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_7424180.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7424180.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7424180.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.47, per 1000 atoms: 0.37 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: 2.641 distance_ideal: 2.720 ideal - model: 0.079 slack: 0.000 delta_slack: 0.079 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: 2.597 distance_ideal: 2.710 ideal - model: 0.113 slack: 0.000 delta_slack: 0.113 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: 1.18 Conformation dependent library (CDL) restraints added in 209.2 milliseconds Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.00: 533 1.00 - 1.22: 2568 1.22 - 1.44: 1350 1.44 - 1.66: 1396 1.66 - 1.88: 87 Bond restraints: 5934 Sorted by residual: bond pdb=" CA ILE A 134 " pdb=" C ILE A 134 " ideal model delta sigma weight residual 1.522 1.347 0.176 7.10e-03 1.98e+04 6.11e+02 bond pdb=" NE ARG A 143 " pdb=" CZ ARG A 143 " ideal model delta sigma weight residual 1.326 1.539 -0.213 1.10e-02 8.26e+03 3.74e+02 bond pdb=" N VAL B 150 " pdb=" H VAL B 150 " ideal model delta sigma weight residual 0.860 1.243 -0.383 2.00e-02 2.50e+03 3.67e+02 bond pdb=" OG1 THR A 86 " pdb=" HG1 THR A 86 " ideal model delta sigma weight residual 0.840 1.220 -0.380 2.00e-02 2.50e+03 3.61e+02 bond pdb=" N SER A 36 " pdb=" CA SER A 36 " ideal model delta sigma weight residual 1.455 1.213 0.242 1.30e-02 5.92e+03 3.46e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 5566 4.13 - 8.26: 3529 8.26 - 12.38: 1411 12.38 - 16.51: 268 16.51 - 20.64: 36 Bond angle restraints: 10810 Sorted by residual: angle pdb=" C THR A 125 " pdb=" N GLY A 126 " pdb=" CA GLY A 126 " ideal model delta sigma weight residual 120.51 140.12 -19.61 1.22e+00 6.72e-01 2.58e+02 angle pdb=" O ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 121.71 131.96 -10.25 6.40e-01 2.44e+00 2.56e+02 angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" O ILE A 134 " ideal model delta sigma weight residual 119.51 128.58 -9.07 6.20e-01 2.60e+00 2.14e+02 angle pdb=" CA HIS A 179 " pdb=" C HIS A 179 " pdb=" O HIS A 179 " ideal model delta sigma weight residual 120.42 105.05 15.37 1.06e+00 8.90e-01 2.10e+02 angle pdb=" CA VAL B 102 " pdb=" C VAL B 102 " pdb=" O VAL B 102 " ideal model delta sigma weight residual 120.48 105.68 14.80 1.06e+00 8.90e-01 1.95e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 1822 16.01 - 32.03: 150 32.03 - 48.04: 50 48.04 - 64.05: 23 64.05 - 80.06: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -155.81 -24.19 0 5.00e+00 4.00e-02 2.34e+01 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 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.281: 265 0.281 - 0.561: 163 0.561 - 0.842: 52 0.842 - 1.122: 11 1.122 - 1.402: 1 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA THR A 91 " pdb=" N THR A 91 " pdb=" C THR A 91 " pdb=" CB THR A 91 " both_signs ideal model delta sigma weight residual False 2.53 3.93 -1.40 2.00e-01 2.50e+01 4.92e+01 chirality pdb=" CB THR B 111 " pdb=" CA THR B 111 " pdb=" OG1 THR B 111 " pdb=" CG2 THR B 111 " both_signs ideal model delta sigma weight residual False 2.55 3.60 -1.05 2.00e-01 2.50e+01 2.75e+01 chirality pdb=" CA ASP B 132 " pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CB ASP B 132 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.70e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.079 2.00e-02 2.50e+03 6.00e-02 1.44e+02 pdb=" CG TRP A 146 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.057 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.060 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.124 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.011 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.065 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.036 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.122 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.026 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.020 2.00e-02 2.50e+03 5.93e-02 1.41e+02 pdb=" CG TRP A 139 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.034 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.088 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.107 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.031 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.022 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.136 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.097 2.00e-02 2.50e+03 6.59e-02 1.30e+02 pdb=" CG PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.111 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.100 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.094 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.063 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.061 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.006 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.60: 27 1.60 - 2.35: 2212 2.35 - 3.10: 22198 3.10 - 3.85: 33045 3.85 - 4.60: 52762 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110244 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.847 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.913 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.020 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.106 2.620 nonbonded pdb=" HG2 GLN B 184 " pdb=" O HOH S1490 " model vdw 1.206 2.620 ... (remaining 110239 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_7424180_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= 0.2040 r_free= 0.1960 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.305477 | | target function (ml) not normalized (work): 806471.878060 | | target function (ml) not normalized (free): 16563.894952 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2140 0.1992 6.6806 6.3313| | 2: 2.94 - 2.33 1.00 7339 128 0.1621 0.1466 5.5445 5.5683| | 3: 2.33 - 2.04 0.96 6939 150 0.1643 0.1442 5.1406 5.0707| | 4: 2.04 - 1.85 1.00 7170 155 0.1744 0.1598 4.9663 5.0353| | 5: 1.85 - 1.72 0.99 7113 159 0.1930 0.1609 4.8001 4.7286| | 6: 1.72 - 1.62 0.99 7102 142 0.2018 0.1999 4.6781 4.7152| | 7: 1.62 - 1.54 0.99 7104 148 0.2021 0.1813 4.5771 4.5788| | 8: 1.54 - 1.47 0.96 6798 152 0.2041 0.2265 4.4765 4.5465| | 9: 1.47 - 1.41 0.98 6938 155 0.2085 0.2453 4.3982 4.5463| | 10: 1.41 - 1.36 0.99 7022 150 0.2127 0.2307 4.3378 4.4018| | 11: 1.36 - 1.32 0.99 6997 151 0.2101 0.2199 4.2446 4.3213| | 12: 1.32 - 1.28 0.98 6976 149 0.2114 0.1877 4.1837 4.1821| | 13: 1.28 - 1.25 0.98 6907 166 0.2039 0.2116 4.1251 4.1765| | 14: 1.25 - 1.22 0.98 7015 113 0.2097 0.2140 4.0874 4.2281| | 15: 1.22 - 1.19 0.98 6957 137 0.2076 0.2108 4.0389 4.0896| | 16: 1.19 - 1.17 0.93 6604 132 0.2114 0.2230 4.0084 4.1176| | 17: 1.17 - 1.14 0.98 6941 135 0.2180 0.1812 3.9616 3.9674| | 18: 1.14 - 1.12 0.98 6875 142 0.2246 0.2388 3.9346 3.9488| | 19: 1.12 - 1.10 0.97 6949 106 0.2294 0.2306 3.8821 3.9245| | 20: 1.10 - 1.08 0.97 6884 147 0.2311 0.2212 3.8178 3.8229| | 21: 1.08 - 1.07 0.97 6852 152 0.2433 0.2612 3.7922 3.8297| | 22: 1.07 - 1.05 0.97 6838 135 0.2605 0.2439 3.7628 3.7488| | 23: 1.05 - 1.03 0.97 6829 159 0.2735 0.2640 3.737 3.8182| | 24: 1.03 - 1.02 0.96 6785 133 0.2881 0.2532 3.7084 3.7207| | 25: 1.02 - 1.01 0.93 6552 130 0.3093 0.2867 3.6807 3.705| | 