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_2943615.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2943615.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2943615.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } 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 =============================================================================== 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: 2.71, per 1000 atoms: 0.40 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: 2.617 distance_ideal: 2.720 ideal - model: 0.103 slack: 0.000 delta_slack: 0.103 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: 2.641 distance_ideal: 2.710 ideal - model: 0.069 slack: 0.000 delta_slack: 0.069 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 199.7 milliseconds Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 1.00: 559 1.00 - 1.23: 2585 1.23 - 1.46: 1453 1.46 - 1.69: 1296 1.69 - 1.92: 41 Bond restraints: 5934 Sorted by residual: bond pdb=" N GLY B 41 " pdb=" H GLY B 41 " ideal model delta sigma weight residual 0.860 1.231 -0.371 2.00e-02 2.50e+03 3.45e+02 bond pdb=" N SER A 155 " pdb=" H SER A 155 " ideal model delta sigma weight residual 0.860 1.230 -0.370 2.00e-02 2.50e+03 3.43e+02 bond pdb=" N VAL A 181 " pdb=" CA VAL A 181 " ideal model delta sigma weight residual 1.460 1.241 0.219 1.19e-02 7.06e+03 3.40e+02 bond pdb=" N GLU A 80 " pdb=" H GLU A 80 " ideal model delta sigma weight residual 0.860 1.225 -0.365 2.00e-02 2.50e+03 3.34e+02 bond pdb=" NE ARG A 49 " pdb=" CZ ARG A 49 " ideal model delta sigma weight residual 1.326 1.526 -0.200 1.10e-02 8.26e+03 3.31e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 6127 4.69 - 9.38: 3567 9.38 - 14.07: 980 14.07 - 18.76: 129 18.76 - 23.44: 7 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ALA A 57 " pdb=" C ALA A 57 " pdb=" O ALA A 57 " ideal model delta sigma weight residual 120.13 133.61 -13.48 8.60e-01 1.35e+00 2.46e+02 angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.71 131.00 -9.29 6.40e-01 2.44e+00 2.10e+02 angle pdb=" O LYS A 93 " pdb=" C LYS A 93 " pdb=" N GLN A 94 " ideal model delta sigma weight residual 122.15 105.68 16.47 1.14e+00 7.69e-01 2.09e+02 angle pdb=" O ALA A 178 " pdb=" C ALA A 178 " pdb=" N HIS A 179 " ideal model delta sigma weight residual 122.12 136.61 -14.49 1.06e+00 8.90e-01 1.87e+02 angle pdb=" NE ARG A 143 " pdb=" CZ ARG A 143 " pdb=" NH2 ARG A 143 " ideal model delta sigma weight residual 119.20 107.13 12.07 9.00e-01 1.23e+00 1.80e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 1839 16.65 - 33.30: 140 33.30 - 49.94: 50 49.94 - 66.59: 15 66.59 - 83.24: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -152.07 -27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ALA A 188 " pdb=" C ALA A 188 " pdb=" N ALA A 189 " pdb=" CA ALA A 189 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LEU B 172 " pdb=" C LEU B 172 " pdb=" N VAL B 173 " pdb=" CA VAL B 173 " ideal model delta harmonic sigma weight residual 180.00 -156.46 -23.54 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.233: 215 0.233 - 0.465: 175 0.465 - 0.698: 80 0.698 - 0.930: 18 0.930 - 1.162: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 144 " pdb=" N VAL A 144 " pdb=" C VAL A 144 " pdb=" CB VAL A 144 " both_signs ideal model delta sigma weight residual False 2.44 3.60 -1.16 2.00e-01 2.50e+01 3.38e+01 chirality pdb=" CA VAL B 32 " pdb=" N VAL B 32 " pdb=" C VAL B 32 " pdb=" CB VAL B 32 " both_signs ideal model delta sigma weight residual False 2.44 3.49 -1.05 2.00e-01 2.50e+01 2.76e+01 chirality pdb=" CA ASN A 193 " pdb=" N ASN A 193 " pdb=" C ASN A 193 " pdb=" CB ASN A 193 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.170 2.00e-02 2.50e+03 7.99e-02 1.92e+02 pdb=" CG PHE B 164 " 0.004 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.104 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.094 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.060 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.062 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.029 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 42 " 0.063 2.00e-02 2.50e+03 9.61e-02 1.38e+02 pdb=" CG ASN B 42 " 0.086 2.00e-02 2.50e+03 pdb=" OD1 ASN B 42 " -0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN B 42 " -0.022 2.00e-02 2.50e+03 pdb="HD21 ASN B 42 " 0.118 2.00e-02 2.50e+03 pdb="HD22 ASN B 42 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.136 2.00e-02 2.50e+03 6.75e-02 1.37e+02 pdb=" CG PHE A 164 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.067 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.057 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.109 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 30 1.64 - 2.38: 2669 2.38 - 3.12: 22424 3.12 - 3.86: 32757 3.86 - 4.60: 52480 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110360 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.896 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.941 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.968 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.098 2.620 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.159 2.100 ... (remaining 110355 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_2943615_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= 0.2036 r_free= 0.2010 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.303702 | | target function (ml) not normalized (work): 806139.337220 | | target function (ml) not normalized (free): 16607.095044 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2135 0.1908 6.6936 6.3142| | 2: 2.94 - 2.33 1.00 7339 128 0.1616 0.1763 5.5406 5.5973| | 3: 2.33 - 2.04 0.96 6939 150 0.1622 0.1566 5.1438 5.1434| | 4: 2.04 - 1.85 1.00 7170 155 0.1747 0.1667 4.9651 5.0217| | 5: 1.85 - 1.72 0.99 7113 159 0.1944 0.1532 4.7994 4.7266| | 6: 1.72 - 1.62 0.99 7102 142 0.1979 0.2182 4.6715 4.8346| | 7: 1.62 - 1.54 0.99 7104 148 0.2035 0.1821 4.5658 4.5847| | 8: 1.54 - 1.47 0.96 6798 152 0.2062 0.2156 4.49 4.5383| | 9: 1.47 - 1.41 0.98 6938 155 0.2088 0.2431 4.397 4.4971| | 10: 1.41 - 1.36 0.99 7022 150 0.2134 0.2178 4.3221 4.3962| | 11: 1.36 - 1.32 0.99 6997 151 0.2112 0.2069 4.2384 4.2576| | 12: 1.32 - 1.28 0.98 6976 149 0.2108 0.1853 4.1837 4.1779| | 13: 1.28 - 1.25 0.98 6907 166 0.2066 0.2157 4.1345 4.2096| | 14: 1.25 - 1.22 0.98 7015 113 0.2075 0.2421 4.0836 4.3281| | 15: 1.22 - 1.19 0.98 6957 137 0.2088 0.2218 4.0449 4.1033| | 16: 1.19 - 1.17 0.93 6604 132 0.2114 0.2343 4.0017 4.0642| | 17: 1.17 - 1.14 0.98 6941 135 0.2163 0.1951 3.9516 3.9809| | 18: 1.14 - 1.12 0.98 6875 142 0.2192 0.2442 3.9123 3.9427| | 19: 1.12 - 1.10 0.97 6949 106 0.2269 0.2370 3.8744 3.9328| | 20: 1.10 - 1.08 0.97 6884 147 0.2331 0.2245 3.8274 3.8423| | 21: 1.08 - 1.07 0.97 6852 152 0.2464 0.2774 3.803 3.8644| | 22: 1.07 - 1.05 0.97 6838 135 0.2569 0.2743 3.7567 3.8047| | 23: 1.05 - 1.03 0.97 6829 159 0.2713 0.2685 3.7268 3.7871| | 24: 1.03 - 1.02 0.96 6785 133 0.2848 0.2787 3.6953 3.7554| | 25: 1.02 - 1.01 0.93 6552 130 0.3079 0.3307 3.6815 3.8283| | 26: 1.01 - 0.99 0.96 6767 158 0.3183 0.3001 3.6313 3.6251| | 27: 0.99 - 0.98 0.94 6648 131 0.3423 0.3175 3.6507 3.6034| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.32 0.91 0.98 35324.82| | 2: 2.94 - 2.33 7339 128 0.86 21.15 1.08 1.02 