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_3788076.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3788076.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3788076.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.48, per 1000 atoms: 0.37 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.689 distance_ideal: 2.720 ideal - model: 0.031 slack: 0.000 delta_slack: 0.031 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: 2.760 distance_ideal: 2.710 ideal - model: -0.050 slack: 0.000 delta_slack: -0.050 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 117.6 milliseconds Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.04: 1016 1.04 - 1.30: 2520 1.30 - 1.55: 1797 1.55 - 1.80: 591 1.80 - 2.05: 10 Bond restraints: 5934 Sorted by residual: bond pdb=" C VAL B 69 " pdb=" O VAL B 69 " ideal model delta sigma weight residual 1.236 1.457 -0.222 1.01e-02 9.80e+03 4.82e+02 bond pdb=" CA LYS B 142 " pdb=" C LYS B 142 " ideal model delta sigma weight residual 1.521 1.757 -0.236 1.20e-02 6.94e+03 3.87e+02 bond pdb=" N GLY A 12 " pdb=" H GLY A 12 " ideal model delta sigma weight residual 0.860 1.234 -0.374 2.00e-02 2.50e+03 3.50e+02 bond pdb=" CG2 ILE A 134 " pdb="HG22 ILE A 134 " ideal model delta sigma weight residual 0.970 1.336 -0.366 2.00e-02 2.50e+03 3.34e+02 bond pdb=" NE ARG B 143 " pdb=" HE ARG B 143 " ideal model delta sigma weight residual 0.860 1.225 -0.365 2.00e-02 2.50e+03 3.33e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 5557 4.10 - 8.20: 3564 8.20 - 12.30: 1359 12.30 - 16.40: 288 16.40 - 20.50: 42 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 120.13 136.40 -16.27 8.60e-01 1.35e+00 3.58e+02 angle pdb=" CA ILE B 134 " pdb=" C ILE B 134 " pdb=" N PRO B 135 " ideal model delta sigma weight residual 119.22 132.90 -13.68 7.80e-01 1.64e+00 3.07e+02 angle pdb=" O LYS B 142 " pdb=" C LYS B 142 " pdb=" N ARG B 143 " ideal model delta sigma weight residual 123.27 143.31 -20.04 1.16e+00 7.43e-01 2.99e+02 angle pdb=" CA GLY A 190 " pdb=" C GLY A 190 " pdb=" O GLY A 190 " ideal model delta sigma weight residual 119.56 104.87 14.69 8.70e-01 1.32e+00 2.85e+02 angle pdb=" O PHE A 95 " pdb=" C PHE A 95 " pdb=" N HIS A 96 " ideal model delta sigma weight residual 122.07 139.33 -17.26 1.03e+00 9.43e-01 2.81e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 1821 16.32 - 32.63: 151 32.63 - 48.95: 56 48.95 - 65.26: 16 65.26 - 81.58: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ALA B 107 " pdb=" C ALA B 107 " pdb=" N ALA B 108 " pdb=" CA ALA B 108 " ideal model delta harmonic sigma weight residual -180.00 -157.96 -22.04 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CG TRP A 146 " pdb=" CD2 TRP A 146 " pdb=" CE3 TRP A 146 " pdb=" HE3 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 21.73 -21.73 0 5.00e+00 4.00e-02 1.89e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.252: 241 0.252 - 0.503: 161 0.503 - 0.754: 73 0.754 - 1.006: 14 1.006 - 1.257: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ALA B 38 " pdb=" N ALA B 38 " pdb=" C ALA B 38 " pdb=" CB ALA B 38 " both_signs ideal model delta sigma weight residual False 2.48 3.74 -1.26 2.00e-01 2.50e+01 3.95e+01 chirality pdb=" CA TRP A 139 " pdb=" N TRP A 139 " pdb=" C TRP A 139 " pdb=" CB TRP A 139 " both_signs ideal model delta sigma weight residual False 2.51 3.59 -1.08 2.00e-01 2.50e+01 2.92e+01 chirality pdb=" CA ALA B 57 " pdb=" N ALA B 57 " pdb=" C ALA B 57 " pdb=" CB ALA B 57 " both_signs ideal model delta sigma weight residual False 2.48 3.55 -1.06 2.00e-01 2.50e+01 2.82e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.134 2.00e-02 2.50e+03 7.15e-02 1.53e+02 pdb=" CG PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.088 2.00e-02 2.50e+03 6.92e-02 1.44e+02 pdb=" CG PHE A 119 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.112 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.070 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.044 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.055 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.128 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.048 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.058 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG TYR A 194 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " 0.119 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.080 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.123 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " -0.082 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " 0.048 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 30 1.64 - 2.38: 2785 2.38 - 3.12: 22437 3.12 - 3.86: 32752 3.86 - 4.60: 52321 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110325 Sorted by model distance: nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.905 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.929 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.938 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 0.989 2.620 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.172 2.100 ... (remaining 110320 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_3788076_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= 0.2035 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.300774 | | target function (ml) not normalized (work): 805590.882042 | | target function (ml) not normalized (free): 16545.697960 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2133 0.1888 6.7064 6.3008| | 2: 2.94 - 2.33 1.00 7339 128 0.1616 0.1459 5.522 5.5327| | 3: 2.33 - 2.04 0.96 6939 150 0.1643 0.1449 5.139 5.0768| | 4: 2.04 - 1.85 1.00 7170 155 0.1752 0.1455 4.9635 4.9303| | 5: 1.85 - 1.72 0.99 7113 159 0.1931 0.1666 4.8042 4.7684| | 6: 1.72 - 1.62 0.99 7102 142 0.1978 0.1787 4.6755 4.589| | 7: 1.62 - 1.54 0.99 7104 148 0.2029 0.1788 4.5584 4.5177| | 8: 1.54 - 1.47 0.96 6798 152 0.2008 0.2305 4.4657 4.5236| | 9: 1.47 - 1.41 0.98 6938 155 0.2083 0.2318 4.3948 4.5202| | 10: 1.41 - 1.36 0.99 7022 150 0.2125 0.2117 4.3082 4.3286| | 11: 1.36 - 1.32 0.99 6997 151 0.2096 0.2199 4.2249 4.2844| | 12: 1.32 - 1.28 0.98 6976 149 0.2094 0.2120 4.1829 4.2779| | 13: 1.28 - 1.25 0.98 6907 166 0.2010 0.2336 4.1148 4.2631| | 14: 1.25 - 1.22 0.98 7015 113 0.2078 0.2221 4.0766 4.2375| | 15: 1.22 - 1.19 0.98 6957 137 0.2127 0.2109 4.048 4.0781| | 16: 1.19 - 1.17 0.93 6604 132 0.2121 0.2468 4.0097 4.1746| | 17: 1.17 - 1.14 0.98 6941 135 0.2167 0.1716 3.9523 3.9113| | 18: 1.14 - 1.12 0.98 6875 142 0.2224 0.2543 3.9138 3.999| | 19: 1.12 - 1.10 0.97 6949 106 0.2298 0.2431 3.8817 3.9282| | 20: 1.10 - 1.08 0.97 6884 147 0.2347 0.2268 3.8281 3.8466| | 21: 1.08 - 1.07 0.97 6852 152 0.2444 0.2729 3.7919 3.8111| | 22: 1.07 - 1.05 0.97 6838 135 0.2552 0.2531 3.7514 3.7296| | 23: 1.05 - 1.03 0.97 6829 159 0.2721 0.2790 3.7336 3.8579| | 24: 1.03 - 1.02 0.96 6785 133 0.2931 0.2771 3.7088 3.7785| | 25: 1.02 - 1.01 0.93 6552 130 0.3091 0.3032 3.6844 3.7393| | 26: 1.01 - 0.99 0.96 6767 158 0.3204 0.3433 3.628 3.6389| | 27: 0.99 - 0.98 0.94 6648 131 0.3414 0.3529 3.6392 3.6451| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.05 0.91 0.98 34379.45| | 2: 2.94 - 2.33 7339 128 0.86 20.55 1.09 1.02 14251.44| | 3: 2.33 - 2.04 6939 150 0.94 11.30 1.11 1.05 3557.65| | 4: 2.04 - 1.85 7170 155 0.93 12.07 1.11 1.07 2336.90| | 5: 