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_5912678.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5912678.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5912678.pdb" 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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } 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: 2.14, per 1000 atoms: 0.32 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: 2.639 distance_ideal: 2.720 ideal - model: 0.081 slack: 0.000 delta_slack: 0.081 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: 2.725 distance_ideal: 2.710 ideal - model: -0.015 slack: 0.000 delta_slack: -0.015 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 168.2 milliseconds Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.74 - 0.99: 431 0.99 - 1.24: 2729 1.24 - 1.49: 1643 1.49 - 1.73: 1114 1.73 - 1.98: 17 Bond restraints: 5934 Sorted by residual: bond pdb=" C SER B 4 " pdb=" O SER B 4 " ideal model delta sigma weight residual 1.234 1.470 -0.237 1.26e-02 6.30e+03 3.52e+02 bond pdb=" CZ ARG A 100 " pdb=" NH2 ARG A 100 " ideal model delta sigma weight residual 1.330 1.574 -0.244 1.30e-02 5.92e+03 3.52e+02 bond pdb=" NZ LYS B 167 " pdb=" HZ2 LYS B 167 " ideal model delta sigma weight residual 0.890 1.265 -0.375 2.00e-02 2.50e+03 3.51e+02 bond pdb=" C VAL A 32 " pdb=" O VAL A 32 " ideal model delta sigma weight residual 1.237 1.436 -0.199 1.07e-02 8.73e+03 3.47e+02 bond pdb=" CA GLY A 50 " pdb=" HA2 GLY A 50 " ideal model delta sigma weight residual 0.970 1.332 -0.362 2.00e-02 2.50e+03 3.28e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.48: 5987 4.48 - 8.95: 3509 8.95 - 13.43: 1116 13.43 - 17.90: 185 17.90 - 22.38: 13 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O PHE B 95 " pdb=" C PHE B 95 " pdb=" N HIS B 96 " ideal model delta sigma weight residual 122.07 103.47 18.60 1.03e+00 9.43e-01 3.26e+02 angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" O ILE A 134 " ideal model delta sigma weight residual 119.19 107.60 11.59 6.50e-01 2.37e+00 3.18e+02 angle pdb=" CA GLU A 180 " pdb=" C GLU A 180 " pdb=" O GLU A 180 " ideal model delta sigma weight residual 120.55 103.02 17.53 1.06e+00 8.90e-01 2.74e+02 angle pdb=" CA VAL A 112 " pdb=" C VAL A 112 " pdb=" N LEU A 113 " ideal model delta sigma weight residual 117.37 129.46 -12.09 7.40e-01 1.83e+00 2.67e+02 angle pdb=" NE ARG B 83 " pdb=" CZ ARG B 83 " pdb=" NH1 ARG B 83 " ideal model delta sigma weight residual 121.50 137.00 -15.50 1.00e+00 1.00e+00 2.40e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 1840 16.60 - 33.20: 139 33.20 - 49.80: 40 49.80 - 66.41: 26 66.41 - 83.01: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA LYS B 52 " pdb=" C LYS B 52 " pdb=" N LEU B 53 " pdb=" CA LEU B 53 " ideal model delta harmonic sigma weight residual 180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA VAL A 145 " pdb=" C VAL A 145 " pdb=" N TRP A 146 " pdb=" CA TRP A 146 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ALA A 57 " pdb=" C ALA A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.221: 224 0.221 - 0.441: 140 0.441 - 0.662: 82 0.662 - 0.882: 34 0.882 - 1.103: 12 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA PRO A 158 " pdb=" N PRO A 158 " pdb=" C PRO A 158 " pdb=" CB PRO A 158 " both_signs ideal model delta sigma weight residual False 2.72 1.62 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" CB VAL B 51 " pdb=" CA VAL B 51 " pdb=" CG1 VAL B 51 " pdb=" CG2 VAL B 51 " both_signs ideal model delta sigma weight residual False -2.63 -1.56 -1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CA VAL B 112 " pdb=" N VAL B 112 " pdb=" C VAL B 112 " pdb=" CB VAL B 112 " both_signs ideal model delta sigma weight residual False 2.44 3.46 -1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.114 2.00e-02 2.50e+03 7.64e-02 1.75e+02 pdb=" CG PHE A 164 " 0.136 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.058 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.070 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.015 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 143 " 0.060 9.50e-02 1.11e+02 7.74e-02 1.26e+02 pdb=" NE ARG B 143 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG B 143 " 0.065 2.00e-02 2.50e+03 pdb=" NH1 ARG B 143 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG B 143 " 0.022 2.00e-02 2.50e+03 pdb="HH11 ARG B 143 " -0.132 2.00e-02 2.50e+03 pdb="HH12 ARG B 143 " 0.130 2.00e-02 2.50e+03 pdb="HH21 ARG B 143 " -0.048 2.00e-02 2.50e+03 pdb="HH22 ARG B 143 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.013 2.00e-02 2.50e+03 5.37e-02 1.15e+02 pdb=" CG TRP A 139 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.104 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.046 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.063 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.029 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.094 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.034 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.067 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.012 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.065 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.067 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.61: 27 1.61 - 2.36: 2300 2.36 - 3.10: 22351 3.10 - 3.85: 32968 3.85 - 4.60: 52429 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110075 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.859 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.876 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.049 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.155 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.198 2.620 ... (remaining 110070 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_5912678_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= 0.2037 r_free= 0.1984 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.300970 | | target function (ml) not normalized (work): 805627.646530 | | target function (ml) not normalized (free): 16556.607869 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2137 0.1960 6.6825 6.3184| | 2: 2.94 - 2.33 1.00 7339 128 0.1624 0.1546 5.5431 5.5744| | 3: 2.33 - 2.04 0.96 6939 150 0.1638 0.1683 5.1359 5.1702| | 4: 2.04 - 1.85 1.00 7170 155 0.1750 0.1485 4.9627 4.9778| | 5: 1.85 - 1.72 0.99 7113 159 0.1905 0.1807 4.7955 4.8542| | 6: 1.72 - 1.62 0.99 7102 142 0.2019 0.1858 4.6809 4.6837| | 7: 1.62 - 1.54 0.99 7104 148 0.2012 0.1955 4.5633 4.6416| | 8: 1.54 - 1.47 0.96 6798 152 0.2054 0.2143 4.4717 4.5263| | 9: 1.47 - 1.41 0.98 6938 155 0.2120 0.2083 4.4129 4.4495| | 10: 1.41 - 1.36 0.99 7022 150 0.2146 0.2186 4.324 4.3697| | 11: 1.36 - 1.32 0.99 6997 151 0.2118 0.2232 4.2556 4.2962| | 12: 1.32 - 1.28 0.98 6976 149 0.2103 0.2038 4.1808 4.2378| | 13: 1.28 - 1.25 0.98 6907 166 0.2026 0.1953 4.1173 4.0804| | 14: 1.25 - 1.22 0.98 7015 113 0.2060 0.2486 4.0736 4.3308| | 15: 1.22 - 1.19 0.98 6957 137 0.2133 0.1945 4.0533 4.0036| | 16: 1.19 - 1.17 0.93 6604 132 0.2122 0.2232 4.004 4.1034| | 17: 1.17 - 1.14 0.98 6941 135 0.2197 0.2000 3.9673 4.077| | 18: 1.14 - 1.12 0.98 6875 142 0.2178 0.2399 3.908 3.9697| | 19: 1.12 - 1.10 0.97 6949 106 0.2270 0.2336 3.8626 3.9005| | 20: 1.10 - 1.08 0.97 6884 147 