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_2738015.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2738015.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2738015.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.22, per 1000 atoms: 0.33 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: 2.755 distance_ideal: 2.720 ideal - model: -0.035 slack: 0.000 delta_slack: -0.035 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: 2.731 distance_ideal: 2.710 ideal - model: -0.021 slack: 0.000 delta_slack: -0.021 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: 0.84 Conformation dependent library (CDL) restraints added in 160.4 milliseconds Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.02: 681 1.02 - 1.25: 2579 1.25 - 1.48: 1551 1.48 - 1.72: 1098 1.72 - 1.95: 25 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL B 114 " pdb=" CB VAL B 114 " ideal model delta sigma weight residual 1.539 1.398 0.141 5.40e-03 3.43e+04 6.78e+02 bond pdb=" N ARG A 149 " pdb=" CA ARG A 149 " ideal model delta sigma weight residual 1.459 1.690 -0.231 1.20e-02 6.94e+03 3.70e+02 bond pdb=" CG1 VAL A 62 " pdb="HG13 VAL A 62 " ideal model delta sigma weight residual 0.970 1.337 -0.367 2.00e-02 2.50e+03 3.37e+02 bond pdb=" N GLY A 165 " pdb=" CA GLY A 165 " ideal model delta sigma weight residual 1.454 1.217 0.236 1.29e-02 6.01e+03 3.36e+02 bond pdb=" N VAL A 7 " pdb=" H VAL A 7 " ideal model delta sigma weight residual 0.860 1.223 -0.363 2.00e-02 2.50e+03 3.30e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.45: 5843 4.45 - 8.90: 3559 8.90 - 13.34: 1193 13.34 - 17.79: 204 17.79 - 22.24: 11 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O PHE B 127 " pdb=" C PHE B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 121.30 136.72 -15.42 8.90e-01 1.26e+00 3.00e+02 angle pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" O VAL B 114 " ideal model delta sigma weight residual 118.69 129.81 -11.12 6.70e-01 2.23e+00 2.76e+02 angle pdb=" O GLU A 17 " pdb=" C GLU A 17 " pdb=" N ALA A 18 " ideal model delta sigma weight residual 122.12 105.54 16.58 1.06e+00 8.90e-01 2.45e+02 angle pdb=" O LEU A 166 " pdb=" C LEU A 166 " pdb=" N LYS A 167 " ideal model delta sigma weight residual 122.12 138.40 -16.28 1.06e+00 8.90e-01 2.36e+02 angle pdb=" O LEU A 87 " pdb=" C LEU A 87 " pdb=" N LEU A 88 " ideal model delta sigma weight residual 122.09 105.84 16.25 1.08e+00 8.57e-01 2.26e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 1828 16.27 - 32.54: 142 32.54 - 48.81: 54 48.81 - 65.08: 20 65.08 - 81.35: 6 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -156.17 -23.83 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA GLU B 80 " pdb=" C GLU B 80 " pdb=" N CYS B 81 " pdb=" CA CYS B 81 " ideal model delta harmonic sigma weight residual 180.00 157.19 22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.209: 170 0.209 - 0.418: 165 0.418 - 0.628: 95 0.628 - 0.837: 50 0.837 - 1.046: 12 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ILE B 30 " pdb=" N ILE B 30 " pdb=" C ILE B 30 " pdb=" CB ILE B 30 " both_signs ideal model delta sigma weight residual False 2.43 3.48 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA TYR A 192 " pdb=" N TYR A 192 " pdb=" C TYR A 192 " pdb=" CB TYR A 192 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 chirality pdb=" CA ALA A 35 " pdb=" N ALA A 35 " pdb=" C ALA A 35 " pdb=" CB ALA A 35 " both_signs ideal model delta sigma weight residual False 2.48 1.53 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.135 2.00e-02 2.50e+03 8.36e-02 2.10e+02 pdb=" CG PHE B 164 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.068 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.085 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.071 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.111 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.041 2.00e-02 2.50e+03 6.16e-02 1.52e+02 pdb=" CG TRP A 139 " -0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.060 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.042 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.016 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.059 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.073 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.110 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.033 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.073 