26: 1.01 - 0.99 0.96 6767 158 0.3205 0.3394 3.6298 3.6473| | 27: 0.99 - 0.98 0.94 6648 131 0.3443 0.3246 3.6396 3.6494| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.86 0.91 0.98 37259.42| | 2: 2.94 - 2.33 7339 128 0.85 21.28 1.08 1.02 15307.38| | 3: 2.33 - 2.04 6939 150 0.94 11.60 1.11 1.06 3644.48| | 4: 2.04 - 1.85 7170 155 0.93 12.45 1.11 1.06 2419.20| | 5: 1.85 - 1.72 7113 159 0.92 14.54 1.11 1.08 1851.19| | 6: 1.72 - 1.62 7102 142 0.91 16.10 1.12 1.08 1547.11| | 7: 1.62 - 1.54 7104 148 0.89 17.55 1.10 1.08 1340.85| | 8: 1.54 - 1.47 6798 152 0.88 19.22 1.10 1.06 1244.05| | 9: 1.47 - 1.41 6938 155 0.87 20.44 1.10 1.06 1125.17| | 10: 1.41 - 1.36 7022 150 0.86 21.53 1.09 1.06 989.18| | 11: 1.36 - 1.32 6997 151 0.86 20.82 1.08 1.05 805.12| | 12: 1.32 - 1.28 6976 149 0.87 19.88 1.08 1.04 653.44| | 13: 1.28 - 1.25 6907 166 0.88 19.48 1.07 1.04 588.52| | 14: 1.25 - 1.22 7015 113 0.87 20.55 1.07 1.03 569.83| | 15: 1.22 - 1.19 6957 137 0.86 21.32 1.07 1.03 558.50| | 16: 1.19 - 1.17 6604 132 0.87 20.84 1.07 1.02 502.78| | 17: 1.17 - 1.14 6941 135 0.87 20.77 1.08 1.02 436.62| | 18: 1.14 - 1.12 6875 142 0.87 20.45 1.08 1.01 379.37| | 19: 1.12 - 1.10 6949 106 0.86 21.34 1.07 1.01 363.01| | 20: 1.10 - 1.08 6884 147 0.86 22.03 1.06 1.00 340.20| | 21: 1.08 - 1.07 6852 152 0.84 23.63 1.06 0.98 331.98| | 22: 1.07 - 1.05 6838 135 0.83 24.96 1.06 0.97 312.98| | 23: 1.05 - 1.03 6829 159 0.81 26.61 1.06 0.98 313.26| | 24: 1.03 - 1.02 6785 133 0.80 27.79 1.05 1.00 306.76| | 25: 1.02 - 1.01 6552 130 0.78 29.94 1.03 0.96 305.03| | 26: 1.01 - 0.99 6767 158 0.75 32.59 1.03 0.92 299.99| | 27: 0.99 - 0.98 6648 131 0.73 34.35 1.04 0.90 303.60| |alpha: min = 0.90 max = 1.08 mean = 1.02| |beta: min = 299.99 max = 37259.42 mean = 2875.82| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 21.51| |phase err.(test): min = 0.00 max = 89.03 mean = 21.53| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.266 2950 Z= 5.543 Angle : 5.271 19.612 4018 Z= 3.748 Chirality : 0.381 1.402 492 Planarity : 0.032 0.135 512 Dihedral : 12.639 80.061 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.61 % Allowed : 3.23 % Favored : 95.16 % Cbeta Deviations : 29.21 % 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: -2.13 (0.40), residues: 386 helix: -2.51 (0.32), residues: 144 sheet: -0.72 (0.55), residues: 82 loop : -0.41 (0.52), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.026 ARG B 149 TYR 0.108 0.031 TYR B 192 PHE 0.090 0.038 PHE A 164 TRP 0.104 0.040 TRP A 146 HIS 0.065 0.023 HIS B 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= 0.2040 r_free= 0.1960 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.305477 | | target function (ml) not normalized (work): 806471.878060 | | target function (ml) not normalized (free): 16563.894952 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2038 0.2040 0.1960 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2038 0.2040 0.1960 n_refl.: 191155 remove outliers: r(all,work,free)=0.2038 0.2041 0.1960 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2036 0.2038 0.1960 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1811 0.1809 0.1893 n_refl.: 191145 remove outliers: r(all,work,free)=0.1809 0.1807 0.1893 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 0.4089 402.814 291.330 0.420 0.935 0.301 13.296-10.522 99.01 99 1 0.2466 528.187 519.008 0.760 0.937 0.253 10.503-8.327 98.90 177 3 0.2442 564.205 559.632 0.942 0.937 0.230 8.318-6.595 100.00 360 8 0.2468 414.736 402.967 0.943 0.937 0.175 6.588-5.215 100.00 711 7 0.2300 381.101 366.314 0.925 0.937 0.170 5.214-4.128 98.38 1367 28 0.1485 557.435 548.699 1.039 0.938 0.060 4.126-3.266 94.74 2603 46 0.1357 508.132 498.664 1.105 0.938 0.019 3.266-2.585 99.86 5447 97 0.1454 342.774 337.549 1.080 0.938 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 254.382 1.086 0.938 0.000 2.046-1.619 99.39 21536 464 0.1630 153.054 149.919 1.104 0.938 0.000 1.619-1.281 98.00 42464 925 0.1933 82.395 80.466 1.089 0.937 0.000 1.281-0.980 96.53 101826 2056 0.2324 44.203 42.006 1.075 0.936 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0431 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1807 r_free=0.1893 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1807 r_free=0.1898 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.056934 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 564.435452 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1267 0.1492 0.0225 0.038 1.2 10.9 0.0 0.3 0 11.528 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.67 14.92 2.25 1.117 13.095 564.435 0.018 12.98 15.69 2.70 1.250 13.359 564.435 0.017 Individual atomic B min max mean iso aniso Overall: 5.20 73.03 15.06 1.40 435 3274 Protein: 5.20 40.31 11.04 1.40 0 2902 Water: 6.39 73.03 29.55 N/A 435 370 Other: 16.04 30.51 23.28 N/A 0 2 Chain A: 5.34 59.82 13.09 N/A 0 1626 Chain B: 5.20 73.03 12.82 N/A 0 1648 Chain S: 11.69 64.73 30.95 N/A 435 0 Histogram: Values Number of atoms 5.20 - 11.99 2158 11.99 - 18.77 641 18.77 - 25.55 317 25.55 - 32.33 259 32.33 - 39.12 167 39.12 - 45.90 97 45.90 - 52.68 46 52.68 - 59.46 19 59.46 - 66.25 4 66.25 - 73.03 1 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1569 r_work=0.1298 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1563 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1553 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015581 | | target function (ls_wunit_k1) not normalized (work): 2918.262463 | | target function (ls_wunit_k1) not normalized (free): 115.404675 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1553 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1472 0.1470 0.1635 n_refl.: 191138 remove outliers: r(all,work,free)=0.1472 0.1470 0.1635 n_refl.: 191138 overall B=0.15 to atoms: r(all,work,free)=0.1494 0.1491 0.1644 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1275 0.1543 n_refl.: 191138 remove outliers: r(all,work,free)=0.1281 0.1275 0.1542 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 0.3629 402.814 376.082 0.468 1.002 0.287 13.296-10.522 99.01 99 1 0.2058 528.187 519.026 0.705 1.004 0.245 10.503-8.327 98.90 177 3 0.1729 564.205 562.464 0.849 1.004 0.223 8.318-6.595 100.00 360 8 0.1720 414.736 411.947 0.874 1.004 0.165 6.588-5.215 100.00 711 7 0.1539 381.101 373.337 0.852 1.004 0.160 5.214-4.128 98.38 1367 28 0.0905 557.435 554.771 0.936 1.005 0.045 4.126-3.266 94.74 2603 46 0.0836 508.132 504.145 1.001 1.005 0.014 3.266-2.585 99.86 5447 97 0.0925 342.774 340.277 0.984 1.005 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.478 0.996 1.006 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.406 1.012 1.006 0.000 1.619-1.281 98.00 42464 925 0.1280 82.395 81.420 1.004 1.007 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.126 0.981 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0335 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1542 | n_water=805 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1279 r_free=0.1548 | n_water=795 | time (s): 103.730 (total time: 105.970) Filter (q & B) r_work=0.1280 r_free=0.1547 | n_water=791 | time (s): 5.470 (total time: 111.440) Compute maps r_work=0.1280 r_free=0.1547 | n_water=791 | time (s): 1.960 (total time: 113.400) Filter (map) r_work=0.1306 r_free=0.1533 | n_water=658 | time (s): 4.170 (total time: 117.570) Find peaks r_work=0.1306 r_free=0.1533 | n_water=658 | time (s): 0.590 (total time: 118.160) Add new water r_work=0.1328 r_free=0.1559 | n_water=948 | time (s): 4.310 (total time: 122.470) Refine new water occ: r_work=0.1286 r_free=0.1516 adp: r_work=0.1274 r_free=0.1512 occ: r_work=0.1277 r_free=0.1511 adp: r_work=0.1271 r_free=0.1511 occ: r_work=0.1272 r_free=0.1508 adp: r_work=0.1270 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1270 r_free=0.1510 r_work=0.1270 r_free=0.1510 | n_water=948 | time (s): 75.860 (total time: 198.330) Filter (q & B) r_work=0.1273 r_free=0.1515 | n_water=882 | time (s): 4.270 (total time: 202.600) Filter (dist only) r_work=0.1273 r_free=0.1513 | n_water=881 | time (s): 116.480 (total time: 319.