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_3537830.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3537830.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3537830.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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.64, per 1000 atoms: 0.39 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: 2.660 distance_ideal: 2.720 ideal - model: 0.060 slack: 0.000 delta_slack: 0.060 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: 2.726 distance_ideal: 2.710 ideal - model: -0.016 slack: 0.000 delta_slack: -0.016 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 222.6 milliseconds Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.05: 1086 1.05 - 1.29: 2405 1.29 - 1.52: 1578 1.52 - 1.75: 855 1.75 - 1.98: 10 Bond restraints: 5934 Sorted by residual: bond pdb=" N CYS A 81 " pdb=" H CYS A 81 " ideal model delta sigma weight residual 0.860 1.247 -0.387 2.00e-02 2.50e+03 3.75e+02 bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.455 1.587 -0.132 7.00e-03 2.04e+04 3.57e+02 bond pdb=" N SER A 85 " pdb=" H SER A 85 " ideal model delta sigma weight residual 0.860 1.232 -0.372 2.00e-02 2.50e+03 3.47e+02 bond pdb=" CD2 HIS B 116 " pdb=" NE2 HIS B 116 " ideal model delta sigma weight residual 1.374 1.169 0.205 1.10e-02 8.26e+03 3.46e+02 bond pdb=" N GLN A 184 " pdb=" H GLN A 184 " ideal model delta sigma weight residual 0.860 1.229 -0.369 2.00e-02 2.50e+03 3.41e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 5525 4.04 - 8.08: 3535 8.08 - 12.12: 1410 12.12 - 16.15: 302 16.15 - 20.19: 38 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY B 174 " pdb=" C GLY B 174 " pdb=" O GLY B 174 " ideal model delta sigma weight residual 122.45 109.67 12.78 7.20e-01 1.93e+00 3.15e+02 angle pdb=" O GLU A 180 " pdb=" C GLU A 180 " pdb=" N VAL A 181 " ideal model delta sigma weight residual 122.07 107.30 14.77 1.03e+00 9.43e-01 2.06e+02 angle pdb=" C LEU A 72 " pdb=" N PRO A 73 " pdb=" CA PRO A 73 " ideal model delta sigma weight residual 120.21 106.61 13.60 9.60e-01 1.09e+00 2.01e+02 angle pdb=" N VAL B 114 " pdb=" CA VAL B 114 " pdb=" CB VAL B 114 " ideal model delta sigma weight residual 110.50 119.39 -8.89 6.30e-01 2.52e+00 1.99e+02 angle pdb=" O VAL B 150 " pdb=" C VAL B 150 " pdb=" N LYS B 151 " ideal model delta sigma weight residual 122.16 134.13 -11.97 9.10e-01 1.21e+00 1.73e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 1876 17.41 - 34.82: 107 34.82 - 52.22: 45 52.22 - 69.63: 17 69.63 - 87.03: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LEU B 72 " pdb=" C LEU B 72 " pdb=" N PRO B 73 " pdb=" CA PRO B 73 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL A 69 " pdb=" C VAL A 69 " pdb=" N ILE A 70 " pdb=" CA ILE A 70 " ideal model delta harmonic sigma weight residual 180.00 158.91 21.09 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.298: 280 0.298 - 0.596: 158 0.596 - 0.895: 42 0.895 - 1.193: 11 1.193 - 1.491: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.10 -1.49 2.00e-01 2.50e+01 5.56e+01 chirality pdb=" CA ASP A 132 " pdb=" N ASP A 132 " pdb=" C ASP A 132 " pdb=" CB ASP A 132 " both_signs ideal model delta sigma weight residual False 2.51 1.37 1.14 2.00e-01 2.50e+01 3.22e+01 chirality pdb=" CB VAL A 144 " pdb=" CA VAL A 144 " pdb=" CG1 VAL A 144 " pdb=" CG2 VAL A 144 " both_signs ideal model delta sigma weight residual False -2.63 -3.70 1.07 2.00e-01 2.50e+01 2.86e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.050 2.00e-02 2.50e+03 6.40e-02 1.64e+02 pdb=" CG TRP B 146 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.097 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.109 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.082 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.016 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.069 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.081 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.023 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.063 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.012 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.096 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.071 2.00e-02 2.50e+03 5.35e-02 1.15e+02 pdb=" CG TRP A 146 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.032 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.015 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.094 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.041 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.061 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.024 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.056 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.075 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.022 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 192 " -0.002 2.00e-02 2.50e+03 5.64e-02 9.56e+01 pdb=" CG TYR B 192 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR B 192 " 0.108 2.00e-02 2.50e+03 pdb=" CD2 TYR B 192 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR B 192 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR B 192 " 0.074 2.00e-02 2.50e+03 pdb=" CZ TYR B 192 " 0.061 2.00e-02 2.50e+03 pdb=" OH TYR B 192 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR B 192 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 TYR B 192 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR B 192 " -0.093 2.00e-02 2.50e+03 pdb=" HE2 TYR B 192 " -0.049 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.66: 31 1.66 - 2.39: 2906 2.39 - 3.13: 22575 3.13 - 3.86: 32819 3.86 - 4.60: 51801 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110132 Sorted by model distance: nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.922 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.975 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 1.001 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.043 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.188 2.620 ... (remaining 110127 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_3537830_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= 0.2045 r_free= 0.1973 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.306191 | | target function (ml) not normalized (work): 806605.507035 | | target function (ml) not normalized (free): 16576.872724 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2134 0.1890 6.7095 6.2899| | 2: 2.94 - 2.33 1.00 7339 128 0.1614 0.1541 5.5312 5.5596| | 3: 2.33 - 2.04 0.96 6939 150 0.1637 0.1557 5.1442 5.1503| | 4: 2.04 - 1.85 1.00 7170 155 0.1778 0.1673 4.9755 5.0527| | 5: 1.85 - 1.72 0.99 7113 159 0.1939 0.1646 4.7956 4.7795| | 6: 1.72 - 1.62 0.99 7102 142 0.2016 0.2056 4.683 4.7519| | 7: 1.62 - 1.54 0.99 7104 148 0.2032 0.1793 4.5674 4.5462| | 8: 1.54 - 1.47 0.96 6798 152 0.2055 0.2146 4.4683 4.5281| | 9: 1.47 - 1.41 0.98 6938 155 0.2099 0.2261 4.3886 4.5211| | 10: 1.41 - 1.36 0.99 7022 150 0.2145 0.1989 4.3135 4.2284| | 11: 1.36 - 1.32 0.99 6997 151 0.2113 0.1950 4.2406 4.1851| | 12: 1.32 - 1.28 0.98 6976 149 0.2078 0.1922 4.1692 4.198| | 13: 1.28 - 1.25 0.98 6907 166 0.2048 0.2452 4.1333 4.3132| | 14: 1.25 - 1.22 0.98 7015 113 0.2107 0.2223 4.0895 4.1559| | 15: 1.22 - 1.19 0.98 6957 137 0.2120 0.1995 4.0447 3.9924| | 16: 1.19 - 1.17 0.93 6604 132 0.2154 0.2176 4.0201 4.1073| | 17: 1.17 - 1.14 0.98 6941 135 0.2190 0.1857 3.9617 3.9632| | 18: 1.14 - 1.12 0.98 6875 142 0.2211 0.2360 3.9265 3.9139| | 19: 1.12 - 1.10 0.97 6949 106 0.2302 0.2611 3.8784 4.0382| | 20: 1.10 - 1.08 0.97 6884 147 0.2328 0.2337 3.825 3.8609| | 21: 1.08 - 1.07 0.97 6852 152 0.2464 0.2667 3.8009 3.8471| | 22: 1.07 - 1.05 0.97 6838 135 0.2583 0.2892 3.7717 3.9007| | 23: 1.05 - 1.03 0.97 6829 159 0.2738 0.2771 3.7457 3.8617| | 24: 1.03 - 1.02 0.96 6785 133 0.2895 0.2708 3.7088 3.7668| | 25: 1.02 - 1.01 0.93 6552 130 0.3118 0.3065 3.6873 3.7365| | 26: 1.01 - 0.99 0.96 6767 158 0.3260 0.3385 3.6381 3.6363| | 27: 0.99 - 0.98 0.94 6648 131 0.3402 0.3217 3.6358 3.6237| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 19.92 0.91 0.97 33759.20| | 2: 2.94 - 2.33 7339 128 0.86 20.84 1.09 1.01 14596.01| | 3: 2.33 - 2.04 6939 150 0.93 12.67 1.11 1.05 4197.07| | 4: 2.04 - 1.85 7170 155 0.93 13.43 1.11 1.06 2771.34| | 5: 1.85 - 1.72 7113 159 0.91 15.42 1.12 1.08 2026.61| | 6: 1.72 - 1.62 7102 142 0.90 16.58 1.11 1.08 1620.29| | 7: 1.62 - 1.54 7104 148 0.89 17.55 1.11 1.08 1336.19| | 8: 1.54 - 1.47 6798 152 0.88 18.55 1.11 1.06 1155.91| | 9: 1.47 - 1.41 6938 155 0.88 19.17 1.10 1.05 975.67| | 10: 1.41 - 1.36 7022 150 0.87 19.60 1.10 1.04 804.94| | 11: 1.36 - 1.32 6997 151 0.88 19.14 1.08 1.04 681.45| | 12: 1.32 - 1.28 6976 149 0.88 19.36 1.08 1.02 620.51| | 13: 1.28 - 1.25 6907 166 0.87 20.01 1.07 1.03 607.96| | 14: 1.25 - 1.22 7015 113 0.86 21.19 1.07 1.03 598.94| | 15: 1.22 - 1.19 6957 137 0.86 21.27 1.08 1.04 551.59| | 16: 1.19 - 1.17 6604 132 0.87 20.77 1.07 1.03 498.61| | 17: 1.17 - 1.14 6941 135 0.86 21.23 1.08 1.01 445.12| | 18: 1.14 - 1.12 6875 142 0.86 21.35 1.08 0.99 405.33| | 19: 1.12 - 1.10 6949 106 0.85 22.38 1.07 1.00 386.44| | 20: 1.10 - 1.08 6884 147 0.85 23.06 1.06 0.98 358.51| | 21: 1.08 - 1.07 6852 152 0.83 25.08 1.06 0.99 370.90| | 22: 1.07 - 1.05 6838 135 0.80 27.29 1.05 0.97 371.99| | 23: 1.05 - 1.03 6829 159 0.78 29.53 1.05 0.97 375.80| | 24: 1.03 - 1.02 6785 133 0.76 30.86 1.05 0.96 357.21| | 25: 1.02 - 1.01 6552 130 0.75 31.83 1.02 0.92 328.71| | 26: 1.01 - 0.99 6767 158 0.73 33.68 1.04 0.90 308.81| | 27: 0.99 - 0.98 6648 131 0.73 33.93 1.05 0.87 289.60| |alpha: min = 0.87 max = 1.08 mean = 1.01| |beta: min = 289.60 max = 33759.20 mean = 2743.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.97| |phase err.(test): min = 0.00 max = 89.99 mean = 22.10| |-----------------------------------------------------------------------------| ----------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 0.313 2950 Z= 5.476 Angle : 5.100 16.715 4018 Z= 3.627 Chirality : 0.380 1.491 492 Planarity : 0.033 0.136 512 Dihedral : 12.893 87.033 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.92 % Favored : 94.82 % Rotamer: Outliers : 0.32 % Allowed : 5.48 % Favored : 94.19 % Cbeta Deviations : 29.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.38), residues: 386 helix: -2.67 (0.32), residues: 146 sheet: -1.30 (0.49), residues: 82 loop : -0.25 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.110 0.018 ARG B 27 TYR 0.109 0.036 TYR A 192 PHE 0.084 0.031 PHE A 82 TRP 0.103 0.047 TRP B 146 HIS 0.086 0.035 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2045 r_free= 0.1973 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.306191 | | target function (ml) not normalized (work): 806605.507035 | | target function (ml) not normalized (free): 16576.872724 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2043 0.2045 0.1973 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2043 0.2045 0.1973 n_refl.: 191155 remove outliers: r(all,work,free)=0.2043 0.2045 0.1973 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2044 0.2046 0.1973 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1814 0.1812 0.1909 n_refl.: 191145 remove outliers: r(all,work,free)=0.1811 0.1809 0.1909 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 0.4129 402.814 291.914 0.435 0.912 0.301 13.296-10.522 99.01 99 1 0.2522 528.187 518.992 0.785 0.914 0.250 10.503-8.327 98.90 177 3 0.2503 564.205 557.633 0.971 0.914 0.223 8.318-6.595 100.00 360 8 0.2488 414.736 404.580 0.970 0.914 0.171 6.588-5.215 100.00 711 7 0.2268 381.101 365.637 0.951 0.914 0.140 5.214-4.128 98.38 1367 28 0.1485 557.435 550.228 1.072 0.914 0.090 4.126-3.266 94.74 2603 46 0.1337 508.132 499.748 1.143 0.914 0.028 3.266-2.585 99.86 5447 97 0.1434 342.774 337.648 1.117 0.913 0.005 2.585-2.046 97.45 10613 204 0.1398 258.603 254.506 1.123 0.913 0.000 2.046-1.619 99.39 21536 464 0.1640 153.054 149.723 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1930 82.395 80.194 1.129 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2343 44.203 41.615 1.111 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0069 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1809 r_free=0.1909 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN Total number of N/Q/H flips: 1 r_work=0.1812 r_free=0.1913 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.020029 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.420020 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1273 0.1505 0.0232 0.038 1.2 10.9 0.0 0.0 0 11.510 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.05 2.32 1.119 13.115 573.420 0.018 12.98 15.69 2.72 1.225 13.311 573.420 0.017 Individual atomic B min max mean iso aniso Overall: 5.22 73.05 14.96 1.39 435 3274 Protein: 5.22 40.32 10.99 1.39 0 2902 Water: 6.32 73.05 29.23 N/A 435 370 Other: 16.09 30.80 23.45 N/A 0 2 Chain A: 5.38 59.97 13.01 N/A 0 1626 Chain B: 5.22 73.05 12.74 N/A 0 1648 Chain S: 11.14 62.40 30.65 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.00 2167 12.00 - 18.78 638 18.78 - 25.57 319 25.57 - 32.35 270 32.35 - 39.13 150 39.13 - 45.91 106 45.91 - 52.70 38 52.70 - 59.48 16 59.48 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1570 r_work=0.1297 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1565 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 = 0.1282 r_free = 0.1555 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 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= 0.1282 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015539 | | target function (ls_wunit_k1) not normalized (work): 2910.479194 | | target function (ls_wunit_k1) not normalized (free): 117.052792 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1555 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1469 0.1466 0.1629 n_refl.: 191138 remove outliers: r(all,work,free)=0.1469 0.1466 0.1629 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1492 0.1490 0.1639 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1546 n_refl.: 191138 remove outliers: r(all,work,free)=0.1279 0.1274 0.1545 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3617 402.814 378.080 0.469 0.997 0.281 13.296-10.522 99.01 99 1 0.2106 528.187 522.592 0.717 0.998 0.255 10.503-8.327 98.90 177 3 0.1711 564.205 561.804 0.855 0.998 0.203 8.318-6.595 100.00 360 8 0.1717 414.736 413.018 0.877 0.998 0.150 6.588-5.215 100.00 711 7 0.1546 381.101 373.143 0.855 0.998 0.140 5.214-4.128 98.38 1367 28 0.0906 557.435 555.237 0.943 0.999 0.054 4.126-3.266 94.74 2603 46 0.0833 508.132 504.140 1.008 1.000 0.014 3.266-2.585 99.86 5447 97 0.0920 342.774 340.305 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.359 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.384 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.411 