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.114 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.017 2.00e-02 2.50e+03 6.04e-02 1.46e+02 pdb=" CG TRP A 146 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.075 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.088 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.083 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.098 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.052 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.022 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " 0.071 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.089 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.089 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 27 1.62 - 2.37: 2453 2.37 - 3.11: 22289 3.11 - 3.86: 33069 3.86 - 4.60: 52416 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110254 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.881 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.988 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.037 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.130 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.147 2.620 ... (remaining 110249 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_2738015_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= 0.2025 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.304233 | | target function (ml) not normalized (work): 806238.711226 | | target function (ml) not normalized (free): 16618.339661 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2138 0.2056 6.6636 6.3223| | 2: 2.94 - 2.33 1.00 7339 128 0.1626 0.1633 5.5537 5.5979| | 3: 2.33 - 2.04 0.96 6939 150 0.1630 0.1582 5.1458 5.1511| | 4: 2.04 - 1.85 1.00 7170 155 0.1755 0.1668 4.9615 5.0906| | 5: 1.85 - 1.72 0.99 7113 159 0.1906 0.1804 4.7936 4.8561| | 6: 1.72 - 1.62 0.99 7102 142 0.1982 0.1942 4.6711 4.7565| | 7: 1.62 - 1.54 0.99 7104 148 0.2019 0.1761 4.5608 4.5148| | 8: 1.54 - 1.47 0.96 6798 152 0.2042 0.2066 4.47 4.4248| | 9: 1.47 - 1.41 0.98 6938 155 0.2085 0.2159 4.3884 4.4644| | 10: 1.41 - 1.36 0.99 7022 150 0.2157 0.2033 4.3149 4.3271| | 11: 1.36 - 1.32 0.99 6997 151 0.2112 0.2237 4.2357 4.3189| | 12: 1.32 - 1.28 0.98 6976 149 0.2096 0.2127 4.1891 4.3195| | 13: 1.28 - 1.25 0.98 6907 166 0.2035 0.2149 4.1314 4.1917| | 14: 1.25 - 1.22 0.98 7015 113 0.2069 0.2484 4.085 4.246| | 15: 1.22 - 1.19 0.98 6957 137 0.2105 0.2096 4.0546 4.0715| | 16: 1.19 - 1.17 0.93 6604 132 0.2127 0.2285 4.0082 4.0923| | 17: 1.17 - 1.14 0.98 6941 135 0.2191 0.1877 3.9708 3.9985| | 18: 1.14 - 1.12 0.98 6875 142 0.2210 0.2402 3.9322 3.9869| | 19: 1.12 - 1.10 0.97 6949 106 0.2298 0.2461 3.8919 3.986| | 20: 1.10 - 1.08 0.97 6884 147 0.2333 0.2373 3.8378 3.85| | 21: 1.08 - 1.07 0.97 6852 152 0.2440 0.2704 3.798 3.8219| | 22: 1.07 - 1.05 0.97 6838 135 0.2568 0.2549 3.7573 3.7605| | 23: 1.05 - 1.03 0.97 6829 159 0.2741 0.2635 3.7331 3.8022| | 24: 1.03 - 1.02 0.96 6785 133 0.2868 0.2997 3.7032 3.7918| | 25: 1.02 - 1.01 0.93 6552 130 0.3086 0.3247 3.6769 3.8113| | 26: 1.01 - 0.99 0.96 6767 158 0.3241 0.3442 3.6375 3.6345| | 27: 0.99 - 0.98 0.94 6648 131 0.3417 0.3337 3.6362 3.6403| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 21.02 0.91 0.97 37122.43| | 2: 2.94 - 2.33 7339 128 0.85 21.78 1.08 1.01 15735.81| | 3: 2.33 - 2.04 6939 150 0.93 12.90 1.11 1.05 4311.43| | 4: 2.04 - 1.85 7170 155 0.92 13.89 1.12 1.06 2902.29| | 5: 1.85 - 1.72 7113 159 0.90 16.15 1.11 1.07 2186.91| | 6: 1.72 - 1.62 7102 142 0.90 16.69 1.11 1.07 1637.73| | 7: 1.62 - 1.54 7104 148 0.90 16.94 1.11 1.07 1251.78| | 8: 1.54 - 1.47 6798 152 0.90 17.29 1.10 1.06 1029.19| | 9: 1.47 - 1.41 6938 155 0.89 18.38 1.10 1.04 912.88| | 10: 1.41 - 1.36 7022 150 0.87 20.14 1.10 1.03 838.12| | 11: 1.36 - 1.32 6997 151 0.87 20.72 1.08 1.03 777.99| | 12: 1.32 - 1.28 6976 149 0.86 21.03 1.07 1.03 711.63| | 13: 1.28 - 1.25 6907 166 0.87 20.70 1.07 1.04 660.40| | 14: 1.25 - 1.22 7015 113 0.85 21.88 1.07 1.04 630.87| | 15: 1.22 - 1.19 6957 137 0.86 21.56 1.08 1.04 575.53| | 16: 1.19 - 1.17 6604 132 0.86 21.20 1.08 1.02 518.55| | 17: 1.17 - 1.14 6941 135 0.86 21.50 1.09 1.01 456.98| | 18: 1.14 - 1.12 6875 142 0.85 22.19 1.08 0.98 429.59| | 19: 1.12 - 1.10 6949 106 0.85 23.04 1.08 0.98 404.22| | 20: 1.10 - 1.08 6884 147 0.84 23.79 1.06 0.96 371.15| | 21: 1.08 - 1.07 6852 152 0.83 24.40 1.06 0.96 344.25| | 22: 1.07 - 1.05 6838 135 0.82 25.97 1.05 0.96 333.85| | 23: 1.05 - 1.03 6829 159 0.79 28.29 1.05 0.96 343.74| | 24: 1.03 - 1.02 6785 133 0.76 30.83 1.04 0.96 359.15| | 25: 1.02 - 1.01 6552 130 0.74 32.72 1.02 0.91 346.57| | 26: 1.01 - 0.99 6767 158 0.73 34.14 1.02 0.89 320.52| | 27: 0.99 - 0.98 6648 131 0.74 33.16 1.04 0.90 285.67| |alpha: min = 0.89 max = 1.07 mean = 1.01| |beta: min = 285.67 max = 37122.43 mean = 2940.