Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8239628.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8239628.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8239628.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.95, per 1000 atoms: 0.29 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.804 distance_ideal: 2.720 ideal - model: -0.084 slack: 0.000 delta_slack: -0.084 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: 2.726 distance_ideal: 2.710 ideal - model: -0.016 slack: 0.000 delta_slack: -0.016 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: 0.70 Conformation dependent library (CDL) restraints added in 119.4 milliseconds Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.05: 1100 1.05 - 1.30: 2437 1.30 - 1.54: 1695 1.54 - 1.78: 693 1.78 - 2.02: 9 Bond restraints: 5934 Sorted by residual: bond pdb=" CA TRP A 146 " pdb=" C TRP A 146 " ideal model delta sigma weight residual 1.523 1.263 0.260 1.21e-02 6.83e+03 4.62e+02 bond pdb=" NE1 TRP A 146 " pdb=" CE2 TRP A 146 " ideal model delta sigma weight residual 1.370 1.162 0.208 1.10e-02 8.26e+03 3.56e+02 bond pdb=" N ILE B 30 " pdb=" H ILE B 30 " ideal model delta sigma weight residual 0.860 1.236 -0.376 2.00e-02 2.50e+03 3.53e+02 bond pdb=" C ILE B 70 " pdb=" O ILE B 70 " ideal model delta sigma weight residual 1.237 1.445 -0.208 1.11e-02 8.12e+03 3.52e+02 bond pdb=" N THR A 33 " pdb=" H THR A 33 " ideal model delta sigma weight residual 0.860 1.235 -0.375 2.00e-02 2.50e+03 3.51e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 5646 4.21 - 8.43: 3567 8.43 - 12.64: 1332 12.64 - 16.85: 240 16.85 - 21.06: 25 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" N PRO A 135 " ideal model delta sigma weight residual 119.22 133.20 -13.98 7.80e-01 1.64e+00 3.21e+02 angle pdb=" O ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 121.32 134.41 -13.09 8.50e-01 1.38e+00 2.37e+02 angle pdb=" O VAL B 89 " pdb=" C VAL B 89 " pdb=" N GLU B 90 " ideal model delta sigma weight residual 121.94 137.28 -15.34 1.00e+00 1.00e+00 2.35e+02 angle pdb=" NE ARG B 97 " pdb=" CZ ARG B 97 " pdb=" NH1 ARG B 97 " ideal model delta sigma weight residual 121.50 135.90 -14.40 1.00e+00 1.00e+00 2.07e+02 angle pdb=" O ILE A 118 " pdb=" C ILE A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 121.91 135.69 -13.78 9.80e-01 1.04e+00 1.98e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 1852 17.66 - 35.31: 128 35.31 - 52.97: 48 52.97 - 70.63: 18 70.63 - 88.28: 4 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 180.00 154.91 25.09 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -155.50 -24.50 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.231: 215 0.231 - 0.461: 163 0.461 - 0.691: 82 0.691 - 0.921: 26 0.921 - 1.150: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA TRP B 139 " pdb=" N TRP B 139 " pdb=" C TRP B 139 " pdb=" CB TRP B 139 " both_signs ideal model delta sigma weight residual False 2.51 3.66 -1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CA ALA B 3 " pdb=" N ALA B 3 " pdb=" C ALA B 3 " pdb=" CB ALA B 3 " both_signs ideal model delta sigma weight residual False 2.48 3.58 -1.09 2.00e-01 2.50e+01 2.97e+01 chirality pdb=" CB ILE B 76 " pdb=" CA ILE B 76 " pdb=" CG1 ILE B 76 " pdb=" CG2 ILE B 76 " both_signs ideal model delta sigma weight residual False 2.64 1.56 1.09 2.00e-01 2.50e+01 2.96e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.055 2.00e-02 2.50e+03 6.12e-02 1.50e+02 pdb=" CG TRP B 146 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.062 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.092 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.040 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.078 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.071 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.029 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.018 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.081 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.057 2.00e-02 2.50e+03 5.68e-02 1.29e+02 pdb=" CG TRP A 139 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.087 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.061 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.020 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.011 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.059 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.046 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 194 " -0.062 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG TYR B 194 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 194 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B 194 " -0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR B 194 " 0.065 2.00e-02 2.50e+03 pdb=" CE2 TYR B 194 " -0.042 2.00e-02 2.50e+03 pdb=" CZ TYR B 194 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR B 194 " -0.129 2.00e-02 2.50e+03 pdb=" HD1 TYR B 194 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 TYR B 194 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 TYR B 194 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 TYR B 194 " 0.118 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.83 - 1.58: 22 1.58 - 2.34: 2135 2.34 - 3.09: 21996 3.09 - 3.85: 33067 3.85 - 4.60: 53112 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110332 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.829 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.935 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.950 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.113 2.620 nonbonded pdb="HG22 VAL A 181 " pdb=" O HOH S1566 " model vdw 1.172 2.620 ... (remaining 110327 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_8239628_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= 0.2038 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299989 | | target function (ml) not normalized (work): 805443.773589 | | target function (ml) not normalized (free): 16459.861159 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2147 0.1959 6.6951 6.3103| | 2: 2.94 - 2.33 1.00 7339 128 0.1627 0.1739 5.5425 5.6081| | 3: 2.33 - 2.04 0.96 6939 150 0.1633 0.1500 5.1542 5.1098| | 4: 2.04 - 1.85 1.00 7170 155 0.1748 0.1691 4.9678 5.0881| | 5: 1.85 - 1.72 0.99 7113 159 0.1928 0.1890 4.8011 4.8774| | 6: 1.72 - 1.62 0.99 7102 142 0.2014 0.2009 4.6831 4.6861| | 7: 1.62 - 1.54 0.99 7104 148 0.2019 0.1732 4.5612 4.5304| | 8: 1.54 - 1.47 0.96 6798 152 0.2039 0.2322 4.4718 4.5376| | 9: 1.47 - 1.41 0.98 6938 155 0.2083 0.2176 4.3929 4.418| | 10: 1.41 - 1.36 0.99 7022 150 0.2097 0.1981 4.303 4.251| | 11: 1.36 - 1.32 0.99 6997 151 0.2111 0.2173 4.2337 4.2629| | 12: 1.32 - 1.28 0.98 6976 149 0.2094 0.1991 4.1773 4.2536| | 13: 1.28 - 1.25 0.98 6907 166 0.2035 0.1834 4.1239 4.079| | 14: 1.25 - 1.22 0.98 7015 113 0.2115 0.2159 4.0817 4.2095| | 15: 1.22 - 1.19 0.98 6957 137 0.2085 0.1839 4.0344 3.9719| | 16: 1.19 - 1.17 0.93 6604 132 0.2082 0.2166 3.9855 4.0485| | 17: 1.17 - 1.14 0.98 6941 135 0.2178 0.1769 3.9591 3.9235| | 18: 1.14 - 1.12 0.98 6875 142 0.2238 0.2247 3.9403 3.8698| | 19: 1.12 - 1.10 0.97 6949 106 0.2277 0.2276 3.8739 3.8669| | 20: 1.10 - 1.08 0.97 6884 147 0.2308 0.2437 3.8134 3.902| | 21: 1.08 - 1.07 0.97 6852 152 0.2431 0.2544 3.793 3.7746| | 22: 1.07 - 1.05 0.97 6838 135 0.2532 0.2453 3.7425 3.7242| | 23: 1.05 - 1.03 0.97 6829 159 0.2699 0.2561 