1.85 - 1.72 7113 159 0.92 14.24 1.11 1.09 1773.66| | 6: 1.72 - 1.62 7102 142 0.91 15.18 1.11 1.09 1403.43| | 7: 1.62 - 1.54 7104 148 0.90 16.62 1.11 1.09 1239.33| | 8: 1.54 - 1.47 6798 152 0.89 18.18 1.10 1.08 1146.73| | 9: 1.47 - 1.41 6938 155 0.88 19.52 1.10 1.06 1040.71| | 10: 1.41 - 1.36 7022 150 0.87 20.30 1.09 1.05 874.15| | 11: 1.36 - 1.32 6997 151 0.87 20.35 1.08 1.03 750.15| | 12: 1.32 - 1.28 6976 149 0.87 20.20 1.08 1.04 675.82| | 13: 1.28 - 1.25 6907 166 0.86 20.95 1.08 1.03 658.55| | 14: 1.25 - 1.22 7015 113 0.85 21.93 1.08 1.02 624.13| | 15: 1.22 - 1.19 6957 137 0.86 21.79 1.08 1.03 576.27| | 16: 1.19 - 1.17 6604 132 0.87 21.04 1.07 1.03 510.86| | 17: 1.17 - 1.14 6941 135 0.86 21.11 1.08 1.03 447.44| | 18: 1.14 - 1.12 6875 142 0.86 21.43 1.08 1.00 402.93| | 19: 1.12 - 1.10 6949 106 0.86 21.99 1.07 1.01 380.88| | 20: 1.10 - 1.08 6884 147 0.85 22.78 1.07 0.99 350.60| | 21: 1.08 - 1.07 6852 152 0.84 23.81 1.07 0.99 338.56| | 22: 1.07 - 1.05 6838 135 0.82 25.62 1.05 0.97 328.85| | 23: 1.05 - 1.03 6829 159 0.79 28.38 1.06 0.95 337.80| | 24: 1.03 - 1.02 6785 133 0.77 30.46 1.05 0.95 341.05| | 25: 1.02 - 1.01 6552 130 0.76 31.59 1.02 0.92 327.59| | 26: 1.01 - 0.99 6767 158 0.73 34.06 1.03 0.90 320.99| | 27: 0.99 - 0.98 6648 131 0.70 36.09 1.04 0.85 319.81| |alpha: min = 0.85 max = 1.09 mean = 1.01| |beta: min = 319.81 max = 34379.45 mean = 2702.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 21.81| |phase err.(test): min = 0.00 max = 88.91 mean = 21.95| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.250 2950 Z= 5.506 Angle : 5.277 20.042 4018 Z= 3.820 Chirality : 0.376 1.257 492 Planarity : 0.031 0.121 512 Dihedral : 12.778 81.576 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.81 % Favored : 97.93 % Rotamer: Outliers : 1.29 % Allowed : 4.84 % Favored : 93.87 % Cbeta Deviations : 28.37 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.38), residues: 386 helix: -2.15 (0.33), residues: 142 sheet: -0.35 (0.60), residues: 66 loop : -0.28 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.107 0.018 ARG A 143 TYR 0.098 0.033 TYR A 192 PHE 0.115 0.035 PHE B 82 TRP 0.113 0.040 TRP B 139 HIS 0.046 0.018 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2035 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.300774 | | target function (ml) not normalized (work): 805590.882042 | | target function (ml) not normalized (free): 16545.697960 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2035 0.1951 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2035 0.1951 n_refl.: 191155 remove outliers: r(all,work,free)=0.2033 0.2036 0.1951 n_refl.: 191145 overall B=-0.03 to atoms: r(all,work,free)=0.2029 0.2032 0.1950 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1803 0.1895 n_refl.: 191145 remove outliers: r(all,work,free)=0.1802 0.1800 0.1894 n_refl.: 191136 ======================== 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 0.4070 398.008 290.410 0.431 0.915 0.299 13.296-10.522 99.01 99 1 0.2507 528.187 519.122 0.778 0.917 0.248 10.503-8.327 98.90 177 3 0.2447 564.205 558.798 0.963 0.917 0.223 8.318-6.595 100.00 360 8 0.2467 414.736 402.278 0.962 0.917 0.165 6.588-5.215 100.00 711 7 0.2269 381.101 365.693 0.948 0.917 0.160 5.214-4.128 98.38 1367 28 0.1498 557.435 549.346 1.064 0.918 0.090 4.126-3.266 94.74 2603 46 0.1332 508.132 499.181 1.132 0.920 0.023 3.266-2.585 99.86 5447 97 0.1443 342.774 337.424 1.105 0.921 0.000 2.585-2.046 97.45 10613 204 0.1397 258.603 254.425 1.109 0.923 0.000 2.046-1.619 99.39 21536 464 0.1634 153.054 149.847 1.118 0.926 0.000 1.619-1.281 98.00 42464 925 0.1912 82.395 80.527 1.102 0.931 0.000 1.281-0.980 96.53 101826 2055 0.2325 44.202 42.010 1.077 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0716 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1894 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1800 r_free=0.1894 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.510312 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 573.757652 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 0.1274 0.1484 0.0210 0.035 1.2 11.4 0.0 0.0 0 11.255 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.74 14.84 2.10 1.118 13.085 573.758 0.019 12.97 15.47 2.50 1.206 13.303 573.758 0.018 Individual atomic B min max mean iso aniso Overall: 5.15 73.02 14.97 1.40 435 3274 Protein: 5.15 40.76 11.00 1.40 0 2902 Water: 6.35 73.02 29.25 N/A 435 370 Other: 16.07 30.42 23.25 N/A 0 2 Chain A: 5.38 60.45 13.03 N/A 0 1626 Chain B: 5.15 73.02 12.76 N/A 0 1648 Chain S: 11.47 64.08 30.56 N/A 435 0 Histogram: Values Number of atoms 5.15 - 11.94 2149 11.94 - 18.72 652 18.72 - 25.51 327 25.51 - 32.30 264 32.30 - 39.08 149 39.08 - 45.87 108 45.87 - 52.66 39 52.66 - 59.44 16 59.44 - 66.23 4 66.23 - 73.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1547 r_work=0.1296 r_free=0.1543 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1543 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1281 r_free = 0.1530 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1530 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015701 | | target function (ls_wunit_k1) not normalized (work): 2940.756513 | | target function (ls_wunit_k1) not normalized (free): 112.453681 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1530 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1470 0.1468 0.1607 n_refl.: 191136 remove outliers: r(all,work,free)=0.1470 0.1468 0.1607 n_refl.: 191136 overall B=0.15 to atoms: r(all,work,free)=0.1492 0.1490 0.1617 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1277 0.1272 0.1518 n_refl.: 191136 remove outliers: r(all,work,free)=0.1277 0.1272 0.1518 n_refl.: 191136 ======================== 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 0.3675 398.008 370.385 0.460 1.002 0.287 13.296-10.522 99.01 99 1 0.2087 528.187 518.962 0.704 1.003 0.243 10.503-8.327 98.90 177 3 0.1733 564.205 561.775 0.850 1.003 0.220 8.318-6.595 100.00 360 8 0.1763 414.736 410.998 0.873 1.003 0.160 6.588-5.215 100.00 711 7 0.1592 381.101 372.917 0.853 1.003 0.160 5.214-4.128 98.38 1367 28 0.0935 557.435 554.814 0.938 1.004 0.064 4.126-3.266 94.74 2603 46 0.0860 508.132 503.904 1.003 1.005 0.024 3.266-2.585 99.86 5447 97 0.0934 342.774 340.225 0.985 1.004 0.010 2.585-2.046 97.45 10613 204 0.0945 258.603 256.419 0.996 1.005 0.000 2.046-1.619 99.39 21536 464 0.1071 153.054 151.398 1.013 1.005 0.000 1.619-1.281 98.00 42464 925 0.1266 82.395 81.430 1.006 1.006 0.000 1.281-0.980 96.53 101826 2055 0.1868 44.202 42.143 0.983 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0331 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1272 r_free=0.1518 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1272 r_free=0.1518 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1272 r_free=0.1518 | n_water=805 | time (s): 3.180 (total time: 3.180) Filter (dist) r_work=0.1274 r_free=0.1521 | n_water=800 | time (s): 105.760 (total time: 108.940) Filter (q & B) r_work=0.1275 r_free=0.1522 | n_water=794 | time (s): 4.870 (total time: 113.810) Compute maps r_work=0.1275 r_free=0.1522 | n_water=794 | time (s): 1.760 (total time: 115.570) Filter (map) r_work=0.1296 r_free=0.1511 | n_water=665 | time (s): 5.380 (total time: 120.950) Find peaks r_work=0.1296 r_free=0.1511 | n_water=665 | time (s): 0.830 (total time: 121.780) Add new water r_work=0.1322 r_free=0.1544 | n_water=986 | time (s): 4.920 (total time: 126.700) Refine new water occ: r_work=0.1278 r_free=0.1498 adp: r_work=0.1266 r_free=0.1491 occ: r_work=0.1268 r_free=0.1489 adp: r_work=0.1262 r_free=0.1485 occ: r_work=0.1263 r_free=0.1483 adp: r_work=0.1263 r_free=0.1483 ADP+occupancy (water only), MIN, final r_work=0.1263 r_free=0.1483 r_work=0.1263 r_free=0.1483 | n_water=986 | time (s): 120.060 (total time: 246.760) Filter (q & B) r_work=0.1266 r_free=0.1486 | n_water=909 | time (s): 4.480 (total time: 251.240) Filter (dist only) r_work=0.1266 r_free=0.1485 | n_water=908 | time (s): 114.640 (total time: 365.