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_5598907.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 { 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_5598907.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5598907.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.04, per 1000 atoms: 0.30 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: 2.730 distance_ideal: 2.720 ideal - model: -0.010 slack: 0.000 delta_slack: -0.010 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: 2.743 distance_ideal: 2.710 ideal - model: -0.033 slack: 0.000 delta_slack: -0.033 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.81 Conformation dependent library (CDL) restraints added in 114.3 milliseconds Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.04: 933 1.04 - 1.26: 2441 1.26 - 1.49: 1489 1.49 - 1.72: 1050 1.72 - 1.95: 21 Bond restraints: 5934 Sorted by residual: bond pdb=" C CYS A 47 " pdb=" O CYS A 47 " ideal model delta sigma weight residual 1.233 1.518 -0.284 1.28e-02 6.10e+03 4.93e+02 bond pdb=" N ILE A 162 " pdb=" CA ILE A 162 " ideal model delta sigma weight residual 1.461 1.696 -0.235 1.17e-02 7.31e+03 4.04e+02 bond pdb=" CA VAL B 114 " pdb=" C VAL B 114 " ideal model delta sigma weight residual 1.524 1.721 -0.196 1.05e-02 9.07e+03 3.50e+02 bond pdb=" CG1 VAL B 51 " pdb="HG12 VAL B 51 " ideal model delta sigma weight residual 0.970 1.337 -0.367 2.00e-02 2.50e+03 3.37e+02 bond pdb=" CD1 LEU A 54 " pdb="HD13 LEU A 54 " ideal model delta sigma weight residual 0.970 1.329 -0.359 2.00e-02 2.50e+03 3.22e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 5727 4.24 - 8.48: 3561 8.48 - 12.73: 1267 12.73 - 16.97: 224 16.97 - 21.21: 31 Bond angle restraints: 10810 Sorted by residual: angle pdb=" N PRO A 135 " pdb=" CA PRO A 135 " pdb=" CB PRO A 135 " ideal model delta sigma weight residual 103.32 89.90 13.42 8.40e-01 1.42e+00 2.55e+02 angle pdb=" NE ARG B 100 " pdb=" CZ ARG B 100 " pdb=" NH2 ARG B 100 " ideal model delta sigma weight residual 119.20 132.58 -13.38 9.00e-01 1.23e+00 2.21e+02 angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 106.17 13.03 9.00e-01 1.23e+00 2.09e+02 angle pdb=" CA ILE A 191 " pdb=" C ILE A 191 " pdb=" O ILE A 191 " ideal model delta sigma weight residual 120.84 137.46 -16.62 1.16e+00 7.43e-01 2.05e+02 angle pdb=" O HIS B 116 " pdb=" C HIS B 116 " pdb=" N ASP B 117 " ideal model delta sigma weight residual 122.34 140.19 -17.85 1.25e+00 6.40e-01 2.04e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.81: 1818 15.81 - 31.62: 159 31.62 - 47.42: 39 47.42 - 63.23: 28 63.23 - 79.03: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP A 139 " pdb=" C TRP A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA MET B 124 " pdb=" C MET B 124 " pdb=" N THR B 125 " pdb=" CA THR B 125 " ideal model delta harmonic sigma weight residual 180.00 157.99 22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 218 0.228 - 0.457: 142 0.457 - 0.685: 96 0.685 - 0.913: 30 0.913 - 1.141: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA SER B 4 " pdb=" N SER B 4 " pdb=" C SER B 4 " pdb=" CB SER B 4 " both_signs ideal model delta sigma weight residual False 2.51 3.65 -1.14 2.00e-01 2.50e+01 3.26e+01 chirality pdb=" CB ILE B 70 " pdb=" CA ILE B 70 " pdb=" CG1 ILE B 70 " pdb=" CG2 ILE B 70 " both_signs ideal model delta sigma weight residual False 2.64 1.52 1.13 2.00e-01 2.50e+01 3.18e+01 chirality pdb=" CA ARG B 97 " pdb=" N ARG B 97 " pdb=" C ARG B 97 " pdb=" CB ARG B 97 " both_signs ideal model delta sigma weight residual False 2.51 1.45 1.06 2.00e-01 2.50e+01 2.78e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.006 2.00e-02 2.50e+03 7.20e-02 2.07e+02 pdb=" CG TRP A 139 " 0.118 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.042 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.080 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.178 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.010 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.082 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.078 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.051 2.00e-02 2.50e+03 7.41e-02 1.65e+02 pdb=" CG TYR A 194 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.074 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " 0.092 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " 0.021 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.089 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " -0.026 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " -0.158 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.086 2.00e-02 2.50e+03 6.14e-02 1.51e+02 pdb=" CG TRP A 146 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.126 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.048 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.092 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.086 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.049 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.042 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.040 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.064 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.013 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.068 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.009 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.67: 38 1.67 - 2.40: 3046 2.40 - 3.14: 22658 3.14 - 3.87: 32869 3.87 - 4.60: 51533 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110144 Sorted by model distance: nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.941 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.945 2.620 nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.958 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.026 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.078 2.620 ... (remaining 110139 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_5598907_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= 0.2024 r_free= 0.1990 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.295122 | | target function (ml) not normalized (work): 804532.117122 | | target function (ml) not normalized (free): 16548.769302 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2127 0.1988 6.6709 6.3201| | 2: 2.94 - 2.33 1.00 7339 128 0.1595 0.1632 5.5422 5.5961| | 3: 2.33 - 2.04 0.96 6939 150 0.1627 0.1615 5.142 5.2306| | 4: 2.04 - 1.85 1.00 7170 155 0.1751 0.1506 4.9598 4.9747| | 5: 1.85 - 1.72 0.99 7113 159 0.1919 0.1729 4.7858 4.7465| | 6: 1.72 - 1.62 0.99 7102 142 0.1957 0.2109 4.6513 4.7378| | 7: 1.62 - 1.54 0.99 7104 148 0.1981 0.1628 4.5527 4.5361| | 8: 1.54 - 1.47 0.96 6798 152 0.2044 0.2202 4.4636 4.5336| | 9: 1.47 - 1.41 0.98 6938 155 0.2118 0.2272 4.4035 4.496| | 10: 1.41 - 1.36 0.99 7022 150 0.2131 0.2246 4.3191 4.3838| | 11: 1.36 - 1.32 0.99 6997 151 0.2107 0.2268 4.2407 4.3218| | 12: 1.32 - 1.28 0.98 6976 149 0.2092 0.1974 4.1808 4.2185| | 13: 1.28 - 1.25 0.98 6907 166 0.2031 0.2173 4.1215 4.206| | 14: 1.25 - 1.22 0.98 7015 113 0.2078 0.2337 4.0724 4.2453| | 15: 1.22 - 1.19 0.98 6957 137 0.2091 0.1932 4.0297 4.0123| | 16: 1.19 - 1.17 0.93 6604 132 0.2076 0.2270 3.9905 4.0545| | 17: 1.17 - 1.14 0.98 6941 135 0.2164 0.2074 3.9576 4.0073| | 18: 1.14 - 1.12 0.98 6875 142 0.2182 0.2414 3.9069 3.881| | 19: 1.12 - 1.10 0.97 6949 106 0.2238 0.2425 3.8635 3.9979| | 20: 1.10 - 1.08 0.97 6884 147 0.2302 