3.7188 3.7659| | 24: 1.03 - 1.02 0.96 6785 133 0.2900 0.2755 3.7006 3.7351| | 25: 1.02 - 1.01 0.93 6552 130 0.3072 0.2862 3.6692 3.6928| | 26: 1.01 - 0.99 0.96 6767 158 0.3242 0.3185 3.6299 3.5815| | 27: 0.99 - 0.98 0.94 6648 131 0.3393 0.3275 3.6334 3.6062| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.35 0.91 0.98 35269.64| | 2: 2.94 - 2.33 7339 128 0.86 21.15 1.08 1.02 15040.53| | 3: 2.33 - 2.04 6939 150 0.93 12.75 1.10 1.04 4236.76| | 4: 2.04 - 1.85 7170 155 0.92 14.06 1.11 1.05 2948.16| | 5: 1.85 - 1.72 7113 159 0.90 16.20 1.12 1.07 2197.59| | 6: 1.72 - 1.62 7102 142 0.90 16.71 1.11 1.08 1662.85| | 7: 1.62 - 1.54 7104 148 0.89 17.42 1.11 1.08 1311.07| | 8: 1.54 - 1.47 6798 152 0.89 17.74 1.10 1.07 1094.38| | 9: 1.47 - 1.41 6938 155 0.88 18.48 1.10 1.06 923.97| | 10: 1.41 - 1.36 7022 150 0.88 18.81 1.09 1.06 772.98| | 11: 1.36 - 1.32 6997 151 0.88 18.95 1.08 1.05 673.20| | 12: 1.32 - 1.28 6976 149 0.88 19.14 1.08 1.03 614.66| | 13: 1.28 - 1.25 6907 166 0.88 19.46 1.07 1.03 578.49| | 14: 1.25 - 1.22 7015 113 0.87 20.19 1.08 1.03 535.15| | 15: 1.22 - 1.19 6957 137 0.87 19.80 1.07 1.04 492.64| | 16: 1.19 - 1.17 6604 132 0.88 19.23 1.07 1.04 439.44| | 17: 1.17 - 1.14 6941 135 0.88 19.41 1.08 1.02 381.65| | 18: 1.14 - 1.12 6875 142 0.88 19.53 1.08 1.00 346.13| | 19: 1.12 - 1.10 6949 106 0.87 20.56 1.07 0.99 333.39| | 20: 1.10 - 1.08 6884 147 0.86 21.91 1.06 0.99 324.52| | 21: 1.08 - 1.07 6852 152 0.85 22.54 1.06 1.00 310.01| | 22: 1.07 - 1.05 6838 135 0.84 24.10 1.06 0.99 300.91| | 23: 1.05 - 1.03 6829 159 0.82 26.09 1.06 0.98 299.46| | 24: 1.03 - 1.02 6785 133 0.79 28.33 1.05 0.98 305.33| | 25: 1.02 - 1.01 6552 130 0.78 29.74 1.04 0.93 291.25| | 26: 1.01 - 0.99 6767 158 0.75 32.25 1.03 0.91 286.30| | 27: 0.99 - 0.98 6648 131 0.73 33.99 1.04 0.87 287.14| |alpha: min = 0.87 max = 1.08 mean = 1.02| |beta: min = 286.30 max = 35269.64 mean = 2803.23| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 20.99| |phase err.(test): min = 0.00 max = 89.50 mean = 21.11| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.260 2950 Z= 5.493 Angle : 5.264 19.363 4018 Z= 3.787 Chirality : 0.383 1.150 492 Planarity : 0.033 0.111 512 Dihedral : 13.073 88.282 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.15 % Favored : 95.34 % Rotamer: Outliers : 1.29 % Allowed : 4.52 % Favored : 94.19 % Cbeta Deviations : 33.99 % 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: -2.38 (0.37), residues: 386 helix: -2.25 (0.34), residues: 146 sheet: -1.46 (0.45), residues: 86 loop : -0.60 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.015 ARG B 83 TYR 0.101 0.037 TYR B 192 PHE 0.090 0.037 PHE A 164 TRP 0.091 0.039 TRP A 139 HIS 0.062 0.021 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2038 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299989 | | target function (ml) not normalized (work): 805443.773589 | | target function (ml) not normalized (free): 16459.861159 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2038 0.1978 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2038 0.1978 n_refl.: 191155 remove outliers: r(all,work,free)=0.2036 0.2038 0.1978 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2036 0.2038 0.1979 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1809 0.1807 0.1912 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1805 0.1912 n_refl.: 191140 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4249 400.535 295.761 0.434 0.914 0.299 13.296-10.522 100.00 100 1 0.2554 534.497 519.889 0.788 0.915 0.250 10.503-8.327 98.90 177 3 0.2457 564.205 559.686 0.973 0.915 0.227 8.318-6.595 100.00 360 8 0.2502 414.736 402.698 0.971 0.914 0.175 6.588-5.215 100.00 711 7 0.2253 381.101 366.371 0.955 0.914 0.170 5.214-4.128 98.38 1367 28 0.1478 557.435 549.716 1.080 0.915 0.100 4.126-3.266 94.74 2603 46 0.1347 508.132 498.785 1.147 0.915 0.023 3.266-2.585 99.86 5447 97 0.1437 342.774 337.923 1.117 0.914 0.000 2.585-2.046 97.45 10613 204 0.1419 258.603 254.351 1.122 0.913 0.000 2.046-1.619 99.39 21536 464 0.1631 153.054 149.681 1.144 0.912 0.000 1.619-1.281 98.00 42464 925 0.1922 82.395 80.218 1.128 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2324 44.203 41.622 1.112 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0033 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1805 r_free=0.1912 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN B 138 GLN Total number of N/Q/H flips: 2 r_work=0.1808 r_free=0.1912 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.129261 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 581.766614 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1273 0.1502 0.0230 0.038 1.2 10.9 0.0 0.0 0 11.565 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 15.02 2.30 1.117 13.113 581.767 0.018 12.97 15.67 2.70 1.239 13.297 581.767 0.017 Individual atomic B min max mean iso aniso Overall: 5.14 73.05 14.94 1.41 435 3274 Protein: 5.14 40.32 10.98 1.41 0 2902 Water: 6.38 73.05 29.20 N/A 435 370 Other: 16.01 30.32 23.17 N/A 0 2 Chain A: 5.32 59.99 13.00 N/A 0 1626 Chain B: 5.14 73.05 12.73 N/A 0 1648 Chain S: 11.55 61.29 30.55 N/A 435 0 Histogram: Values Number of atoms 5.14 - 11.93 2162 11.93 - 18.72 643 18.72 - 25.51 311 25.51 - 32.30 273 32.30 - 39.09 155 39.09 - 45.88 103 45.88 - 52.67 38 52.67 - 59.46 20 59.46 - 66.25 3 66.25 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1567 r_work=0.1296 r_free=0.1564 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1564 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1282 r_free = 0.1555 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191140 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1555 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015603 | | target function (ls_wunit_k1) not normalized (work): 2922.332936 | | target function (ls_wunit_k1) not normalized (free): 116.615416 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1555 n_refl.: 191140 re-set all scales: r(all,work,free)=0.1470 0.1468 0.1628 n_refl.: 191140 remove outliers: r(all,work,free)=0.1470 0.1468 0.1628 n_refl.: 191140 overall B=0.17 to atoms: r(all,work,free)=0.1495 0.1493 0.1638 n_refl.: 191140 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1545 n_refl.: 191140 remove outliers: r(all,work,free)=0.1279 0.1273 0.1545 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3588 402.814 377.471 0.481 0.962 0.269 13.296-10.522 100.00 100 1 0.2120 534.497 527.904 0.744 0.964 0.235 10.503-8.327 98.90 177 3 0.1737 564.205 562.265 0.890 0.964 0.199 8.318-6.595 100.00 360 8 0.1699 414.736 412.901 0.912 0.964 0.165 6.588-5.215 100.00 711 7 0.1536 381.101 373.747 0.890 0.964 0.160 5.214-4.128 98.38 1367 28 0.0904 557.435 555.123 0.979 0.964 0.059 4.126-3.266 94.74 2603 46 0.0834 508.132 504.339 1.046 0.965 0.018 3.266-2.585 99.86 5447 97 0.0923 342.774 340.246 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.370 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1087 153.054 151.366 1.056 0.965 0.000 1.619-1.281 98.00 42464 925 0.1275 82.395 81.429 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.185 1.024 0.964 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0391 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 138 GLN Total number of N/Q/H flips: 1 r_work=0.1275 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1546 | n_water=805 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1279 