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.164 0.989 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0361 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1545 | n_water=805 | time (s): 3.000 (total time: 3.000) Filter (dist) r_work=0.1279 r_free=0.1553 | n_water=794 | time (s): 102.580 (total time: 105.580) Filter (q & B) r_work=0.1280 r_free=0.1553 | n_water=789 | time (s): 4.820 (total time: 110.400) Compute maps r_work=0.1280 r_free=0.1553 | n_water=789 | time (s): 2.070 (total time: 112.470) Filter (map) r_work=0.1305 r_free=0.1535 | n_water=653 | time (s): 4.340 (total time: 116.810) Find peaks r_work=0.1305 r_free=0.1535 | n_water=653 | time (s): 0.820 (total time: 117.630) Add new water r_work=0.1327 r_free=0.1560 | n_water=960 | time (s): 4.690 (total time: 122.320) Refine new water occ: r_work=0.1285 r_free=0.1514 adp: r_work=0.1272 r_free=0.1510 occ: r_work=0.1274 r_free=0.1512 adp: r_work=0.1267 r_free=0.1509 occ: r_work=0.1269 r_free=0.1510 adp: r_work=0.1267 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1509 r_work=0.1267 r_free=0.1509 | n_water=960 | time (s): 78.770 (total time: 201.090) Filter (q & B) r_work=0.1270 r_free=0.1510 | n_water=892 | time (s): 4.800 (total time: 205.890) Filter (dist only) r_work=0.1270 r_free=0.1509 | n_water=890 | time (s): 111.750 (total time: 317.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.708105 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 590.699258 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 0.1256 0.1534 0.0278 0.040 1.1 18.4 0.0 0.3 0 11.854 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.34 2.78 2.035 15.092 590.699 0.014 12.32 15.11 2.80 2.384 15.174 590.699 0.014 Individual atomic B min max mean iso aniso Overall: 5.44 68.21 16.23 1.20 522 3272 Protein: 5.44 40.30 10.98 1.20 0 2902 Water: 6.66 68.21 33.33 N/A 522 368 Other: 16.29 32.98 24.64 N/A 0 2 Chain A: 5.53 56.29 12.97 N/A 0 1624 Chain B: 5.44 68.21 12.80 N/A 0 1648 Chain S: 12.72 67.44 37.24 N/A 522 0 Histogram: Values Number of atoms 5.44 - 11.72 2068 11.72 - 17.99 704 17.99 - 24.27 267 24.27 - 30.55 218 30.55 - 36.82 176 36.82 - 43.10 179 43.10 - 49.38 97 49.38 - 55.65 43 55.65 - 61.93 32 61.93 - 68.21 10 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1512 r_work=0.1232 r_free=0.1513 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1513 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 = 0.1226 r_free = 0.1513 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1513 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013439 | | target function (ls_wunit_k1) not normalized (work): 2517.106327 | | target function (ls_wunit_k1) not normalized (free): 100.953632 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1513 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1604 n_refl.: 191137 remove outliers: r(all,work,free)=0.1436 0.1433 0.1604 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1430 0.1602 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1519 n_refl.: 191137 remove outliers: r(all,work,free)=0.1239 0.1233 0.1519 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3271 402.814 379.350 0.485 0.963 0.273 13.296-10.522 99.01 99 1 0.1898 528.187 523.201 0.765 0.964 0.260 10.503-8.327 98.90 177 3 0.1383 564.205 567.370 0.919 0.964 0.176 8.318-6.595 100.00 360 8 0.1566 414.736 413.921 0.934 0.963 0.145 6.588-5.215 100.00 711 7 0.1346 381.101 376.520 0.910 0.964 0.127 5.214-4.128 98.38 1367 28 0.0831 557.435 556.018 0.995 0.964 0.080 4.126-3.266 94.74 2603 46 0.0766 508.132 505.469 1.060 0.964 0.025 3.266-2.585 99.86 5447 97 0.0865 342.774 341.443 1.046 0.962 0.020 2.585-2.046 97.45 10613 204 0.0900 258.603 256.721 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.636 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1252 82.395 81.360 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.220 1.061 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0529 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1519 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1519 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1519 | n_water=890 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1235 r_free=0.1520 | n_water=885 | time (s): 108.570 (total time: 110.960) Filter (q & B) r_work=0.1235 r_free=0.1521 | n_water=881 | time (s): 4.030 (total time: 114.990) Compute maps r_work=0.1235 r_free=0.1521 | n_water=881 | time (s): 2.150 (total time: 117.140) Filter (map) r_work=0.1275 r_free=0.1521 | n_water=688 | time (s): 4.710 (total time: 121.850) Find peaks r_work=0.1275 r_free=0.1521 | n_water=688 | time (s): 0.590 (total time: 122.440) Add new water r_work=0.1298 r_free=0.1557 | n_water=1026 | time (s): 4.160 (total time: 126.600) Refine new water occ: r_work=0.1250 r_free=0.1516 adp: r_work=0.1250 r_free=0.1517 occ: r_work=0.1246 r_free=0.1509 adp: r_work=0.1246 r_free=0.1511 occ: r_work=0.1243 r_free=0.1504 adp: r_work=0.1242 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1506 r_work=0.1242 r_free=0.1506 | n_water=1026 | time (s): 349.470 (total time: 476.070) Filter (q & B) r_work=0.1247 r_free=0.1514 | n_water=894 | time (s): 4.180 (total time: 480.250) Filter (dist only) r_work=0.1248 r_free=0.1514 | n_water=893 | time (s): 119.030 (total time: 599.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.656138 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.175877 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 0.1237 0.1434 0.0197 0.035 1.1 7.1 0.0 0.0 0 0.828 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.34 1.97 1.930 14.590 16.176 3.938 12.34 13.97 1.63 2.234 14.494 16.176 3.896 Individual atomic B min max mean iso aniso Overall: 5.54 67.76 15.26 1.06 526 3271 Protein: 5.54 36.61 10.74 1.06 0 2902 Water: 6.70 67.76 29.96 N/A 526 367 Other: 13.98 28.44 21.21 N/A 0 2 Chain A: 5.56 55.43 12.73 N/A 0 1624 Chain B: 5.54 67.76 12.51 N/A 0 1647 Chain S: 14.29 60.77 31.71 N/A 526 0 Histogram: Values Number of atoms 5.54 - 11.76 2136 11.76 - 17.98 685 17.98 - 24.20 297 24.20 - 30.43 244 30.43 - 36.65 190 36.65 - 42.87 141 42.87 - 49.09 72 49.09 - 55.32 25 55.32 - 61.54 6 61.54 - 67.76 1 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1397 r_work=0.1235 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1397 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1388 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890390 | | target function (ml) not normalized (work): 728654.491656 | | target function (ml) not normalized (free): 15220.882421 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1387 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1440 0.1440 0.1491 n_refl.: 191137 remove outliers: r(all,work,free)=0.1440 0.1440 0.1491 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1434 0.1434 0.1487 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1378 n_refl.: 191137 remove outliers: r(all,work,free)=0.1227 0.1224 0.1378 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 0.3782 393.525 362.094 0.425 0.946 0.251 13.296-10.522 99.01 99 1 0.2595 528.187 508.094 0.701 0.947 0.214 10.503-8.327 97.80 175 3 0.1938 554.286 558.308 0.886 0.947 0.200 8.318-6.595 100.00 360 8 0.2075 414.736 410.610 0.897 0.947 0.120 6.588-5.215 100.00 711 7 0.1804 381.101 370.437 0.887 0.947 0.110 5.214-4.128 98.38 1367 28 0.1167 557.435 552.413 0.971 0.947 0.060 4.126-3.266 94.74 2603 46 0.1101 508.132 