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.22| |phase err.(test): min = 0.00 max = 89.99 mean = 22.31| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.277 2950 Z= 5.401 Angle : 5.264 17.025 4018 Z= 3.780 Chirality : 0.401 1.046 492 Planarity : 0.033 0.160 512 Dihedral : 12.798 81.355 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.60 % Rotamer: Outliers : 0.97 % Allowed : 6.13 % Favored : 92.90 % Cbeta Deviations : 35.96 % 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: -2.52 (0.37), residues: 386 helix: -2.12 (0.36), residues: 144 sheet: -1.37 (0.48), residues: 86 loop : -1.12 (0.46), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.081 0.014 ARG A 143 TYR 0.107 0.038 TYR B 192 PHE 0.138 0.037 PHE B 119 TRP 0.100 0.036 TRP B 146 HIS 0.078 0.033 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= 0.2025 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.304233 | | target function (ml) not normalized (work): 806238.711226 | | target function (ml) not normalized (free): 16618.339661 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2037 0.2038 0.2025 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2037 0.2038 0.2025 n_refl.: 191155 remove outliers: r(all,work,free)=0.2037 0.2038 0.2025 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2037 0.2038 0.2025 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1805 0.1970 n_refl.: 191145 remove outliers: r(all,work,free)=0.1807 0.1803 0.1970 n_refl.: 191141 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4254 400.535 295.637 0.437 0.911 0.303 13.296-10.522 100.00 100 1 0.2503 534.497 521.886 0.793 0.912 0.256 10.503-8.327 99.45 178 3 0.2518 565.118 555.459 0.974 0.912 0.233 8.318-6.595 100.00 360 8 0.2488 414.736 402.997 0.969 0.912 0.175 6.588-5.215 100.00 711 7 0.2247 381.101 366.397 0.961 0.912 0.170 5.214-4.128 98.38 1367 28 0.1495 557.435 549.867 1.075 0.912 0.080 4.126-3.266 94.74 2603 46 0.1334 508.132 498.775 1.147 0.912 0.023 3.266-2.585 99.86 5447 97 0.1451 342.774 337.444 1.120 0.911 0.000 2.585-2.046 97.45 10613 204 0.1400 258.603 254.324 1.125 0.911 0.000 2.046-1.619 99.39 21536 464 0.1614 153.054 149.870 1.147 0.909 0.000 1.619-1.281 98.00 42464 925 0.1928 82.395 80.176 1.129 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2331 44.203 41.697 1.113 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0053 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1803 r_free=0.1970 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1803 r_free=0.1970 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.177671 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.326226 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 0.1276 0.1488 0.0212 0.036 1.2 11.9 0.0 0.3 0 11.589 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.76 14.88 2.12 1.118 13.114 575.326 0.019 13.05 15.60 2.56 1.264 13.346 575.326 0.018 Individual atomic B min max mean iso aniso Overall: 5.12 73.05 15.02 1.41 435 3274 Protein: 5.12 40.35 11.01 1.41 0 2902 Water: 6.26 73.05 29.46 N/A 435 370 Other: 15.98 31.38 23.68 N/A 0 2 Chain A: 5.38 59.73 13.07 N/A 0 1626 Chain B: 5.12 73.05 12.80 N/A 0 1648 Chain S: 11.46 65.49 30.76 N/A 435 0 Histogram: Values Number of atoms 5.12 - 11.92 2154 11.92 - 18.71 643 18.71 - 25.50 310 25.50 - 32.29 276 32.29 - 39.08 154 39.08 - 45.88 105 45.88 - 52.67 45 52.67 - 59.46 17 59.46 - 66.25 4 66.25 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1305 r_free=0.1561 r_work=0.1304 r_free=0.1556 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1304 r_free = 0.1556 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1288 r_free = 0.1543 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1288 r_free= 0.1543 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015889 | | target function (ls_wunit_k1) not normalized (work): 2976.084940 | | target function (ls_wunit_k1) not normalized (free): 114.522568 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1288 0.1543 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1481 0.1478 0.1617 n_refl.: 191141 remove outliers: r(all,work,free)=0.1481 0.1478 0.1617 n_refl.: 191141 overall B=0.16 to atoms: r(all,work,free)=0.1505 0.1503 0.1628 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1286 0.1281 0.1535 n_refl.: 191141 remove outliers: r(all,work,free)=0.1286 0.1281 0.1534 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3666 402.814 371.412 0.460 0.997 0.281 13.296-10.522 100.00 100 1 0.2156 534.497 526.951 0.724 0.999 0.260 10.503-8.327 99.45 178 3 0.1766 565.118 560.599 0.856 0.999 0.208 8.318-6.595 100.00 360 8 0.1759 414.736 410.887 0.876 0.998 0.160 6.588-5.215 100.00 711 7 0.1574 381.101 373.216 0.857 0.999 0.160 5.214-4.128 98.38 1367 28 0.0927 557.435 554.678 0.942 0.999 0.059 4.126-3.266 94.74 2603 46 0.0855 508.132 504.203 1.008 1.000 0.018 3.266-2.585 99.86 5447 97 0.0930 342.774 340.234 0.990 0.999 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.363 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1083 153.054 151.371 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1284 82.395 81.404 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1883 44.202 42.162 0.989 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0377 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1281 r_free=0.1534 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1281 r_free=0.1534 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1281 r_free=0.1534 | n_water=805 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1282 r_free=0.1535 | n_water=800 | time (s): 105.040 (total time: 107.410) Filter (q & B) r_work=0.1283 r_free=0.1537 | n_water=795 | time (s): 5.980 (total time: 113.390) Compute maps r_work=0.1283 r_free=0.1537 | n_water=795 | time (s): 1.890 (total time: 115.280) Filter (map) r_work=0.1305 r_free=0.1532 | n_water=667 | time (s): 4.810 (total time: 120.090) Find peaks r_work=0.1305 r_free=0.1532 | n_water=667 | time (s): 0.560 (total time: 120.650) Add new water r_work=0.1328 r_free=0.1562 | n_water=981 | time (s): 4.890 (total time: 125.540) Refine new water occ: r_work=0.1285 r_free=0.1520 adp: r_work=0.1274 r_free=0.1516 occ: r_work=0.1276 r_free=0.1513 adp: r_work=0.1271 r_free=0.1512 occ: r_work=0.1272 r_free=0.1511 adp: r_work=0.1269 r_free=0.1511 ADP+occupancy (water only), MIN, final r_work=0.1269 r_free=0.1511 r_work=0.1269 r_free=0.1511 | n_water=981 | time (s): 77.210 (total time: 202.750) Filter (q & B) r_work=0.1271 r_free=0.1515 | n_water=903 | time (s): 5.220 (total time: 207.970) Filter (dist only) r_work=0.1272 r_free=0.1514 | n_water=902 | time (s): 120.170 (total time: 328.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.422099 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 580.874708 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 0.1524 0.0269 0.039 1.1 18.0 0.0 0.3 0 11.711 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.24 2.69 2.051 15.228 580.875 0.015 12.31 15.08 2.77 2.431 15.261 580.875 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.21 16.35 1.20 532 3274 Protein: 5.38 40.56 10.99 1.20 0 2902 Water: 6.57 68.21 33.59 N/A 532 370 Other: 16.16 32.25 24.21 N/A 0 2 Chain A: 5.56 55.41 13.07 N/A 0 1626 Chain B: 5.38 68.21 12.83 N/A 0 1648 Chain S: 12.98 67.16 37.31 N/A 532 0 Histogram: Values Number of atoms 5.38 - 11.66 2044 11.66 - 17.94 728 17.94 - 24.23 272 24.23 - 30.51 215 30.51 - 36.79 177 36.79 - 43.08 162 43.08 - 49.36 111 49.36 - 55.64 51 55.64 - 61.93 38 61.93 - 68.21 8 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1508 r_work=0.1231 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1509 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 = 0.1225 r_free = 0.1503 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1503 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013435 | | target function (ls_wunit_k1) not normalized (work): 2516.348700 | | target function (ls_wunit_k1) not normalized (free): 103.645041 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1225 0.1502 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1606 n_refl.: 191139 remove outliers: r(all,work,free)=0.1434 0.1431 0.1606 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1428 0.1604 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1512 n_refl.: 191139 remove outliers: r(all,work,free)=0.1237 0.1231 0.1512 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3346 402.814 378.265 0.487 0.963 0.273 13.296-10.522 100.00 100 1 0.1909 534.497 528.316 0.772 0.964 0.260 