Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2565062.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2565062.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2565062.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.67, 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: 2.822 distance_ideal: 2.720 ideal - model: -0.102 slack: 0.000 delta_slack: -0.102 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: 2.822 distance_ideal: 2.710 ideal - model: -0.112 slack: 0.000 delta_slack: -0.112 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: 0.67 Conformation dependent library (CDL) restraints added in 223.0 milliseconds Time building geometry restraints manager: 1.06 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: 887 1.04 - 1.27: 2500 1.27 - 1.50: 1586 1.50 - 1.74: 948 1.74 - 1.97: 13 Bond restraints: 5934 Sorted by residual: bond pdb=" CE1 HIS A 116 " pdb=" NE2 HIS A 116 " ideal model delta sigma weight residual 1.321 1.546 -0.225 1.00e-02 1.00e+04 5.06e+02 bond pdb=" C ALA A 189 " pdb=" N GLY A 190 " ideal model delta sigma weight residual 1.335 1.117 0.218 9.80e-03 1.04e+04 4.96e+02 bond pdb=" CA TYR A 192 " pdb=" C TYR A 192 " ideal model delta sigma weight residual 1.524 1.782 -0.259 1.31e-02 5.83e+03 3.90e+02 bond pdb=" CA PHE A 127 " pdb=" C PHE A 127 " ideal model delta sigma weight residual 1.527 1.726 -0.199 1.02e-02 9.61e+03 3.82e+02 bond pdb=" CA ILE A 118 " pdb=" HA ILE A 118 " ideal model delta sigma weight residual 0.970 1.352 -0.382 2.00e-02 2.50e+03 3.65e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.02: 5531 4.02 - 8.03: 3546 8.03 - 12.05: 1386 12.05 - 16.06: 303 16.06 - 20.08: 44 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA LEU A 72 " pdb=" C LEU A 72 " pdb=" O LEU A 72 " ideal model delta sigma weight residual 119.71 107.49 12.22 8.10e-01 1.52e+00 2.28e+02 angle pdb=" CA THR A 16 " pdb=" C THR A 16 " pdb=" O THR A 16 " ideal model delta sigma weight residual 120.55 106.21 14.34 1.06e+00 8.90e-01 1.83e+02 angle pdb=" CA PHE A 119 " pdb=" C PHE A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 117.59 103.83 13.76 1.03e+00 9.43e-01 1.78e+02 angle pdb=" N VAL B 92 " pdb=" CA VAL B 92 " pdb=" CB VAL B 92 " ideal model delta sigma weight residual 110.62 124.10 -13.48 1.05e+00 9.07e-01 1.65e+02 angle pdb=" CA GLY A 190 " pdb=" C GLY A 190 " pdb=" O GLY A 190 " ideal model delta sigma weight residual 119.83 108.95 10.88 8.50e-01 1.38e+00 1.64e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 1871 17.89 - 35.77: 127 35.77 - 53.66: 33 53.66 - 71.54: 16 71.54 - 89.43: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA CYS B 47 " pdb=" C CYS B 47 " pdb=" N SER B 48 " pdb=" CA SER B 48 " ideal model delta harmonic sigma weight residual 180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+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 -156.85 -23.15 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CB TRP B 146 " pdb=" CG TRP B 146 " pdb=" CD1 TRP B 146 " pdb=" HD1 TRP B 146 " ideal model delta harmonic sigma weight residual 0.00 -21.01 21.01 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.207: 212 0.207 - 0.413: 145 0.413 - 0.619: 91 0.619 - 0.826: 31 0.826 - 1.032: 13 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE A 118 " pdb=" N ILE A 118 " pdb=" C ILE A 118 " pdb=" CB ILE A 118 " both_signs ideal model delta sigma weight residual False 2.43 1.40 1.03 2.00e-01 2.50e+01 2.66e+01 chirality pdb=" CA GLU A 66 " pdb=" N GLU A 66 " pdb=" C GLU A 66 " pdb=" CB GLU A 66 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA ILE B 70 " pdb=" N ILE B 70 " pdb=" C ILE B 70 " pdb=" CB ILE B 70 " both_signs ideal model delta sigma weight residual False 2.43 3.44 -1.01 2.00e-01 2.50e+01 2.54e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.122 2.00e-02 2.50e+03 7.29e-02 1.59e+02 pdb=" CG PHE A 164 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.060 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.065 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.131 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.098 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.064 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.076 2.00e-02 2.50e+03 6.19e-02 1.53e+02 pdb=" CG TRP A 146 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.030 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.097 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.129 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.118 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.044 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.020 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.020 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.016 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.036 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.023 2.00e-02 2.50e+03 5.91e-02 1.40e+02 pdb=" CG TRP B 139 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.067 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.142 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.067 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.076 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.014 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " -0.019 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.019 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.082 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.043 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.048 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.91 - 1.64: 34 1.64 - 2.38: 2765 2.38 - 3.12: 22450 3.12 - 3.86: 32865 3.86 - 4.60: 52124 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110238 Sorted by model distance: nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.906 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.911 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.060 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.107 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.154 2.620 ... (remaining 110233 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_2565062_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2036 r_free= 0.1949 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300598 | | target function (ml) not normalized (work): 805557.943630 | | target function (ml) not normalized (free): 16516.144298 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2138 0.1931 6.6668 6.3217| | 2: 2.94 - 2.33 1.00 7339 128 0.1602 0.1602 5.5422 5.5949| | 3: 2.33 - 2.04 0.96 6939 150 0.1651 0.1624 5.1456 5.1606| | 4: 2.04 - 1.85 1.00 7170 155 0.1732 0.1635 4.9484 5.0524| | 5: 1.85 - 1.72 0.99 7113 159 0.1921 0.1512 4.7926 4.7369| | 6: 1.72 - 1.62 0.99 7102 142 0.2002 0.2021 4.6723 4.7858| | 7: 1.62 - 1.54 0.99 7104 148 0.2022 0.1746 4.5621 4.6063| | 8: 1.54 - 1.47 0.96 6798 152 0.2047 0.2087 4.4848 4.4517| | 9: 1.47 - 1.41 0.98 6938 155 0.2119 0.2378 4.3954 4.5117| | 10: 1.41 - 1.36 0.99 7022 150 0.2106 0.1962 4.3038 4.3025| | 11: 1.36 - 1.32 0.99 6997 151 0.2121 0.2140 4.2265 4.2482| | 12: 1.32 - 1.28 0.98 6976 149 0.2100 0.1727 4.1701 4.1471| | 13: 1.28 - 1.25 0.98 6907 166 0.2022 0.2032 4.123 4.1327| | 14: 1.25 - 1.22 0.98 7015 113 0.2057 0.2124 4.0672 4.0974| | 15: 1.22 - 1.19 0.98 6957 137 0.2111 0.2091 4.0515 4.0634| | 16: 1.19 - 1.17 0.93 6604 132 0.2099 0.2234 4.0058 