15027.40| | 3: 2.33 - 2.04 6939 150 0.93 12.32 1.11 1.05 4027.23| | 4: 2.04 - 1.85 7170 155 0.93 13.02 1.11 1.05 2614.02| | 5: 1.85 - 1.72 7113 159 0.91 15.14 1.12 1.07 1940.91| | 6: 1.72 - 1.62 7102 142 0.90 16.93 1.11 1.06 1657.39| | 7: 1.62 - 1.54 7104 148 0.89 18.08 1.11 1.06 1394.22| | 8: 1.54 - 1.47 6798 152 0.88 19.21 1.10 1.05 1243.45| | 9: 1.47 - 1.41 6938 155 0.87 19.82 1.10 1.06 1059.15| | 10: 1.41 - 1.36 7022 150 0.86 21.06 1.09 1.04 931.25| | 11: 1.36 - 1.32 6997 151 0.86 20.78 1.08 1.04 782.79| | 12: 1.32 - 1.28 6976 149 0.87 20.58 1.08 1.03 679.99| | 13: 1.28 - 1.25 6907 166 0.87 20.35 1.07 1.03 630.12| | 14: 1.25 - 1.22 7015 113 0.86 21.19 1.07 1.04 604.64| | 15: 1.22 - 1.19 6957 137 0.86 21.36 1.07 1.04 565.52| | 16: 1.19 - 1.17 6604 132 0.87 20.90 1.08 1.03 504.68| | 17: 1.17 - 1.14 6941 135 0.87 20.88 1.08 1.04 442.82| | 18: 1.14 - 1.12 6875 142 0.86 20.99 1.07 1.02 398.46| | 19: 1.12 - 1.10 6949 106 0.86 21.82 1.07 1.01 374.20| | 20: 1.10 - 1.08 6884 147 0.85 22.96 1.07 0.99 361.37| | 21: 1.08 - 1.07 6852 152 0.83 24.62 1.06 0.98 354.53| | 22: 1.07 - 1.05 6838 135 0.81 26.45 1.06 0.98 348.71| | 23: 1.05 - 1.03 6829 159 0.79 28.05 1.06 0.97 340.22| | 24: 1.03 - 1.02 6785 133 0.78 29.67 1.06 1.00 343.08| | 25: 1.02 - 1.01 6552 130 0.77 30.72 1.03 0.97 323.45| | 26: 1.01 - 0.99 6767 158 0.76 31.61 1.03 0.95 295.78| | 27: 0.99 - 0.98 6648 131 0.77 30.52 1.04 0.93 255.97| |alpha: min = 0.93 max = 1.07 mean = 1.02| |beta: min = 255.97 max = 35324.82 mean = 2823.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.79| |phase err.(test): min = 0.00 max = 88.26 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 0.254 2950 Z= 5.473 Angle : 5.213 17.154 4018 Z= 3.728 Chirality : 0.367 1.162 492 Planarity : 0.033 0.138 512 Dihedral : 12.729 83.235 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.32 % Allowed : 5.16 % Favored : 94.52 % Cbeta Deviations : 28.65 % 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: -2.31 (0.39), residues: 386 helix: -2.59 (0.30), residues: 146 sheet: -1.34 (0.54), residues: 86 loop : -0.15 (0.50), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.022 ARG A 143 TYR 0.105 0.037 TYR A 194 PHE 0.111 0.037 PHE A 164 TRP 0.089 0.039 TRP B 139 HIS 0.058 0.025 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2036 r_free= 0.2010 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.303702 | | target function (ml) not normalized (work): 806139.337220 | | target function (ml) not normalized (free): 16607.095044 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2036 0.2010 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2036 0.2010 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2036 0.2010 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2034 0.2036 0.2010 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1806 0.1804 0.1950 n_refl.: 191145 remove outliers: r(all,work,free)=0.1804 0.1801 0.1949 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 0.4110 402.814 292.166 0.436 0.913 0.305 13.296-10.522 100.00 100 1 0.2519 534.497 522.892 0.792 0.914 0.263 10.503-8.327 98.90 177 3 0.2456 564.205 559.531 0.972 0.914 0.243 8.318-6.595 100.00 360 8 0.2485 414.736 402.476 0.974 0.914 0.185 6.588-5.215 100.00 711 7 0.2230 381.101 366.480 0.961 0.914 0.170 5.214-4.128 98.38 1367 28 0.1495 557.435 550.415 1.077 0.914 0.090 4.126-3.266 94.74 2603 46 0.1329 508.132 499.778 1.146 0.914 0.029 3.266-2.585 99.86 5447 97 0.1447 342.774 337.919 1.118 0.913 0.010 2.585-2.046 97.45 10613 204 0.1410 258.603 254.328 1.123 0.913 0.000 2.046-1.619 99.39 21536 464 0.1613 153.054 149.789 1.143 0.912 0.000 1.619-1.281 98.00 42464 925 0.1938 82.395 80.154 1.128 0.910 0.000 1.281-0.980 96.53 101826 2055 0.2315 44.202 41.651 1.112 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0016 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1801 r_free=0.1949 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 156 GLN Total number of N/Q/H flips: 2 r_work=0.1803 r_free=0.1948 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.297567 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 574.993383 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1273 0.1479 0.0207 0.035 1.2 11.9 0.0 0.0 0 11.649 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 14.79 2.07 1.117 13.110 574.993 0.019 13.02 15.49 2.48 1.261 13.348 574.993 0.018 Individual atomic B min max mean iso aniso Overall: 5.28 73.04 15.03 1.41 435 3274 Protein: 5.28 40.73 11.02 1.41 0 2902 Water: 6.31 73.04 29.48 N/A 435 370 Other: 15.97 30.49 23.23 N/A 0 2 Chain A: 5.33 60.85 13.08 N/A 0 1626 Chain B: 5.28 73.04 12.80 N/A 0 1648 Chain S: 11.54 62.44 30.76 N/A 435 0 Histogram: Values Number of atoms 5.28 - 12.06 2178 12.06 - 18.83 627 18.83 - 25.61 321 25.61 - 32.38 259 32.38 - 39.16 154 39.16 - 45.94 103 45.94 - 52.71 45 52.71 - 59.49 17 59.49 - 66.27 4 66.27 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1302 r_free=0.1550 r_work=0.1301 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1301 r_free = 0.1544 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1286 r_free = 0.1532 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= 0.1286 r_free= 0.1532 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015826 | | target function (ls_wunit_k1) not normalized (work): 2964.150996 | | target function (ls_wunit_k1) not normalized (free): 112.468907 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1286 0.1532 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1473 0.1471 0.1608 n_refl.: 191138 remove outliers: r(all,work,free)=0.1473 0.1471 0.1608 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1497 0.1495 0.1621 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1278 0.1524 n_refl.: 191138 remove outliers: r(all,work,free)=0.1283 0.1278 0.1524 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 0.3675 402.814 368.214 0.477 0.963 0.287 13.296-10.522 99.01 99 1 0.2116 528.187 526.022 0.753 0.964 0.270 10.503-8.327 98.90 177 3 0.1713 564.205 565.446 0.892 0.964 0.218 8.318-6.595 100.00 360 8 0.1764 414.736 410.599 0.909 0.964 0.165 6.588-5.215 100.00 711 7 0.1584 381.101 373.658 0.892 0.964 0.160 5.214-4.128 98.38 1367 28 0.0933 557.435 554.179 0.976 0.964 0.059 4.126-3.266 94.74 2603 46 0.0854 508.132 503.994 1.045 0.965 0.024 3.266-2.585 99.86 5447 97 0.0933 342.774 340.368 1.027 0.964 0.010 2.585-2.046 97.45 10613 204 0.0945 258.603 256.335 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1079 153.054 151.380 1.057 0.964 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.331 1.047 0.964 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.174 1.027 0.963 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0383 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1278 r_free=0.1524 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1278 r_free=0.1524 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1278 r_free=0.1524 | n_water=805 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1279 r_free=0.1526 | n_water=801 | time (s): 94.690 (total time: 97.630) Filter (q & B) r_work=0.1280 r_free=0.1526 | n_water=795 | time (s): 4.120 (total time: 101.750) Compute maps r_work=0.1280 r_free=0.1526 | n_water=795 | time (s): 2.230 (total time: 103.980) Filter (map) r_work=0.1303 r_free=0.1512 | n_water=672 | time (s): 4.070 (total time: 108.050) Find peaks r_work=0.1303 r_free=0.1512 | n_water=672 | time (s): 0.620 (total time: 108.670) Add new water r_work=0.1327 r_free=0.1544 | n_water=984 | time (s): 4.990 (total time: 113.660) Refine new water occ: r_work=0.1284 r_free=0.1508 adp: r_work=0.1273 r_free=0.1497 occ: r_work=0.1275 r_free=0.1501 adp: r_work=0.1270 r_free=0.1495 occ: r_work=0.1271 r_free=0.1498 adp: r_work=0.1268 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1495 r_work=0.1268 r_free=0.1495 | n_water=984 | time (s): 74.720 (total time: 188.380) Filter (q & B) r_work=0.1271 r_free=0.1502 | n_water=908 | time (s): 4.450 (total time: 192.830) Filter (dist only) r_work=0.1272 r_free=0.1501 | n_water=905 | time (s): 119.150 (total time: 311.