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.361867 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.623508 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 0.1248 0.1499 0.0251 0.038 1.1 15.8 0.0 0.3 0 11.681 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.48 14.99 2.51 2.040 15.063 571.624 0.014 12.31 14.96 2.65 2.406 15.186 571.624 0.014 Individual atomic B min max mean iso aniso Overall: 5.45 71.07 16.25 1.19 539 3273 Protein: 5.45 40.00 10.98 1.19 0 2902 Water: 6.64 71.07 33.08 N/A 539 369 Other: 16.33 33.22 24.77 N/A 0 2 Chain A: 5.55 57.00 13.00 N/A 0 1625 Chain B: 5.45 68.16 12.79 N/A 0 1648 Chain S: 12.35 71.07 36.60 N/A 539 0 Histogram: Values Number of atoms 5.45 - 12.01 2127 12.01 - 18.57 681 18.57 - 25.13 266 25.13 - 31.70 238 31.70 - 38.26 189 38.26 - 44.82 167 44.82 - 51.38 87 51.38 - 57.94 32 57.94 - 64.51 21 64.51 - 71.07 4 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1496 r_work=0.1231 r_free=0.1498 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1498 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 = 0.1225 r_free = 0.1495 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1495 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013331 | | target function (ls_wunit_k1) not normalized (work): 2496.857560 | | target function (ls_wunit_k1) not normalized (free): 97.995389 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1225 0.1495 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1433 0.1431 0.1577 n_refl.: 191136 remove outliers: r(all,work,free)=0.1433 0.1431 0.1577 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1576 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1232 0.1501 n_refl.: 191136 remove outliers: r(all,work,free)=0.1237 0.1232 0.1501 n_refl.: 191136 ======================== 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 0.3207 398.008 376.020 0.489 0.963 0.277 13.296-10.522 99.01 99 1 0.1925 528.187 519.940 0.754 0.964 0.228 10.503-8.327 98.90 177 3 0.1406 564.205 566.047 0.921 0.964 0.184 8.318-6.595 100.00 360 8 0.1513 414.736 412.913 0.935 0.963 0.149 6.588-5.215 100.00 711 7 0.1376 381.101 376.398 0.911 0.963 0.130 5.214-4.128 98.38 1367 28 0.0824 557.435 555.632 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0762 508.132 505.441 1.059 0.963 0.019 3.266-2.585 99.86 5447 97 0.0857 342.774 341.361 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0895 258.603 256.774 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1040 153.054 151.640 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.347 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.213 1.059 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0588 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1501 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1501 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1501 | n_water=908 | time (s): 2.730 (total time: 2.730) Filter (dist) r_work=0.1234 r_free=0.1503 | n_water=903 | time (s): 121.600 (total time: 124.330) Filter (q & B) r_work=0.1234 r_free=0.1503 | n_water=900 | time (s): 5.220 (total time: 129.550) Compute maps r_work=0.1234 r_free=0.1503 | n_water=900 | time (s): 2.150 (total time: 131.700) Filter (map) r_work=0.1271 r_free=0.1513 | n_water=728 | time (s): 4.790 (total time: 136.490) Find peaks r_work=0.1271 r_free=0.1513 | n_water=728 | time (s): 0.920 (total time: 137.410) Add new water r_work=0.1292 r_free=0.1538 | n_water=1030 | time (s): 4.400 (total time: 141.810) Refine new water occ: r_work=0.1248 r_free=0.1501 adp: r_work=0.1248 r_free=0.1501 occ: r_work=0.1245 r_free=0.1500 adp: r_work=0.1245 r_free=0.1501 occ: r_work=0.1242 r_free=0.1500 adp: r_work=0.1241 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1500 r_work=0.1241 r_free=0.1500 | n_water=1030 | time (s): 312.150 (total time: 453.960) Filter (q & B) r_work=0.1246 r_free=0.1504 | n_water=908 | time (s): 5.080 (total time: 459.040) Filter (dist only) r_work=0.1246 r_free=0.1504 | n_water=907 | time (s): 116.190 (total time: 575.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.709478 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.848631 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1236 0.1432 0.0196 0.035 1.1 6.8 0.0 0.0 0 0.855 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.36 14.32 1.96 1.925 14.659 15.849 3.939 12.30 13.91 1.61 2.265 14.552 15.849 3.896 Individual atomic B min max mean iso aniso Overall: 5.50 67.59 15.38 1.03 540 3271 Protein: 5.50 35.74 10.70 1.03 0 2902 Water: 6.69 67.59 30.31 N/A 540 367 Other: 14.03 28.58 21.31 N/A 0 2 Chain A: 5.55 55.70 12.72 N/A 0 1624 Chain B: 5.50 67.59 12.48 N/A 0 1647 Chain S: 14.11 61.37 32.21 N/A 540 0 Histogram: Values Number of atoms 5.50 - 11.71 2117 11.71 - 17.92 703 17.92 - 24.13 301 24.13 - 30.33 241 30.33 - 36.54 193 36.54 - 42.75 147 42.75 - 48.96 74 48.96 - 55.17 24 55.17 - 61.38 10 61.38 - 67.59 1 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1391 r_work=0.1231 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1392 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1387 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890416 | | target function (ml) not normalized (work): 728655.459663 | | target function (ml) not normalized (free): 15214.742540 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1225 0.1386 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1435 0.1434 0.1492 n_refl.: 191136 remove outliers: r(all,work,free)=0.1435 0.1434 0.1492 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1428 0.1428 0.1488 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1222 0.1382 n_refl.: 191136 remove outliers: r(all,work,free)=0.1225 0.1222 0.1382 n_refl.: 191135 ======================== 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 0.3792 398.895 352.112 0.415 0.947 0.250 13.296-10.522 99.01 99 1 0.2497 528.187 507.158 0.712 0.948 0.234 10.503-8.327 98.90 177 3 0.1935 564.205 562.980 0.879 0.948 0.220 8.318-6.595 100.00 360 8 0.2024 414.736 410.128 0.898 0.948 0.120 6.588-5.215 100.00 711 7 0.1823 381.101 370.578 0.886 0.948 0.120 5.214-4.128 98.38 1367 28 0.1154 557.435 552.063 0.972 0.948 0.070 4.126-3.266 94.74 2603 46 0.1092 508.132 501.131 1.031 0.949 0.009 3.266-2.585 99.86 5447 97 0.1085 342.774 339.164 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0965 258.603 255.794 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0965 153.054 151.451 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.508 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.317 1.038 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1042 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1382 