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_3774798.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3774798.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3774798.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } 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: 1.93, per 1000 atoms: 0.29 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: 2.718 distance_ideal: 2.720 ideal - model: 0.002 slack: 0.000 delta_slack: 0.002 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: 2.728 distance_ideal: 2.710 ideal - model: -0.018 slack: 0.000 delta_slack: -0.018 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: 0.81 Conformation dependent library (CDL) restraints added in 210.4 milliseconds Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.04: 987 1.04 - 1.27: 2399 1.27 - 1.49: 1474 1.49 - 1.72: 1054 1.72 - 1.94: 20 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL B 150 " pdb=" CB VAL B 150 " ideal model delta sigma weight residual 1.541 1.777 -0.236 1.05e-02 9.07e+03 5.07e+02 bond pdb=" C LEU A 172 " pdb=" N VAL A 173 " ideal model delta sigma weight residual 1.332 1.147 0.184 8.70e-03 1.32e+04 4.50e+02 bond pdb=" CA ILE A 134 " pdb=" CB ILE A 134 " ideal model delta sigma weight residual 1.540 1.699 -0.159 7.70e-03 1.69e+04 4.28e+02 bond pdb=" CD2 HIS B 96 " pdb=" NE2 HIS B 96 " ideal model delta sigma weight residual 1.374 1.160 0.214 1.10e-02 8.26e+03 3.80e+02 bond pdb=" N GLY B 126 " pdb=" CA GLY B 126 " ideal model delta sigma weight residual 1.447 1.646 -0.199 1.03e-02 9.43e+03 3.72e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 5890 4.37 - 8.74: 3448 8.74 - 13.11: 1233 13.11 - 17.49: 213 17.49 - 21.86: 26 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA LYS A 77 " pdb=" C LYS A 77 " pdb=" O LYS A 77 " ideal model delta sigma weight residual 120.70 106.36 14.34 1.03e+00 9.43e-01 1.94e+02 angle pdb=" CA VAL B 145 " pdb=" C VAL B 145 " pdb=" O VAL B 145 " ideal model delta sigma weight residual 120.36 135.04 -14.68 1.06e+00 8.90e-01 1.92e+02 angle pdb=" O PHE B 164 " pdb=" C PHE B 164 " pdb=" N GLY B 165 " ideal model delta sigma weight residual 122.07 136.25 -14.18 1.03e+00 9.43e-01 1.89e+02 angle pdb=" O VAL A 102 " pdb=" C VAL A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 123.18 137.43 -14.25 1.05e+00 9.07e-01 1.84e+02 angle pdb=" ND1 HIS A 116 " pdb=" CE1 HIS A 116 " pdb=" NE2 HIS A 116 " ideal model delta sigma weight residual 108.40 95.00 13.40 1.00e+00 1.00e+00 1.80e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 1834 16.49 - 32.98: 140 32.98 - 49.47: 49 49.47 - 65.96: 22 65.96 - 82.45: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CB TRP A 146 " pdb=" CG TRP A 146 " pdb=" CD1 TRP A 146 " pdb=" HD1 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 26.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual 180.00 -155.67 -24.33 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -156.26 -23.74 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.225: 216 0.225 - 0.449: 147 0.449 - 0.673: 88 0.673 - 0.897: 34 0.897 - 1.121: 7 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA PRO B 115 " pdb=" N PRO B 115 " pdb=" C PRO B 115 " pdb=" CB PRO B 115 " both_signs ideal model delta sigma weight residual False 2.72 3.84 -1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CA VAL B 144 " pdb=" N VAL B 144 " pdb=" C VAL B 144 " pdb=" CB VAL B 144 " both_signs ideal model delta sigma weight residual False 2.44 3.49 -1.04 2.00e-01 2.50e+01 2.73e+01 chirality pdb=" CA MET B 124 " pdb=" N MET B 124 " pdb=" C MET B 124 " pdb=" CB MET B 124 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.68e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.166 2.00e-02 2.50e+03 6.66e-02 1.33e+02 pdb=" CG PHE B 164 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.073 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.034 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.041 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.068 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.046 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.043 2.00e-02 2.50e+03 5.69e-02 1.29e+02 pdb=" CG TRP B 139 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.017 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.042 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.069 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " 0.073 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.152 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.040 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.013 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.019 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " -0.070 2.00e-02 2.50e+03 6.36e-02 1.21e+02 pdb=" CG TYR A 192 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " 0.069 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " -0.124 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " 0.038 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " 0.049 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.064 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " 0.069 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " -0.060 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.61: 24 1.61 - 2.36: 2406 2.36 - 3.11: 22287 3.11 - 3.85: 32813 3.85 - 4.60: 52670 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110200 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.868 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.919 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.031 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.097 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.141 2.620 ... (remaining 110195 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_3774798_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= 0.2034 r_free= 0.1969 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299465 | | target function (ml) not normalized (work): 805345.631525 | | target function (ml) not normalized (free): 16552.344148 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2141 0.1861 6.6876 6.2969| | 2: 2.94 - 2.33 1.00 7339 128 0.1600 0.1488 5.5316 5.5663| | 3: 2.33 - 2.04 0.96 6939 150 0.1639 0.1573 5.1432 5.1662| | 4: 2.04 - 1.85 1.00 7170 155 0.1765 0.1702 4.9689 5.11| | 5: 1.85 - 1.72 0.99 7113 159 0.1900 0.1882 4.799 4.8948| | 6: 1.72 - 1.62 0.99 7102 142 0.1990 0.2033 4.6674 4.671| | 7: 1.62 - 1.54 0.99 7104 148 0.2032 0.1778 4.563 4.5583| | 8: 1.54 - 1.47 0.96 6798 152 0.2068 0.2179 4.4696 4.5233| | 9: 1.47 - 1.41 0.98 6938 155 0.2094 0.2150 4.4003 4.4203| | 10: 1.41 - 1.36 0.99 7022 150 0.2135 0.2132 4.3034 4.336| | 11: 1.36 - 1.32 0.99 6997 151 0.2088 0.1949 4.2377 4.2185| | 12: 1.32 - 1.28 0.98 6976 149 0.2048 0.2062 4.1716 4.2973| | 13: 1.28 - 1.25 0.98 6907 166 0.2012 0.2307 4.122 4.2719| | 14: 1.25 - 1.22 0.98 7015 113 0.2084 0.2467 4.0894 4.3222| | 15: 1.22 - 1.19 0.98 6957 137 0.2109 0.1935 4.0542 3.9469| | 16: 1.19 - 1.17 0.93 6604 132 0.2162 0.2226 4.0247 4.0766| | 17: 1.17 - 1.14 0.98 6941 135 0.2167 0.1873 3.9498 3.9748| | 18: 1.14 - 1.12 0.98 6875 142 0.2185 0.2351 3.9061 3.9517| | 19: 1.12 - 1.10 0.97 6949 106 0.2269 0.2441 3.8673 3.9629| | 20: 1.10 - 1.08 0.97 6884 147 0.2309 0.2290 3.824 3.8698| | 21: 1.08 - 1.07 0.97 6852 152 0.2423 0.2524 3.7791 3.7401| | 22: 1.07 - 1.05 