r_free=0.1553 | n_water=794 | time (s): 102.670 (total time: 104.950) Filter (q & B) r_work=0.1280 r_free=0.1552 | n_water=791 | time (s): 5.100 (total time: 110.050) Compute maps r_work=0.1280 r_free=0.1552 | n_water=791 | time (s): 2.430 (total time: 112.480) Filter (map) r_work=0.1305 r_free=0.1537 | n_water=652 | time (s): 5.240 (total time: 117.720) Find peaks r_work=0.1305 r_free=0.1537 | n_water=652 | time (s): 0.870 (total time: 118.590) Add new water r_work=0.1329 r_free=0.1566 | n_water=952 | time (s): 4.330 (total time: 122.920) Refine new water occ: r_work=0.1285 r_free=0.1513 adp: r_work=0.1273 r_free=0.1516 occ: r_work=0.1276 r_free=0.1510 adp: r_work=0.1269 r_free=0.1513 occ: r_work=0.1270 r_free=0.1511 adp: r_work=0.1268 r_free=0.1513 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1513 r_work=0.1268 r_free=0.1513 | n_water=952 | time (s): 97.770 (total time: 220.690) Filter (q & B) r_work=0.1271 r_free=0.1514 | n_water=891 | time (s): 4.800 (total time: 225.490) Filter (dist only) r_work=0.1272 r_free=0.1514 | n_water=890 | time (s): 117.300 (total time: 342.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.034201 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 580.510436 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 0.1255 0.1530 0.0275 0.041 1.1 15.8 0.0 0.0 0 11.517 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.30 2.75 2.040 15.188 580.510 0.014 12.33 15.11 2.78 2.419 15.272 580.510 0.014 Individual atomic B min max mean iso aniso Overall: 5.36 70.97 16.41 1.20 522 3272 Protein: 5.36 40.52 10.96 1.20 0 2902 Water: 6.61 70.97 34.19 N/A 522 368 Other: 16.35 33.07 24.71 N/A 0 2 Chain A: 5.52 55.87 12.98 N/A 0 1624 Chain B: 5.36 68.22 12.79 N/A 0 1648 Chain S: 12.82 70.97 38.52 N/A 522 0 Histogram: Values Number of atoms 5.36 - 11.92 2118 11.92 - 18.48 685 18.48 - 25.04 255 25.04 - 31.60 216 31.60 - 38.16 167 38.16 - 44.72 169 44.72 - 51.28 94 51.28 - 57.84 53 57.84 - 64.41 26 64.41 - 70.97 11 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1511 r_work=0.1233 r_free=0.1512 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1512 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1503 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1503 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013453 | | target function (ls_wunit_k1) not normalized (work): 2519.708960 | | target function (ls_wunit_k1) not normalized (free): 99.176740 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1503 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1603 n_refl.: 191138 remove outliers: r(all,work,free)=0.1434 0.1431 0.1603 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1429 0.1601 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1232 0.1512 n_refl.: 191138 remove outliers: r(all,work,free)=0.1238 0.1232 0.1512 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3225 402.814 377.736 0.494 0.963 0.271 13.296-10.522 100.00 100 1 0.1903 534.497 525.971 0.765 0.964 0.228 10.503-8.327 98.90 177 3 0.1353 564.205 566.079 0.920 0.964 0.189 8.318-6.595 100.00 360 8 0.1528 414.736 414.750 0.940 0.963 0.170 6.588-5.215 100.00 711 7 0.1359 381.101 376.684 0.914 0.963 0.160 5.214-4.128 98.38 1367 28 0.0832 557.435 556.011 0.995 0.963 0.080 4.126-3.266 94.74 2603 46 0.0763 508.132 505.145 1.059 0.963 0.014 3.266-2.585 99.86 5447 97 0.0859 342.774 341.322 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.745 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.616 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.360 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.222 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0474 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1512 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1512 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1512 | n_water=890 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1234 r_free=0.1514 | n_water=885 | time (s): 114.600 (total time: 117.160) Filter (q & B) r_work=0.1234 r_free=0.1514 | n_water=883 | time (s): 4.920 (total time: 122.080) Compute maps r_work=0.1234 r_free=0.1514 | n_water=883 | time (s): 1.740 (total time: 123.820) Filter (map) r_work=0.1273 r_free=0.1525 | n_water=695 | time (s): 4.390 (total time: 128.210) Find peaks r_work=0.1273 r_free=0.1525 | n_water=695 | time (s): 0.680 (total time: 128.890) Add new water r_work=0.1299 r_free=0.1551 | n_water=1011 | time (s): 4.660 (total time: 133.550) Refine new water occ: r_work=0.1255 r_free=0.1509 adp: r_work=0.1255 r_free=0.1510 occ: r_work=0.1250 r_free=0.1505 adp: r_work=0.1250 r_free=0.1506 occ: r_work=0.1247 r_free=0.1500 adp: r_work=0.1246 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1246 r_free=0.1502 r_work=0.1246 r_free=0.1502 | n_water=1011 | time (s): 297.710 (total time: 431.260) Filter (q & B) r_work=0.1249 r_free=0.1511 | n_water=894 | time (s): 5.010 (total time: 436.270) Filter (dist only) r_work=0.1251 r_free=0.1509 | n_water=892 | time (s): 116.540 (total time: 552.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.700858 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.727484 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 0.1427 0.0190 0.035 1.1 8.3 0.0 0.0 0 0.850 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.27 1.90 1.927 14.644 15.727 3.937 12.37 13.90 1.53 2.269 14.536 15.727 3.898 Individual atomic B min max mean iso aniso Overall: 5.53 67.72 15.37 1.03 525 3271 Protein: 5.53 36.05 10.70 1.03 0 2902 Water: 6.71 67.72 30.55 N/A 525 367 Other: 13.84 28.97 21.40 N/A 0 2 Chain A: 5.57 55.63 12.72 N/A 0 1624 Chain B: 5.53 67.72 12.49 N/A 0 1647 Chain S: 14.97 67.57 32.57 N/A 525 0 Histogram: Values Number of atoms 5.53 - 11.75 2135 11.75 - 17.97 695 17.97 - 24.19 287 24.19 - 30.41 235 30.41 - 36.63 181 36.63 - 42.85 145 42.85 - 49.06 84 49.06 - 55.28 25 55.28 - 61.50 7 61.50 - 67.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1391 r_work=0.1238 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1391 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1378 target_work(ml) = 3.891 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1378 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891318 | | target function (ml) not normalized (work): 728832.219420 | | target function (ml) not normalized (free): 15220.017208 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1378 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1441 0.1490 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1441 0.1490 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1435 0.1486 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1374 n_refl.: 191138 remove outliers: r(all,work,free)=0.1229 0.1226 0.1374 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3775 393.525 361.570 0.429 0.948 0.255 13.296-10.522 99.01 99 1 0.2426 528.187 513.396 0.720 0.949 0.219 10.503-8.327 98.35 176 3 0.1940 556.299 557.323 0.880 0.949 0.174 8.318-6.595 100.00 360 8 0.2053 414.736 410.568 0.897 0.949 0.130 6.588-5.215 100.00 711 7 0.1823 381.101 371.037 0.884 0.949 0.120 5.214-4.128 98.38 1367 28 0.1164 557.435 552.646 0.972 0.949 0.090 4.126-3.266 94.74 2603 46 0.1102 508.132 501.265 1.031 0.949 0.009 3.266-2.585 99.86 5447 97 0.1086 342.774 339.214 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0974 258.603 255.727 1.032 0.948 0.000 2.046-1.619 