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_9350771.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9350771.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9350771.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } 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 2 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: 1.66, per 1000 atoms: 0.25 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: 2.657 distance_ideal: 2.720 ideal - model: 0.063 slack: 0.000 delta_slack: 0.063 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: 2.612 distance_ideal: 2.710 ideal - model: 0.098 slack: 0.000 delta_slack: 0.098 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: 0.77 Conformation dependent library (CDL) restraints added in 202.5 milliseconds Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.04: 991 1.04 - 1.28: 2438 1.28 - 1.51: 1583 1.51 - 1.75: 907 1.75 - 1.98: 15 Bond restraints: 5934 Sorted by residual: bond pdb=" NE ARG B 175 " pdb=" CZ ARG B 175 " ideal model delta sigma weight residual 1.326 1.109 0.217 1.10e-02 8.26e+03 3.91e+02 bond pdb=" CA VAL A 62 " pdb=" CB VAL A 62 " ideal model delta sigma weight residual 1.544 1.314 0.230 1.19e-02 7.06e+03 3.74e+02 bond pdb=" N ILE A 101 " pdb=" CA ILE A 101 " ideal model delta sigma weight residual 1.459 1.702 -0.243 1.26e-02 6.30e+03 3.71e+02 bond pdb=" C SER A 4 " pdb=" O SER A 4 " ideal model delta sigma weight residual 1.234 1.468 -0.234 1.22e-02 6.72e+03 3.67e+02 bond pdb=" C ALA B 136 " pdb=" O ALA B 136 " ideal model delta sigma weight residual 1.236 1.017 0.220 1.18e-02 7.18e+03 3.46e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.19: 5706 4.19 - 8.37: 3517 8.37 - 12.56: 1316 12.56 - 16.75: 246 16.75 - 20.93: 25 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.22 134.58 -12.36 6.50e-01 2.37e+00 3.62e+02 angle pdb=" O ALA A 57 " pdb=" C ALA A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 121.65 134.12 -12.47 7.30e-01 1.88e+00 2.92e+02 angle pdb=" O PHE B 119 " pdb=" C PHE B 119 " pdb=" N PRO B 120 " ideal model delta sigma weight residual 121.34 136.46 -15.12 8.90e-01 1.26e+00 2.89e+02 angle pdb=" CA GLY A 126 " pdb=" C GLY A 126 " pdb=" O GLY A 126 " ideal model delta sigma weight residual 121.21 137.28 -16.07 1.07e+00 8.73e-01 2.26e+02 angle pdb=" N LEU B 113 " pdb=" CA LEU B 113 " pdb=" C LEU B 113 " ideal model delta sigma weight residual 111.36 126.25 -14.89 1.09e+00 8.42e-01 1.87e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 1831 16.78 - 33.55: 144 33.55 - 50.32: 50 50.32 - 67.09: 20 67.09 - 83.87: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 153.00 27.00 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA GLY B 75 " pdb=" C GLY B 75 " pdb=" N ILE B 76 " pdb=" CA ILE B 76 " ideal model delta harmonic sigma weight residual -180.00 -154.70 -25.30 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.271: 236 0.271 - 0.540: 167 0.540 - 0.809: 74 0.809 - 1.078: 12 1.078 - 1.348: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 59 " pdb=" CB LEU B 59 " pdb=" CD1 LEU B 59 " pdb=" CD2 LEU B 59 " both_signs ideal model delta sigma weight residual False -2.59 -3.94 1.35 2.00e-01 2.50e+01 4.54e+01 chirality pdb=" CA SER A 85 " pdb=" N SER A 85 " pdb=" C SER A 85 " pdb=" CB SER A 85 " both_signs ideal model delta sigma weight residual False 2.51 3.77 -1.26 2.00e-01 2.50e+01 3.98e+01 chirality pdb=" CG LEU B 172 " pdb=" CB LEU B 172 " pdb=" CD1 LEU B 172 " pdb=" CD2 LEU B 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.38 -1.21 2.00e-01 2.50e+01 3.65e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.156 2.00e-02 2.50e+03 7.78e-02 1.81e+02 pdb=" CG PHE B 164 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.072 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.085 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.103 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.127 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " 0.010 2.00e-02 2.50e+03 6.58e-02 1.73e+02 pdb=" CG TRP B 146 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.124 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " -0.046 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.055 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.101 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.056 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.118 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.028 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.007 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.060 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 82 " 0.039 2.00e-02 2.50e+03 7.47e-02 1.67e+02 pdb=" CG PHE B 82 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 PHE B 82 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE B 82 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 82 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE B 82 " 0.144 2.00e-02 2.50e+03 pdb=" CZ PHE B 82 " -0.093 2.00e-02 2.50e+03 pdb=" HD1 PHE B 82 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 PHE B 82 " -0.094 2.00e-02 2.50e+03 pdb=" HE1 PHE B 82 " -0.084 2.00e-02 2.50e+03 pdb=" HE2 PHE B 82 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE B 82 " 0.076 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 30 1.64 - 2.38: 2637 2.38 - 3.12: 22434 3.12 - 3.86: 32827 3.86 - 4.60: 52330 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110258 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.896 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.937 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.031 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.063 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.170 2.620 ... (remaining 110253 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_9350771_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= 0.2033 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300537 | | target function (ml) not normalized (work): 805546.410333 | | target function (ml) not normalized (free): 16544.214378 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2136 0.1814 6.7016 6.3005| | 2: 2.94 - 2.33 1.00 7339 128 0.1603 0.1570 5.5311 5.5553| | 3: 2.33 - 2.04 0.96 6939 150 0.1632 0.1662 5.1421 5.1969| | 4: 2.04 - 1.85 1.00 7170 155 0.1766 0.1561 4.9691 4.9936| | 5: 1.85 - 1.72 0.99 7113 159 0.1926 0.1879 4.8027 4.858| | 6: 1.72 - 1.62 0.99 7102 142 0.1979 0.1819 4.6668 4.6641| | 7: 1.62 - 1.54 0.99 7104 148 0.2015 0.1640 4.559 4.5313| | 8: 1.54 - 1.47 0.96 6798 152 0.2023 0.2226 4.469 4.4768| | 9: 1.47 - 1.41 0.98 6938 155 0.2050 0.2339 4.3894 4.5213| | 10: 1.41 - 1.36 0.99 7022 150 0.2121 0.1954 4.2978 4.2905| | 11: 1.36 - 1.32 0.99 6997 151 0.2105 0.2069 4.2215 4.2428| | 12: 1.32 - 1.28 0.98 6976 149 0.2096 0.1978 4.1739 4.23| | 13: 1.28 - 1.25 0.98 6907 166 0.2017 0.2111 4.1045 4.1629| | 14: 1.25 - 1.22 0.98 7015 113 0.2080 0.2406 4.0745 4.2431| | 15: 1.22 - 1.19 0.98 6957 137 0.2105 0.1905 4.0425 3.9856| | 16: 1.19 - 1.17 0.93 6604 132 0.2124 0.2257 4.004 4.0725| | 17: 1.17 - 1.14 0.98 6941 135 0.2187 0.1895 3.9669 3.9786| | 18: 1.14 - 1.12 0.98 6875 142 0.2247 0.2297 3.9245 3.8877| | 19: 1.12 - 1.10 0.97 6949 106 0.2271 0.2519 3.8759 3.9546| | 20: 1.10 - 1.08 0.97 6884 147 0.2345 0.2185 3.8338 3.8122| | 21: 1.08 - 1.07 0.97 6852 152 0.2429 0.2820 3.7989 