0.2260 3.8072 3.8312| | 21: 1.08 - 1.07 0.97 6852 152 0.2396 0.2510 3.7683 3.795| | 22: 1.07 - 1.05 0.97 6838 135 0.2554 0.2398 3.749 3.7037| | 23: 1.05 - 1.03 0.97 6829 159 0.2712 0.2518 3.7191 3.7786| | 24: 1.03 - 1.02 0.96 6785 133 0.2877 0.2713 3.6965 3.7355| | 25: 1.02 - 1.01 0.93 6552 130 0.3091 0.3105 3.6758 3.7953| | 26: 1.01 - 0.99 0.96 6767 158 0.3221 0.3317 3.6342 3.6323| | 27: 0.99 - 0.98 0.94 6648 131 0.3402 0.2891 3.6511 3.5651| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.82 0.91 0.97 36688.74| | 2: 2.94 - 2.33 7339 128 0.85 21.56 1.08 1.01 15457.16| | 3: 2.33 - 2.04 6939 150 0.93 12.44 1.11 1.04 4036.33| | 4: 2.04 - 1.85 7170 155 0.93 13.05 1.11 1.07 2610.24| | 5: 1.85 - 1.72 7113 159 0.91 15.19 1.12 1.08 1979.25| | 6: 1.72 - 1.62 7102 142 0.90 16.41 1.11 1.08 1606.43| | 7: 1.62 - 1.54 7104 148 0.89 17.48 1.10 1.06 1311.30| | 8: 1.54 - 1.47 6798 152 0.88 18.66 1.11 1.04 1144.97| | 9: 1.47 - 1.41 6938 155 0.87 19.73 1.10 1.04 1032.57| | 10: 1.41 - 1.36 7022 150 0.86 21.17 1.10 1.04 930.15| | 11: 1.36 - 1.32 6997 151 0.86 21.17 1.08 1.04 814.63| | 12: 1.32 - 1.28 6976 149 0.87 20.39 1.08 1.03 678.31| | 13: 1.28 - 1.25 6907 166 0.87 20.01 1.08 1.04 617.27| | 14: 1.25 - 1.22 7015 113 0.87 20.37 1.08 1.03 549.14| | 15: 1.22 - 1.19 6957 137 0.87 20.76 1.08 1.03 526.73| | 16: 1.19 - 1.17 6604 132 0.87 20.31 1.07 1.02 480.11| | 17: 1.17 - 1.14 6941 135 0.86 21.01 1.08 1.02 446.65| | 18: 1.14 - 1.12 6875 142 0.86 21.05 1.08 1.00 394.43| | 19: 1.12 - 1.10 6949 106 0.86 21.41 1.07 1.00 361.99| | 20: 1.10 - 1.08 6884 147 0.86 21.76 1.07 1.00 326.37| | 21: 1.08 - 1.07 6852 152 0.85 22.57 1.07 1.01 311.69| | 22: 1.07 - 1.05 6838 135 0.83 24.25 1.05 0.99 301.39| | 23: 1.05 - 1.03 6829 159 0.81 26.79 1.05 0.98 311.08| | 24: 1.03 - 1.02 6785 133 0.78 29.28 1.05 0.97 326.93| | 25: 1.02 - 1.01 6552 130 0.76 31.07 1.03 0.93 315.84| | 26: 1.01 - 0.99 6767 158 0.75 31.80 1.03 0.91 284.65| | 27: 0.99 - 0.98 6648 131 0.78 29.60 1.04 0.91 234.34| |alpha: min = 0.91 max = 1.08 mean = 1.01| |beta: min = 234.34 max = 36688.74 mean = 2874.50| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.96 mean = 21.41| |phase err.(test): min = 0.00 max = 89.87 mean = 21.44| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.284 2950 Z= 5.333 Angle : 5.283 18.094 4018 Z= 3.766 Chirality : 0.387 1.141 492 Planarity : 0.032 0.105 512 Dihedral : 12.708 79.035 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.97 % Allowed : 3.55 % Favored : 95.48 % Cbeta Deviations : 32.58 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.38), residues: 386 helix: -2.53 (0.32), residues: 144 sheet: -0.58 (0.56), residues: 66 loop : -0.79 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.111 0.026 ARG B 149 TYR 0.122 0.041 TYR A 195 PHE 0.107 0.045 PHE B 164 TRP 0.122 0.042 TRP A 146 HIS 0.089 0.039 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2024 r_free= 0.1990 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.295122 | | target function (ml) not normalized (work): 804532.117122 | | target function (ml) not normalized (free): 16548.769302 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2023 0.2024 0.1990 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2023 0.2024 0.1990 n_refl.: 191155 remove outliers: r(all,work,free)=0.2023 0.2024 0.1990 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2023 0.2024 0.1990 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1793 0.1791 0.1935 n_refl.: 191145 remove outliers: r(all,work,free)=0.1792 0.1789 0.1935 n_refl.: 191141 ======================== 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 0.4193 400.535 294.611 0.433 0.912 0.298 13.296-10.522 100.00 100 1 0.2518 534.497 522.101 0.788 0.914 0.250 10.503-8.327 99.45 178 3 0.2524 565.118 555.640 0.971 0.914 0.230 8.318-6.595 100.00 360 8 0.2452 414.736 404.013 0.975 0.914 0.200 6.588-5.215 100.00 711 7 0.2282 381.101 366.794 0.961 0.914 0.180 5.214-4.128 98.38 1367 28 0.1472 557.435 550.308 1.077 0.914 0.080 4.126-3.266 94.74 2603 46 0.1346 508.132 498.977 1.144 0.914 0.019 3.266-2.585 99.86 5447 97 0.1427 342.774 337.519 1.120 0.913 0.000 2.585-2.046 97.45 10613 204 0.1377 258.603 254.305 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1606 153.054 149.908 1.143 0.912 0.000 1.619-1.281 98.00 42464 925 0.1922 82.395 80.212 1.129 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2304 44.203 41.679 1.113 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0047 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1789 r_free=0.1935 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1789 r_free=0.1935 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.225419 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 580.372989 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 0.1272 0.1500 0.0228 0.039 1.2 10.9 0.0 0.3 0 11.113 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.00 2.28 1.117 13.109 580.373 0.019 12.98 15.71 2.72 1.254 13.337 580.373 0.017 Individual atomic B min max mean iso aniso Overall: 5.17 73.04 15.01 1.41 435 3274 Protein: 5.17 40.31 11.01 1.41 0 2902 Water: 6.28 73.04 29.43 N/A 435 370 Other: 16.02 29.95 22.99 N/A 0 2 Chain A: 5.29 59.83 13.05 N/A 0 1626 Chain B: 5.17 73.04 12.78 N/A 0 1648 Chain S: 11.22 64.90 30.80 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2163 11.96 - 18.74 640 18.74 - 25.53 323 25.53 - 32.32 255 32.32 - 39.11 162 39.11 - 45.89 100 45.89 - 52.68 43 52.68 - 59.47 18 59.47 - 66.25 4 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1571 r_work=0.1298 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1565 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 = 0.1284 r_free = 0.1554 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1284 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015672 | | target function (ls_wunit_k1) not normalized (work): 2935.390607 | | target function (ls_wunit_k1) not normalized (free): 116.266274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1284 0.1554 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1474 0.1471 0.1633 n_refl.: 191141 remove outliers: r(all,work,free)=0.1474 0.1471 0.1633 n_refl.: 191141 overall B=0.17 to atoms: r(all,work,free)=0.1499 0.1496 0.1643 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1543 n_refl.: 191141 remove outliers: r(all,work,free)=0.1281 0.1275 0.1542 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3567 402.814 378.215 0.483 0.962 0.269 13.296-10.522 100.00 100 1 0.2129 534.497 526.593 0.745 0.964 0.240 10.503-8.327 99.45 178 3 0.1761 565.118 562.169 0.890 0.964 0.208 8.318-6.595 100.00 360 8 0.1703 414.736 411.974 0.914 0.964 0.175 6.588-5.215 100.00 711 7 0.1531 381.101 373.785 0.890 0.964 0.170 5.214-4.128 98.38 1367 28 0.0901 557.435 554.395 0.979 0.964 0.080 4.126-3.266 94.74 2603 46 0.0833 508.132 504.385 1.044 0.965 0.014 3.266-2.585 99.86 5447 97 0.0924 342.774 340.337 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.375 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1091 153.054 151.373 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.409 1.048 0.964 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.174 1.026 0.963 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0384 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1542 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1542 