99.39 21536 464 0.0979 153.054 151.402 1.055 0.946 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.476 1.052 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.310 1.038 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1012 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1374 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1226 r_free=0.1374 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1226 r_free=0.1374 | n_water=892 | time (s): 2.940 (total time: 2.940) Filter (dist) r_work=0.1226 r_free=0.1374 | n_water=891 | time (s): 113.200 (total time: 116.140) Filter (q & B) r_work=0.1227 r_free=0.1375 | n_water=881 | time (s): 4.650 (total time: 120.790) Compute maps r_work=0.1227 r_free=0.1375 | n_water=881 | time (s): 2.420 (total time: 123.210) Filter (map) r_work=0.1250 r_free=0.1384 | n_water=730 | time (s): 4.760 (total time: 127.970) Find peaks r_work=0.1250 r_free=0.1384 | n_water=730 | time (s): 0.760 (total time: 128.730) Add new water r_work=0.1265 r_free=0.1400 | n_water=962 | time (s): 5.210 (total time: 133.940) Refine new water occ: r_work=0.1217 r_free=0.1361 adp: r_work=0.1209 r_free=0.1358 occ: r_work=0.1206 r_free=0.1356 adp: r_work=0.1206 r_free=0.1356 occ: r_work=0.1206 r_free=0.1356 adp: r_work=0.1206 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1356 r_work=0.1206 r_free=0.1356 | n_water=962 | time (s): 191.050 (total time: 324.990) Filter (q & B) r_work=0.1211 r_free=0.1367 | n_water=860 | time (s): 4.310 (total time: 329.300) Filter (dist only) r_work=0.1211 r_free=0.1366 | n_water=859 | time (s): 110.150 (total time: 439.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.644983 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.869937 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 0.1210 0.1364 0.0154 0.037 1.1 5.6 0.0 0.3 0 0.822 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.64 1.54 1.812 14.101 15.870 3.875 12.00 13.59 1.59 1.896 14.071 15.870 3.865 Individual atomic B min max mean iso aniso Overall: 5.52 67.28 14.86 0.99 492 3271 Protein: 5.52 33.19 10.63 0.99 0 2902 Water: 6.14 67.28 29.12 N/A 492 367 Other: 13.91 27.66 20.78 N/A 0 2 Chain A: 5.54 55.40 12.60 N/A 0 1624 Chain B: 5.52 67.28 12.41 N/A 0 1647 Chain S: 6.14 61.50 30.50 N/A 492 0 Histogram: Values Number of atoms 5.52 - 11.70 2118 11.70 - 17.88 732 17.88 - 24.05 329 24.05 - 30.23 211 30.23 - 36.40 139 36.40 - 42.58 135 42.58 - 48.76 70 48.76 - 54.93 21 54.93 - 61.11 6 61.11 - 67.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1360 r_work=0.1200 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1358 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863227 | | target function (ml) not normalized (work): 723555.463655 | | target function (ml) not normalized (free): 15137.984256 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1358 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1430 0.1429 0.1475 n_refl.: 191134 remove outliers: r(all,work,free)=0.1430 0.1429 0.1475 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1423 0.1422 0.1470 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1356 n_refl.: 191134 remove outliers: r(all,work,free)=0.1199 0.1196 0.1356 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3756 348.290 319.100 0.409 0.946 0.250 13.296-10.522 98.02 98 1 0.2424 481.128 457.622 0.699 0.948 0.201 10.503-8.327 97.80 175 3 0.2071 502.543 499.970 0.863 0.948 0.178 8.318-6.595 100.00 360 8 0.2219 376.020 370.401 0.889 0.947 0.120 6.588-5.215 100.00 711 7 0.1901 345.525 335.790 0.883 0.947 0.110 5.214-4.128 98.38 1367 28 0.1212 505.398 500.604 0.975 0.948 0.080 4.126-3.266 94.74 2603 46 0.1126 460.698 454.342 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1079 310.776 307.580 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0941 234.462 231.986 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0915 138.766 137.442 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.0987 74.704 73.969 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1658 40.075 38.409 1.038 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1165 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1355 | n_water=859 | time (s): 3.360 (total time: 3.360) Filter (dist) r_work=0.1196 r_free=0.1355 | n_water=858 | time (s): 106.370 (total time: 109.730) Filter (q & B) r_work=0.1196 r_free=0.1355 | n_water=852 | time (s): 4.600 (total time: 114.330) Compute maps r_work=0.1196 r_free=0.1355 | n_water=852 | time (s): 1.800 (total time: 116.130) Filter (map) r_work=0.1220 r_free=0.1357 | n_water=726 | time (s): 5.060 (total time: 121.190) Find peaks r_work=0.1220 r_free=0.1357 | n_water=726 | time (s): 0.680 (total time: 121.870) Add new water r_work=0.1232 r_free=0.1377 | n_water=969 | time (s): 4.060 (total time: 125.930) Refine new water occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1194 r_free=0.1348 occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1191 r_free=0.1347 occ: r_work=0.1189 r_free=0.1347 adp: r_work=0.1189 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1347 r_work=0.1189 r_free=0.1347 | n_water=969 | time (s): 253.860 (total time: 379.790) Filter (q & B) r_work=0.1193 r_free=0.1348 | n_water=884 | time (s): 5.320 (total time: 385.110) Filter (dist only) r_work=0.1194 r_free=0.1348 | n_water=883 | time (s): 110.140 (total time: 495.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.573546 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.435542 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 0.1351 0.0154 0.037 1.1 5.6 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.51 1.54 1.784 14.077 15.436 3.764 12.01 13.54 1.53 1.854 14.048 15.436 3.762 Individual atomic B min max mean iso aniso Overall: 5.56 66.86 14.88 0.95 516 3271 Protein: 5.56 31.62 10.56 0.95 0 2902 Water: 5.94 66.86 29.05 N/A 516 367 Other: 13.80 26.33 20.06 N/A 0 2 Chain A: 5.58 55.17 12.50 N/A 0 1624 Chain B: 5.56 66.86 12.32 N/A 0 1647 Chain S: 5.94 61.57 30.53 N/A 516 0 Histogram: Values Number of atoms 5.56 - 11.69 2131 11.69 - 17.82 743 17.82 - 23.95 302 23.95 - 30.08 218 30.08 - 36.21 161 36.21 - 42.34 135 42.34 - 48.47 66 48.47 - 54.60 23 54.60 - 60.73 6 60.73 - 66.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1354 r_work=0.1202 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1355 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1355 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760741 | | target function (ml) not normalized (work): 704349.118228 | | target function (ml) not normalized (free): 14740.977926 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1355 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1426 0.1425 0.1471 n_refl.: 191131 remove outliers: r(all,work,free)=0.1426 0.1425 0.1471 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1418 0.1417 0.1466 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1354 n_refl.: 191131 remove outliers: r(all,work,free)=0.1202 0.1199 0.1354 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3779 348.290 311.534 0.391 0.946 0.236 13.296-10.522 97.03 97 1 0.2471 481.803 458.102 0.693 0.947 0.169 10.503-8.327 97.80 175 3 0.2148 502.543 495.866 0.858 0.948 0.140 8.318-6.595 100.00 360 8 0.2212 376.020 370.845 0.888 0.947 0.116 6.588-5.215 100.00 711 7 0.1890 345.525 336.019 0.884 0.948 0.097 5.214-4.128 98.38 1367 28 0.1214 505.398 500.351 