3.8513| | 22: 1.07 - 1.05 0.97 6838 135 0.2532 0.2754 3.7526 3.8625| | 23: 1.05 - 1.03 0.97 6829 159 0.2756 0.2961 3.7467 3.8559| | 24: 1.03 - 1.02 0.96 6785 133 0.2903 0.2830 3.7051 3.7888| | 25: 1.02 - 1.01 0.93 6552 130 0.3083 0.2883 3.6774 3.7135| | 26: 1.01 - 0.99 0.96 6767 158 0.3199 0.3390 3.6245 3.6608| | 27: 0.99 - 0.98 0.94 6648 131 0.3407 0.3075 3.6458 3.591| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.09 0.91 0.97 34152.97| | 2: 2.94 - 2.33 7339 128 0.86 20.83 1.08 1.02 14701.28| | 3: 2.33 - 2.04 6939 150 0.93 12.76 1.11 1.05 4235.83| | 4: 2.04 - 1.85 7170 155 0.92 13.64 1.12 1.06 2797.65| | 5: 1.85 - 1.72 7113 159 0.91 15.94 1.11 1.06 2100.85| | 6: 1.72 - 1.62 7102 142 0.90 16.64 1.12 1.04 1597.11| | 7: 1.62 - 1.54 7104 148 0.89 17.59 1.11 1.04 1280.78| | 8: 1.54 - 1.47 6798 152 0.89 18.15 1.10 1.04 1122.66| | 9: 1.47 - 1.41 6938 155 0.88 18.97 1.09 1.06 987.85| | 10: 1.41 - 1.36 7022 150 0.87 20.34 1.09 1.05 860.56| | 11: 1.36 - 1.32 6997 151 0.87 19.97 1.08 1.03 707.53| | 12: 1.32 - 1.28 6976 149 0.87 19.76 1.08 1.02 629.95| | 13: 1.28 - 1.25 6907 166 0.88 19.50 1.07 1.03 577.57| | 14: 1.25 - 1.22 7015 113 0.86 20.79 1.07 1.03 575.07| | 15: 1.22 - 1.19 6957 137 0.87 20.68 1.07 1.03 523.58| | 16: 1.19 - 1.17 6604 132 0.87 20.40 1.07 1.02 479.12| | 17: 1.17 - 1.14 6941 135 0.87 20.24 1.08 1.02 414.99| | 18: 1.14 - 1.12 6875 142 0.87 20.75 1.08 1.01 384.99| | 19: 1.12 - 1.10 6949 106 0.86 21.61 1.07 1.01 371.14| | 20: 1.10 - 1.08 6884 147 0.85 23.07 1.06 0.99 360.21| | 21: 1.08 - 1.07 6852 152 0.83 25.11 1.06 0.96 364.98| | 22: 1.07 - 1.05 6838 135 0.80 27.63 1.05 0.96 371.81| | 23: 1.05 - 1.03 6829 159 0.78 29.61 1.05 0.95 369.74| | 24: 1.03 - 1.02 6785 133 0.76 31.03 1.05 0.97 360.07| | 25: 1.02 - 1.01 6552 130 0.76 31.26 1.03 0.94 322.93| | 26: 1.01 - 0.99 6767 158 0.75 32.04 1.03 0.93 291.66| | 27: 0.99 - 0.98 6648 131 0.77 30.60 1.04 0.91 250.71| |alpha: min = 0.91 max = 1.06 mean = 1.01| |beta: min = 250.71 max = 34152.97 mean = 2759.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 21.73| |phase err.(test): min = 0.00 max = 88.24 mean = 21.89| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.269 2950 Z= 5.499 Angle : 5.143 18.321 4018 Z= 3.653 Chirality : 0.395 1.348 492 Planarity : 0.032 0.128 512 Dihedral : 12.750 83.867 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.52 % Allowed : 2.59 % Favored : 96.89 % Rotamer: Outliers : 0.65 % Allowed : 4.52 % Favored : 94.84 % Cbeta Deviations : 29.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.39), residues: 386 helix: -2.50 (0.30), residues: 148 sheet: -0.31 (0.57), residues: 86 loop : -0.29 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.160 0.020 ARG A 149 TYR 0.112 0.032 TYR A 192 PHE 0.115 0.045 PHE B 82 TRP 0.111 0.044 TRP A 139 HIS 0.078 0.034 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2033 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300537 | | target function (ml) not normalized (work): 805546.410333 | | target function (ml) not normalized (free): 16544.214378 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2031 0.2033 0.1961 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2031 0.2033 0.1961 n_refl.: 191155 remove outliers: r(all,work,free)=0.2031 0.2033 0.1961 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2032 0.2034 0.1961 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1801 0.1799 0.1907 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1797 0.1907 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 94.06 92 3 0.4036 398.008 292.824 0.422 0.932 0.297 13.296-10.522 99.01 99 1 0.2558 528.187 517.791 0.762 0.934 0.245 10.503-8.327 99.45 178 3 0.2514 565.118 556.677 0.949 0.933 0.220 8.318-6.595 100.00 360 8 0.2477 414.736 404.172 0.945 0.933 0.165 6.588-5.215 100.00 711 7 0.2291 381.101 365.296 0.938 0.933 0.160 5.214-4.128 98.38 1367 28 0.1481 557.435 550.431 1.056 0.932 0.110 4.126-3.266 94.74 2603 46 0.1334 508.132 499.623 1.122 0.931 0.018 3.266-2.585 99.86 5447 97 0.1450 342.774 337.390 1.093 0.929 0.000 2.585-2.046 97.45 10613 204 0.1388 258.603 254.210 1.104 0.926 0.000 2.046-1.619 99.39 21536 464 0.1626 153.054 149.783 1.131 0.920 0.000 1.619-1.281 98.00 42464 925 0.1906 82.395 80.225 1.123 0.912 0.000 1.281-0.980 96.53 101826 2056 0.2320 44.203 41.660 1.121 0.896 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0142 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1797 r_free=0.1907 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 123 ASN Total number of N/Q/H flips: 2 r_work=0.1798 r_free=0.1910 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.788707 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 571.019216 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1273 0.1503 0.0231 0.039 1.2 10.7 0.0 0.0 0 10.894 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.03 2.31 1.119 13.119 571.019 0.018 12.98 15.69 2.70 1.270 13.375 571.019 0.017 Individual atomic B min max mean iso aniso Overall: 5.10 73.05 15.07 1.42 435 3274 Protein: 5.10 40.34 11.04 1.42 0 2902 Water: 6.32 73.05 29.58 N/A 435 370 Other: 16.03 29.99 23.01 N/A 0 2 Chain A: 5.35 59.49 13.11 N/A 0 1626 Chain B: 5.10 73.05 12.82 N/A 0 1648 Chain S: 11.60 67.80 30.93 N/A 435 0 Histogram: Values Number of atoms 5.10 - 11.90 2146 11.90 - 18.69 645 18.69 - 25.49 325 25.49 - 32.28 261 32.28 - 39.08 159 39.08 - 45.87 104 45.87 - 52.67 44 52.67 - 59.46 21 59.46 - 66.26 2 66.26 - 73.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1569 r_work=0.1298 r_free=0.1564 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1564 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1554 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015577 | | target function (ls_wunit_k1) not normalized (work): 2917.589756 | | target function (ls_wunit_k1) not normalized (free): 115.103366 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1554 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1470 0.1467 0.1635 n_refl.: 191138 remove outliers: r(all,work,free)=0.1470 0.1467 0.1635 n_refl.: 191138 overall B=0.15 to atoms: r(all,work,free)=0.1492 0.1490 0.1644 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1282 0.1277 0.1545 n_refl.: 191138 remove outliers: r(all,work,free)=0.1282 0.1277 0.1544 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3564 398.008 377.250 0.484 0.963 0.276 13.296-10.522 99.01 99 1 0.2070 528.187 524.323 0.739 0.964 0.234 10.503-8.327 99.45 178 3 0.1749 565.118 564.950 0.891 0.964 0.220 8.318-6.595 100.00 360 8 0.1710 414.736 411.406 0.909 0.964 0.160 6.588-5.215 100.00 711 7 0.1525 381.101 373.403 0.890 0.964 0.160 5.214-4.128 98.38 1367 28 0.0907 557.435 555.189 0.978 0.965 0.059 4.126-3.266 94.74 2603 46 0.0834 508.132 504.077 1.044 0.965 0.014 3.266-2.585 99.86 5447 97 0.0927 342.774 340.196 1.024 0.965 0.000 2.585-2.046 97.45 10613 204 0.0954 258.603 256.262 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1093 153.054 151.373 1.055 0.966 0.000 1.619-1.281 98.00 42464 925 0.1280 82.395 81.412 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.181 1.023 0.967 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0349 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1544 | n_water=805 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1281 r_free=0.1548 | n_water=794 | time (s): 99.550 (total time: 102.640) Filter (q & B) r_work=0.1282 r_free=0.1550 | n_water=789 | time (s): 5.000 (total time: 107.640) Compute maps r_work=0.1282 r_free=0.1550 | n_water=789 | time (s): 1.990 (total time: 109.630) Filter (map) r_work=0.1306 r_free=0.1531 | n_water=657 | time (s): 4.250 (total time: 113.880) Find peaks r_work=0.1306 r_free=0.1531 | n_water=657 | time (s): 0.920 (total time: 114.800) Add new water r_work=0.1330 r_free=0.1561 | n_water=966 | time (s): 5.410 (total time: 120.210) Refine new water occ: r_work=0.1286 r_free=0.1512 adp: r_work=0.1273 r_free=0.1510 occ: r_work=0.1276 r_free=0.1507 adp: r_work=0.1269 r_free=0.1508 occ: r_work=0.1270 r_free=0.1506 adp: r_work=0.1268 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1507 r_work=0.1268 r_free=0.1507 | n_water=966 | time (s): 81.850 (total time: 202.060) Filter (q & B) r_work=0.1272 r_free=0.1511 | n_water=890 | time (s): 5.730 (total time: 207.790) Filter (dist only) r_work=0.1272 r_free=0.1511 | n_water=889 | time (s): 114.710 (total time: 322.