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1542 | n_water=805 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1280 r_free=0.1546 | n_water=794 | time (s): 102.130 (total time: 104.640) Filter (q & B) r_work=0.1280 r_free=0.1545 | n_water=792 | time (s): 5.260 (total time: 109.900) Compute maps r_work=0.1280 r_free=0.1545 | n_water=792 | time (s): 1.780 (total time: 111.680) Filter (map) r_work=0.1307 r_free=0.1531 | n_water=647 | time (s): 5.120 (total time: 116.800) Find peaks r_work=0.1307 r_free=0.1531 | n_water=647 | time (s): 0.740 (total time: 117.540) Add new water r_work=0.1332 r_free=0.1567 | n_water=951 | time (s): 4.400 (total time: 121.940) Refine new water occ: r_work=0.1286 r_free=0.1509 adp: r_work=0.1273 r_free=0.1509 occ: r_work=0.1275 r_free=0.1505 adp: r_work=0.1269 r_free=0.1506 occ: r_work=0.1270 r_free=0.1505 adp: r_work=0.1267 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1505 r_work=0.1267 r_free=0.1505 | n_water=951 | time (s): 84.750 (total time: 206.690) Filter (q & B) r_work=0.1271 r_free=0.1507 | n_water=886 | time (s): 4.320 (total time: 211.010) Filter (dist only) r_work=0.1271 r_free=0.1507 | n_water=884 | time (s): 113.020 (total time: 324.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.617044 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 596.416194 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 0.1256 0.1532 0.0276 0.042 1.1 19.0 0.0 0.3 0 11.309 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.32 2.76 2.046 15.195 596.416 0.015 12.35 15.20 2.85 2.391 15.230 596.416 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 68.24 16.31 1.21 516 3272 Protein: 5.39 40.05 11.01 1.21 0 2902 Water: 6.63 68.24 33.69 N/A 516 368 Other: 16.22 31.85 24.04 N/A 0 2 Chain A: 5.53 56.63 13.00 N/A 0 1624 Chain B: 5.39 68.24 12.83 N/A 0 1648 Chain S: 8.37 65.70 37.82 N/A 516 0 Histogram: Values Number of atoms 5.39 - 11.67 2054 11.67 - 17.96 711 17.96 - 24.24 266 24.24 - 30.53 219 30.53 - 36.81 166 36.81 - 43.10 174 43.10 - 49.38 101 49.38 - 55.67 53 55.67 - 61.95 34 61.95 - 68.24 10 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1520 r_work=0.1235 r_free=0.1522 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1522 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 = 0.1229 r_free = 0.1516 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1516 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013511 | | target function (ls_wunit_k1) not normalized (work): 2530.569480 | | target function (ls_wunit_k1) not normalized (free): 101.597293 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1516 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1440 0.1438 0.1603 n_refl.: 191139 remove outliers: r(all,work,free)=0.1440 0.1438 0.1603 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1437 0.1435 0.1602 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1242 0.1236 0.1525 n_refl.: 191139 remove outliers: r(all,work,free)=0.1242 0.1236 0.1525 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3284 402.814 377.572 0.494 0.962 0.265 13.296-10.522 100.00 100 1 0.1874 534.497 527.493 0.765 0.963 0.218 10.503-8.327 99.45 178 3 0.1429 565.118 566.771 0.923 0.963 0.191 8.318-6.595 100.00 360 8 0.1541 414.736 413.707 0.939 0.963 0.166 6.588-5.215 100.00 711 7 0.1344 381.101 376.674 0.914 0.963 0.150 5.214-4.128 98.38 1367 28 0.0836 557.435 555.981 0.995 0.963 0.100 4.126-3.266 94.74 2603 46 0.0763 508.132 505.298 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0859 342.774 341.334 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0900 258.603 256.774 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1048 153.054 151.609 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1259 82.395 81.361 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.222 1.060 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0494 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1525 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1525 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1525 | n_water=884 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1238 r_free=0.1525 | n_water=879 | time (s): 107.620 (total time: 110.110) Filter (q & B) r_work=0.1238 r_free=0.1524 | n_water=876 | time (s): 5.120 (total time: 115.230) Compute maps r_work=0.1238 r_free=0.1524 | n_water=876 | time (s): 1.740 (total time: 116.970) Filter (map) r_work=0.1273 r_free=0.1523 | n_water=696 | time (s): 4.850 (total time: 121.820) Find peaks r_work=0.1273 r_free=0.1523 | n_water=696 | time (s): 0.830 (total time: 122.650) Add new water r_work=0.1297 r_free=0.1555 | n_water=1028 | time (s): 5.150 (total time: 127.800) Refine new water occ: r_work=0.1252 r_free=0.1513 adp: r_work=0.1252 r_free=0.1515 occ: r_work=0.1248 r_free=0.1510 adp: r_work=0.1248 r_free=0.1512 occ: r_work=0.1245 r_free=0.1508 adp: r_work=0.1244 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1510 r_work=0.1244 r_free=0.1510 | n_water=1028 | time (s): 358.480 (total time: 486.280) Filter (q & B) r_work=0.1250 r_free=0.1517 | n_water=888 | time (s): 5.340 (total time: 491.620) Filter (dist only) r_work=0.1250 r_free=0.1517 | n_water=887 | time (s): 122.620 (total time: 614.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.707675 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.433912 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 0.1238 0.1435 0.0196 0.035 1.1 8.3 0.0 0.0 0 0.854 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.35 1.96 1.940 14.636 17.434 3.941 12.30 13.92 1.63 2.207 14.553 17.434 3.896 Individual atomic B min max mean iso aniso Overall: 5.53 67.88 15.34 1.09 520 3271 Protein: 5.53 36.84 10.79 1.09 0 2902 Water: 6.69 67.88 30.23 N/A 520 367 Other: 14.15 27.65 20.90 N/A 0 2 Chain A: 5.53 55.87 12.80 N/A 0 1624 Chain B: 5.54 67.88 12.57 N/A 0 1647 Chain S: 12.55 61.96 32.08 N/A 520 0 Histogram: Values Number of atoms 5.53 - 11.77 2129 11.77 - 18.00 680 18.00 - 24.24 297 24.24 - 30.47 251 30.47 - 36.71 180 36.71 - 42.94 154 42.94 - 49.17 65 49.17 - 55.41 23 55.41 - 61.64 10 61.64 - 67.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1393 r_work=0.1230 r_free=0.1394 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1394 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1384 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889984 | | target function (ml) not normalized (work): 728586.135106 | | target function (ml) not normalized (free): 15224.851213 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1228 0.1224 0.1383 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1438 0.1438 0.1466 n_refl.: 191139 remove outliers: r(all,work,free)=0.1438 0.1438 0.1466 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1432 0.1432 0.1463 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1224 0.1220 0.1377 n_refl.: 191139 remove outliers: r(all,work,free)=0.1223 0.1220 0.1377 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 0.3787 398.008 361.624 0.416 0.947 0.236 13.296-10.522 99.01 99 1 0.2455 528.187 513.280 0.708 0.948 0.194 10.503-8.327 98.35 176 3 0.1982 555.265 557.911 0.888 0.948 0.160 8.318-6.595 100.00 360 8 0.2015 414.736 410.002 0.895 0.948 0.125 6.588-5.215 100.00 711 7 0.1806 381.101 371.017 0.886 0.948 0.110 5.214-4.128 98.38 1367 28 0.1170 557.435 551.603 0.971 0.948 0.090 4.126-3.266 94.74 2603 46 0.1091 508.132 500.671 1.031 0.948 