0.2279 0.2061 3.8075 3.7399| | 21: 1.08 - 1.07 0.97 6852 152 0.2415 0.2750 3.7878 3.8345| | 22: 1.07 - 1.05 0.97 6838 135 0.2537 0.2460 3.7465 3.7407| | 23: 1.05 - 1.03 0.97 6829 159 0.2761 0.2964 3.7387 3.8423| | 24: 1.03 - 1.02 0.96 6785 133 0.2839 0.2909 3.6946 3.7939| | 25: 1.02 - 1.01 0.93 6552 130 0.3047 0.2874 3.6732 3.6794| | 26: 1.01 - 0.99 0.96 6767 158 0.3194 0.3344 3.6267 3.6231| | 27: 0.99 - 0.98 0.94 6648 131 0.3429 0.3155 3.6419 3.5731| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.58 0.91 0.97 36056.55| | 2: 2.94 - 2.33 7339 128 0.85 21.29 1.08 1.02 15193.89| | 3: 2.33 - 2.04 6939 150 0.93 12.43 1.11 1.05 4047.00| | 4: 2.04 - 1.85 7170 155 0.93 13.03 1.11 1.06 2623.81| | 5: 1.85 - 1.72 7113 159 0.91 15.67 1.11 1.07 2079.14| | 6: 1.72 - 1.62 7102 142 0.90 16.95 1.12 1.07 1669.61| | 7: 1.62 - 1.54 7104 148 0.89 18.34 1.11 1.06 1409.25| | 8: 1.54 - 1.47 6798 152 0.88 18.81 1.11 1.06 1188.43| | 9: 1.47 - 1.41 6938 155 0.88 19.46 1.10 1.06 1027.10| | 10: 1.41 - 1.36 7022 150 0.87 20.55 1.09 1.07 900.13| | 11: 1.36 - 1.32 6997 151 0.87 20.47 1.08 1.05 779.83| | 12: 1.32 - 1.28 6976 149 0.87 20.34 1.08 1.03 671.33| | 13: 1.28 - 1.25 6907 166 0.87 19.99 1.07 1.02 596.72| | 14: 1.25 - 1.22 7015 113 0.87 20.57 1.07 1.04 565.58| | 15: 1.22 - 1.19 6957 137 0.86 20.98 1.08 1.04 544.21| | 16: 1.19 - 1.17 6604 132 0.86 21.11 1.08 1.03 516.77| | 17: 1.17 - 1.14 6941 135 0.85 22.00 1.08 1.01 464.92| | 18: 1.14 - 1.12 6875 142 0.86 21.30 1.08 1.00 403.91| | 19: 1.12 - 1.10 6949 106 0.86 21.24 1.07 1.01 354.22| | 20: 1.10 - 1.08 6884 147 0.87 20.95 1.06 1.02 314.56| | 21: 1.08 - 1.07 6852 152 0.85 22.76 1.06 1.01 319.21| | 22: 1.07 - 1.05 6838 135 0.82 25.34 1.05 1.01 330.17| | 23: 1.05 - 1.03 6829 159 0.79 28.54 1.05 0.97 349.77| | 24: 1.03 - 1.02 6785 133 0.77 30.51 1.04 0.95 344.74| | 25: 1.02 - 1.01 6552 130 0.76 31.68 1.03 0.90 320.13| | 26: 1.01 - 0.99 6767 158 0.75 32.59 1.03 0.89 292.87| | 27: 0.99 - 0.98 6648 131 0.75 32.33 1.04 0.90 271.85| |alpha: min = 0.89 max = 1.07 mean = 1.01| |beta: min = 271.85 max = 36056.55 mean = 2855.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.76| |phase err.(test): min = 0.00 max = 89.60 mean = 21.89| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.270 2950 Z= 5.490 Angle : 5.308 18.596 4018 Z= 3.798 Chirality : 0.384 1.103 492 Planarity : 0.034 0.146 512 Dihedral : 12.672 83.007 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.65 % Allowed : 5.48 % Favored : 93.87 % Cbeta Deviations : 30.90 % 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: -2.06 (0.39), residues: 386 helix: -2.47 (0.32), residues: 148 sheet: -0.88 (0.52), residues: 86 loop : -0.10 (0.51), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.069 0.018 ARG A 27 TYR 0.130 0.039 TYR B 195 PHE 0.125 0.037 PHE A 164 TRP 0.105 0.031 TRP A 139 HIS 0.077 0.037 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.1984 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.300970 | | target function (ml) not normalized (work): 805627.646530 | | target function (ml) not normalized (free): 16556.607869 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2035 0.2037 0.1984 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2035 0.2037 0.1984 n_refl.: 191155 remove outliers: r(all,work,free)=0.2035 0.2037 0.1984 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2035 0.2037 0.1984 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1806 0.1934 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1803 0.1934 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4077 402.814 292.303 0.435 0.911 0.297 13.296-10.522 99.01 99 1 0.2515 528.187 518.787 0.785 0.912 0.245 10.503-8.327 98.90 177 3 0.2469 564.205 559.786 0.973 0.912 0.220 8.318-6.595 100.00 360 8 0.2478 414.736 402.371 0.973 0.912 0.160 6.588-5.215 100.00 711 7 0.2303 381.101 364.860 0.958 0.912 0.150 5.214-4.128 98.38 1367 28 0.1481 557.435 550.352 1.076 0.912 0.070 4.126-3.266 94.74 2603 46 0.1350 508.132 499.489 1.147 0.912 0.009 3.266-2.585 99.86 5447 97 0.1447 342.774 337.293 1.122 0.911 0.000 2.585-2.046 97.45 10613 204 0.1401 258.603 254.291 1.128 0.911 0.000 2.046-1.619 99.39 21536 464 0.1624 153.054 149.739 1.144 0.910 0.000 1.619-1.281 98.00 42464 925 0.1937 82.395 80.167 1.130 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2314 44.203 41.678 1.113 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0017 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1803 r_free=0.1934 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1803 r_free=0.1934 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.374653 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.783150 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 0.1269 0.1481 0.0211 0.035 1.2 11.0 0.0 0.0 0 11.187 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.69 14.81 2.11 1.118 13.111 573.783 0.019 13.00 15.54 2.55 1.274 13.373 573.783 0.018 Individual atomic B min max mean iso aniso Overall: 5.12 73.04 15.07 1.42 435 3274 Protein: 5.12 40.62 11.02 1.42 0 2902 Water: 6.30 73.04 29.67 N/A 435 370 Other: 16.03 30.65 23.34 N/A 0 2 Chain A: 5.32 60.58 13.09 N/A 0 1626 Chain B: 5.12 73.04 12.81 N/A 0 1648 Chain S: 11.36 63.04 31.05 N/A 435 0 Histogram: Values Number of atoms 5.12 - 11.91 2154 11.91 - 18.70 642 18.70 - 25.50 318 25.50 - 32.29 259 32.29 - 39.08 152 39.08 - 45.87 113 45.87 - 52.67 49 52.67 - 59.46 17 59.46 - 66.25 4 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1554 r_work=0.1299 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1549 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 = 0.1535 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.10 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= 0.1535 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015725 | | target function (ls_wunit_k1) not normalized (work): 2945.136167 | | target function (ls_wunit_k1) not normalized (free): 112.480561 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1535 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1471 0.1468 0.1611 n_refl.: 191138 remove outliers: r(all,work,free)=0.1471 0.1468 0.1611 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1494 0.1492 0.1623 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1527 n_refl.: 191138 remove outliers: r(all,work,free)=0.1281 0.1276 0.1526 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 0.3650 402.814 367.512 0.452 0.997 0.275 13.296-10.522 99.01 99 1 0.2094 528.187 520.106 0.712 0.999 0.250 10.503-8.327 98.90 177 3 0.1727 564.205 564.480 0.861 0.999 0.203 8.318-6.595 100.00 360 8 0.1752 414.736 411.793 0.876 0.998 0.150 6.588-5.215 100.00 711 7 0.1582 381.101 373.744 0.857 0.999 0.140 5.214-4.128 98.38 1367 28 0.0930 557.435 554.201 0.942 0.999 0.049 4.126-3.266 94.74 2603 46 0.0856 508.132 503.968 1.009 1.000 0.019 3.266-2.585 99.86 5447 97 0.0928 342.774 340.382 0.992 0.999 0.010 2.585-2.046 97.45 10613 204 0.0940 258.603 256.403 1.002 0.999 0.000 2.046-1.619 99.39 21536 464 0.1077 153.054 151.407 1.019 0.999 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.384 1.010 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.223 0.990 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0371 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1526 | n_water=805 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1278 r_free=0.1530 | n_water=800 | time (s): 100.930 (total time: 103.660) Filter (q & B) r_work=0.1278 r_free=0.1530 | n_water=795 | time (s): 4.840 (total time: 108.500) Compute maps r_work=0.1278 r_free=0.1530 | n_water=795 | time (s): 1.920 (total time: 110.420) Filter (map) r_work=0.1302 r_free=0.1522 | n_water=672 | time (s): 5.380 (total time: 115.800) Find peaks r_work=0.1302 r_free=0.1522 | n_water=672 | time (s): 0.780 (total time: 116.580) Add new water r_work=0.1324 r_free=0.1551 | n_water=972 | time (s): 4.850 (total time: 121.430) Refine new water occ: r_work=0.1283 r_free=0.1520 adp: r_work=0.1273 r_free=0.1511 occ: r_work=0.1275 r_free=0.1514 adp: r_work=0.1268 r_free=0.1507 occ: r_work=0.1269 r_free=0.1508 adp: r_work=0.1266 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1505 r_work=0.1266 r_free=0.1505 | n_water=972 | time (s): 68.480 (total time: 189.910) Filter (q & B) r_work=0.1269 r_free=0.1507 | n_water=903 | time (s): 6.190 (total time: 196.100) Filter (dist only) r_work=0.1270 r_free=0.1505 | n_water=901 | time (s): 117.810 (total time: 313.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.619882 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 576.361099 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1253 0.1522 0.0269 0.038 1.1 16.8 0.0 0.3 0 12.310 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.22 2.69 2.054 15.207 576.361 0.014 12.31 15.09 2.78 2.452 15.226 576.361 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 68.21 16.29 1.20 532 3273 Protein: 5.42 40.89 10.98 1.20 0 2902 Water: 6.57 68.21 33.36 N/A 532 369 Other: 16.62 33.32 24.97 N/A 0 2 Chain A: 5.54 56.64 13.03 N/A 0 1625 Chain B: 5.42 68.21 12.83 N/A 0 1648 Chain S: 12.88 66.79 36.93 N/A 532 0 Histogram: Values Number of atoms 5.42 - 11.70 2059 11.70 - 17.97 714 17.97 - 24.25 274 24.25 - 30.53 214 30.53 - 36.81 185 36.81 - 43.09 162 43.09 - 49.37 105 49.37 - 55.65 44 55.65 - 61.93 42 61.93 - 68.21 6 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1510 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 = 0.1509 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1509 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013444 | | target function (ls_wunit_k1) not normalized (work): 2518.033934 | | target function (ls_wunit_k1) not normalized (free): 100.941286 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1509 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1432 0.1429 0.1595 n_refl.: 191137 remove outliers: r(all,work,free)=0.1432 0.1429 0.1595 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1594 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1233 0.1517 n_refl.: 191137 remove outliers: r(all,work,free)=0.1238 0.1233 0.1517 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 0.3295 402.814 377.964 0.486 0.964 0.277 13.296-10.522 99.01 99 1 0.1852 528.187 524.213 0.762 0.965 0.260 10.503-8.327 98.90 177 3 0.1420 564.205 565.417 0.922 0.965 0.159 8.318-6.595 100.00 360 8 0.1545 414.736 414.351 0.927 0.964 0.130 6.588-5.215 100.00 711 7 0.1340 381.101 376.818 0.908 0.964 0.120 5.214-4.128 98.38 1367 28 0.0824 557.435 555.536 0.992 0.964 0.080 4.126-3.266 94.74 2603 46 0.0770 508.132 505.246 1.059 0.964 0.024 3.266-2.585 99.86 5447 97 0.0862 342.774 341.260 1.045 0.963 0.010 2.585-2.046 97.45 10613 204 0.0896 258.603 256.777 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1040 153.054 151.621 1.079 0.959 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.349 1.072 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.210 1.059 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0430 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1517 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1517 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1517 | n_water=901 | time (s): 3.520 (total time: 3.520) Filter (dist) r_work=0.1236 r_free=0.1520 | n_water=893 | time (s): 131.880 (total time: 135.400) Filter (q & B) r_work=0.1236 r_free=0.1521 | n_water=891 | time (s): 5.230 (total time: 140.630) Compute maps r_work=0.1236 r_free=0.1521 | n_water=891 | time (s): 2.020 (total time: 142.650) Filter (map) r_work=0.1272 r_free=0.1514 | n_water=706 | time (s): 4.760 (total time: 147.410) Find peaks r_work=0.1272 r_free=0.1514 | n_water=706 | time (s): 0.930 (total time: 148.340) Add new water r_work=0.1293 r_free=0.1545 | n_water=1021 | time (s): 5.020 (total time: 153.360) Refine new water occ: r_work=0.1249 r_free=0.1507 adp: r_work=0.1250 r_free=0.1508 occ: r_work=0.1245 r_free=0.1505 adp: r_work=0.1245 r_free=0.1506 occ: r_work=0.1242 r_free=0.1504 adp: r_work=0.1242 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1505 r_work=0.1242 r_free=0.1505 | n_water=1021 | time (s): 262.170 (total time: 415.530) Filter (q & B) r_work=0.1247 r_free=0.1508 | n_water=888 | time (s): 4.710 (total time: 420.240) Filter (dist only) r_work=0.1247 r_free=0.1507 | n_water=887 | time (s): 130.350 (total time: 550.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.704325 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.962778 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1239 0.1439 0.0200 0.034 1.1 7.0 0.0 0.0 0 0.852 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.39 2.00 1.934 14.600 16.963 3.940 12.31 13.96 1.65 2.232 14.508 16.963 3.895 Individual atomic B min max mean iso aniso Overall: 5.53 67.77 15.29 1.07 520 3271 Protein: 5.53 36.94 10.75 1.07 0 2902 Water: 6.70 67.77 30.14 N/A 520 367 Other: 14.11 28.55 21.33 N/A 0 2 Chain A: 5.53 55.66 12.80 N/A 0 1625 Chain B: 5.53 67.77 12.54 N/A 0 1646 Chain S: 14.06 60.72 31.79 N/A 520 0 Histogram: Values Number of atoms 5.53 - 11.75 2127 11.75 - 17.98 689 17.98 - 24.20 290 24.20 - 30.43 243 30.43 - 36.65 206 36.65 - 42.87 133 42.87 - 49.10 70 49.10 - 55.32 20 55.32 - 61.54 12 61.54 - 67.77 1 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1396 r_work=0.1231 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1397 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1389 target_work(ml) = 3.890 | | 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= 0.1389 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890023 | | target function (ml) not normalized (work): 728585.666245 | | target function (ml) not normalized (free): 15216.671354 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1227 0.1388 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1439 0.1439 0.1479 n_refl.: 191137 remove outliers: r(all,work,free)=0.1439 0.1439 0.1479 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1433 0.1433 0.1476 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1223 0.1380 n_refl.: 191137 remove outliers: r(all,work,free)=0.1226 0.1223 0.1380 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3956 398.895 352.386 0.411 0.947 0.244 13.296-10.522 99.01 99 1 0.2393 528.187 507.794 0.704 0.948 0.213 10.503-8.327 97.80 175 3 0.1970 554.286 556.548 0.884 0.948 0.148 8.318-6.595 100.00 360 8 0.2122 414.736 408.871 0.892 0.948 0.110 6.588-5.215 100.00 711 7 0.1817 381.101 371.085 0.884 0.948 0.110 5.214-4.128 98.38 1367 28 0.1158 557.435 551.682 0.972 0.948 0.090 4.126-3.266 94.74 2603 46 0.1104 508.132 500.785 1.031 0.948 0.009 