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.833265 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 597.712723 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 0.1254 0.1526 0.0272 0.041 1.1 16.5 0.0 0.3 0 11.917 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.26 2.72 2.056 15.172 597.713 0.014 12.33 15.13 2.80 2.462 15.241 597.713 0.014 Individual atomic B min max mean iso aniso Overall: 5.43 68.21 16.30 1.21 521 3272 Protein: 5.43 40.47 10.99 1.21 0 2902 Water: 6.70 68.21 33.61 N/A 521 368 Other: 16.16 32.15 24.16 N/A 0 2 Chain A: 5.49 55.86 13.01 N/A 0 1624 Chain B: 5.43 68.21 12.85 N/A 0 1648 Chain S: 9.75 67.68 37.45 N/A 521 0 Histogram: Values Number of atoms 5.43 - 11.70 2064 11.70 - 17.98 704 17.98 - 24.26 268 24.26 - 30.54 219 30.54 - 36.82 167 36.82 - 43.09 177 43.09 - 49.37 98 49.37 - 55.65 54 55.65 - 61.93 28 61.93 - 68.21 14 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1513 r_work=0.1233 r_free=0.1513 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1513 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 = 0.1517 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1517 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013382 | | target function (ls_wunit_k1) not normalized (work): 2506.425777 | | target function (ls_wunit_k1) not normalized (free): 103.937058 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1517 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1622 n_refl.: 191137 remove outliers: r(all,work,free)=0.1436 0.1433 0.1622 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1429 0.1620 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1524 n_refl.: 191137 remove outliers: r(all,work,free)=0.1239 0.1233 0.1524 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3253 398.008 369.468 0.477 0.962 0.256 13.296-10.522 99.01 99 1 0.1882 528.187 519.405 0.757 0.963 0.214 10.503-8.327 99.45 178 3 0.1469 565.118 567.506 0.919 0.963 0.200 8.318-6.595 100.00 360 8 0.1539 414.736 414.368 0.940 0.963 0.167 6.588-5.215 100.00 711 7 0.1360 381.101 376.652 0.913 0.963 0.127 5.214-4.128 98.38 1367 28 0.0822 557.435 556.188 0.997 0.963 0.080 4.126-3.266 94.74 2603 46 0.0752 508.132 505.730 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0851 342.774 341.382 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0897 258.603 256.720 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.622 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.350 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.222 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0555 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1524 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1524 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1524 | n_water=889 | time (s): 3.290 (total time: 3.290) Filter (dist) r_work=0.1234 r_free=0.1525 | n_water=888 | time (s): 115.410 (total time: 118.700) Filter (q & B) r_work=0.1234 r_free=0.1524 | n_water=885 | time (s): 5.490 (total time: 124.190) Compute maps r_work=0.1234 r_free=0.1524 | n_water=885 | time (s): 1.830 (total time: 126.020) Filter (map) r_work=0.1277 r_free=0.1513 | n_water=694 | time (s): 4.270 (total time: 130.290) Find peaks r_work=0.1277 r_free=0.1513 | n_water=694 | time (s): 0.630 (total time: 130.920) Add new water r_work=0.1300 r_free=0.1544 | n_water=1009 | time (s): 5.090 (total time: 136.010) Refine new water occ: r_work=0.1255 r_free=0.1510 adp: r_work=0.1255 r_free=0.1509 occ: r_work=0.1251 r_free=0.1508 adp: r_work=0.1250 r_free=0.1507 occ: r_work=0.1247 r_free=0.1506 adp: r_work=0.1247 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1247 r_free=0.1505 r_work=0.1247 r_free=0.1505 | n_water=1009 | time (s): 292.190 (total time: 428.200) Filter (q & B) r_work=0.1251 r_free=0.1511 | n_water=884 | time (s): 6.290 (total time: 434.490) Filter (dist only) r_work=0.1251 r_free=0.1510 | n_water=883 | time (s): 117.620 (total time: 552.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.664385 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.383976 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 0.1241 0.1444 0.0203 0.035 1.1 6.6 0.0 0.0 0 0.832 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.44 2.03 1.935 14.627 16.384 3.942 12.36 14.01 1.65 2.245 14.528 16.384 3.898 Individual atomic B min max mean iso aniso Overall: 5.54 67.76 15.33 1.06 517 3270 Protein: 5.54 36.71 10.74 1.06 0 2902 Water: 6.71 67.76 30.38 N/A 517 366 Other: 13.88 28.04 20.96 N/A 0 2 Chain A: 5.55 54.86 12.75 N/A 0 1623 Chain B: 5.54 67.76 12.55 N/A 0 1647 Chain S: 13.67 60.64 32.25 N/A 517 0 Histogram: Values Number of atoms 5.54 - 11.76 2131 11.76 - 17.99 687 17.99 - 24.21 290 24.21 - 30.43 249 30.43 - 36.65 171 36.65 - 42.87 155 42.87 - 49.10 67 49.10 - 55.32 28 55.32 - 61.54 8 61.54 - 67.76 1 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1401 r_work=0.1237 r_free=0.1402 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1402 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1394 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1394 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892109 | | target function (ml) not normalized (work): 728976.460591 | | target function (ml) not normalized (free): 15223.977717 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1393 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1443 0.1442 0.1506 n_refl.: 191137 remove outliers: r(all,work,free)=0.1443 0.1442 0.1506 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1436 0.1501 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1390 n_refl.: 191137 remove outliers: r(all,work,free)=0.1230 0.1226 0.1390 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3805 393.525 358.174 0.421 0.947 0.259 13.296-10.522 98.02 98 1 0.2382 528.900 506.112 0.707 0.948 0.216 10.503-8.327 98.90 177 3 0.2035 557.261 557.155 0.882 0.948 0.193 8.318-6.595 100.00 360 8 0.2076 414.736 410.892 0.900 0.948 0.130 6.588-5.215 100.00 711 7 0.1807 381.101 370.876 0.888 0.948 0.130 5.214-4.128 98.38 1367 28 0.1172 557.435 551.512 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1082 508.132 501.793 1.032 0.948 0.000 3.266-2.585 99.86 5447 97 0.1095 342.774 339.154 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0969 258.603 255.741 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0980 