0.009 3.266-2.585 99.86 5447 97 0.1074 342.774 339.115 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0960 258.603 255.753 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0972 153.054 151.383 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1047 82.395 81.489 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.322 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1015 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1220 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1220 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1220 r_free=0.1377 | n_water=887 | time (s): 2.900 (total time: 2.900) Filter (dist) r_work=0.1220 r_free=0.1378 | n_water=886 | time (s): 109.370 (total time: 112.270) Filter (q & B) r_work=0.1221 r_free=0.1375 | n_water=874 | time (s): 4.160 (total time: 116.430) Compute maps r_work=0.1221 r_free=0.1375 | n_water=874 | time (s): 1.880 (total time: 118.310) Filter (map) r_work=0.1245 r_free=0.1378 | n_water=726 | time (s): 5.670 (total time: 123.980) Find peaks r_work=0.1245 r_free=0.1378 | n_water=726 | time (s): 0.680 (total time: 124.660) Add new water r_work=0.1259 r_free=0.1387 | n_water=977 | time (s): 5.000 (total time: 129.660) Refine new water occ: r_work=0.1210 r_free=0.1352 adp: r_work=0.1203 r_free=0.1346 occ: r_work=0.1200 r_free=0.1349 adp: r_work=0.1200 r_free=0.1346 occ: r_work=0.1198 r_free=0.1350 adp: r_work=0.1198 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1350 r_work=0.1198 r_free=0.1350 | n_water=977 | time (s): 332.370 (total time: 462.030) Filter (q & B) r_work=0.1202 r_free=0.1353 | n_water=882 | time (s): 5.250 (total time: 467.280) Filter (dist only) r_work=0.1203 r_free=0.1352 | n_water=880 | time (s): 111.020 (total time: 578.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.605757 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.563250 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 0.1200 0.1354 0.0154 0.036 1.1 6.6 0.0 0.0 0 0.803 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.54 1.54 1.853 14.255 15.563 3.872 11.96 13.52 1.55 1.934 14.230 15.563 3.866 Individual atomic B min max mean iso aniso Overall: 5.55 67.57 15.03 1.02 513 3271 Protein: 5.55 34.55 10.72 1.02 0 2902 Water: 6.00 67.57 29.22 N/A 513 367 Other: 13.94 27.40 20.67 N/A 0 2 Chain A: 5.57 55.15 12.69 N/A 0 1624 Chain B: 5.55 67.57 12.49 N/A 0 1647 Chain S: 6.00 60.97 30.59 N/A 513 0 Histogram: Values Number of atoms 5.55 - 11.75 2128 11.75 - 17.95 703 17.95 - 24.15 314 24.15 - 30.36 255 30.36 - 36.56 160 36.56 - 42.76 137 42.76 - 48.97 62 48.97 - 55.17 19 55.17 - 61.37 5 61.37 - 67.57 1 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1352 r_work=0.1196 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1352 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1349 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863971 | | target function (ml) not normalized (work): 723698.535330 | | target function (ml) not normalized (free): 15130.655885 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1420 0.1420 0.1458 n_refl.: 191135 remove outliers: r(all,work,free)=0.1420 0.1420 0.1458 n_refl.: 191135 overall B=-0.04 to atoms: r(all,work,free)=0.1412 0.1412 0.1453 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1348 n_refl.: 191135 remove outliers: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3405 351.947 309.162 0.400 0.947 0.235 13.296-10.522 96.04 96 1 0.2363 480.251 445.931 0.692 0.949 0.182 10.503-8.327 98.35 176 3 0.2129 502.605 494.969 0.869 0.949 0.139 8.318-6.595 100.00 360 8 0.2160 375.404 369.670 0.887 0.949 0.110 6.588-5.215 100.00 711 7 0.1859 344.958 335.462 0.886 0.949 0.100 5.214-4.128 98.38 1367 28 0.1181 504.569 499.406 0.971 0.949 0.060 4.126-3.266 94.74 2603 46 0.1102 459.942 453.309 1.032 0.949 0.000 3.266-2.585 99.86 5447 97 0.1069 310.266 307.295 1.020 0.949 0.000 2.585-2.046 97.45 10613 204 0.0930 234.078 231.776 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0916 138.539 137.309 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0991 74.581 73.887 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1664 40.010 38.360 1.040 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9647 b_overall=-0.1258 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1348 | n_water=880 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1192 r_free=0.1348 | n_water=880 | time (s): 109.930 (total time: 112.380) Filter (q & B) r_work=0.1192 r_free=0.1348 | n_water=871 | time (s): 4.390 (total time: 116.770) Compute maps r_work=0.1192 r_free=0.1348 | n_water=871 | time (s): 2.240 (total time: 119.010) Filter (map) r_work=0.1214 r_free=0.1354 | n_water=750 | time (s): 4.580 (total time: 123.590) Find peaks r_work=0.1214 r_free=0.1354 | n_water=750 | time (s): 0.670 (total time: 124.260) Add new water r_work=0.1224 r_free=0.1357 | n_water=963 | time (s): 4.350 (total time: 128.610) Refine new water occ: r_work=0.1190 r_free=0.1335 adp: r_work=0.1190 r_free=0.1334 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1335 occ: r_work=0.1186 r_free=0.1337 adp: r_work=0.1186 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1337 r_work=0.1186 r_free=0.1337 | n_water=963 | time (s): 318.690 (total time: 447.300) Filter (q & B) r_work=0.1189 r_free=0.1344 | n_water=893 | time (s): 4.490 (total time: 451.790) Filter (dist only) r_work=0.1189 r_free=0.1343 | n_water=892 | time (s): 114.530 (total time: 566.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.562116 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.777538 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1356 0.0164 0.037 1.1 7.1 0.0 0.3 0 0.781 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.56 1.64 1.813 14.225 14.778 3.764 11.97 13.58 1.61 1.901 14.194 14.778 3.762 Individual atomic B min max mean iso aniso Overall: 5.59 67.21 15.04 0.97 525 3271 Protein: 5.59 32.83 10.64 0.97 0 2902 Water: 6.03 67.21 29.35 N/A 525 367 Other: 13.78 26.04 19.91 N/A 0 2 Chain A: 5.59 54.35 12.58 N/A 0 1624 Chain B: 5.60 67.21 12.39 N/A 0 1647 Chain S: 6.03 60.87 30.97 N/A 525 0 Histogram: Values Number of atoms 5.59 - 11.76 2147 11.76 - 17.92 707 17.92 - 24.08 303 24.08 - 30.24 236 30.24 - 36.40 162 36.40 - 42.57 152 42.57 - 48.73 61 48.73 - 54.89 22 54.89 - 61.05 5 61.05 - 67.21 1 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1358 r_work=0.1198 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1358 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1360 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.