0.976 0.948 0.090 4.126-3.266 94.74 2603 46 0.1150 460.698 454.201 1.036 0.948 0.005 3.266-2.585 99.86 5447 97 0.1106 310.776 307.505 1.022 0.948 0.000 2.585-2.046 97.45 10613 204 0.0949 234.462 232.003 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0911 138.766 137.492 1.056 0.948 0.000 1.619-1.281 98.00 42464 925 0.0976 74.704 73.990 1.052 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.075 38.402 1.037 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1291 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1354 | n_water=883 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1199 r_free=0.1354 | n_water=883 | time (s): 110.980 (total time: 113.500) Filter (q & B) r_work=0.1199 r_free=0.1353 | n_water=875 | time (s): 4.320 (total time: 117.820) Compute maps r_work=0.1199 r_free=0.1353 | n_water=875 | time (s): 1.690 (total time: 119.510) Filter (map) r_work=0.1221 r_free=0.1352 | n_water=749 | time (s): 4.620 (total time: 124.130) Find peaks r_work=0.1221 r_free=0.1352 | n_water=749 | time (s): 0.670 (total time: 124.800) Add new water r_work=0.1232 r_free=0.1369 | n_water=972 | time (s): 4.060 (total time: 128.860) Refine new water occ: r_work=0.1196 r_free=0.1345 adp: r_work=0.1196 r_free=0.1344 occ: r_work=0.1194 r_free=0.1343 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1193 r_free=0.1341 adp: r_work=0.1192 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1341 r_work=0.1192 r_free=0.1341 | n_water=972 | time (s): 236.400 (total time: 365.260) Filter (q & B) r_work=0.1197 r_free=0.1341 | n_water=893 | time (s): 4.760 (total time: 370.020) Filter (dist only) r_work=0.1197 r_free=0.1340 | n_water=892 | time (s): 119.140 (total time: 489.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.603305 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.449842 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1345 0.0146 0.038 1.1 6.1 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.45 1.46 1.752 14.000 14.450 3.761 12.01 13.49 1.48 1.870 13.959 14.450 3.759 Individual atomic B min max mean iso aniso Overall: 5.58 65.81 14.81 0.90 525 3271 Protein: 5.58 29.40 10.47 0.90 0 2902 Water: 5.94 65.81 28.92 N/A 525 367 Other: 13.83 23.38 18.61 N/A 0 2 Chain A: 5.61 54.60 12.37 N/A 0 1624 Chain B: 5.58 65.81 12.20 N/A 0 1647 Chain S: 5.94 61.87 30.51 N/A 525 0 Histogram: Values Number of atoms 5.58 - 11.60 2113 11.60 - 17.63 783 17.63 - 23.65 278 23.65 - 29.67 214 29.67 - 35.70 169 35.70 - 41.72 124 41.72 - 47.74 77 47.74 - 53.77 30 53.77 - 59.79 6 59.79 - 65.81 2 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1349 r_work=0.1202 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1350 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1347 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758484 | | target function (ml) not normalized (work): 703922.684914 | | target function (ml) not normalized (free): 14732.908076 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1348 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1421 0.1420 0.1462 n_refl.: 191130 remove outliers: r(all,work,free)=0.1421 0.1420 0.1462 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1382 0.1381 0.1440 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1347 n_refl.: 191130 remove outliers: r(all,work,free)=0.1201 0.1198 0.1347 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3838 348.290 310.629 0.396 0.946 0.234 13.296-10.522 96.04 96 1 0.2403 481.040 458.024 0.717 0.947 0.167 10.503-8.327 97.80 175 3 0.2119 502.543 496.230 0.881 0.948 0.140 8.318-6.595 100.00 360 8 0.2207 376.020 371.108 0.908 0.947 0.097 6.588-5.215 100.00 711 7 0.1882 345.525 336.409 0.906 0.948 0.078 5.214-4.128 98.38 1367 28 0.1212 505.398 500.403 1.001 0.948 0.064 4.126-3.266 94.74 2603 46 0.1162 460.698 454.037 1.061 0.949 0.005 3.266-2.585 99.86 5447 97 0.1113 310.776 307.583 1.045 0.949 0.000 2.585-2.046 97.45 10613 204 0.0952 234.462 231.999 1.052 0.949 0.000 2.046-1.619 99.39 21536 464 0.0909 138.766 137.515 1.068 0.949 0.000 1.619-1.281 98.00 42464 925 0.0971 74.704 74.001 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.075 38.401 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=0.0496 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1347 | n_water=892 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1199 r_free=0.1347 | n_water=892 | time (s): 109.230 (total time: 111.820) Filter (q & B) r_work=0.1199 r_free=0.1348 | n_water=883 | time (s): 4.620 (total time: 116.440) Compute maps r_work=0.1199 r_free=0.1348 | n_water=883 | time (s): 2.010 (total time: 118.450) Filter (map) r_work=0.1221 r_free=0.1351 | n_water=763 | time (s): 4.320 (total time: 122.770) Find peaks r_work=0.1221 r_free=0.1351 | n_water=763 | time (s): 0.850 (total time: 123.620) Add new water r_work=0.1231 r_free=0.1364 | n_water=979 | time (s): 4.110 (total time: 127.730) Refine new water occ: r_work=0.1197 r_free=0.1342 adp: r_work=0.1197 r_free=0.1342 occ: r_work=0.1195 r_free=0.1342 adp: r_work=0.1195 r_free=0.1341 occ: r_work=0.1194 r_free=0.1341 adp: r_work=0.1193 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1341 r_work=0.1193 r_free=0.1341 | n_water=979 | time (s): 197.380 (total time: 325.110) Filter (q & B) r_work=0.1198 r_free=0.1342 | n_water=903 | time (s): 4.440 (total time: 329.550) Filter (dist only) r_work=0.1198 r_free=0.1341 | n_water=902 | time (s): 114.310 (total time: 443.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.513321 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.635247 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1356 0.0154 0.038 1.1 7.7 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.56 1.54 1.713 13.712 14.635 3.761 12.02 13.60 1.58 1.751 13.693 14.635 3.758 Individual atomic B min max mean iso aniso Overall: 5.38 64.54 14.59 0.88 535 3271 Protein: 5.38 28.67 10.23 0.88 0 2902 Water: 5.85 64.54 28.61 N/A 535 367 Other: 13.68 21.92 17.80 N/A 0 2 Chain A: 5.43 53.95 12.09 N/A 0 1624 Chain B: 5.38 64.54 11.94 N/A 0 1647 Chain S: 5.85 61.91 30.31 N/A 535 0 Histogram: Values Number of atoms 5.38 - 11.30 2087 11.30 - 17.21 800 17.21 - 23.13 283 23.13 - 29.04 217 29.04 - 34.96 176 34.96 - 40.88 120 40.88 - 46.79 83 46.79 - 52.71 30 52.71 - 58.62 7 58.62 - 64.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1360 r_work=0.1202 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757328 | | target function (ml) not normalized (work): 703702.516054 | | target function (ml) not normalized (free): 14738.948154 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1360 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1388 0.1387 0.1457 n_refl.: 191129 remove outliers: r(all,work,free)=0.1388 0.1387 0.1457 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1397 0.1396 0.1462 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1190 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 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 91.09 89 3 0.3809 348.976 305.079 0.409 0.905 0.229 13.296-10.522 95.05 95 1 0.2369 480.141 457.478 0.762 0.906 0.167 10.503-8.327 97.80 175 3 0.2138 502.543 496.066 0.928 0.907 0.140 8.318-6.595 100.00 360 8 0.2217 376.020 370.354 0.956 0.906 0.088 6.588-5.215 100.00 711 7 0.1907 345.525 335.980 0.956 0.907 0.087 5.214-4.128 98.38 1367 28 0.1219 505.398 499.875 1.057 0.908 0.060 4.126-3.266 94.74 2603 46 