3.266-2.585 99.86 5447 97 0.1078 342.774 339.148 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0967 258.603 255.749 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0969 153.054 151.417 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.496 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.316 1.039 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0954 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1380 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1380 | n_water=887 | time (s): 2.170 (total time: 2.170) Filter (dist) r_work=0.1225 r_free=0.1384 | n_water=882 | time (s): 108.940 (total time: 111.110) Filter (q & B) r_work=0.1225 r_free=0.1380 | n_water=863 | time (s): 5.010 (total time: 116.120) Compute maps r_work=0.1225 r_free=0.1380 | n_water=863 | time (s): 1.650 (total time: 117.770) Filter (map) r_work=0.1246 r_free=0.1385 | n_water=735 | time (s): 4.190 (total time: 121.960) Find peaks r_work=0.1246 r_free=0.1385 | n_water=735 | time (s): 0.680 (total time: 122.640) Add new water r_work=0.1261 r_free=0.1404 | n_water=972 | time (s): 4.350 (total time: 126.990) Refine new water occ: r_work=0.1214 r_free=0.1366 adp: r_work=0.1206 r_free=0.1362 occ: r_work=0.1203 r_free=0.1364 adp: r_work=0.1203 r_free=0.1363 occ: r_work=0.1200 r_free=0.1366 adp: r_work=0.1200 r_free=0.1365 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1365 r_work=0.1200 r_free=0.1365 | n_water=972 | time (s): 272.220 (total time: 399.210) Filter (q & B) r_work=0.1205 r_free=0.1370 | n_water=881 | time (s): 4.460 (total time: 403.670) Filter (dist only) r_work=0.1206 r_free=0.1369 | n_water=880 | time (s): 107.330 (total time: 511.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.530885 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.024180 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 0.1205 0.1370 0.0164 0.035 1.1 6.0 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.70 1.64 1.837 14.252 16.024 3.873 11.99 13.67 1.68 1.947 14.210 16.024 3.865 Individual atomic B min max mean iso aniso Overall: 5.50 67.26 15.04 1.01 513 3271 Protein: 5.50 33.78 10.67 1.01 0 2902 Water: 5.88 67.26 29.41 N/A 513 367 Other: 14.03 27.41 20.72 N/A 0 2 Chain A: 5.55 54.47 12.67 N/A 0 1625 Chain B: 5.50 67.26 12.44 N/A 0 1646 Chain S: 5.88 60.77 30.85 N/A 513 0 Histogram: Values Number of atoms 5.50 - 11.67 2108 11.67 - 17.85 732 17.85 - 24.03 292 24.03 - 30.20 244 30.20 - 36.38 178 36.38 - 42.56 141 42.56 - 48.73 63 48.73 - 54.91 19 54.91 - 61.09 6 61.09 - 67.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1367 r_work=0.1199 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1367 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1366 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862480 | | target function (ml) not normalized (work): 723411.654768 | | target function (ml) not normalized (free): 15131.085625 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1366 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1405 0.1404 0.1469 n_refl.: 191133 remove outliers: r(all,work,free)=0.1405 0.1404 0.1469 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1397 0.1396 0.1465 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1363 n_refl.: 191133 remove outliers: r(all,work,free)=0.1198 0.1195 0.1363 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3933 360.801 322.068 0.402 0.951 0.227 13.296-10.522 97.03 97 1 0.2336 480.661 452.022 0.692 0.952 0.193 10.503-8.327 97.80 175 3 0.2068 501.352 495.996 0.864 0.952 0.150 8.318-6.595 100.00 360 8 0.2158 375.129 369.857 0.885 0.952 0.109 6.588-5.215 100.00 711 7 0.1881 344.706 334.965 0.881 0.952 0.092 5.214-4.128 98.38 1367 28 0.1191 504.200 499.030 0.969 0.952 0.090 4.126-3.266 94.74 2603 46 0.1119 459.606 453.140 1.030 0.952 0.005 3.266-2.585 99.86 5447 97 0.1090 310.039 306.811 1.016 0.952 0.000 2.585-2.046 97.45 10613 204 0.0935 233.907 231.530 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0910 138.437 137.152 1.052 0.950 0.000 1.619-1.281 98.00 42464 925 0.0985 74.527 73.825 1.049 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1661 39.980 38.324 1.035 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1185 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1363 | n_water=880 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1195 r_free=0.1363 | n_water=880 | time (s): 105.770 (total time: 108.430) Filter (q & B) r_work=0.1195 r_free=0.1363 | n_water=872 | time (s): 4.970 (total time: 113.400) Compute maps r_work=0.1195 r_free=0.1363 | n_water=872 | time (s): 2.140 (total time: 115.540) Filter (map) r_work=0.1216 r_free=0.1362 | n_water=753 | time (s): 4.170 (total time: 119.710) Find peaks r_work=0.1216 r_free=0.1362 | n_water=753 | time (s): 0.560 (total time: 120.270) Add new water r_work=0.1229 r_free=0.1378 | n_water=989 | time (s): 4.240 (total time: 124.510) Refine new water occ: r_work=0.1195 r_free=0.1350 adp: r_work=0.1195 r_free=0.1350 occ: r_work=0.1192 r_free=0.1349 adp: r_work=0.1192 r_free=0.1349 occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1190 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1350 r_work=0.1190 r_free=0.1350 | n_water=989 | time (s): 240.790 (total time: 365.300) Filter (q & B) r_work=0.1195 r_free=0.1356 | n_water=891 | time (s): 5.200 (total time: 370.500) Filter (dist only) r_work=0.1196 r_free=0.1356 | n_water=890 | time (s): 115.660 (total time: 486.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.563707 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.301464 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1364 0.0166 0.036 1.1 7.3 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.64 1.66 1.796 14.153 15.301 3.762 12.02 13.67 1.65 1.855 14.127 15.301 3.760 Individual atomic B min max mean iso aniso Overall: 5.56 66.95 14.98 0.96 523 3271 Protein: 5.56 32.44 10.61 0.96 0 2902 Water: 5.95 66.95 29.21 N/A 523 367 Other: 13.82 26.38 20.10 N/A 0 2 Chain A: 5.56 53.72 12.58 N/A 0 1625 Chain B: 5.59 66.95 12.36 N/A 0 1646 Chain S: 5.95 60.78 30.67 N/A 523 0 Histogram: Values Number of atoms 5.56 - 11.70 2135 11.70 - 17.84 724 17.84 - 23.98 294 23.98 - 30.12 234 30.12 - 36.25 179 36.25 - 42.39 132 42.39 - 48.53 70 48.53 - 54.67 20 54.67 - 60.81 5 60.81 - 66.95 1 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1368 r_work=0.1202 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1368 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1369 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759150 | | target function (ml) not normalized (work): 704051.136928 | | target function (ml) not normalized (free): 14740.148477 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1369 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1476 n_refl.: 191131 remove outliers: r(all,work,free)=0.1407 0.1406 0.1476 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1399 0.1398 0.1470 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1366 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1366 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3924 360.801 321.059 0.389 0.951 0.213 13.296-10.522 97.03 97 1 0.2397 480.661 460.897 0.695 0.953 0.168 10.503-8.327 97.80 175 3 0.2137 501.352 495.151 0.855 0.953 0.122 8.318-6.595 100.00 360 8 0.2185 