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.582122 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 567.319318 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 0.1255 0.1521 0.0266 0.038 1.1 20.2 0.0 0.3 0 11.791 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.21 2.66 2.051 15.273 567.319 0.015 12.34 15.07 2.73 2.441 15.300 567.319 0.014 Individual atomic B min max mean iso aniso Overall: 5.35 68.21 16.42 1.19 536 3273 Protein: 5.35 40.54 10.98 1.19 0 2902 Water: 6.48 68.21 33.83 N/A 536 369 Other: 16.23 32.59 24.41 N/A 0 2 Chain A: 5.49 57.62 13.04 N/A 0 1625 Chain B: 5.35 68.21 12.83 N/A 0 1648 Chain S: 11.85 65.77 37.70 N/A 536 0 Histogram: Values Number of atoms 5.35 - 11.63 2042 11.63 - 17.92 728 17.92 - 24.21 270 24.21 - 30.49 211 30.49 - 36.78 189 36.78 - 43.07 157 43.07 - 49.35 104 49.35 - 55.64 54 55.64 - 61.92 46 61.92 - 68.21 8 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1507 r_work=0.1234 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1509 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1505 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013453 | | target function (ls_wunit_k1) not normalized (work): 2519.640317 | | target function (ls_wunit_k1) not normalized (free): 102.091729 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1227 0.1505 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1433 0.1430 0.1594 n_refl.: 191137 remove outliers: r(all,work,free)=0.1433 0.1430 0.1594 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1428 0.1593 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1510 n_refl.: 191137 remove outliers: r(all,work,free)=0.1239 0.1234 0.1510 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 0.3211 402.814 381.619 0.491 0.963 0.277 13.296-10.522 99.01 99 1 0.1923 528.187 523.837 0.765 0.964 0.260 10.503-8.327 98.90 177 3 0.1417 564.205 564.632 0.923 0.964 0.174 8.318-6.595 100.00 360 8 0.1532 414.736 413.825 0.934 0.963 0.150 6.588-5.215 100.00 711 7 0.1352 381.101 376.855 0.914 0.963 0.150 5.214-4.128 98.38 1367 28 0.0823 557.435 555.934 0.993 0.964 0.080 4.126-3.266 94.74 2603 46 0.0760 508.132 505.178 1.059 0.963 0.015 3.266-2.585 99.86 5447 97 0.0859 342.774 341.215 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0898 258.603 256.712 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.644 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1259 82.395 81.342 1.072 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.213 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=-0.0447 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1510 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1510 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1510 | n_water=905 | time (s): 2.440 (total time: 2.440) Filter (dist) r_work=0.1236 r_free=0.1511 | n_water=899 | time (s): 125.020 (total time: 127.460) Filter (q & B) r_work=0.1236 r_free=0.1511 | n_water=896 | time (s): 5.730 (total time: 133.190) Compute maps r_work=0.1236 r_free=0.1511 | n_water=896 | time (s): 2.300 (total time: 135.490) Filter (map) r_work=0.1278 r_free=0.1514 | n_water=691 | time (s): 4.290 (total time: 139.780) Find peaks r_work=0.1278 r_free=0.1514 | n_water=691 | time (s): 0.760 (total time: 140.540) Add new water r_work=0.1302 r_free=0.1553 | n_water=1021 | time (s): 4.670 (total time: 145.210) Refine new water occ: r_work=0.1256 r_free=0.1510 adp: r_work=0.1257 r_free=0.1512 occ: r_work=0.1252 r_free=0.1507 adp: r_work=0.1252 r_free=0.1509 occ: r_work=0.1249 r_free=0.1505 adp: r_work=0.1249 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1249 r_free=0.1507 r_work=0.1249 r_free=0.1507 | n_water=1021 | time (s): 325.890 (total time: 471.100) Filter (q & B) r_work=0.1255 r_free=0.1507 | n_water=869 | time (s): 6.270 (total time: 477.370) Filter (dist only) r_work=0.1255 r_free=0.1507 | n_water=868 | time (s): 125.480 (total time: 602.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.730025 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.483848 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 0.1245 0.1437 0.0193 0.034 1.1 6.1 0.0 0.0 0 0.865 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.45 14.37 1.93 1.931 14.582 16.484 3.942 12.37 13.95 1.58 2.258 14.479 16.484 3.897 Individual atomic B min max mean iso aniso Overall: 5.53 67.74 15.24 1.05 501 3271 Protein: 5.53 36.59 10.73 1.05 0 2902 Water: 6.66 67.74 30.32 N/A 501 367 Other: 13.98 28.16 21.07 N/A 0 2 Chain A: 5.53 56.48 12.79 N/A 0 1625 Chain B: 5.53 67.74 12.51 N/A 0 1646 Chain S: 12.73 61.70 32.19 N/A 501 0 Histogram: Values Number of atoms 5.53 - 11.75 2128 11.75 - 17.97 691 17.97 - 24.19 289 24.19 - 30.41 226 30.41 - 36.63 184 36.63 - 42.85 149 42.85 - 49.08 69 49.08 - 55.30 24 55.30 - 61.52 9 61.52 - 67.74 3 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1395 r_work=0.1238 r_free=0.1397 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1397 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1391 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1232 r_free= 0.1391 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891513 | | target function (ml) not normalized (work): 728864.902038 | | target function (ml) not normalized (free): 15218.174333 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1232 0.1391 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1446 0.1445 0.1497 n_refl.: 191137 remove outliers: r(all,work,free)=0.1446 0.1445 0.1497 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1439 0.1493 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1228 0.1384 n_refl.: 191137 remove outliers: r(all,work,free)=0.1230 0.1227 0.1384 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3756 398.008 364.482 0.429 0.946 0.251 13.296-10.522 99.01 99 1 0.2453 528.187 508.251 0.706 0.948 0.219 10.503-8.327 97.80 175 3 0.1991 554.286 556.610 0.888 0.948 0.174 8.318-6.595 100.00 360 8 0.2152 414.736 407.971 0.896 0.947 0.140 6.588-5.215 100.00 711 7 0.1867 381.101 370.673 0.886 0.947 0.140 5.214-4.128 98.38 1367 28 0.1192 557.435 551.409 0.971 0.947 0.090 4.126-3.266 94.74 2603 46 0.1111 508.132 500.909 1.032 0.948 0.009 3.266-2.585 99.86 5447 97 0.1093 342.774 339.044 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0961 258.603 255.739 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0968 153.054 151.406 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.491 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.323 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.0971 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1384 