0.1169 460.698 453.380 1.120 0.909 0.005 3.266-2.585 99.86 5447 97 0.1123 310.776 307.243 1.103 0.909 0.000 2.585-2.046 97.45 10613 204 0.0954 234.462 231.893 1.111 0.911 0.000 2.046-1.619 99.39 21536 464 0.0905 138.766 137.428 1.129 0.913 0.000 1.619-1.281 98.00 42464 925 0.0949 74.704 74.049 1.116 0.917 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.075 38.381 1.080 0.923 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0611 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1350 | n_water=902 | time (s): 2.470 (total time: 2.470) Filter (dist) r_work=0.1190 r_free=0.1349 | n_water=901 | time (s): 110.800 (total time: 113.270) Filter (q & B) r_work=0.1191 r_free=0.1351 | n_water=889 | time (s): 4.620 (total time: 117.890) Compute maps r_work=0.1191 r_free=0.1351 | n_water=889 | time (s): 1.750 (total time: 119.640) Filter (map) r_work=0.1213 r_free=0.1355 | n_water=768 | time (s): 5.100 (total time: 124.740) Find peaks r_work=0.1213 r_free=0.1355 | n_water=768 | time (s): 0.850 (total time: 125.590) Add new water r_work=0.1222 r_free=0.1372 | n_water=987 | time (s): 4.740 (total time: 130.330) Refine new water occ: r_work=0.1188 r_free=0.1344 adp: r_work=0.1188 r_free=0.1343 occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1186 r_free=0.1342 occ: r_work=0.1184 r_free=0.1341 adp: r_work=0.1184 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1341 r_work=0.1184 r_free=0.1341 | n_water=987 | time (s): 225.910 (total time: 356.240) Filter (q & B) r_work=0.1189 r_free=0.1347 | n_water=900 | time (s): 5.680 (total time: 361.920) Filter (dist only) r_work=0.1190 r_free=0.1347 | n_water=899 | time (s): 119.300 (total time: 481.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566900 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.458212 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 0.1350 0.0158 0.038 1.1 6.8 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.50 1.58 1.674 13.712 14.458 3.756 11.92 13.53 1.61 1.676 13.708 14.458 3.754 Individual atomic B min max mean iso aniso Overall: 5.47 64.25 14.62 0.88 532 3271 Protein: 5.47 28.54 10.31 0.88 0 2902 Water: 5.88 64.25 28.52 N/A 532 367 Other: 13.75 22.00 17.87 N/A 0 2 Chain A: 5.55 53.86 12.14 N/A 0 1624 Chain B: 5.47 64.25 12.00 N/A 0 1647 Chain S: 5.88 62.05 30.27 N/A 532 0 Histogram: Values Number of atoms 5.47 - 11.34 2078 11.34 - 17.22 812 17.22 - 23.10 279 23.10 - 28.98 219 28.98 - 34.86 169 34.86 - 40.73 122 40.73 - 46.61 78 46.61 - 52.49 36 52.49 - 58.37 7 58.37 - 64.25 3 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1353 r_work=0.1192 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1354 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753687 | | target function (ml) not normalized (work): 703013.009986 | | target function (ml) not normalized (free): 14727.872054 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1354 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1389 0.1388 0.1472 n_refl.: 191127 remove outliers: r(all,work,free)=0.1389 0.1388 0.1472 n_refl.: 191127 overall B=0.02 to atoms: r(all,work,free)=0.1392 0.1390 0.1473 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1353 n_refl.: 191127 remove outliers: r(all,work,free)=0.1193 0.1190 0.1353 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 91.09 89 3 0.3844 348.976 308.795 0.373 0.975 0.210 13.296-10.522 95.05 95 1 0.2335 480.141 465.777 0.718 0.976 0.158 10.503-8.327 97.80 175 3 0.2197 502.543 495.004 0.856 0.977 0.132 8.318-6.595 100.00 360 8 0.2224 376.020 369.637 0.888 0.976 0.103 6.588-5.215 100.00 711 7 0.1940 345.525 335.242 0.885 0.977 0.090 5.214-4.128 98.38 1367 28 0.1244 505.398 499.435 0.980 0.978 0.063 4.126-3.266 94.74 2603 46 0.1173 460.698 453.068 1.039 0.979 0.000 3.266-2.585 99.86 5447 97 0.1127 310.776 307.110 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0954 234.462 231.834 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0903 138.766 137.436 1.049 0.984 0.000 1.619-1.281 98.00 42464 925 0.0942 74.704 74.048 1.040 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.075 38.363 1.009 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0240 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1353 | n_water=899 | time (s): 3.420 (total time: 3.420) Filter (dist) r_work=0.1190 r_free=0.1352 | n_water=898 | time (s): 111.880 (total time: 115.300) Filter (q & B) r_work=0.1191 r_free=0.1352 | n_water=890 | time (s): 4.860 (total time: 120.160) Compute maps r_work=0.1191 r_free=0.1352 | n_water=890 | time (s): 2.210 (total time: 122.370) Filter (map) r_work=0.1211 r_free=0.1350 | n_water=780 | time (s): 5.350 (total time: 127.720) Find peaks r_work=0.1211 r_free=0.1350 | n_water=780 | time (s): 0.840 (total time: 128.560) Add new water r_work=0.1220 r_free=0.1370 | n_water=989 | time (s): 4.340 (total time: 132.900) Refine new water occ: r_work=0.1187 r_free=0.1344 adp: r_work=0.1187 r_free=0.1344 occ: r_work=0.1185 r_free=0.1343 adp: r_work=0.1185 r_free=0.1343 occ: r_work=0.1183 r_free=0.1343 adp: r_work=0.1183 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1342 r_work=0.1183 r_free=0.1342 | n_water=989 | time (s): 249.300 (total time: 382.200) Filter (q & B) r_work=0.1188 r_free=0.1345 | n_water=903 | time (s): 4.390 (total time: 386.590) Filter (dist only) r_work=0.1188 r_free=0.1345 | n_water=901 | time (s): 119.450 (total time: 506.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.570734 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.090490 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 0.1348 0.0158 0.038 1.1 5.6 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.48 1.58 1.680 13.735 15.090 3.754 11.89 13.49 1.60 1.685 13.733 15.090 3.751 Individual atomic B min max mean iso aniso Overall: 5.54 63.49 14.63 0.88 534 3271 Protein: 5.54 28.47 10.34 0.88 0 2902 Water: 5.95 63.49 28.43 N/A 534 367 Other: 13.81 22.02 17.91 N/A 0 2 Chain A: 5.61 53.52 12.14 N/A 0 1624 Chain B: 5.54 63.49 12.01 N/A 0 1647 Chain S: 5.95 62.27 30.27 N/A 534 0 Histogram: Values Number of atoms 5.54 - 11.34 2066 11.34 - 17.13 827 17.13 - 22.93 281 22.93 - 28.72 208 28.72 - 34.51 165 34.51 - 40.31 127 40.31 - 46.10 85 46.10 - 51.90 31 51.90 - 57.69 11 57.69 - 63.49 4 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1349 r_work=0.1189 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1349 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1348 target_work(ml) = 3.751 | | 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= 0.1188 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751113 | | target function (ml) not normalized (work): 702531.031365 | | target function (ml) not normalized (free): 14721.207590 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1348 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1394 0.1393 0.1485 n_refl.: 191127 remove outliers: r(all,work,free)=0.1394 0.1393 0.1485 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1394 0.1393 0.1484 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1347 n_refl.: 191127 remove outliers: r(all,work,free)=0.1190 0.1187 0.1347 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 91.09 89 3 0.3855 348.976 308.659 0.388 0.915 0.195 13.296-10.522 95.05 95 1 0.2348 480.141 465.503 0.758 0.916 0.143 10.503-8.327 97.80 175 3 0.2205 502.543 494.835 0.914 0.917 0.120 8.318-6.595 100.00 360 8 0.2209 376.020 