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.883056 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 590.711306 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1257 0.1527 0.0270 0.042 1.2 17.8 0.0 0.3 0 12.442 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.27 2.70 2.046 15.155 590.711 0.015 12.31 15.10 2.79 2.425 15.236 590.711 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 70.11 16.31 1.22 513 3272 Protein: 5.38 40.80 10.99 1.22 0 2902 Water: 6.57 70.11 33.82 N/A 513 368 Other: 16.16 32.93 24.54 N/A 0 2 Chain A: 5.49 55.66 13.03 N/A 0 1624 Chain B: 5.38 68.17 12.85 N/A 0 1648 Chain S: 13.16 70.11 37.80 N/A 513 0 Histogram: Values Number of atoms 5.38 - 11.86 2101 11.86 - 18.33 696 18.33 - 24.80 247 24.80 - 31.27 228 31.27 - 37.75 161 37.75 - 44.22 173 44.22 - 50.69 105 50.69 - 57.16 38 57.16 - 63.63 25 63.63 - 70.11 11 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1511 r_work=0.1232 r_free=0.1511 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1511 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1508 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 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= 0.1508 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013493 | | target function (ls_wunit_k1) not normalized (work): 2527.263153 | | target function (ls_wunit_k1) not normalized (free): 103.919015 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1508 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1438 0.1435 0.1604 n_refl.: 191137 remove outliers: r(all,work,free)=0.1438 0.1435 0.1604 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1432 0.1602 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1512 n_refl.: 191137 remove outliers: r(all,work,free)=0.1238 0.1233 0.1512 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 0.3337 402.814 376.883 0.489 0.961 0.268 13.296-10.522 99.01 99 1 0.1955 528.187 520.264 0.755 0.962 0.226 10.503-8.327 98.90 177 3 0.1443 564.205 566.048 0.919 0.962 0.191 8.318-6.595 100.00 360 8 0.1548 414.736 414.931 0.938 0.962 0.151 6.588-5.215 100.00 711 7 0.1333 381.101 376.760 0.914 0.962 0.130 5.214-4.128 98.38 1367 28 0.0828 557.435 556.218 0.996 0.962 0.080 4.126-3.266 94.74 2603 46 0.0771 508.132 505.216 1.061 0.962 0.014 3.266-2.585 99.86 5447 97 0.0864 342.774 341.292 1.048 0.961 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.742 1.060 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.603 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1250 82.395 81.344 1.074 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1867 44.202 42.219 1.059 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0614 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1512 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1512 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1512 | n_water=881 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1234 r_free=0.1511 | n_water=876 | time (s): 114.880 (total time: 117.400) Filter (q & B) r_work=0.1234 r_free=0.1511 | n_water=874 | time (s): 5.380 (total time: 122.780) Compute maps r_work=0.1234 r_free=0.1511 | n_water=874 | time (s): 1.780 (total time: 124.560) Filter (map) r_work=0.1273 r_free=0.1513 | n_water=688 | time (s): 5.430 (total time: 129.990) Find peaks r_work=0.1273 r_free=0.1513 | n_water=688 | time (s): 0.640 (total time: 130.630) Add new water r_work=0.1294 r_free=0.1542 | n_water=998 | time (s): 4.200 (total time: 134.830) Refine new water occ: r_work=0.1252 r_free=0.1512 adp: r_work=0.1252 r_free=0.1513 occ: r_work=0.1248 r_free=0.1506 adp: r_work=0.1247 r_free=0.1508 occ: r_work=0.1244 r_free=0.1502 adp: r_work=0.1244 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1503 r_work=0.1244 r_free=0.1503 | n_water=998 | time (s): 271.440 (total time: 406.270) Filter (q & B) r_work=0.1248 r_free=0.1506 | n_water=867 | time (s): 5.440 (total time: 411.710) Filter (dist only) r_work=0.1248 r_free=0.1506 | n_water=866 | time (s): 113.610 (total time: 525.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.652654 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.267916 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 0.1236 0.1432 0.0195 0.036 1.1 6.5 0.0 0.0 0 0.826 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.32 1.95 1.937 14.620 15.268 3.936 12.31 13.95 1.64 2.152 14.547 15.268 3.899 Individual atomic B min max mean iso aniso Overall: 5.53 67.92 15.36 1.07 501 3269 Protein: 5.53 37.60 10.80 1.07 0 2902 Water: 6.69 67.92 30.62 N/A 501 365 Other: 14.14 29.34 21.74 N/A 0 2 Chain A: 5.54 55.12 12.83 N/A 0 1623 Chain B: 5.53 67.92 12.60 N/A 0 1646 Chain S: 13.67 66.96 32.64 N/A 501 0 Histogram: Values Number of atoms 5.53 - 11.77 2119 11.77 - 18.01 694 18.01 - 24.25 290 24.25 - 30.49 240 30.49 - 36.72 167 36.72 - 42.96 142 42.96 - 49.20 82 49.20 - 55.44 24 55.44 - 61.68 7 61.68 - 67.92 5 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1395 r_work=0.1232 r_free=0.1396 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1396 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1386 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1386 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892927 | | target function (ml) not normalized (work): 729129.608276 | | target function (ml) not normalized (free): 15220.979491 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1227 0.1386 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1445 0.1444 0.1485 n_refl.: 191137 remove outliers: r(all,work,free)=0.1445 0.1444 0.1485 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1438 0.1438 0.1481 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1224 0.1382 n_refl.: 191137 remove outliers: r(all,work,free)=0.1226 0.1223 0.1382 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3718 398.895 357.497 0.422 0.946 0.241 13.296-10.522 98.02 98 1 0.2399 528.900 508.561 0.709 0.947 0.215 10.503-8.327 98.90 177 3 0.1964 564.205 562.759 0.882 0.947 0.210 8.318-6.595 100.00 360 8 0.2032 414.736 410.845 0.899 0.947 0.135 6.588-5.215 100.00 711 7 0.1796 381.101 371.345 0.888 0.947 0.120 5.214-4.128 98.38 1367 28 0.1157 557.435 552.359 0.972 0.947 0.080 4.126-3.266 94.74 2603 46 0.1083 508.132 501.789 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1073 342.774 339.272 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0961 258.603 255.870 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0977 153.054 151.455 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1055 82.395 81.495 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1696 