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1382 | n_water=907 | time (s): 2.630 (total time: 2.630) Filter (dist) r_work=0.1239 r_free=0.1403 | n_water=903 | time (s): 112.330 (total time: 114.960) Filter (q & B) r_work=0.1239 r_free=0.1402 | n_water=894 | time (s): 4.280 (total time: 119.240) Compute maps r_work=0.1239 r_free=0.1402 | n_water=894 | time (s): 1.790 (total time: 121.030) Filter (map) r_work=0.1258 r_free=0.1399 | n_water=754 | time (s): 5.410 (total time: 126.440) Find peaks r_work=0.1258 r_free=0.1399 | n_water=754 | time (s): 0.550 (total time: 126.990) Add new water r_work=0.1271 r_free=0.1421 | n_water=975 | time (s): 5.060 (total time: 132.050) Refine new water occ: r_work=0.1238 r_free=0.1392 adp: r_work=0.1238 r_free=0.1392 occ: r_work=0.1235 r_free=0.1390 adp: r_work=0.1235 r_free=0.1390 occ: r_work=0.1233 r_free=0.1388 adp: r_work=0.1232 r_free=0.1388 ADP+occupancy (water only), MIN, final r_work=0.1232 r_free=0.1388 r_work=0.1232 r_free=0.1388 | n_water=975 | time (s): 233.470 (total time: 365.520) Filter (q & B) r_work=0.1236 r_free=0.1388 | n_water=903 | time (s): 4.480 (total time: 370.000) Filter (dist only) r_work=0.1237 r_free=0.1387 | n_water=902 | time (s): 112.010 (total time: 482.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.607555 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.808370 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1237 0.1396 0.0158 0.036 1.1 6.1 0.0 0.3 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 13.96 1.58 1.814 14.276 14.808 3.895 12.35 13.99 1.63 1.891 14.243 14.808 3.889 Individual atomic B min max mean iso aniso Overall: 5.53 67.25 15.14 0.97 536 3270 Protein: 5.53 32.97 10.64 0.97 0 2902 Water: 6.70 67.25 29.61 N/A 536 366 Other: 13.92 27.95 20.94 N/A 0 2 Chain A: 5.56 54.85 12.61 N/A 0 1623 Chain B: 5.53 67.25 12.40 N/A 0 1647 Chain S: 13.84 61.32 31.24 N/A 536 0 Histogram: Values Number of atoms 5.53 - 11.70 2121 11.70 - 17.88 727 17.88 - 24.05 298 24.05 - 30.22 232 30.22 - 36.39 185 36.39 - 42.56 148 42.56 - 48.74 67 48.74 - 54.91 21 54.91 - 61.08 5 61.08 - 67.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1399 r_work=0.1235 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1399 target_work(ml) = 3.889 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1233 r_free = 0.1395 target_work(ml) = 3.887 | | 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.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1233 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.887010 | | target function (ml) not normalized (work): 728013.600710 | | target function (ml) not normalized (free): 15217.201101 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1233 0.1395 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1432 0.1431 0.1506 n_refl.: 191135 remove outliers: r(all,work,free)=0.1432 0.1431 0.1506 n_refl.: 191135 overall B=-0.04 to atoms: r(all,work,free)=0.1425 0.1423 0.1502 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1232 0.1387 n_refl.: 191135 remove outliers: r(all,work,free)=0.1234 0.1231 0.1387 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3833 356.816 324.705 0.375 0.949 0.179 13.296-10.522 99.01 99 1 0.2543 478.466 455.973 0.689 0.951 0.175 10.503-8.327 97.80 175 3 0.2055 502.108 504.414 0.883 0.951 0.172 8.318-6.595 100.00 360 8 0.2102 375.695 370.159 0.891 0.950 0.120 6.588-5.215 100.00 711 7 0.1894 345.226 335.001 0.884 0.950 0.120 5.214-4.128 98.38 1367 28 0.1199 504.961 499.668 0.972 0.951 0.090 4.126-3.266 94.74 2603 46 0.1132 460.299 453.251 1.031 0.951 0.014 3.266-2.585 99.86 5447 97 0.1139 310.507 307.048 1.018 0.951 0.000 2.585-2.046 97.45 10613 204 0.0979 234.260 231.706 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0971 138.646 137.188 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.1032 74.639 73.868 1.050 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1679 40.041 38.339 1.035 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1302 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1386 | n_water=902 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1231 r_free=0.1386 | n_water=901 | time (s): 114.060 (total time: 116.710) Filter (q & B) r_work=0.1231 r_free=0.1387 | n_water=892 | time (s): 5.370 (total time: 122.080) Compute maps r_work=0.1231 r_free=0.1387 | n_water=892 | time (s): 2.170 (total time: 124.250) Filter (map) r_work=0.1248 r_free=0.1388 | n_water=782 | time (s): 5.390 (total time: 129.640) Find peaks r_work=0.1248 r_free=0.1388 | n_water=782 | time (s): 0.730 (total time: 130.370) Add new water r_work=0.1261 r_free=0.1400 | n_water=996 | time (s): 4.200 (total time: 134.570) Refine new water occ: r_work=0.1211 r_free=0.1351 adp: r_work=0.1200 r_free=0.1342 occ: r_work=0.1198 r_free=0.1343 adp: r_work=0.1198 r_free=0.1343 occ: r_work=0.1198 r_free=0.1343 adp: r_work=0.1198 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1343 r_work=0.1198 r_free=0.1343 | n_water=996 | time (s): 180.620 (total time: 315.190) Filter (q & B) r_work=0.1203 r_free=0.1355 | n_water=889 | time (s): 4.270 (total time: 319.460) Filter (dist only) r_work=0.1203 r_free=0.1354 | n_water=887 | time (s): 117.840 (total time: 437.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.562758 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.823175 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1203 0.1354 0.0151 0.036 1.1 5.3 0.0 0.3 0 0.781 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.03 13.54 1.51 1.779 14.040 15.823 3.769 12.01 13.55 1.54 1.885 14.013 15.823 3.761 Individual atomic B min max mean iso aniso Overall: 5.51 66.53 14.82 0.95 522 3269 Protein: 5.51 30.82 10.56 0.95 0 2902 Water: 5.81 66.53 28.73 N/A 522 365 Other: 13.82 25.70 19.76 N/A 0 2 Chain A: 5.59 53.08 12.47 N/A 0 1622 Chain B: 5.51 66.53 12.29 N/A 0 1647 Chain S: 5.81 61.32 30.06 N/A 522 0 Histogram: Values Number of atoms 5.51 - 11.62 2111 11.62 - 17.72 753 17.72 - 23.82 319 23.82 - 29.92 216 29.92 - 36.02 171 36.02 - 42.12 132 42.12 - 48.22 60 48.22 - 54.32 21 54.32 - 60.43 6 60.43 - 66.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1355 r_work=0.1201 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1355 target_work(ml) = 3.761 | | 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: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (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): 3.760203 | | target function (ml) not normalized (work): 704252.129522 | | target function (ml) not normalized (free): 14742.233910 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1354 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1488 n_refl.: 191132 remove outliers: r(all,work,free)=0.1406 0.1404 0.1488 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1398 0.1396 0.1482 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191132 remove outliers: r(all,work,free)=0.1201 0.1197 0.1355 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 0.3757 356.816 320.916 0.384 0.948 0.200 13.296-10.522 97.03 97 1 0.2455 481.386 451.739 0.684 0.949 0.167 10.503-8.327 97.80 175 3 0.2112 502.108 495.771 0.867 0.949 0.146 8.318-6.595 100.00 360 8 0.2125 375.695 368.599 0.892 0.949 0.112 6.588-5.215 100.00 711 7 0.1929 345.226 335.176 0.884 0.949 0.097 5.214-4.128 98.38 1367 28 0.1208 