501.139 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1086 342.774 339.076 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0967 258.603 255.686 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.373 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.479 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.314 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1017 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1378 | n_water=893 | time (s): 3.300 (total time: 3.300) Filter (dist) r_work=0.1224 r_free=0.1378 | n_water=893 | time (s): 111.790 (total time: 115.090) Filter (q & B) r_work=0.1225 r_free=0.1375 | n_water=881 | time (s): 4.560 (total time: 119.650) Compute maps r_work=0.1225 r_free=0.1375 | n_water=881 | time (s): 2.280 (total time: 121.930) Filter (map) r_work=0.1249 r_free=0.1384 | n_water=734 | time (s): 5.690 (total time: 127.620) Find peaks r_work=0.1249 r_free=0.1384 | n_water=734 | time (s): 0.690 (total time: 128.310) Add new water r_work=0.1262 r_free=0.1402 | n_water=973 | time (s): 5.180 (total time: 133.490) Refine new water occ: r_work=0.1215 r_free=0.1356 adp: r_work=0.1207 r_free=0.1353 occ: r_work=0.1205 r_free=0.1352 adp: r_work=0.1205 r_free=0.1351 occ: r_work=0.1203 r_free=0.1350 adp: r_work=0.1203 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1350 r_work=0.1203 r_free=0.1350 | n_water=973 | time (s): 223.230 (total time: 356.720) Filter (q & B) r_work=0.1209 r_free=0.1365 | n_water=873 | time (s): 4.110 (total time: 360.830) Filter (dist only) r_work=0.1209 r_free=0.1364 | n_water=872 | time (s): 116.550 (total time: 477.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.660996 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.717577 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 0.1206 0.1369 0.0163 0.036 1.1 5.8 0.0 0.3 0 0.830 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.69 1.63 1.829 14.153 15.718 3.873 11.99 13.68 1.69 1.932 14.117 15.718 3.865 Individual atomic B min max mean iso aniso Overall: 5.51 67.28 14.89 1.00 505 3271 Protein: 5.51 33.39 10.66 1.00 0 2902 Water: 5.99 67.28 28.96 N/A 505 367 Other: 13.98 27.52 20.75 N/A 0 2 Chain A: 5.57 54.36 12.60 N/A 0 1624 Chain B: 5.51 67.28 12.41 N/A 0 1647 Chain S: 5.99 60.77 30.32 N/A 505 0 Histogram: Values Number of atoms 5.51 - 11.68 2115 11.68 - 17.86 730 17.86 - 24.04 311 24.04 - 30.22 244 30.22 - 36.39 156 36.39 - 42.57 136 42.57 - 48.75 53 48.75 - 54.93 24 54.93 - 61.11 6 61.11 - 67.28 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1368 r_work=0.1199 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1368 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1365 target_work(ml) = 3.863 | | 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.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862778 | | target function (ml) not normalized (work): 723467.460657 | | target function (ml) not normalized (free): 15137.617390 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1365 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1424 0.1423 0.1482 n_refl.: 191133 remove outliers: r(all,work,free)=0.1424 0.1423 0.1482 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1416 0.1477 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191133 remove outliers: r(all,work,free)=0.1199 0.1196 0.1362 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3849 357.392 315.774 0.402 0.946 0.243 13.296-10.522 97.03 97 1 0.2418 481.578 454.702 0.692 0.947 0.192 10.503-8.327 97.80 175 3 0.2099 502.309 495.675 0.864 0.948 0.167 8.318-6.595 100.00 360 8 0.2187 375.845 370.252 0.890 0.947 0.100 6.588-5.215 100.00 711 7 0.1911 345.364 335.331 0.883 0.947 0.084 5.214-4.128 98.38 1367 28 0.1208 505.163 500.500 0.972 0.948 0.039 4.126-3.266 94.74 2603 46 0.1126 460.483 453.804 1.035 0.948 0.005 3.266-2.585 99.86 5447 97 0.1089 310.631 307.483 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0929 234.353 231.941 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0910 138.702 137.430 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0986 74.669 73.958 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.057 38.401 1.038 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1199 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1362 | n_water=872 | time (s): 2.320 (total time: 2.320) Filter (dist) r_work=0.1196 r_free=0.1362 | n_water=872 | time (s): 99.990 (total time: 102.310) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=866 | time (s): 4.940 (total time: 107.250) Compute maps r_work=0.1196 r_free=0.1362 | n_water=866 | time (s): 2.160 (total time: 109.410) Filter (map) r_work=0.1219 r_free=0.1361 | n_water=746 | time (s): 5.550 (total time: 114.960) Find peaks r_work=0.1219 r_free=0.1361 | n_water=746 | time (s): 0.660 (total time: 115.620) Add new water r_work=0.1228 r_free=0.1375 | n_water=957 | time (s): 5.060 (total time: 120.680) Refine new water occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1193 r_free=0.1349 occ: r_work=0.1190 r_free=0.1350 adp: r_work=0.1190 r_free=0.1349 occ: r_work=0.1189 r_free=0.1351 adp: r_work=0.1188 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1349 r_work=0.1188 r_free=0.1349 | n_water=957 | time (s): 298.020 (total time: 418.700) Filter (q & B) r_work=0.1192 r_free=0.1355 | n_water=893 | time (s): 4.180 (total time: 422.880) Filter (dist only) r_work=0.1192 r_free=0.1355 | n_water=892 | time (s): 110.420 (total time: 533.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.569888 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.193742 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 0.1366 0.0170 0.037 1.1 9.0 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.66 1.70 1.791 14.118 15.194 3.765 11.99 13.69 1.69 1.836 14.100 15.194 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 67.01 14.94 0.96 525 3271 Protein: 5.58 32.43 10.60 0.96 0 2902 Water: 6.03 67.01 29.05 N/A 525 367 Other: 13.77 26.69 20.23 N/A 0 2 Chain A: 5.61 53.79 12.53 N/A 0 1624 Chain B: 5.58 67.01 12.34 N/A 0 1647 Chain S: 6.03 60.73 30.57 N/A 525 0 Histogram: Values Number of atoms 5.58 - 11.72 2143 11.72 - 17.86 716 17.86 - 24.01 310 24.01 - 30.15 227 30.15 - 36.29 168 36.29 - 42.44 149 42.44 - 48.58 53 48.58 - 54.73 23 54.73 - 60.87 6 60.87 - 67.01 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1369 r_work=0.1200 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1369 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1369 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761074 | | target function (ml) not normalized (work): 704407.780818 | | target function (ml) not normalized (free): 14754.926964 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1369 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1501 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1401 0.1501 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1396 0.1394 0.1495 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1368 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1368 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3764 357.392 322.728 0.396 0.950 0.225 13.296-10.522 97.03 97 1 0.2394 481.578 462.671 0.698 0.952 0.178 10.503-8.327 97.80 175 3 0.2117 502.309 495.117 0.860 0.952 0.153 8.318-6.595 100.00 360 8 0.2146 375.845 371.023 0.887 0.951 0.108 6.588-5.215 100.00 711 7 0.1897 345.364 335.486 0.879 0.952 0.071 5.214-4.128 