375.129 370.016 0.882 0.953 0.095 6.588-5.215 100.00 711 7 0.1921 344.706 334.758 0.880 0.953 0.080 5.214-4.128 98.38 1367 28 0.1215 504.200 498.526 0.968 0.953 0.070 4.126-3.266 94.74 2603 46 0.1147 459.606 452.799 1.031 0.953 0.010 3.266-2.585 99.86 5447 97 0.1114 310.039 306.594 1.016 0.952 0.000 2.585-2.046 97.45 10613 204 0.0946 233.907 231.435 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0913 138.437 137.119 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0975 74.527 73.817 1.052 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1652 39.980 38.311 1.040 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1329 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1366 | n_water=890 | time (s): 2.960 (total time: 2.960) Filter (dist) r_work=0.1199 r_free=0.1366 | n_water=887 | time (s): 108.860 (total time: 111.820) Filter (q & B) r_work=0.1200 r_free=0.1363 | n_water=875 | time (s): 4.300 (total time: 116.120) Compute maps r_work=0.1200 r_free=0.1363 | n_water=875 | time (s): 2.450 (total time: 118.570) Filter (map) r_work=0.1219 r_free=0.1365 | n_water=765 | time (s): 4.630 (total time: 123.200) Find peaks r_work=0.1219 r_free=0.1365 | n_water=765 | time (s): 0.610 (total time: 123.810) Add new water r_work=0.1229 r_free=0.1380 | n_water=981 | time (s): 4.780 (total time: 128.590) Refine new water occ: r_work=0.1196 r_free=0.1348 adp: r_work=0.1196 r_free=0.1348 occ: r_work=0.1194 r_free=0.1346 adp: r_work=0.1194 r_free=0.1347 occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1192 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1345 r_work=0.1192 r_free=0.1345 | n_water=981 | time (s): 197.820 (total time: 326.410) Filter (q & B) r_work=0.1197 r_free=0.1351 | n_water=898 | time (s): 4.880 (total time: 331.290) Filter (dist only) r_work=0.1197 r_free=0.1351 | n_water=897 | time (s): 120.910 (total time: 452.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.597505 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.433823 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 0.1356 0.0157 0.037 1.1 7.2 0.0 0.3 0 0.799 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.56 1.57 1.767 14.064 14.434 3.758 12.02 13.60 1.58 1.920 14.011 14.434 3.757 Individual atomic B min max mean iso aniso Overall: 5.58 65.78 14.85 0.90 530 3271 Protein: 5.58 29.33 10.49 0.90 0 2902 Water: 5.95 65.78 28.94 N/A 530 367 Other: 13.87 23.54 18.71 N/A 0 2 Chain A: 5.62 52.67 12.43 N/A 0 1625 Chain B: 5.58 65.78 12.22 N/A 0 1646 Chain S: 5.95 60.87 30.45 N/A 530 0 Histogram: Values Number of atoms 5.58 - 11.60 2112 11.60 - 17.62 769 17.62 - 23.64 286 23.64 - 29.66 207 29.66 - 35.68 189 35.68 - 41.70 135 41.70 - 47.72 73 47.72 - 53.74 24 53.74 - 59.76 3 59.76 - 65.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1357 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755803 | | target function (ml) not normalized (work): 703424.283401 | | target function (ml) not normalized (free): 14724.822959 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1357 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1406 0.1405 0.1470 n_refl.: 191131 remove outliers: r(all,work,free)=0.1406 0.1405 0.1470 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1398 0.1397 0.1464 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1356 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1356 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3656 356.360 313.091 0.388 0.951 0.213 13.296-10.522 97.03 97 1 0.2394 480.661 461.261 0.693 0.952 0.158 10.503-8.327 97.80 175 3 0.2140 501.352 495.261 0.854 0.952 0.111 8.318-6.595 100.00 360 8 0.2177 375.129 370.095 0.882 0.952 0.090 6.588-5.215 100.00 711 7 0.1934 344.706 334.839 0.881 0.952 0.080 5.214-4.128 98.38 1367 28 0.1222 504.200 498.641 0.968 0.952 0.039 4.126-3.266 94.74 2603 46 0.1152 459.606 452.533 1.032 0.953 0.005 3.266-2.585 99.86 5447 97 0.1120 310.039 306.647 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0951 233.907 231.432 1.030 0.952 0.000 2.046-1.619 99.39 21536 464 0.0911 138.437 137.157 1.053 0.951 0.000 1.619-1.281 98.00 42464 925 0.0968 74.527 73.836 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1650 39.980 38.317 1.039 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1385 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1356 | n_water=897 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1199 r_free=0.1356 | n_water=897 | time (s): 107.040 (total time: 110.270) Filter (q & B) r_work=0.1199 r_free=0.1355 | n_water=887 | time (s): 5.010 (total time: 115.280) Compute maps r_work=0.1199 r_free=0.1355 | n_water=887 | time (s): 2.290 (total time: 117.570) Filter (map) r_work=0.1219 r_free=0.1357 | n_water=772 | time (s): 4.350 (total time: 121.920) Find peaks r_work=0.1219 r_free=0.1357 | n_water=772 | time (s): 0.550 (total time: 122.470) Add new water r_work=0.1227 r_free=0.1366 | n_water=975 | time (s): 4.020 (total time: 126.490) Refine new water occ: r_work=0.1197 r_free=0.1342 adp: r_work=0.1197 r_free=0.1342 occ: r_work=0.1195 r_free=0.1343 adp: r_work=0.1195 r_free=0.1342 occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1344 r_work=0.1194 r_free=0.1344 | n_water=975 | time (s): 251.750 (total time: 378.240) Filter (q & B) r_work=0.1198 r_free=0.1354 | n_water=900 | time (s): 5.230 (total time: 383.470) Filter (dist only) r_work=0.1198 r_free=0.1353 | n_water=898 | time (s): 117.280 (total time: 500.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.531019 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.687114 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 0.1358 0.0156 0.037 1.1 6.5 0.0 0.3 0 0.766 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.58 1.56 1.719 13.908 13.687 3.757 12.04 13.61 1.57 1.771 13.887 13.687 3.756 Individual atomic B min max mean iso aniso Overall: 5.57 64.65 14.76 0.88 531 3271 Protein: 5.57 28.55 10.43 0.88 0 2902 Water: 5.94 64.65 28.75 N/A 531 367 Other: 13.88 22.51 18.19 N/A 0 2 Chain A: 5.61 52.18 12.33 N/A 0 1625 Chain B: 5.57 64.65 12.14 N/A 0 1646 Chain S: 5.94 60.90 30.36 N/A 531 0 Histogram: Values Number of atoms 5.57 - 11.48 2086 11.48 - 17.39 796 17.39 - 23.30 272 23.30 - 29.21 213 29.21 - 35.11 188 35.11 - 41.02 140 41.02 - 46.93 71 46.93 - 52.84 29 52.84 - 58.74 4 58.74 - 64.65 3 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1361 r_work=0.1204 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1361 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755468 | | target function (ml) not normalized (work): 703354.138186 | | target function (ml) not normalized (free): 14723.619702 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1398 0.1397 0.1476 n_refl.: 191129 remove outliers: r(all,work,free)=0.1398 0.1397 0.1476 n_refl.: 191129 overall B=-0.24 to atoms: r(all,work,free)=0.1362 0.1361 0.1453 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1202 0.1359 n_refl.: 191129 remove outliers: r(all,work,free)=0.1205 0.1202 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3668 356.360 328.648 0.410 0.953 0.203 13.296-10.522 97.03 97 1 0.2378 480.661 461.662 0.706 0.954 0.146 10.503-8.327 97.80 175 3 0.2176 501.352 495.698 0.873 0.954 0.115 8.318-6.595 100.00 360 8 0.2215 375.129 370.134 0.903 0.954 0.093 6.588-5.215 100.00 711 7 