4.064| | 17: 1.17 - 1.14 0.98 6941 135 0.2166 0.1832 3.9629 3.9742| | 18: 1.14 - 1.12 0.98 6875 142 0.2264 0.2506 3.9475 4.0149| | 19: 1.12 - 1.10 0.97 6949 106 0.2268 0.2324 3.8727 3.9573| | 20: 1.10 - 1.08 0.97 6884 147 0.2353 0.2159 3.834 3.8171| | 21: 1.08 - 1.07 0.97 6852 152 0.2458 0.2601 3.7904 3.8097| | 22: 1.07 - 1.05 0.97 6838 135 0.2584 0.2408 3.7599 3.7187| | 23: 1.05 - 1.03 0.97 6829 159 0.2724 0.2532 3.7318 3.7632| | 24: 1.03 - 1.02 0.96 6785 133 0.2916 0.2754 3.7055 3.7407| | 25: 1.02 - 1.01 0.93 6552 130 0.3050 0.3079 3.6711 3.8061| | 26: 1.01 - 0.99 0.96 6767 158 0.3214 0.3114 3.6312 3.6032| | 27: 0.99 - 0.98 0.94 6648 131 0.3409 0.3287 3.6403 3.6203| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.89 0.91 0.97 36579.75| | 2: 2.94 - 2.33 7339 128 0.85 21.61 1.08 1.02 15494.37| | 3: 2.33 - 2.04 6939 150 0.93 12.46 1.11 1.06 4113.84| | 4: 2.04 - 1.85 7170 155 0.93 13.33 1.11 1.06 2709.18| | 5: 1.85 - 1.72 7113 159 0.91 15.20 1.12 1.07 1977.97| | 6: 1.72 - 1.62 7102 142 0.90 16.62 1.12 1.07 1618.35| | 7: 1.62 - 1.54 7104 148 0.89 17.69 1.11 1.06 1325.81| | 8: 1.54 - 1.47 6798 152 0.89 18.22 1.10 1.07 1152.06| | 9: 1.47 - 1.41 6938 155 0.88 19.05 1.11 1.05 956.45| | 10: 1.41 - 1.36 7022 150 0.88 19.47 1.09 1.05 809.82| | 11: 1.36 - 1.32 6997 151 0.88 18.99 1.09 1.04 657.48| | 12: 1.32 - 1.28 6976 149 0.88 18.63 1.08 1.04 580.91| | 13: 1.28 - 1.25 6907 166 0.89 18.41 1.07 1.06 538.57| | 14: 1.25 - 1.22 7015 113 0.88 19.34 1.08 1.06 520.72| | 15: 1.22 - 1.19 6957 137 0.87 19.87 1.07 1.04 502.55| | 16: 1.19 - 1.17 6604 132 0.87 20.28 1.07 1.02 483.02| | 17: 1.17 - 1.14 6941 135 0.86 21.61 1.08 0.99 453.70| | 18: 1.14 - 1.12 6875 142 0.85 22.11 1.08 0.98 420.46| | 19: 1.12 - 1.10 6949 106 0.85 22.62 1.07 0.98 389.05| | 20: 1.10 - 1.08 6884 147 0.85 22.83 1.07 0.99 352.61| | 21: 1.08 - 1.07 6852 152 0.84 23.41 1.06 0.99 324.39| | 22: 1.07 - 1.05 6838 135 0.83 24.40 1.05 0.98 303.68| | 23: 1.05 - 1.03 6829 159 0.81 26.58 1.06 0.97 308.03| | 24: 1.03 - 1.02 6785 133 0.79 28.76 1.06 0.98 313.02| | 25: 1.02 - 1.01 6552 130 0.77 30.37 1.03 0.95 309.32| | 26: 1.01 - 0.99 6767 158 0.75 32.14 1.03 0.92 296.05| | 27: 0.99 - 0.98 6648 131 0.74 33.53 1.03 0.86 283.68| |alpha: min = 0.86 max = 1.07 mean = 1.01| |beta: min = 283.68 max = 36579.75 mean = 2862.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.99 mean = 21.34| |phase err.(test): min = 0.00 max = 89.81 mean = 21.28| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.259 2950 Z= 5.499 Angle : 5.033 15.869 4018 Z= 3.544 Chirality : 0.372 1.032 492 Planarity : 0.034 0.159 512 Dihedral : 12.734 89.428 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.92 % Favored : 94.56 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % Cbeta Deviations : 28.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.40), residues: 386 helix: -2.08 (0.34), residues: 144 sheet: -1.38 (0.48), residues: 86 loop : 0.35 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.025 ARG B 27 TYR 0.107 0.042 TYR A 192 PHE 0.107 0.035 PHE B 119 TRP 0.140 0.047 TRP A 146 HIS 0.059 0.027 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2036 r_free= 0.1949 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.300598 | | target function (ml) not normalized (work): 805557.943630 | | target function (ml) not normalized (free): 16516.144298 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2036 0.1949 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2036 0.1949 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2036 0.1949 n_refl.: 191145 overall B=0.01 to atoms: r(all,work,free)=0.2036 0.2038 0.1949 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1801 0.1800 0.1879 n_refl.: 191145 remove outliers: r(all,work,free)=0.1799 0.1798 0.1879 n_refl.: 191140 ======================== 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 96.04 94 3 0.4227 400.535 295.929 0.424 0.930 0.300 13.296-10.522 99.01 99 1 0.2470 528.187 519.469 0.769 0.931 0.254 10.503-8.327 99.45 178 3 0.2509 565.118 555.661 0.947 0.931 0.234 8.318-6.595 100.00 360 8 0.2485 414.736 403.330 0.953 0.931 0.179 6.588-5.215 100.00 711 7 0.2261 381.101 365.565 0.936 0.930 0.160 5.214-4.128 98.38 1367 28 0.1464 557.435 549.910 1.053 0.930 0.090 4.126-3.266 94.74 2603 46 0.1357 508.132 498.780 1.122 0.929 0.009 3.266-2.585 99.86 5447 97 0.1425 342.774 337.321 1.097 0.927 0.000 2.585-2.046 97.45 10613 204 0.1405 258.603 254.034 1.106 0.924 0.000 2.046-1.619 99.39 21536 464 0.1604 153.054 149.904 1.132 0.919 0.000 1.619-1.281 98.00 42464 925 0.1924 82.395 80.103 1.124 0.911 0.000 1.281-0.980 96.53 101826 2056 0.2324 44.203 41.679 1.120 0.896 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0202 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1798 r_free=0.1879 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1798 r_free=0.1879 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.251476 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.177384 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 0.1271 0.1502 0.0231 0.039 1.2 11.0 0.0 0.3 0 11.126 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.02 2.31 1.119 13.124 575.177 0.018 12.96 15.66 2.70 1.254 13.359 575.177 0.017 Individual atomic B min max mean iso aniso Overall: 5.20 73.06 15.04 1.41 435 3274 Protein: 5.20 40.34 11.02 1.41 0 2902 Water: 6.37 73.06 29.50 N/A 435 370 Other: 15.97 30.03 23.00 N/A 0 2 Chain A: 5.33 60.13 13.08 N/A 0 1626 Chain B: 5.20 73.06 12.79 N/A 0 1648 Chain S: 11.56 63.59 30.88 N/A 435 0 Histogram: Values Number of atoms 5.20 - 11.98 2161 11.98 - 18.77 640 18.77 - 25.56 314 25.56 - 32.34 264 32.34 - 39.13 164 39.13 - 45.91 101 45.91 - 52.70 42 52.70 - 59.48 19 59.48 - 66.27 3 66.27 - 73.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1296 r_free=0.1566 r_work=0.1296 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1561 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1281 r_free = 0.1553 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015605 | | target function (ls_wunit_k1) not normalized (work): 2922.822303 | | target function (ls_wunit_k1) not normalized (free): 116.626300 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1553 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1476 0.1474 0.1632 n_refl.: 191140 remove outliers: r(all,work,free)=0.1476 0.1474 0.1632 n_refl.: 191140 overall B=0.16 to atoms: r(all,work,free)=0.1500 0.1498 0.1642 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1545 n_refl.: 191140 remove outliers: r(all,work,free)=0.1280 0.1275 0.1544 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3606 402.814 371.295 0.481 0.962 0.283 13.296-10.522 99.01 99 1 0.2069 528.187 517.772 0.733 0.964 0.238 10.503-8.327 99.45 178 3 0.1773 565.118 562.417 0.887 0.964 0.217 8.318-6.595 100.00 360 8 0.1699 414.736 412.742 0.913 0.963 0.165 6.588-5.215 100.00 711 7 0.1534 381.101 373.997 0.889 0.964 0.160 5.214-4.128 98.38 1367 28 0.0902 557.435 554.414 0.977 0.964 0.080 4.126-3.266 94.74 2603 46 0.0832 508.132 504.491 1.044 0.965 0.009 3.266-2.585 99.86 5447 97 0.0923 342.774 340.452 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.457 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.414 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1278 82.395 81.411 1.048 0.964 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.146 