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760978 | | target function (ml) not normalized (work): 704382.215774 | | target function (ml) not normalized (free): 14751.055024 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1360 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1395 0.1393 0.1487 n_refl.: 191128 remove outliers: r(all,work,free)=0.1395 0.1393 0.1487 n_refl.: 191128 overall B=-0.04 to atoms: r(all,work,free)=0.1386 0.1385 0.1481 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191128 remove outliers: r(all,work,free)=0.1197 0.1194 0.1360 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3471 351.947 327.366 0.414 0.952 0.227 13.296-10.522 96.04 96 1 0.2388 480.251 459.688 0.712 0.953 0.199 10.503-8.327 98.35 176 3 0.2078 502.605 495.801 0.867 0.954 0.143 8.318-6.595 100.00 360 8 0.2160 375.404 369.652 0.881 0.953 0.100 6.588-5.215 100.00 711 7 0.1876 344.958 335.307 0.883 0.954 0.100 5.214-4.128 98.38 1367 28 0.1197 504.569 499.266 0.967 0.954 0.039 4.126-3.266 94.74 2603 46 0.1112 459.942 453.087 1.029 0.954 0.005 3.266-2.585 99.86 5447 97 0.1095 310.266 307.146 1.016 0.954 0.000 2.585-2.046 97.45 10613 204 0.0944 234.078 231.629 1.027 0.954 0.000 2.046-1.619 99.39 21536 464 0.0917 138.539 137.232 1.050 0.954 0.000 1.619-1.281 98.00 42464 925 0.0983 74.581 73.860 1.047 0.954 0.000 1.281-0.980 96.53 101826 2055 0.1655 40.010 38.346 1.034 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1455 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1360 | n_water=892 | time (s): 2.950 (total time: 2.950) Filter (dist) r_work=0.1194 r_free=0.1360 | n_water=892 | time (s): 104.630 (total time: 107.580) Filter (q & B) r_work=0.1195 r_free=0.1361 | n_water=881 | time (s): 4.870 (total time: 112.450) Compute maps r_work=0.1195 r_free=0.1361 | n_water=881 | time (s): 2.500 (total time: 114.950) Filter (map) r_work=0.1217 r_free=0.1348 | n_water=765 | time (s): 4.920 (total time: 119.870) Find peaks r_work=0.1217 r_free=0.1348 | n_water=765 | time (s): 0.680 (total time: 120.550) Add new water r_work=0.1226 r_free=0.1358 | n_water=985 | time (s): 4.840 (total time: 125.390) Refine new water occ: r_work=0.1194 r_free=0.1338 adp: r_work=0.1194 r_free=0.1337 occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1192 r_free=0.1339 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1341 r_work=0.1190 r_free=0.1341 | n_water=985 | time (s): 228.040 (total time: 353.430) Filter (q & B) r_work=0.1193 r_free=0.1348 | n_water=908 | time (s): 3.970 (total time: 357.400) Filter (dist only) r_work=0.1194 r_free=0.1347 | n_water=907 | time (s): 116.710 (total time: 474.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.563159 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.207157 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1346 0.0149 0.037 1.1 5.8 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.46 1.49 1.776 14.144 15.207 3.761 11.99 13.50 1.51 1.942 14.092 15.207 3.757 Individual atomic B min max mean iso aniso Overall: 5.59 66.06 14.96 0.91 540 3271 Protein: 5.59 29.76 10.51 0.91 0 2902 Water: 5.97 66.06 29.18 N/A 540 367 Other: 13.86 23.33 18.59 N/A 0 2 Chain A: 5.62 51.36 12.41 N/A 0 1624 Chain B: 5.59 66.06 12.25 N/A 0 1647 Chain S: 5.97 60.71 30.90 N/A 540 0 Histogram: Values Number of atoms 5.59 - 11.64 2120 11.64 - 17.69 768 17.69 - 23.73 280 23.73 - 29.78 222 29.78 - 35.83 177 35.83 - 41.87 134 41.87 - 47.92 73 47.92 - 53.97 29 53.97 - 60.01 6 60.01 - 66.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1350 r_work=0.1199 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1350 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1353 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756503 | | target function (ml) not normalized (work): 703544.183969 | | target function (ml) not normalized (free): 14734.088498 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1489 n_refl.: 191128 remove outliers: r(all,work,free)=0.1393 0.1391 0.1489 n_refl.: 191128 overall B=-0.24 to atoms: r(all,work,free)=0.1355 0.1353 0.1463 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1350 n_refl.: 191128 remove outliers: r(all,work,free)=0.1198 0.1195 0.1350 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3441 351.947 326.968 0.411 0.953 0.205 13.296-10.522 95.05 95 1 0.2292 479.353 452.835 0.713 0.955 0.151 10.503-8.327 98.35 176 3 0.2144 502.605 496.152 0.886 0.955 0.127 8.318-6.595 100.00 360 8 0.2165 375.404 369.905 0.901 0.955 0.105 6.588-5.215 100.00 711 7 0.1898 344.958 335.497 0.903 0.955 0.087 5.214-4.128 98.38 1367 28 0.1210 504.569 499.249 0.991 0.955 0.039 4.126-3.266 94.74 2603 46 0.1137 459.942 452.898 1.052 0.955 0.005 3.266-2.585 99.86 5447 97 0.1111 310.266 307.147 1.037 0.955 0.000 2.585-2.046 97.45 10613 204 0.0951 234.078 231.609 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0910 138.539 137.262 1.062 0.954 0.000 1.619-1.281 98.00 42464 925 0.0971 74.581 73.888 1.050 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.010 38.355 1.022 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0532 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1350 | n_water=907 | time (s): 3.350 (total time: 3.350) Filter (dist) r_work=0.1195 r_free=0.1350 | n_water=907 | time (s): 106.700 (total time: 110.050) Filter (q & B) r_work=0.1196 r_free=0.1350 | n_water=899 | time (s): 5.570 (total time: 115.620) Compute maps r_work=0.1196 r_free=0.1350 | n_water=899 | time (s): 2.360 (total time: 117.980) Filter (map) r_work=0.1215 r_free=0.1351 | n_water=782 | time (s): 5.130 (total time: 123.110) Find peaks r_work=0.1215 r_free=0.1351 | n_water=782 | time (s): 0.630 (total time: 123.740) Add new water r_work=0.1224 r_free=0.1354 | n_water=988 | time (s): 4.260 (total time: 128.000) Refine new water occ: r_work=0.1194 r_free=0.1333 adp: r_work=0.1194 r_free=0.1333 occ: r_work=0.1192 r_free=0.1335 adp: r_work=0.1192 r_free=0.1334 occ: r_work=0.1190 r_free=0.1336 adp: r_work=0.1190 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1336 r_work=0.1190 r_free=0.1336 | n_water=988 | time (s): 194.270 (total time: 322.270) Filter (q & B) r_work=0.1195 r_free=0.1347 | n_water=909 | time (s): 4.440 (total time: 326.710) Filter (dist only) r_work=0.1195 r_free=0.1346 | n_water=905 | time (s): 115.930 (total time: 442.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.540771 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.782268 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1352 0.0155 0.037 1.1 4.8 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.52 1.55 1.727 13.785 14.782 3.758 11.99 13.52 1.53 1.787 13.762 14.782 3.756 Individual atomic B min max mean iso aniso Overall: 5.40 64.65 14.67 0.89 538 3271 Protein: 5.40 28.54 10.25 0.89 0 2902 Water: 5.82 64.65 28.86 N/A 538 367 Other: 13.68 22.06 17.87 N/A 0 2 Chain A: 5.43 50.45 12.10 N/A 0 1624 Chain B: 5.40 64.65 11.96 N/A 0 1647 Chain S: 5.82 60.32 30.75 N/A 538 0 Histogram: Values Number of atoms 5.40 - 11.33 2096 11.33 - 17.25 787 17.25 - 23.18 274 23.18 - 29.10 225 29.10 - 35.03 175 35.03 - 40.95 124 40.95 - 46.88 87 46.88 - 52.80 32 52.80 - 58.73 6 58.73 - 64.65 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1353 r_work=0.1199 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1353 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1356 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755408 | | target function (ml) not normalized (work): 703335.298959 | | target function (ml) not normalized (free): 14732.741666 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1356 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1361 0.1359 0.1476 n_refl.: 191127 remove outliers: r(all,work,free)=0.1361 0.1359 0.1476 n_refl.: 191127 overall B=0.06 to atoms: r(all,work,free)=0.1369 0.1366 0.1481 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1348 n_refl.: 191127 remove outliers: r(all,work,free)=0.1191 0.1188 0.1348 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3424 351.947 326.155 0.406 0.976 0.205 13.296-10.522 95.05 95 1 0.2296 479.353 461.569 0.719 0.977 0.153 10.503-8.327 98.35 176 3 0.2161 502.605 495.708 0.872 0.977 0.120 8.318-6.595 100.00 360 8 0.2168 375.404 369.257 0.885 