153.054 151.414 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.495 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.319 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1050 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1389 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1389 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1389 | n_water=883 | time (s): 2.920 (total time: 2.920) Filter (dist) r_work=0.1226 r_free=0.1388 | n_water=882 | time (s): 112.150 (total time: 115.070) Filter (q & B) r_work=0.1227 r_free=0.1385 | n_water=874 | time (s): 4.240 (total time: 119.310) Compute maps r_work=0.1227 r_free=0.1385 | n_water=874 | time (s): 1.620 (total time: 120.930) Filter (map) r_work=0.1252 r_free=0.1385 | n_water=718 | time (s): 4.250 (total time: 125.180) Find peaks r_work=0.1252 r_free=0.1385 | n_water=718 | time (s): 0.560 (total time: 125.740) Add new water r_work=0.1267 r_free=0.1402 | n_water=973 | time (s): 4.900 (total time: 130.640) Refine new water occ: r_work=0.1216 r_free=0.1366 adp: r_work=0.1208 r_free=0.1360 occ: r_work=0.1205 r_free=0.1360 adp: r_work=0.1205 r_free=0.1359 occ: r_work=0.1203 r_free=0.1359 adp: r_work=0.1203 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1358 r_work=0.1203 r_free=0.1358 | n_water=973 | time (s): 291.790 (total time: 422.430) Filter (q & B) r_work=0.1207 r_free=0.1364 | n_water=879 | time (s): 4.480 (total time: 426.910) Filter (dist only) r_work=0.1208 r_free=0.1364 | n_water=878 | time (s): 114.440 (total time: 541.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.635116 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.664322 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1363 0.0158 0.036 1.1 5.8 0.0 0.0 0 0.818 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.63 1.58 1.831 14.242 14.664 3.874 11.98 13.61 1.63 1.909 14.215 14.664 3.867 Individual atomic B min max mean iso aniso Overall: 5.55 67.41 15.06 1.00 513 3269 Protein: 5.55 33.70 10.68 1.00 0 2902 Water: 5.95 67.41 29.52 N/A 513 365 Other: 13.95 27.46 20.70 N/A 0 2 Chain A: 5.55 53.98 12.63 N/A 0 1622 Chain B: 5.55 67.41 12.48 N/A 0 1647 Chain S: 5.95 60.58 31.04 N/A 513 0 Histogram: Values Number of atoms 5.55 - 11.73 2123 11.73 - 17.92 719 17.92 - 24.10 286 24.10 - 30.29 261 30.29 - 36.48 167 36.48 - 42.66 130 42.66 - 48.85 67 48.85 - 55.04 21 55.04 - 61.22 7 61.22 - 67.41 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 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) = 3.867 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1358 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865553 | | target function (ml) not normalized (work): 723991.072730 | | target function (ml) not normalized (free): 15136.751092 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1358 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1422 0.1422 0.1479 n_refl.: 191134 remove outliers: r(all,work,free)=0.1422 0.1422 0.1479 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1415 0.1414 0.1474 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191134 remove outliers: r(all,work,free)=0.1197 0.1194 0.1356 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3822 356.250 319.878 0.412 0.948 0.257 13.296-10.522 98.02 98 1 0.2442 478.802 460.342 0.710 0.949 0.211 10.503-8.327 98.35 176 3 0.2060 502.669 497.421 0.868 0.949 0.187 8.318-6.595 100.00 360 8 0.2179 375.452 369.773 0.891 0.949 0.115 6.588-5.215 100.00 711 7 0.1860 345.003 335.463 0.887 0.949 0.110 5.214-4.128 98.38 1367 28 0.1179 504.634 499.469 0.971 0.949 0.070 4.126-3.266 94.74 2603 46 0.1096 460.001 453.684 1.031 0.949 0.000 3.266-2.585 99.86 5447 97 0.1073 310.306 307.067 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0935 234.108 231.617 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0922 138.557 137.238 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0991 74.591 73.861 1.055 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.015 38.349 1.044 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1217 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1356 | n_water=878 | time (s): 3.030 (total time: 3.030) Filter (dist) r_work=0.1194 r_free=0.1357 | n_water=877 | time (s): 110.190 (total time: 113.220) Filter (q & B) r_work=0.1195 r_free=0.1357 | n_water=869 | time (s): 4.920 (total time: 118.140) Compute maps r_work=0.1195 r_free=0.1357 | n_water=869 | time (s): 2.540 (total time: 120.680) Filter (map) r_work=0.1219 r_free=0.1358 | n_water=738 | time (s): 4.580 (total time: 125.260) Find peaks r_work=0.1219 r_free=0.1358 | n_water=738 | time (s): 0.620 (total time: 125.880) Add new water r_work=0.1232 r_free=0.1379 | n_water=962 | time (s): 3.880 (total time: 129.760) Refine new water occ: r_work=0.1195 r_free=0.1352 adp: r_work=0.1195 r_free=0.1352 occ: r_work=0.1192 r_free=0.1350 adp: r_work=0.1193 r_free=0.1350 occ: r_work=0.1191 r_free=0.1349 adp: r_work=0.1191 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1349 r_work=0.1191 r_free=0.1349 | n_water=962 | time (s): 238.270 (total time: 368.030) Filter (q & B) r_work=0.1194 r_free=0.1357 | n_water=879 | time (s): 5.020 (total time: 373.050) Filter (dist only) r_work=0.1194 r_free=0.1357 | n_water=878 | time (s): 117.790 (total time: 490.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.564217 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.182707 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1370 0.0173 0.037 1.1 4.9 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.70 1.73 1.795 14.146 15.183 3.766 12.01 13.75 1.74 1.906 14.102 15.183 3.762 Individual atomic B min max mean iso aniso Overall: 5.54 66.90 14.93 0.95 513 3269 Protein: 5.54 31.87 10.59 0.95 0 2902 Water: 6.08 66.90 29.27 N/A 513 365 Other: 13.83 25.68 19.75 N/A 0 2 Chain A: 5.54 52.82 12.50 N/A 0 1622 Chain B: 5.57 66.90 12.36 N/A 0 1647 Chain S: 6.08 60.69 30.87 N/A 513 0 Histogram: Values Number of atoms 5.54 - 11.68 2124 11.68 - 17.81 737 17.81 - 23.95 291 23.95 - 30.09 236 30.09 - 36.22 165 36.22 - 42.36 129 42.36 - 48.49 71 48.49 - 54.63 21 54.63 - 60.77 7 60.77 - 66.90 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1375 r_work=0.1201 r_free=0.1376 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1376 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1373 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761150 | | target function (ml) not normalized (work): 704433.228384 | | target function (ml) not normalized (free): 14749.136682 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1373 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1429 0.1428 0.1492 n_refl.: 191133 remove outliers: r(all,work,free)=0.1429 0.1428 0.1492 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1421 0.1420 0.1487 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1369 n_refl.: 191133 remove outliers: r(all,work,free)=0.1202 0.1199 0.1369 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3800 347.764 317.477 0.400 0.948 0.239 13.296-10.522 98.02 98 1 0.2439 478.802 462.104 0.702 0.949 0.190 10.503-8.327 98.35 176 3 0.2109 502.669 494.448 0.864 0.949 0.167 8.318-6.595 100.00 360 8 0.2185 375.452 368.922 0.889 0.949 0.124 6.588-5.215 100.00 711 7 0.1897 345.003 335.867 0.887 0.949 0.103 5.214-4.128 98.38 1367 28 0.1216 504.634 499.124 0.973 