1.026 0.964 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0365 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1544 | n_water=805 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1278 r_free=0.1545 | n_water=795 | time (s): 98.800 (total time: 101.400) Filter (q & B) r_work=0.1278 r_free=0.1545 | n_water=792 | time (s): 5.310 (total time: 106.710) Compute maps r_work=0.1278 r_free=0.1545 | n_water=792 | time (s): 1.740 (total time: 108.450) Filter (map) r_work=0.1305 r_free=0.1528 | n_water=651 | time (s): 4.940 (total time: 113.390) Find peaks r_work=0.1305 r_free=0.1528 | n_water=651 | time (s): 0.660 (total time: 114.050) Add new water r_work=0.1329 r_free=0.1553 | n_water=955 | time (s): 3.950 (total time: 118.000) Refine new water occ: r_work=0.1286 r_free=0.1504 adp: r_work=0.1273 r_free=0.1503 occ: r_work=0.1276 r_free=0.1500 adp: r_work=0.1269 r_free=0.1501 occ: r_work=0.1271 r_free=0.1499 adp: r_work=0.1268 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1501 r_work=0.1268 r_free=0.1501 | n_water=955 | time (s): 101.900 (total time: 219.900) Filter (q & B) r_work=0.1271 r_free=0.1506 | n_water=881 | time (s): 4.710 (total time: 224.610) Filter (dist only) r_work=0.1271 r_free=0.1505 | n_water=880 | time (s): 115.390 (total time: 340.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.993314 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 598.473857 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 0.0271 0.042 1.1 18.9 0.0 0.0 0 11.997 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.26 2.71 2.049 15.226 598.474 0.015 12.32 15.11 2.79 2.400 15.250 598.474 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 68.76 16.34 1.22 512 3272 Protein: 5.39 39.94 11.01 1.22 0 2902 Water: 6.60 68.76 33.90 N/A 512 368 Other: 16.32 32.85 24.58 N/A 0 2 Chain A: 5.50 56.23 13.02 N/A 0 1624 Chain B: 5.39 68.76 12.85 N/A 0 1648 Chain S: 9.68 67.33 38.11 N/A 512 0 Histogram: Values Number of atoms 5.39 - 11.73 2066 11.73 - 18.06 704 18.06 - 24.40 271 24.40 - 30.74 211 30.74 - 37.08 169 37.08 - 43.41 167 43.41 - 49.75 91 49.75 - 56.09 55 56.09 - 62.43 39 62.43 - 68.76 11 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1511 r_work=0.1233 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1512 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1513 target_work(ls_wunit_k1) = 0.014 | | 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1513 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013507 | | target function (ls_wunit_k1) not normalized (work): 2529.819136 | | target function (ls_wunit_k1) not normalized (free): 107.003132 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1513 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1439 0.1622 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1439 0.1622 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1439 0.1435 0.1620 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1518 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1233 0.1518 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3321 402.814 375.076 0.489 0.962 0.269 13.296-10.522 99.01 99 1 0.1846 528.187 522.103 0.756 0.963 0.225 10.503-8.327 99.45 178 3 0.1437 565.118 567.455 0.920 0.963 0.179 8.318-6.595 100.00 360 8 0.1544 414.736 414.811 0.938 0.962 0.160 6.588-5.215 100.00 711 7 0.1346 381.101 376.706 0.914 0.962 0.140 5.214-4.128 98.38 1367 28 0.0834 557.435 555.934 0.995 0.963 0.100 4.126-3.266 94.74 2603 46 0.0770 508.132 505.326 1.061 0.963 0.019 3.266-2.585 99.86 5447 97 0.0854 342.774 341.343 1.047 0.961 0.010 2.585-2.046 97.45 10613 204 0.0899 258.603 256.765 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1042 153.054 151.615 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.354 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.216 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0562 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1518 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1518 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1518 | n_water=880 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1235 r_free=0.1518 | n_water=877 | time (s): 108.050 (total time: 111.250) Filter (q & B) r_work=0.1235 r_free=0.1519 | n_water=876 | time (s): 5.540 (total time: 116.790) Compute maps r_work=0.1235 r_free=0.1519 | n_water=876 | time (s): 2.010 (total time: 118.800) Filter (map) r_work=0.1271 r_free=0.1527 | n_water=689 | time (s): 4.200 (total time: 123.000) Find peaks r_work=0.1271 r_free=0.1527 | n_water=689 | time (s): 0.580 (total time: 123.580) Add new water r_work=0.1297 r_free=0.1575 | n_water=1010 | time (s): 5.480 (total time: 129.060) Refine new water occ: r_work=0.1252 r_free=0.1528 adp: r_work=0.1252 r_free=0.1529 occ: r_work=0.1248 r_free=0.1526 adp: r_work=0.1248 r_free=0.1527 occ: r_work=0.1245 r_free=0.1523 adp: r_work=0.1245 r_free=0.1524 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1524 r_work=0.1245 r_free=0.1524 | n_water=1010 | time (s): 241.660 (total time: 370.720) Filter (q & B) r_work=0.1249 r_free=0.1526 | n_water=864 | time (s): 6.030 (total time: 376.750) Filter (dist only) r_work=0.1250 r_free=0.1526 | n_water=862 | time (s): 119.180 (total time: 495.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.648628 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.556190 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 0.1240 0.1439 0.0198 0.036 1.1 7.0 0.0 0.0 0 0.824 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.39 1.98 1.942 14.559 16.556 3.940 12.33 14.03 1.70 2.218 14.472 16.556 3.897 Individual atomic B min max mean iso aniso Overall: 5.52 68.42 15.20 1.08 495 3271 Protein: 5.52 36.64 10.78 1.08 0 2902 Water: 6.67 68.42 30.06 N/A 495 367 Other: 14.11 28.49 21.30 N/A 0 2 Chain A: 5.52 55.41 12.80 N/A 0 1624 Chain B: 5.55 68.42 12.58 N/A 0 1647 Chain S: 12.00 62.88 31.79 N/A 495 0 Histogram: Values Number of atoms 5.52 - 11.81 2140 11.81 - 18.10 679 18.10 - 24.39 303 24.39 - 30.68 240 30.68 - 36.97 167 36.97 - 43.26 143 43.26 - 49.55 55 49.55 - 55.84 26 55.84 - 62.13 11 62.13 - 68.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1404 r_work=0.1234 r_free=0.1404 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1404 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1396 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1396 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891646 | | target function (ml) not normalized (work): 728893.590363 | | target function (ml) not normalized (free): 15226.254248 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1396 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1449 0.1448 0.1506 n_refl.: 191138 remove outliers: r(all,work,free)=0.1449 0.1448 0.1506 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1442 0.1442 0.1502 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1225 0.1388 n_refl.: 191138 remove outliers: r(all,work,free)=0.1228 0.1225 0.1388 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3850 398.008 360.510 0.423 0.945 0.247 13.296-10.522 99.01 99 1 0.2508 528.187 506.928 0.704 0.947 0.214 10.503-8.327 98.35 176 3 0.1990 555.265 556.515 0.887 0.947 0.169 8.318-6.595 100.00 360 8 0.2099 414.736 410.879 0.900 0.946 0.140 6.588-5.215 100.00 711 7 0.1830 381.101 369.610 0.889 0.946 0.140 5.214-4.128 98.38 1367 28 0.1166 557.435 