0.1962 344.706 334.564 0.903 0.954 0.077 5.214-4.128 98.38 1367 28 0.1228 504.200 498.487 0.992 0.954 0.035 4.126-3.266 94.74 2603 46 0.1166 459.606 452.366 1.056 0.955 0.005 3.266-2.585 99.86 5447 97 0.1124 310.039 306.623 1.038 0.954 0.000 2.585-2.046 97.45 10613 204 0.0957 233.907 231.362 1.046 0.954 0.000 2.046-1.619 99.39 21536 464 0.0910 138.437 137.137 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0966 74.527 73.833 1.050 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1650 39.980 38.315 1.020 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0529 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1359 | n_water=898 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1202 r_free=0.1361 | n_water=897 | time (s): 112.100 (total time: 114.870) Filter (q & B) r_work=0.1203 r_free=0.1359 | n_water=887 | time (s): 4.430 (total time: 119.300) Compute maps r_work=0.1203 r_free=0.1359 | n_water=887 | time (s): 1.830 (total time: 121.130) Filter (map) r_work=0.1222 r_free=0.1368 | n_water=777 | time (s): 5.450 (total time: 126.580) Find peaks r_work=0.1222 r_free=0.1368 | n_water=777 | time (s): 0.590 (total time: 127.170) Add new water r_work=0.1229 r_free=0.1379 | n_water=986 | time (s): 4.520 (total time: 131.690) Refine new water occ: r_work=0.1199 r_free=0.1344 adp: r_work=0.1199 r_free=0.1344 occ: r_work=0.1197 r_free=0.1343 adp: r_work=0.1197 r_free=0.1344 occ: r_work=0.1196 r_free=0.1343 adp: r_work=0.1195 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1344 r_work=0.1195 r_free=0.1344 | n_water=986 | time (s): 241.490 (total time: 373.180) Filter (q & B) r_work=0.1200 r_free=0.1354 | n_water=905 | time (s): 4.370 (total time: 377.550) Filter (dist only) r_work=0.1200 r_free=0.1354 | n_water=903 | time (s): 117.390 (total time: 494.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.551107 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.829313 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1359 0.0156 0.038 1.1 6.3 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.59 1.56 1.698 13.642 14.829 3.757 12.02 13.60 1.58 1.711 13.630 14.829 3.753 Individual atomic B min max mean iso aniso Overall: 5.37 63.39 14.53 0.88 536 3271 Protein: 5.37 28.24 10.20 0.88 0 2902 Water: 5.78 63.39 28.43 N/A 536 367 Other: 13.66 22.22 17.94 N/A 0 2 Chain A: 5.44 51.57 12.06 N/A 0 1625 Chain B: 5.37 63.39 11.88 N/A 0 1646 Chain S: 5.78 60.75 30.16 N/A 536 0 Histogram: Values Number of atoms 5.37 - 11.17 2062 11.17 - 16.97 814 16.97 - 22.78 274 22.78 - 28.58 207 28.58 - 34.38 194 34.38 - 40.18 132 40.18 - 45.99 82 45.99 - 51.79 34 51.79 - 57.59 4 57.59 - 63.39 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1360 r_work=0.1202 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1360 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1359 target_work(ml) = 3.753 | | 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.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.752893 | | target function (ml) not normalized (work): 702871.783350 | | target function (ml) not normalized (free): 14723.265269 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1359 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1369 0.1367 0.1458 n_refl.: 191129 remove outliers: r(all,work,free)=0.1369 0.1367 0.1458 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1369 0.1367 0.1458 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1349 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1190 0.1349 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3647 356.360 328.815 0.401 0.975 0.207 13.296-10.522 97.03 97 1 0.2375 480.661 461.295 0.683 0.976 0.142 10.503-8.327 97.80 175 3 0.2183 501.352 494.688 0.844 0.977 0.108 8.318-6.595 100.00 360 8 0.2192 375.129 369.837 0.873 0.977 0.088 6.588-5.215 100.00 711 7 0.1965 344.706 333.904 0.875 0.977 0.073 5.214-4.128 98.38 1367 28 0.1232 504.200 498.240 0.961 0.978 0.034 4.126-3.266 94.74 2603 46 0.1173 459.606 451.868 1.022 0.979 0.000 3.266-2.585 99.86 5447 97 0.1124 310.039 306.368 1.004 0.980 0.000 2.585-2.046 97.45 10613 204 0.0957 233.907 231.231 1.011 0.982 0.000 2.046-1.619 99.39 21536 464 0.0904 138.437 137.063 1.024 0.985 0.000 1.619-1.281 98.00 42464 925 0.0943 74.527 73.877 1.009 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1627 39.980 38.295 0.969 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1208 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1349 | n_water=903 | time (s): 2.260 (total time: 2.260) Filter (dist) r_work=0.1190 r_free=0.1349 | n_water=903 | time (s): 108.270 (total time: 110.530) Filter (q & B) r_work=0.1191 r_free=0.1347 | n_water=893 | time (s): 5.350 (total time: 115.880) Compute maps r_work=0.1191 r_free=0.1347 | n_water=893 | time (s): 1.600 (total time: 117.480) Filter (map) r_work=0.1212 r_free=0.1362 | n_water=785 | time (s): 4.200 (total time: 121.680) Find peaks r_work=0.1212 r_free=0.1362 | n_water=785 | time (s): 0.550 (total time: 122.230) Add new water r_work=0.1219 r_free=0.1372 | n_water=1001 | time (s): 4.040 (total time: 126.270) Refine new water occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1187 r_free=0.1335 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1334 occ: r_work=0.1183 r_free=0.1334 adp: r_work=0.1183 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1334 r_work=0.1183 r_free=0.1334 | n_water=1001 | time (s): 216.490 (total time: 342.760) Filter (q & B) r_work=0.1189 r_free=0.1350 | n_water=913 | time (s): 5.320 (total time: 348.080) Filter (dist only) r_work=0.1189 r_free=0.1349 | n_water=911 | time (s): 115.200 (total time: 463.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.602904 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.961337 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1352 0.0160 0.038 1.1 7.2 0.0 0.3 0 0.801 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.52 1.60 1.667 13.625 13.961 3.752 11.94 13.55 1.62 1.667 13.622 13.961 3.752 Individual atomic B min max mean iso aniso Overall: 5.39 63.11 14.54 0.86 544 3271 Protein: 5.39 28.04 10.22 0.86 0 2902 Water: 5.86 63.11 28.31 N/A 544 367 Other: 13.69 22.20 17.95 N/A 0 2 Chain A: 5.44 51.45 12.05 N/A 0 1625 Chain B: 5.39 63.11 11.87 N/A 0 1646 Chain S: 5.86 60.78 30.07 N/A 544 0 Histogram: Values Number of atoms 5.39 - 11.16 2057 11.16 - 16.93 825 16.93 - 22.70 265 22.70 - 28.48 223 28.48 - 34.25 190 34.25 - 40.02 127 40.02 - 45.79 82 45.79 - 51.56 37 51.56 - 57.33 5 57.33 - 63.11 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1356 r_work=0.1194 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1356 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 = 0.1355 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751366 | | target function (ml) not normalized (work): 702585.858149 | | target function (ml) not normalized (free): 14720.585294 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1375 0.1374 0.1464 n_refl.: 191129 remove outliers: r(all,work,free)=0.1375 0.1374 0.1464 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1375 0.1374 0.1464 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191129 remove outliers: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3643 356.360 327.682 0.394 0.976 0.201 13.296-10.522 97.03 97 1 0.2367 480.661 