0.977 0.094 6.588-5.215 100.00 711 7 0.1908 344.958 335.188 0.889 0.978 0.083 5.214-4.128 98.38 1367 28 0.1224 504.569 498.590 0.977 0.978 0.034 4.126-3.266 94.74 2603 46 0.1152 459.942 452.273 1.039 0.979 0.005 3.266-2.585 99.86 5447 97 0.1118 310.266 306.865 1.023 0.980 0.000 2.585-2.046 97.45 10613 204 0.0957 234.078 231.498 1.031 0.982 0.000 2.046-1.619 99.39 21536 464 0.0906 138.539 137.161 1.047 0.984 0.000 1.619-1.281 98.00 42464 925 0.0951 74.581 73.919 1.035 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.010 38.327 1.001 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0628 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1348 | n_water=905 | time (s): 2.640 (total time: 2.640) Filter (dist) r_work=0.1188 r_free=0.1348 | n_water=905 | time (s): 120.690 (total time: 123.330) Filter (q & B) r_work=0.1189 r_free=0.1348 | n_water=900 | time (s): 4.220 (total time: 127.550) Compute maps r_work=0.1189 r_free=0.1348 | n_water=900 | time (s): 1.690 (total time: 129.240) Filter (map) r_work=0.1207 r_free=0.1351 | n_water=784 | time (s): 4.780 (total time: 134.020) Find peaks r_work=0.1207 r_free=0.1351 | n_water=784 | time (s): 0.650 (total time: 134.670) Add new water r_work=0.1215 r_free=0.1358 | n_water=1008 | time (s): 4.610 (total time: 139.280) Refine new water occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1185 r_free=0.1331 occ: r_work=0.1182 r_free=0.1331 adp: r_work=0.1182 r_free=0.1332 occ: r_work=0.1181 r_free=0.1333 adp: r_work=0.1181 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1333 r_work=0.1181 r_free=0.1333 | n_water=1008 | time (s): 271.110 (total time: 410.390) Filter (q & B) r_work=0.1186 r_free=0.1345 | n_water=915 | time (s): 5.360 (total time: 415.750) Filter (dist only) r_work=0.1186 r_free=0.1345 | n_water=914 | time (s): 114.020 (total time: 529.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.519847 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.975607 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1350 0.0161 0.038 1.1 6.3 0.0 0.3 0 0.760 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.50 1.61 1.680 13.800 13.976 3.755 11.92 13.54 1.62 1.697 13.787 13.976 3.754 Individual atomic B min max mean iso aniso Overall: 5.46 64.11 14.74 0.87 547 3271 Protein: 5.46 28.17 10.31 0.87 0 2902 Water: 5.91 64.11 28.81 N/A 547 367 Other: 13.76 22.10 17.93 N/A 0 2 Chain A: 5.56 50.33 12.13 N/A 0 1624 Chain B: 5.46 64.11 11.99 N/A 0 1647 Chain S: 5.91 60.30 30.78 N/A 547 0 Histogram: Values Number of atoms 5.46 - 11.32 2071 11.32 - 17.19 817 17.19 - 23.05 262 23.05 - 28.92 231 28.92 - 34.78 185 34.78 - 40.65 120 40.65 - 46.51 91 46.51 - 52.38 32 52.38 - 58.24 6 58.24 - 64.11 3 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1354 r_work=0.1192 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753867 | | target function (ml) not normalized (work): 703046.798936 | | target function (ml) not normalized (free): 14735.622164 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1190 0.1359 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1376 0.1374 0.1493 n_refl.: 191127 remove outliers: r(all,work,free)=0.1376 0.1374 0.1493 n_refl.: 191127 overall B=0.01 to atoms: r(all,work,free)=0.1378 0.1376 0.1494 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1357 n_refl.: 191127 remove outliers: r(all,work,free)=0.1192 0.1189 0.1357 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3456 351.947 325.726 0.388 0.995 0.191 13.296-10.522 95.05 95 1 0.2294 479.353 462.464 0.700 0.996 0.137 10.503-8.327 98.35 176 3 0.2156 502.605 495.519 0.854 0.997 0.107 8.318-6.595 100.00 360 8 0.2163 375.404 368.886 0.864 0.997 0.087 6.588-5.215 100.00 711 7 0.1924 344.958 335.222 0.871 0.997 0.080 5.214-4.128 98.38 1367 28 0.1229 504.569 498.623 0.958 0.998 0.029 4.126-3.266 94.74 2603 46 0.1156 459.942 452.086 1.018 0.999 0.000 3.266-2.585 99.86 5447 97 0.1124 310.266 306.878 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0961 234.078 231.440 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0908 138.539 137.174 1.028 1.005 0.000 1.619-1.281 98.00 42464 925 0.0947 74.581 73.928 1.018 1.010 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.010 38.314 0.987 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0198 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1357 | n_water=914 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1189 r_free=0.1357 | n_water=914 | time (s): 115.760 (total time: 118.900) Filter (q & B) r_work=0.1190 r_free=0.1358 | n_water=903 | time (s): 4.960 (total time: 123.860) Compute maps r_work=0.1190 r_free=0.1358 | n_water=903 | time (s): 2.310 (total time: 126.170) Filter (map) r_work=0.1211 r_free=0.1351 | n_water=783 | time (s): 4.920 (total time: 131.090) Find peaks r_work=0.1211 r_free=0.1351 | n_water=783 | time (s): 0.700 (total time: 131.790) Add new water r_work=0.1218 r_free=0.1360 | n_water=1001 | time (s): 5.030 (total time: 136.820) Refine new water occ: r_work=0.1188 r_free=0.1332 adp: r_work=0.1188 r_free=0.1333 occ: r_work=0.1186 r_free=0.1332 adp: r_work=0.1186 r_free=0.1333 occ: r_work=0.1184 r_free=0.1332 adp: r_work=0.1184 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1334 r_work=0.1184 r_free=0.1334 | n_water=1001 | time (s): 196.190 (total time: 333.010) Filter (q & B) r_work=0.1189 r_free=0.1347 | n_water=911 | time (s): 5.790 (total time: 338.800) Filter (dist only) r_work=0.1189 r_free=0.1346 | n_water=909 | time (s): 115.180 (total time: 453.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.548806 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.181502 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1347 0.0155 0.038 1.1 5.3 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.47 1.55 1.678 13.792 14.182 3.754 11.91 13.48 1.57 1.691 13.787 14.182 3.752 Individual atomic B min max mean iso aniso Overall: 5.55 63.08 14.73 0.86 542 3271 Protein: 5.55 28.07 10.33 0.86 0 2902 Water: 5.96 63.08 28.75 N/A 542 367 Other: 13.82 22.13 17.97 N/A 0 2 Chain A: 5.61 49.94 12.12 N/A 0 1624 Chain B: 5.55 63.08 11.99 N/A 0 1647 Chain S: 5.96 60.15 30.85 N/A 542 0 Histogram: Values Number of atoms 5.55 - 11.30 2060 11.30 - 17.05 827 17.05 - 22.81 253 22.81 - 28.56 221 28.56 - 34.32 187 34.32 - 40.07 121 40.07 - 45.82 95 45.82 - 51.58 36 51.58 - 57.33 9 57.33 - 63.08 4 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1348 r_work=0.1191 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1349 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1351 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752166 | | target function (ml) not normalized (work): 702728.094724 | | target function (ml) not normalized (free): 14726.868998 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1351 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1387 0.1385 0.1489 n_refl.: 191127 remove outliers: r(all,work,free)=0.1387 0.1385 0.1489 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1386 0.1384 0.1488 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1188 0.1350 n_refl.: 191127 remove outliers: r(all,work,free)=0.1192 0.1188 0.1350 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3549 351.947 324.097 0.389 0.975 0.183 13.296-10.522 95.05 95 1 0.2288 479.353 462.929 0.711 0.977 0.130 10.503-8.327 98.35 176 3 0.2165 502.605 495.962 0.869 0.977 0.101 8.318-6.595 100.00 360 8 