0.949 0.070 4.126-3.266 94.74 2603 46 0.1136 460.001 453.369 1.034 0.949 0.000 3.266-2.585 99.86 5447 97 0.1103 310.306 306.941 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0949 234.108 231.603 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0918 138.557 137.222 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0978 74.591 73.870 1.055 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.015 38.343 1.043 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1329 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1369 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1369 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1369 | n_water=878 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1199 r_free=0.1369 | n_water=878 | time (s): 111.920 (total time: 114.580) Filter (q & B) r_work=0.1199 r_free=0.1370 | n_water=870 | time (s): 4.850 (total time: 119.430) Compute maps r_work=0.1199 r_free=0.1370 | n_water=870 | time (s): 2.270 (total time: 121.700) Filter (map) r_work=0.1225 r_free=0.1371 | n_water=745 | time (s): 5.120 (total time: 126.820) Find peaks r_work=0.1225 r_free=0.1371 | n_water=745 | time (s): 0.570 (total time: 127.390) Add new water r_work=0.1238 r_free=0.1388 | n_water=962 | time (s): 4.250 (total time: 131.640) Refine new water occ: r_work=0.1198 r_free=0.1353 adp: r_work=0.1199 r_free=0.1352 occ: r_work=0.1196 r_free=0.1353 adp: r_work=0.1196 r_free=0.1352 occ: r_work=0.1193 r_free=0.1353 adp: r_work=0.1193 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1353 r_work=0.1193 r_free=0.1353 | n_water=962 | time (s): 241.110 (total time: 372.750) Filter (q & B) r_work=0.1197 r_free=0.1355 | n_water=893 | time (s): 4.660 (total time: 377.410) Filter (dist only) r_work=0.1197 r_free=0.1354 | n_water=892 | time (s): 118.370 (total time: 495.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.483916 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.508721 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 0.1201 0.1358 0.0157 0.037 1.1 6.5 0.0 0.3 0 0.742 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.58 1.57 1.758 14.051 14.509 3.762 12.02 13.59 1.57 1.863 14.014 14.509 3.759 Individual atomic B min max mean iso aniso Overall: 5.59 65.98 14.88 0.91 527 3269 Protein: 5.59 29.39 10.50 0.91 0 2902 Water: 5.97 65.98 29.14 N/A 527 365 Other: 13.88 23.56 18.72 N/A 0 2 Chain A: 5.64 52.46 12.37 N/A 0 1622 Chain B: 5.59 65.98 12.24 N/A 0 1647 Chain S: 5.97 60.98 30.87 N/A 527 0 Histogram: Values Number of atoms 5.59 - 11.63 2119 11.63 - 17.66 762 17.66 - 23.70 288 23.70 - 29.74 218 29.74 - 35.78 171 35.78 - 41.82 126 41.82 - 47.86 74 47.86 - 53.90 30 53.90 - 59.94 5 59.94 - 65.98 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1359 r_work=0.1202 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1359 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1361 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758389 | | target function (ml) not normalized (work): 703912.485848 | | target function (ml) not normalized (free): 14732.814448 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1361 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1426 0.1424 0.1502 n_refl.: 191132 remove outliers: r(all,work,free)=0.1426 0.1424 0.1502 n_refl.: 191132 overall B=-0.23 to atoms: r(all,work,free)=0.1386 0.1384 0.1477 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191132 remove outliers: r(all,work,free)=0.1202 0.1199 0.1363 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3861 347.764 310.174 0.397 0.948 0.237 13.296-10.522 98.02 98 1 0.2445 478.802 462.176 0.717 0.949 0.181 10.503-8.327 98.35 176 3 0.2119 502.669 494.613 0.886 0.949 0.153 8.318-6.595 100.00 360 8 0.2149 375.452 370.108 0.911 0.949 0.113 6.588-5.215 100.00 711 7 0.1895 345.003 336.076 0.910 0.949 0.097 5.214-4.128 98.38 1367 28 0.1237 504.634 499.270 1.000 0.949 0.090 4.126-3.266 94.74 2603 46 0.1140 460.001 453.076 1.059 0.949 0.000 3.266-2.585 99.86 5447 97 0.1110 310.306 307.020 1.043 0.949 0.000 2.585-2.046 97.45 10613 204 0.0954 234.108 231.645 1.052 0.949 0.000 2.046-1.619 99.39 21536 464 0.0917 138.557 137.246 1.069 0.948 0.000 1.619-1.281 98.00 42464 925 0.0970 74.591 73.880 1.057 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.015 38.339 1.027 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0513 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1363 | n_water=892 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1200 r_free=0.1363 | n_water=891 | time (s): 126.410 (total time: 129.470) Filter (q & B) r_work=0.1200 r_free=0.1364 | n_water=881 | time (s): 4.880 (total time: 134.350) Compute maps r_work=0.1200 r_free=0.1364 | n_water=881 | time (s): 2.490 (total time: 136.840) Filter (map) r_work=0.1224 r_free=0.1355 | n_water=760 | time (s): 4.310 (total time: 141.150) Find peaks r_work=0.1224 r_free=0.1355 | n_water=760 | time (s): 0.620 (total time: 141.770) Add new water r_work=0.1235 r_free=0.1372 | n_water=964 | time (s): 5.140 (total time: 146.910) Refine new water occ: r_work=0.1199 r_free=0.1347 adp: r_work=0.1199 r_free=0.1347 occ: r_work=0.1197 r_free=0.1347 adp: r_work=0.1197 r_free=0.1347 occ: r_work=0.1196 r_free=0.1347 adp: r_work=0.1195 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1347 r_work=0.1195 r_free=0.1347 | n_water=964 | time (s): 261.970 (total time: 408.880) Filter (q & B) r_work=0.1198 r_free=0.1353 | n_water=896 | time (s): 4.990 (total time: 413.870) Filter (dist only) r_work=0.1198 r_free=0.1353 | n_water=895 | time (s): 116.050 (total time: 529.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.597848 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.605990 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 0.1201 0.1359 0.0158 0.038 1.1 5.8 0.0 0.3 0 0.799 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.59 1.58 1.721 13.714 14.606 3.759 12.01 13.61 1.60 1.777 13.695 14.606 3.756 Individual atomic B min max mean iso aniso Overall: 5.40 64.68 14.57 0.89 531 3268 Protein: 5.40 28.46 10.24 0.89 0 2902 Water: 5.77 64.68 28.59 N/A 531 364 Other: 13.69 22.07 17.88 N/A 0 2 Chain A: 5.42 51.89 12.07 N/A 0 1622 Chain B: 5.40 64.68 11.95 N/A 0 1646 Chain S: 5.77 61.11 30.34 N/A 531 0 Histogram: Values Number of atoms 5.40 - 11.32 2098 11.32 - 17.25 786 17.25 - 23.18 279 23.18 - 29.11 221 29.11 - 35.04 176 35.04 - 40.96 116 40.96 - 46.89 85 46.89 - 52.82 29 52.82 - 58.75 6 58.75 - 64.68 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1361 r_work=0.1202 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1362 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755549 | | target function (ml) not normalized (work): 703380.479199 | | target function (ml) not normalized (free): 14722.833841 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1362 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1474 n_refl.: 191132 remove outliers: r(all,work,free)=0.1393 0.1391 0.1474 n_refl.: 191132 overall B=0.06 to atoms: r(all,work,free)=0.1402 0.1401 0.1480 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1350 n_refl.: 191132 remove outliers: r(all,work,free)=0.1194 0.1190 0.1350 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3798 347.764 310.366 0.384 0.970 0.222 13.296-10.522 98.02 98 1 0.2479 478.802 462.445 0.693 0.972 0.154 10.503-8.327 98.35 176 3 0.2175 502.669 