551.406 0.971 0.947 0.070 4.126-3.266 94.74 2603 46 0.1101 508.132 501.003 1.034 0.947 0.009 3.266-2.585 99.86 5447 97 0.1088 342.774 339.119 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0963 258.603 255.778 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0975 153.054 151.374 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.483 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.315 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1042 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1388 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1388 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1388 | n_water=862 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1226 r_free=0.1390 | n_water=859 | time (s): 113.250 (total time: 116.380) Filter (q & B) r_work=0.1226 r_free=0.1388 | n_water=851 | time (s): 5.300 (total time: 121.680) Compute maps r_work=0.1226 r_free=0.1388 | n_water=851 | time (s): 1.750 (total time: 123.430) Filter (map) r_work=0.1247 r_free=0.1377 | n_water=719 | time (s): 4.140 (total time: 127.570) Find peaks r_work=0.1247 r_free=0.1377 | n_water=719 | time (s): 0.640 (total time: 128.210) Add new water r_work=0.1262 r_free=0.1389 | n_water=965 | time (s): 4.740 (total time: 132.950) Refine new water occ: r_work=0.1213 r_free=0.1354 adp: r_work=0.1205 r_free=0.1348 occ: r_work=0.1202 r_free=0.1349 adp: r_work=0.1202 r_free=0.1349 occ: r_work=0.1200 r_free=0.1351 adp: r_work=0.1200 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1351 r_work=0.1200 r_free=0.1351 | n_water=965 | time (s): 351.160 (total time: 484.110) Filter (q & B) r_work=0.1205 r_free=0.1364 | n_water=867 | time (s): 5.210 (total time: 489.320) Filter (dist only) r_work=0.1205 r_free=0.1364 | n_water=866 | time (s): 107.910 (total time: 597.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.573770 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.732031 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1204 0.1368 0.0164 0.036 1.1 6.3 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.68 1.64 1.846 14.197 15.732 3.873 11.98 13.64 1.66 1.952 14.160 15.732 3.865 Individual atomic B min max mean iso aniso Overall: 5.55 68.03 14.92 1.01 499 3271 Protein: 5.55 33.70 10.70 1.01 0 2902 Water: 5.91 68.03 29.04 N/A 499 367 Other: 13.95 27.79 20.87 N/A 0 2 Chain A: 5.55 54.43 12.67 N/A 0 1624 Chain B: 5.55 68.03 12.48 N/A 0 1647 Chain S: 5.91 62.82 30.27 N/A 499 0 Histogram: Values Number of atoms 5.55 - 11.80 2143 11.80 - 18.05 707 18.05 - 24.29 308 24.29 - 30.54 261 30.54 - 36.79 143 36.79 - 43.04 123 43.04 - 49.29 52 49.29 - 55.54 23 55.54 - 61.79 8 61.79 - 68.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1364 r_work=0.1198 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1363 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863362 | | target function (ml) not normalized (work): 723584.555777 | | target function (ml) not normalized (free): 15132.761946 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1363 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1427 0.1427 0.1479 n_refl.: 191135 remove outliers: r(all,work,free)=0.1427 0.1427 0.1479 n_refl.: 191135 overall B=-0.04 to atoms: r(all,work,free)=0.1420 0.1419 0.1474 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1361 n_refl.: 191135 remove outliers: r(all,work,free)=0.1197 0.1194 0.1361 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3958 361.062 315.540 0.408 0.947 0.248 13.296-10.522 97.03 97 1 0.2366 479.573 451.715 0.697 0.949 0.213 10.503-8.327 98.35 176 3 0.2086 502.600 495.039 0.867 0.949 0.169 8.318-6.595 100.00 360 8 0.2200 375.400 369.646 0.897 0.949 0.150 6.588-5.215 100.00 711 7 0.1912 344.955 334.555 0.882 0.949 0.110 5.214-4.128 98.38 1367 28 0.1184 504.564 499.148 0.971 0.949 0.070 4.126-3.266 94.74 2603 46 0.1112 459.938 453.462 1.032 0.949 0.000 3.266-2.585 99.86 5447 97 0.1086 310.263 307.104 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0931 234.076 231.677 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0911 138.538 137.266 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0986 74.581 73.872 1.056 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.009 38.350 1.045 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1233 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1362 | n_water=866 | time (s): 2.710 (total time: 2.710) Filter (dist) r_work=0.1194 r_free=0.1362 | n_water=865 | time (s): 122.730 (total time: 125.440) Filter (q & B) r_work=0.1195 r_free=0.1363 | n_water=852 | time (s): 4.290 (total time: 129.730) Compute maps r_work=0.1195 r_free=0.1363 | n_water=852 | time (s): 2.010 (total time: 131.740) Filter (map) r_work=0.1214 r_free=0.1355 | n_water=738 | time (s): 5.100 (total time: 136.840) Find peaks r_work=0.1214 r_free=0.1355 | n_water=738 | time (s): 0.660 (total time: 137.500) Add new water r_work=0.1226 r_free=0.1375 | n_water=970 | time (s): 4.360 (total time: 141.860) Refine new water occ: r_work=0.1191 r_free=0.1346 adp: r_work=0.1192 r_free=0.1347 occ: r_work=0.1189 r_free=0.1345 adp: r_work=0.1189 r_free=0.1347 occ: r_work=0.1188 r_free=0.1345 adp: r_work=0.1187 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1347 r_work=0.1187 r_free=0.1347 | n_water=970 | time (s): 308.970 (total time: 450.830) Filter (q & B) r_work=0.1192 r_free=0.1348 | n_water=881 | time (s): 5.370 (total time: 456.200) Filter (dist only) r_work=0.1192 r_free=0.1347 | n_water=880 | time (s): 112.790 (total time: 568.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.535147 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.944863 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 0.1195 0.1353 0.0158 0.037 1.1 6.3 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.53 1.58 1.804 14.155 14.945 3.763 12.00 13.57 1.58 1.860 14.134 14.945 3.762 Individual atomic B min max mean iso aniso Overall: 5.61 67.77 14.96 0.97 514 3270 Protein: 5.61 32.75 10.64 0.97 0 2902 Water: 6.09 67.77 29.22 N/A 514 366 Other: 13.75 26.77 20.26 N/A 0 2 Chain A: 5.61 53.76 12.58 N/A 0 1624 Chain B: 5.61 67.77 12.39 N/A 0 1646 Chain S: 6.09 62.77 30.73 N/A 514 0 Histogram: Values Number of atoms 5.61 - 11.82 2166 11.82 - 18.04 696 18.04 - 24.25 301 24.25 - 30.47 238 30.47 - 36.69 165 36.69 - 42.90 132 42.90 - 49.12 53 49.12 - 55.34 23 55.34 - 61.55 8 61.55 - 67.