369.700 0.945 0.917 0.101 6.588-5.215 100.00 711 7 0.1914 345.525 335.589 0.942 0.917 0.090 5.214-4.128 98.38 1367 28 0.1232 505.398 499.402 1.045 0.918 0.090 4.126-3.266 94.74 2603 46 0.1170 460.698 453.158 1.107 0.919 0.000 3.266-2.585 99.86 5447 97 0.1123 310.776 307.122 1.091 0.920 0.000 2.585-2.046 97.45 10613 204 0.0954 234.462 231.824 1.099 0.922 0.000 2.046-1.619 99.39 21536 464 0.0901 138.766 137.434 1.118 0.925 0.000 1.619-1.281 98.00 42464 925 0.0939 74.704 74.049 1.109 0.930 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.075 38.354 1.077 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0043 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1347 After: r_work=0.1187 r_free=0.1348 ================================== NQH flips ================================== r_work=0.1187 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1348 | n_water=901 | time (s): 2.820 (total time: 2.820) Filter (dist) r_work=0.1188 r_free=0.1347 | n_water=900 | time (s): 116.470 (total time: 119.290) Filter (q & B) r_work=0.1189 r_free=0.1347 | n_water=892 | time (s): 4.700 (total time: 123.990) Compute maps r_work=0.1189 r_free=0.1347 | n_water=892 | time (s): 2.030 (total time: 126.020) Filter (map) r_work=0.1209 r_free=0.1344 | n_water=791 | time (s): 5.150 (total time: 131.170) Find peaks r_work=0.1209 r_free=0.1344 | n_water=791 | time (s): 0.870 (total time: 132.040) Add new water r_work=0.1217 r_free=0.1358 | n_water=987 | time (s): 4.670 (total time: 136.710) Refine new water occ: r_work=0.1187 r_free=0.1339 adp: r_work=0.1187 r_free=0.1339 occ: r_work=0.1185 r_free=0.1339 adp: r_work=0.1185 r_free=0.1338 occ: r_work=0.1184 r_free=0.1338 adp: r_work=0.1184 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1338 r_work=0.1184 r_free=0.1338 | n_water=987 | time (s): 267.700 (total time: 404.410) Filter (q & B) r_work=0.1188 r_free=0.1347 | n_water=905 | time (s): 5.470 (total time: 409.880) Filter (dist only) r_work=0.1188 r_free=0.1347 | n_water=903 | time (s): 118.950 (total time: 528.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.522014 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.917391 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 0.1349 0.0159 0.038 1.1 6.1 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.49 1.59 1.682 13.733 13.917 3.753 11.92 13.53 1.61 1.680 13.732 13.917 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 63.26 14.62 0.86 536 3271 Protein: 5.56 28.31 10.35 0.86 0 2902 Water: 6.00 63.26 28.31 N/A 536 367 Other: 13.83 22.03 17.93 N/A 0 2 Chain A: 5.63 53.43 12.14 N/A 0 1624 Chain B: 5.56 63.26 12.01 N/A 0 1647 Chain S: 6.00 62.31 30.14 N/A 536 0 Histogram: Values Number of atoms 5.56 - 11.33 2060 11.33 - 17.10 835 17.10 - 22.87 275 22.87 - 28.64 213 28.64 - 34.41 175 34.41 - 40.18 119 40.18 - 45.95 84 45.95 - 51.72 31 51.72 - 57.49 11 57.49 - 63.26 4 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1353 r_work=0.1192 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1353 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | 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: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753909 | | target function (ml) not normalized (work): 703054.581528 | | target function (ml) not normalized (free): 14726.602828 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1366 0.1469 5.6943 5.7705| | 2: 2.94 - 2.33 1.00 7339 128 0.1072 0.1387 5.0815 5.1911| | 3: 2.33 - 2.04 0.96 6939 150 0.0899 0.1143 4.651 4.7254| | 4: 2.04 - 1.85 1.00 7170 155 0.0895 0.1039 4.3873 4.5526| | 5: 1.85 - 1.72 0.99 7113 159 0.0926 0.0974 4.1448 4.2308| | 6: 1.72 - 1.62 0.99 7102 142 0.0895 0.1114 3.9475 4.0925| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0961 3.8004 3.9301| | 8: 1.54 - 1.47 0.96 6798 152 0.0886 0.1322 3.6975 3.9081| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1123 3.6205 3.7514| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1192 3.5567 3.6774| | 11: 1.36 - 1.32 0.99 6997 151 0.0990 0.1118 3.4841 3.5891| | 12: 1.32 - 1.28 0.98 6975 149 0.1029 0.1119 3.4579 3.5801| | 13: 1.28 - 1.25 0.98 6907 166 0.1039 0.1239 3.4355 3.5616| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1607 3.4317 3.6863| | 15: 1.22 - 1.19 0.98 6956 137 0.1165 0.1233 3.4475 3.4871| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1557 3.465 3.6609| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1233 3.434 3.4451| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1702 3.439 3.5306| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1745 3.4196 3.596| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1576 3.4099 3.4312| | 21: 1.08 - 1.07 0.97 6852 152 0.1725 0.2122 3.418 3.5018| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1950 3.4136 3.4171| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2028 3.4342 3.4893| | 24: 1.03 - 1.02 0.96 6784 133 0.2329 0.2254 3.4362 3.5119| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2512 3.4505 3.5246| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2849 3.417 3.4248| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2807 3.4697 3.3971| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11.71 1.00 0.95 11236.53| | 2: 2.94 - 2.33 7339 128 0.93 12.80 0.99 0.96 5145.90| | 3: 2.33 - 2.04 6939 150 0.96 7.61 1.01 0.96 1694.57| | 4: 2.04 - 1.85 7170 155 0.96 7.52 1.00 0.96 986.82| | 5: 1.85 - 1.72 7113 159 0.96 7.96 1.00 0.96 623.78| | 6: 1.72 - 1.62 7102 142 0.96 8.02 1.00 0.96 444.21| | 7: 1.62 - 1.54 7104 148 0.96 8.16 1.01 0.97 338.44| | 8: 1.54 - 1.47 6798 152 0.96 8.29 1.01 0.97 281.24| | 9: 1.47 - 1.41 6938 155 0.96 8.49 1.00 0.98 232.19| | 10: 1.41 - 1.36 7022 150 0.96 8.93 1.00 0.97 203.93| | 11: 1.36 - 1.32 6997 151 0.96 8.93 0.99 0.96 175.25| | 12: 1.32 - 1.28 6975 149 0.96 8.96 0.98 0.95 160.45| | 13: 1.28 - 1.25 6907 166 0.96 9.48 1.01 0.96 157.54| | 14: 1.25 - 1.22 7015 112 0.95 10.64 1.01 0.97 162.55| | 15: 1.22 - 1.19 6956 137 0.95 11.20 1.01 0.98 166.40| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.96 160.44| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.96 154.08| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.95 147.57| | 19: 1.12 - 1.10 6948 106 0.93 14.09 1.00 0.95 150.72| | 20: 1.10 - 1.08 6884 147 0.92 15.16 1.00 0.94 149.84| | 21: 1.08 - 1.07 6852 152 0.91 16.60 1.00 0.93 153.14| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.93 155.21| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 165.43| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.93 179.87| | 25: 1.02 - 1.01 6552 130 0.83 25.15 0.98 0.90 182.75| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.89 177.08| | 27: 0.99 - 0.98 6647 131 0.82 26.28 0.99 0.87 161.44| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.57 max = 11236.53 mean = 926.53| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.88 mean = 13.27| |phase err.(test): min = 0.00 max = 85.79 mean = 13.