462.171 0.680 0.977 0.139 10.503-8.327 97.80 175 3 0.2214 501.352 494.336 0.843 0.977 0.103 8.318-6.595 100.00 360 8 0.2185 375.129 369.601 0.872 0.977 0.080 6.588-5.215 100.00 711 7 0.1961 344.706 333.827 0.873 0.978 0.063 5.214-4.128 98.38 1367 28 0.1240 504.200 498.143 0.960 0.979 0.024 4.126-3.266 94.74 2603 46 0.1174 459.606 451.975 1.023 0.980 0.000 3.266-2.585 99.86 5447 97 0.1127 310.039 306.369 1.005 0.981 0.000 2.585-2.046 97.45 10613 204 0.0960 233.907 231.218 1.011 0.983 0.000 2.046-1.619 99.39 21536 464 0.0906 138.437 137.084 1.025 0.987 0.000 1.619-1.281 98.00 42464 925 0.0942 74.527 73.876 1.011 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1625 39.980 38.280 0.974 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0833 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1353 After: r_work=0.1192 r_free=0.1353 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1353 | n_water=911 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1192 r_free=0.1353 | n_water=911 | time (s): 110.830 (total time: 113.190) Filter (q & B) r_work=0.1193 r_free=0.1353 | n_water=900 | time (s): 5.240 (total time: 118.430) Compute maps r_work=0.1193 r_free=0.1353 | n_water=900 | time (s): 1.620 (total time: 120.050) Filter (map) r_work=0.1215 r_free=0.1371 | n_water=791 | time (s): 4.180 (total time: 124.230) Find peaks r_work=0.1215 r_free=0.1371 | n_water=791 | time (s): 0.650 (total time: 124.880) Add new water r_work=0.1220 r_free=0.1380 | n_water=999 | time (s): 3.990 (total time: 128.870) Refine new water occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 occ: r_work=0.1187 r_free=0.1341 adp: r_work=0.1187 r_free=0.1342 occ: r_work=0.1186 r_free=0.1341 adp: r_work=0.1186 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1341 r_work=0.1186 r_free=0.1341 | n_water=999 | time (s): 256.280 (total time: 385.150) Filter (q & B) r_work=0.1191 r_free=0.1353 | n_water=915 | time (s): 4.150 (total time: 389.300) Filter (dist only) r_work=0.1191 r_free=0.1352 | n_water=913 | time (s): 121.490 (total time: 510.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.622040 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.996841 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 0.1194 0.1358 0.0164 0.038 1.2 8.0 0.0 0.3 0 0.811 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.58 1.64 1.662 13.620 13.997 3.754 11.96 13.62 1.67 1.667 13.614 13.997 3.754 Individual atomic B min max mean iso aniso Overall: 5.44 62.27 14.52 0.86 546 3271 Protein: 5.44 27.83 10.23 0.86 0 2902 Water: 5.90 62.27 28.14 N/A 546 367 Other: 13.73 22.07 17.90 N/A 0 2 Chain A: 5.53 51.15 12.04 N/A 0 1625 Chain B: 5.44 62.27 11.86 N/A 0 1646 Chain S: 5.90 60.76 29.91 N/A 546 0 Histogram: Values Number of atoms 5.44 - 11.13 2040 11.13 - 16.81 841 16.81 - 22.49 270 22.49 - 28.17 216 28.17 - 33.86 195 33.86 - 39.54 123 39.54 - 45.22 84 45.22 - 50.90 34 50.90 - 56.59 9 56.59 - 62.27 5 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1362 r_work=0.1196 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1362 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753835 | | target function (ml) not normalized (work): 703048.333142 | | target function (ml) not normalized (free): 14732.247858 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1365 0.1460 5.6892 5.7746| | 2: 2.94 - 2.33 1.00 7339 128 0.1076 0.1376 5.0853 5.1919| | 3: 2.33 - 2.04 0.96 6939 150 0.0903 0.1175 4.6571 4.7347| | 4: 2.04 - 1.85 1.00 7170 155 0.0898 0.1079 4.3936 4.5969| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.0995 4.1534 4.2476| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1068 3.946 4.0668| | 7: 1.62 - 1.54 0.99 7104 148 0.0896 0.0992 3.801 3.9411| | 8: 1.54 - 1.47 0.96 6798 152 0.0895 0.1312 3.7013 3.898| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1149 3.6219 3.7641| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1186 3.5542 3.6734| | 11: 1.36 - 1.32 0.99 6997 151 0.0995 0.1128 3.4847 3.5859| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1112 3.458 3.5769| | 13: 1.28 - 1.25 0.98 6907 166 0.1045 0.1266 3.4359 3.5677| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1581 3.4276 3.6694| | 15: 1.22 - 1.19 0.98 6956 137 0.1171 0.1244 3.4457 3.4855| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1544 3.463 3.6526| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1237 3.4324 3.4461| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1724 3.4386 3.5343| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1784 3.4194 3.603| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1579 3.409 3.4348| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2145 3.4164 3.5009| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1964 3.4117 3.4167| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2026 3.4317 3.4844| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2247 3.4344 3.5096| | 25: 1.02 - 1.01 0.93 6552 130 0.2617 0.2512 3.448 3.5226| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2868 3.4143 3.4216| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2804 3.4681 3.3935| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.94 1.00 0.96 11441.92| | 2: 2.94 - 2.33 7339 128 0.92 12.96 0.99 0.97 5235.04| | 3: 2.33 - 2.04 6939 150 0.96 7.76 1.01 0.97 1730.08| | 4: 2.04 - 1.85 7170 155 0.96 7.76 1.00 0.97 1019.10| | 5: 1.85 - 1.72 7113 159 0.96 8.16 1.00 0.97 639.79| | 6: 1.72 - 1.62 7102 142 0.96 8.03 1.00 0.97 444.68| | 7: 1.62 - 1.54 7104 148 0.96 8.19 1.01 0.99 339.08| | 8: 1.54 - 1.47 6798 152 0.96 8.33 1.01 0.99 280.14| | 9: 1.47 - 1.41 6938 155 0.96 8.52 1.00 0.99 231.72| | 10: 1.41 - 1.36 7022 150 0.96 8.94 1.00 0.98 202.53| | 11: 1.36 - 1.32 6997 151 0.96 8.97 0.99 0.97 175.13| | 12: 1.32 - 1.28 6975 149 0.96 8.96 0.98 0.96 160.13| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.01 0.97 157.30| | 14: 1.25 - 1.22 7015 112 0.95 10.63 1.02 0.98 161.28| | 15: 1.22 - 1.19 6956 137 0.95 11.19 1.01 0.99 165.01| | 16: 1.19 - 1.17 6604 132 0.95 11.40 1.01 0.98 159.38| | 17: 1.17 - 1.14 6940 135 0.94 12.29 1.01 0.98 154.43| | 18: 1.14 - 1.12 6875 142 0.94 12.84 1.01 0.96 148.72| | 19: 1.12 - 1.10 6948 106 0.93 14.23 1.00 0.96 152.00| | 20: 1.10 - 1.08 6884 147 0.92 15.27 1.00 0.95 150.57| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.94 153.28| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.94 154.82| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.93 164.53| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.93 178.83| | 25: 1.02 - 1.01 6552 130 0.83 25.15 0.97 0.90 181.57| | 26: 1.01 - 0.99 6767 158 0.81 26.59 0.97 0.89 175.79| | 27: 0.99 - 0.98 6647 131 0.82 26.20 0.98 0.88 159.66| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 148.72 max = 11441.92 mean = 941.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.33| |phase err.