0.97 6838 135 0.2584 0.2600 3.7527 3.7309| | 23: 1.05 - 1.03 0.97 6829 159 0.2733 0.2433 3.7304 3.7422| | 24: 1.03 - 1.02 0.96 6785 133 0.2869 0.2827 3.6909 3.7515| | 25: 1.02 - 1.01 0.93 6552 130 0.3088 0.3061 3.6771 3.7596| | 26: 1.01 - 0.99 0.96 6767 158 0.3201 0.3160 3.6278 3.5937| | 27: 0.99 - 0.98 0.94 6648 131 0.3375 0.3214 3.6336 3.5944| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.44 0.91 0.97 35069.51| | 2: 2.94 - 2.33 7339 128 0.86 21.05 1.08 1.02 14880.93| | 3: 2.33 - 2.04 6939 150 0.93 12.52 1.11 1.05 4171.08| | 4: 2.04 - 1.85 7170 155 0.92 14.05 1.11 1.06 2916.34| | 5: 1.85 - 1.72 7113 159 0.90 16.19 1.11 1.07 2222.53| | 6: 1.72 - 1.62 7102 142 0.90 16.86 1.12 1.08 1691.44| | 7: 1.62 - 1.54 7104 148 0.89 17.67 1.11 1.07 1333.05| | 8: 1.54 - 1.47 6798 152 0.89 18.24 1.11 1.06 1125.95| | 9: 1.47 - 1.41 6938 155 0.89 18.51 1.10 1.07 944.68| | 10: 1.41 - 1.36 7022 150 0.87 19.80 1.10 1.07 836.08| | 11: 1.36 - 1.32 6997 151 0.88 19.55 1.08 1.07 721.12| | 12: 1.32 - 1.28 6976 149 0.87 20.43 1.07 1.04 686.65| | 13: 1.28 - 1.25 6907 166 0.86 20.85 1.07 1.03 658.39| | 14: 1.25 - 1.22 7015 113 0.85 22.20 1.08 1.03 644.19| | 15: 1.22 - 1.19 6957 137 0.86 21.33 1.07 1.04 565.13| | 16: 1.19 - 1.17 6604 132 0.87 20.54 1.08 1.03 496.49| | 17: 1.17 - 1.14 6941 135 0.87 20.49 1.08 1.03 425.25| | 18: 1.14 - 1.12 6875 142 0.86 21.13 1.07 1.00 397.67| | 19: 1.12 - 1.10 6949 106 0.86 21.87 1.07 1.00 371.65| | 20: 1.10 - 1.08 6884 147 0.85 22.60 1.06 0.99 348.33| | 21: 1.08 - 1.07 6852 152 0.85 23.06 1.06 0.99 319.77| | 22: 1.07 - 1.05 6838 135 0.83 24.70 1.06 0.98 307.70| | 23: 1.05 - 1.03 6829 159 0.81 26.58 1.05 0.97 304.98| | 24: 1.03 - 1.02 6785 133 0.79 28.80 1.05 0.96 312.12| | 25: 1.02 - 1.01 6552 130 0.77 30.24 1.03 0.95 307.09| | 26: 1.01 - 0.99 6767 158 0.75 32.24 1.03 0.92 295.46| | 27: 0.99 - 0.98 6648 131 0.74 33.06 1.04 0.88 278.85| |alpha: min = 0.88 max = 1.08 mean = 1.02| |beta: min = 278.85 max = 35069.51 mean = 2816.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.59| |phase err.(test): min = 0.00 max = 89.75 mean = 21.86| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.238 2950 Z= 5.502 Angle : 5.226 19.297 4018 Z= 3.740 Chirality : 0.387 1.121 492 Planarity : 0.034 0.137 512 Dihedral : 13.168 82.448 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.78 % Allowed : 2.85 % Favored : 96.37 % Rotamer: Outliers : 1.29 % Allowed : 5.48 % Favored : 93.23 % Cbeta Deviations : 31.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.38), residues: 386 helix: -2.57 (0.32), residues: 144 sheet: -0.95 (0.52), residues: 86 loop : -0.29 (0.48), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.018 ARG B 143 TYR 0.147 0.039 TYR A 194 PHE 0.108 0.037 PHE B 164 TRP 0.094 0.036 TRP A 146 HIS 0.071 0.030 HIS B 96 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= 0.2034 r_free= 0.1969 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299465 | | target function (ml) not normalized (work): 805345.631525 | | target function (ml) not normalized (free): 16552.344148 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2032 0.2034 0.1969 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2032 0.2034 0.1969 n_refl.: 191155 remove outliers: r(all,work,free)=0.2032 0.2034 0.1969 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2034 0.2036 0.1970 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1801 0.1799 0.1904 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1797 0.1904 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4045 402.814 292.360 0.423 0.934 0.299 13.296-10.522 99.01 99 1 0.2505 528.187 519.216 0.765 0.934 0.248 10.503-8.327 99.45 178 3 0.2529 565.118 556.593 0.943 0.934 0.223 8.318-6.595 100.00 360 8 0.2466 414.736 403.020 0.949 0.934 0.170 6.588-5.215 100.00 711 7 0.2226 381.101 366.550 0.938 0.933 0.170 5.214-4.128 98.38 1367 28 0.1486 557.435 550.136 1.048 0.933 0.090 4.126-3.266 94.74 2603 46 0.1354 508.132 498.822 1.121 0.932 0.050 3.266-2.585 99.86 5447 97 0.1441 342.774 337.223 1.096 0.929 0.000 2.585-2.046 97.45 10613 204 0.1394 258.603 254.242 1.102 0.926 0.000 2.046-1.619 99.39 21536 464 0.1613 153.054 149.779 1.128 0.920 0.000 1.619-1.281 98.00 42464 925 0.1921 82.395 80.190 1.125 0.911 0.000 1.281-0.980 96.53 101826 2056 0.2316 44.203 41.653 1.122 0.894 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0173 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1904 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1797 r_free=0.1904 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.676928 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 578.695072 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 0.1268 0.1497 0.0229 0.039 1.2 11.2 0.0 0.3 0 11.338 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.68 14.97 2.29 1.118 13.122 578.695 0.018 12.94 15.63 2.69 1.226 13.321 578.695 0.017 Individual atomic B min max mean iso aniso Overall: 5.18 73.05 14.97 1.40 435 3274 Protein: 5.18 40.33 10.99 1.40 0 2902 Water: 6.34 73.05 29.30 N/A 435 370 Other: 15.94 29.59 22.76 N/A 0 2 Chain A: 5.36 59.82 13.03 N/A 0 1626 Chain B: 5.18 73.05 12.76 N/A 0 1648 Chain S: 11.73 63.21 30.60 N/A 435 0 Histogram: Values Number of atoms 5.18 - 11.97 2168 11.97 - 18.75 638 18.75 - 25.54 322 25.54 - 32.33 262 32.33 - 39.12 153 39.12 - 45.90 104 45.90 - 52.69 38 52.69 - 59.48 19 59.48 - 66.27 4 66.27 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1294 r_free=0.1563 r_work=0.1293 r_free=0.1558 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1293 r_free = 0.1558 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 = 0.1279 r_free = 0.1546 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1279 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015571 | | target function (ls_wunit_k1) not normalized (work): 2916.344110 | | target function (ls_wunit_k1) not normalized (free): 116.101508 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1284 0.1279 0.1546 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1466 0.1464 0.1629 n_refl.: 191139 remove outliers: r(all,work,free)=0.1466 0.1464 0.1629 n_refl.: 191139 overall B=0.16 to atoms: r(all,work,free)=0.1490 0.1487 0.1639 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1278 0.1273 0.1541 n_refl.: 191139 remove outliers: r(all,work,free)=0.1278 0.1273 0.1540 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3623 402.814 378.413 0.472 0.997 0.281 13.296-10.522 99.01 99 1 0.2110 528.187 522.004 0.718 0.999 0.255 10.503-8.327 99.45 178 3 0.1758 565.118 561.357 0.855 0.999 0.203 8.318-6.595 100.00 360 8 0.1723 414.736 411.436 0.878 0.998 0.160 6.588-5.215 100.00 711 7 0.1531 381.101 373.652 0.859 0.999 0.160 5.214-4.128 98.38 1367 28 0.0907 557.435 554.766 0.942 0.999 0.065 4.126-3.266 94.74 2603 46 0.0833 508.132 504.396 1.009 1.000 0.023 3.266-2.585 99.86 5447 97 0.0925 342.774 340.310 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.355 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1084 153.054 151.392 1.018 1.000 0.000 1.619-1.281 98.00 42464 925 0.1274 82.395 81.426 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.155 0.988 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0371 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1540 | n_water=805 | time (s): 2.980 (total time: 2.980) Filter (dist) r_work=0.1277 r_free=0.1544 | n_water=794 | time (s): 99.060 (total time: 102.040) Filter (q & B) r_work=0.1278 r_free=0.1543 | n_water=790 | time (s): 4.570 (total time: 106.610) Compute maps r_work=0.1278 r_free=0.1543 | n_water=790 | time (s): 2.280 (total time: 108.890) Filter (map) r_work=0.1304 r_free=0.1527 | n_water=651 | time (s): 5.250 (total time: 114.140) Find peaks r_work=0.1304 r_free=0.1527 | n_water=651 | time (s): 0.700 (total time: 114.840) Add new water r_work=0.1328 r_free=0.1554 | n_water=955 | time (s): 5.600 (total time: 120.440) Refine new water occ: r_work=0.1284 r_free=0.1504 adp: r_work=0.1270 r_free=0.1501 occ: r_work=0.1273 r_free=0.1499 adp: r_work=0.1266 r_free=0.1498 occ: r_work=0.1267 r_free=0.1497 adp: r_work=0.1264 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1264 r_free=0.1497 r_work=0.1264 r_free=0.1497 | n_water=955 | time (s): 81.910 (total time: 202.350) Filter (q & B) r_work=0.1268 r_free=0.1503 | n_water=887 | time (s): 5.390 (total time: 207.740) Filter (dist only) r_work=0.1268 r_free=0.1500 | n_water=885 | time (s): 109.980 (total time: 317.