10.503-8.327 99.45 178 3 0.1481 565.118 565.950 0.923 0.964 0.179 8.318-6.595 100.00 360 8 0.1561 414.736 413.439 0.935 0.964 0.157 6.588-5.215 100.00 711 7 0.1342 381.101 376.767 0.914 0.964 0.155 5.214-4.128 98.38 1367 28 0.0821 557.435 555.945 0.993 0.964 0.080 4.126-3.266 94.74 2603 46 0.0763 508.132 505.256 1.058 0.964 0.014 3.266-2.585 99.86 5447 97 0.0861 342.774 341.304 1.046 0.963 0.000 2.585-2.046 97.45 10613 204 0.0892 258.603 256.738 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1039 153.054 151.654 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.351 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.213 1.060 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0522 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1512 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1512 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1512 | n_water=902 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1233 r_free=0.1515 | n_water=899 | time (s): 125.590 (total time: 128.830) Filter (q & B) r_work=0.1233 r_free=0.1515 | n_water=897 | time (s): 4.870 (total time: 133.700) Compute maps r_work=0.1233 r_free=0.1515 | n_water=897 | time (s): 2.410 (total time: 136.110) Filter (map) r_work=0.1271 r_free=0.1502 | n_water=704 | time (s): 4.320 (total time: 140.430) Find peaks r_work=0.1271 r_free=0.1502 | n_water=704 | time (s): 0.700 (total time: 141.130) Add new water r_work=0.1296 r_free=0.1549 | n_water=1019 | time (s): 3.910 (total time: 145.040) Refine new water occ: r_work=0.1252 r_free=0.1500 adp: r_work=0.1253 r_free=0.1501 occ: r_work=0.1249 r_free=0.1497 adp: r_work=0.1249 r_free=0.1498 occ: r_work=0.1246 r_free=0.1496 adp: r_work=0.1245 r_free=0.1497 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1497 r_work=0.1245 r_free=0.1497 | n_water=1019 | time (s): 336.970 (total time: 482.010) Filter (q & B) r_work=0.1250 r_free=0.1497 | n_water=880 | time (s): 5.860 (total time: 487.870) Filter (dist only) r_work=0.1251 r_free=0.1497 | n_water=879 | time (s): 121.660 (total time: 609.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.714506 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.734486 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1240 0.1433 0.0193 0.034 1.1 8.2 0.0 0.0 0 0.857 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.33 1.93 1.934 14.610 15.734 3.939 12.36 13.94 1.58 2.238 14.512 15.734 3.898 Individual atomic B min max mean iso aniso Overall: 5.53 67.81 15.29 1.05 511 3272 Protein: 5.53 36.63 10.75 1.05 0 2902 Water: 6.69 67.81 30.27 N/A 511 368 Other: 14.13 28.68 21.40 N/A 0 2 Chain A: 5.53 54.51 12.81 N/A 0 1625 Chain B: 5.53 67.81 12.55 N/A 0 1647 Chain S: 13.92 64.63 32.04 N/A 511 0 Histogram: Values Number of atoms 5.53 - 11.75 2127 11.75 - 17.98 686 17.98 - 24.21 306 24.21 - 30.44 229 30.44 - 36.67 178 36.67 - 42.89 145 42.89 - 49.12 79 49.12 - 55.35 24 55.35 - 61.58 6 61.58 - 67.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1395 r_work=0.1237 r_free=0.1395 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1395 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1393 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892699 | | target function (ml) not normalized (work): 729094.826569 | | target function (ml) not normalized (free): 15227.365357 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1393 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1445 0.1445 0.1490 n_refl.: 191139 remove outliers: r(all,work,free)=0.1445 0.1445 0.1490 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1439 0.1438 0.1486 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1387 n_refl.: 191139 remove outliers: r(all,work,free)=0.1230 0.1227 0.1387 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3992 398.008 357.914 0.423 0.947 0.253 13.296-10.522 100.00 100 1 0.2482 534.497 514.147 0.720 0.948 0.229 10.503-8.327 98.35 176 3 0.2059 555.265 556.695 0.885 0.948 0.163 8.318-6.595 100.00 360 8 0.2077 414.736 410.444 0.892 0.948 0.110 6.588-5.215 100.00 711 7 0.1820 381.101 371.020 0.883 0.948 0.110 5.214-4.128 98.38 1367 28 0.1186 557.435 551.804 0.970 0.948 0.090 4.126-3.266 94.74 2603 46 0.1101 508.132 500.882 1.031 0.948 0.009 3.266-2.585 99.86 5447 97 0.1094 342.774 339.100 1.019 0.947 0.000 2.585-2.046 97.45 10613 204 0.0958 258.603 255.748 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0969 153.054 151.430 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.485 