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1384 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1384 | n_water=868 | time (s): 3.000 (total time: 3.000) Filter (dist) r_work=0.1228 r_free=0.1387 | n_water=867 | time (s): 109.580 (total time: 112.580) Filter (q & B) r_work=0.1228 r_free=0.1383 | n_water=859 | time (s): 4.490 (total time: 117.070) Compute maps r_work=0.1228 r_free=0.1383 | n_water=859 | time (s): 2.020 (total time: 119.090) Filter (map) r_work=0.1253 r_free=0.1378 | n_water=714 | time (s): 4.470 (total time: 123.560) Find peaks r_work=0.1253 r_free=0.1378 | n_water=714 | time (s): 0.560 (total time: 124.120) Add new water r_work=0.1269 r_free=0.1395 | n_water=977 | time (s): 4.850 (total time: 128.970) Refine new water occ: r_work=0.1217 r_free=0.1361 adp: r_work=0.1210 r_free=0.1357 occ: r_work=0.1207 r_free=0.1359 adp: r_work=0.1207 r_free=0.1357 occ: r_work=0.1204 r_free=0.1359 adp: r_work=0.1204 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1359 r_work=0.1204 r_free=0.1359 | n_water=977 | time (s): 388.950 (total time: 517.920) Filter (q & B) r_work=0.1209 r_free=0.1366 | n_water=875 | time (s): 4.950 (total time: 522.870) Filter (dist only) r_work=0.1210 r_free=0.1365 | n_water=874 | time (s): 111.620 (total time: 634.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.634649 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.686529 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 0.1208 0.1366 0.0158 0.035 1.1 6.0 0.0 0.0 0 0.817 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.66 1.58 1.828 14.181 15.687 3.874 12.01 13.64 1.63 1.907 14.153 15.687 3.866 Individual atomic B min max mean iso aniso Overall: 5.50 67.36 14.96 1.01 508 3270 Protein: 5.50 33.77 10.67 1.01 0 2902 Water: 6.06 67.36 29.19 N/A 508 366 Other: 14.04 27.33 20.69 N/A 0 2 Chain A: 5.50 55.59 12.68 N/A 0 1625 Chain B: 5.52 67.36 12.42 N/A 0 1645 Chain S: 6.06 61.61 30.49 N/A 508 0 Histogram: Values Number of atoms 5.50 - 11.68 2114 11.68 - 17.87 725 17.87 - 24.05 308 24.05 - 30.24 245 30.24 - 36.43 160 36.43 - 42.61 135 42.61 - 48.80 60 48.80 - 54.99 21 54.99 - 61.17 8 61.17 - 67.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1364 r_work=0.1201 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1365 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1360 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864414 | | target function (ml) not normalized (work): 723777.771545 | | target function (ml) not normalized (free): 15139.402822 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1199 0.1360 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1425 0.1425 0.1473 n_refl.: 191134 remove outliers: r(all,work,free)=0.1425 0.1425 0.1473 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1418 0.1418 0.1469 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1360 n_refl.: 191134 remove outliers: r(all,work,free)=0.1201 0.1198 0.1360 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 94.06 92 3 0.3909 360.464 321.508 0.416 0.945 0.250 13.296-10.522 98.02 98 1 0.2364 480.609 457.152 0.694 0.947 0.200 10.503-8.327 97.80 175 3 0.2122 502.001 496.663 0.865 0.947 0.184 8.318-6.595 100.00 360 8 0.2222 375.615 368.524 0.889 0.947 0.115 6.588-5.215 100.00 711 7 0.1939 345.153 335.091 0.881 0.947 0.084 5.214-4.128 98.38 1367 28 0.1200 504.853 499.368 0.972 0.947 0.060 4.126-3.266 94.74 2603 46 0.1113 460.201 453.726 1.035 0.947 0.005 3.266-2.585 99.86 5447 97 0.1092 310.441 307.108 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0936 234.210 231.814 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0913 138.617 137.320 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0989 74.623 73.906 1.053 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.032 38.368 1.038 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1126 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1360 | n_water=874 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1198 r_free=0.1360 | n_water=874 | time (s): 106.730 (total time: 109.440) Filter (q & B) r_work=0.1198 r_free=0.1359 | n_water=865 | time (s): 4.190 (total time: 113.630) Compute maps r_work=0.1198 r_free=0.1359 | n_water=865 | time (s): 1.830 (total time: 115.460) Filter (map) r_work=0.1222 r_free=0.1358 | n_water=733 | time (s): 5.140 (total time: 120.600) Find peaks r_work=0.1222 r_free=0.1358 | n_water=733 | time (s): 0.650 (total time: 121.250) Add new water r_work=0.1235 r_free=0.1375 | n_water=998 | time (s): 5.110 (total time: 126.360) Refine new water occ: r_work=0.1195 r_free=0.1340 adp: r_work=0.1195 r_free=0.1340 occ: r_work=0.1192 r_free=0.1337 adp: r_work=0.1192 r_free=0.1337 occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1189 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1335 r_work=0.1189 r_free=0.1335 | n_water=998 | time (s): 265.510 (total time: 391.870) Filter (q & B) r_work=0.1195 r_free=0.1345 | n_water=894 | time (s): 5.260 (total time: 397.130) Filter (dist only) r_work=0.1195 r_free=0.1345 | n_water=893 | time (s): 112.180 (total time: 509.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554436 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.349482 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 0.1353 0.0155 0.036 1.1 8.2 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.53 1.55 1.796 14.168 15.349 3.764 12.01 13.55 1.54 1.873 14.137 15.349 3.761 Individual atomic B min max mean iso aniso Overall: 5.57 66.97 14.99 0.96 528 3269 Protein: 5.57 32.42 10.60 0.96 0 2902 Water: 6.00 66.97 29.28 N/A 528 365 Other: 13.81 26.08 19.95 N/A 0 2 Chain A: 5.58 54.68 12.55 N/A 0 1624 Chain B: 5.57 66.97 12.33 N/A 0 1645 Chain S: 6.00 59.79 30.81 N/A 528 0 Histogram: Values Number of atoms 5.57 - 11.71 2134 11.71 - 17.85 724 17.85 - 23.99 298 23.99 - 30.13 226 30.13 - 36.27 181 36.27 - 42.41 135 42.41 - 48.55 68 48.55 - 54.69 24 54.69 - 60.83 6 60.83 - 66.97 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1355 r_work=0.1201 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1356 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1354 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760281 | | target function (ml) not normalized (work): 704270.628351 | | target function (ml) not normalized (free): 14739.239178 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1355 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1421 0.1420 0.1465 n_refl.: 191133 remove outliers: r(all,work,free)=0.1421 0.1420 0.1465 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1413 0.1413 0.1460 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1353 n_refl.: 191133 remove outliers: r(all,work,free)=0.1200 0.1197 0.1353 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 0.3629 360.155 312.543 0.401 0.948 0.234 13.296-10.522 97.03 97 1 0.2354 481.284 457.488 0.688 0.949 0.178 10.503-8.327 97.80 175 3 0.2134 502.001 494.828 0.864 0.949 0.129 8.318-6.595 100.00 360 8 0.2168 375.615 369.368 0.887 0.949 0.100 6.588-5.215 100.00 711 7 0.1934 345.153 335.031 0.884 0.949 0.100 5.214-4.128 98.38 1367 28 0.1204 504.853 499.751 0.971 0.949 0.034 4.126-3.266 94.74 2603 46 0.1131 460.201 453.507 1.034 0.949 0.005 3.266-2.585 99.86 5447 97 0.1106 310.441 307.101 1.020 0.949 0.000 2.585-2.046 97.45 10613 204 0.0942 