98.38 1367 28 0.1208 505.163 500.229 0.969 0.952 0.040 4.126-3.266 94.74 2603 46 0.1138 460.483 453.711 1.031 0.953 0.009 3.266-2.585 99.86 5447 97 0.1106 310.631 307.404 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0943 234.353 231.841 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0913 138.702 137.395 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0978 74.669 73.954 1.047 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1655 40.057 38.386 1.032 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1298 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1368 | n_water=892 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1197 r_free=0.1367 | n_water=890 | time (s): 118.000 (total time: 120.510) Filter (q & B) r_work=0.1198 r_free=0.1366 | n_water=877 | time (s): 4.860 (total time: 125.370) Compute maps r_work=0.1198 r_free=0.1366 | n_water=877 | time (s): 1.670 (total time: 127.040) Filter (map) r_work=0.1219 r_free=0.1358 | n_water=765 | time (s): 5.270 (total time: 132.310) Find peaks r_work=0.1219 r_free=0.1358 | n_water=765 | time (s): 0.690 (total time: 133.000) Add new water r_work=0.1228 r_free=0.1365 | n_water=971 | time (s): 4.770 (total time: 137.770) Refine new water occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1195 r_free=0.1340 occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1341 occ: r_work=0.1191 r_free=0.1342 adp: r_work=0.1190 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1341 r_work=0.1190 r_free=0.1341 | n_water=971 | time (s): 200.400 (total time: 338.170) Filter (q & B) r_work=0.1194 r_free=0.1346 | n_water=905 | time (s): 5.440 (total time: 343.610) Filter (dist only) r_work=0.1195 r_free=0.1346 | n_water=903 | time (s): 114.160 (total time: 457.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.533306 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.181629 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1355 0.0157 0.037 1.1 6.8 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.55 1.57 1.767 14.064 14.182 3.761 12.04 13.60 1.56 1.948 14.007 14.182 3.761 Individual atomic B min max mean iso aniso Overall: 5.61 65.72 14.84 0.89 536 3271 Protein: 5.61 29.13 10.47 0.89 0 2902 Water: 5.90 65.72 28.90 N/A 536 367 Other: 13.83 23.42 18.62 N/A 0 2 Chain A: 5.64 51.37 12.36 N/A 0 1624 Chain B: 5.61 65.72 12.19 N/A 0 1647 Chain S: 5.90 60.52 30.53 N/A 536 0 Histogram: Values Number of atoms 5.61 - 11.62 2117 11.62 - 17.63 772 17.63 - 23.64 281 23.64 - 29.65 220 29.65 - 35.66 174 35.66 - 41.67 148 41.67 - 47.68 58 47.68 - 53.69 30 53.69 - 59.71 5 59.71 - 65.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1360 r_work=0.1204 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1361 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1361 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760093 | | target function (ml) not normalized (work): 704223.968820 | | target function (ml) not normalized (free): 14748.681225 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1201 0.1361 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1499 n_refl.: 191130 remove outliers: r(all,work,free)=0.1404 0.1403 0.1499 n_refl.: 191130 overall B=-0.22 to atoms: r(all,work,free)=0.1368 0.1367 0.1474 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1358 n_refl.: 191130 remove outliers: r(all,work,free)=0.1203 0.1200 0.1358 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3774 357.392 322.757 0.392 0.951 0.205 13.296-10.522 97.03 97 1 0.2432 481.578 462.187 0.705 0.952 0.151 10.503-8.327 97.80 175 3 0.2141 502.309 495.055 0.882 0.953 0.127 8.318-6.595 100.00 360 8 0.2151 375.845 371.260 0.907 0.952 0.093 6.588-5.215 100.00 711 7 0.1903 345.364 335.701 0.902 0.953 0.073 5.214-4.128 98.38 1367 28 0.1224 505.163 499.972 0.993 0.953 0.040 4.126-3.266 94.74 2603 46 0.1157 460.483 453.429 1.056 0.953 0.009 3.266-2.585 99.86 5447 97 0.1113 310.631 307.328 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0953 234.353 231.794 1.047 0.952 0.000 2.046-1.619 99.39 21536 464 0.0914 138.702 137.397 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0973 74.669 73.963 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.057 38.387 1.025 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0492 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1358 | n_water=903 | time (s): 3.160 (total time: 3.160) Filter (dist) r_work=0.1201 r_free=0.1358 | n_water=902 | time (s): 118.760 (total time: 121.920) Filter (q & B) r_work=0.1201 r_free=0.1358 | n_water=891 | time (s): 4.360 (total time: 126.280) Compute maps r_work=0.1201 r_free=0.1358 | n_water=891 | time (s): 2.210 (total time: 128.490) Filter (map) r_work=0.1223 r_free=0.1361 | n_water=773 | time (s): 4.590 (total time: 133.080) Find peaks r_work=0.1223 r_free=0.1361 | n_water=773 | time (s): 0.590 (total time: 133.670) Add new water r_work=0.1231 r_free=0.1371 | n_water=975 | time (s): 3.930 (total time: 137.600) Refine new water occ: r_work=0.1199 r_free=0.1349 adp: r_work=0.1199 r_free=0.1349 occ: r_work=0.1197 r_free=0.1348 adp: r_work=0.1197 r_free=0.1348 occ: r_work=0.1196 r_free=0.1348 adp: r_work=0.1195 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1348 r_work=0.1195 r_free=0.1348 | n_water=975 | time (s): 189.700 (total time: 327.300) Filter (q & B) r_work=0.1200 r_free=0.1354 | n_water=902 | time (s): 4.230 (total time: 331.530) Filter (dist only) r_work=0.1201 r_free=0.1355 | n_water=899 | time (s): 115.100 (total time: 446.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.594969 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.671609 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 0.1203 0.1360 0.0157 0.038 1.1 7.0 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.60 1.57 1.712 13.692 13.672 3.761 12.05 13.63 1.58 1.766 13.671 13.672 3.759 Individual atomic B min max mean iso aniso Overall: 5.40 64.13 14.55 0.87 532 3271 Protein: 5.40 27.93 10.23 0.87 0 2902 Water: 5.81 64.13 28.50 N/A 532 367 Other: 13.73 21.74 17.74 N/A 0 2 Chain A: 5.44 50.60 12.07 N/A 0 1624 Chain B: 5.40 64.13 11.92 N/A 0 1647 Chain S: 5.81 59.97 30.26 N/A 532 0 Histogram: Values Number of atoms 5.40 - 11.28 2081 11.28 - 17.15 806 17.15 - 23.02 268 23.02 - 28.89 223 28.89 - 34.77 180 34.77 - 40.64 138 40.64 - 46.51 66 46.51 - 52.38 31 52.38 - 58.26 8 58.26 - 64.