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.197683 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 595.184615 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 0.1252 0.1512 0.0260 0.041 1.2 16.1 0.0 0.3 0 12.099 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.12 2.60 2.040 15.203 595.185 0.014 12.31 15.05 2.73 2.388 15.254 595.185 0.014 Individual atomic B min max mean iso aniso Overall: 5.36 68.22 16.37 1.21 517 3272 Protein: 5.36 40.05 10.99 1.21 0 2902 Water: 6.63 68.22 34.00 N/A 517 368 Other: 16.24 32.62 24.43 N/A 0 2 Chain A: 5.55 56.20 13.00 N/A 0 1624 Chain B: 5.36 68.22 12.82 N/A 0 1648 Chain S: 10.63 67.92 38.27 N/A 517 0 Histogram: Values Number of atoms 5.36 - 11.65 2053 11.65 - 17.93 715 17.93 - 24.22 266 24.22 - 30.50 213 30.50 - 36.79 168 36.79 - 43.08 164 43.08 - 49.36 99 49.36 - 55.65 55 55.65 - 61.93 42 61.93 - 68.22 14 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1505 r_work=0.1232 r_free=0.1506 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1506 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1501 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1501 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013414 | | target function (ls_wunit_k1) not normalized (work): 2512.333092 | | target function (ls_wunit_k1) not normalized (free): 95.860374 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1501 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1602 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1436 0.1602 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1433 0.1600 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1506 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1234 0.1506 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3231 402.814 380.901 0.493 0.962 0.265 13.296-10.522 99.01 99 1 0.1900 528.187 517.921 0.757 0.963 0.219 10.503-8.327 99.45 178 3 0.1478 565.118 568.384 0.923 0.962 0.186 8.318-6.595 100.00 360 8 0.1557 414.736 413.162 0.940 0.962 0.173 6.588-5.215 100.00 711 7 0.1349 381.101 376.705 0.914 0.962 0.137 5.214-4.128 98.38 1367 28 0.0828 557.435 556.253 0.996 0.962 0.090 4.126-3.266 94.74 2603 46 0.0765 508.132 505.438 1.061 0.962 0.019 3.266-2.585 99.86 5447 97 0.0859 342.774 341.322 1.047 0.961 0.000 2.585-2.046 97.45 10613 204 0.0898 258.603 256.776 1.059 0.960 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.625 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.359 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.222 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0541 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1506 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1506 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1506 | n_water=885 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1235 r_free=0.1505 | n_water=881 | time (s): 107.330 (total time: 109.990) Filter (q & B) r_work=0.1235 r_free=0.1505 | n_water=879 | time (s): 5.190 (total time: 115.180) Compute maps r_work=0.1235 r_free=0.1505 | n_water=879 | time (s): 1.740 (total time: 116.920) Filter (map) r_work=0.1274 r_free=0.1507 | n_water=687 | time (s): 5.020 (total time: 121.940) Find peaks r_work=0.1274 r_free=0.1507 | n_water=687 | time (s): 0.680 (total time: 122.620) Add new water r_work=0.1299 r_free=0.1529 | n_water=1017 | time (s): 4.140 (total time: 126.760) Refine new water occ: r_work=0.1252 r_free=0.1500 adp: r_work=0.1252 r_free=0.1500 occ: r_work=0.1247 r_free=0.1500 adp: r_work=0.1247 r_free=0.1499 occ: r_work=0.1244 r_free=0.1501 adp: r_work=0.1243 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1500 r_work=0.1243 r_free=0.1500 | n_water=1017 | time (s): 280.320 (total time: 407.080) Filter (q & B) r_work=0.1248 r_free=0.1501 | n_water=881 | time (s): 4.780 (total time: 411.860) Filter (dist only) r_work=0.1248 r_free=0.1502 | n_water=880 | time (s): 117.970 (total time: 529.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.714173 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.992791 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 0.1424 0.0188 0.035 1.1 7.5 0.0 0.0 0 0.857 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.24 1.88 1.935 14.627 16.993 3.939 12.31 13.83 1.52 2.248 14.532 16.993 3.895 Individual atomic B min max mean iso aniso Overall: 5.53 67.79 15.33 1.06 515 3269 Protein: 5.53 36.30 10.74 1.06 0 2902 Water: 6.67 67.79 30.43 N/A 515 365 Other: 14.00 28.77 21.39 N/A 0 2 Chain A: 5.54 55.24 12.76 N/A 0 1624 Chain B: 5.53 67.79 12.49 N/A 0 1645 Chain S: 12.73 64.56 32.46 N/A 515 0 Histogram: Values Number of atoms 5.53 - 11.75 2130 11.75 - 17.98 685 17.98 - 24.21 296 24.21 - 30.43 236 30.43 - 36.66 175 36.66 - 42.88 154 42.88 - 49.11 70 49.11 - 55.34 23 55.34 - 61.56 9 61.56 - 67.79 6 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1384 r_work=0.1232 r_free=0.1384 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1384 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1379 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1379 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889859 | | target function (ml) not normalized (work): 728558.967588 | | target function (ml) not normalized (free): 15222.291173 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1226 0.1378 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1438 0.1438 0.1484 n_refl.: 191138 remove outliers: r(all,work,free)=0.1438 0.1438 0.1484 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1432 0.1431 0.1480 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1222 0.1378 n_refl.: 191138 remove outliers: r(all,work,free)=0.1225 0.1222 0.1378 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 94.06 92 3 0.3759 398.008 361.416 0.433 0.947 0.251 13.296-10.522 99.01 99 1 0.2430 528.187 507.734 0.707 0.948 0.211 10.503-8.327 98.35 176 3 0.1933 555.265 559.483 0.887 0.948 0.169 8.318-6.595 100.00 360 8 0.2030 414.736 410.056 0.899 0.947 0.122 6.588-5.215 100.00 711 7 0.1845 381.101 370.572 0.883 0.947 0.100 5.214-4.128 98.38 1367 28 0.1146 557.435 552.479 0.972 0.948 0.060 4.126-3.266 94.74 2603 46 0.1094 508.132 501.166 1.032 0.948 0.025 3.266-2.585 99.86 5447 97 0.1082 342.774 339.199 1.020 0.947 0.010 2.585-2.046 97.45 10613 204 0.0965 258.603 