234.210 231.855 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0913 138.617 137.340 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0979 74.623 73.924 1.054 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.032 38.367 1.042 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1272 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1353 | n_water=893 | time (s): 3.250 (total time: 3.250) Filter (dist) r_work=0.1197 r_free=0.1354 | n_water=892 | time (s): 112.890 (total time: 116.140) Filter (q & B) r_work=0.1197 r_free=0.1353 | n_water=885 | time (s): 4.870 (total time: 121.010) Compute maps r_work=0.1197 r_free=0.1353 | n_water=885 | time (s): 1.680 (total time: 122.690) Filter (map) r_work=0.1222 r_free=0.1358 | n_water=760 | time (s): 4.990 (total time: 127.680) Find peaks r_work=0.1222 r_free=0.1358 | n_water=760 | time (s): 0.580 (total time: 128.260) Add new water r_work=0.1231 r_free=0.1367 | n_water=985 | time (s): 4.940 (total time: 133.200) Refine new water occ: r_work=0.1195 r_free=0.1344 adp: r_work=0.1195 r_free=0.1344 occ: r_work=0.1193 r_free=0.1342 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1191 r_free=0.1340 adp: r_work=0.1191 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1340 r_work=0.1191 r_free=0.1340 | n_water=985 | time (s): 206.480 (total time: 339.680) Filter (q & B) r_work=0.1196 r_free=0.1347 | n_water=904 | time (s): 5.470 (total time: 345.150) Filter (dist only) r_work=0.1196 r_free=0.1347 | n_water=902 | time (s): 113.430 (total time: 458.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.527043 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.763043 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1357 0.0158 0.036 1.1 7.0 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.57 1.58 1.764 14.057 14.763 3.761 12.02 13.61 1.59 1.906 14.009 14.763 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 65.80 14.86 0.90 537 3269 Protein: 5.58 29.49 10.49 0.90 0 2902 Water: 6.21 65.80 28.90 N/A 537 365 Other: 13.84 23.40 18.62 N/A 0 2 Chain A: 5.61 53.18 12.41 N/A 0 1624 Chain B: 5.58 65.80 12.20 N/A 0 1645 Chain S: 6.21 59.96 30.41 N/A 537 0 Histogram: Values Number of atoms 5.58 - 11.60 2109 11.60 - 17.62 775 17.62 - 23.65 288 23.65 - 29.67 217 29.67 - 35.69 176 35.69 - 41.71 137 41.71 - 47.73 73 47.73 - 53.75 24 53.75 - 59.78 5 59.78 - 65.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1362 r_work=0.1202 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1362 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1361 target_work(ml) = 3.758 | | 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= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758312 | | target function (ml) not normalized (work): 703894.237808 | | target function (ml) not normalized (free): 14737.007259 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1361 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1412 0.1411 0.1471 n_refl.: 191131 remove outliers: r(all,work,free)=0.1412 0.1411 0.1471 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1404 0.1403 0.1466 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1360 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1360 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 0.3655 360.155 329.003 0.420 0.949 0.236 13.296-10.522 97.03 97 1 0.2377 481.284 461.180 0.690 0.950 0.167 10.503-8.327 97.80 175 3 0.2157 502.001 494.337 0.860 0.951 0.137 8.318-6.595 100.00 360 8 0.2156 375.615 369.630 0.884 0.950 0.098 6.588-5.215 100.00 711 7 0.1948 345.153 335.309 0.880 0.951 0.077 5.214-4.128 98.38 1367 28 0.1216 504.853 499.418 0.971 0.951 0.040 4.126-3.266 94.74 2603 46 0.1158 460.201 453.234 1.034 0.951 0.014 3.266-2.585 99.86 5447 97 0.1116 310.441 307.114 1.019 0.950 0.000 2.585-2.046 97.45 10613 204 0.0950 234.210 231.736 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0910 138.617 137.307 1.054 0.950 0.000 1.619-1.281 98.00 42464 925 0.0971 74.623 73.917 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.032 38.365 1.039 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1355 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1360 | n_water=902 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1199 r_free=0.1360 | n_water=902 | time (s): 110.010 (total time: 113.150) Filter (q & B) r_work=0.1200 r_free=0.1357 | n_water=893 | time (s): 5.020 (total time: 118.170) Compute maps r_work=0.1200 r_free=0.1357 | n_water=893 | time (s): 1.980 (total time: 120.150) Filter (map) r_work=0.1222 r_free=0.1362 | n_water=764 | time (s): 4.160 (total time: 124.310) Find peaks r_work=0.1222 r_free=0.1362 | n_water=764 | time (s): 0.740 (total time: 125.050) Add new water r_work=0.1231 r_free=0.1371 | n_water=990 | time (s): 4.450 (total time: 129.500) Refine new water occ: r_work=0.1196 r_free=0.1352 adp: r_work=0.1196 r_free=0.1353 occ: r_work=0.1193 r_free=0.1350 adp: r_work=0.1193 r_free=0.1351 occ: r_work=0.1192 r_free=0.1348 adp: r_work=0.1191 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1349 r_work=0.1191 r_free=0.1349 | n_water=990 | time (s): 312.300 (total time: 441.800) Filter (q & B) r_work=0.1196 r_free=0.1354 | n_water=909 | time (s): 4.320 (total time: 446.120) Filter (dist only) r_work=0.1196 r_free=0.1353 | n_water=907 | time (s): 115.230 (total time: 561.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.627287 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.830873 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 0.0158 0.037 1.1 6.3 0.0 0.3 0 0.814 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.56 1.58 1.720 13.942 14.831 3.758 11.98 13.56 1.59 1.765 13.924 14.831 3.755 Individual atomic B min max mean iso aniso Overall: 5.59 64.64 14.83 0.89 542 3269 Protein: 5.59 28.81 10.44 0.89 0 2902 Water: 5.88 64.64 28.88 N/A 542 365 Other: 13.87 22.34 18.10 N/A 0 2 Chain A: 5.64 52.66 12.31 N/A 0 1624 Chain B: 5.59 64.64 12.12 N/A 0 1645 Chain S: 5.88 60.18 30.60 N/A 542 0 Histogram: Values Number of atoms 5.59 - 11.50 2092 11.50 - 17.40 788 17.40 - 23.31 279 23.31 - 29.21 212 29.21 - 35.12 185 35.12 - 41.02 140 41.02 - 46.92 78 46.92 - 52.83 30 52.83 - 58.73 4 58.73 - 64.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1356 r_work=0.1198 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1357 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.754383 | | target function (ml) not normalized (work): 703158.448172 | | target function (ml) not normalized (free): 14719.819172 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1353 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1410 0.1409 0.1473 n_refl.: 191131 remove outliers: r(all,work,free)=0.1410 0.1409 0.1473 n_refl.: 191131 overall B=-0.23 to atoms: r(all,work,free)=0.1374 0.1372 0.1452 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1352 n_refl.: 191131 remove outliers: r(all,work,free)=0.1198 0.1195 0.1352 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3573 360.964 325.442 0.424 0.949 0.222 13.296-10.522 97.03 97 1 0.2364 481.284 462.071 0.704 0.950 0.150 10.503-8.327 97.80 175 3 0.2156 502.001 494.670 0.882 0.951 0.120 8.318-6.595 100.00 360 8 0.2141 375.615 370.053 0.906 0.950 0.090 6.588-5.215 100.00 711 7 0.1930 345.153 335.698 0.904 0.950 0.070 5.214-4.128 98.38 1367 28 0.1207 504.853 499.598 0.996 0.951 