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1363 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1363 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761122 | | target function (ml) not normalized (work): 704424.222113 | | target function (ml) not normalized (free): 14749.128291 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1363 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1480 n_refl.: 191132 remove outliers: r(all,work,free)=0.1409 0.1408 0.1480 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1401 0.1400 0.1475 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191132 remove outliers: r(all,work,free)=0.1200 0.1197 0.1361 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3872 361.062 321.124 0.398 0.952 0.223 13.296-10.522 96.04 96 1 0.2406 480.246 454.218 0.703 0.953 0.199 10.503-8.327 98.35 176 3 0.2056 502.600 495.436 0.863 0.953 0.164 8.318-6.595 100.00 360 8 0.2184 375.400 369.716 0.890 0.953 0.121 6.588-5.215 100.00 711 7 0.1902 344.955 334.719 0.880 0.953 0.103 5.214-4.128 98.38 1367 28 0.1196 504.564 499.232 0.969 0.953 0.080 4.126-3.266 94.74 2603 46 0.1130 459.938 453.249 1.029 0.954 0.000 3.266-2.585 99.86 5447 97 0.1103 310.263 307.014 1.017 0.953 0.000 2.585-2.046 97.45 10613 204 0.0944 234.076 231.660 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0916 138.538 137.229 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0979 74.581 73.864 1.051 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.009 38.339 1.040 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1367 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1361 | n_water=880 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1197 r_free=0.1362 | n_water=879 | time (s): 112.950 (total time: 115.720) Filter (q & B) r_work=0.1197 r_free=0.1361 | n_water=871 | time (s): 5.010 (total time: 120.730) Compute maps r_work=0.1197 r_free=0.1361 | n_water=871 | time (s): 2.350 (total time: 123.080) Filter (map) r_work=0.1218 r_free=0.1359 | n_water=762 | time (s): 5.730 (total time: 128.810) Find peaks r_work=0.1218 r_free=0.1359 | n_water=762 | time (s): 0.900 (total time: 129.710) Add new water r_work=0.1228 r_free=0.1372 | n_water=969 | time (s): 4.920 (total time: 134.630) Refine new water occ: r_work=0.1195 r_free=0.1349 adp: r_work=0.1195 r_free=0.1349 occ: r_work=0.1193 r_free=0.1349 adp: r_work=0.1193 r_free=0.1348 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=969 | time (s): 180.510 (total time: 315.140) Filter (q & B) r_work=0.1196 r_free=0.1354 | n_water=890 | time (s): 4.890 (total time: 320.030) Filter (dist only) r_work=0.1196 r_free=0.1354 | n_water=889 | time (s): 112.650 (total time: 432.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.585580 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.809454 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1356 0.0157 0.037 1.1 5.4 0.0 0.3 0 0.793 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.56 1.57 1.776 14.079 14.809 3.762 12.02 13.60 1.59 1.942 14.030 14.809 3.759 Individual atomic B min max mean iso aniso Overall: 5.60 66.64 14.85 0.91 523 3270 Protein: 5.60 29.66 10.51 0.91 0 2902 Water: 6.02 66.64 29.03 N/A 523 366 Other: 13.85 23.99 18.92 N/A 0 2 Chain A: 5.63 51.37 12.42 N/A 0 1624 Chain B: 5.60 66.64 12.24 N/A 0 1646 Chain S: 6.02 62.61 30.65 N/A 523 0 Histogram: Values Number of atoms 5.60 - 11.70 2139 11.70 - 17.81 755 17.81 - 23.91 277 23.91 - 30.02 226 30.02 - 36.12 170 36.12 - 42.22 129 42.22 - 48.33 60 48.33 - 54.43 26 54.43 - 60.54 9 60.54 - 66.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1361 r_work=0.1202 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1361 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1362 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758449 | | target function (ml) not normalized (work): 703919.856232 | | target function (ml) not normalized (free): 14738.002431 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1363 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1409 0.1408 0.1488 n_refl.: 191131 remove outliers: r(all,work,free)=0.1409 0.1408 0.1488 n_refl.: 191131 overall B=-0.24 to atoms: r(all,work,free)=0.1371 0.1370 0.1464 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1201 0.1198 0.1357 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 91.09 89 3 0.3573 356.180 313.383 0.398 0.951 0.211 13.296-10.522 95.05 95 1 0.2350 479.349 452.387 0.717 0.952 0.170 10.503-8.327 98.35 176 3 0.2124 502.600 495.018 0.886 0.953 0.153 8.318-6.595 100.00 360 8 0.2214 375.400 369.575 0.915 0.953 0.125 6.588-5.215 100.00 711 7 0.1901 344.955 334.960 0.904 0.953 0.120 5.214-4.128 98.38 1367 28 0.1213 504.564 499.207 0.993 0.953 0.063 4.126-3.266 94.74 2603 46 0.1152 459.938 453.020 1.056 0.953 0.021 3.266-2.585 99.86 5447 97 0.1114 310.263 307.029 1.039 0.953 0.007 2.585-2.046 97.45 10613 204 0.0952 234.076 231.669 1.047 0.952 0.000 2.046-1.619 99.39 21536 464 0.0915 138.538 137.261 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0971 74.581 73.887 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.009 38.349 1.024 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9912 b_overall=0.0520 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1357 | n_water=889 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1199 r_free=0.1357 | n_water=889 | time (s): 106.860 (total time: 109.340) Filter (q & B) r_work=0.1199 r_free=0.1357 | n_water=882 | time (s): 4.080 (total time: 113.420) Compute maps r_work=0.1199 r_free=0.1357 | n_water=882 | time (s): 2.120 (total time: 115.540) Filter (map) r_work=0.1217 r_free=0.1358 | n_water=778 | time (s): 6.140 (total time: 121.680) Find peaks r_work=0.1217 r_free=0.1358 | n_water=778 | time (s): 0.850 (total time: 122.530) Add new water r_work=0.1227 r_free=0.1370 | n_water=971 | time (s): 4.140 (total time: 126.670) Refine new water occ: r_work=0.1197 r_free=0.1353 adp: r_work=0.1197 r_free=0.1353 occ: r_work=0.1195 r_free=0.1353 adp: r_work=0.1195 r_free=0.1353 occ: r_work=0.1194 r_free=0.1354 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=971 | time (s): 179.190 (total time: 305.860) Filter (q & B) r_work=0.1197 r_free=0.1357 | n_water=904 | time (s): 5.390 (total time: 311.250) Filter (dist only) r_work=0.1198 r_free=0.1357 | n_water=903 | time (s): 112.260 (total time: 423.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.558059 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.060282 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 0.1363 0.0163 0.037 1.1 8.7 0.0 0.3 0 0.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.63 1.63 1.725 13.769 14.060 3.760 12.03 13.68 1.65 1.781 13.748 14.060 3.759 Individual atomic B min max mean iso aniso Overall: 5.40 65.50 14.65 0.88 537 3270 Protein: 5.40 28.48 10.25 0.88 0 2902 Water: 5.76 65.50 28.77 N/A 537 366 Other: 13.67 22.38 18.02 N/A 0 2 Chain A: 5.47 50.76 12.12 N/A 0 1624 Chain B: 5.40 65.50 11.96 N/A 0 1646 Chain S: 5.76 62.27 30.55 N/A 537 0 Histogram: Values Number of atoms 5.40 - 11.41 2122 11.41 - 17.42 775 17.42 - 23.43 265 23.43 - 29.44 226 29.44 - 35.45 184 35.45 - 41.46 129 41.46 - 47.47 64 47.47 - 53.48 30 53.48 - 59.49 9 59.49 - 65.50 3 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1368 r_work=0.1203 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1368 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1370 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758269 | | target function (ml) not normalized (work): 703874.889747 | | target function (ml) not normalized (free): 14743.753434 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1370 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1371 0.1369 0.1485 n_refl.: 191128 remove outliers: r(all,work,free)=0.1371 0.1369 0.1485 n_refl.: 191128 overall B=0.06 to atoms: r(all,work,free)=0.1378 0.1376 0.1489 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1362 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1362 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 91.09 89 3 0.3596 356.180 327.783 0.408 0.974 0.207 13.296-10.522 95.05 95 1 0.2297 479.349 462.183 0.715 0.976 0.152 10.503-8.327 98.35 176 3 0.2136 502.600 494.115 0.874 0.976 0.121 8.318-6.595 100.00 360 8 0.2212 375.400 368.746 0.896 0.976 0.107 6.588-5.215 100.00 711 7 0.1913 344.955 334.442 0.888 0.977 0.098 5.214-4.128 