n/a 4_nqh: 0.1222 0.1380 0.035 1.106 5.5 67.9 15.1 868 n/a 4_sol: 0.1208 0.1364 0.035 1.106 5.5 67.9 14.9 829 n/a 4_weight: 0.1208 0.1364 0.035 1.106 5.5 67.9 14.9 829 n/a 4_xyzrec: 0.1207 0.1364 0.035 1.132 5.5 67.9 14.9 829 n/a 4_adp: 0.1203 0.1362 0.035 1.132 5.5 67.4 14.8 829 n/a 4_regHadp: 0.1204 0.1362 0.035 1.132 5.5 67.4 14.8 829 n/a 4_occ: 0.1201 0.1359 0.035 1.132 5.5 67.4 14.8 829 n/a 5_bss: 0.1200 0.1359 0.035 1.132 5.5 67.4 14.8 829 n/a 5_settarget: 0.1200 0.1359 0.035 1.132 5.5 67.4 14.8 829 n/a 5_updatecdl: 0.1200 0.1359 0.035 1.132 5.5 67.4 14.8 829 n/a 5_nqh: 0.1200 0.1359 0.035 1.132 5.5 67.4 14.8 829 n/a 5_sol: 0.1196 0.1358 0.035 1.132 5.5 67.4 15.0 870 n/a 5_weight: 0.1196 0.1358 0.035 1.132 5.5 67.4 15.0 870 n/a 5_xyzrec: 0.1199 0.1358 0.036 1.127 5.5 67.4 15.0 870 n/a 5_adp: 0.1205 0.1365 0.036 1.127 5.6 67.0 14.9 870 n/a 5_regHadp: 0.1205 0.1365 0.036 1.127 5.6 67.0 14.9 870 n/a 5_occ: 0.1203 0.1366 0.036 1.127 5.6 67.0 14.9 870 n/a 6_bss: 0.1201 0.1363 0.036 1.127 5.5 66.9 14.8 870 n/a 6_settarget: 0.1201 0.1363 0.036 1.127 5.5 66.9 14.8 870 n/a 6_updatecdl: 0.1201 0.1363 0.036 1.128 5.5 66.9 14.8 870 n/a 6_nqh: 0.1201 0.1363 0.036 1.128 5.5 66.9 14.8 870 n/a 6_sol: 0.1199 0.1356 0.036 1.128 5.5 66.9 14.9 875 n/a 6_weight: 0.1199 0.1356 0.036 1.128 5.5 66.9 14.9 875 n/a 6_xyzrec: 0.1202 0.1361 0.037 1.127 5.5 66.9 14.9 875 n/a 6_adp: 0.1202 0.1363 0.037 1.127 5.6 65.9 14.8 875 n/a 6_regHadp: 0.1202 0.1364 0.037 1.127 5.6 65.9 14.8 875 n/a 6_occ: 0.1200 0.1364 0.037 1.127 5.6 65.9 14.8 875 n/a 7_bss: 0.1199 0.1366 0.037 1.127 5.3 65.7 14.6 875 n/a 7_settarget: 0.1199 0.1366 0.037 1.127 5.3 65.7 14.6 875 n/a 7_updatecdl: 0.1199 0.1366 0.037 1.127 5.3 65.7 14.6 875 n/a 7_nqh: 0.1199 0.1366 0.037 1.127 5.3 65.7 14.6 875 n/a 7_sol: 0.1196 0.1358 0.037 1.127 5.3 65.7 14.6 895 n/a 7_weight: 0.1196 0.1358 0.037 1.127 5.3 65.7 14.6 895 n/a 7_xyzrec: 0.1201 0.1367 0.038 1.124 5.3 65.7 14.6 895 n/a 7_adp: 0.1203 0.1368 0.038 1.124 5.4 64.6 14.6 895 n/a 7_regHadp: 0.1203 0.1368 0.038 1.124 5.4 64.6 14.6 895 n/a 7_occ: 0.1201 0.1369 0.038 1.124 5.4 64.6 14.6 895 n/a 8_bss: 0.1193 0.1358 0.038 1.124 5.4 64.6 14.6 895 n/a 8_settarget: 0.1193 0.1358 0.038 1.124 5.4 64.6 14.6 895 n/a 8_updatecdl: 0.1193 0.1358 0.038 1.124 5.4 64.6 14.6 895 n/a 8_nqh: 0.1193 0.1358 