0.035 4.126-3.266 94.74 2603 46 0.1151 460.201 453.277 1.060 0.951 0.009 3.266-2.585 99.86 5447 97 0.1115 310.441 307.083 1.042 0.951 0.000 2.585-2.046 97.45 10613 204 0.0950 234.210 231.770 1.050 0.951 0.000 2.046-1.619 99.39 21536 464 0.0907 138.617 137.331 1.067 0.951 0.000 1.619-1.281 98.00 42464 925 0.0963 74.623 73.931 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.032 38.363 1.023 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0508 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1352 | n_water=907 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1195 r_free=0.1352 | n_water=907 | time (s): 109.050 (total time: 111.450) Filter (q & B) r_work=0.1195 r_free=0.1352 | n_water=901 | time (s): 5.380 (total time: 116.830) Compute maps r_work=0.1195 r_free=0.1352 | n_water=901 | time (s): 2.330 (total time: 119.160) Filter (map) r_work=0.1216 r_free=0.1349 | n_water=788 | time (s): 5.240 (total time: 124.400) Find peaks r_work=0.1216 r_free=0.1349 | n_water=788 | time (s): 0.610 (total time: 125.010) Add new water r_work=0.1223 r_free=0.1359 | n_water=996 | time (s): 5.190 (total time: 130.200) Refine new water occ: r_work=0.1193 r_free=0.1336 adp: r_work=0.1193 r_free=0.1337 occ: r_work=0.1191 r_free=0.1335 adp: r_work=0.1191 r_free=0.1336 occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1190 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1335 r_work=0.1190 r_free=0.1335 | n_water=996 | time (s): 253.310 (total time: 383.510) Filter (q & B) r_work=0.1194 r_free=0.1350 | n_water=916 | time (s): 4.330 (total time: 387.840) Filter (dist only) r_work=0.1194 r_free=0.1349 | n_water=915 | time (s): 114.930 (total time: 502.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.507650 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.803012 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 0.1354 0.0156 0.037 1.1 5.6 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.54 1.56 1.704 13.689 14.803 3.757 12.00 13.59 1.59 1.724 13.679 14.803 3.755 Individual atomic B min max mean iso aniso Overall: 5.37 63.38 14.60 0.88 550 3269 Protein: 5.37 28.19 10.21 0.88 0 2902 Water: 5.75 63.38 28.50 N/A 550 365 Other: 13.64 22.03 17.84 N/A 0 2 Chain A: 5.46 52.06 12.05 N/A 0 1624 Chain B: 5.37 63.38 11.87 N/A 0 1645 Chain S: 5.75 60.18 30.30 N/A 550 0 Histogram: Values Number of atoms 5.37 - 11.17 2057 11.17 - 16.97 824 16.97 - 22.77 277 22.77 - 28.57 211 28.57 - 34.37 188 34.37 - 40.17 134 40.17 - 45.97 87 45.97 - 51.77 31 51.77 - 57.58 7 57.58 - 63.38 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1359 r_work=0.1200 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1359 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1359 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.754845 | | target function (ml) not normalized (work): 703241.215604 | | target function (ml) not normalized (free): 14728.200787 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1369 0.1368 0.1460 n_refl.: 191130 remove outliers: r(all,work,free)=0.1369 0.1368 0.1460 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1369 0.1368 0.1460 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1346 n_refl.: 191130 remove outliers: r(all,work,free)=0.1192 0.1189 0.1346 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3690 360.964 328.411 0.386 0.995 0.193 13.296-10.522 97.03 97 1 0.2404 481.284 461.531 0.661 0.997 0.136 10.503-8.327 97.80 175 3 0.2182 502.001 493.776 0.831 0.997 0.110 8.318-6.595 100.00 360 8 0.2158 375.615 369.692 0.855 0.997 0.085 6.588-5.215 100.00 711 7 0.1946 345.153 334.989 0.855 0.998 0.067 5.214-4.128 98.38 1367 28 0.1218 504.853 499.199 0.941 0.998 0.030 4.126-3.266 94.74 2603 46 0.1160 460.201 452.574 1.001 1.000 0.005 3.266-2.585 99.86 5447 97 0.1118 310.441 306.800 0.984 1.000 0.000 2.585-2.046 97.45 10613 204 0.0955 234.210 231.626 0.990 1.002 0.000 2.046-1.619 99.39 21536 464 0.0906 138.617 137.242 1.003 1.006 0.000 1.619-1.281 98.00 42464 925 0.0944 74.623 73.967 0.989 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.032 38.333 0.950 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.1167 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1346 | n_water=915 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1189 r_free=0.1346 | n_water=915 | time (s): 108.960 (total time: 112.050) Filter (q & B) r_work=0.1190 r_free=0.1344 | n_water=904 | time (s): 4.290 (total time: 116.340) Compute maps r_work=0.1190 r_free=0.1344 | n_water=904 | time (s): 2.040 (total time: 118.380) Filter (map) r_work=0.1210 r_free=0.1347 | n_water=796 | time (s): 4.490 (total time: 122.870) Find peaks r_work=0.1210 r_free=0.1347 | n_water=796 | time (s): 0.660 (total time: 123.530) Add new water r_work=0.1217 r_free=0.1351 | n_water=996 | time (s): 4.040 (total time: 127.570) Refine new water occ: r_work=0.1187 r_free=0.1330 adp: r_work=0.1187 r_free=0.1330 occ: r_work=0.1185 r_free=0.1329 adp: r_work=0.1185 r_free=0.1330 occ: r_work=0.1184 r_free=0.1329 adp: r_work=0.1183 r_free=0.1330 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1330 r_work=0.1183 r_free=0.1330 | n_water=996 | time (s): 194.730 (total time: 322.300) Filter (q & B) r_work=0.1187 r_free=0.1342 | n_water=922 | time (s): 4.950 (total time: 327.250) Filter (dist only) r_work=0.1188 r_free=0.1341 | n_water=921 | time (s): 115.230 (total time: 442.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.543213 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.787647 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 0.1190 0.1345 0.0155 0.037 1.1 5.3 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.45 1.55 1.668 13.677 14.788 3.753 11.89 13.45 1.56 1.667 13.675 14.788 3.752 Individual atomic B min max mean iso aniso Overall: 5.38 62.84 14.63 0.87 556 3269 Protein: 5.38 28.12 10.23 0.87 0 2902 Water: 5.81 62.84 28.47 N/A 556 365 Other: 13.69 22.17 17.93 N/A 0 2 Chain A: 5.49 51.88 12.04 N/A 0 1624 Chain B: 5.38 62.84 11.86 N/A 0 1645 Chain S: 5.81 60.23 30.38 N/A 556 0 Histogram: Values Number of atoms 5.38 - 11.13 2042 11.13 - 16.87 833 16.87 - 22.62 284 22.62 - 28.36 210 28.36 - 34.11 184 34.11 - 39.86 131 39.86 - 45.60 96 45.60 - 51.35 31 51.35 - 57.10 11 57.10 - 62.84 3 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1345 r_work=0.1190 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1345 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1344 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751261 | | target function (ml) not normalized (work): 702569.974231 | | target function (ml) not normalized (free): 14716.988216 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1344 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1372 0.1371 0.1465 n_refl.: 191130 remove outliers: r(all,work,free)=0.1372 0.1371 0.1465 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1372 0.1371 0.1465 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1343 n_refl.: 191130 remove outliers: r(all,work,free)=0.1190 0.1187 0.1343 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3725 360.964 328.660 0.385 0.995 0.193 13.296-10.522 97.03 97 1 0.2418 481.284 460.844 0.657 0.996 0.126 10.503-8.327 97.80 175 3 0.2205 502.001 493.576 0.830 0.997 0.097 8.318-6.595 100.00 360 8 0.2149 375.615 370.091 0.852 0.997 0.065 6.588-5.215 100.00 711 7 