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1692 44.202 42.309 1.039 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1024 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1387 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1387 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1387 | n_water=879 | time (s): 2.980 (total time: 2.980) Filter (dist) r_work=0.1228 r_free=0.1387 | n_water=876 | time (s): 108.880 (total time: 111.860) Filter (q & B) r_work=0.1229 r_free=0.1383 | n_water=865 | time (s): 5.230 (total time: 117.090) Compute maps r_work=0.1229 r_free=0.1383 | n_water=865 | time (s): 2.160 (total time: 119.250) Filter (map) r_work=0.1249 r_free=0.1384 | n_water=726 | time (s): 4.480 (total time: 123.730) Find peaks r_work=0.1249 r_free=0.1384 | n_water=726 | time (s): 0.900 (total time: 124.630) Add new water r_work=0.1266 r_free=0.1402 | n_water=987 | time (s): 5.200 (total time: 129.830) 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=0.1358 adp: r_work=0.1206 r_free=0.1357 occ: r_work=0.1204 r_free=0.1358 adp: r_work=0.1204 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1358 r_work=0.1204 r_free=0.1358 | n_water=987 | time (s): 248.750 (total time: 378.580) Filter (q & B) r_work=0.1210 r_free=0.1364 | n_water=874 | time (s): 5.190 (total time: 383.770) Filter (dist only) r_work=0.1210 r_free=0.1364 | n_water=873 | time (s): 112.830 (total time: 496.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.650900 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.273960 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 0.1208 0.1362 0.0154 0.034 1.1 5.6 0.0 0.3 0 0.825 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.62 1.54 1.831 14.205 15.274 3.875 12.01 13.61 1.60 1.980 14.155 15.274 3.866 Individual atomic B min max mean iso aniso Overall: 5.46 67.21 14.94 0.99 505 3272 Protein: 5.46 33.13 10.65 0.99 0 2902 Water: 5.88 67.21 29.22 N/A 505 368 Other: 13.95 27.35 20.65 N/A 0 2 Chain A: 5.57 53.16 12.64 N/A 0 1625 Chain B: 5.46 67.21 12.42 N/A 0 1647 Chain S: 5.88 64.45 30.58 N/A 505 0 Histogram: Values Number of atoms 5.46 - 11.63 2101 11.63 - 17.81 736 17.81 - 23.98 316 23.98 - 30.16 241 30.16 - 36.33 158 36.33 - 42.51 121 42.51 - 48.68 72 48.68 - 54.86 24 54.86 - 61.03 5 61.03 - 67.21 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1361 r_work=0.1201 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1361 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1357 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863552 | | target function (ml) not normalized (work): 723624.034840 | | target function (ml) not normalized (free): 15134.540967 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1425 0.1425 0.1470 n_refl.: 191136 remove outliers: r(all,work,free)=0.1425 0.1425 0.1470 n_refl.: 191136 overall B=-0.04 to atoms: r(all,work,free)=0.1417 0.1417 0.1465 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1354 n_refl.: 191136 remove outliers: r(all,work,free)=0.1200 0.1196 0.1354 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3667 361.012 311.677 0.409 0.946 0.245 13.296-10.522 98.02 98 1 0.2519 479.073 456.043 0.703 0.947 0.203 10.503-8.327 98.35 176 3 0.2201 502.955 495.938 0.868 0.948 0.158 8.318-6.595 100.00 360 8 0.2172 375.665 369.953 0.892 0.947 0.115 6.588-5.215 100.00 711 7 0.1903 345.198 335.735 0.882 0.947 0.084 5.214-4.128 98.38 1367 28 0.1202 504.920 499.995 0.972 0.948 0.070 4.126-3.266 94.74 2603 46 0.1122 460.262 453.525 1.033 0.948 0.000 3.266-2.585 99.86 5447 97 0.1091 310.482 307.277 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0931 234.241 231.864 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0907 138.635 137.390 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0988 74.633 73.936 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.037 38.384 1.039 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1252 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1354 | n_water=873 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1197 r_free=0.1354 | n_water=870 | time (s): 113.790 (total time: 116.340) Filter (q & B) r_work=0.1197 r_free=0.1353 | n_water=864 | time (s): 4.550 (total time: 120.890) Compute maps r_work=0.1197 r_free=0.1353 | n_water=864 | time (s): 2.010 (total time: 122.900) Filter (map) r_work=0.1219 r_free=0.1358 | n_water=740 | time (s): 5.090 (total time: 127.990) Find peaks