98.38 1367 28 0.1235 504.564 498.346 0.980 0.978 0.062 4.126-3.266 94.74 2603 46 0.1160 459.938 452.249 1.040 0.979 0.010 3.266-2.585 99.86 5447 97 0.1122 310.263 306.681 1.024 0.979 0.010 2.585-2.046 97.45 10613 204 0.0958 234.076 231.476 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0915 138.538 137.141 1.047 0.984 0.000 1.619-1.281 98.00 42464 925 0.0951 74.581 73.911 1.036 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.009 38.320 1.002 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0609 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1362 | n_water=903 | time (s): 3.100 (total time: 3.100) Filter (dist) r_work=0.1193 r_free=0.1362 | n_water=903 | time (s): 108.000 (total time: 111.100) Filter (q & B) r_work=0.1193 r_free=0.1362 | n_water=892 | time (s): 5.180 (total time: 116.280) Compute maps r_work=0.1193 r_free=0.1362 | n_water=892 | time (s): 1.820 (total time: 118.100) Filter (map) r_work=0.1213 r_free=0.1361 | n_water=784 | time (s): 5.440 (total time: 123.540) Find peaks r_work=0.1213 r_free=0.1361 | n_water=784 | time (s): 0.550 (total time: 124.090) Add new water r_work=0.1222 r_free=0.1376 | n_water=987 | time (s): 3.810 (total time: 127.900) Refine new water occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1190 r_free=0.1351 occ: r_work=0.1188 r_free=0.1352 adp: r_work=0.1188 r_free=0.1352 occ: r_work=0.1186 r_free=0.1353 adp: r_work=0.1186 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1353 r_work=0.1186 r_free=0.1353 | n_water=987 | time (s): 286.610 (total time: 414.510) Filter (q & B) r_work=0.1190 r_free=0.1357 | n_water=910 | time (s): 4.520 (total time: 419.030) Filter (dist only) r_work=0.1190 r_free=0.1357 | n_water=909 | time (s): 118.830 (total time: 537.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.592461 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.816163 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 0.1359 0.0166 0.038 1.1 7.0 0.0 0.3 0 0.796 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.59 1.66 1.678 13.775 13.816 3.757 11.95 13.62 1.67 1.707 13.762 13.816 3.755 Individual atomic B min max mean iso aniso Overall: 5.49 64.71 14.70 0.87 543 3270 Protein: 5.49 28.03 10.31 0.87 0 2902 Water: 5.94 64.71 28.71 N/A 543 366 Other: 13.76 22.11 17.94 N/A 0 2 Chain A: 5.59 50.42 12.13 N/A 0 1624 Chain B: 5.49 64.71 11.98 N/A 0 1646 Chain S: 5.94 62.20 30.61 N/A 543 0 Histogram: Values Number of atoms 5.49 - 11.41 2099 11.41 - 17.33 799 17.33 - 23.25 266 23.25 - 29.18 223 29.18 - 35.10 180 35.10 - 41.02 129 41.02 - 46.94 73 46.94 - 52.87 31 52.87 - 58.79 8 58.79 - 64.71 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1362 r_work=0.1195 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1362 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1364 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1364 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754913 | | target function (ml) not normalized (work): 703246.401666 | | target function (ml) not normalized (free): 14736.631899 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1364 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1385 0.1383 0.1492 n_refl.: 191128 remove outliers: r(all,work,free)=0.1385 0.1383 0.1492 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1387 0.1385 0.1493 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1362 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1362 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 91.09 89 3 0.3630 356.180 326.644 0.398 0.974 0.195 13.296-10.522 95.05 95 1 0.2309 479.349 462.186 0.710 0.976 0.142 10.503-8.327 98.35 176 3 0.2147 502.600 494.951 0.870 0.976 0.119 8.318-6.595 100.00 360 8 0.2214 375.400 368.303 0.893 0.976 0.104 6.588-5.215 100.00 711 7 0.1929 344.955 334.457 0.886 0.977 0.090 5.214-4.128 98.38 1367 28 0.1237 504.564 498.433 0.978 0.978 0.049 4.126-3.266 94.74 2603 46 0.1170 459.938 452.075 1.041 0.979 0.015 3.266-2.585 99.86 5447 97 0.1124 310.263 306.649 1.024 0.980 0.010 2.585-2.046 97.45 10613 204 0.0960 234.076 231.440 1.032 0.982 0.000 2.046-1.619 99.39 21536 464 0.0912 138.538 137.165 1.048 0.985 0.000 1.619-1.281 98.00 42464 925 0.0945 74.581 73.925 1.039 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.009 38.308 1.007 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1362 | n_water=909 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1192 r_free=0.1362 | n_water=908 | time (s): 116.800 (total time: 119.390) Filter (q & B) r_work=0.1193 r_free=0.1361 | n_water=899 | time (s): 5.630 (total time: 125.020) Compute maps r_work=0.1193 r_free=0.1361 | n_water=899 | time (s): 1.590 (total time: 126.610) Filter (map) r_work=0.1215 r_free=0.1364 | n_water=785 | time (s): 4.930 (total time: 131.540) Find peaks r_work=0.1215 r_free=0.1364 | n_water=785 | time (s): 0.730 (total time: 132.270) Add new water r_work=0.1223 r_free=0.1374 | n_water=993 | time (s): 4.890 (total time: 137.160) Refine new water occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1191 r_free=0.1348 occ: r_work=0.1189 r_free=0.1348 adp: r_work=0.1189 r_free=0.1349 occ: r_work=0.1187 r_free=0.1349 adp: r_work=0.1187 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1350 r_work=0.1187 r_free=0.1350 | n_water=993 | time (s): 316.670 (total time: 453.830) Filter (q & B) r_work=0.1192 r_free=0.1358 | n_water=911 | time (s): 5.130 (total time: 458.960) Filter (dist only) r_work=0.1192 r_free=0.1358 | n_water=910 | time (s): 119.280 (total time: 578.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.508682 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.591779 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 0.1361 0.0167 0.038 1.1 5.4 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.61 1.67 1.676 13.761 13.592 3.757 11.95 13.63 1.68 1.681 13.758 13.592 3.755 Individual atomic B min max mean iso aniso Overall: 5.49 64.28 14.68 0.86 544 3270 Protein: 5.49 27.92 10.33 0.86 0 2902 Water: 5.95 64.28 28.54 N/A 544 366 Other: 13.82 22.15 17.99 N/A 0 2 Chain A: 5.61 50.22 12.13 N/A 0 1624 Chain B: 5.49 64.28 11.99 N/A 0 1646 Chain S: 5.95 62.14 30.45 N/A 544 0 Histogram: Values Number of atoms 5.49 - 11.37 2076 11.37 - 17.25 818 17.25 - 23.13 268 23.13 - 29.00 227 29.00 - 34.88 180 34.88 - 40.76 127 40.76 - 46.64 74 46.64 - 52.52 30 52.52 - 58.40 9 58.40 - 64.28 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1363 r_work=0.1195 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1363 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1365 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755212 | | target function (ml) not normalized (work): 703302.345546 | | target function (ml) not normalized (free): 14736.234911 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1365 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1394 0.1392 0.1501 n_refl.: 191128 remove outliers: r(all,work,free)=0.1394 0.1392 0.1501 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1394 0.1392 0.1500 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1193 0.1365 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1193 0.1365 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 91.09 89 3 0.3587 356.180 326.694 0.399 0.975 0.198 13.296-10.522 95.05 95 1 0.2242 479.349 464.815 0.708 0.977 0.134 10.503-8.327 98.35 176 3 0.2174 502.600 494.607 