0.1924 345.153 335.163 0.854 0.997 0.050 5.214-4.128 98.38 1367 28 0.1212 504.853 499.124 0.941 0.998 0.020 4.126-3.266 94.74 2603 46 0.1156 460.201 452.628 1.002 0.999 0.000 3.266-2.585 99.86 5447 97 0.1122 310.441 306.794 0.985 1.000 0.000 2.585-2.046 97.45 10613 204 0.0954 234.210 231.610 0.992 1.003 0.000 2.046-1.619 99.39 21536 464 0.0907 138.617 137.259 1.005 1.006 0.000 1.619-1.281 98.00 42464 925 0.0941 74.623 73.974 0.992 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.032 38.323 0.956 1.022 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9978 b_overall=0.0787 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1343 After: r_work=0.1188 r_free=0.1344 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1346 | n_water=921 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1189 r_free=0.1345 | n_water=920 | time (s): 120.770 (total time: 123.330) Filter (q & B) r_work=0.1189 r_free=0.1347 | n_water=910 | time (s): 4.560 (total time: 127.890) Compute maps r_work=0.1189 r_free=0.1347 | n_water=910 | time (s): 1.630 (total time: 129.520) Filter (map) r_work=0.1210 r_free=0.1357 | n_water=806 | time (s): 4.990 (total time: 134.510) Find peaks r_work=0.1210 r_free=0.1357 | n_water=806 | time (s): 0.740 (total time: 135.250) Add new water r_work=0.1215 r_free=0.1361 | n_water=1011 | time (s): 4.080 (total time: 139.330) Refine new water occ: r_work=0.1186 r_free=0.1334 adp: r_work=0.1186 r_free=0.1335 occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1184 r_free=0.1333 occ: r_work=0.1183 r_free=0.1331 adp: r_work=0.1183 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1333 r_work=0.1183 r_free=0.1333 | n_water=1011 | time (s): 205.020 (total time: 344.350) Filter (q & B) r_work=0.1187 r_free=0.1345 | n_water=927 | time (s): 5.350 (total time: 349.700) Filter (dist only) r_work=0.1187 r_free=0.1344 | n_water=926 | time (s): 121.760 (total time: 471.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554931 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.586874 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 0.1188 0.1346 0.0158 0.037 1.1 8.2 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.46 1.58 1.667 13.700 14.587 3.753 11.89 13.47 1.59 1.671 13.703 14.587 3.752 Individual atomic B min max mean iso aniso Overall: 5.47 61.57 14.66 0.87 561 3269 Protein: 5.47 27.96 10.25 0.87 0 2902 Water: 5.75 61.57 28.49 N/A 561 365 Other: 13.77 22.14 17.95 N/A 0 2 Chain A: 5.53 51.53 12.03 N/A 0 1624 Chain B: 5.47 61.57 11.86 N/A 0 1645 Chain S: 5.75 60.50 30.50 N/A 561 0 Histogram: Values Number of atoms 5.47 - 11.08 2023 11.08 - 16.69 856 16.69 - 22.30 276 22.30 - 27.91 198 27.91 - 33.52 183 33.52 - 39.13 137 39.13 - 44.74 103 44.74 - 50.35 33 50.35 - 55.96 15 55.96 - 61.57 6 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1348 r_work=0.1189 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1348 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1345 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752106 | | target function (ml) not normalized (work): 702728.215523 | | target function (ml) not normalized (free): 14719.869622 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1343 0.1389 5.6779 5.739| | 2: 2.94 - 2.33 1.00 7339 128 0.1065 0.1388 5.066 5.182| | 3: 2.33 - 2.04 0.96 6939 150 0.0902 0.1177 4.6536 4.732| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1058 4.3919 4.566| | 5: 1.85 - 1.72 0.99 7113 159 0.0925 0.0998 4.1457 4.2449| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1095 3.9453 4.085| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0960 3.796 3.9235| | 8: 1.54 - 1.47 0.96 6798 152 0.0892 0.1297 3.698 3.891| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1113 3.6191 3.7499| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1185 3.5548 3.681| | 11: 1.36 - 1.32 0.99 6997 151 0.0992 0.1124 3.4837 3.5822| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1124 3.4566 3.5793| | 13: 1.28 - 1.25 0.98 6907 166 0.1045 0.1239 3.4367 3.5644| | 14: 1.25 - 1.22 0.98 7015 112 0.1108 0.1590 3.4308 3.6749| | 15: 1.22 - 1.19 0.98 6956 137 0.1170 0.1241 3.4471 3.4896| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1545 3.4643 3.6611| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1231 3.4332 3.447| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1694 3.4377 3.527| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1754 3.4191 3.5954| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1585 3.4094 3.4383| | 21: 1.08 - 1.07 0.97 6852 152 0.1724 0.2128 3.4167 3.5016| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1967 3.4125 3.4151| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2023 3.4326 3.4856| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2244 3.4356 3.509| | 25: 1.02 - 1.01 0.93 6552 130 0.2615 0.2504 3.4487 3.5245| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2874 3.4152 3.4233| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2810 3.4691 3.3961| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7398 127 0.93 11.15 1.00 0.97 10573.26| | 2: 2.94 - 2.33 7339 128 0.93 12.48 0.99 0.97 4921.30| | 3: 2.33 - 2.04 6939 150 0.96 7.63 1.01 0.97 1697.92| | 4: 2.04 - 1.85 7170 155 0.96 7.60 1.00 0.97 1000.55| | 5: 1.85 - 1.72 7113 159 0.96 8.05 1.00 0.97 631.40| | 6: 1.72 - 1.62 7102 142 0.96 8.02 1.00 0.98 442.72| | 7: 1.62 - 1.54 7104 148 0.96 8.12 1.01 0.99 335.70| | 8: 1.54 - 1.47 6798 152 0.96 8.23 1.01 0.99 277.53| | 9: 1.47 - 1.41 6938 155 0.96 8.45 1.01 0.99 230.22| | 10: 1.41 - 1.36 7022 150 0.96 8.89 1.00 0.99 201.92| | 11: 1.36 - 1.32 6997 151 0.96 8.91 0.99 0.97 173.78| | 12: 1.32 - 1.28 6975 149 0.96 8.91 0.98 0.96 159.40| | 13: 1.28 - 1.25 6907 166 0.96 9.49 1.01 0.98 156.94| | 14: 1.25 - 1.22 7015 112 0.95 10.67 1.02 0.98 162.46| | 15: 1.22 - 1.19 6956 137 0.95 11.22 1.01 1.00 166.38| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.98 160.35| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.98 153.84| | 18: 1.14 - 1.12 6875 142 0.94 12.73 1.01 0.96 147.52| | 19: 1.12 - 1.10 6948 106 0.93 14.15 1.00 0.96 151.07| | 20: 1.10 - 1.08 6884 147 0.92 15.24 1.00 0.95 150.61| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.95 153.57| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.94 154.95| | 23: 1.05 - 1.03 6827 159 0.87 20.46 0.99 0.93 164.37| | 24: 1.03 - 1.02 6784 133 0.85 23.12 0.99 0.94 178.65| | 25: 1.02 - 1.01 6552 130 0.83 25.12 0.97 0.91 181.73| | 26: 1.01 - 0.99 6767 158 0.81 26.60 0.98 0.89 176.40| | 27: 0.99 - 0.98 6647 131 0.82 26.26 0.98 0.88 160.90| |alpha: min = 0.88 max = 1.00 mean = 0.96| |beta: min = 147.52 max = 10573.26 mean = 891.95| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.24| |phase err.