504.961 500.176 0.971 0.950 0.034 4.126-3.266 94.74 2603 46 0.1130 460.299 453.302 1.032 0.950 0.000 3.266-2.585 99.86 5447 97 0.1105 310.507 307.221 1.020 0.950 0.000 2.585-2.046 97.45 10613 204 0.0944 234.260 231.848 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0915 138.646 137.348 1.054 0.951 0.000 1.619-1.281 98.00 42464 925 0.0977 74.639 73.946 1.049 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1656 40.041 38.376 1.033 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1343 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1355 | n_water=887 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1212 r_free=0.1370 | n_water=886 | time (s): 108.320 (total time: 111.030) Filter (q & B) r_work=0.1213 r_free=0.1369 | n_water=877 | time (s): 4.430 (total time: 115.460) Compute maps r_work=0.1213 r_free=0.1369 | n_water=877 | time (s): 1.750 (total time: 117.210) Filter (map) r_work=0.1229 r_free=0.1374 | n_water=792 | time (s): 4.410 (total time: 121.620) Find peaks r_work=0.1229 r_free=0.1374 | n_water=792 | time (s): 0.800 (total time: 122.420) Add new water r_work=0.1238 r_free=0.1384 | n_water=998 | time (s): 5.210 (total time: 127.630) Refine new water occ: r_work=0.1198 r_free=0.1345 adp: r_work=0.1193 r_free=0.1342 occ: r_work=0.1191 r_free=0.1342 adp: r_work=0.1191 r_free=0.1341 occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1190 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1341 r_work=0.1190 r_free=0.1341 | n_water=998 | time (s): 223.240 (total time: 350.870) Filter (q & B) r_work=0.1195 r_free=0.1350 | n_water=905 | time (s): 4.930 (total time: 355.800) Filter (dist only) r_work=0.1195 r_free=0.1349 | n_water=904 | time (s): 115.390 (total time: 471.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.473142 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.946055 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 0.1359 0.0161 0.037 1.1 5.6 0.0 0.3 0 0.737 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.59 1.61 1.750 13.971 13.946 3.761 12.01 13.61 1.60 1.756 13.971 13.946 3.761 Individual atomic B min max mean iso aniso Overall: 5.57 66.37 14.83 0.92 539 3269 Protein: 5.57 30.44 10.53 0.92 0 2902 Water: 5.90 66.37 28.61 N/A 539 365 Other: 13.78 25.54 19.66 N/A 0 2 Chain A: 5.67 52.74 12.43 N/A 0 1622 Chain B: 5.57 66.37 12.25 N/A 0 1647 Chain S: 5.90 61.29 29.92 N/A 539 0 Histogram: Values Number of atoms 5.57 - 11.65 2131 11.65 - 17.73 742 17.73 - 23.81 309 23.81 - 29.89 239 29.89 - 35.97 169 35.97 - 42.05 129 42.05 - 48.13 61 48.13 - 54.21 21 54.21 - 60.29 5 60.29 - 66.37 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1361 r_work=0.1201 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1362 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1362 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760356 | | target function (ml) not normalized (work): 704273.222851 | | target function (ml) not normalized (free): 14743.790020 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1362 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1505 n_refl.: 191130 remove outliers: r(all,work,free)=0.1404 0.1403 0.1505 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1368 0.1366 0.1480 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1360 n_refl.: 191130 remove outliers: r(all,work,free)=0.1202 0.1198 0.1360 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3830 356.816 318.367 0.384 0.951 0.194 13.296-10.522 96.04 96 1 0.2368 480.505 452.360 0.703 0.952 0.145 10.503-8.327 97.80 175 3 0.2181 502.108 494.782 0.884 0.953 0.127 8.318-6.595 100.00 360 8 0.2126 375.695 369.474 0.911 0.952 0.105 6.588-5.215 100.00 711 7 0.1921 345.226 335.137 0.905 0.952 0.100 5.214-4.128 98.38 1367 28 0.1203 504.961 500.245 0.993 0.953 0.020 4.126-3.266 94.74 2603 46 0.1137 460.299 453.088 1.055 0.953 0.000 3.266-2.585 99.86 5447 97 0.1111 310.507 307.222 1.039 0.952 0.000 2.585-2.046 97.45 10613 204 0.0950 234.260 231.796 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0917 138.646 137.353 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0973 74.639 73.946 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.041 38.367 1.024 0.949 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=0.1199 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=904 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1199 r_free=0.1360 | n_water=904 | time (s): 108.080 (total time: 110.630) Filter (q & B) r_work=0.1200 r_free=0.1358 | n_water=892 | time (s): 4.200 (total time: 114.830) Compute maps r_work=0.1200 r_free=0.1358 | n_water=892 | time (s): 1.860 (total time: 116.690) Filter (map) r_work=0.1218 r_free=0.1358 | n_water=796 | time (s): 5.000 (total time: 121.690) Find peaks r_work=0.1218 r_free=0.1358 | n_water=796 | time (s): 0.540 (total time: 122.230) Add new water r_work=0.1225 r_free=0.1370 | n_water=1007 | time (s): 4.880 (total time: 127.110) Refine new water occ: r_work=0.1194 r_free=0.1344 adp: r_work=0.1194 r_free=0.1345 occ: r_work=0.1192 r_free=0.1343 adp: r_work=0.1192 r_free=0.1344 occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1343 r_work=0.1191 r_free=0.1343 | n_water=1007 | time (s): 290.370 (total time: 417.480) Filter (q & B) r_work=0.1195 r_free=0.1354 | n_water=927 | time (s): 4.990 (total time: 422.470) Filter (dist only) r_work=0.1196 r_free=0.1353 | n_water=925 | time (s): 118.490 (total time: 540.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.573604 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.599364 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 0.1358 0.0161 0.037 1.1 7.8 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.58 1.61 1.734 13.832 14.599 3.760 11.99 13.62 1.63 1.803 13.810 14.599 3.758 Individual atomic B min max mean iso aniso Overall: 5.41 65.26 14.72 0.89 560 3269 Protein: 5.41 28.95 10.27 0.89 0 2902 Water: 5.79 65.26 28.69 N/A 560 365 Other: 13.68 23.28 18.48 N/A 0 2 Chain A: 5.48 50.70 12.13 N/A 0 1622 Chain B: 5.41 65.26 11.97 N/A 0 1647 Chain S: 5.79 58.60 30.32 N/A 560 0 Histogram: Values Number of atoms 5.41 - 11.39 2110 11.39 - 17.38 772 17.38 - 23.36 286 23.36 - 29.35 228 29.35 - 35.33 192 35.33 - 41.32 140 41.32 - 47.30 67 47.30 - 53.29 28 53.29 - 59.27 5 59.27 - 65.26 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1362 r_work=0.1199 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 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 = 0.1197 r_free = 0.1362 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757943 | | target function (ml) not normalized (work): 703817.611461 | | target function (ml) not normalized (free): 14741.812520 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1366 0.1364 0.1484 n_refl.: 191129 remove outliers: r(all,work,free)=0.1366 0.1364 0.1484 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1373 0.1371 0.1489 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1191 0.1188 0.1351 n_refl.: 191127 ======================== 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 90.10 88 3 0.3662 356.257 309.007 0.320 0.985 0.090 13.296-10.522 96.04 96 1 0.2368 480.505 458.405 0.686 0.986 0.108 10.503-8.327 97.80 175 3 0.2141 502.108 494.795 0.863 0.987 0.107 8.318-6.595 100.00 360 8 0.2117 375.695 369.591 0.885 0.986 0.088 6.588-5.215 100.00 711 7 0.1907 345.226 334.893 