255.757 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0976 153.054 151.390 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.480 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1684 44.202 42.318 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1025 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1378 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1378 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1378 | n_water=880 | time (s): 2.830 (total time: 2.830) Filter (dist) r_work=0.1222 r_free=0.1379 | n_water=879 | time (s): 108.250 (total time: 111.080) Filter (q & B) r_work=0.1222 r_free=0.1376 | n_water=873 | time (s): 5.390 (total time: 116.470) Compute maps r_work=0.1222 r_free=0.1376 | n_water=873 | time (s): 2.010 (total time: 118.480) Filter (map) r_work=0.1245 r_free=0.1367 | n_water=729 | time (s): 4.780 (total time: 123.260) Find peaks r_work=0.1245 r_free=0.1367 | n_water=729 | time (s): 0.900 (total time: 124.160) Add new water r_work=0.1259 r_free=0.1381 | n_water=982 | time (s): 4.440 (total time: 128.600) Refine new water occ: r_work=0.1212 r_free=0.1355 adp: r_work=0.1204 r_free=0.1351 occ: r_work=0.1201 r_free=0.1353 adp: r_work=0.1201 r_free=0.1352 occ: r_work=0.1199 r_free=0.1354 adp: r_work=0.1199 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1199 r_free=0.1354 r_work=0.1199 r_free=0.1354 | n_water=982 | time (s): 344.820 (total time: 473.420) Filter (q & B) r_work=0.1204 r_free=0.1367 | n_water=881 | time (s): 4.680 (total time: 478.100) Filter (dist only) r_work=0.1206 r_free=0.1366 | n_water=878 | time (s): 110.030 (total time: 588.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.629798 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.115933 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 0.1204 0.1363 0.0158 0.036 1.1 6.8 0.0 0.3 0 0.815 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.63 1.58 1.831 14.204 16.116 3.872 11.97 13.60 1.63 1.922 14.174 16.116 3.864 Individual atomic B min max mean iso aniso Overall: 5.50 67.38 14.98 1.01 513 3269 Protein: 5.50 33.23 10.68 1.01 0 2902 Water: 5.73 67.38 29.21 N/A 513 365 Other: 14.00 27.75 20.87 N/A 0 2 Chain A: 5.53 54.24 12.64 N/A 0 1624 Chain B: 5.50 67.38 12.41 N/A 0 1645 Chain S: 5.73 64.46 30.64 N/A 513 0 Histogram: Values Number of atoms 5.50 - 11.69 2114 11.69 - 17.88 727 17.88 - 24.06 309 24.06 - 30.25 252 30.25 - 36.44 150 36.44 - 42.63 136 42.63 - 48.82 63 48.82 - 55.01 21 55.01 - 61.19 6 61.19 - 67.38 4 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1361 r_work=0.1198 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1361 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1357 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862890 | | target function (ml) not normalized (work): 723496.076513 | | target function (ml) not normalized (free): 15139.108975 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1357 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1425 0.1424 0.1471 n_refl.: 191135 remove outliers: r(all,work,free)=0.1425 0.1424 0.1471 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1419 0.1418 0.1467 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1351 n_refl.: 191135 remove outliers: r(all,work,free)=0.1193 0.1190 0.1351 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3842 361.066 315.830 0.392 0.971 0.237 13.296-10.522 97.03 97 1 0.2427 479.579 450.503 0.671 0.972 0.193 10.503-8.327 98.35 176 3 0.2099 502.607 496.467 0.842 0.972 0.156 8.318-6.595 100.00 360 8 0.2164 375.405 369.932 0.865 0.971 0.119 6.588-5.215 100.00 711 7 0.1906 344.960 335.143 0.859 0.971 0.097 5.214-4.128 98.38 1367 28 0.1188 504.571 499.553 0.947 0.970 0.070 4.126-3.266 94.74 2603 46 0.1117 459.944 453.183 1.007 0.969 0.000 3.266-2.585 99.86 5447 97 0.1085 310.267 307.022 0.997 0.966 0.000 2.585-2.046 97.45 10613 204 0.0930 234.079 231.682 1.014 0.962 0.000 2.046-1.619 99.39 21536 464 0.0908 138.539 137.252 1.043 0.955 0.000 1.619-1.281 98.00 42464 925 0.0979 74.582 73.885 1.051 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.010 38.347 1.056 0.924 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0946 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== 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=878 | time (s): 3.300 (total time: 3.300) Filter (dist) r_work=0.1191 r_free=0.1352 | n_water=875 | time (s): 110.110 (total time: 113.410) Filter (q & B) r_work=0.1191 r_free=0.1352 | n_water=867 | time (s): 4.530 (total time: 117.940) Compute maps r_work=0.1191 r_free=0.1352 | n_water=867 | time (s): 2.410 (total time: 120.350) Filter (map) r_work=0.1213 r_free=0.1354 | n_water=749 | time (s): 4.740 (total time: 125.090) Find peaks r_work=0.1213 r_free=0.1354 | n_water=749 | time (s): 0.770 (total time: 125.860) Add new water r_work=0.1224 r_free=0.1371 | n_water=985 | time (s): 4.330 (total time: 130.190) Refine new water occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1188 r_free=0.1339 occ: r_work=0.1185 r_free=0.1339 adp: r_work=0.1185 r_free=0.1339 occ: r_work=0.1183 r_free=0.1340 adp: r_work=0.1182 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1340 r_work=0.1182 r_free=0.1340 | n_water=985 | time (s): 310.340 (total time: 440.530) Filter (q & B) r_work=0.1186 r_free=0.1345 | n_water=899 | time (s): 4.240 (total time: 444.770) Filter (dist only) r_work=0.1187 r_free=0.1344 | n_water=898 | time (s): 115.670 (total time: 560.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.572970 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.784878 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1354 0.0165 0.036 1.1 7.0 0.0 0.3 0 0.786 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.54 1.65 1.796 14.185 14.785 3.761 11.95 13.57 1.62 1.844 14.165 14.785 3.761 Individual atomic B min max mean iso aniso Overall: 5.60 67.16 15.03 0.96 533 3269 Protein: 5.60 32.26 10.63 0.96 0 2902 Water: 5.88 67.16 29.26 N/A 533 365 Other: 13.83 26.95 20.39 N/A 0 2 Chain A: 5.62 53.67 12.57 N/A 0 1624 Chain B: 5.60 67.16 12.35 N/A 0 1645 Chain S: 5.88 64.40 30.82 N/A 533 0 Histogram: Values Number of atoms 5.60 - 11.76 2147 11.76 - 17.91 710 17.91 - 24.07 314 24.07 - 30.22 235 30.22 - 36.38 155 36.38 - 42.53 142 42.53 - 48.69 68 48.69 - 54.85 22 54.85 - 61.00 5 61.00 - 67.16 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1357 r_work=0.1195 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1358 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1358 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759955 | | target function (ml) not normalized (work): 704205.786748 | | target function (ml) not normalized (free): 14748.477138 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1480 n_refl.: 191132 remove outliers: r(all,work,free)=0.1407 0.1405 0.1480 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1398 0.1397 0.1475 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1359 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3800 361.066 323.274 0.397 0.952 0.215 13.296-10.522 95.05 95 1 0.2295 479.355 450.892 0.687 0.953 0.163 10.503-8.327 97.80 175 3 0.2097 501.721 496.195 0.863 0.954 0.140 8.318-6.595 100.00 360 8 0.2157 375.405 371.195 0.881 0.953 0.100 6.588-5.215 100.00 711 7 0.1907 344.960 335.475 0.879 0.953 0.090 5.214-4.128 98.38 1367 28 0.1197 504.571 499.574 