(test): min = 0.00 max = 89.66 mean = 13.39| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1345 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1380 0.1378 0.1470 n_refl.: 191130 remove outliers: r(all,work,free)=0.1380 0.1378 0.1470 n_refl.: 191130 overall B=0.00 to atoms: r(all,work,free)=0.1380 0.1378 0.1470 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1345 n_refl.: 191130 remove outliers: r(all,work,free)=0.1190 0.1187 0.1345 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3680 360.964 329.892 0.383 0.994 0.194 13.296-10.522 97.03 97 1 0.2392 481.284 462.129 0.652 0.996 0.125 10.503-8.327 97.80 175 3 0.2185 502.001 493.558 0.823 0.996 0.086 8.318-6.595 100.00 360 8 0.2132 375.615 370.216 0.848 0.996 0.065 6.588-5.215 100.00 711 7 0.1915 345.153 335.415 0.848 0.997 0.053 5.214-4.128 98.38 1367 28 0.1209 504.853 499.152 0.935 0.998 0.024 4.126-3.266 94.74 2603 46 0.1152 460.201 452.658 0.998 0.999 0.000 3.266-2.585 99.86 5447 97 0.1120 310.441 306.833 0.980 1.000 0.000 2.585-2.046 97.45 10613 204 0.0957 234.210 231.587 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0908 138.617 137.244 1.000 1.007 0.000 1.619-1.281 98.00 42464 925 0.0944 74.623 73.971 0.988 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.032 38.323 0.953 1.027 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0434 ================= 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 : 0.2036 0.2010 0.082 5.213 5.2 78.0 14.6 805 0.000 1_bss: 0.1801 0.1949 0.082 5.213 5.2 78.0 14.6 805 0.000 1_settarget: 0.1801 0.1949 0.082 5.213 5.2 78.0 14.6 805 0.000 1_nqh: 0.1803 0.1948 0.082 5.213 5.2 78.0 14.6 805 0.003 1_weight: 0.1803 0.1948 0.082 5.213 5.2 78.0 14.6 805 0.003 1_xyzrec: 0.1273 0.1479 0.035 1.164 5.2 78.0 14.6 805 0.144 1_adp: 0.1302 0.1550 0.035 1.164 5.3 73.0 15.0 805 0.144 1_regHadp: 0.1301 0.1544 0.035 1.164 5.3 73.0 15.0 805 0.144 1_occ: 0.1286 0.1532 0.035 1.164 5.3 73.0 15.0 805 0.144 2_bss: 0.1278 0.1524 0.035 1.164 5.4 73.2 15.2 805 0.144 2_settarget: 0.1278 0.1524 0.035 1.164 5.4 73.2 15.2 805 0.144 2_updatecdl: 0.1278 0.1524 0.035 1.180 5.4 73.2 15.2 805 0.144 2_nqh: 0.1278 0.1524 0.035 1.180 5.4 73.2 15.2 805 0.144 2_sol: 0.1272 0.1501 0.035 1.180 5.4 73.2 16.4 905 n/a 2_weight: 0.1272 0.1501 0.035 1.180 5.4 73.2 16.4 905 n/a 2_xyzrec: 0.1255 0.1521 0.038 1.146 5.4 73.2 16.4 905 n/a 2_adp: 0.1234 0.1507 0.038 1.146 5.3 68.2 16.4 905 n/a 2_regHadp: 0.1234 0.1509 0.038 1.146 5.3 68.2 16.4 905 n/a 2_occ: 0.1227 0.1505 0.038 1.146 5.3 68.2 16.4 905 n/a 3_bss: 0.1234 0.1510 0.038 1.146 5.3 68.2 16.4 905 n/a 3_settarget: 0.1234 0.1510 0.038 1.146 5.3 68.2 16.4 905 n/a 3_updatecdl: 0.1234 0.1510 0.038 1.154 5.3 68.2 16.4 905 n/a 3_nqh: 0.1234 0.1510 0.038 1.154 5.3 68.2 16.4 905 n/a 3_sol: 0.1255 0.1507 0.038 1.154 5.3 68.2 15.4 868 n/a 3_weight: 0.1255 0.1507 0.038 1.154 5.3 68.2 15.4 868 n/a 3_xyzrec: 0.1245 0.1437 0.034 1.105 5.3 68.2 15.4 868 n/a 3_adp: 0.1237 0.1395 0.034 1.105 5.5 67.7 15.2 868 n/a 3_regHadp: 0.1238 0.1397 0.034 1.105 5.5 67.7 15.2 868 n/a 3_occ: 0.1232 0.1391 0.034 1.105 5.5 67.7 15.2 868 n/a 4_bss: 0.1227 0.1384 0.034 1.105 5.5 67.7 15.2 868 n/a 4_settarget: 0.1227 0.1384 0.034 1.105 5.5 67.7 15.2 868 n/a 4_updatecdl: 0.1227 0.1384 0.034 1.105 5.5 67.7 15.2 868 n/a 4_nqh: 0.1227 0.1384 0.034 1.105 5.5 67.7 15.2 868 n/a 4_sol: 0.1210 0.1365 0.034 1.105 5.5 67.7 15.0 874 n/a 4_weight: 0.1210 0.1365 0.034 1.105 5.5 67.7 15.0 874 n/a 4_xyzrec: 0.1208 0.1366 0.035 1.132 5.5 67.7 15.0 874 n/a 4_adp: 0.1201 0.1364 0.035 1.132 5.5 67.4 15.0 874 n/a 4_regHadp: 0.1201 0.1365 0.035 1.132 5.5 67.4 15.0 874 n/a 4_occ: 0.1199 0.1360 0.035 1.132 5.5 67.4 15.0 874 n/a 5_bss: 0.1198 0.1360 0.035 1.132 5.5 67.3 14.9 874 n/a 5_settarget: 0.1198 0.1360 0.035 1.132 5.5 67.3 14.9 874 n/a 5_updatecdl: 0.1198 0.1360 0.035 1.132 5.5 67.3 14.9 874 n/a 5_nqh: 0.1198 0.1360 0.035 1.132 5.5 67.3 14.9 874 n/a 5_sol: 0.1195 0.1345 0.035 1.132 5.5 67.3 15.0 893 n/a 5_weight: 0.1195 0.1345 0.035 1.132 5.5 67.3 15.0 893 n/a 5_xyzrec: 0.1197 0.1353 0.036 1.126 5.5 67.3 15.0 893 n/a 5_adp: 0.1201 0.1355 0.036 1.126 5.6 67.0 15.0 893 n/a 5_regHadp: 0.1201 0.1356 0.036 1.126 5.6 67.0 15.0 893 n/a 5_occ: 0.1199 0.1354 0.036 1.126 5.6 67.0 15.0 893 n/a 6_bss: 0.1197 0.1353 0.036 1.126 5.5 66.9 15.0 893 n/a 6_settarget: 0.1197 0.1353 0.036 1.126 5.5 66.9 15.0 893 n/a 6_updatecdl: 0.1197 0.1353 0.036 1.126 5.5 66.9 15.0 893 n/a 6_nqh: 0.1197 0.1353 0.036 1.126 5.5 66.9 15.0 893 n/a 6_sol: 0.1196 0.1347 0.036 1.126 5.5 66.9 14.9 902 n/a 6_weight: 0.1196 0.1347 0.036 1.126 5.5 66.9 14.9 902 n/a 6_xyzrec: 0.1199 0.1357 0.036 1.127 5.5 66.9 14.9 902 n/a 6_adp: 0.1202 0.1362 0.036 1.127 5.6 65.8 14.9 902 n/a 6_regHadp: 0.1202 0.1362 0.036 1.127 5.6 65.8 14.9 902 n/a 6_occ: 0.1200 0.1361 0.036 1.127 5.6 65.8 14.9 902 n/a 7_bss: 0.1199 0.1360 0.036 1.127 5.5 65.8 14.8 902 n/a 7_settarget: 0.1199 0.1360 0.036 1.127 5.5 65.8 14.8 902 n/a 7_updatecdl: 0.1199 0.1360 0.036 1.128 5.5 65.8 14.8 902 n/a 7_nqh: 0.1199 0.1360 0.036 1.128 5.5 65.8 14.8 902 n/a 7_sol: 0.1196 0.1353 0.036 1.128 5.5 65.8 14.9 907 n/a 7_weight: 0.1196 0.1353 0.036 1.128 5.5 65.8 14.9 907 n/a 7_xyzrec: 0.1198 0.1356 0.037 1.133 5.5 65.8 14.9 907 n/a 7_adp: 0.1198 0.1356 0.037 1.133 5.6 64.6 14.8 907 n/a 7_regHadp: 0.1198 0.1357 0.037 1.133 5.6 64.6 14.8 907 n/a 7_occ: 0.1196 0.1353 0.037 1.133 5.6 64.6 14.8 907 n/a 8_bss: 0.1195 0.1352 0.037 1.133 5.4 64.4 14.6 907 n/a 8_settarget: 0.1195 0.1352 0.037 1.133 5.4 64.4 14.6 907 n/a 8_updatecdl: 0.1195 0.1352 0.037 1.133 5.4 64.4 14.6 907 n/a 8_nqh: 0.1195 0.1352 0.037 1.133 5.4 64.4 14.6 907 n/a 8_sol: 0.1194 0.1349 0.037 1.133 5.4 64.4 14.6 915 n/a 8_weight: 0.1194 0.1349 0.037 1.133 5.4 64.4 14.6 915 n/a 8_xyzrec: 0.1198 0.1354 0.037 1.124 5.4 64.4 14.6 915 n/a 8_adp: 0.1200 0.1359 0.037 1.124 5.4 63.4 14.6 915 n/a 8_regHadp: 0.1200 0.1359 0.037 1.124 5.4 63.4 14.6 915 n/a 8_occ: 0.1198 0.1359 0.037 1.124 5.4 63.4 14.6 915 n/a 9_bss: 0.1189 0.1346 0.037 1.124 5.4 63.4 14.6 915 n/a 9_settarget: 0.1189 0.1346 0.037 1.124 5.4 63.4 14.6 915 n/a 9_updatecdl: 0.1189 0.1346 0.037 1.123 5.4 63.4 14.6 915 n/a 9_nqh: 0.1189 0.1346 0.037 1.123 5.4 63.4 14.6 915 n/a 9_sol: 0.1188 0.1341 0.037 1.123 5.4 63.4 14.6 921 n/a 9_weight: 0.1188 0.1341 0.037 1.123 5.4 63.4 14.6 921 n/a 9_xyzrec: 0.1190 0.1345 0.037 1.124 5.4 63.4 14.6 921 n/a 9_adp: 0.1190 0.1345 0.037 1.124 5.4 62.8 14.6 921 n/a 9_regHadp: 0.1190 0.1345 0.037 1.124 5.4 62.8 14.6 921 n/a 9_occ: 0.1188 0.1344 0.037 1.124 5.4 62.8 14.6 921 n/a 10_bss: 0.1187 0.1343 0.037 1.124 5.4 62.8 14.6 921 n/a 10_settarget: 0.1187 0.1343 0.037 1.124 5.4 62.8 14.6 921 n/a 10_updatecdl: 0.1187 0.1343 0.037 1.125 5.4 62.8 14.6 921 n/a 10_setrh: 0.1188 0.1344 0.037 1.125 5.4 62.8 14.6 921 n/a 10_nqh: 0.1189 0.1346 0.037 1.125 5.4 62.8 14.6 921 n/a 10_sol: 0.1187 0.1344 0.037 1.125 5.4 62.8 14.7 926 n/a 10_weight: 0.1187 0.1344 0.037 1.125 5.4 62.8 14.7 926 n/a 10_xyzrec: 0.1188 0.1346 0.037 1.149 5.4 62.8 14.7 926 n/a 10_adp: 0.1189 0.1348 0.037 1.149 5.5 61.6 14.7 926 n/a 10_regHadp: 0.1189 0.1348 0.037 1.149 5.5 61.6 14.7 926 n/a 10_occ: 0.1188 0.1345 0.037 1.149 5.5 61.6 14.7 926 n/a end: 0.1187 0.1345 0.037 1.149 5.5 61.6 14.7 926 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2943615_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2943615_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.6700 Refinement macro-cycles (run) : 12139.4800 Write final files (write_after_run_outputs) : 178.3100 Total : 12324.4600 Total CPU time: 3.43 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:38 PST -0800 (1736736158.67 s) Start R-work = 0.1801, R-free = 0.1949 Final R-work = 0.1187, R-free = 0.1345 =============================================================================== Job complete usr+sys time: 12623.44 seconds wall clock time: 211 minutes 24.33 seconds (12684.33 seconds total)