0.2180 375.404 368.905 0.879 0.977 0.084 6.588-5.215 100.00 711 7 0.1919 344.958 335.290 0.886 0.978 0.079 5.214-4.128 98.38 1367 28 0.1232 504.569 498.419 0.976 0.979 0.033 4.126-3.266 94.74 2603 46 0.1163 459.942 452.172 1.039 0.980 0.000 3.266-2.585 99.86 5447 97 0.1124 310.266 306.846 1.023 0.981 0.000 2.585-2.046 97.45 10613 204 0.0960 234.078 231.460 1.031 0.983 0.000 2.046-1.619 99.39 21536 464 0.0907 138.539 137.184 1.048 0.987 0.000 1.619-1.281 98.00 42464 925 0.0942 74.581 73.933 1.039 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.010 38.307 1.009 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0108 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1188 r_free=0.1350 After: r_work=0.1189 r_free=0.1350 ================================== NQH flips ================================== r_work=0.1189 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1350 | n_water=909 | time (s): 2.750 (total time: 2.750) Filter (dist) r_work=0.1189 r_free=0.1350 | n_water=909 | time (s): 112.590 (total time: 115.340) Filter (q & B) r_work=0.1190 r_free=0.1351 | n_water=901 | time (s): 5.130 (total time: 120.470) Compute maps r_work=0.1190 r_free=0.1351 | n_water=901 | time (s): 2.120 (total time: 122.590) Filter (map) r_work=0.1211 r_free=0.1355 | n_water=789 | time (s): 5.170 (total time: 127.760) Find peaks r_work=0.1211 r_free=0.1355 | n_water=789 | time (s): 0.610 (total time: 128.370) Add new water r_work=0.1218 r_free=0.1366 | n_water=1002 | time (s): 4.760 (total time: 133.130) Refine new water occ: r_work=0.1188 r_free=0.1333 adp: r_work=0.1188 r_free=0.1333 occ: r_work=0.1186 r_free=0.1333 adp: r_work=0.1186 r_free=0.1333 occ: r_work=0.1185 r_free=0.1332 adp: r_work=0.1185 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1333 r_work=0.1185 r_free=0.1333 | n_water=1002 | time (s): 206.060 (total time: 339.190) Filter (q & B) r_work=0.1189 r_free=0.1343 | n_water=905 | time (s): 5.130 (total time: 344.320) Filter (dist only) r_work=0.1190 r_free=0.1342 | n_water=903 | time (s): 118.420 (total time: 462.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.553140 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.417104 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1343 0.0153 0.038 1.1 7.7 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.43 1.53 1.676 13.761 14.417 3.753 11.90 13.43 1.53 1.670 13.761 14.417 3.751 Individual atomic B min max mean iso aniso Overall: 5.55 62.46 14.68 0.86 537 3270 Protein: 5.55 28.05 10.35 0.86 0 2902 Water: 6.01 62.46 28.58 N/A 537 366 Other: 13.84 22.18 18.01 N/A 0 2 Chain A: 5.63 49.71 12.12 N/A 0 1624 Chain B: 5.55 62.46 11.97 N/A 0 1646 Chain S: 6.01 60.08 30.74 N/A 537 0 Histogram: Values Number of atoms 5.55 - 11.24 2040 11.24 - 16.93 836 16.93 - 22.62 262 22.62 - 28.31 218 28.31 - 34.00 186 34.00 - 39.70 117 39.70 - 45.39 95 45.39 - 51.08 39 51.08 - 56.77 10 56.77 - 62.46 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1344 r_work=0.1190 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1344 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1344 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750777 | | target function (ml) not normalized (work): 702468.007867 | | target function (ml) not normalized (free): 14714.293084 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1349 0.1418 5.675 5.7293| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1316 5.0658 5.1546| | 3: 2.33 - 2.04 0.96 6939 150 0.0901 0.1177 4.6528 4.7534| | 4: 2.04 - 1.85 1.00 7170 155 0.0897 0.1088 4.3911 4.5848| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.0998 4.1514 4.2388| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1079 3.9452 4.0701| | 7: 1.62 - 1.54 0.99 7104 148 0.0885 0.0966 3.7953 3.9346| | 8: 1.54 - 1.47 0.96 6798 152 0.0885 0.1302 3.6926 3.8912| | 9: 1.47 - 1.41 0.98 6938 155 0.0921 0.1098 3.6124 3.7372| | 10: 1.41 - 1.36 0.99 7022 150 0.0970 0.1169 3.5497 3.6648| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1121 3.4804 3.585| | 12: 1.32 - 1.28 0.98 6975 149 0.1028 0.1124 3.4551 3.5785| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1234 3.4328 3.5529| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1586 3.43 3.6835| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1241 3.4469 3.4925| | 16: 1.19 - 1.17 0.93 6604 132 0.1247 0.1564 3.4637 3.6651| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1226 3.4328 3.4396| | 18: 1.14 - 1.12 0.98 6875 142 0.1381 0.1700 3.4364 3.5321| | 19: 1.12 - 1.10 0.97 6948 106 0.1467 0.1737 3.4176 3.5945| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1570 3.4084 3.4294| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2134 3.417 3.5042| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1962 3.4123 3.4166| | 23: 1.05 - 1.03 0.97 6827 159 0.2115 0.2027 3.4318 3.4846| | 24: 1.03 - 1.02 0.96 6784 133 0.2328 0.2247 3.4347 3.5057| | 25: 1.02 - 1.01 0.93 6552 130 0.2609 0.2518 3.4476 3.5276| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2871 3.4151 3.425| | 27: 0.99 - 0.98 0.94 6647 131 0.3037 0.2800 3.468 3.3925| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7395 127 0.93 11.07 1.00 0.96 10411.12| | 2: 2.94 - 2.33 7339 128 0.93 12.33 0.99 0.95 4849.77| | 3: 2.33 - 2.04 6939 150 0.96 7.61 1.01 0.95 1688.42| | 4: 2.04 - 1.85 7170 155 0.96 7.73 1.00 0.95 1013.59| | 5: 1.85 - 1.72 7113 159 0.96 8.14 1.00 0.96 640.04| | 6: 1.72 - 1.62 7102 142 0.96 8.01 1.00 0.96 444.06| | 7: 1.62 - 1.54 7104 148 0.96 8.12 1.01 0.97 335.10| | 8: 1.54 - 1.47 6798 152 0.96 8.19 1.01 0.97 274.98| | 9: 1.47 - 1.41 6938 155 0.96 8.32 1.00 0.98 225.47| | 10: 1.41 - 1.36 7022 150 0.96 8.75 1.00 0.97 197.93| | 11: 1.36 - 1.32 6997 151 0.96 8.83 0.99 0.96 172.30| | 12: 1.32 - 1.28 6975 149 0.96 8.92 0.98 0.95 159.24| | 13: 1.28 - 1.25 6907 166 0.96 9.47 1.01 0.96 157.10| | 14: 1.25 - 1.22 7015 112 0.95 10.66 1.01 0.96 162.14| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 0.98 166.49| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.96 160.21| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.96 153.81| | 18: 1.14 - 1.12 6875 142 0.94 12.71 1.01 0.95 146.77| | 19: 1.12 - 1.10 6948 106 0.93 14.08 1.00 0.95 150.12| | 20: 1.10 - 1.08 6884 147 0.92 15.16 1.00 0.94 149.42| | 21: 1.08 - 1.07 6852 152 0.91 16.63 1.00 0.93 152.86| | 22: 1.07 - 1.05 6836 135 0.89 18.28 0.99 0.93 154.62| | 23: 1.05 - 1.03 6827 159 0.87 20.47 0.99 0.92 164.46| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.93 178.84| | 25: 1.02 - 1.01 6552 130 0.83 25.16 0.98 0.90 182.09| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.88 176.37| | 27: 0.99 - 0.98 6647 131 0.82 26.22 0.99 0.87 160.13| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.77 max = 10411.12 mean = 882.45| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 90.00 mean = 13.22| |phase err.