0.969 0.954 0.080 4.126-3.266 94.74 2603 46 0.1123 459.944 453.275 1.029 0.954 0.000 3.266-2.585 99.86 5447 97 0.1100 310.267 307.013 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0938 234.079 231.668 1.029 0.953 0.000 2.046-1.619 99.39 21536 464 0.0915 138.539 137.268 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0979 74.582 73.874 1.051 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.010 38.342 1.040 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1407 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1359 | n_water=898 | time (s): 3.430 (total time: 3.430) Filter (dist) r_work=0.1195 r_free=0.1361 | n_water=895 | time (s): 112.260 (total time: 115.690) Filter (q & B) r_work=0.1196 r_free=0.1363 | n_water=887 | time (s): 4.110 (total time: 119.800) Compute maps r_work=0.1196 r_free=0.1363 | n_water=887 | time (s): 1.830 (total time: 121.630) Filter (map) r_work=0.1218 r_free=0.1356 | n_water=773 | time (s): 5.220 (total time: 126.850) Find peaks r_work=0.1218 r_free=0.1356 | n_water=773 | time (s): 0.770 (total time: 127.620) Add new water r_work=0.1228 r_free=0.1366 | n_water=977 | time (s): 4.510 (total time: 132.130) Refine new water occ: r_work=0.1195 r_free=0.1338 adp: r_work=0.1195 r_free=0.1338 occ: r_work=0.1193 r_free=0.1338 adp: r_work=0.1192 r_free=0.1339 occ: r_work=0.1191 r_free=0.1339 adp: r_work=0.1191 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1340 r_work=0.1191 r_free=0.1340 | n_water=977 | time (s): 283.020 (total time: 415.150) Filter (q & B) r_work=0.1194 r_free=0.1347 | n_water=909 | time (s): 4.930 (total time: 420.080) Filter (dist only) r_work=0.1194 r_free=0.1347 | n_water=908 | time (s): 119.150 (total time: 539.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.629325 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.943072 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1348 0.0152 0.037 1.1 6.3 0.0 0.3 0 0.815 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.48 1.52 1.769 14.111 14.943 3.760 11.98 13.51 1.53 1.900 14.067 14.943 3.757 Individual atomic B min max mean iso aniso Overall: 5.60 66.23 14.93 0.91 543 3269 Protein: 5.60 29.55 10.52 0.91 0 2902 Water: 5.93 66.23 29.02 N/A 543 365 Other: 13.86 24.48 19.17 N/A 0 2 Chain A: 5.66 51.18 12.43 N/A 0 1624 Chain B: 5.60 66.23 12.23 N/A 0 1645 Chain S: 5.93 64.20 30.62 N/A 543 0 Histogram: Values Number of atoms 5.60 - 11.66 2122 11.66 - 17.73 770 17.73 - 23.79 284 23.79 - 29.85 230 29.85 - 35.92 166 35.92 - 41.98 134 41.98 - 48.04 72 48.04 - 54.11 24 54.11 - 60.17 6 60.17 - 66.23 4 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1352 r_work=0.1198 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1352 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1354 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756090 | | target function (ml) not normalized (work): 703470.670900 | | target function (ml) not normalized (free): 14728.864717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1354 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1476 n_refl.: 191129 remove outliers: r(all,work,free)=0.1402 0.1401 0.1476 n_refl.: 191129 overall B=-0.24 to atoms: r(all,work,free)=0.1364 0.1363 0.1452 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1354 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1195 0.1354 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 93.07 91 3 0.3892 361.066 321.750 0.399 0.951 0.211 13.296-10.522 95.05 95 1 0.2333 479.355 463.136 0.727 0.952 0.164 10.503-8.327 97.80 175 3 0.2089 501.721 495.746 0.881 0.953 0.143 8.318-6.595 100.00 360 8 0.2129 375.405 370.986 0.907 0.952 0.100 6.588-5.215 100.00 711 7 0.1897 344.960 335.831 0.904 0.953 0.095 5.214-4.128 98.38 1367 28 0.1228 504.571 499.290 0.995 0.953 0.090 4.126-3.266 94.74 2603 46 0.1141 459.944 452.846 1.056 0.953 0.009 3.266-2.585 99.86 5447 97 0.1114 310.267 306.864 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0944 234.079 231.592 1.047 0.952 0.000 2.046-1.619 99.39 21536 464 0.0912 138.539 137.245 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0968 74.582 73.872 1.052 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.010 38.340 1.023 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0530 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1354 | n_water=908 | time (s): 2.750 (total time: 2.750) Filter (dist) r_work=0.1196 r_free=0.1355 | n_water=907 | time (s): 115.500 (total time: 118.250) Filter (q & B) r_work=0.1197 r_free=0.1355 | n_water=894 | time (s): 5.480 (total time: 123.730) Compute maps r_work=0.1197 r_free=0.1355 | n_water=894 | time (s): 2.070 (total time: 125.800) Filter (map) r_work=0.1219 r_free=0.1354 | n_water=775 | time (s): 4.390 (total time: 130.190) Find peaks r_work=0.1219 r_free=0.1354 | n_water=775 | time (s): 0.540 (total time: 130.730) Add new water r_work=0.1229 r_free=0.1364 | n_water=986 | time (s): 3.830 (total time: 134.560) Refine new water occ: r_work=0.1196 r_free=0.1340 adp: r_work=0.1196 r_free=0.1340 occ: r_work=0.1194 r_free=0.1340 adp: r_work=0.1194 r_free=0.1341 occ: r_work=0.1192 r_free=0.1341 adp: r_work=0.1192 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1342 r_work=0.1192 r_free=0.1342 | n_water=986 | time (s): 229.120 (total time: 363.680) Filter (q & B) r_work=0.1195 r_free=0.1351 | n_water=913 | time (s): 5.650 (total time: 369.330) Filter (dist only) r_work=0.1195 r_free=0.1350 | n_water=911 | time (s): 121.060 (total time: 490.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.512620 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.019032 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1357 0.0157 0.038 1.1 6.8 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.57 1.57 1.728 13.773 15.019 3.759 12.00 13.59 1.59 1.790 13.746 15.019 3.756 Individual atomic B min max mean iso aniso Overall: 5.40 64.80 14.64 0.89 546 3269 Protein: 5.40 28.52 10.26 0.89 0 2902 Water: 5.73 64.80 28.58 N/A 546 365 Other: 13.69 22.30 17.99 N/A 0 2 Chain A: 5.45 50.30 12.12 N/A 0 1624 Chain B: 5.40 64.80 11.93 N/A 0 1645 Chain S: 5.73 63.77 30.27 N/A 546 0 Histogram: Values Number of atoms 5.40 - 11.34 2100 11.34 - 17.28 784 17.28 - 23.22 281 23.22 - 29.16 234 29.16 - 35.10 173 35.10 - 41.04 123 41.04 - 46.98 84 46.98 - 52.92 25 52.92 - 58.86 6 58.86 - 64.80 5 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1359 r_work=0.1200 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1359 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1361 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755401 | | target function (ml) not normalized (work): 703341.506530 | | target function (ml) not normalized (free): 14730.873352 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1373 0.1371 0.1467 n_refl.: 191129 remove outliers: r(all,work,free)=0.1373 0.1371 0.1467 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1381 0.1379 0.1472 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1189 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1189 0.1350 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 93.07 91 3 0.3857 361.066 320.351 0.393 0.974 0.215 13.296-10.522 95.05 95 1 0.2334 479.355 463.853 0.717 0.976 0.159 10.503-8.327 97.80 175 3 0.2101 501.721 495.412 0.866 0.976 0.133 8.318-6.595 100.00 360 8 0.2161 375.405 370.378 0.893 0.976 0.115 6.588-5.215 