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1363 r_work=0.1205 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1364 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1362 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758510 | | target function (ml) not normalized (work): 703927.512538 | | target function (ml) not normalized (free): 14737.353072 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1203 0.1362 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1377 0.1375 0.1481 n_refl.: 191130 remove outliers: r(all,work,free)=0.1377 0.1375 0.1481 n_refl.: 191130 overall B=0.06 to atoms: r(all,work,free)=0.1385 0.1383 0.1486 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1353 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1194 0.1353 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3829 357.392 320.514 0.371 0.996 0.195 13.296-10.522 97.03 97 1 0.2441 481.578 462.360 0.674 0.997 0.141 10.503-8.327 97.80 175 3 0.2174 502.309 493.703 0.848 0.997 0.117 8.318-6.595 100.00 360 8 0.2166 375.845 369.901 0.872 0.997 0.095 6.588-5.215 100.00 711 7 0.1942 345.364 335.178 0.870 0.998 0.080 5.214-4.128 98.38 1367 28 0.1246 505.163 499.299 0.959 0.999 0.054 4.126-3.266 94.74 2603 46 0.1174 460.483 452.846 1.019 1.000 0.014 3.266-2.585 99.86 5447 97 0.1119 310.631 306.990 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0960 234.353 231.709 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0907 138.702 137.329 1.026 1.004 0.000 1.619-1.281 98.00 42464 925 0.0951 74.669 74.005 1.015 1.008 0.000 1.281-0.980 96.53 101826 2055 0.1632 40.057 38.358 0.982 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0623 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1353 | n_water=899 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1194 r_free=0.1353 | n_water=899 | time (s): 118.600 (total time: 120.940) Filter (q & B) r_work=0.1195 r_free=0.1353 | n_water=888 | time (s): 5.030 (total time: 125.970) Compute maps r_work=0.1195 r_free=0.1353 | n_water=888 | time (s): 2.100 (total time: 128.070) Filter (map) r_work=0.1217 r_free=0.1355 | n_water=773 | time (s): 5.120 (total time: 133.190) Find peaks r_work=0.1217 r_free=0.1355 | n_water=773 | time (s): 0.570 (total time: 133.760) Add new water r_work=0.1225 r_free=0.1371 | n_water=977 | time (s): 4.270 (total time: 138.030) Refine new water occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1192 r_free=0.1339 occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1190 r_free=0.1338 occ: r_work=0.1189 r_free=0.1338 adp: r_work=0.1188 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1338 r_work=0.1188 r_free=0.1338 | n_water=977 | time (s): 273.900 (total time: 411.930) Filter (q & B) r_work=0.1193 r_free=0.1344 | n_water=900 | time (s): 5.170 (total time: 417.100) Filter (dist only) r_work=0.1193 r_free=0.1345 | n_water=898 | time (s): 115.190 (total time: 532.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540104 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.553364 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1359 0.0162 0.039 1.1 5.8 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.59 1.62 1.669 13.673 13.553 3.758 11.98 13.63 1.65 1.674 13.665 13.553 3.757 Individual atomic B min max mean iso aniso Overall: 5.46 63.78 14.56 0.86 531 3271 Protein: 5.46 27.82 10.30 0.86 0 2902 Water: 5.90 63.78 28.32 N/A 531 367 Other: 13.72 21.88 17.80 N/A 0 2 Chain A: 5.56 50.52 12.11 N/A 0 1624 Chain B: 5.46 63.78 11.97 N/A 0 1647 Chain S: 5.90 59.95 30.08 N/A 531 0 Histogram: Values Number of atoms 5.46 - 11.29 2066 11.29 - 17.12 824 17.12 - 22.96 271 22.96 - 28.79 222 28.79 - 34.62 173 34.62 - 40.45 137 40.45 - 46.29 71 46.29 - 52.12 28 52.12 - 57.95 7 57.95 - 63.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1363 r_work=0.1198 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1363 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1364 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756646 | | target function (ml) not normalized (work): 703578.515792 | | target function (ml) not normalized (free): 14743.916942 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1364 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1502 n_refl.: 191130 remove outliers: r(all,work,free)=0.1395 0.1393 0.1502 n_refl.: 191130 overall B=0.01 to atoms: r(all,work,free)=0.1397 0.1395 0.1503 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1362 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1195 0.1362 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3840 357.392 319.774 0.403 0.912 0.195 13.296-10.522 97.03 97 1 0.2444 481.578 461.205 0.734 0.913 0.141 10.503-8.327 97.80 175 3 0.2181 502.309 493.986 0.923 0.914 0.117 8.318-6.595 100.00 360 8 0.2174 375.845 369.633 0.950 0.914 0.094 6.588-5.215 100.00 711 7 0.1956 345.364 334.905 0.947 0.914 0.077 5.214-4.128 98.38 1367 28 0.1259 505.163 499.424 1.045 0.915 0.044 4.126-3.266 94.74 2603 46 0.1181 460.483 452.688 1.112 0.916 0.009 3.266-2.585 99.86 5447 97 0.1135 310.631 306.903 1.094 0.917 0.000 2.585-2.046 97.45 10613 204 0.0962 234.353 231.640 1.103 0.918 0.000 2.046-1.619 99.39 21536 464 0.0908 138.702 137.327 1.121 0.921 0.000 1.619-1.281 98.00 42464 925 0.0945 74.669 74.017 1.111 0.926 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.057 38.347 1.078 0.933 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0210 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1362 | n_water=898 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1195 r_free=0.1362 | n_water=898 | time (s): 109.780 (total time: 112.180) Filter (q & B) r_work=0.1196 r_free=0.1362 | n_water=887 | time (s): 5.490 (total time: 117.670) Compute maps r_work=0.1196 r_free=0.1362 | n_water=887 | time (s): 2.280 (total time: 119.950) Filter (map) r_work=0.1219 r_free=0.1365 | n_water=769 | time (s): 4.340 (total time: 124.290) Find peaks r_work=0.1219 r_free=0.1365 | n_water=769 | time (s): 0.870 (total time: 125.160) Add new water r_work=0.1227 r_free=0.1382 | n_water=977 | time (s): 5.360 (total time: 130.520) Refine new water occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1193 r_free=0.1350 occ: r_work=0.1191 r_free=0.1351 adp: r_work=0.1191 r_free=0.1350 occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1190 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1350 r_work=0.1190 r_free=0.1350 | n_water=977 | time (s): 195.760 (total time: 326.280) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=903 | time (s): 4.200 (total time: 330.480) Filter (dist only) r_work=0.1194 r_free=0.1356 | n_water=901 | time (s): 114.500 (total time: 444.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.491508 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.856571 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 0.1362 0.0163 0.040 1.1 6.0 0.0 0.3 0 0.746 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.62 1.63 1.672 13.686 13.857 3.758 11.99 13.65 1.66 1.682 13.677 13.857 3.756 Individual atomic B min max mean iso aniso Overall: 5.56 62.79 14.55 0.86 534 3271 Protein: 5.56 27.68 10.32 0.86 0 2902 Water: 5.92 62.79 28.18 N/A 534 367 Other: 13.81 21.96 17.89 N/A 0 2 Chain A: 5.65 50.23 12.10 N/A 0 1624 Chain B: 5.56 62.79 11.97 N/A 0 1647 Chain S: 5.92 59.68 29.98 N/A 534 0 Histogram: Values Number of atoms 5.56 - 11.29 2058 11.29 - 17.01 829 17.01 - 22.73 269 22.73 - 28.46 216 28.46 - 34.18 184 34.18 - 39.90 133 39.90 - 45.62 74 45.62 - 51.35 29 51.35 - 57.07 8 57.07 - 62.79 5 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1365 r_work=0.1199 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1365 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756083 | | target function (ml) not normalized (work): 703473.099417 | | target function (ml) not normalized (free): 14745.975376 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1365 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1508 n_refl.: 191130 remove outliers: r(all,work,free)=0.1406 0.1404 0.1508 n_refl.: 191130 overall B=-0.00 to atoms: r(all,work,free)=0.1405 0.1404 0.1508 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3841 357.392 319.218 0.373 0.976 0.191 13.296-10.522 97.03 97 1 0.2479 481.578 460.696 0.685 0.977 0.143 10.503-8.327 97.80 175 3 0.2173 502.309 493.926 0.861 0.978 0.126 8.318-6.595 100.00 360 8 0.2172 375.845 369.733 0.885 0.977 0.082 6.588-5.215 100.00 711 7 0.1966 345.364 334.910 0.884 0.978 0.070 