492.660 0.871 0.972 0.127 8.315-6.595 100.00 359 8 0.2154 374.506 370.322 0.896 0.972 0.106 6.588-5.215 100.00 711 7 0.1922 345.003 335.376 0.895 0.972 0.092 5.214-4.128 98.38 1367 28 0.1247 504.634 498.535 0.986 0.973 0.090 4.126-3.266 94.74 2603 46 0.1151 460.001 452.533 1.046 0.974 0.005 3.266-2.585 99.86 5447 97 0.1115 310.306 306.720 1.028 0.975 0.000 2.585-2.046 97.45 10613 204 0.0957 234.108 231.499 1.037 0.976 0.000 2.046-1.619 99.39 21536 464 0.0909 138.557 137.183 1.053 0.979 0.000 1.619-1.281 98.00 42464 925 0.0947 74.591 73.927 1.041 0.983 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.015 38.317 1.007 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0606 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1350 | n_water=895 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1191 r_free=0.1349 | n_water=894 | time (s): 124.590 (total time: 126.870) Filter (q & B) r_work=0.1192 r_free=0.1346 | n_water=885 | time (s): 3.980 (total time: 130.850) Compute maps r_work=0.1192 r_free=0.1346 | n_water=885 | time (s): 2.410 (total time: 133.260) Filter (map) r_work=0.1214 r_free=0.1346 | n_water=770 | time (s): 4.640 (total time: 137.900) Find peaks r_work=0.1214 r_free=0.1346 | n_water=770 | time (s): 0.690 (total time: 138.590) Add new water r_work=0.1224 r_free=0.1360 | n_water=970 | time (s): 4.200 (total time: 142.790) Refine new water occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1190 r_free=0.1337 occ: r_work=0.1188 r_free=0.1338 adp: r_work=0.1188 r_free=0.1337 occ: r_work=0.1186 r_free=0.1339 adp: r_work=0.1186 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1339 r_work=0.1186 r_free=0.1339 | n_water=970 | time (s): 258.450 (total time: 401.240) Filter (q & B) r_work=0.1189 r_free=0.1348 | n_water=898 | time (s): 5.480 (total time: 406.720) Filter (dist only) r_work=0.1189 r_free=0.1348 | n_water=897 | time (s): 115.260 (total time: 521.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.543753 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.403186 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1352 0.0159 0.038 1.1 5.6 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.52 1.59 1.678 13.719 14.403 3.754 11.94 13.54 1.61 1.684 13.713 14.403 3.753 Individual atomic B min max mean iso aniso Overall: 5.46 64.29 14.62 0.88 533 3268 Protein: 5.46 28.32 10.32 0.88 0 2902 Water: 5.89 64.29 28.51 N/A 533 364 Other: 13.78 22.14 17.96 N/A 0 2 Chain A: 5.55 51.79 12.12 N/A 0 1622 Chain B: 5.46 64.29 12.00 N/A 0 1646 Chain S: 5.89 61.32 30.31 N/A 533 0 Histogram: Values Number of atoms 5.46 - 11.35 2077 11.35 - 17.23 809 17.23 - 23.11 277 23.11 - 28.99 225 28.99 - 34.88 170 34.88 - 40.76 120 40.76 - 46.64 81 46.64 - 52.52 32 52.52 - 58.40 7 58.40 - 64.29 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1355 r_work=0.1194 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1355 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1357 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752853 | | target function (ml) not normalized (work): 702871.783456 | | target function (ml) not normalized (free): 14717.715389 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1357 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1411 0.1410 0.1499 n_refl.: 191131 remove outliers: r(all,work,free)=0.1411 0.1410 0.1499 n_refl.: 191131 overall B=0.01 to atoms: r(all,work,free)=0.1413 0.1412 0.1500 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1353 n_refl.: 191131 remove outliers: r(all,work,free)=0.1194 0.1191 0.1353 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3841 347.764 309.383 0.379 0.970 0.218 13.296-10.522 98.02 98 1 0.2493 478.802 461.611 0.687 0.971 0.146 10.503-8.327 98.35 176 3 0.2200 502.669 492.710 0.869 0.972 0.117 8.315-6.595 100.00 359 8 0.2159 374.506 369.566 0.892 0.972 0.106 6.588-5.215 100.00 711 7 0.1934 345.003 335.311 0.894 0.972 0.100 5.214-4.128 98.38 1367 28 0.1254 504.634 498.654 0.984 0.973 0.054 4.126-3.266 94.74 2603 46 0.1165 460.001 452.450 1.046 0.974 0.005 3.266-2.585 99.86 5447 97 0.1121 310.306 306.656 1.029 0.975 0.000 2.585-2.046 97.45 10613 204 0.0957 234.108 231.485 1.037 0.977 0.000 2.046-1.619 99.39 21536 464 0.0910 138.557 137.197 1.054 0.980 0.000 1.619-1.281 98.00 42464 925 0.0942 74.591 73.939 1.044 0.985 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.015 38.304 1.012 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1353 | n_water=897 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1191 r_free=0.1353 | n_water=897 | time (s): 119.000 (total time: 121.450) Filter (q & B) r_work=0.1192 r_free=0.1352 | n_water=888 | time (s): 5.070 (total time: 126.520) Compute maps r_work=0.1192 r_free=0.1352 | n_water=888 | time (s): 1.940 (total time: 128.460) Filter (map) r_work=0.1217 r_free=0.1350 | n_water=766 | time (s): 4.740 (total time: 133.200) Find peaks r_work=0.1217 r_free=0.1350 | n_water=766 | time (s): 0.630 (total time: 133.830) Add new water r_work=0.1226 r_free=0.1366 | n_water=969 | time (s): 3.910 (total time: 137.740) Refine new water occ: r_work=0.1191 r_free=0.1336 adp: r_work=0.1191 r_free=0.1337 occ: r_work=0.1189 r_free=0.1335 adp: r_work=0.1189 r_free=0.1335 occ: r_work=0.1188 r_free=0.1334 adp: r_work=0.1188 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1334 r_work=0.1188 r_free=0.1334 | n_water=969 | time (s): 155.890 (total time: 293.630) Filter (q & B) r_work=0.1191 r_free=0.1341 | n_water=888 | time (s): 4.630 (total time: 298.260) Filter (dist only) r_work=0.1191 r_free=0.1340 | n_water=887 | time (s): 119.170 (total time: 417.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.544362 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.252775 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 0.1346 0.0152 0.039 1.1 5.1 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.46 1.52 1.682 13.699 14.253 3.753 11.94 13.47 1.53 1.693 13.693 14.253 3.752 Individual atomic B min max mean iso aniso Overall: 5.55 63.51 14.56 0.87 523 3268 Protein: 5.55 28.12 10.34 0.87 0 2902 Water: 5.95 63.51 28.33 N/A 523 364 Other: 13.83 22.20 18.02 N/A 0 2 Chain A: 5.61 51.54 12.12 N/A 0 1622 Chain B: 5.55 63.51 12.00 N/A 0 1646 Chain S: 5.95 61.58 30.17 N/A 523 0 Histogram: Values Number of atoms 5.55 - 11.35 2070 11.35 - 17.14 816 17.14 - 22.94 274 22.94 - 28.73 219 28.73 - 34.53 176 34.53 - 40.32 111 40.32 - 46.12 82 46.12 - 51.92 30 51.92 - 57.71 10 57.71 - 63.51 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1347 r_work=0.1195 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1347 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1346 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751792 | | target function (ml) not normalized (work): 702673.095577 | | target function (ml) not normalized (free): 14715.084233 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1346 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1425 0.1423 0.1504 n_refl.: 191131 remove outliers: r(all,work,free)=0.1425 0.1423 0.1504 n_refl.: 191131 overall B=-0.00 to atoms: r(all,work,free)=0.1424 0.1423 0.1503 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1345 n_refl.: 191131 remove outliers: r(all,work,free)=0.1195 0.1192 0.1345 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3727 343.683 303.850 0.396 0.908 0.208 13.296-10.522 97.03 97 