100.00 711 7 0.1910 344.960 335.206 0.890 0.977 0.100 5.214-4.128 98.38 1367 28 0.1249 504.571 498.734 0.978 0.978 0.059 4.126-3.266 94.74 2603 46 0.1155 459.944 452.275 1.042 0.979 0.009 3.266-2.585 99.86 5447 97 0.1120 310.267 306.574 1.024 0.979 0.000 2.585-2.046 97.45 10613 204 0.0952 234.079 231.453 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0907 138.539 137.172 1.048 0.984 0.000 1.619-1.281 98.00 42464 925 0.0947 74.582 73.915 1.036 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.010 38.312 1.002 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0588 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1350 | n_water=911 | time (s): 3.040 (total time: 3.040) Filter (dist) r_work=0.1189 r_free=0.1350 | n_water=911 | time (s): 108.850 (total time: 111.890) Filter (q & B) r_work=0.1190 r_free=0.1348 | n_water=901 | time (s): 5.770 (total time: 117.660) Compute maps r_work=0.1190 r_free=0.1348 | n_water=901 | time (s): 2.180 (total time: 119.840) Filter (map) r_work=0.1212 r_free=0.1345 | n_water=780 | time (s): 4.440 (total time: 124.280) Find peaks r_work=0.1212 r_free=0.1345 | n_water=780 | time (s): 0.540 (total time: 124.820) Add new water r_work=0.1221 r_free=0.1355 | n_water=986 | time (s): 4.040 (total time: 128.860) Refine new water occ: r_work=0.1188 r_free=0.1326 adp: r_work=0.1189 r_free=0.1327 occ: r_work=0.1186 r_free=0.1327 adp: r_work=0.1186 r_free=0.1328 occ: r_work=0.1185 r_free=0.1329 adp: r_work=0.1185 r_free=0.1330 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1330 r_work=0.1185 r_free=0.1330 | n_water=986 | time (s): 245.310 (total time: 374.170) Filter (q & B) r_work=0.1188 r_free=0.1338 | n_water=917 | time (s): 5.200 (total time: 379.370) Filter (dist only) r_work=0.1188 r_free=0.1338 | n_water=915 | time (s): 112.890 (total time: 492.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.536332 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.891169 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 0.1191 0.1342 0.0151 0.038 1.1 7.0 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.42 1.51 1.682 13.770 14.891 3.753 11.91 13.44 1.53 1.702 13.762 14.891 3.751 Individual atomic B min max mean iso aniso Overall: 5.50 63.89 14.69 0.88 550 3269 Protein: 5.50 28.24 10.33 0.88 0 2902 Water: 5.91 63.89 28.51 N/A 550 365 Other: 13.79 22.34 18.06 N/A 0 2 Chain A: 5.58 50.09 12.15 N/A 0 1624 Chain B: 5.50 63.89 11.97 N/A 0 1645 Chain S: 5.91 63.75 30.28 N/A 550 0 Histogram: Values Number of atoms 5.50 - 11.34 2069 11.34 - 17.18 820 17.18 - 23.02 273 23.02 - 28.85 230 28.85 - 34.69 177 34.69 - 40.53 126 40.53 - 46.37 84 46.37 - 52.21 29 52.21 - 58.05 7 58.05 - 63.89 4 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1344 r_work=0.1191 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1344 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1347 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751217 | | target function (ml) not normalized (work): 702557.889550 | | target function (ml) not normalized (free): 14714.439509 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1347 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1390 0.1388 0.1475 n_refl.: 191129 remove outliers: r(all,work,free)=0.1390 0.1388 0.1475 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1392 0.1390 0.1476 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1345 n_refl.: 191129 remove outliers: r(all,work,free)=0.1191 0.1188 0.1345 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3877 361.066 319.956 0.379 0.995 0.207 13.296-10.522 95.05 95 1 0.2328 479.355 463.595 0.703 0.996 0.163 10.503-8.327 97.80 175 3 0.2092 501.721 496.021 0.846 0.997 0.129 8.318-6.595 100.00 360 8 0.2149 375.405 369.918 0.870 0.997 0.100 6.588-5.215 100.00 711 7 0.1912 344.960 335.192 0.869 0.997 0.087 5.214-4.128 98.38 1367 28 0.1254 504.571 498.577 0.956 0.998 0.049 4.126-3.266 94.74 2603 46 0.1159 459.944 452.187 1.019 1.000 0.009 3.266-2.585 99.86 5447 97 0.1126 310.267 306.533 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0951 234.079 231.460 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0905 138.539 137.186 1.027 1.006 0.000 1.619-1.281 98.00 42464 925 0.0941 74.582 73.927 1.018 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.010 38.299 0.986 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0184 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1345 | n_water=915 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1188 r_free=0.1345 | n_water=915 | time (s): 109.910 (total time: 112.300) Filter (q & B) r_work=0.1189 r_free=0.1345 | n_water=905 | time (s): 5.050 (total time: 117.350) Compute maps r_work=0.1189 r_free=0.1345 | n_water=905 | time (s): 2.020 (total time: 119.370) Filter (map) r_work=0.1212 r_free=0.1348 | n_water=787 | time (s): 4.790 (total time: 124.160) Find peaks r_work=0.1212 r_free=0.1348 | n_water=787 | time (s): 0.880 (total time: 125.040) Add new water r_work=0.1220 r_free=0.1355 | n_water=991 | time (s): 5.410 (total time: 130.450) Refine new water occ: r_work=0.1188 r_free=0.1329 adp: r_work=0.1188 r_free=0.1329 occ: r_work=0.1186 r_free=0.1329 adp: r_work=0.1186 r_free=0.1330 occ: r_work=0.1184 r_free=0.1330 adp: r_work=0.1184 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1331 r_work=0.1184 r_free=0.1331 | n_water=991 | time (s): 260.020 (total time: 390.470) Filter (q & B) r_work=0.1188 r_free=0.1339 | n_water=917 | time (s): 4.320 (total time: 394.790) Filter (dist only) r_work=0.1188 r_free=0.1339 | n_water=916 | time (s): 117.820 (total time: 512.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.563518 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.923262 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 0.1191 0.1348 0.0156 0.039 1.1 5.1 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.48 1.56 1.684 13.773 14.923 3.752 11.92 13.49 1.57 1.684 13.769 14.923 3.751 Individual atomic B min max mean iso aniso Overall: 5.50 63.74 14.68 0.88 551 3269 Protein: 5.50 28.25 10.35 0.88 0 2902 Water: 5.94 63.74 28.37 N/A 551 365 Other: 13.81 22.29 18.05 N/A 0 2 Chain A: 5.62 49.98 12.15 N/A 0 1624 Chain B: 5.50 63.40 11.98 N/A 0 1645 Chain S: 5.94 63.74 30.19 N/A 551 0 Histogram: Values Number of atoms 5.50 - 11.33 2065 11.33 - 17.15 827 17.15 - 22.98 275 22.98 - 28.80 229 28.80 - 34.62 181 34.62 - 40.45 119 40.45 - 46.27 82 46.27 - 52.10 31 52.10 - 57.92 7 57.92 - 63.74 4 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1349 r_work=0.1192 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1349 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1351 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750589 | | target function (ml) not normalized (work): 702440.251451 | | target function (ml) not normalized (free): 14717.362032 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1351 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1399 0.1398 0.1492 n_refl.: 191129 remove outliers: r(all,work,free)=0.1399 0.1398 0.1492 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1399 0.1397 0.1492 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1348 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 93.07 91 3 0.3918 361.066 318.622 0.366 0.994 0.189 13.296-10.522 95.05 95 1 0.2275 479.355 464.672 0.694 0.996 0.139 10.503-8.327 97.80 175 3 0.2159 