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1354 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1496 n_refl.: 191127 remove outliers: r(all,work,free)=0.1407 0.1405 0.1496 n_refl.: 191127 overall B=-0.05 to atoms: r(all,work,free)=0.1399 0.1397 0.1491 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1351 n_refl.: 191127 remove outliers: r(all,work,free)=0.1194 0.1191 0.1351 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3834 348.976 308.142 0.353 0.975 0.191 13.296-10.522 95.05 95 1 0.2338 480.141 465.167 0.694 0.977 0.144 10.503-8.327 97.80 175 3 0.2221 502.543 494.648 0.834 0.977 0.128 8.318-6.595 100.00 360 8 0.2212 376.020 369.361 0.863 0.977 0.099 6.588-5.215 100.00 711 7 0.1937 345.525 335.342 0.862 0.978 0.096 5.214-4.128 98.38 1367 28 0.1261 505.398 499.286 0.955 0.979 0.059 4.126-3.266 94.74 2603 46 0.1172 460.698 453.188 1.015 0.980 0.000 3.266-2.585 99.86 5447 97 0.1124 310.776 307.140 0.999 0.981 0.000 2.585-2.046 97.45 10613 204 0.0958 234.462 231.838 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0906 138.766 137.427 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0942 74.704 74.052 1.012 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.075 38.349 0.981 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0108 ================= 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 : 0.2038 0.1978 0.082 5.264 5.2 78.0 14.6 805 0.000 1_bss: 0.1805 0.1912 0.082 5.264 5.2 78.0 14.6 805 0.000 1_settarget: 0.1805 0.1912 0.082 5.264 5.2 78.0 14.6 805 0.000 1_nqh: 0.1808 0.1912 0.082 5.264 5.2 78.0 14.6 805 0.003 1_weight: 0.1808 0.1912 0.082 5.264 5.2 78.0 14.6 805 0.003 1_xyzrec: 0.1273 0.1502 0.038 1.165 5.2 78.0 14.6 805 0.156 1_adp: 0.1297 0.1567 0.038 1.165 5.1 73.0 14.9 805 0.156 1_regHadp: 0.1296 0.1564 0.038 1.165 5.1 73.0 14.9 805 0.156 1_occ: 0.1282 0.1555 0.038 1.165 5.1 73.0 14.9 805 0.156 2_bss: 0.1273 0.1545 0.038 1.165 5.3 73.2 15.1 805 0.156 2_settarget: 0.1273 0.1545 0.038 1.165 5.3 73.2 15.1 805 0.156 2_updatecdl: 0.1273 0.1545 0.038 1.181 5.3 73.2 15.1 805 0.156 2_nqh: 0.1275 0.1546 0.038 1.181 5.3 73.2 15.1 805 0.155 2_sol: 0.1272 0.1514 0.038 1.181 5.3 73.2 16.3 890 n/a 2_weight: 0.1272 0.1514 0.038 1.181 5.3 73.2 16.3 890 n/a 2_xyzrec: 0.1255 0.1530 0.041 1.145 5.3 73.2 16.3 890 n/a 2_adp: 0.1233 0.1511 0.041 1.145 5.4 71.0 16.4 890 n/a 2_regHadp: 0.1233 0.1512 0.041 1.145 5.4 71.0 16.4 890 n/a 2_occ: 0.1226 0.1503 0.041 1.145 5.4 71.0 16.4 890 n/a 3_bss: 0.1232 0.1512 0.041 1.145 5.3 70.9 16.4 890 n/a 3_settarget: 0.1232 0.1512 0.041 1.145 5.3 70.9 16.4 890 n/a 3_updatecdl: 0.1232 0.1512 0.041 1.146 5.3 70.9 16.4 890 n/a 3_nqh: 0.1232 0.1512 0.041 1.146 5.3 70.9 16.4 890 n/a 3_sol: 0.1251 0.1509 0.041 1.146 5.3 68.2 15.6 892 n/a 3_weight: 0.1251 0.1509 0.041 1.146 5.3 68.2 15.6 892 n/a 3_xyzrec: 0.1238 0.1427 0.035 1.098 5.3 68.2 15.6 892 n/a 3_adp: 0.1237 0.1391 0.035 1.098 5.5 67.7 15.4 892 n/a 3_regHadp: 0.1238 0.1391 0.035 1.098 5.5 67.7 15.4 892 n/a 3_occ: 0.1231 0.1378 0.035 1.098 5.5 67.7 15.4 892 n/a 4_bss: 0.1226 0.1374 0.035 1.098 5.5 67.7 15.3 892 n/a 4_settarget: 0.1226 0.1374 0.035 1.098 5.5 67.7 15.3 892 n/a 4_updatecdl: 0.1226 0.1374 0.035 1.103 5.5 67.7 15.3 892 n/a 4_nqh: 0.1226 0.1374 0.035 1.103 5.5 67.7 15.3 892 n/a 4_sol: 0.1211 0.1366 0.035 1.103 5.5 67.7 14.9 859 n/a 4_weight: 0.1211 0.1366 0.035 1.103 5.5 67.7 14.9 859 n/a 4_xyzrec: 0.1210 0.1364 0.037 1.125 5.5 67.7 14.9 859 n/a 4_adp: 0.1200 0.1360 0.037 1.125 5.5 67.3 14.9 859 n/a 4_regHadp: 0.1200 0.1360 0.037 1.125 5.5 67.3 14.9 859 n/a 4_occ: 0.1198 0.1358 0.037 1.125 5.5 67.3 14.9 859 n/a 5_bss: 0.1196 0.1355 0.037 1.125 5.5 67.3 14.8 859 n/a 5_settarget: 0.1196 0.1355 0.037 1.125 5.5 67.3 14.8 859 n/a 5_updatecdl: 0.1196 0.1355 0.037 1.125 5.5 67.3 14.8 859 n/a 5_nqh: 0.1196 0.1355 0.037 1.125 5.5 67.3 14.8 859 n/a 5_sol: 0.1194 0.1348 0.037 1.125 5.5 67.3 14.9 883 n/a 5_weight: 0.1194 0.1348 0.037 1.125 5.5 67.3 14.9 883 n/a 5_xyzrec: 0.1197 0.1351 0.037 1.131 5.5 67.3 14.9 883 n/a 5_adp: 0.1201 0.1354 0.037 1.131 5.6 66.9 14.9 883 n/a 5_regHadp: 0.1202 0.1355 0.037 1.131 5.6 66.9 14.9 883 n/a 5_occ: 0.1199 0.1355 0.037 1.131 5.6 66.9 14.9 883 n/a 6_bss: 0.1199 0.1354 0.037 1.131 5.5 66.8 14.8 883 n/a 6_settarget: 0.1199 0.1354 0.037 1.131 5.5 66.8 14.8 883 n/a 6_updatecdl: 0.1199 0.1354 0.037 1.131 5.5 66.8 14.8 883 n/a 6_nqh: 0.1199 0.1354 0.037 1.131 5.5 66.8 14.8 883 n/a 6_sol: 0.1197 0.1340 0.037 1.131 5.5 66.8 14.9 892 n/a 6_weight: 0.1197 0.1340 0.037 1.131 5.5 66.8 14.9 892 n/a 6_xyzrec: 0.1199 0.1345 0.038 1.132 5.5 66.8 14.9 892 n/a 6_adp: 0.1202 0.1349 0.038 1.132 5.6 65.8 14.8 892 n/a 6_regHadp: 0.1202 0.1350 0.038 1.132 5.6 65.8 14.8 892 n/a 6_occ: 0.1199 0.1347 0.038 1.132 5.6 65.8 14.8 892 n/a 7_bss: 0.1199 0.1347 0.038 1.132 5.4 65.6 14.6 892 n/a 7_settarget: 0.1199 0.1347 0.038 1.132 5.4 65.6 14.6 892 n/a 7_updatecdl: 0.1199 0.1347 0.038 1.133 5.4 65.6 14.6 892 n/a 7_nqh: 0.1199 0.1347 0.038 1.133 5.4 65.6 14.6 892 n/a 7_sol: 0.1198 0.1341 0.038 1.133 5.4 65.6 14.6 902 n/a 7_weight: 0.1198 0.1341 0.038 1.133 5.4 65.6 14.6 902 n/a 7_xyzrec: 0.1201 0.1356 0.038 1.119 5.4 65.6 14.6 902 n/a 7_adp: 0.1202 0.1360 0.038 1.119 5.4 64.5 14.6 902 n/a 7_regHadp: 0.1202 0.1360 0.038 1.119 5.4 64.5 14.6 902 n/a 7_occ: 0.1200 0.1360 0.038 1.119 5.4 64.5 14.6 902 n/a 8_bss: 0.1190 0.1350 0.038 1.119 5.4 64.6 14.7 902 n/a 8_settarget: 0.1190 0.1350 0.038 1.119 5.4 64.6 14.7 902 n/a 8_updatecdl: 0.1190 0.1350 0.038 1.118 5.4 64.6 14.7 902 n/a 8_nqh: 0.1190 0.1350 0.038 1.118 5.4 64.6 14.7 902 n/a 8_sol: 0.1190 0.1347 0.038 1.118 5.4 64.6 14.6 899 n/a 8_weight: 0.1190 0.1347 0.038 1.118 5.4 64.6 14.6 899 n/a 8_xyzrec: 0.1192 0.1350 0.038 1.119 5.4 64.6 14.6 899 n/a 8_adp: 0.1192 0.1353 0.038 1.119 5.5 64.2 14.6 899 n/a 8_regHadp: 0.1192 0.1353 0.038 1.119 5.5 64.2 14.6 899 n/a 8_occ: 0.1191 0.1354 0.038 1.119 5.5 64.2 14.6 899 n/a 9_bss: 0.1190 0.1353 0.038 1.119 5.5 64.3 14.6 899 n/a 9_settarget: 0.1190 0.1353 0.038 1.119 5.5 64.3 14.6 899 n/a 9_updatecdl: 0.1190 0.1353 0.038 1.119 5.5 64.3 14.6 899 n/a 9_nqh: 0.1190 0.1353 0.038 1.119 5.5 64.3 14.6 899 n/a 9_sol: 0.1188 0.1345 0.038 1.119 5.5 64.3 14.6 901 n/a 9_weight: 0.1188 0.1345 0.038 1.119 5.5 64.3 14.6 901 n/a 9_xyzrec: 0.1190 0.1348 0.038 1.125 5.5 64.3 14.6 901 n/a 9_adp: 0.1189 0.1349 0.038 1.125 5.5 63.5 14.6 901 n/a 9_regHadp: 0.1189 0.1349 0.038 1.125 5.5 63.5 14.6 901 n/a 9_occ: 0.1188 0.1348 0.038 1.125 5.5 63.5 14.6 901 n/a 10_bss: 0.1187 0.1347 0.038 1.125 5.5 63.5 14.6 901 n/a 10_settarget: 0.1187 0.1347 0.038 1.125 5.5 63.5 14.6 901 n/a 10_updatecdl: 0.1187 0.1347 0.038 1.126 5.5 63.5 14.6 901 n/a 10_setrh: 0.1187 0.1348 0.038 1.126 5.5 63.5 14.6 901 n/a 10_nqh: 0.1187 0.1348 0.038 1.126 5.5 63.5 14.6 901 n/a 10_sol: 0.1188 0.1347 0.038 1.126 5.5 63.5 14.6 903 n/a 10_weight: 0.1188 0.1347 0.038 1.126 5.5 63.5 14.6 903 n/a 10_xyzrec: 0.1190 0.1349 0.038 1.148 5.5 63.5 14.6 903 n/a 10_adp: 0.1192 0.1353 0.038 1.148 5.6 63.3 14.6 903 n/a 10_regHadp: 0.1192 0.1353 0.038 1.148 5.6 63.3 14.6 903 n/a 10_occ: 0.1192 0.1354 0.038 1.148 5.6 63.3 14.6 903 n/a end: 0.1191 0.1351 0.038 1.148 5.5 63.2 14.6 903 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8239628_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8239628_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.4200 Refinement macro-cycles (run) : 12056.3300 Write final files (write_after_run_outputs) : 170.6900 Total : 12233.4400 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:07 PST -0800 (1736736067.12 s) Start R-work = 0.1805, R-free = 0.1912 Final R-work = 0.1191, R-free = 0.1351 =============================================================================== Job complete usr+sys time: 12523.74 seconds wall clock time: 209 minutes 43.80 seconds (12583.80 seconds total)