44.202 42.318 1.037 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1067 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1382 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1382 | n_water=866 | time (s): 2.610 (total time: 2.610) Filter (dist) r_work=0.1224 r_free=0.1383 | n_water=865 | time (s): 110.020 (total time: 112.630) Filter (q & B) r_work=0.1224 r_free=0.1383 | n_water=858 | time (s): 5.380 (total time: 118.010) Compute maps r_work=0.1224 r_free=0.1383 | n_water=858 | time (s): 2.380 (total time: 120.390) Filter (map) r_work=0.1246 r_free=0.1387 | n_water=721 | time (s): 6.040 (total time: 126.430) Find peaks r_work=0.1246 r_free=0.1387 | n_water=721 | time (s): 0.890 (total time: 127.320) Add new water r_work=0.1261 r_free=0.1399 | n_water=953 | time (s): 5.110 (total time: 132.430) Refine new water occ: r_work=0.1214 r_free=0.1368 adp: r_work=0.1207 r_free=0.1361 occ: r_work=0.1205 r_free=0.1363 adp: r_work=0.1205 r_free=0.1362 occ: r_work=0.1203 r_free=0.1363 adp: r_work=0.1203 r_free=0.1362 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1362 r_work=0.1203 r_free=0.1362 | n_water=953 | time (s): 364.260 (total time: 496.690) Filter (q & B) r_work=0.1207 r_free=0.1369 | n_water=862 | time (s): 4.360 (total time: 501.050) Filter (dist only) r_work=0.1207 r_free=0.1368 | n_water=861 | time (s): 110.190 (total time: 611.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550878 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.892980 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1366 0.0160 0.036 1.1 6.6 0.0 0.0 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.66 1.60 1.849 14.308 15.893 3.877 12.01 13.63 1.62 2.013 14.248 15.893 3.866 Individual atomic B min max mean iso aniso Overall: 5.51 67.41 15.06 1.01 496 3269 Protein: 5.51 33.99 10.68 1.01 0 2902 Water: 5.81 67.41 29.82 N/A 496 365 Other: 13.83 27.85 20.84 N/A 0 2 Chain A: 5.54 53.97 12.65 N/A 0 1623 Chain B: 5.51 67.41 12.46 N/A 0 1646 Chain S: 5.81 66.89 31.56 N/A 496 0 Histogram: Values Number of atoms 5.51 - 11.70 2119 11.70 - 17.89 724 17.89 - 24.08 288 24.08 - 30.27 235 30.27 - 36.46 161 36.46 - 42.65 134 42.65 - 48.84 69 48.84 - 55.03 25 55.03 - 61.22 5 61.22 - 67.41 5 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1363 r_work=0.1201 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1364 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1364 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863622 | | target function (ml) not normalized (work): 723629.370283 | | target function (ml) not normalized (free): 15131.690003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1364 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1408 0.1407 0.1469 n_refl.: 191134 remove outliers: r(all,work,free)=0.1408 0.1407 0.1469 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1401 0.1400 0.1465 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1196 0.1365 n_refl.: 191134 remove outliers: r(all,work,free)=0.1199 0.1196 0.1365 n_refl.: 191132 ======================== 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 0.3879 361.182 325.206 0.412 0.952 0.240 13.296-10.522 97.03 97 1 0.2418 478.117 457.600 0.712 0.953 0.224 10.503-8.327 98.35 176 3 0.2065 503.703 503.685 0.872 0.953 0.210 8.318-6.595 100.00 360 8 0.2155 375.525 370.393 0.889 0.953 0.120 6.588-5.215 100.00 711 7 0.1871 345.070 335.032 0.879 0.953 0.099 5.214-4.128 98.38 1367 28 0.1190 504.732 499.117 0.968 0.953 0.080 4.126-3.266 94.74 2603 46 0.1114 460.091 453.515 1.029 0.953 0.005 3.266-2.585 99.86 5447 97 0.1090 310.366 307.000 1.015 0.952 0.000 2.585-2.046 97.45 10613 204 0.0938 234.153 231.657 1.028 0.951 0.000 2.046-1.619 99.39 21536 464 0.0917 138.584 137.240 1.052 0.950 0.000 1.619-1.281 98.00 42464 925 0.0987 74.605 73.870 1.050 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.023 38.341 1.038 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1197 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1365 | n_water=861 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1196 r_free=0.1365 | n_water=861 | time (s): 104.330 (total time: 107.040) Filter (q & B) r_work=0.1196 r_free=0.1365 | n_water=853 | time (s): 4.810 (total time: 111.850) Compute maps r_work=0.1196 r_free=0.1365 | n_water=853 | time (s): 1.780 (total time: 113.630) Filter (map) r_work=0.1218 r_free=0.1364 | n_water=727 | time (s): 5.690 (total time: 119.320) Find peaks r_work=0.1218 r_free=0.1364 | n_water=727 | time (s): 0.890 (total time: 120.210) Add new water r_work=0.1230 r_free=0.1388 | n_water=953 | time (s): 4.140 (total time: 124.350) Refine new water occ: r_work=0.1195 r_free=0.1358 adp: r_work=0.1195 r_free=0.1358 occ: r_work=0.1193 r_free=0.1356 adp: r_work=0.1193 r_free=0.1357 occ: r_work=0.1191 r_free=0.1356 adp: r_work=0.1191 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1357 r_work=0.1191 r_free=0.1357 | n_water=953 | time (s): 220.770 (total time: 345.120) Filter (q & B) r_work=0.1195 r_free=0.1359 | n_water=877 | time (s): 5.080 (total time: 350.200) Filter (dist only) r_work=0.1195 r_free=0.1358 | n_water=876 | time (s): 115.130 (total time: 465.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.528732 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.369563 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 0.1364 0.0165 0.037 1.1 6.3 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.64 1.65 1.799 14.175 15.370 3.765 12.04 13.68 1.64 1.871 14.144 15.370 3.764 Individual atomic B min max mean iso aniso Overall: 5.58 67.03 15.00 0.96 512 3268 Protein: 5.58 32.27 10.60 0.96 0 2902 Water: 5.96 67.03 29.58 N/A 512 364 Other: 13.81 26.65 20.23 N/A 0 2 Chain A: 5.59 53.75 12.55 N/A 0 1623 Chain B: 5.58 67.03 12.34 N/A 0 1645 Chain S: 5.96 66.82 31.33 N/A 512 0 Histogram: Values Number of atoms 5.58 - 11.72 2140 11.72 - 17.87 719 17.87 - 24.01 292 24.01 - 30.16 230 30.16 - 36.30 156 36.30 - 42.45 137 42.45 - 48.59 71 48.59 - 54.74 25 54.74 - 60.88 5 60.88 - 67.03 5 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1368 r_work=0.1204 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1369 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1370 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.762813 | | target function (ml) not normalized (work): 704740.942420 | | target function (ml) not normalized (free): 14753.626081 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1370 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1477 n_refl.: 191132 remove outliers: r(all,work,free)=0.1411 0.1410 0.1477 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1403 0.1402 0.1472 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1368 n_refl.: 191132 remove outliers: r(all,work,free)=0.1204 0.1201 0.1368 n_refl.: 191132 ======================== 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 0.3864 361.182 323.605 0.407 0.950 0.234 13.296-10.522 97.03 97 1 0.2428 478.117 462.983 0.713 0.952 0.214 10.503-8.327 98.35 176 3 0.2110 503.703 497.298 0.862 0.952 0.169 8.318-6.595 100.00 360 8 0.2158 375.525 370.168 0.889 0.952 0.119 6.588-5.215 100.00 711 7 0.1898 345.070 335.362 0.881 0.952 0.100 5.214-4.128 98.38 1367 28 0.1209 504.732 499.112 0.970 0.952 0.080 4.126-3.266 94.74 2603 46 0.1145 460.091 453.292 1.031 0.953 