r_work=0.1219 r_free=0.1358 | n_water=740 | time (s): 0.530 (total time: 128.520) Add new water r_work=0.1231 r_free=0.1372 | n_water=964 | time (s): 4.580 (total time: 133.100) Refine new water occ: r_work=0.1195 r_free=0.1351 adp: r_work=0.1195 r_free=0.1351 occ: r_work=0.1193 r_free=0.1349 adp: r_work=0.1192 r_free=0.1349 occ: r_work=0.1190 r_free=0.1347 adp: r_work=0.1190 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1348 r_work=0.1190 r_free=0.1348 | n_water=964 | time (s): 323.520 (total time: 456.620) Filter (q & B) r_work=0.1195 r_free=0.1355 | n_water=882 | time (s): 4.990 (total time: 461.610) Filter (dist only) r_work=0.1196 r_free=0.1354 | n_water=881 | time (s): 116.880 (total time: 578.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.581391 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.970274 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1354 0.0156 0.034 1.1 6.3 0.0 0.3 0 0.791 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.54 1.56 1.783 14.125 14.970 3.764 12.02 13.56 1.54 1.838 14.102 14.970 3.761 Individual atomic B min max mean iso aniso Overall: 5.57 66.88 14.97 0.95 514 3271 Protein: 5.57 31.63 10.58 0.95 0 2902 Water: 6.00 66.88 29.39 N/A 514 367 Other: 13.79 26.28 20.04 N/A 0 2 Chain A: 5.57 52.71 12.54 N/A 0 1624 Chain B: 5.57 66.88 12.34 N/A 0 1647 Chain S: 6.00 64.35 31.05 N/A 514 0 Histogram: Values Number of atoms 5.57 - 11.70 2138 11.70 - 17.83 715 17.83 - 23.96 302 23.96 - 30.09 221 30.09 - 36.22 180 36.22 - 42.35 120 42.35 - 48.48 77 48.48 - 54.61 25 54.61 - 60.75 4 60.75 - 66.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1356 r_work=0.1202 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1357 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1355 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760344 | | target function (ml) not normalized (work): 704278.578621 | | target function (ml) not normalized (free): 14736.233254 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1355 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1398 0.1396 0.1476 n_refl.: 191132 remove outliers: r(all,work,free)=0.1398 0.1396 0.1476 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1390 0.1389 0.1470 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1353 n_refl.: 191132 remove outliers: r(all,work,free)=0.1202 0.1199 0.1353 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3672 361.012 333.136 0.430 0.951 0.235 13.296-10.522 98.02 98 1 0.2482 479.073 458.028 0.696 0.953 0.183 10.503-8.327 98.35 176 3 0.2203 502.955 495.765 0.863 0.953 0.139 8.318-6.595 100.00 360 8 0.2136 375.665 370.603 0.889 0.953 0.110 6.588-5.215 100.00 711 7 0.1892 345.198 335.235 0.880 0.953 0.100 5.214-4.128 98.38 1367 28 0.1205 504.920 500.160 0.968 0.953 0.070 4.126-3.266 94.74 2603 46 0.1136 460.262 453.264 1.029 0.954 0.005 3.266-2.585 99.86 5447 97 0.1107 310.482 307.116 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0947 234.241 231.742 1.028 0.954 0.000 2.046-1.619 99.39 21536 464 0.0916 138.635 137.337 1.050 0.953 0.000 1.619-1.281 98.00 42464 925 0.0978 74.633 73.922 1.046 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1656 40.037 38.371 1.032 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1369 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1353 | n_water=881 | time (s): 2.750 (total time: 2.750) Filter (dist) r_work=0.1199 r_free=0.1354 | n_water=880 | time (s): 106.200 (total time: 108.950) Filter (q & B) r_work=0.1199 r_free=0.1353 | n_water=874 | time (s): 4.200 (total time: 113.150) Compute maps r_work=0.1199 r_free=0.1353 | n_water=874 | time (s): 2.020 (total time: 115.170) Filter (map) r_work=0.1217 r_free=0.1353 | n_water=774 | time (s): 4.320 (total time: 119.490) Find peaks r_work=0.1217 r_free=0.1353 | n_water=774 | time (s): 0.870 (total time: 120.360) Add new water r_work=0.1228 r_free=0.1364 | n_water=980 | time (s): 4.330 (total time: 124.690) Refine new water occ: r_work=0.1195 r_free=0.1342 adp: r_work=0.1195 r_free=0.1342 occ: r_work=0.1193 r_free=0.1340 adp: r_work=0.1193 r_free=0.1341 occ: r_work=0.1191 r_free=0.1339 adp: r_work=0.1191 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1340 r_work=0.1191 r_free=0.1340 | n_water=980 | time (s): 257.510 (total time: 382.200) Filter (q & B) r_work=0.1195 r_free=0.1348 | n_water=906 | time (s): 5.830 (total time: 388.030) Filter (dist only) r_work=0.1196 r_free=0.1347 | n_water=905 | time (s): 118.570 (total time: 506.