0.880 0.987 0.070 5.214-4.128 98.38 1367 28 0.1196 504.961 499.695 0.970 0.988 0.020 4.126-3.266 94.74 2603 46 0.1142 460.299 452.574 1.030 0.989 0.000 3.266-2.585 99.86 5447 97 0.1113 310.507 306.976 1.013 0.989 0.000 2.585-2.046 97.45 10613 204 0.0953 234.260 231.688 1.022 0.991 0.000 2.046-1.619 99.39 21536 464 0.0911 138.646 137.294 1.037 0.994 0.000 1.619-1.281 98.00 42464 925 0.0953 74.639 73.989 1.026 0.998 0.000 1.281-0.980 96.53 101826 2055 0.1631 40.041 38.350 0.991 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0615 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1351 | n_water=925 | time (s): 2.420 (total time: 2.420) Filter (dist) r_work=0.1202 r_free=0.1367 | n_water=924 | time (s): 114.710 (total time: 117.130) Filter (q & B) r_work=0.1203 r_free=0.1367 | n_water=913 | time (s): 4.310 (total time: 121.440) Compute maps r_work=0.1203 r_free=0.1367 | n_water=913 | time (s): 2.180 (total time: 123.620) Filter (map) r_work=0.1222 r_free=0.1363 | n_water=805 | time (s): 5.820 (total time: 129.440) Find peaks r_work=0.1222 r_free=0.1363 | n_water=805 | time (s): 0.620 (total time: 130.060) Add new water r_work=0.1228 r_free=0.1371 | n_water=1018 | time (s): 4.880 (total time: 134.940) Refine new water occ: r_work=0.1189 r_free=0.1341 adp: r_work=0.1184 r_free=0.1335 occ: r_work=0.1182 r_free=0.1335 adp: r_work=0.1182 r_free=0.1335 occ: r_work=0.1182 r_free=0.1335 adp: r_work=0.1182 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1335 r_work=0.1182 r_free=0.1335 | n_water=1018 | time (s): 278.650 (total time: 413.590) Filter (q & B) r_work=0.1190 r_free=0.1348 | n_water=891 | time (s): 5.270 (total time: 418.860) Filter (dist only) r_work=0.1191 r_free=0.1346 | n_water=889 | time (s): 114.050 (total time: 532.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.525964 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.926013 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1354 0.0160 0.038 1.1 4.8 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.54 1.60 1.686 13.684 13.926 3.758 11.96 13.57 1.60 1.719 13.674 13.926 3.757 Individual atomic B min max mean iso aniso Overall: 5.50 64.40 14.52 0.87 524 3269 Protein: 5.50 28.28 10.32 0.87 0 2902 Water: 5.90 64.40 28.23 N/A 524 365 Other: 13.75 22.38 18.06 N/A 0 2 Chain A: 5.57 50.53 12.15 N/A 0 1622 Chain B: 5.50 64.40 12.00 N/A 0 1647 Chain S: 5.90 58.66 29.79 N/A 524 0 Histogram: Values Number of atoms 5.50 - 11.39 2083 11.39 - 17.28 800 17.28 - 23.17 298 23.17 - 29.06 208 29.06 - 34.95 177 34.95 - 40.84 109 40.84 - 46.73 83 46.73 - 52.62 28 52.62 - 58.51 5 58.51 - 64.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1357 r_work=0.1197 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757197 | | target function (ml) not normalized (work): 703670.372404 | | target function (ml) not normalized (free): 14743.895828 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1358 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1376 0.1373 0.1509 n_refl.: 191127 remove outliers: r(all,work,free)=0.1376 0.1373 0.1509 n_refl.: 191127 overall B=0.01 to atoms: r(all,work,free)=0.1378 0.1375 0.1511 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191127 remove outliers: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191127 ======================== 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 90.10 88 3 0.3752 356.257 323.863 0.329 0.995 0.090 13.296-10.522 96.04 96 1 0.2368 480.505 459.482 0.680 0.996 0.120 10.503-8.327 97.80 175 3 0.2186 502.108 494.099 0.848 0.997 0.118 8.318-6.595 100.00 360 8 0.2170 375.695 368.350 0.873 0.997 0.100 6.588-5.215 100.00 711 7 0.1947 345.226 334.904 0.868 0.997 0.083 5.214-4.128 98.38 1367 28 0.1237 504.961 499.422 0.958 0.998 0.029 4.126-3.266 94.74 2603 46 0.1162 460.299 452.313 1.019 0.999 0.000 3.266-2.585 99.86 5447 97 0.1124 310.507 306.818 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0961 234.260 231.604 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0913 138.646 137.269 1.027 1.005 0.000 1.619-1.281 98.00 42464 925 0.0949 74.639 73.979 1.018 1.010 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.041 38.321 0.986 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0217 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1356 | n_water=889 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1208 r_free=0.1373 | n_water=886 | time (s): 112.280 (total time: 114.840) Filter (q & B) r_work=0.1208 r_free=0.1374 | n_water=878 | time (s): 5.300 (total time: 120.140) Compute maps r_work=0.1208 r_free=0.1374 | n_water=878 | time (s): 2.300 (total time: 122.440) Filter (map) r_work=0.1224 r_free=0.1365 | n_water=800 | time (s): 5.620 (total time: 128.060) Find peaks r_work=0.1224 r_free=0.1365 | n_water=800 | time (s): 0.560 (total time: 128.620) Add new water r_work=0.1230 r_free=0.1376 | n_water=1001 | time (s): 5.220 (total time: 133.840) Refine new water occ: r_work=0.1192 r_free=0.1345 adp: r_work=0.1187 r_free=0.1340 occ: r_work=0.1185 r_free=0.1338 adp: r_work=0.1185 r_free=0.1339 occ: r_work=0.1184 r_free=0.1338 adp: r_work=0.1184 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1338 r_work=0.1184 r_free=0.1338 | n_water=1001 | time (s): 290.560 (total time: 424.400) Filter (q & B) r_work=0.1189 r_free=0.1348 | n_water=922 | time (s): 4.860 (total time: 429.260) Filter (dist only) r_work=0.1189 r_free=0.1346 | n_water=920 | time (s): 121.910 (total time: 551.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.615050 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.322059 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1351 0.0159 0.038 1.1 6.5 0.0 0.3 0 0.808 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.51 1.59 1.681 13.784 14.322 3.756 11.91 13.53 1.63 1.692 13.777 14.322 3.754 Individual atomic B min max mean iso aniso Overall: 5.54 63.49 14.70 0.87 555 3269 Protein: 5.54 28.17 10.35 0.87 0 2902 Water: 5.99 63.49 28.41 N/A 555 365 Other: 13.81 22.26 18.04 N/A 0 2 Chain A: 5.65 50.36 12.14 N/A 0 1622 Chain B: 5.54 63.49 12.01 N/A 0 1647 Chain S: 5.99 58.69 30.14 N/A 555 0 Histogram: Values Number of atoms 5.54 - 11.34 2060 11.34 - 17.13 821 17.13 - 22.93 269 22.93 - 28.72 226 28.72 - 34.52 209 34.52 - 40.31 110 40.31 - 46.11 90 46.11 - 51.90 30 51.90 - 57.69 6 57.69 - 63.49 3 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1353 r_work=0.1191 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 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 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753917 | | target function (ml) not normalized (work): 703056.122476 | | target function (ml) not normalized (free): 14737.143815 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1189 0.1353 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1378 0.1375 0.1511 n_refl.: 191127 remove outliers: r(all,work,free)=0.1378 0.1375 0.1511 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1377 0.1375 0.1511 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1351 n_refl.: 191127 remove outliers: r(all,work,free)=0.1192 0.1189 0.1351 n_refl.: 191127 ======================== 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 90.10 88 3 0.3723 356.257 324.900 0.330 0.986 0.080 13.296-10.522 96.04 96 1 0.2381 480.505 459.277 0.683 0.987 0.103 10.503-8.327 97.80 175 3 0.2169 