(test): min = 0.00 max = 89.12 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1384 0.1383 0.1481 n_refl.: 191129 remove outliers: r(all,work,free)=0.1384 0.1383 0.1481 n_refl.: 191129 overall B=0.00 to atoms: r(all,work,free)=0.1384 0.1383 0.1481 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3601 356.360 328.121 0.394 0.975 0.207 13.296-10.522 97.03 97 1 0.2403 480.661 461.736 0.672 0.977 0.138 10.503-8.327 97.80 175 3 0.2186 501.352 494.883 0.836 0.977 0.106 8.318-6.595 100.00 360 8 0.2193 375.129 370.073 0.866 0.977 0.079 6.588-5.215 100.00 711 7 0.1967 344.706 333.620 0.868 0.977 0.070 5.214-4.128 98.38 1367 28 0.1239 504.200 498.266 0.954 0.978 0.020 4.126-3.266 94.74 2603 46 0.1179 459.606 451.818 1.017 0.980 0.000 3.266-2.585 99.86 5447 97 0.1122 310.039 306.464 1.000 0.981 0.000 2.585-2.046 97.45 10613 204 0.0965 233.907 231.202 1.005 0.983 0.000 2.046-1.619 99.39 21536 464 0.0910 138.437 137.071 1.019 0.988 0.000 1.619-1.281 98.00 42464 925 0.0948 74.527 73.868 1.007 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1625 39.980 38.278 0.971 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0487 ================= 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 : 0.2037 0.1984 0.082 5.308 5.2 78.0 14.6 805 0.000 1_bss: 0.1803 0.1934 0.082 5.308 5.2 78.0 14.6 805 0.000 1_settarget: 0.1803 0.1934 0.082 5.308 5.2 78.0 14.6 805 0.000 1_nqh: 0.1803 0.1934 0.082 5.308 5.2 78.0 14.6 805 0.000 1_weight: 0.1803 0.1934 0.082 5.308 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1269 0.1481 0.035 1.172 5.2 78.0 14.6 805 0.142 1_adp: 0.1300 0.1554 0.035 1.172 5.1 73.0 15.1 805 0.142 1_regHadp: 0.1299 0.1549 0.035 1.172 5.1 73.0 15.1 805 0.142 1_occ: 0.1283 0.1535 0.035 1.172 5.1 73.0 15.1 805 0.142 2_bss: 0.1276 0.1526 0.035 1.172 5.3 73.2 15.2 805 0.142 2_settarget: 0.1276 0.1526 0.035 1.172 5.3 73.2 15.2 805 0.142 2_updatecdl: 0.1276 0.1526 0.035 1.183 5.3 73.2 15.2 805 0.142 2_nqh: 0.1276 0.1526 0.035 1.183 5.3 73.2 15.2 805 0.142 2_sol: 0.1270 0.1505 0.035 1.183 5.3 73.2 16.3 901 n/a 2_weight: 0.1270 0.1505 0.035 1.183 5.3 73.2 16.3 901 n/a 2_xyzrec: 0.1253 0.1522 0.038 1.145 5.3 73.2 16.3 901 n/a 2_adp: 0.1232 0.1510 0.038 1.145 5.4 68.2 16.3 901 n/a 2_regHadp: 0.1232 0.1511 0.038 1.145 5.4 68.2 16.3 901 n/a 2_occ: 0.1226 0.1509 0.038 1.145 5.4 68.2 16.3 901 n/a 3_bss: 0.1233 0.1517 0.038 1.145 5.4 68.2 16.3 901 n/a 3_settarget: 0.1233 0.1517 0.038 1.145 5.4 68.2 16.3 901 n/a 3_updatecdl: 0.1233 0.1517 0.038 1.152 5.4 68.2 16.3 901 n/a 3_nqh: 0.1233 0.1517 0.038 1.152 5.4 68.2 16.3 901 n/a 3_sol: 0.1247 0.1507 0.038 1.152 5.4 68.2 15.5 887 n/a 3_weight: 0.1247 0.1507 0.038 1.152 5.4 68.2 15.5 887 n/a 3_xyzrec: 0.1239 0.1439 0.034 1.104 5.4 68.2 15.5 887 n/a 3_adp: 0.1231 0.1396 0.034 1.104 5.5 67.8 15.3 887 n/a 3_regHadp: 0.1231 0.1397 0.034 1.104 5.5 67.8 15.3 887 n/a 3_occ: 0.1227 0.1389 0.034 1.104 5.5 67.8 15.3 887 n/a 4_bss: 0.1223 0.1380 0.034 1.104 5.5 67.7 15.3 887 n/a 4_settarget: 0.1223 0.1380 0.034 1.104 5.5 67.7 15.3 887 n/a 4_updatecdl: 0.1223 0.1380 0.034 1.101 5.5 67.7 15.3 887 n/a 4_nqh: 0.1223 0.1380 0.034 1.101 5.5 67.7 15.3 887 n/a 4_sol: 0.1206 0.1369 0.034 1.101 5.5 67.7 15.1 880 n/a 4_weight: 0.1206 0.1369 0.034 1.101 5.5 67.7 15.1 880 n/a 4_xyzrec: 0.1205 0.1370 0.035 1.109 5.5 67.7 15.1 880 n/a 4_adp: 0.1199 0.1367 0.035 1.109 5.5 67.3 15.0 880 n/a 4_regHadp: 0.1199 0.1367 0.035 1.109 5.5 67.3 15.0 880 n/a 4_occ: 0.1196 0.1366 0.035 1.109 5.5 67.3 15.0 880 n/a 5_bss: 0.1195 0.1363 0.035 1.109 5.5 67.2 15.0 880 n/a 5_settarget: 0.1195 0.1363 0.035 1.109 5.5 67.2 15.0 880 n/a 5_updatecdl: 0.1195 0.1363 0.035 1.109 5.5 67.2 15.0 880 n/a 5_nqh: 0.1195 0.1363 0.035 1.109 5.5 67.2 15.0 880 n/a 5_sol: 0.1196 0.1356 0.035 1.109 5.5 67.2 15.0 890 n/a 5_weight: 0.1196 0.1356 0.035 1.109 5.5 67.2 15.0 890 n/a 5_xyzrec: 0.1197 0.1364 0.036 1.123 5.5 67.2 15.0 890 n/a 5_adp: 0.1202 0.1368 0.036 1.123 5.6 66.9 15.0 890 n/a 5_regHadp: 0.1202 0.1368 0.036 1.123 5.6 66.9 15.0 890 n/a 5_occ: 0.1201 0.1369 0.036 1.123 5.6 66.9 15.0 890 n/a 6_bss: 0.1199 0.1366 0.036 1.123 5.5 66.9 14.9 890 n/a 6_settarget: 0.1199 0.1366 0.036 1.123 5.5 66.9 14.9 890 n/a 6_updatecdl: 0.1199 0.1366 0.036 1.124 5.5 66.9 14.9 890 n/a 6_nqh: 0.1199 0.1366 0.036 1.124 5.5 66.9 14.9 890 n/a 6_sol: 0.1197 0.1351 0.036 1.124 5.5 66.9 14.9 897 n/a 6_weight: 0.1197 0.1351 0.036 1.124 5.5 66.9 14.9 897 n/a 6_xyzrec: 0.1198 0.1356 0.037 1.132 5.5 66.9 14.9 897 n/a 6_adp: 0.1202 0.1361 0.037 1.132 5.6 65.8 14.8 897 n/a 6_regHadp: 0.1202 0.1361 0.037 1.132 5.6 65.8 14.8 897 n/a 6_occ: 0.1200 0.1357 0.037 1.132 5.6 65.8 14.8 897 n/a 7_bss: 0.1199 0.1356 0.037 1.132 5.5 65.7 14.8 897 n/a 7_settarget: 0.1199 0.1356 0.037 1.132 5.5 65.7 14.8 897 n/a 7_updatecdl: 0.1199 0.1356 0.037 1.131 5.5 65.7 14.8 897 n/a 7_nqh: 0.1199 0.1356 0.037 1.131 5.5 65.7 14.8 897 n/a 7_sol: 0.1198 0.1353 0.037 1.131 5.5 65.7 14.8 898 n/a 7_weight: 0.1198 0.1353 0.037 1.131 5.5 65.7 14.8 898 n/a 7_xyzrec: 0.1202 0.1358 0.037 1.123 5.5 65.7 14.8 898 n/a 7_adp: 0.1204 0.1361 0.037 1.123 5.6 64.7 14.8 898 n/a 7_regHadp: 0.1204 0.1361 0.037 1.123 5.6 64.7 14.8 898 n/a 7_occ: 0.1202 0.1361 0.037 1.123 5.6 64.7 14.8 898 n/a 8_bss: 0.1202 0.1359 0.037 1.123 5.3 64.4 14.5 898 n/a 8_settarget: 0.1202 0.1359 0.037 1.123 5.3 64.4 14.5 898 n/a 8_updatecdl: 0.1202 0.1359 0.037 1.124 5.3 64.4 14.5 898 n/a 8_nqh: 0.1202 0.1359 0.037 1.124 5.3 64.4 14.5 898 n/a 8_sol: 0.1200 0.1354 0.037 1.124 5.3 64.4 14.6 903 n/a 8_weight: 0.1200 0.1354 0.037 1.124 5.3 64.4 14.6 903 n/a 8_xyzrec: 0.1203 0.1359 0.038 1.115 5.3 64.4 14.6 903 n/a 8_adp: 0.1202 0.1360 0.038 1.115 5.4 63.4 14.5 903 n/a 8_regHadp: 0.1202 0.1360 0.038 1.115 5.4 63.4 14.5 903 n/a 8_occ: 0.1200 0.1359 0.038 1.115 5.4 63.4 14.5 903 n/a 9_bss: 0.1190 0.1349 0.038 1.115 5.4 63.4 14.5 903 n/a 9_settarget: 0.1190 0.1349 0.038 1.115 5.4 63.4 14.5 903 n/a 9_updatecdl: 0.1190 0.1349 0.038 1.114 5.4 63.4 14.5 903 n/a 9_nqh: 0.1190 0.1349 0.038 1.114 5.4 63.4 14.5 903 n/a 9_sol: 0.1189 0.1349 0.038 1.114 5.4 63.4 14.5 911 n/a 9_weight: 0.1189 0.1349 0.038 1.114 5.4 63.4 14.5 911 n/a 9_xyzrec: 0.1192 0.1352 0.038 1.128 5.4 63.4 14.5 911 n/a 9_adp: 0.1194 0.1356 0.038 1.128 5.4 63.1 14.5 911 n/a 9_regHadp: 0.1194 0.1356 0.038 1.128 5.4 63.1 14.5 911 n/a 9_occ: 0.1192 0.1355 0.038 1.128 5.4 63.1 14.5 911 n/a 10_bss: 0.1192 0.1353 0.038 1.128 5.4 63.1 14.5 911 n/a 10_settarget: 0.1192 0.1353 0.038 1.128 5.4 63.1 14.5 911 n/a 10_updatecdl: 0.1192 0.1353 0.038 1.128 5.4 63.1 14.5 911 n/a 10_setrh: 0.1192 0.1353 0.038 1.128 5.4 63.1 14.5 911 n/a 10_nqh: 0.1192 0.1353 0.038 1.128 5.4 63.1 14.5 911 n/a 10_sol: 0.1191 0.1352 0.038 1.128 5.4 63.1 14.5 913 n/a 10_weight: 0.1191 0.1352 0.038 1.128 5.4 63.1 14.5 913 n/a 10_xyzrec: 0.1194 0.1358 0.038 1.173 5.4 63.1 14.5 913 n/a 10_adp: 0.1196 0.1362 0.038 1.173 5.4 62.3 14.5 913 n/a 10_regHadp: 0.1196 0.1362 0.038 1.173 5.4 62.3 14.5 913 n/a 10_occ: 0.1195 0.1361 0.038 1.173 5.4 62.3 14.5 913 n/a end: 0.1194 0.1359 0.038 1.173 5.4 62.3 14.5 913 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5912678_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5912678_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1800 Refinement macro-cycles (run) : 11990.1000 Write final files (write_after_run_outputs) : 170.5500 Total : 12167.8300 Total CPU time: 3.39 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:01 PST -0800 (1736736001.62 s) Start R-work = 0.1803, R-free = 0.1934 Final R-work = 0.1194, R-free = 0.1359 =============================================================================== Job complete usr+sys time: 12484.86 seconds wall clock time: 209 minutes 5.86 seconds (12545.86 seconds total)