0.038 1.124 5.4 64.6 14.6 895 n/a 8_sol: 0.1191 0.1354 0.038 1.124 5.4 64.6 14.6 900 n/a 8_weight: 0.1191 0.1354 0.038 1.124 5.4 64.6 14.6 900 n/a 8_xyzrec: 0.1195 0.1359 0.038 1.114 5.4 64.6 14.6 900 n/a 8_adp: 0.1196 0.1362 0.038 1.114 5.5 64.1 14.6 900 n/a 8_regHadp: 0.1196 0.1362 0.038 1.114 5.5 64.1 14.6 900 n/a 8_occ: 0.1195 0.1365 0.038 1.114 5.5 64.1 14.6 900 n/a 9_bss: 0.1194 0.1363 0.038 1.114 5.5 64.1 14.6 900 n/a 9_settarget: 0.1194 0.1363 0.038 1.114 5.5 64.1 14.6 900 n/a 9_updatecdl: 0.1194 0.1363 0.038 1.114 5.5 64.1 14.6 900 n/a 9_nqh: 0.1194 0.1363 0.038 1.114 5.5 64.1 14.6 900 n/a 9_sol: 0.1192 0.1355 0.038 1.114 5.5 64.1 14.6 900 n/a 9_weight: 0.1192 0.1355 0.038 1.114 5.5 64.1 14.6 900 n/a 9_xyzrec: 0.1196 0.1359 0.038 1.108 5.5 64.1 14.6 900 n/a 9_adp: 0.1196 0.1359 0.038 1.108 5.5 63.1 14.6 900 n/a 9_regHadp: 0.1196 0.1359 0.038 1.108 5.5 63.1 14.6 900 n/a 9_occ: 0.1194 0.1360 0.038 1.108 5.5 63.1 14.6 900 n/a 10_bss: 0.1194 0.1359 0.038 1.108 5.5 63.1 14.6 900 n/a 10_settarget: 0.1194 0.1359 0.038 1.108 5.5 63.1 14.6 900 n/a 10_updatecdl: 0.1194 0.1359 0.038 1.108 5.5 63.1 14.6 900 n/a 10_setrh: 0.1194 0.1360 0.038 1.108 5.5 63.1 14.6 900 n/a 10_nqh: 0.1194 0.1360 0.038 1.108 5.5 63.1 14.6 900 n/a 10_sol: 0.1193 0.1353 0.038 1.108 5.5 63.1 14.6 901 n/a 10_weight: 0.1193 0.1353 0.038 1.108 5.5 63.1 14.6 901 n/a 10_xyzrec: 0.1196 0.1358 0.038 1.162 5.5 63.1 14.6 901 n/a 10_adp: 0.1195 0.1360 0.038 1.162 5.5 62.6 14.6 901 n/a 10_regHadp: 0.1195 0.1360 0.038 1.162 5.5 62.6 14.6 901 n/a 10_occ: 0.1194 0.1360 0.038 1.162 5.5 62.6 14.6 901 n/a end: 0.1194 0.1358 0.038 1.162 5.5 62.6 14.5 901 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4021785_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4021785_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.7700 Refinement macro-cycles (run) : 11799.9100 Write final files (write_after_run_outputs) : 156.8600 Total : 11962.5400 Total CPU time: 3.33 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:36:36 PST -0800 (1736735796.90 s) Start R-work = 0.1797, R-free = 0.1922 Final R-work = 0.1194, R-free = 0.1358 =============================================================================== Job complete usr+sys time: 12274.95 seconds wall clock time: 205 minutes 36.65 seconds (12336.65 seconds total)