0.009 3.266-2.585 99.86 5447 97 0.1111 310.366 306.999 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0947 234.153 231.642 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0921 138.584 137.253 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0982 74.605 73.879 1.050 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.023 38.346 1.037 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1303 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1368 | n_water=876 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1201 r_free=0.1368 | n_water=876 | time (s): 122.980 (total time: 125.610) Filter (q & B) r_work=0.1202 r_free=0.1367 | n_water=862 | time (s): 5.690 (total time: 131.300) Compute maps r_work=0.1202 r_free=0.1367 | n_water=862 | time (s): 2.550 (total time: 133.850) Filter (map) r_work=0.1222 r_free=0.1366 | n_water=740 | time (s): 4.620 (total time: 138.470) Find peaks r_work=0.1222 r_free=0.1366 | n_water=740 | time (s): 0.870 (total time: 139.340) Add new water r_work=0.1233 r_free=0.1385 | n_water=955 | time (s): 5.150 (total time: 144.490) Refine new water occ: r_work=0.1199 r_free=0.1361 adp: r_work=0.1200 r_free=0.1361 occ: r_work=0.1197 r_free=0.1361 adp: r_work=0.1197 r_free=0.1361 occ: r_work=0.1195 r_free=0.1361 adp: r_work=0.1195 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1361 r_work=0.1195 r_free=0.1361 | n_water=955 | time (s): 337.540 (total time: 482.030) Filter (q & B) r_work=0.1198 r_free=0.1365 | n_water=890 | time (s): 4.110 (total time: 486.140) Filter (dist only) r_work=0.1199 r_free=0.1365 | n_water=889 | time (s): 117.200 (total time: 603.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570854 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.070844 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1369 0.0167 0.038 1.1 8.7 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.69 1.67 1.764 14.085 15.071 3.764 12.03 13.70 1.67 1.859 14.048 15.071 3.760 Individual atomic B min max mean iso aniso Overall: 5.56 66.73 14.92 0.92 525 3268 Protein: 5.56 30.41 10.52 0.92 0 2902 Water: 5.92 66.73 29.30 N/A 525 364 Other: 13.81 24.60 19.21 N/A 0 2 Chain A: 5.64 53.38 12.43 N/A 0 1623 Chain B: 5.56 66.28 12.24 N/A 0 1645 Chain S: 5.92 66.73 31.06 N/A 525 0 Histogram: Values Number of atoms 5.56 - 11.68 2132 11.68 - 17.79 756 17.79 - 23.91 287 23.91 - 30.03 217 30.03 - 36.14 161 36.14 - 42.26 131 42.26 - 48.38 76 48.38 - 54.49 24 54.49 - 60.61 5 60.61 - 66.73 4 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1370 r_work=0.1203 r_free=0.1370 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1370 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1373 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759575 | | target function (ml) not normalized (work): 704134.508313 | | target function (ml) not normalized (free): 14748.635754 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1373 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1476 n_refl.: 191132 remove outliers: r(all,work,free)=0.1409 0.1408 0.1476 n_refl.: 191132 overall B=-0.22 to atoms: r(all,work,free)=0.1374 0.1373 0.1459 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1373 n_refl.: 191132 remove outliers: r(all,work,free)=0.1203 0.1200 0.1373 n_refl.: 191132 ======================== 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 0.3913 361.182 323.129 0.414 0.950 0.234 13.296-10.522 97.03 97 1 0.2432 478.117 463.743 0.733 0.951 0.219 10.503-8.327 98.35 176 3 0.2118 503.703 498.850 0.880 0.952 0.210 8.318-6.595 100.00 360 8 0.2146 375.525 370.249 0.911 0.951 0.110 6.588-5.215 100.00 711 7 0.1900 345.070 335.451 0.905 0.952 0.110 5.214-4.128 98.38 1367 28 0.1224 504.732 499.071 0.996 0.952 0.080 4.126-3.266 94.74 2603 46 0.1154 460.091 453.092 1.057 0.952 0.005 3.266-2.585 99.86 5447 97 0.1117 310.366 306.969 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0950 234.153 231.648 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0913 138.584 137.255 1.066 0.952 0.000 1.619-1.281 98.00 42464 925 0.0974 74.605 73.887 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.023 38.348 1.023 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0492 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1373 | n_water=889 | time (s): 2.860 (total time: 2.860) Filter (dist) r_work=0.1200 r_free=0.1372 | n_water=886 | time (s): 109.760 (total time: 112.620) Filter (q & B) r_work=0.1201 r_free=0.1372 | n_water=873 | time (s): 5.680 (total time: 118.300) Compute maps r_work=0.1201 r_free=0.1372 | n_water=873 | time (s): 2.290 (total time: 120.590) Filter (map) r_work=0.1222 r_free=0.1367 | n_water=743 | time (s): 4.280 (total time: 124.870) Find peaks r_work=0.1222 r_free=0.1367 | n_water=743 | time (s): 0.560 (total time: 125.430) Add new water r_work=0.1234 r_free=0.1381 | n_water=954 | time (s): 4.100 (total time: 129.530) Refine new water occ: r_work=0.1200 r_free=0.1353 adp: r_work=0.1200 r_free=0.1354 occ: r_work=0.1198 r_free=0.1352 adp: r_work=0.1198 r_free=0.1353 occ: r_work=0.1196 r_free=0.1353 adp: r_work=0.1196 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1354 r_work=0.1196 r_free=0.1354 | n_water=954 | time (s): 212.360 (total time: 341.890) Filter (q & B) r_work=0.1199 r_free=0.1356 | n_water=891 | time (s): 5.000 (total time: 346.890) Filter (dist only) r_work=0.1199 r_free=0.1355 | n_water=890 | time (s): 116.500 (total time: 463.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.493347 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.812481 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1202 0.1356 0.0153 0.038 1.1 7.5 0.0 0.3 0 0.747 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.56 1.53 1.732 13.783 13.812 3.761 12.06 13.60 1.54 1.816 13.750 13.812 3.760 Individual atomic B min max mean iso aniso Overall: 5.41 66.39 14.64 0.88 526 3268 Protein: 5.41 28.62 10.25 0.88 0 2902 Water: 5.75 66.39 28.93 N/A 526 364 Other: 13.69 22.36 18.03 N/A 0 2 Chain A: 5.44 52.74 12.12 N/A 0 1623 Chain B: 5.41 64.98 11.95 N/A 0 1645 Chain S: 5.75 66.39 30.79 N/A 526 0 Histogram: Values Number of atoms 5.41 - 11.51 2148 11.51 - 17.61 758 17.61 - 23.70 271 23.70 - 29.80 210 29.80 - 35.90 166 35.90 - 42.00 133 42.00 - 48.10 74 48.10 - 54.19 26 54.19 - 60.29 4 60.29 - 66.39 4 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1360 r_work=0.1206 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1360 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1361 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759366 | | target function (ml) not normalized (work): 704095.351461 | | target function (ml) not normalized (free): 14737.614439 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1361 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1385 0.1384 0.1451 n_refl.: 191132 remove outliers: r(all,work,free)=0.1385 0.1384 0.1451 n_refl.: 191132 overall B=0.00 to atoms: r(all,work,free)=0.1385 0.1384 0.1451 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1352 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1194 0.1352 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3668 360.878 313.761 0.431 0.906 0.233 13.296-10.522 97.03 97 1 0.2452 478.117 462.948 0.762 0.908 0.215 10.503-8.327 98.35 176 3 0.2153 503.703 497.638 0.913 0.908 0.211 8.318-6.595 100.00 360 8 