5.214-4.128 98.38 1367 28 0.1266 505.163 499.211 0.976 0.979 0.040 4.126-3.266 94.74 2603 46 0.1188 460.483 452.552 1.040 0.980 0.009 3.266-2.585 99.86 5447 97 0.1138 310.631 306.951 1.024 0.981 0.000 2.585-2.046 97.45 10613 204 0.0966 234.353 231.627 1.031 0.983 0.000 2.046-1.619 99.39 21536 464 0.0909 138.702 137.332 1.049 0.987 0.000 1.619-1.281 98.00 42464 925 0.0943 74.669 74.017 1.040 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.057 38.336 1.010 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0082 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1197 r_free=0.1363 After: r_work=0.1197 r_free=0.1364 ================================== NQH flips ================================== r_work=0.1197 r_free=0.1364 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1364 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1364 | n_water=901 | time (s): 2.200 (total time: 2.200) Filter (dist) r_work=0.1197 r_free=0.1364 | n_water=901 | time (s): 115.220 (total time: 117.420) Filter (q & B) r_work=0.1198 r_free=0.1364 | n_water=890 | time (s): 5.850 (total time: 123.270) Compute maps r_work=0.1198 r_free=0.1364 | n_water=890 | time (s): 1.840 (total time: 125.110) Filter (map) r_work=0.1222 r_free=0.1364 | n_water=769 | time (s): 5.160 (total time: 130.270) Find peaks r_work=0.1222 r_free=0.1364 | n_water=769 | time (s): 0.760 (total time: 131.030) Add new water r_work=0.1229 r_free=0.1379 | n_water=970 | time (s): 3.730 (total time: 134.760) Refine new water occ: r_work=0.1197 r_free=0.1345 adp: r_work=0.1197 r_free=0.1345 occ: r_work=0.1195 r_free=0.1345 adp: r_work=0.1195 r_free=0.1345 occ: r_work=0.1194 r_free=0.1345 adp: r_work=0.1194 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1345 r_work=0.1194 r_free=0.1345 | n_water=970 | time (s): 241.660 (total time: 376.420) Filter (q & B) r_work=0.1198 r_free=0.1352 | n_water=898 | time (s): 4.520 (total time: 380.940) Filter (dist only) r_work=0.1198 r_free=0.1352 | n_water=896 | time (s): 122.850 (total time: 503.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524176 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.795501 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 0.1355 0.0155 0.040 1.1 8.7 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.55 1.55 1.671 13.664 13.796 3.757 11.99 13.56 1.57 1.664 13.665 13.796 3.756 Individual atomic B min max mean iso aniso Overall: 5.56 62.47 14.53 0.85 530 3270 Protein: 5.56 27.68 10.34 0.85 0 2902 Water: 5.99 62.47 28.08 N/A 530 366 Other: 13.83 21.96 17.90 N/A 0 2 Chain A: 5.65 50.14 12.10 N/A 0 1624 Chain B: 5.56 62.47 11.95 N/A 0 1646 Chain S: 5.99 59.58 29.95 N/A 530 0 Histogram: Values Number of atoms 5.56 - 11.25 2044 11.25 - 16.94 840 16.94 - 22.63 273 22.63 - 28.32 213 28.32 - 34.01 179 34.01 - 39.70 127 39.70 - 45.39 80 45.39 - 51.09 32 51.09 - 56.78 7 56.78 - 62.47 5 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1356 r_work=0.1200 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1356 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1357 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755936 | | target function (ml) not normalized (work): 703445.422730 | | target function (ml) not normalized (free): 14738.135195 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1383 0.1474 5.7062 5.7883| | 2: 2.94 - 2.33 1.00 7339 128 0.1085 0.1376 5.0934 5.2058| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1153 4.6556 4.7276| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1070 4.3949 4.581| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.0976 4.1528 4.2399| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1080 3.9474 4.082| | 7: 1.62 - 1.54 0.99 7104 148 0.0891 0.0980 3.8018 3.9482| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1317 3.7002 3.9005| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1115 3.6214 3.7492| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1190 3.5556 3.6809| | 11: 1.36 - 1.32 0.99 6997 151 0.0990 0.1130 3.4841 3.5911| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1130 3.4587 3.5841| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1242 3.4369 3.5621| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1586 3.4339 3.6817| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1251 3.4493 3.4937| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1542 3.4658 3.6637| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1225 3.4336 3.4418| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1698 3.4384 3.5292| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1742 3.4191 3.5933| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1574 3.4098 3.431| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2128 3.4188 3.5049| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1959 3.4133 3.4177| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2037 3.4342 3.4893| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2252 3.4363 3.5095| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2509 3.4499 3.5261| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2862 3.4167 3.4235| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2807 3.4687 3.3968| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 12.01 1.00 0.96 11764.44| | 2: 2.94 - 2.33 7339 128 0.92 13.03 0.99 0.96 5313.48| | 3: 2.33 - 2.04 6939 150 0.96 7.62 1.01 0.96 1694.97| | 4: 2.04 - 1.85 7170 155 0.96 7.67 1.00 0.96 1012.15| | 5: 1.85 - 1.72 7113 159 0.96 8.06 1.00 0.96 635.51| | 6: 1.72 - 1.62 7102 142 0.96 8.06 1.00 0.96 447.28| | 7: 1.62 - 1.54 7104 148 0.96 8.21 1.01 0.97 341.17| | 8: 1.54 - 1.47 6798 152 0.96 8.34 1.01 0.97 282.12| | 9: 1.47 - 1.41 6938 155 0.96 8.52 1.00 0.98 232.79| | 10: 1.41 - 1.36 7022 150 0.96 8.94 1.00 0.97 203.58| | 11: 1.36 - 1.32 6997 151 0.96 8.94 0.99 0.96 175.45| | 12: 1.32 - 1.28 6975 149 0.96 8.99 0.98 0.95 161.18| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.01 0.96 158.34| | 14: 1.25 - 1.22 7015 112 0.95 10.71 1.01 0.97 163.62| | 15: 1.22 - 1.19 6956 137 0.95 11.26 1.01 0.98 167.30| | 16: 1.19 - 1.17 6604 132 0.95 11.45 1.01 0.96 160.94| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.96 153.92| | 18: 1.14 - 1.12 6875 142 0.94 12.70 1.01 0.95 146.98| | 19: 1.12 - 1.10 6948 106 0.93 14.09 1.00 0.95 150.31| | 20: 1.10 - 1.08 6884 147 0.92 15.18 1.00 0.94 149.85| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.93 153.54| | 22: 1.07 - 1.05 6836 135 0.89 18.32 0.99 0.93 155.62| | 23: 1.05 - 1.03 6827 159 0.87 20.55 0.99 0.92 165.59| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.93 179.72| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.98 0.90 182.40| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.89 176.88| | 27: 0.99 - 0.98 6647 131 0.82 26.31 0.99 0.87 161.58| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.98 max = 11764.44 mean = 955.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.32| |phase err.