(test): min = 0.00 max = 88.19 mean = 13.35| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1344 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1395 0.1394 0.1488 n_refl.: 191127 remove outliers: r(all,work,free)=0.1395 0.1394 0.1488 n_refl.: 191127 overall B=-0.06 to atoms: r(all,work,free)=0.1387 0.1385 0.1482 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1343 n_refl.: 191127 remove outliers: r(all,work,free)=0.1191 0.1188 0.1343 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3519 351.947 322.842 0.407 0.916 0.189 13.296-10.522 95.05 95 1 0.2273 479.353 462.720 0.738 0.917 0.132 10.503-8.327 98.35 176 3 0.2165 502.605 495.876 0.899 0.917 0.101 8.318-6.595 100.00 360 8 0.2161 375.404 369.315 0.913 0.917 0.080 6.588-5.215 100.00 711 7 0.1914 344.958 335.440 0.921 0.918 0.073 5.214-4.128 98.38 1367 28 0.1232 504.569 498.636 1.014 0.919 0.030 4.126-3.266 94.74 2603 46 0.1162 459.942 452.187 1.081 0.920 0.005 3.266-2.585 99.86 5447 97 0.1127 310.266 306.920 1.063 0.921 0.000 2.585-2.046 97.45 10613 204 0.0962 234.078 231.491 1.070 0.924 0.000 2.046-1.619 99.39 21536 464 0.0908 138.539 137.183 1.087 0.928 0.000 1.619-1.281 98.00 42464 925 0.0941 74.581 73.937 1.075 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.010 38.299 1.041 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0126 ================= 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 : 0.2024 0.1990 0.079 5.283 5.2 78.0 14.6 805 0.000 1_bss: 0.1789 0.1935 0.079 5.283 5.2 78.0 14.6 805 0.000 1_settarget: 0.1789 0.1935 0.079 5.283 5.2 78.0 14.6 805 0.000 1_nqh: 0.1789 0.1935 0.079 5.283 5.2 78.0 14.6 805 0.000 1_weight: 0.1789 0.1935 0.079 5.283 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1272 0.1500 0.039 1.158 5.2 78.0 14.6 805 0.156 1_adp: 0.1299 0.1571 0.039 1.158 5.2 73.0 15.0 805 0.156 1_regHadp: 0.1298 0.1565 0.039 1.158 5.2 73.0 15.0 805 0.156 1_occ: 0.1284 0.1554 0.039 1.158 5.2 73.0 15.0 805 0.156 2_bss: 0.1275 0.1542 0.039 1.158 5.3 73.2 15.2 805 0.156 2_settarget: 0.1275 0.1542 0.039 1.158 5.3 73.2 15.2 805 0.156 2_updatecdl: 0.1275 0.1542 0.039 1.176 5.3 73.2 15.2 805 0.156 2_nqh: 0.1275 0.1542 0.039 1.176 5.3 73.2 15.2 805 0.156 2_sol: 0.1271 0.1507 0.039 1.176 5.3 73.2 16.2 884 n/a 2_weight: 0.1271 0.1507 0.039 1.176 5.3 73.2 16.2 884 n/a 2_xyzrec: 0.1256 0.1532 0.042 1.144 5.3 73.2 16.2 884 n/a 2_adp: 0.1235 0.1520 0.042 1.144 5.4 68.2 16.3 884 n/a 2_regHadp: 0.1235 0.1522 0.042 1.144 5.4 68.2 16.3 884 n/a 2_occ: 0.1229 0.1516 0.042 1.144 5.4 68.2 16.3 884 n/a 3_bss: 0.1236 0.1525 0.042 1.144 5.4 68.2 16.3 884 n/a 3_settarget: 0.1236 0.1525 0.042 1.144 5.4 68.2 16.3 884 n/a 3_updatecdl: 0.1236 0.1525 0.042 1.147 5.4 68.2 16.3 884 n/a 3_nqh: 0.1236 0.1525 0.042 1.147 5.4 68.2 16.3 884 n/a 3_sol: 0.1250 0.1517 0.042 1.147 5.4 68.2 15.5 887 n/a 3_weight: 0.1250 0.1517 0.042 1.147 5.4 68.2 15.5 887 n/a 3_xyzrec: 0.1238 0.1435 0.035 1.106 5.4 68.2 15.5 887 n/a 3_adp: 0.1230 0.1393 0.035 1.106 5.5 67.9 15.3 887 n/a 3_regHadp: 0.1230 0.1394 0.035 1.106 5.5 67.9 15.3 887 n/a 3_occ: 0.1224 0.1384 0.035 1.106 5.5 67.9 15.3 887 n/a 4_bss: 0.1220 0.1377 0.035 1.106 5.5 67.9 15.3 887 n/a 4_settarget: 0.1220 0.1377 0.035 1.106 5.5 67.9 15.3 887 n/a 4_updatecdl: 0.1220 0.1377 0.035 1.107 5.5 67.9 15.3 887 n/a 4_nqh: 0.1220 0.1377 0.035 1.107 5.5 67.9 15.3 887 n/a 4_sol: 0.1203 0.1352 0.035 1.107 5.5 67.9 15.1 880 n/a 4_weight: 0.1203 0.1352 0.035 1.107 5.5 67.9 15.1 880 n/a 4_xyzrec: 0.1200 0.1354 0.036 1.127 5.5 67.9 15.1 880 n/a 4_adp: 0.1196 0.1352 0.036 1.127 5.5 67.6 15.0 880 n/a 4_regHadp: 0.1196 0.1352 0.036 1.127 5.5 67.6 15.0 880 n/a 4_occ: 0.1194 0.1349 0.036 1.127 5.5 67.6 15.0 880 n/a 5_bss: 0.1192 0.1348 0.036 1.127 5.5 67.5 15.0 880 n/a 5_settarget: 0.1192 0.1348 0.036 1.127 5.5 67.5 15.0 880 n/a 5_updatecdl: 0.1192 0.1348 0.036 1.127 5.5 67.5 15.0 880 n/a 5_nqh: 0.1192 0.1348 0.036 1.127 5.5 67.5 15.0 880 n/a 5_sol: 0.1189 0.1343 0.036 1.127 5.5 67.5 15.1 892 n/a 5_weight: 0.1189 0.1343 0.036 1.127 5.5 67.5 15.1 892 n/a 5_xyzrec: 0.1192 0.1356 0.037 1.135 5.5 67.5 15.1 892 n/a 5_adp: 0.1197 0.1358 0.037 1.135 5.6 67.2 15.0 892 n/a 5_regHadp: 0.1198 0.1358 0.037 1.135 5.6 67.2 15.0 892 n/a 5_occ: 0.1195 0.1360 0.037 1.135 5.6 67.2 15.0 892 n/a 6_bss: 0.1194 0.1360 0.037 1.135 5.6 67.2 15.0 892 n/a 6_settarget: 0.1194 0.1360 0.037 1.135 5.6 67.2 15.0 892 n/a 6_updatecdl: 0.1194 0.1360 0.037 1.135 5.6 67.2 15.0 892 n/a 6_nqh: 0.1194 0.1360 0.037 1.135 5.6 67.2 15.0 892 n/a 6_sol: 0.1194 0.1347 0.037 1.135 5.6 67.2 15.1 907 n/a 6_weight: 0.1194 0.1347 0.037 1.135 5.6 67.2 15.1 907 n/a 6_xyzrec: 0.1197 0.1346 0.037 1.133 5.6 67.2 15.1 907 n/a 6_adp: 0.1199 0.1350 0.037 1.133 5.6 66.1 15.0 907 n/a 6_regHadp: 0.1199 0.1350 0.037 1.133 5.6 66.1 15.0 907 n/a 6_occ: 0.1196 0.1353 0.037 1.133 5.6 66.1 15.0 907 n/a 7_bss: 0.1195 0.1350 0.037 1.133 5.4 65.8 14.7 907 n/a 7_settarget: 0.1195 0.1350 0.037 1.133 5.4 65.8 14.7 907 n/a 7_updatecdl: 0.1195 0.1350 0.037 1.133 5.4 65.8 14.7 907 n/a 7_nqh: 0.1195 0.1350 0.037 1.133 5.4 65.8 14.7 907 n/a 7_sol: 0.1195 0.1346 0.037 1.133 5.4 65.8 14.7 905 n/a 7_weight: 0.1195 0.1346 0.037 1.133 5.4 65.8 14.7 905 n/a 7_xyzrec: 0.1198 0.1352 0.037 1.129 5.4 65.8 14.7 905 n/a 7_adp: 0.1199 0.1353 0.037 1.129 5.4 64.7 14.7 905 n/a 7_regHadp: 0.1199 0.1353 0.037 1.129 5.4 64.7 14.7 905 n/a 7_occ: 0.1197 0.1356 0.037 1.129 5.4 64.7 14.7 905 n/a 8_bss: 0.1188 0.1348 0.037 1.129 5.5 64.7 14.7 905 n/a 8_settarget: 0.1188 0.1348 0.037 1.129 5.5 64.7 14.7 905 n/a 8_updatecdl: 0.1188 0.1348 0.037 1.129 5.5 64.7 14.7 905 n/a 8_nqh: 0.1188 0.1348 0.037 1.129 5.5 64.7 14.7 905 n/a 8_sol: 0.1186 0.1345 0.037 1.129 5.5 64.7 14.8 914 n/a 8_weight: 0.1186 0.1345 0.037 1.129 5.5 64.7 14.8 914 n/a 8_xyzrec: 0.1190 0.1350 0.038 1.116 5.5 64.7 14.8 914 n/a 8_adp: 0.1192 0.1354 0.038 1.116 5.5 64.1 14.7 914 n/a 8_regHadp: 0.1192 0.1354 0.038 1.116 5.5 64.1 14.7 914 n/a 8_occ: 0.1190 0.1359 0.038 1.116 5.5 64.1 14.7 914 n/a 9_bss: 0.1189 0.1357 0.038 1.116 5.5 64.1 14.8 914 n/a 9_settarget: 0.1189 0.1357 0.038 1.116 5.5 64.1 14.8 914 n/a 9_updatecdl: 0.1189 0.1357 0.038 1.116 5.5 64.1 14.8 914 n/a 9_nqh: 0.1189 0.1357 0.038 1.116 5.5 64.1 14.8 914 n/a 9_sol: 0.1189 0.1346 0.038 1.116 5.5 64.1 14.7 909 n/a 9_weight: 0.1189 0.1346 0.038 1.116 5.5 64.1 14.7 909 n/a 9_xyzrec: 0.1191 0.1347 0.038 1.124 5.5 64.1 14.7 909 n/a 9_adp: 0.1191 0.1348 0.038 1.124 5.5 63.1 14.7 909 n/a 9_regHadp: 0.1191 0.1349 0.038 1.124 5.5 63.1 14.7 909 n/a 9_occ: 0.1190 0.1351 0.038 1.124 5.5 63.1 14.7 909 n/a 10_bss: 0.1188 0.1350 0.038 1.124 5.5 63.1 14.7 909 n/a 10_settarget: 0.1188 0.1350 0.038 1.124 5.5 63.1 14.7 909 n/a 10_updatecdl: 0.1188 0.1350 0.038 1.125 5.5 63.1 14.7 909 n/a 10_setrh: 0.1189 0.1350 0.038 1.125 5.5 63.1 14.7 909 n/a 10_nqh: 0.1189 0.1350 0.038 1.125 5.5 63.1 14.7 909 n/a 10_sol: 0.1190 0.1342 0.038 1.125 5.5 63.1 14.7 903 n/a 10_weight: 0.1190 0.1342 0.038 1.125 5.5 63.1 14.7 903 n/a 10_xyzrec: 0.1190 0.1343 0.038 1.136 5.5 63.1 14.7 903 n/a 10_adp: 0.1190 0.1344 0.038 1.136 5.6 62.5 14.7 903 n/a 10_regHadp: 0.1190 0.1344 0.038 1.136 5.6 62.5 14.7 903 n/a 10_occ: 0.1189 0.1344 0.038 1.136 5.6 62.5 14.7 903 n/a end: 0.1188 0.1343 0.038 1.136 5.5 62.4 14.6 903 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5598907_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5598907_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.6000 Refinement macro-cycles (run) : 12164.9000 Write final files (write_after_run_outputs) : 162.9100 Total : 12334.4100 Total CPU time: 3.44 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:48 PST -0800 (1736736168.75 s) Start R-work = 0.1789, R-free = 0.1935 Final R-work = 0.1188, R-free = 0.1343 =============================================================================== Job complete usr+sys time: 12611.36 seconds wall clock time: 211 minutes 14.38 seconds (12674.38 seconds total)