0.2161 375.525 370.049 0.946 0.908 0.116 6.588-5.215 100.00 711 7 0.1907 345.070 335.502 0.942 0.909 0.097 5.214-4.128 98.38 1367 28 0.1240 504.732 498.592 1.036 0.909 0.090 4.126-3.266 94.74 2603 46 0.1160 460.091 452.614 1.099 0.911 0.005 3.266-2.585 99.86 5447 97 0.1122 310.366 306.782 1.080 0.911 0.000 2.585-2.046 97.45 10613 204 0.0957 234.153 231.587 1.087 0.913 0.000 2.046-1.619 99.39 21536 464 0.0912 138.584 137.207 1.101 0.916 0.000 1.619-1.281 98.00 42464 925 0.0958 74.605 73.938 1.086 0.920 0.000 1.281-0.980 96.53 101826 2055 0.1632 40.023 38.328 1.044 0.928 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1352 | n_water=890 | time (s): 3.470 (total time: 3.470) Filter (dist) r_work=0.1194 r_free=0.1352 | n_water=890 | time (s): 105.640 (total time: 109.110) Filter (q & B) r_work=0.1195 r_free=0.1351 | n_water=880 | time (s): 4.810 (total time: 113.920) Compute maps r_work=0.1195 r_free=0.1351 | n_water=880 | time (s): 2.070 (total time: 115.990) Filter (map) r_work=0.1215 r_free=0.1349 | n_water=758 | time (s): 4.830 (total time: 120.820) Find peaks r_work=0.1215 r_free=0.1349 | n_water=758 | time (s): 0.750 (total time: 121.570) Add new water r_work=0.1226 r_free=0.1370 | n_water=955 | time (s): 4.890 (total time: 126.460) Refine new water occ: r_work=0.1194 r_free=0.1337 adp: r_work=0.1194 r_free=0.1337 occ: r_work=0.1192 r_free=0.1336 adp: r_work=0.1192 r_free=0.1336 occ: r_work=0.1191 r_free=0.1335 adp: r_work=0.1191 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1335 r_work=0.1191 r_free=0.1335 | n_water=955 | time (s): 303.320 (total time: 429.780) Filter (q & B) r_work=0.1194 r_free=0.1341 | n_water=889 | time (s): 5.110 (total time: 434.890) Filter (dist only) r_work=0.1195 r_free=0.1340 | n_water=887 | time (s): 115.640 (total time: 550.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.484945 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.105805 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 0.1349 0.0151 0.039 1.1 5.1 0.0 0.3 0 0.742 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.49 1.51 1.677 13.672 15.106 3.758 11.94 13.47 1.53 1.686 13.665 15.106 3.753 Individual atomic B min max mean iso aniso Overall: 5.43 66.29 14.58 0.89 523 3268 Protein: 5.43 28.59 10.27 0.89 0 2902 Water: 5.85 66.29 28.67 N/A 523 364 Other: 13.72 22.06 17.89 N/A 0 2 Chain A: 5.50 52.42 12.11 N/A 0 1623 Chain B: 5.43 63.97 11.94 N/A 0 1645 Chain S: 5.85 66.29 30.55 N/A 523 0 Histogram: Values Number of atoms 5.43 - 11.52 2145 11.52 - 17.60 772 17.60 - 23.69 270 23.69 - 29.78 208 29.78 - 35.86 169 35.86 - 41.95 123 41.95 - 48.03 73 48.03 - 54.12 24 54.12 - 60.21 4 60.21 - 66.29 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1347 r_work=0.1194 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1347 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1350 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752286 | | target function (ml) not normalized (work): 702765.698292 | | target function (ml) not normalized (free): 14717.048414 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1192 0.1350 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1382 0.1381 0.1458 n_refl.: 191131 remove outliers: r(all,work,free)=0.1382 0.1381 0.1458 n_refl.: 191131 overall B=0.00 to atoms: r(all,work,free)=0.1382 0.1381 0.1458 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191131 remove outliers: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3726 360.878 330.215 0.444 0.909 0.221 13.296-10.522 97.03 97 1 0.2476 478.117 460.989 0.747 0.911 0.181 10.503-8.327 97.80 175 3 0.2196 501.881 495.412 0.910 0.911 0.160 8.315-6.595 100.00 359 8 0.2174 374.579 370.184 0.942 0.911 0.116 6.588-5.215 100.00 711 7 0.1933 345.070 335.051 0.939 0.911 0.097 5.214-4.128 98.38 1367 28 0.1247 504.732 498.687 1.030 0.912 0.054 4.126-3.266 94.74 2603 46 0.1171 460.091 452.645 1.097 0.913 0.009 3.266-2.585 99.86 5447 97 0.1127 310.366 306.662 1.077 0.914 0.000 2.585-2.046 97.45 10613 204 0.0956 234.153 231.538 1.084 0.916 0.000 2.046-1.619 99.39 21536 464 0.0902 138.584 137.213 1.100 0.920 0.000 1.619-1.281 98.00 42464 925 0.0946 74.605 73.941 1.085 0.925 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.023 38.319 1.046 0.934 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0801 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1192 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1347 | n_water=887 | time (s): 3.410 (total time: 3.410) Filter (dist) r_work=0.1192 r_free=0.1347 | n_water=885 | time (s): 115.050 (total time: 118.460) Filter (q & B) r_work=0.1193 r_free=0.1345 | n_water=875 | time (s): 4.730 (total time: 123.190) Compute maps r_work=0.1193 r_free=0.1345 | n_water=875 | time (s): 1.780 (total time: 124.970) Filter (map) r_work=0.1215 r_free=0.1350 | n_water=752 | time (s): 4.460 (total time: 129.430) Find peaks r_work=0.1215 r_free=0.1350 | n_water=752 | time (s): 0.880 (total time: 130.310) Add new water r_work=0.1225 r_free=0.1363 | n_water=970 | time (s): 4.480 (total time: 134.790) Refine new water occ: r_work=0.1191 r_free=0.1332 adp: r_work=0.1191 r_free=0.1332 occ: r_work=0.1189 r_free=0.1332 adp: r_work=0.1189 r_free=0.1332 occ: r_work=0.1187 r_free=0.1332 adp: r_work=0.1187 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1332 r_work=0.1187 r_free=0.1332 | n_water=970 | time (s): 238.350 (total time: 373.140) Filter (q & B) r_work=0.1191 r_free=0.1340 | n_water=895 | time (s): 4.590 (total time: 377.730) Filter (dist only) r_work=0.1191 r_free=0.1339 | n_water=894 | time (s): 122.400 (total time: 500.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554624 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.339939 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1340 0.0147 0.040 1.1 7.7 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.40 1.47 1.680 13.693 14.340 3.753 11.94 13.43 1.49 1.679 13.691 14.340 3.752 Individual atomic B min max mean iso aniso Overall: 5.44 66.27 14.61 0.87 530 3268 Protein: 5.44 28.42 10.28 0.87 0 2902 Water: 5.89 66.27 28.63 N/A 530 364 Other: 13.74 22.12 17.93 N/A 0 2 Chain A: 5.53 52.33 12.10 N/A 0 1623 Chain B: 5.44 63.70 11.94 N/A 0 1645 Chain S: 5.89 66.27 30.58 N/A 530 0 Histogram: Values Number of atoms 5.44 - 11.53 2143 11.53 - 17.61 775 17.61 - 23.69 266 23.69 - 29.77 217 29.77 - 35.86 168 35.86 - 41.94 129 41.94 - 48.02 69 48.02 - 54.10 25 54.10 - 60.18 3 60.18 - 66.27 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1343 r_work=0.1194 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1343 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1345 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751875 | | target function (ml) not normalized (work): 702681.114627 | | target function (ml) not normalized (free): 14715.528901 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1345 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1389 0.1388 0.1467 n_refl.: 191129 remove outliers: r(all,work,free)=0.1389 0.1388 0.1467 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1389 0.1388 0.1467 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3690 360.878 330.841 0.406 0.973 0.213 13.296-10.522 97.03 97 1 0.2494 478.117 460.167 0.687 0.974 0.168 10.503-8.327 97.80 175 3 0.2207 501.881 494.435 0.841 0.975 0.147 8.315-6.595 