1 0.2450 481.075 459.896 0.729 0.910 0.137 10.503-8.327 98.35 176 3 0.2227 502.669 491.876 0.924 0.910 0.110 8.315-6.595 100.00 359 8 0.2164 374.506 370.226 0.948 0.910 0.083 6.588-5.215 100.00 711 7 0.1938 345.003 335.290 0.952 0.910 0.074 5.214-4.128 98.38 1367 28 0.1270 504.634 498.225 1.049 0.911 0.060 4.126-3.266 94.74 2603 46 0.1174 460.001 452.332 1.117 0.913 0.005 3.266-2.585 99.86 5447 97 0.1128 310.306 306.710 1.099 0.913 0.000 2.585-2.046 97.45 10613 204 0.0959 234.108 231.474 1.108 0.916 0.000 2.046-1.619 99.39 21536 464 0.0909 138.557 137.210 1.126 0.919 0.000 1.619-1.281 98.00 42464 925 0.0940 74.591 73.945 1.117 0.925 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.015 38.299 1.084 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0107 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1345 After: r_work=0.1193 r_free=0.1345 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1194 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1348 | n_water=887 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1194 r_free=0.1347 | n_water=885 | time (s): 124.360 (total time: 126.520) Filter (q & B) r_work=0.1195 r_free=0.1344 | n_water=876 | time (s): 4.750 (total time: 131.270) Compute maps r_work=0.1195 r_free=0.1344 | n_water=876 | time (s): 1.790 (total time: 133.060) Filter (map) r_work=0.1217 r_free=0.1356 | n_water=764 | time (s): 4.670 (total time: 137.730) Find peaks r_work=0.1217 r_free=0.1356 | n_water=764 | time (s): 0.540 (total time: 138.270) Add new water r_work=0.1225 r_free=0.1363 | n_water=965 | time (s): 5.120 (total time: 143.390) Refine new water occ: r_work=0.1191 r_free=0.1336 adp: r_work=0.1191 r_free=0.1336 occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1189 r_free=0.1337 occ: r_work=0.1188 r_free=0.1337 adp: r_work=0.1187 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1337 r_work=0.1187 r_free=0.1337 | n_water=965 | time (s): 209.570 (total time: 352.960) Filter (q & B) r_work=0.1190 r_free=0.1348 | n_water=897 | time (s): 4.210 (total time: 357.170) Filter (dist only) r_work=0.1191 r_free=0.1348 | n_water=895 | time (s): 120.800 (total time: 477.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.604007 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.979454 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1350 0.0157 0.039 1.2 7.5 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.50 1.57 1.679 13.710 13.979 3.754 11.94 13.53 1.59 1.681 13.710 13.979 3.753 Individual atomic B min max mean iso aniso Overall: 5.57 62.69 14.58 0.86 531 3268 Protein: 5.57 27.98 10.36 0.86 0 2902 Water: 6.02 62.69 28.28 N/A 531 364 Other: 13.86 22.10 17.98 N/A 0 2 Chain A: 5.64 51.24 12.10 N/A 0 1622 Chain B: 5.57 62.69 11.99 N/A 0 1646 Chain S: 6.02 61.69 30.18 N/A 531 0 Histogram: Values Number of atoms 5.57 - 11.28 2047 11.28 - 16.99 834 16.99 - 22.71 271 22.71 - 28.42 220 28.42 - 34.13 179 34.13 - 39.84 116 39.84 - 45.56 84 45.56 - 51.27 32 51.27 - 56.98 10 56.98 - 62.69 6 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1353 r_work=0.1194 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1353 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1353 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753183 | | target function (ml) not normalized (work): 702922.409704 | | target function (ml) not normalized (free): 14718.991135 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1361 0.1467 5.6898 5.7669| | 2: 2.94 - 2.33 1.00 7339 128 0.1073 0.1346 5.0787 5.1629| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1199 4.654 4.7519| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1044 4.3915 4.5576| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0988 4.1463 4.2331| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1062 3.9423 4.0595| | 7: 1.62 - 1.54 0.99 7104 148 0.0890 0.0960 3.7961 3.934| | 8: 1.54 - 1.47 0.96 6798 152 0.0889 0.1282 3.6954 3.8884| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1116 3.6167 3.7476| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1173 3.5531 3.6705| | 11: 1.36 - 1.32 0.99 6997 151 0.0992 0.1151 3.486 3.5941| | 12: 1.32 - 1.28 0.98 6975 149 0.1036 0.1129 3.4627 3.59| | 13: 1.28 - 1.25 0.98 6907 166 0.1045 0.1250 3.4405 3.573| | 14: 1.25 - 1.22 0.98 7015 112 0.1108 0.1572 3.434 3.6742| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1235 3.4474 3.485| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1542 3.464 3.6535| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1226 3.4326 3.4416| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1700 3.437 3.5316| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1754 3.4184 3.5958| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1582 3.4088 3.432| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2143 3.417 3.506| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1946 3.4118 3.4107| | 23: 1.05 - 1.03 0.97 6827 159 0.2118 0.2021 3.4325 3.4867| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2260 3.4356 3.5105| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2522 3.4491 3.5248| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2853 3.4152 3.4228| | 27: 0.99 - 0.98 0.94 6647 131 0.3045 0.2806 3.4688 3.3965| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7396 127 0.93 11.72 1.00 0.95 11281.76| | 2: 2.94 - 2.33 7339 128 0.93 12.80 0.99 0.95 5124.24| | 3: 2.33 - 2.04 6939 150 0.96 7.53 1.01 0.95 1663.09| | 4: 2.04 - 1.85 7170 155 0.96 7.53 1.00 0.95 985.90| | 5: 1.85 - 1.72 7113 159 0.96 7.98 1.00 0.96 623.47| | 6: 1.72 - 1.62 7102 142 0.96 7.94 1.00 0.96 436.03| | 7: 1.62 - 1.54 7104 148 0.96 8.03 1.01 0.97 332.37| | 8: 1.54 - 1.47 6798 152 0.96 8.17 1.01 0.97 274.45| | 9: 1.47 - 1.41 6938 155 0.96 8.35 1.00 0.98 227.05| | 10: 1.41 - 1.36 7022 150 0.96 8.86 1.00 0.97 200.80| | 11: 1.36 - 1.32 6997 151 0.96 8.96 0.99 0.96 175.72| | 12: 1.32 - 1.28 6975 149 0.96 9.09 0.98 0.95 162.81| | 13: 1.28 - 1.25 6907 166 0.96 9.62 1.01 0.96 159.93| | 14: 1.25 - 1.22 7015 112 0.95 10.75 1.01 0.97 163.80| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 0.98 166.19| | 16: 1.19 - 1.17 6604 132 0.95 11.39 1.01 0.96 159.46| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.96 153.23| | 18: 1.14 - 1.12 6875 142 0.94 12.71 1.01 0.95 147.27| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.95 150.80| | 20: 1.10 - 1.08 6884 147 0.92 15.19 1.00 0.94 149.79| | 21: 1.08 - 1.07 6852 152 0.91 16.61 1.00 0.93 152.84| | 22: 1.07 - 1.05 6836 135 0.89 18.26 0.99 0.93 154.28| | 23: 1.05 - 1.03 6827 159 0.87 20.49 0.99 0.92 164.50| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.93 179.10| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.90 182.42| | 26: 1.01 - 0.99 6767 158 0.81 26.66 0.98 0.89 176.93| | 27: 0.99 - 0.98 6647 131 0.82 26.35 0.99 0.87 161.37| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.27 max = 11281.76 mean = 925.25| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.90 mean = 13.27| |phase err.