501.721 495.422 0.842 0.997 0.117 8.318-6.595 100.00 360 8 0.2158 375.405 369.717 0.870 0.996 0.095 6.588-5.215 100.00 711 7 0.1951 344.960 334.881 0.866 0.997 0.080 5.214-4.128 98.38 1367 28 0.1272 504.571 498.552 0.957 0.998 0.049 4.126-3.266 94.74 2603 46 0.1166 459.944 452.155 1.020 0.999 0.015 3.266-2.585 99.86 5447 97 0.1132 310.267 306.504 1.003 1.000 0.010 2.585-2.046 97.45 10613 204 0.0953 234.079 231.410 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0906 138.539 137.187 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0936 74.582 73.935 1.020 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.010 38.295 0.990 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0114 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1348 After: r_work=0.1190 r_free=0.1349 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1349 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1349 | n_water=916 | time (s): 3.220 (total time: 3.220) Filter (dist) r_work=0.1190 r_free=0.1349 | n_water=916 | time (s): 114.450 (total time: 117.670) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=903 | time (s): 5.290 (total time: 122.960) Compute maps r_work=0.1192 r_free=0.1349 | n_water=903 | time (s): 2.570 (total time: 125.530) Filter (map) r_work=0.1214 r_free=0.1353 | n_water=794 | time (s): 4.160 (total time: 129.690) Find peaks r_work=0.1214 r_free=0.1353 | n_water=794 | time (s): 0.660 (total time: 130.350) Add new water r_work=0.1221 r_free=0.1361 | n_water=990 | time (s): 4.160 (total time: 134.510) Refine new water occ: r_work=0.1187 r_free=0.1331 adp: r_work=0.1188 r_free=0.1332 occ: r_work=0.1186 r_free=0.1332 adp: r_work=0.1186 r_free=0.1333 occ: r_work=0.1184 r_free=0.1333 adp: r_work=0.1184 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1334 r_work=0.1184 r_free=0.1334 | n_water=990 | time (s): 368.660 (total time: 503.170) Filter (q & B) r_work=0.1188 r_free=0.1342 | n_water=916 | time (s): 5.680 (total time: 508.850) Filter (dist only) r_work=0.1189 r_free=0.1342 | n_water=915 | time (s): 120.810 (total time: 629.660) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.523499 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.569973 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 0.1349 0.0155 0.039 1.2 10.9 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.49 1.55 1.684 13.767 14.570 3.755 11.96 13.53 1.57 1.688 13.768 14.570 3.755 Individual atomic B min max mean iso aniso Overall: 5.55 63.70 14.67 0.87 550 3269 Protein: 5.55 28.00 10.36 0.87 0 2902 Water: 6.04 63.70 28.31 N/A 550 365 Other: 13.86 22.24 18.05 N/A 0 2 Chain A: 5.67 49.76 12.14 N/A 0 1624 Chain B: 5.55 62.47 11.97 N/A 0 1645 Chain S: 6.04 63.70 30.21 N/A 550 0 Histogram: Values Number of atoms 5.55 - 11.37 2063 11.37 - 17.18 837 17.18 - 23.00 271 23.00 - 28.81 227 28.81 - 34.63 187 34.63 - 40.44 104 40.44 - 46.25 85 46.25 - 52.07 32 52.07 - 57.88 9 57.88 - 63.70 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1353 r_work=0.1196 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1353 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1354 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754850 | | target function (ml) not normalized (work): 703238.263361 | | target function (ml) not normalized (free): 14730.220371 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1366 0.1464 5.6914 5.7652| | 2: 2.94 - 2.33 1.00 7339 128 0.1077 0.1329 5.0828 5.1734| | 3: 2.33 - 2.04 0.96 6939 150 0.0899 0.1156 4.6465 4.7259| | 4: 2.04 - 1.85 1.00 7170 155 0.0900 0.1062 4.3916 4.5715| | 5: 1.85 - 1.72 0.99 7113 159 0.0934 0.1001 4.1557 4.2635| | 6: 1.72 - 1.62 0.99 7102 142 0.0902 0.1092 3.9537 4.0784| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0980 3.8031 3.9482| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1308 3.7042 3.9045| | 9: 1.47 - 1.41 0.98 6938 155 0.0930 0.1149 3.625 3.7591| | 10: 1.41 - 1.36 0.99 7022 150 0.0976 0.1181 3.5562 3.6649| | 11: 1.36 - 1.32 0.99 6997 151 0.0994 0.1123 3.4851 3.5816| | 12: 1.32 - 1.28 0.98 6975 149 0.1033 0.1133 3.4578 3.5858| | 13: 1.28 - 1.25 0.98 6907 166 0.1042 0.1241 3.4369 3.5664| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1586 3.4315 3.6764| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1246 3.4482 3.4877| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1530 3.4634 3.6451| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1231 3.4328 3.4452| | 18: 1.14 - 1.12 0.98 6875 142 0.1387 0.1714 3.4386 3.5355| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1774 3.4209 3.6011| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1592 3.4105 3.4404| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2148 3.4179 3.5038| | 22: 1.07 - 1.05 0.97 6836 135 0.1907 0.1945 3.4131 3.413| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2021 3.4325 3.4871| | 24: 1.03 - 1.02 0.96 6784 133 0.2333 0.2263 3.4355 3.5127| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2519 3.4493 3.5243| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2852 3.4156 3.4228| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2794 3.4693 3.395| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.84 1.00 0.95 11411.71| | 2: 2.94 - 2.33 7339 128 0.93 12.84 0.99 0.96 5147.08| | 3: 2.33 - 2.04 6939 150 0.96 7.47 1.01 0.96 1652.59| | 4: 2.04 - 1.85 7170 155 0.96 7.65 1.00 0.96 1007.60| | 5: 1.85 - 1.72 7113 159 0.96 8.20 1.00 0.96 647.94| | 6: 1.72 - 1.62 7102 142 0.96 8.16 1.00 0.96 454.08| | 7: 1.62 - 1.54 7104 148 0.96 8.27 1.01 0.97 343.73| | 8: 1.54 - 1.47 6798 152 0.96 8.36 1.01 0.97 282.98| | 9: 1.47 - 1.41 6938 155 0.96 8.52 1.00 0.98 232.41| | 10: 1.41 - 1.36 7022 150 0.96 8.91 1.00 0.97 202.05| | 11: 1.36 - 1.32 6997 151 0.96 8.88 0.99 0.96 173.95| | 12: 1.32 - 1.28 6975 149 0.96 8.93 0.98 0.95 159.78| | 13: 1.28 - 1.25 6907 166 0.96 9.53 1.01 0.96 157.85| | 14: 1.25 - 1.22 7015 112 0.95 10.67 1.01 0.97 162.45| | 15: 1.22 - 1.19 6956 137 0.95 11.21 1.01 0.98 165.98| | 16: 1.19 - 1.17 6604 132 0.95 11.41 1.01 0.96 159.56| | 17: 1.17 - 1.14 6940 135 0.94 12.26 1.01 0.96 154.08| | 18: 1.14 - 1.12 6875 142 0.94 12.80 1.01 0.95 148.41| | 19: 1.12 - 1.10 6948 106 0.93 14.24 1.00 0.95 152.49| | 20: 1.10 - 1.08 6884 147 0.92 15.30 1.00 0.94 151.38| | 21: 1.08 - 1.07 6852 152 0.91 16.68 1.00 0.93 153.86| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.93 154.90| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.92 164.80| | 24: 1.03 - 1.02 6784 133 0.85 23.20 0.99 0.93 179.43| | 25: 1.02 - 1.01 6552 130 0.83 25.20 0.98 0.90 182.49| | 26: 1.01 - 0.99 6767 158 0.81 26.64 0.98 0.88 176.61| | 27: 0.99 - 0.98 6647 131 0.82 26.27 0.99 0.87 160.51| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.41 max = 11411.71 mean = 934.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 13.32| |phase err.