100.00 359 8 0.2173 374.579 369.510 0.870 0.975 0.100 6.588-5.215 100.00 711 7 0.1928 345.070 334.939 0.872 0.975 0.100 5.214-4.128 98.38 1367 28 0.1245 504.732 498.786 0.956 0.976 0.049 4.126-3.266 94.74 2603 46 0.1169 460.091 452.566 1.019 0.977 0.009 3.266-2.585 99.86 5447 97 0.1130 310.366 306.757 1.000 0.979 0.000 2.585-2.046 97.45 10613 204 0.0957 234.153 231.532 1.007 0.981 0.000 2.046-1.619 99.39 21536 464 0.0905 138.584 137.220 1.022 0.985 0.000 1.619-1.281 98.00 42464 925 0.0944 74.605 73.950 1.010 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.023 38.314 0.975 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0462 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1344 After: r_work=0.1192 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1344 | n_water=894 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1192 r_free=0.1343 | n_water=893 | time (s): 117.770 (total time: 120.420) Filter (q & B) r_work=0.1193 r_free=0.1344 | n_water=885 | time (s): 4.190 (total time: 124.610) Compute maps r_work=0.1193 r_free=0.1344 | n_water=885 | time (s): 1.940 (total time: 126.550) Filter (map) r_work=0.1215 r_free=0.1349 | n_water=760 | time (s): 4.800 (total time: 131.350) Find peaks r_work=0.1215 r_free=0.1349 | n_water=760 | time (s): 0.730 (total time: 132.080) Add new water r_work=0.1224 r_free=0.1360 | n_water=971 | time (s): 5.040 (total time: 137.120) Refine new water occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1191 r_free=0.1333 occ: r_work=0.1189 r_free=0.1333 adp: r_work=0.1189 r_free=0.1333 occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1333 r_work=0.1187 r_free=0.1333 | n_water=971 | time (s): 187.700 (total time: 324.820) Filter (q & B) r_work=0.1191 r_free=0.1343 | n_water=899 | time (s): 4.360 (total time: 329.180) Filter (dist only) r_work=0.1191 r_free=0.1342 | n_water=898 | time (s): 119.620 (total time: 448.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.518435 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.871168 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1345 0.0152 0.040 1.1 7.3 0.0 0.3 0 0.759 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.45 1.52 1.675 13.687 14.871 3.753 11.93 13.46 1.54 1.676 13.687 14.871 3.752 Individual atomic B min max mean iso aniso Overall: 5.48 66.25 14.59 0.88 534 3268 Protein: 5.48 28.28 10.30 0.88 0 2902 Water: 5.98 66.25 28.43 N/A 534 364 Other: 13.80 22.15 17.98 N/A 0 2 Chain A: 5.58 52.02 12.09 N/A 0 1623 Chain B: 5.48 62.72 11.93 N/A 0 1645 Chain S: 5.98 66.25 30.36 N/A 534 0 Histogram: Values Number of atoms 5.48 - 11.56 2140 11.56 - 17.64 791 17.64 - 23.72 261 23.72 - 29.79 223 29.79 - 35.87 172 35.87 - 41.95 118 41.95 - 48.02 66 48.02 - 54.10 25 54.10 - 60.18 3 60.18 - 66.25 3 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1346 r_work=0.1193 r_free=0.1346 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1346 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1347 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751387 | | target function (ml) not normalized (work): 702589.742258 | | target function (ml) not normalized (free): 14709.900132 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1366 0.1468 5.6908 5.7528| | 2: 2.94 - 2.33 1.00 7339 128 0.1068 0.1324 5.0715 5.1657| | 3: 2.33 - 2.04 0.96 6939 150 0.0896 0.1159 4.6439 4.7255| | 4: 2.04 - 1.85 1.00 7170 155 0.0894 0.1056 4.3822 4.5697| | 5: 1.85 - 1.72 0.99 7113 159 0.0925 0.0970 4.1398 4.2165| | 6: 1.72 - 1.62 0.99 7102 142 0.0890 0.1059 3.9383 4.06| | 7: 1.62 - 1.54 0.99 7104 148 0.0888 0.0958 3.7936 3.9184| | 8: 1.54 - 1.47 0.96 6798 152 0.0890 0.1303 3.6949 3.9048| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1101 3.6176 3.7424| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1195 3.5535 3.6769| | 11: 1.36 - 1.32 0.99 6997 151 0.0995 0.1112 3.4846 3.5786| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1142 3.4589 3.5886| | 13: 1.28 - 1.25 0.98 6907 166 0.1043 0.1239 3.4359 3.5589| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1580 3.4302 3.6757| | 15: 1.22 - 1.19 0.98 6956 137 0.1170 0.1249 3.4475 3.496| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1556 3.4645 3.6588| | 17: 1.17 - 1.14 0.98 6940 135 0.1302 0.1229 3.4341 3.4431| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1705 3.4375 3.5304| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1755 3.4186 3.5993| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1575 3.4092 3.4305| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2134 3.4169 3.5009| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1959 3.4124 3.4133| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2030 3.4328 3.4884| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2243 3.4352 3.5078| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2513 3.449 3.5232| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2871 3.4153 3.4229| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2798 3.4688 3.3937| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.51 1.00 0.97 10967.72| | 2: 2.94 - 2.33 7339 128 0.93 12.58 0.99 0.98 4983.60| | 3: 2.33 - 2.04 6939 150 0.96 7.33 1.01 0.98 1617.94| | 4: 2.04 - 1.85 7170 155 0.96 7.38 1.00 0.98 966.76| | 5: 1.85 - 1.72 7113 159 0.96 7.77 1.00 0.98 607.29| | 6: 1.72 - 1.62 7102 142 0.96 7.81 1.00 0.98 428.68| | 7: 1.62 - 1.54 7104 148 0.96 8.00 1.01 0.99 328.59| | 8: 1.54 - 1.47 6798 152 0.96 8.19 1.01 1.00 275.27| | 9: 1.47 - 1.41 6938 155 0.96 8.38 1.00 1.00 227.97| | 10: 1.41 - 1.36 7022 150 0.96 8.87 1.00 0.99 200.85| | 11: 1.36 - 1.32 6997 151 0.96 8.90 0.99 0.98 173.90| | 12: 1.32 - 1.28 6975 149 0.96 8.96 0.98 0.97 160.18| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.01 0.98 157.28| | 14: 1.25 - 1.22 7015 112 0.95 10.65 1.01 0.99 161.96| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 1.00 165.99| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.98 160.15| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.98 154.24| | 18: 1.14 - 1.12 6875 142 0.94 12.75 1.01 0.97 147.68| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.97 150.76| | 20: 1.10 - 1.08 6884 147 0.92 15.17 1.00 0.96 149.51| | 21: 1.08 - 1.07 6852 152 0.91 16.58 1.00 0.95 152.54| | 22: 1.07 - 1.05 6836 135 0.89 18.26 0.99 0.95 154.35| | 23: 1.05 - 1.03 6827 159 0.87 20.49 0.99 0.94 164.57| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.95 178.82| | 25: 1.02 - 1.01 6552 130 0.83 25.14 0.97 0.91 181.74| | 26: 1.01 - 0.99 6767 158 0.81 26.57 0.98 0.90 175.89| | 27: 0.99 - 0.98 6647 131 0.82 26.19 0.98 0.89 160.13| |alpha: min = 0.89 max = 1.00 mean = 0.97| |beta: min = 147.68 max = 10967.72 mean = 903.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.20| |phase err.