(test): min = 0.00 max = 89.40 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1357 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1503 n_refl.: 191130 remove outliers: r(all,work,free)=0.1415 0.1414 0.1503 n_refl.: 191130 overall B=-0.05 to atoms: r(all,work,free)=0.1407 0.1405 0.1498 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1356 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1356 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3780 348.813 317.057 0.361 0.976 0.191 13.296-10.522 97.03 97 1 0.2450 481.578 462.062 0.662 0.977 0.131 10.503-8.327 97.80 175 3 0.2192 502.309 494.110 0.837 0.978 0.105 8.318-6.595 100.00 360 8 0.2187 375.845 370.390 0.860 0.978 0.086 6.588-5.215 100.00 711 7 0.1958 345.364 334.702 0.863 0.978 0.070 5.214-4.128 98.38 1367 28 0.1274 505.163 499.262 0.951 0.979 0.039 4.126-3.266 94.74 2603 46 0.1191 460.483 452.418 1.015 0.981 0.005 3.266-2.585 99.86 5447 97 0.1136 310.631 306.925 0.999 0.982 0.000 2.585-2.046 97.45 10613 204 0.0967 234.353 231.626 1.005 0.984 0.000 2.046-1.619 99.39 21536 464 0.0911 138.702 137.326 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0943 74.669 74.015 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.057 38.329 0.979 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0116 ================= 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 : 0.2045 0.1973 0.082 5.100 5.2 78.0 14.6 805 0.000 1_bss: 0.1809 0.1909 0.082 5.100 5.2 78.0 14.6 805 0.000 1_settarget: 0.1809 0.1909 0.082 5.100 5.2 78.0 14.6 805 0.000 1_nqh: 0.1812 0.1913 0.082 5.100 5.2 78.0 14.6 805 0.002 1_weight: 0.1812 0.1913 0.082 5.100 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1273 0.1505 0.038 1.158 5.2 78.0 14.6 805 0.155 1_adp: 0.1298 0.1570 0.038 1.158 5.2 73.0 15.0 805 0.155 1_regHadp: 0.1297 0.1565 0.038 1.158 5.2 73.0 15.0 805 0.155 1_occ: 0.1282 0.1555 0.038 1.158 5.2 73.0 15.0 805 0.155 2_bss: 0.1274 0.1545 0.038 1.158 5.4 73.2 15.1 805 0.155 2_settarget: 0.1274 0.1545 0.038 1.158 5.4 73.2 15.1 805 0.155 2_updatecdl: 0.1274 0.1545 0.038 1.173 5.4 73.2 15.1 805 0.155 2_nqh: 0.1274 0.1545 0.038 1.173 5.4 73.2 15.1 805 0.155 2_sol: 0.1270 0.1509 0.038 1.173 5.4 73.2 16.1 890 n/a 2_weight: 0.1270 0.1509 0.038 1.173 5.4 73.2 16.1 890 n/a 2_xyzrec: 0.1256 0.1534 0.040 1.138 5.4 73.2 16.1 890 n/a 2_adp: 0.1232 0.1512 0.040 1.138 5.4 68.2 16.2 890 n/a 2_regHadp: 0.1232 0.1513 0.040 1.138 5.4 68.2 16.2 890 n/a 2_occ: 0.1226 0.1513 0.040 1.138 5.4 68.2 16.2 890 n/a 3_bss: 0.1233 0.1519 0.040 1.138 5.4 68.2 16.2 890 n/a 3_settarget: 0.1233 0.1519 0.040 1.138 5.4 68.2 16.2 890 n/a 3_updatecdl: 0.1233 0.1519 0.040 1.142 5.4 68.2 16.2 890 n/a 3_nqh: 0.1233 0.1519 0.040 1.142 5.4 68.2 16.2 890 n/a 3_sol: 0.1248 0.1514 0.040 1.142 5.4 68.2 15.4 893 n/a 3_weight: 0.1248 0.1514 0.040 1.142 5.4 68.2 15.4 893 n/a 3_xyzrec: 0.1237 0.1434 0.035 1.097 5.4 68.2 15.4 893 n/a 3_adp: 0.1234 0.1397 0.035 1.097 5.5 67.8 15.3 893 n/a 3_regHadp: 0.1235 0.1397 0.035 1.097 5.5 67.8 15.3 893 n/a 3_occ: 0.1229 0.1388 0.035 1.097 5.5 67.8 15.3 893 n/a 4_bss: 0.1224 0.1378 0.035 1.097 5.5 67.7 15.2 893 n/a 4_settarget: 0.1224 0.1378 0.035 1.097 5.5 67.7 15.2 893 n/a 4_updatecdl: 0.1224 0.1378 0.035 1.101 5.5 67.7 15.2 893 n/a 4_nqh: 0.1224 0.1378 0.035 1.101 5.5 67.7 15.2 893 n/a 4_sol: 0.1209 0.1364 0.035 1.101 5.5 67.7 15.0 872 n/a 4_weight: 0.1209 0.1364 0.035 1.101 5.5 67.7 15.0 872 n/a 4_xyzrec: 0.1206 0.1369 0.036 1.124 5.5 67.7 15.0 872 n/a 4_adp: 0.1199 0.1368 0.036 1.124 5.5 67.3 14.9 872 n/a 4_regHadp: 0.1199 0.1368 0.036 1.124 5.5 67.3 14.9 872 n/a 4_occ: 0.1197 0.1365 0.036 1.124 5.5 67.3 14.9 872 n/a 5_bss: 0.1196 0.1362 0.036 1.124 5.5 67.3 14.9 872 n/a 5_settarget: 0.1196 0.1362 0.036 1.124 5.5 67.3 14.9 872 n/a 5_updatecdl: 0.1196 0.1362 0.036 1.124 5.5 67.3 14.9 872 n/a 5_nqh: 0.1196 0.1362 0.036 1.124 5.5 67.3 14.9 872 n/a 5_sol: 0.1192 0.1355 0.036 1.124 5.5 67.3 15.0 892 n/a 5_weight: 0.1192 0.1355 0.036 1.124 5.5 67.3 15.0 892 n/a 5_xyzrec: 0.1196 0.1366 0.037 1.130 5.5 67.3 15.0 892 n/a 5_adp: 0.1199 0.1369 0.037 1.130 5.6 67.0 14.9 892 n/a 5_regHadp: 0.1200 0.1369 0.037 1.130 5.6 67.0 14.9 892 n/a 5_occ: 0.1198 0.1369 0.037 1.130 5.6 67.0 14.9 892 n/a 6_bss: 0.1197 0.1368 0.037 1.130 5.5 67.0 14.9 892 n/a 6_settarget: 0.1197 0.1368 0.037 1.130 5.5 67.0 14.9 892 n/a 6_updatecdl: 0.1197 0.1368 0.037 1.130 5.5 67.0 14.9 892 n/a 6_nqh: 0.1197 0.1368 0.037 1.130 5.5 67.0 14.9 892 n/a 6_sol: 0.1195 0.1346 0.037 1.130 5.5 67.0 14.9 903 n/a 6_weight: 0.1195 0.1346 0.037 1.130 5.5 67.0 14.9 903 n/a 6_xyzrec: 0.1198 0.1355 0.037 1.126 5.5 67.0 14.9 903 n/a 6_adp: 0.1204 0.1360 0.037 1.126 5.6 65.7 14.8 903 n/a 6_regHadp: 0.1204 0.1361 0.037 1.126 5.6 65.7 14.8 903 n/a 6_occ: 0.1201 0.1361 0.037 1.126 5.6 65.7 14.8 903 n/a 7_bss: 0.1201 0.1358 0.037 1.126 5.4 65.5 14.6 903 n/a 7_settarget: 0.1201 0.1358 0.037 1.126 5.4 65.5 14.6 903 n/a 7_updatecdl: 0.1201 0.1358 0.037 1.126 5.4 65.5 14.6 903 n/a 7_nqh: 0.1201 0.1358 0.037 1.126 5.4 65.5 14.6 903 n/a 7_sol: 0.1201 0.1355 0.037 1.126 5.4 65.5 14.6 899 n/a 7_weight: 0.1201 0.1355 0.037 1.126 5.4 65.5 14.6 899 n/a 7_xyzrec: 0.1203 0.1360 0.038 1.131 5.4 65.5 14.6 899 n/a 7_adp: 0.1205 0.1363 0.038 1.131 5.4 64.1 14.5 899 n/a 7_regHadp: 0.1205 0.1364 0.038 1.131 5.4 64.1 14.5 899 n/a 7_occ: 0.1203 0.1362 0.038 1.131 5.4 64.1 14.5 899 n/a 8_bss: 0.1194 0.1353 0.038 1.131 5.5 64.2 14.6 899 n/a 8_settarget: 0.1194 0.1353 0.038 1.131 5.5 64.2 14.6 899 n/a 8_updatecdl: 0.1194 0.1353 0.038 1.131 5.5 64.2 14.6 899 n/a 8_nqh: 0.1194 0.1353 0.038 1.131 5.5 64.2 14.6 899 n/a 8_sol: 0.1193 0.1345 0.038 1.131 5.5 64.2 14.6 898 n/a 8_weight: 0.1193 0.1345 0.038 1.131 5.5 64.2 14.6 898 n/a 8_xyzrec: 0.1197 0.1359 0.039 1.119 5.5 64.2 14.6 898 n/a 8_adp: 0.1198 0.1363 0.039 1.119 5.5 63.8 14.6 898 n/a 8_regHadp: 0.1198 0.1363 0.039 1.119 5.5 63.8 14.6 898 n/a 8_occ: 0.1197 0.1364 0.039 1.119 5.5 63.8 14.6 898 n/a 9_bss: 0.1195 0.1362 0.039 1.119 5.5 63.8 14.6 898 n/a 9_settarget: 0.1195 0.1362 0.039 1.119 5.5 63.8 14.6 898 n/a 9_updatecdl: 0.1195 0.1362 0.039 1.118 5.5 63.8 14.6 898 n/a 9_nqh: 0.1195 0.1362 0.039 1.118 5.5 63.8 14.6 898 n/a 9_sol: 0.1194 0.1356 0.039 1.118 5.5 63.8 14.6 901 n/a 9_weight: 0.1194 0.1356 0.039 1.118 5.5 63.8 14.6 901 n/a 9_xyzrec: 0.1199 0.1362 0.040 1.110 5.5 63.8 14.6 901 n/a 9_adp: 0.1199 0.1365 0.040 1.110 5.6 62.8 14.6 901 n/a 9_regHadp: 0.1199 0.1365 0.040 1.110 5.6 62.8 14.6 901 n/a 9_occ: 0.1198 0.1365 0.040 1.110 5.6 62.8 14.6 901 n/a 10_bss: 0.1197 0.1363 0.040 1.110 5.6 62.8 14.5 901 n/a 10_settarget: 0.1197 0.1363 0.040 1.110 5.6 62.8 14.5 901 n/a 10_updatecdl: 0.1197 0.1363 0.040 1.111 5.6 62.8 14.5 901 n/a 10_setrh: 0.1197 0.1364 0.040 1.111 5.6 62.8 14.5 901 n/a 10_nqh: 0.1197 0.1364 0.040 1.111 5.6 62.8 14.5 901 n/a 10_sol: 0.1198 0.1352 0.040 1.111 5.6 62.8 14.5 896 n/a 10_weight: 0.1198 0.1352 0.040 1.111 5.6 62.8 14.5 896 n/a 10_xyzrec: 0.1199 0.1355 0.040 1.145 5.6 62.8 14.5 896 n/a 10_adp: 0.1199 0.1356 0.040 1.145 5.6 62.5 14.5 896 n/a 10_regHadp: 0.1200 0.1356 0.040 1.145 5.6 62.5 14.5 896 n/a 10_occ: 0.1198 0.1357 0.040 1.145 5.6 62.5 14.5 896 n/a end: 0.1197 0.1356 0.040 1.145 5.5 62.4 14.5 896 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3537830_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3537830_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.2500 Refinement macro-cycles (run) : 12121.4200 Write final files (write_after_run_outputs) : 165.3600 Total : 12293.0300 Total CPU time: 3.42 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:04 PST -0800 (1736736124.92 s) Start R-work = 0.1809, R-free = 0.1909 Final R-work = 0.1197, R-free = 0.1356 =============================================================================== Job complete usr+sys time: 12571.34 seconds wall clock time: 210 minutes 30.70 seconds (12630.70 seconds total)