502.108 494.882 0.856 0.988 0.103 8.318-6.595 100.00 360 8 0.2119 375.695 369.307 0.880 0.988 0.088 6.588-5.215 100.00 711 7 0.1943 345.226 334.796 0.874 0.988 0.073 5.214-4.128 98.38 1367 28 0.1218 504.961 499.488 0.967 0.989 0.020 4.126-3.266 94.74 2603 46 0.1154 460.299 452.417 1.028 0.990 0.000 3.266-2.585 99.86 5447 97 0.1125 310.507 306.835 1.012 0.991 0.000 2.585-2.046 97.45 10613 204 0.0959 234.260 231.608 1.021 0.993 0.000 2.046-1.619 99.39 21536 464 0.0908 138.646 137.279 1.038 0.997 0.000 1.619-1.281 98.00 42464 925 0.0942 74.639 73.984 1.029 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.041 38.311 0.999 1.014 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0083 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1351 After: r_work=0.1190 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1351 | n_water=920 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1204 r_free=0.1370 | n_water=918 | time (s): 125.970 (total time: 129.200) Filter (q & B) r_work=0.1205 r_free=0.1369 | n_water=907 | time (s): 4.910 (total time: 134.110) Compute maps r_work=0.1205 r_free=0.1369 | n_water=907 | time (s): 1.770 (total time: 135.880) Filter (map) r_work=0.1223 r_free=0.1371 | n_water=808 | time (s): 4.670 (total time: 140.550) Find peaks r_work=0.1223 r_free=0.1371 | n_water=808 | time (s): 0.880 (total time: 141.430) Add new water r_work=0.1228 r_free=0.1379 | n_water=1016 | time (s): 4.900 (total time: 146.330) Refine new water occ: r_work=0.1189 r_free=0.1345 adp: r_work=0.1185 r_free=0.1340 occ: r_work=0.1183 r_free=0.1339 adp: r_work=0.1183 r_free=0.1339 occ: r_work=0.1183 r_free=0.1339 adp: r_work=0.1183 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1339 r_work=0.1183 r_free=0.1339 | n_water=1016 | time (s): 157.990 (total time: 304.320) Filter (q & B) r_work=0.1190 r_free=0.1351 | n_water=902 | time (s): 5.620 (total time: 309.940) Filter (dist only) r_work=0.1191 r_free=0.1350 | n_water=900 | time (s): 115.560 (total time: 425.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.548631 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.599230 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1352 0.0159 0.039 1.1 6.1 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.52 1.59 1.681 13.684 13.599 3.756 11.95 13.55 1.60 1.677 13.686 13.599 3.757 Individual atomic B min max mean iso aniso Overall: 5.56 63.19 14.53 0.85 535 3269 Protein: 5.56 28.05 10.36 0.85 0 2902 Water: 6.01 63.19 27.96 N/A 535 365 Other: 13.83 22.26 18.04 N/A 0 2 Chain A: 5.66 50.31 12.14 N/A 0 1622 Chain B: 5.56 63.19 12.01 N/A 0 1647 Chain S: 6.01 58.68 29.55 N/A 535 0 Histogram: Values Number of atoms 5.56 - 11.33 2058 11.33 - 17.09 827 17.09 - 22.85 297 22.85 - 28.61 214 28.61 - 34.38 173 34.38 - 40.14 103 40.14 - 45.90 90 45.90 - 51.66 32 51.66 - 57.43 7 57.43 - 63.19 3 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1355 r_work=0.1195 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1355 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1356 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756700 | | target function (ml) not normalized (work): 703577.238271 | | target function (ml) not normalized (free): 14739.684320 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1362 0.1456 5.6866 5.757| | 2: 2.94 - 2.33 1.00 7339 128 0.1070 0.1349 5.0733 5.1734| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1184 4.6607 4.7583| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1064 4.3962 4.5791| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.1004 4.1535 4.2495| | 6: 1.72 - 1.62 0.99 7102 142 0.0905 0.1076 3.9538 4.0862| | 7: 1.62 - 1.54 0.99 7104 148 0.0893 0.0969 3.8064 3.9392| | 8: 1.54 - 1.47 0.96 6798 152 0.0896 0.1318 3.7069 3.9169| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1117 3.6252 3.7571| | 10: 1.41 - 1.36 0.99 7022 150 0.0981 0.1195 3.5595 3.6705| | 11: 1.36 - 1.32 0.99 6997 151 0.0994 0.1116 3.4868 3.5743| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1117 3.4599 3.5781| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1258 3.4389 3.5706| | 14: 1.25 - 1.22 0.98 7015 112 0.1109 0.1594 3.4357 3.6859| | 15: 1.22 - 1.19 0.98 6956 137 0.1176 0.1249 3.4535 3.4964| | 16: 1.19 - 1.17 0.93 6604 132 0.1252 0.1557 3.4684 3.6639| | 17: 1.17 - 1.14 0.98 6940 135 0.1308 0.1260 3.4389 3.4571| | 18: 1.14 - 1.12 0.98 6875 142 0.1389 0.1706 3.4416 3.5361| | 19: 1.12 - 1.10 0.97 6948 106 0.1474 0.1745 3.4218 3.5973| | 20: 1.10 - 1.08 0.97 6884 147 0.1586 0.1593 3.4117 3.4417| | 21: 1.08 - 1.07 0.97 6852 152 0.1731 0.2133 3.4193 3.5015| | 22: 1.07 - 1.05 0.97 6836 135 0.1907 0.1961 3.4143 3.4159| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2014 3.4342 3.4831| | 24: 1.03 - 1.02 0.96 6784 133 0.2335 0.2240 3.4374 3.5095| | 25: 1.02 - 1.01 0.93 6552 130 0.2615 0.2515 3.45 3.5269| | 26: 1.01 - 0.99 0.96 6767 158 0.2760 0.2880 3.4166 3.4273| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2809 3.4697 3.3935| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7395 127 0.93 11.42 1.00 0.96 10866.24| | 2: 2.94 - 2.33 7339 128 0.93 12.67 0.99 0.95 5039.44| | 3: 2.33 - 2.04 6939 150 0.96 7.72 1.01 0.95 1726.36| | 4: 2.04 - 1.85 7170 155 0.96 7.75 1.00 0.96 1023.08| | 5: 1.85 - 1.72 7113 159 0.96 8.16 1.00 0.96 643.00| | 6: 1.72 - 1.62 7102 142 0.96 8.10 1.00 0.96 449.78| | 7: 1.62 - 1.54 7104 148 0.96 8.26 1.01 0.97 344.19| | 8: 1.54 - 1.47 6798 152 0.96 8.39 1.01 0.97 284.58| | 9: 1.47 - 1.41 6938 155 0.96 8.52 1.00 0.98 233.72| | 10: 1.41 - 1.36 7022 150 0.96 8.89 1.00 0.97 202.28| | 11: 1.36 - 1.32 6997 151 0.96 8.86 0.99 0.96 173.89| | 12: 1.32 - 1.28 6975 149 0.96 8.93 0.98 0.95 159.91| | 13: 1.28 - 1.25 6907 166 0.96 9.51 1.01 0.96 158.23| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.97 163.92| | 15: 1.22 - 1.19 6956 137 0.94 11.34 1.01 0.98 168.79| | 16: 1.19 - 1.17 6604 132 0.95 11.57 1.01 0.96 163.19| | 17: 1.17 - 1.14 6940 135 0.94 12.44 1.01 0.96 157.36| | 18: 1.14 - 1.12 6875 142 0.94 12.90 1.01 0.95 150.39| | 19: 1.12 - 1.10 6948 106 0.93 14.25 1.00 0.95 153.09| | 20: 1.10 - 1.08 6884 147 0.92 15.30 1.00 0.94 151.40| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.73| | 22: 1.07 - 1.05 6836 135 0.89 18.30 0.99 0.93 154.91| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.92 164.43| | 24: 1.03 - 1.02 6784 133 0.85 23.16 0.99 0.93 179.17| | 25: 1.02 - 1.01 6552 130 0.83 25.15 0.98 0.90 182.40| | 26: 1.01 - 0.99 6767 158 0.81 26.63 0.98 0.89 176.75| | 27: 0.99 - 0.98 6647 131 0.82 26.21 0.99 0.88 160.38| |alpha: min = 0.88 max = 0.98 mean = 0.95| |beta: min = 150.39 max = 10866.24 mean = 912.03| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.93 mean = 13.32| |phase err.