(test): min = 0.00 max = 88.77 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1354 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1489 n_refl.: 191129 remove outliers: r(all,work,free)=0.1411 0.1410 0.1489 n_refl.: 191129 overall B=-0.06 to atoms: r(all,work,free)=0.1402 0.1400 0.1483 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1350 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 93.07 91 3 0.3830 361.066 320.798 0.359 0.994 0.190 13.296-10.522 95.05 95 1 0.2275 479.355 464.506 0.672 0.995 0.129 10.503-8.327 97.80 175 3 0.2151 501.721 495.397 0.822 0.996 0.103 8.318-6.595 100.00 360 8 0.2143 375.405 369.537 0.850 0.996 0.093 6.588-5.215 100.00 711 7 0.1940 344.960 334.746 0.846 0.997 0.090 5.214-4.128 98.38 1367 28 0.1271 504.571 498.569 0.934 0.998 0.035 4.126-3.266 94.74 2603 46 0.1172 459.944 452.046 0.996 0.999 0.005 3.266-2.585 99.86 5447 97 0.1129 310.267 306.584 0.980 1.000 0.000 2.585-2.046 97.45 10613 204 0.0959 234.079 231.404 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0912 138.539 137.177 1.001 1.008 0.000 1.619-1.281 98.00 42464 925 0.0947 74.582 73.923 0.991 1.015 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.010 38.289 0.958 1.028 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0132 ================= 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 : 0.2034 0.1969 0.081 5.226 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1904 0.081 5.226 5.2 78.1 14.6 805 0.000 1_settarget: 0.1797 0.1904 0.081 5.226 5.2 78.1 14.6 805 0.000 1_nqh: 0.1797 0.1904 0.081 5.226 5.2 78.1 14.6 805 0.000 1_weight: 0.1797 0.1904 0.081 5.226 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1268 0.1497 0.039 1.168 5.2 78.1 14.6 805 0.154 1_adp: 0.1294 0.1563 0.039 1.168 5.2 73.1 15.0 805 0.154 1_regHadp: 0.1293 0.1558 0.039 1.168 5.2 73.1 15.0 805 0.154 1_occ: 0.1279 0.1546 0.039 1.168 5.2 73.1 15.0 805 0.154 2_bss: 0.1273 0.1540 0.039 1.168 5.3 73.2 15.1 805 0.154 2_settarget: 0.1273 0.1540 0.039 1.168 5.3 73.2 15.1 805 0.154 2_updatecdl: 0.1273 0.1540 0.039 1.174 5.3 73.2 15.1 805 0.154 2_nqh: 0.1273 0.1540 0.039 1.174 5.3 73.2 15.1 805 0.154 2_sol: 0.1268 0.1500 0.039 1.174 5.3 73.2 16.3 885 n/a 2_weight: 0.1268 0.1500 0.039 1.174 5.3 73.2 16.3 885 n/a 2_xyzrec: 0.1252 0.1512 0.041 1.150 5.3 73.2 16.3 885 n/a 2_adp: 0.1232 0.1505 0.041 1.150 5.4 68.2 16.4 885 n/a 2_regHadp: 0.1232 0.1506 0.041 1.150 5.4 68.2 16.4 885 n/a 2_occ: 0.1226 0.1501 0.041 1.150 5.4 68.2 16.4 885 n/a 3_bss: 0.1234 0.1506 0.041 1.150 5.3 68.2 16.4 885 n/a 3_settarget: 0.1234 0.1506 0.041 1.150 5.3 68.2 16.4 885 n/a 3_updatecdl: 0.1234 0.1506 0.041 1.155 5.3 68.2 16.4 885 n/a 3_nqh: 0.1234 0.1506 0.041 1.155 5.3 68.2 16.4 885 n/a 3_sol: 0.1248 0.1502 0.041 1.155 5.3 68.2 15.5 880 n/a 3_weight: 0.1248 0.1502 0.041 1.155 5.3 68.2 15.5 880 n/a 3_xyzrec: 0.1237 0.1424 0.035 1.106 5.3 68.2 15.5 880 n/a 3_adp: 0.1231 0.1384 0.035 1.106 5.5 67.8 15.3 880 n/a 3_regHadp: 0.1232 0.1384 0.035 1.106 5.5 67.8 15.3 880 n/a 3_occ: 0.1226 0.1379 0.035 1.106 5.5 67.8 15.3 880 n/a 4_bss: 0.1222 0.1378 0.035 1.106 5.5 67.8 15.3 880 n/a 4_settarget: 0.1222 0.1378 0.035 1.106 5.5 67.8 15.3 880 n/a 4_updatecdl: 0.1222 0.1378 0.035 1.107 5.5 67.8 15.3 880 n/a 4_nqh: 0.1222 0.1378 0.035 1.107 5.5 67.8 15.3 880 n/a 4_sol: 0.1206 0.1366 0.035 1.107 5.5 67.8 15.0 878 n/a 4_weight: 0.1206 0.1366 0.035 1.107 5.5 67.8 15.0 878 n/a 4_xyzrec: 0.1204 0.1363 0.036 1.124 5.5 67.8 15.0 878 n/a 4_adp: 0.1197 0.1361 0.036 1.124 5.5 67.4 15.0 878 n/a 4_regHadp: 0.1198 0.1361 0.036 1.124 5.5 67.4 15.0 878 n/a 4_occ: 0.1196 0.1357 0.036 1.124 5.5 67.4 15.0 878 n/a 5_bss: 0.1190 0.1351 0.036 1.124 5.5 67.4 15.0 878 n/a 5_settarget: 0.1190 0.1351 0.036 1.124 5.5 67.4 15.0 878 n/a 5_updatecdl: 0.1190 0.1351 0.036 1.124 5.5 67.4 15.0 878 n/a 5_nqh: 0.1190 0.1351 0.036 1.124 5.5 67.4 15.0 878 n/a 5_sol: 0.1187 0.1344 0.036 1.124 5.5 67.4 15.1 898 n/a 5_weight: 0.1187 0.1344 0.036 1.124 5.5 67.4 15.1 898 n/a 5_xyzrec: 0.1190 0.1354 0.036 1.131 5.5 67.4 15.1 898 n/a 5_adp: 0.1195 0.1357 0.036 1.131 5.6 67.2 15.0 898 n/a 5_regHadp: 0.1195 0.1358 0.036 1.131 5.6 67.2 15.0 898 n/a 5_occ: 0.1193 0.1358 0.036 1.131 5.6 67.2 15.0 898 n/a 6_bss: 0.1195 0.1359 0.036 1.131 5.6 67.1 15.0 898 n/a 6_settarget: 0.1195 0.1359 0.036 1.131 5.6 67.1 15.0 898 n/a 6_updatecdl: 0.1195 0.1359 0.036 1.131 5.6 67.1 15.0 898 n/a 6_nqh: 0.1195 0.1359 0.036 1.131 5.6 67.1 15.0 898 n/a 6_sol: 0.1194 0.1347 0.036 1.131 5.6 67.1 15.0 908 n/a 6_weight: 0.1194 0.1347 0.036 1.131 5.6 67.1 15.0 908 n/a 6_xyzrec: 0.1196 0.1348 0.037 1.137 5.6 67.1 15.0 908 n/a 6_adp: 0.1198 0.1352 0.037 1.137 5.6 66.2 14.9 908 n/a 6_regHadp: 0.1198 0.1352 0.037 1.137 5.6 66.2 14.9 908 n/a 6_occ: 0.1196 0.1354 0.037 1.137 5.6 66.2 14.9 908 n/a 7_bss: 0.1196 0.1354 0.037 1.137 5.4 66.0 14.7 908 n/a 7_settarget: 0.1196 0.1354 0.037 1.137 5.4 66.0 14.7 908 n/a 7_updatecdl: 0.1196 0.1354 0.037 1.137 5.4 66.0 14.7 908 n/a 7_nqh: 0.1196 0.1354 0.037 1.137 5.4 66.0 14.7 908 n/a 7_sol: 0.1195 0.1350 0.037 1.137 5.4 66.0 14.7 911 n/a 7_weight: 0.1195 0.1350 0.037 1.137 5.4 66.0 14.7 911 n/a 7_xyzrec: 0.1199 0.1357 0.038 1.122 5.4 66.0 14.7 911 n/a 7_adp: 0.1200 0.1359 0.038 1.122 5.4 64.8 14.6 911 n/a 7_regHadp: 0.1200 0.1359 0.038 1.122 5.4 64.8 14.6 911 n/a 7_occ: 0.1198 0.1361 0.038 1.122 5.4 64.8 14.6 911 n/a 8_bss: 0.1189 0.1350 0.038 1.122 5.5 64.9 14.7 911 n/a 8_settarget: 0.1189 0.1350 0.038 1.122 5.5 64.9 14.7 911 n/a 8_updatecdl: 0.1189 0.1350 0.038 1.123 5.5 64.9 14.7 911 n/a 8_nqh: 0.1189 0.1350 0.038 1.123 5.5 64.9 14.7 911 n/a 8_sol: 0.1188 0.1338 0.038 1.123 5.5 64.9 14.7 915 n/a 8_weight: 0.1188 0.1338 0.038 1.123 5.5 64.9 14.7 915 n/a 8_xyzrec: 0.1191 0.1342 0.038 1.119 5.5 64.9 14.7 915 n/a 8_adp: 0.1191 0.1344 0.038 1.119 5.5 63.9 14.7 915 n/a 8_regHadp: 0.1191 0.1344 0.038 1.119 5.5 63.9 14.7 915 n/a 8_occ: 0.1189 0.1347 0.038 1.119 5.5 63.9 14.7 915 n/a 9_bss: 0.1188 0.1345 0.038 1.119 5.5 63.9 14.7 915 n/a 9_settarget: 0.1188 0.1345 0.038 1.119 5.5 63.9 14.7 915 n/a 9_updatecdl: 0.1188 0.1345 0.038 1.119 5.5 63.9 14.7 915 n/a 9_nqh: 0.1188 0.1345 0.038 1.119 5.5 63.9 14.7 915 n/a 9_sol: 0.1188 0.1339 0.038 1.119 5.5 63.9 14.7 916 n/a 9_weight: 0.1188 0.1339 0.038 1.119 5.5 63.9 14.7 916 n/a 9_xyzrec: 0.1191 0.1348 0.039 1.113 5.5 63.9 14.7 916 n/a 9_adp: 0.1192 0.1349 0.039 1.113 5.5 63.7 14.7 916 n/a 9_regHadp: 0.1192 0.1349 0.039 1.113 5.5 63.7 14.7 916 n/a 9_occ: 0.1190 0.1351 0.039 1.113 5.5 63.7 14.7 916 n/a 10_bss: 0.1190 0.1348 0.039 1.113 5.5 63.7 14.7 916 n/a 10_settarget: 0.1190 0.1348 0.039 1.113 5.5 63.7 14.7 916 n/a 10_updatecdl: 0.1190 0.1348 0.039 1.112 5.5 63.7 14.7 916 n/a 10_setrh: 0.1190 0.1349 0.039 1.112 5.5 63.7 14.7 916 n/a 10_nqh: 0.1190 0.1349 0.039 1.112 5.5 63.7 14.7 916 n/a 10_sol: 0.1189 0.1342 0.039 1.112 5.5 63.7 14.7 915 n/a 10_weight: 0.1189 0.1342 0.039 1.112 5.5 63.7 14.7 915 n/a 10_xyzrec: 0.1194 0.1349 0.039 1.162 5.5 63.7 14.7 915 n/a 10_adp: 0.1196 0.1353 0.039 1.162 5.6 63.7 14.7 915 n/a 10_regHadp: 0.1196 0.1353 0.039 1.162 5.6 63.7 14.7 915 n/a 10_occ: 0.1195 0.1354 0.039 1.162 5.6 63.7 14.7 915 n/a end: 0.1194 0.1351 0.039 1.162 5.5 63.6 14.6 915 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3774798_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3774798_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.6200 Refinement macro-cycles (run) : 12554.0000 Write final files (write_after_run_outputs) : 135.0500 Total : 12695.6700 Total CPU time: 3.54 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:48:48 PST -0800 (1736736528.51 s) Start R-work = 0.1797, R-free = 0.1904 Final R-work = 0.1194, R-free = 0.1351 =============================================================================== Job complete usr+sys time: 12933.92 seconds wall clock time: 216 minutes 33.71 seconds (12993.71 seconds total)