0.866 0.977 0.104 8.318-6.595 100.00 360 8 0.2226 375.400 368.712 0.888 0.977 0.092 6.588-5.215 100.00 711 7 0.1952 344.955 334.177 0.882 0.978 0.083 5.214-4.128 98.38 1367 28 0.1256 504.564 498.189 0.976 0.979 0.044 4.126-3.266 94.74 2603 46 0.1169 459.938 451.968 1.040 0.980 0.005 3.266-2.585 99.86 5447 97 0.1124 310.263 306.727 1.024 0.981 0.000 2.585-2.046 97.45 10613 204 0.0963 234.076 231.418 1.031 0.984 0.000 2.046-1.619 99.39 21536 464 0.0914 138.538 137.163 1.047 0.988 0.000 1.619-1.281 98.00 42464 925 0.0944 74.581 73.925 1.038 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.009 38.302 1.007 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0130 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1193 r_free=0.1365 After: r_work=0.1194 r_free=0.1365 ================================== NQH flips ================================== r_work=0.1194 r_free=0.1365 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1365 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1365 | n_water=910 | time (s): 3.020 (total time: 3.020) Filter (dist) r_work=0.1194 r_free=0.1365 | n_water=910 | time (s): 115.210 (total time: 118.230) Filter (q & B) r_work=0.1194 r_free=0.1365 | n_water=903 | time (s): 4.910 (total time: 123.140) Compute maps r_work=0.1194 r_free=0.1365 | n_water=903 | time (s): 2.000 (total time: 125.140) Filter (map) r_work=0.1216 r_free=0.1367 | n_water=794 | time (s): 4.580 (total time: 129.720) Find peaks r_work=0.1216 r_free=0.1367 | n_water=794 | time (s): 0.560 (total time: 130.280) Add new water r_work=0.1224 r_free=0.1380 | n_water=1002 | time (s): 3.960 (total time: 134.240) Refine new water occ: r_work=0.1192 r_free=0.1350 adp: r_work=0.1192 r_free=0.1351 occ: r_work=0.1190 r_free=0.1349 adp: r_work=0.1190 r_free=0.1350 occ: r_work=0.1188 r_free=0.1350 adp: r_work=0.1188 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1350 r_work=0.1188 r_free=0.1350 | n_water=1002 | time (s): 275.530 (total time: 409.770) Filter (q & B) r_work=0.1193 r_free=0.1360 | n_water=914 | time (s): 5.450 (total time: 415.220) Filter (dist only) r_work=0.1193 r_free=0.1360 | n_water=913 | time (s): 116.060 (total time: 531.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.525897 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.710253 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 0.1361 0.0167 0.038 1.1 7.8 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.61 1.67 1.674 13.761 14.710 3.756 11.91 13.60 1.68 1.661 13.767 14.710 3.752 Individual atomic B min max mean iso aniso Overall: 5.56 63.85 14.69 0.87 547 3270 Protein: 5.56 28.06 10.36 0.87 0 2902 Water: 6.02 63.85 28.46 N/A 547 366 Other: 13.83 22.15 17.99 N/A 0 2 Chain A: 5.65 50.04 12.13 N/A 0 1624 Chain B: 5.56 63.85 12.00 N/A 0 1646 Chain S: 6.02 62.09 30.41 N/A 547 0 Histogram: Values Number of atoms 5.56 - 11.39 2073 11.39 - 17.22 827 17.22 - 23.05 265 23.05 - 28.88 221 28.88 - 34.71 183 34.71 - 40.54 127 40.54 - 46.36 75 46.36 - 52.19 30 52.19 - 58.02 11 58.02 - 63.85 5 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1360 r_work=0.1192 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1360 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1360 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751914 | | target function (ml) not normalized (work): 702684.789596 | | target function (ml) not normalized (free): 14726.495035 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1359 0.1520 5.6938 5.8113| | 2: 2.94 - 2.33 1.00 7339 128 0.1076 0.1298 5.0986 5.1878| | 3: 2.33 - 2.04 0.96 6939 150 0.0897 0.1213 4.6532 4.7632| | 4: 2.04 - 1.85 1.00 7170 155 0.0905 0.1061 4.3957 4.5722| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0984 4.1483 4.2402| | 6: 1.72 - 1.62 0.99 7102 142 0.0893 0.1084 3.9412 4.0715| | 7: 1.62 - 1.54 0.99 7104 148 0.0886 0.0961 3.7926 3.9186| | 8: 1.54 - 1.47 0.96 6798 152 0.0884 0.1295 3.692 3.8879| | 9: 1.47 - 1.41 0.98 6938 155 0.0920 0.1117 3.6144 3.7499| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1170 3.5512 3.6682| | 11: 1.36 - 1.32 0.99 6997 151 0.0986 0.1116 3.4773 3.5764| | 12: 1.32 - 1.28 0.98 6975 149 0.1024 0.1123 3.4502 3.5795| | 13: 1.28 - 1.25 0.98 6907 166 0.1035 0.1230 3.4293 3.5501| | 14: 1.25 - 1.22 0.98 7015 112 0.1101 0.1592 3.4272 3.6776| | 15: 1.22 - 1.19 0.98 6956 137 0.1164 0.1247 3.4449 3.4978| | 16: 1.19 - 1.17 0.93 6604 132 0.1245 0.1569 3.4625 3.6644| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1228 3.4324 3.4437| | 18: 1.14 - 1.12 0.98 6875 142 0.1380 0.1704 3.4362 3.5313| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1740 3.4174 3.5943| | 20: 1.10 - 1.08 0.97 6884 147 0.1580 0.1571 3.4074 3.429| | 21: 1.08 - 1.07 0.97 6852 152 0.1726 0.2126 3.4162 3.501| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1955 3.4113 3.4146| | 23: 1.05 - 1.03 0.97 6827 159 0.2116 0.2028 3.4318 3.4845| | 24: 1.03 - 1.02 0.96 6784 133 0.2329 0.2252 3.4343 3.5093| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2519 3.4476 3.5248| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2849 3.415 3.4225| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2809 3.4674 3.395| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.92 12.49 1.00 0.95 12334.76| | 2: 2.94 - 2.33 7339 128 0.92 13.37 0.99 0.95 5522.15| | 3: 2.33 - 2.04 6939 150 0.96 7.70 1.01 0.95 1718.19| | 4: 2.04 - 1.85 7170 155 0.96 7.71 1.00 0.95 1014.31| | 5: 1.85 - 1.72 7113 159 0.96 8.09 1.00 0.96 634.98| | 6: 1.72 - 1.62 7102 142 0.96 7.94 1.00 0.96 438.24| | 7: 1.62 - 1.54 7104 148 0.96 8.05 1.01 0.97 331.03| | 8: 1.54 - 1.47 6798 152 0.96 8.18 1.01 0.97 274.94| | 9: 1.47 - 1.41 6938 155 0.96 8.41 1.00 0.98 228.19| | 10: 1.41 - 1.36 7022 150 0.96 8.83 1.00 0.97 199.82| | 11: 1.36 - 1.32 6997 151 0.96 8.82 0.99 0.96 171.69| | 12: 1.32 - 1.28 6975 149 0.96 8.84 0.98 0.95 157.66| | 13: 1.28 - 1.25 6907 166 0.96 9.42 1.01 0.96 155.49| | 14: 1.25 - 1.22 7015 112 0.95 10.62 1.01 0.96 161.43| | 15: 1.22 - 1.19 6956 137 0.95 11.21 1.01 0.98 166.31| | 16: 1.19 - 1.17 6604 132 0.95 11.47 1.01 0.96 160.90| | 17: 1.17 - 1.14 6940 135 0.94 12.29 1.01 0.96 154.59| | 18: 1.14 - 1.12 6875 142 0.94 12.75 1.01 0.95 147.46| | 19: 1.12 - 1.10 6948 106 0.93 14.09 1.00 0.95 150.15| | 20: 1.10 - 1.08 6884 147 0.92 15.13 1.00 0.94 148.97| | 21: 1.08 - 1.07 6852 152 0.91 16.59 1.00 0.93 152.08| | 22: 1.07 - 1.05 6836 135 0.89 18.24 0.99 0.93 154.07| | 23: 1.05 - 1.03 6827 159 0.87 20.48 0.99 0.92 164.27| | 24: 1.03 - 1.02 6784 133 0.85 23.17 0.99 0.93 178.90| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.90 182.09| | 26: 1.01 - 0.99 6767 158 0.81 26.66 0.98 0.88 176.69| | 27: 0.99 - 0.98 6647 131 0.82 26.33 0.99 0.87 161.20| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.46 max = 12334.76 mean = 985.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.32| |phase err.