(test): min = 0.00 max = 88.91 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1415 0.1414 0.1513 n_refl.: 191128 remove outliers: r(all,work,free)=0.1415 0.1414 0.1513 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1406 0.1404 0.1506 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3741 343.683 306.017 0.348 0.994 0.198 13.296-10.522 97.03 97 1 0.2475 481.075 462.928 0.656 0.996 0.146 10.503-8.327 98.35 176 3 0.2197 502.669 492.750 0.824 0.997 0.128 8.315-6.595 100.00 359 8 0.2145 374.506 370.071 0.846 0.997 0.089 6.588-5.215 100.00 711 7 0.1933 345.003 334.889 0.847 0.997 0.080 5.214-4.128 98.38 1367 28 0.1261 504.634 498.331 0.933 0.998 0.039 4.126-3.266 94.74 2603 46 0.1164 460.001 452.294 0.995 1.000 0.000 3.266-2.585 99.86 5447 97 0.1122 310.306 306.738 0.979 1.001 0.000 2.585-2.046 97.45 10613 204 0.0964 234.108 231.436 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0910 138.557 137.197 1.001 1.008 0.000 1.619-1.281 98.00 42464 925 0.0944 74.591 73.940 0.991 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.015 38.288 0.960 1.026 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0128 ================= 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 : 0.2033 0.1961 0.083 5.143 5.2 78.0 14.6 805 0.000 1_bss: 0.1797 0.1907 0.083 5.143 5.2 78.1 14.6 805 0.000 1_settarget: 0.1797 0.1907 0.083 5.143 5.2 78.1 14.6 805 0.000 1_nqh: 0.1798 0.1910 0.083 5.143 5.2 78.1 14.6 805 0.003 1_weight: 0.1798 0.1910 0.083 5.143 5.2 78.1 14.6 805 0.003 1_xyzrec: 0.1273 0.1503 0.039 1.151 5.2 78.1 14.6 805 0.158 1_adp: 0.1299 0.1569 0.039 1.151 5.1 73.1 15.1 805 0.158 1_regHadp: 0.1298 0.1564 0.039 1.151 5.1 73.1 15.1 805 0.158 1_occ: 0.1283 0.1554 0.039 1.151 5.1 73.1 15.1 805 0.158 2_bss: 0.1277 0.1544 0.039 1.151 5.3 73.2 15.2 805 0.158 2_settarget: 0.1277 0.1544 0.039 1.151 5.3 73.2 15.2 805 0.158 2_updatecdl: 0.1277 0.1544 0.039 1.152 5.3 73.2 15.2 805 0.158 2_nqh: 0.1277 0.1544 0.039 1.152 5.3 73.2 15.2 805 0.158 2_sol: 0.1272 0.1511 0.039 1.152 5.3 73.2 16.2 889 n/a 2_weight: 0.1272 0.1511 0.039 1.152 5.3 73.2 16.2 889 n/a 2_xyzrec: 0.1254 0.1526 0.041 1.144 5.3 73.2 16.2 889 n/a 2_adp: 0.1233 0.1513 0.041 1.144 5.4 68.2 16.3 889 n/a 2_regHadp: 0.1233 0.1513 0.041 1.144 5.4 68.2 16.3 889 n/a 2_occ: 0.1226 0.1517 0.041 1.144 5.4 68.2 16.3 889 n/a 3_bss: 0.1233 0.1524 0.041 1.144 5.4 68.2 16.3 889 n/a 3_settarget: 0.1233 0.1524 0.041 1.144 5.4 68.2 16.3 889 n/a 3_updatecdl: 0.1233 0.1524 0.041 1.151 5.4 68.2 16.3 889 n/a 3_nqh: 0.1233 0.1524 0.041 1.151 5.4 68.2 16.3 889 n/a 3_sol: 0.1251 0.1510 0.041 1.151 5.4 68.2 15.5 883 n/a 3_weight: 0.1251 0.1510 0.041 1.151 5.4 68.2 15.5 883 n/a 3_xyzrec: 0.1241 0.1444 0.035 1.099 5.4 68.2 15.5 883 n/a 3_adp: 0.1237 0.1401 0.035 1.099 5.5 67.8 15.3 883 n/a 3_regHadp: 0.1237 0.1402 0.035 1.099 5.5 67.8 15.3 883 n/a 3_occ: 0.1231 0.1394 0.035 1.099 5.5 67.8 15.3 883 n/a 4_bss: 0.1226 0.1389 0.035 1.099 5.5 67.7 15.3 883 n/a 4_settarget: 0.1226 0.1389 0.035 1.099 5.5 67.7 15.3 883 n/a 4_updatecdl: 0.1226 0.1389 0.035 1.100 5.5 67.7 15.3 883 n/a 4_nqh: 0.1226 0.1389 0.035 1.100 5.5 67.7 15.3 883 n/a 4_sol: 0.1208 0.1364 0.035 1.100 5.5 67.7 15.1 878 n/a 4_weight: 0.1208 0.1364 0.035 1.100 5.5 67.7 15.1 878 n/a 4_xyzrec: 0.1205 0.1363 0.036 1.136 5.5 67.7 15.1 878 n/a 4_adp: 0.1198 0.1361 0.036 1.136 5.5 67.4 15.1 878 n/a 4_regHadp: 0.1198 0.1361 0.036 1.136 5.5 67.4 15.1 878 n/a 4_occ: 0.1196 0.1358 0.036 1.136 5.5 67.4 15.1 878 n/a 5_bss: 0.1194 0.1356 0.036 1.136 5.5 67.4 15.0 878 n/a 5_settarget: 0.1194 0.1356 0.036 1.136 5.5 67.4 15.0 878 n/a 5_updatecdl: 0.1194 0.1356 0.036 1.136 5.5 67.4 15.0 878 n/a 5_nqh: 0.1194 0.1356 0.036 1.136 5.5 67.4 15.0 878 n/a 5_sol: 0.1194 0.1357 0.036 1.136 5.5 67.4 15.0 878 n/a 5_weight: 0.1194 0.1357 0.036 1.136 5.5 67.4 15.0 878 n/a 5_xyzrec: 0.1198 0.1370 0.037 1.125 5.5 67.4 15.0 878 n/a 5_adp: 0.1201 0.1375 0.037 1.125 5.5 66.9 14.9 878 n/a 5_regHadp: 0.1201 0.1376 0.037 1.125 5.5 66.9 14.9 878 n/a 5_occ: 0.1200 0.1373 0.037 1.125 5.5 66.9 14.9 878 n/a 6_bss: 0.1199 0.1369 0.037 1.125 5.5 66.9 14.9 878 n/a 6_settarget: 0.1199 0.1369 0.037 1.125 5.5 66.9 14.9 878 n/a 6_updatecdl: 0.1199 0.1369 0.037 1.125 5.5 66.9 14.9 878 n/a 6_nqh: 0.1199 0.1369 0.037 1.125 5.5 66.9 14.9 878 n/a 6_sol: 0.1197 0.1354 0.037 1.125 5.5 66.9 14.9 892 n/a 6_weight: 0.1197 0.1354 0.037 1.125 5.5 66.9 14.9 892 n/a 6_xyzrec: 0.1201 0.1358 0.037 1.119 5.5 66.9 14.9 892 n/a 6_adp: 0.1202 0.1359 0.037 1.119 5.6 66.0 14.9 892 n/a 6_regHadp: 0.1202 0.1359 0.037 1.119 5.6 66.0 14.9 892 n/a 6_occ: 0.1200 0.1361 0.037 1.119 5.6 66.0 14.9 892 n/a 7_bss: 0.1200 0.1363 0.037 1.119 5.4 65.8 14.6 892 n/a 7_settarget: 0.1200 0.1363 0.037 1.119 5.4 65.8 14.6 892 n/a 7_updatecdl: 0.1200 0.1363 0.037 1.120 5.4 65.8 14.6 892 n/a 7_nqh: 0.1200 0.1363 0.037 1.120 5.4 65.8 14.6 892 n/a 7_sol: 0.1198 0.1353 0.037 1.120 5.4 65.8 14.6 895 n/a 7_weight: 0.1198 0.1353 0.037 1.120 5.4 65.8 14.6 895 n/a 7_xyzrec: 0.1201 0.1359 0.038 1.132 5.4 65.8 14.6 895 n/a 7_adp: 0.1201 0.1361 0.038 1.132 5.4 64.7 14.6 895 n/a 7_regHadp: 0.1202 0.1361 0.038 1.132 5.4 64.7 14.6 895 n/a 7_occ: 0.1200 0.1362 0.038 1.132 5.4 64.7 14.6 895 n/a 8_bss: 0.1190 0.1350 0.038 1.132 5.5 64.7 14.6 895 n/a 8_settarget: 0.1190 0.1350 0.038 1.132 5.5 64.7 14.6 895 n/a 8_updatecdl: 0.1190 0.1350 0.038 1.132 5.5 64.7 14.6 895 n/a 8_nqh: 0.1190 0.1350 0.038 1.132 5.5 64.7 14.6 895 n/a 8_sol: 0.1189 0.1348 0.038 1.132 5.5 64.7 14.6 897 n/a 8_weight: 0.1189 0.1348 0.038 1.132 5.5 64.7 14.6 897 n/a 8_xyzrec: 0.1193 0.1352 0.038 1.117 5.5 64.7 14.6 897 n/a 8_adp: 0.1194 0.1355 0.038 1.117 5.5 64.3 14.6 897 n/a 8_regHadp: 0.1194 0.1355 0.038 1.117 5.5 64.3 14.6 897 n/a 8_occ: 0.1193 0.1357 0.038 1.117 5.5 64.3 14.6 897 n/a 9_bss: 0.1191 0.1353 0.038 1.117 5.5 64.3 14.6 897 n/a 9_settarget: 0.1191 0.1353 0.038 1.117 5.5 64.3 14.6 897 n/a 9_updatecdl: 0.1191 0.1353 0.038 1.117 5.5 64.3 14.6 897 n/a 9_nqh: 0.1191 0.1353 0.038 1.117 5.5 64.3 14.6 897 n/a 9_sol: 0.1191 0.1340 0.038 1.117 5.5 64.3 14.6 887 n/a 9_weight: 0.1191 0.1340 0.038 1.117 5.5 64.3 14.6 887 n/a 9_xyzrec: 0.1194 0.1346 0.039 1.115 5.5 64.3 14.6 887 n/a 9_adp: 0.1194 0.1347 0.039 1.115 5.6 63.5 14.6 887 n/a 9_regHadp: 0.1195 0.1347 0.039 1.115 5.6 63.5 14.6 887 n/a 9_occ: 0.1194 0.1346 0.039 1.115 5.6 63.5 14.6 887 n/a 10_bss: 0.1192 0.1345 0.039 1.115 5.5 63.5 14.6 887 n/a 10_settarget: 0.1192 0.1345 0.039 1.115 5.5 63.5 14.6 887 n/a 10_updatecdl: 0.1192 0.1345 0.039 1.115 5.5 63.5 14.6 887 n/a 10_setrh: 0.1193 0.1345 0.039 1.115 5.5 63.5 14.6 887 n/a 10_nqh: 0.1194 0.1348 0.039 1.115 5.5 63.5 14.6 887 n/a 10_sol: 0.1191 0.1348 0.039 1.115 5.5 63.5 14.6 895 n/a 10_weight: 0.1191 0.1348 0.039 1.115 5.5 63.5 14.6 895 n/a 10_xyzrec: 0.1193 0.1350 0.039 1.170 5.5 63.5 14.6 895 n/a 10_adp: 0.1194 0.1353 0.039 1.170 5.6 62.7 14.6 895 n/a 10_regHadp: 0.1194 0.1353 0.039 1.170 5.6 62.7 14.6 895 n/a 10_occ: 0.1193 0.1353 0.039 1.170 5.6 62.7 14.6 895 n/a end: 0.1192 0.1350 0.039 1.170 5.5 62.6 14.5 895 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9350771_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9350771_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.6900 Refinement macro-cycles (run) : 12029.8300 Write final files (write_after_run_outputs) : 170.2200 Total : 12206.7400 Total CPU time: 3.40 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:38 PST -0800 (1736736038.76 s) Start R-work = 0.1797, R-free = 0.1907 Final R-work = 0.1192, R-free = 0.1350 =============================================================================== Job complete usr+sys time: 12505.85 seconds wall clock time: 209 minutes 27.35 seconds (12567.35 seconds total)