(test): min = 0.00 max = 88.30 mean = 13.32| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1347 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1396 0.1394 0.1479 n_refl.: 191129 remove outliers: r(all,work,free)=0.1396 0.1394 0.1479 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1396 0.1394 0.1479 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1345 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1345 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3717 360.878 329.319 0.391 0.973 0.197 13.296-10.522 97.03 97 1 0.2502 478.117 460.006 0.678 0.975 0.156 10.503-8.327 97.80 175 3 0.2240 501.881 493.240 0.837 0.976 0.137 8.315-6.595 100.00 359 8 0.2155 374.579 369.751 0.870 0.975 0.106 6.588-5.215 100.00 711 7 0.1950 345.070 334.927 0.867 0.976 0.090 5.214-4.128 98.38 1367 28 0.1251 504.732 498.985 0.956 0.977 0.044 4.126-3.266 94.74 2603 46 0.1171 460.091 452.595 1.019 0.979 0.005 3.266-2.585 99.86 5447 97 0.1121 310.366 306.830 1.001 0.980 0.000 2.585-2.046 97.45 10613 204 0.0957 234.153 231.535 1.007 0.983 0.000 2.046-1.619 99.39 21536 464 0.0903 138.584 137.231 1.023 0.987 0.000 1.619-1.281 98.00 42464 925 0.0945 74.605 73.952 1.011 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.023 38.312 0.978 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0111 ================= 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 : 0.2040 0.1960 0.083 5.271 5.2 78.0 14.6 805 0.000 1_bss: 0.1807 0.1893 0.083 5.271 5.2 78.0 14.6 805 0.000 1_settarget: 0.1807 0.1893 0.083 5.271 5.2 78.0 14.6 805 0.000 1_nqh: 0.1807 0.1898 0.083 5.271 5.2 78.0 14.6 805 0.002 1_weight: 0.1807 0.1898 0.083 5.271 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1267 0.1492 0.038 1.167 5.2 78.0 14.6 805 0.155 1_adp: 0.1299 0.1569 0.038 1.167 5.2 73.0 15.1 805 0.155 1_regHadp: 0.1298 0.1563 0.038 1.167 5.2 73.0 15.1 805 0.155 1_occ: 0.1283 0.1553 0.038 1.167 5.2 73.0 15.1 805 0.155 2_bss: 0.1275 0.1542 0.038 1.167 5.4 73.2 15.2 805 0.155 2_settarget: 0.1275 0.1542 0.038 1.167 5.4 73.2 15.2 805 0.155 2_updatecdl: 0.1275 0.1542 0.038 1.174 5.4 73.2 15.2 805 0.155 2_nqh: 0.1275 0.1542 0.038 1.174 5.4 73.2 15.2 805 0.155 2_sol: 0.1273 0.1513 0.038 1.174 5.4 73.2 16.2 881 n/a 2_weight: 0.1273 0.1513 0.038 1.174 5.4 73.2 16.2 881 n/a 2_xyzrec: 0.1257 0.1527 0.042 1.162 5.4 73.2 16.2 881 n/a 2_adp: 0.1232 0.1511 0.042 1.162 5.4 70.1 16.3 881 n/a 2_regHadp: 0.1232 0.1511 0.042 1.162 5.4 70.1 16.3 881 n/a 2_occ: 0.1226 0.1508 0.042 1.162 5.4 70.1 16.3 881 n/a 3_bss: 0.1233 0.1512 0.042 1.162 5.4 70.1 16.3 881 n/a 3_settarget: 0.1233 0.1512 0.042 1.162 5.4 70.1 16.3 881 n/a 3_updatecdl: 0.1233 0.1512 0.042 1.168 5.4 70.1 16.3 881 n/a 3_nqh: 0.1233 0.1512 0.042 1.168 5.4 70.1 16.3 881 n/a 3_sol: 0.1248 0.1506 0.042 1.168 5.4 68.2 15.5 866 n/a 3_weight: 0.1248 0.1506 0.042 1.168 5.4 68.2 15.5 866 n/a 3_xyzrec: 0.1236 0.1432 0.036 1.104 5.4 68.2 15.5 866 n/a 3_adp: 0.1231 0.1395 0.036 1.104 5.5 67.9 15.4 866 n/a 3_regHadp: 0.1232 0.1396 0.036 1.104 5.5 67.9 15.4 866 n/a 3_occ: 0.1227 0.1386 0.036 1.104 5.5 67.9 15.4 866 n/a 4_bss: 0.1223 0.1382 0.036 1.104 5.5 67.9 15.3 866 n/a 4_settarget: 0.1223 0.1382 0.036 1.104 5.5 67.9 15.3 866 n/a 4_updatecdl: 0.1223 0.1382 0.036 1.103 5.5 67.9 15.3 866 n/a 4_nqh: 0.1223 0.1382 0.036 1.103 5.5 67.9 15.3 866 n/a 4_sol: 0.1207 0.1368 0.036 1.103 5.5 67.9 15.2 861 n/a 4_weight: 0.1207 0.1368 0.036 1.103 5.5 67.9 15.2 861 n/a 4_xyzrec: 0.1207 0.1366 0.036 1.121 5.5 67.9 15.2 861 n/a 4_adp: 0.1201 0.1363 0.036 1.121 5.5 67.4 15.1 861 n/a 4_regHadp: 0.1201 0.1364 0.036 1.121 5.5 67.4 15.1 861 n/a 4_occ: 0.1198 0.1364 0.036 1.121 5.5 67.4 15.1 861 n/a 5_bss: 0.1196 0.1365 0.036 1.121 5.5 67.4 15.0 861 n/a 5_settarget: 0.1196 0.1365 0.036 1.121 5.5 67.4 15.0 861 n/a 5_updatecdl: 0.1196 0.1365 0.036 1.123 5.5 67.4 15.0 861 n/a 5_nqh: 0.1196 0.1365 0.036 1.123 5.5 67.4 15.0 861 n/a 5_sol: 0.1195 0.1358 0.036 1.123 5.5 67.4 15.1 876 n/a 5_weight: 0.1195 0.1358 0.036 1.123 5.5 67.4 15.1 876 n/a 5_xyzrec: 0.1199 0.1364 0.037 1.124 5.5 67.4 15.1 876 n/a 5_adp: 0.1204 0.1368 0.037 1.124 5.6 67.0 15.0 876 n/a 5_regHadp: 0.1204 0.1369 0.037 1.124 5.6 67.0 15.0 876 n/a 5_occ: 0.1202 0.1370 0.037 1.124 5.6 67.0 15.0 876 n/a 6_bss: 0.1201 0.1368 0.037 1.124 5.5 67.0 15.0 876 n/a 6_settarget: 0.1201 0.1368 0.037 1.124 5.5 67.0 15.0 876 n/a 6_updatecdl: 0.1201 0.1368 0.037 1.124 5.5 67.0 15.0 876 n/a 6_nqh: 0.1201 0.1368 0.037 1.124 5.5 67.0 15.0 876 n/a 6_sol: 0.1199 0.1365 0.037 1.124 5.5 67.0 15.0 889 n/a 6_weight: 0.1199 0.1365 0.037 1.124 5.5 67.0 15.0 889 n/a 6_xyzrec: 0.1202 0.1369 0.038 1.128 5.5 67.0 15.0 889 n/a 6_adp: 0.1203 0.1370 0.038 1.128 5.6 66.7 14.9 889 n/a 6_regHadp: 0.1203 0.1370 0.038 1.128 5.6 66.7 14.9 889 n/a 6_occ: 0.1200 0.1373 0.038 1.128 5.6 66.7 14.9 889 n/a 7_bss: 0.1200 0.1373 0.038 1.128 5.3 66.5 14.7 889 n/a 7_settarget: 0.1200 0.1373 0.038 1.128 5.3 66.5 14.7 889 n/a 7_updatecdl: 0.1200 0.1373 0.038 1.129 5.3 66.5 14.7 889 n/a 7_nqh: 0.1200 0.1373 0.038 1.129 5.3 66.5 14.7 889 n/a 7_sol: 0.1199 0.1355 0.038 1.129 5.3 66.5 14.7 890 n/a 7_weight: 0.1199 0.1355 0.038 1.129 5.3 66.5 14.7 890 n/a 7_xyzrec: 0.1202 0.1356 0.038 1.118 5.3 66.5 14.7 890 n/a 7_adp: 0.1206 0.1360 0.038 1.118 5.4 66.4 14.6 890 n/a 7_regHadp: 0.1206 0.1360 0.038 1.118 5.4 66.4 14.6 890 n/a 7_occ: 0.1204 0.1361 0.038 1.118 5.4 66.4 14.6 890 n/a 8_bss: 0.1194 0.1352 0.038 1.118 5.4 66.4 14.6 890 n/a 8_settarget: 0.1194 0.1352 0.038 1.118 5.4 66.4 14.6 890 n/a 8_updatecdl: 0.1194 0.1352 0.038 1.118 5.4 66.4 14.6 890 n/a 8_nqh: 0.1194 0.1352 0.038 1.118 5.4 66.4 14.6 890 n/a 8_sol: 0.1195 0.1340 0.038 1.118 5.4 66.4 14.6 887 n/a 8_weight: 0.1195 0.1340 0.038 1.118 5.4 66.4 14.6 887 n/a 8_xyzrec: 0.1198 0.1349 0.039 1.110 5.4 66.4 14.6 887 n/a 8_adp: 0.1194 0.1347 0.039 1.110 5.4 66.3 14.6 887 n/a 8_regHadp: 0.1194 0.1347 0.039 1.110 5.4 66.3 14.6 887 n/a 8_occ: 0.1192 0.1350 0.039 1.110 5.4 66.3 14.6 887 n/a 9_bss: 0.1191 0.1344 0.039 1.110 5.4 66.3 14.6 887 n/a 9_settarget: 0.1191 0.1344 0.039 1.110 5.4 66.3 14.6 887 n/a 9_updatecdl: 0.1191 0.1344 0.039 1.110 5.4 66.3 14.6 887 n/a 9_nqh: 0.1192 0.1347 0.039 1.110 5.4 66.3 14.6 887 n/a 9_sol: 0.1191 0.1339 0.039 1.110 5.4 66.3 14.6 894 n/a 9_weight: 0.1191 0.1339 0.039 1.110 5.4 66.3 14.6 894 n/a 9_xyzrec: 0.1193 0.1340 0.040 1.119 5.4 66.3 14.6 894 n/a 9_adp: 0.1194 0.1343 0.040 1.119 5.4 66.3 14.6 894 n/a 9_regHadp: 0.1194 0.1343 0.040 1.119 5.4 66.3 14.6 894 n/a 9_occ: 0.1192 0.1345 0.040 1.119 5.4 66.3 14.6 894 n/a 10_bss: 0.1191 0.1344 0.040 1.119 5.4 66.3 14.6 894 n/a 10_settarget: 0.1191 0.1344 0.040 1.119 5.4 66.3 14.6 894 n/a 10_updatecdl: 0.1191 0.1344 0.040 1.119 5.4 66.3 14.6 894 n/a 10_setrh: 0.1192 0.1344 0.040 1.119 5.4 66.3 14.6 894 n/a 10_nqh: 0.1192 0.1344 0.040 1.119 5.4 66.3 14.6 894 n/a 10_sol: 0.1191 0.1342 0.040 1.119 5.4 66.3 14.6 898 n/a 10_weight: 0.1191 0.1342 0.040 1.119 5.4 66.3 14.6 898 n/a 10_xyzrec: 0.1193 0.1345 0.040 1.148 5.4 66.3 14.6 898 n/a 10_adp: 0.1193 0.1346 0.040 1.148 5.5 66.3 14.6 898 n/a 10_regHadp: 0.1193 0.1346 0.040 1.148 5.5 66.3 14.6 898 n/a 10_occ: 0.1191 0.1347 0.040 1.148 5.5 66.3 14.6 898 n/a end: 0.1191 0.1345 0.040 1.148 5.5 66.3 14.6 898 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7424180_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7424180_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.9000 Refinement macro-cycles (run) : 12402.7200 Write final files (write_after_run_outputs) : 127.1300 Total : 12536.7500 Total CPU time: 3.49 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:46:16 PST -0800 (1736736376.60 s) Start R-work = 0.1807, R-free = 0.1893 Final R-work = 0.1191, R-free = 0.1345 =============================================================================== Job complete usr+sys time: 12791.34 seconds wall clock time: 214 minutes 14.63 seconds (12854.63 seconds total)