(test): min = 0.00 max = 87.44 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1392 0.1390 0.1514 n_refl.: 191127 remove outliers: r(all,work,free)=0.1392 0.1390 0.1514 n_refl.: 191127 overall B=-0.01 to atoms: r(all,work,free)=0.1390 0.1388 0.1512 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1355 n_refl.: 191127 remove outliers: r(all,work,free)=0.1197 0.1194 0.1355 n_refl.: 191127 ======================== 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 90.10 88 3 0.3777 356.257 323.118 0.347 0.919 0.080 13.296-10.522 96.04 96 1 0.2379 480.505 458.466 0.721 0.920 0.103 10.503-8.327 97.80 175 3 0.2186 502.108 494.422 0.905 0.921 0.103 8.318-6.595 100.00 360 8 0.2154 375.695 368.772 0.931 0.921 0.088 6.588-5.215 100.00 711 7 0.1957 345.226 334.962 0.925 0.921 0.073 5.214-4.128 98.38 1367 28 0.1244 504.961 499.215 1.026 0.922 0.040 4.126-3.266 94.74 2603 46 0.1171 460.299 452.302 1.093 0.923 0.000 3.266-2.585 99.86 5447 97 0.1123 310.507 306.930 1.076 0.925 0.000 2.585-2.046 97.45 10613 204 0.0962 234.260 231.604 1.084 0.927 0.000 2.046-1.619 99.39 21536 464 0.0913 138.646 137.270 1.102 0.931 0.000 1.619-1.281 98.00 42464 925 0.0948 74.639 73.984 1.094 0.937 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.041 38.307 1.063 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0314 ================= 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 : 0.2035 0.1951 0.083 5.277 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1894 0.083 5.277 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1894 0.083 5.277 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1894 0.083 5.277 5.2 78.0 14.6 805 0.000 1_weight: 0.1800 0.1894 0.083 5.277 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1274 0.1484 0.035 1.163 5.2 78.0 14.6 805 0.140 1_adp: 0.1297 0.1547 0.035 1.163 5.1 73.0 15.0 805 0.140 1_regHadp: 0.1296 0.1543 0.035 1.163 5.1 73.0 15.0 805 0.140 1_occ: 0.1281 0.1530 0.035 1.163 5.1 73.0 15.0 805 0.140 2_bss: 0.1272 0.1518 0.035 1.163 5.3 73.2 15.1 805 0.140 2_settarget: 0.1272 0.1518 0.035 1.163 5.3 73.2 15.1 805 0.140 2_updatecdl: 0.1272 0.1518 0.035 1.183 5.3 73.2 15.1 805 0.140 2_nqh: 0.1272 0.1518 0.035 1.183 5.3 73.2 15.1 805 0.140 2_sol: 0.1266 0.1485 0.035 1.183 5.3 73.2 16.0 908 n/a 2_weight: 0.1266 0.1485 0.035 1.183 5.3 73.2 16.0 908 n/a 2_xyzrec: 0.1248 0.1499 0.038 1.145 5.3 73.2 16.0 908 n/a 2_adp: 0.1231 0.1496 0.038 1.145 5.4 71.1 16.2 908 n/a 2_regHadp: 0.1231 0.1498 0.038 1.145 5.4 71.1 16.2 908 n/a 2_occ: 0.1225 0.1495 0.038 1.145 5.4 71.1 16.2 908 n/a 3_bss: 0.1232 0.1501 0.038 1.145 5.4 71.0 16.2 908 n/a 3_settarget: 0.1232 0.1501 0.038 1.145 5.4 71.0 16.2 908 n/a 3_updatecdl: 0.1232 0.1501 0.038 1.148 5.4 71.0 16.2 908 n/a 3_nqh: 0.1232 0.1501 0.038 1.148 5.4 71.0 16.2 908 n/a 3_sol: 0.1246 0.1504 0.038 1.148 5.4 68.1 15.6 907 n/a 3_weight: 0.1246 0.1504 0.038 1.148 5.4 68.1 15.6 907 n/a 3_xyzrec: 0.1236 0.1432 0.035 1.100 5.4 68.1 15.6 907 n/a 3_adp: 0.1230 0.1391 0.035 1.100 5.5 67.6 15.4 907 n/a 3_regHadp: 0.1231 0.1392 0.035 1.100 5.5 67.6 15.4 907 n/a 3_occ: 0.1225 0.1387 0.035 1.100 5.5 67.6 15.4 907 n/a 4_bss: 0.1222 0.1382 0.035 1.100 5.5 67.6 15.3 907 n/a 4_settarget: 0.1222 0.1382 0.035 1.100 5.5 67.6 15.3 907 n/a 4_updatecdl: 0.1222 0.1382 0.035 1.103 5.5 67.6 15.3 907 n/a 4_nqh: 0.1222 0.1382 0.035 1.103 5.5 67.6 15.3 907 n/a 4_sol: 0.1237 0.1387 0.035 1.103 5.5 67.6 15.2 902 n/a 4_weight: 0.1237 0.1387 0.035 1.103 5.5 67.6 15.2 902 n/a 4_xyzrec: 0.1237 0.1396 0.036 1.121 5.5 67.6 15.2 902 n/a 4_adp: 0.1235 0.1399 0.036 1.121 5.5 67.3 15.1 902 n/a 4_regHadp: 0.1235 0.1399 0.036 1.121 5.5 67.3 15.1 902 n/a 4_occ: 0.1233 0.1395 0.036 1.121 5.5 67.3 15.1 902 n/a 5_bss: 0.1231 0.1386 0.036 1.121 5.5 67.2 15.1 902 n/a 5_settarget: 0.1231 0.1386 0.036 1.121 5.5 67.2 15.1 902 n/a 5_updatecdl: 0.1231 0.1386 0.036 1.121 5.5 67.2 15.1 902 n/a 5_nqh: 0.1231 0.1386 0.036 1.121 5.5 67.2 15.1 902 n/a 5_sol: 0.1203 0.1354 0.036 1.121 5.5 67.2 14.9 887 n/a 5_weight: 0.1203 0.1354 0.036 1.121 5.5 67.2 14.9 887 n/a 5_xyzrec: 0.1203 0.1354 0.036 1.121 5.5 67.2 14.9 887 n/a 5_adp: 0.1201 0.1355 0.036 1.121 5.5 66.5 14.8 887 n/a 5_regHadp: 0.1201 0.1355 0.036 1.121 5.5 66.5 14.8 887 n/a 5_occ: 0.1199 0.1354 0.036 1.121 5.5 66.5 14.8 887 n/a 6_bss: 0.1197 0.1355 0.036 1.121 5.5 66.5 14.8 887 n/a 6_settarget: 0.1197 0.1355 0.036 1.121 5.5 66.5 14.8 887 n/a 6_updatecdl: 0.1197 0.1355 0.036 1.121 5.5 66.5 14.8 887 n/a 6_nqh: 0.1197 0.1355 0.036 1.121 5.5 66.5 14.8 887 n/a 6_sol: 0.1195 0.1349 0.036 1.121 5.5 66.5 14.8 904 n/a 6_weight: 0.1195 0.1349 0.036 1.121 5.5 66.5 14.8 904 n/a 6_xyzrec: 0.1198 0.1359 0.037 1.122 5.5 66.5 14.8 904 n/a 6_adp: 0.1201 0.1361 0.037 1.122 5.6 66.4 14.8 904 n/a 6_regHadp: 0.1201 0.1362 0.037 1.122 5.6 66.4 14.8 904 n/a 6_occ: 0.1200 0.1362 0.037 1.122 5.6 66.4 14.8 904 n/a 7_bss: 0.1199 0.1360 0.037 1.122 5.3 66.1 14.6 904 n/a 7_settarget: 0.1199 0.1360 0.037 1.122 5.3 66.1 14.6 904 n/a 7_updatecdl: 0.1199 0.1360 0.037 1.122 5.3 66.1 14.6 904 n/a 7_nqh: 0.1199 0.1360 0.037 1.122 5.3 66.1 14.6 904 n/a 7_sol: 0.1196 0.1353 0.037 1.122 5.3 66.1 14.8 925 n/a 7_weight: 0.1196 0.1353 0.037 1.122 5.3 66.1 14.8 925 n/a 7_xyzrec: 0.1197 0.1358 0.037 1.127 5.3 66.1 14.8 925 n/a 7_adp: 0.1199 0.1362 0.037 1.127 5.4 65.3 14.7 925 n/a 7_regHadp: 0.1199 0.1362 0.037 1.127 5.4 65.3 14.7 925 n/a 7_occ: 0.1197 0.1362 0.037 1.127 5.4 65.3 14.7 925 n/a 8_bss: 0.1188 0.1351 0.037 1.127 5.5 65.3 14.8 925 n/a 8_settarget: 0.1188 0.1351 0.037 1.127 5.5 65.3 14.8 925 n/a 8_updatecdl: 0.1188 0.1351 0.037 1.126 5.5 65.3 14.8 925 n/a 8_nqh: 0.1188 0.1351 0.037 1.126 5.5 65.3 14.8 925 n/a 8_sol: 0.1191 0.1346 0.037 1.126 5.5 65.3 14.5 889 n/a 8_weight: 0.1191 0.1346 0.037 1.126 5.5 65.3 14.5 889 n/a 8_xyzrec: 0.1194 0.1354 0.038 1.119 5.5 65.3 14.5 889 n/a 8_adp: 0.1196 0.1357 0.038 1.119 5.5 64.4 14.5 889 n/a 8_regHadp: 0.1197 0.1357 0.038 1.119 5.5 64.4 14.5 889 n/a 8_occ: 0.1195 0.1358 0.038 1.119 5.5 64.4 14.5 889 n/a 9_bss: 0.1194 0.1356 0.038 1.119 5.5 64.4 14.5 889 n/a 9_settarget: 0.1194 0.1356 0.038 1.119 5.5 64.4 14.5 889 n/a 9_updatecdl: 0.1194 0.1356 0.038 1.119 5.5 64.4 14.5 889 n/a 9_nqh: 0.1194 0.1356 0.038 1.119 5.5 64.4 14.5 889 n/a 9_sol: 0.1189 0.1346 0.038 1.119 5.5 64.4 14.7 920 n/a 9_weight: 0.1189 0.1346 0.038 1.119 5.5 64.4 14.7 920 n/a 9_xyzrec: 0.1192 0.1351 0.038 1.126 5.5 64.4 14.7 920 n/a 9_adp: 0.1191 0.1353 0.038 1.126 5.5 63.5 14.7 920 n/a 9_regHadp: 0.1191 0.1354 0.038 1.126 5.5 63.5 14.7 920 n/a 9_occ: 0.1189 0.1353 0.038 1.126 5.5 63.5 14.7 920 n/a 10_bss: 0.1189 0.1351 0.038 1.126 5.5 63.5 14.7 920 n/a 10_settarget: 0.1189 0.1351 0.038 1.126 5.5 63.5 14.7 920 n/a 10_updatecdl: 0.1189 0.1351 0.038 1.127 5.5 63.5 14.7 920 n/a 10_setrh: 0.1190 0.1351 0.038 1.127 5.5 63.5 14.7 920 n/a 10_nqh: 0.1190 0.1351 0.038 1.127 5.5 63.5 14.7 920 n/a 10_sol: 0.1191 0.1350 0.038 1.127 5.5 63.5 14.5 900 n/a 10_weight: 0.1191 0.1350 0.038 1.127 5.5 63.5 14.5 900 n/a 10_xyzrec: 0.1193 0.1352 0.039 1.149 5.5 63.5 14.5 900 n/a 10_adp: 0.1195 0.1355 0.039 1.149 5.6 63.2 14.5 900 n/a 10_regHadp: 0.1195 0.1355 0.039 1.149 5.6 63.2 14.5 900 n/a 10_occ: 0.1195 0.1356 0.039 1.149 5.6 63.2 14.5 900 n/a end: 0.1194 0.1355 0.039 1.149 5.6 63.2 14.5 900 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3788076_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3788076_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.4000 Refinement macro-cycles (run) : 12286.9000 Write final files (write_after_run_outputs) : 147.2500 Total : 12441.5500 Total CPU time: 3.47 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:35 PST -0800 (1736736275.06 s) Start R-work = 0.1800, R-free = 0.1894 Final R-work = 0.1194, R-free = 0.1355 =============================================================================== Job complete usr+sys time: 12709.27 seconds wall clock time: 212 minutes 50.00 seconds (12770.00 seconds total)