(test): min = 0.00 max = 89.67 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1360 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1505 n_refl.: 191128 remove outliers: r(all,work,free)=0.1401 0.1399 0.1505 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1391 0.1389 0.1499 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1356 n_refl.: 191128 remove outliers: r(all,work,free)=0.1193 0.1190 0.1356 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 91.09 89 3 0.3502 356.180 328.608 0.372 0.993 0.176 13.296-10.522 95.05 95 1 0.2294 479.349 462.984 0.671 0.995 0.119 10.503-8.327 98.35 176 3 0.2153 502.600 494.788 0.830 0.995 0.101 8.318-6.595 100.00 360 8 0.2213 375.400 369.144 0.850 0.995 0.087 6.588-5.215 100.00 711 7 0.1953 344.955 334.087 0.845 0.996 0.080 5.214-4.128 98.38 1367 28 0.1253 504.564 498.192 0.935 0.997 0.051 4.126-3.266 94.74 2603 46 0.1168 459.938 451.962 0.997 0.999 0.021 3.266-2.585 99.86 5447 97 0.1120 310.263 306.813 0.981 1.000 0.010 2.585-2.046 97.45 10613 204 0.0962 234.076 231.412 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0910 138.538 137.171 1.001 1.008 0.000 1.619-1.281 98.00 42464 925 0.0940 74.581 73.933 0.990 1.016 0.000 1.281-0.980 96.53 101826 2055 0.1620 40.009 38.301 0.957 1.030 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0139 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2036 0.1949 0.081 5.033 5.2 78.0 14.6 805 0.000 1_bss: 0.1798 0.1879 0.081 5.033 5.2 78.1 14.6 805 0.000 1_settarget: 0.1798 0.1879 0.081 5.033 5.2 78.1 14.6 805 0.000 1_nqh: 0.1798 0.1879 0.081 5.033 5.2 78.1 14.6 805 0.000 1_weight: 0.1798 0.1879 0.081 5.033 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1271 0.1502 0.039 1.152 5.2 78.1 14.6 805 0.156 1_adp: 0.1296 0.1566 0.039 1.152 5.2 73.1 15.0 805 0.156 1_regHadp: 0.1296 0.1561 0.039 1.152 5.2 73.1 15.0 805 0.156 1_occ: 0.1281 0.1553 0.039 1.152 5.2 73.1 15.0 805 0.156 2_bss: 0.1275 0.1544 0.039 1.152 5.4 73.2 15.2 805 0.156 2_settarget: 0.1275 0.1544 0.039 1.152 5.4 73.2 15.2 805 0.156 2_updatecdl: 0.1275 0.1544 0.039 1.176 5.4 73.2 15.2 805 0.156 2_nqh: 0.1275 0.1544 0.039 1.176 5.4 73.2 15.2 805 0.156 2_sol: 0.1271 0.1505 0.039 1.176 5.4 73.2 16.3 880 n/a 2_weight: 0.1271 0.1505 0.039 1.176 5.4 73.2 16.3 880 n/a 2_xyzrec: 0.1254 0.1526 0.042 1.137 5.4 73.2 16.3 880 n/a 2_adp: 0.1232 0.1511 0.042 1.137 5.4 68.8 16.3 880 n/a 2_regHadp: 0.1233 0.1512 0.042 1.137 5.4 68.8 16.3 880 n/a 2_occ: 0.1227 0.1513 0.042 1.137 5.4 68.8 16.3 880 n/a 3_bss: 0.1233 0.1518 0.042 1.137 5.4 68.7 16.3 880 n/a 3_settarget: 0.1233 0.1518 0.042 1.137 5.4 68.7 16.3 880 n/a 3_updatecdl: 0.1233 0.1518 0.042 1.140 5.4 68.7 16.3 880 n/a 3_nqh: 0.1233 0.1518 0.042 1.140 5.4 68.7 16.3 880 n/a 3_sol: 0.1250 0.1526 0.042 1.140 5.4 68.7 15.4 862 n/a 3_weight: 0.1250 0.1526 0.042 1.140 5.4 68.7 15.4 862 n/a 3_xyzrec: 0.1240 0.1439 0.036 1.097 5.4 68.7 15.4 862 n/a 3_adp: 0.1233 0.1404 0.036 1.097 5.5 68.4 15.2 862 n/a 3_regHadp: 0.1234 0.1404 0.036 1.097 5.5 68.4 15.2 862 n/a 3_occ: 0.1229 0.1396 0.036 1.097 5.5 68.4 15.2 862 n/a 4_bss: 0.1225 0.1388 0.036 1.097 5.5 68.4 15.2 862 n/a 4_settarget: 0.1225 0.1388 0.036 1.097 5.5 68.4 15.2 862 n/a 4_updatecdl: 0.1225 0.1388 0.036 1.098 5.5 68.4 15.2 862 n/a 4_nqh: 0.1225 0.1388 0.036 1.098 5.5 68.4 15.2 862 n/a 4_sol: 0.1205 0.1364 0.036 1.098 5.5 68.4 15.0 866 n/a 4_weight: 0.1205 0.1364 0.036 1.098 5.5 68.4 15.0 866 n/a 4_xyzrec: 0.1204 0.1368 0.036 1.123 5.5 68.4 15.0 866 n/a 4_adp: 0.1198 0.1364 0.036 1.123 5.5 68.0 14.9 866 n/a 4_regHadp: 0.1198 0.1365 0.036 1.123 5.5 68.0 14.9 866 n/a 4_occ: 0.1196 0.1363 0.036 1.123 5.5 68.0 14.9 866 n/a 5_bss: 0.1194 0.1362 0.036 1.123 5.5 68.0 14.9 866 n/a 5_settarget: 0.1194 0.1362 0.036 1.123 5.5 68.0 14.9 866 n/a 5_updatecdl: 0.1194 0.1362 0.036 1.123 5.5 68.0 14.9 866 n/a 5_nqh: 0.1194 0.1362 0.036 1.123 5.5 68.0 14.9 866 n/a 5_sol: 0.1192 0.1347 0.036 1.123 5.5 68.0 15.0 880 n/a 5_weight: 0.1192 0.1347 0.036 1.123 5.5 68.0 15.0 880 n/a 5_xyzrec: 0.1195 0.1353 0.037 1.130 5.5 68.0 15.0 880 n/a 5_adp: 0.1200 0.1357 0.037 1.130 5.6 67.8 15.0 880 n/a 5_regHadp: 0.1200 0.1358 0.037 1.130 5.6 67.8 15.0 880 n/a 5_occ: 0.1198 0.1363 0.037 1.130 5.6 67.8 15.0 880 n/a 6_bss: 0.1197 0.1361 0.037 1.130 5.6 67.7 14.9 880 n/a 6_settarget: 0.1197 0.1361 0.037 1.130 5.6 67.7 14.9 880 n/a 6_updatecdl: 0.1197 0.1361 0.037 1.130 5.6 67.7 14.9 880 n/a 6_nqh: 0.1197 0.1361 0.037 1.130 5.6 67.7 14.9 880 n/a 6_sol: 0.1196 0.1354 0.037 1.130 5.6 67.7 14.9 889 n/a 6_weight: 0.1196 0.1354 0.037 1.130 5.6 67.7 14.9 889 n/a 6_xyzrec: 0.1199 0.1356 0.037 1.137 5.6 67.7 14.9 889 n/a 6_adp: 0.1202 0.1361 0.037 1.137 5.6 66.6 14.9 889 n/a 6_regHadp: 0.1202 0.1361 0.037 1.137 5.6 66.6 14.9 889 n/a 6_occ: 0.1200 0.1362 0.037 1.137 5.6 66.6 14.9 889 n/a 7_bss: 0.1199 0.1357 0.037 1.137 5.4 66.4 14.6 889 n/a 7_settarget: 0.1199 0.1357 0.037 1.137 5.4 66.4 14.6 889 n/a 7_updatecdl: 0.1199 0.1357 0.037 1.137 5.4 66.4 14.6 889 n/a 7_nqh: 0.1199 0.1357 0.037 1.137 5.4 66.4 14.6 889 n/a 7_sol: 0.1198 0.1357 0.037 1.137 5.4 66.4 14.7 903 n/a 7_weight: 0.1198 0.1357 0.037 1.137 5.4 66.4 14.7 903 n/a 7_xyzrec: 0.1201 0.1363 0.037 1.125 5.4 66.4 14.7 903 n/a 7_adp: 0.1203 0.1368 0.037 1.125 5.4 65.5 14.6 903 n/a 7_regHadp: 0.1203 0.1368 0.037 1.125 5.4 65.5 14.6 903 n/a 7_occ: 0.1202 0.1370 0.037 1.125 5.4 65.5 14.6 903 n/a 8_bss: 0.1193 0.1362 0.037 1.125 5.5 65.6 14.7 903 n/a 8_settarget: 0.1193 0.1362 0.037 1.125 5.5 65.6 14.7 903 n/a 8_updatecdl: 0.1193 0.1362 0.037 1.126 5.5 65.6 14.7 903 n/a 8_nqh: 0.1193 0.1362 0.037 1.126 5.5 65.6 14.7 903 n/a 8_sol: 0.1190 0.1357 0.037 1.126 5.5 65.6 14.7 909 n/a 8_weight: 0.1190 0.1357 0.037 1.126 5.5 65.6 14.7 909 n/a 8_xyzrec: 0.1193 0.1359 0.038 1.125 5.5 65.6 14.7 909 n/a 8_adp: 0.1195 0.1362 0.038 1.125 5.5 64.7 14.7 909 n/a 8_regHadp: 0.1195 0.1362 0.038 1.125 5.5 64.7 14.7 909 n/a 8_occ: 0.1193 0.1364 0.038 1.125 5.5 64.7 14.7 909 n/a 9_bss: 0.1192 0.1362 0.038 1.125 5.5 64.7 14.7 909 n/a 9_settarget: 0.1192 0.1362 0.038 1.125 5.5 64.7 14.7 909 n/a 9_updatecdl: 0.1192 0.1362 0.038 1.124 5.5 64.7 14.7 909 n/a 9_nqh: 0.1192 0.1362 0.038 1.124 5.5 64.7 14.7 909 n/a 9_sol: 0.1192 0.1358 0.038 1.124 5.5 64.7 14.7 910 n/a 9_weight: 0.1192 0.1358 0.038 1.124 5.5 64.7 14.7 910 n/a 9_xyzrec: 0.1194 0.1361 0.038 1.124 5.5 64.7 14.7 910 n/a 9_adp: 0.1195 0.1363 0.038 1.124 5.5 64.3 14.7 910 n/a 9_regHadp: 0.1195 0.1363 0.038 1.124 5.5 64.3 14.7 910 n/a 9_occ: 0.1194 0.1365 0.038 1.124 5.5 64.3 14.7 910 n/a 10_bss: 0.1193 0.1365 0.038 1.124 5.5 64.3 14.7 910 n/a 10_settarget: 0.1193 0.1365 0.038 1.124 5.5 64.3 14.7 910 n/a 10_updatecdl: 0.1193 0.1365 0.038 1.125 5.5 64.3 14.7 910 n/a 10_setrh: 0.1194 0.1365 0.038 1.125 5.5 64.3 14.7 910 n/a 10_nqh: 0.1194 0.1365 0.038 1.125 5.5 64.3 14.7 910 n/a 10_sol: 0.1193 0.1360 0.038 1.125 5.5 64.3 14.7 913 n/a 10_weight: 0.1193 0.1360 0.038 1.125 5.5 64.3 14.7 913 n/a 10_xyzrec: 0.1193 0.1361 0.038 1.142 5.5 64.3 14.7 913 n/a 10_adp: 0.1191 0.1360 0.038 1.142 5.6 63.9 14.7 913 n/a 10_regHadp: 0.1192 0.1360 0.038 1.142 5.6 63.9 14.7 913 n/a 10_occ: 0.1191 0.1360 0.038 1.142 5.6 63.9 14.7 913 n/a end: 0.1190 0.1356 0.038 1.142 5.5 63.8 14.6 913 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2565062_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2565062_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3700 Refinement macro-cycles (run) : 12226.3900 Write final files (write_after_run_outputs) : 151.3300 Total : 12384.0900 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:35 PST -0800 (1736736215.70 s) Start R-work = 0.1798, R-free = 0.1879 Final R-work = 0.1190, R-free = 0.1356 =============================================================================== Job complete usr+sys time: 12648.31 seconds wall clock time: 211 minutes 48.94 seconds (12708.94 seconds total)