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.586416 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.393813 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1349 0.0151 0.036 1.1 7.2 0.0 0.3 0 0.793 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.49 1.51 1.757 14.095 14.394 3.761 12.01 13.51 1.50 1.881 14.051 14.394 3.759 Individual atomic B min max mean iso aniso Overall: 5.57 65.77 14.95 0.90 538 3271 Protein: 5.57 29.20 10.48 0.90 0 2902 Water: 5.98 65.77 29.27 N/A 538 367 Other: 13.84 23.57 18.71 N/A 0 2 Chain A: 5.61 52.57 12.40 N/A 0 1624 Chain B: 5.57 65.77 12.21 N/A 0 1647 Chain S: 5.98 64.08 31.02 N/A 538 0 Histogram: Values Number of atoms 5.57 - 11.59 2111 11.59 - 17.61 763 17.61 - 23.63 280 23.63 - 29.65 229 29.65 - 35.67 185 35.67 - 41.69 122 41.69 - 47.71 82 47.71 - 53.73 27 53.73 - 59.75 6 59.75 - 65.77 4 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1351 r_work=0.1201 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1352 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1351 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.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758046 | | target function (ml) not normalized (work): 703848.109260 | | target function (ml) not normalized (free): 14733.339052 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1351 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1392 0.1391 0.1471 n_refl.: 191132 remove outliers: r(all,work,free)=0.1392 0.1391 0.1471 n_refl.: 191132 overall B=-0.23 to atoms: r(all,work,free)=0.1357 0.1356 0.1448 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1349 n_refl.: 191132 remove outliers: r(all,work,free)=0.1200 0.1197 0.1349 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3663 361.012 333.547 0.436 0.953 0.231 13.296-10.522 98.02 98 1 0.2471 479.073 458.741 0.708 0.955 0.170 10.503-8.327 98.35 176 3 0.2184 502.955 496.211 0.885 0.955 0.134 8.318-6.595 100.00 360 8 0.2108 375.665 370.748 0.911 0.954 0.108 6.588-5.215 100.00 711 7 0.1910 345.198 335.129 0.901 0.955 0.090 5.214-4.128 98.38 1367 28 0.1202 504.920 500.050 0.992 0.955 0.080 4.126-3.266 94.74 2603 46 0.1139 460.262 453.245 1.052 0.955 0.009 3.266-2.585 99.86 5447 97 0.1115 310.482 307.092 1.037 0.955 0.000 2.585-2.046 97.45 10613 204 0.0952 234.241 231.700 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0911 138.635 137.336 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0971 74.633 73.927 1.051 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.037 38.372 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=0.1197 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1350 | n_water=905 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1197 r_free=0.1349 | n_water=904 | time (s): 119.370 (total time: 122.040) Filter (q & B) r_work=0.1198 r_free=0.1348 | n_water=897 | time (s): 4.390 (total time: 126.430) Compute maps r_work=0.1198 r_free=0.1348 | n_water=897 | time (s): 1.690 (total time: 128.120) Filter (map) r_work=0.1218 r_free=0.1358 | n_water=785 | time (s): 5.120 (total time: 133.240) Find peaks r_work=0.1218 r_free=0.1358 | n_water=785 | time (s): 0.650 (total time: 133.890) Add new water r_work=0.1229 r_free=0.1372 | n_water=994 | time (s): 4.190 (total time: 138.080) Refine new water occ: r_work=0.1195 r_free=0.1338 adp: r_work=0.1195 r_free=0.1338 occ: r_work=0.1193 r_free=0.1337 adp: r_work=0.1193 r_free=0.1338 occ: r_work=0.1191 r_free=0.1337 adp: r_work=0.1191 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1337 r_work=0.1191 r_free=0.1337 | n_water=994 | time (s): 306.990 (total time: 445.070) Filter (q & B) r_work=0.1196 r_free=0.1347 | n_water=918 | time (s): 4.690 (total time: 449.760) Filter (dist only) r_work=0.1196 r_free=0.1347 | n_water=917 | time (s): 120.930 (total time: 570.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.522905 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.695883 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 0.1353 0.0154 0.037 1.1 8.9 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.53 1.54 1.717 13.789 14.696 3.760 11.99 13.54 1.55 1.760 13.767 14.696 3.756 Individual atomic B min max mean iso aniso Overall: 5.40 64.44 14.70 0.89 550 3271 Protein: 5.40 28.46 10.24 0.89 0 2902 Water: 5.79 64.44 28.81 N/A 550 367 Other: 13.67 22.16 17.92 N/A 0 2 Chain A: 5.44 52.21 12.12 N/A 0 1624 Chain B: 5.40 64.44 11.95 N/A 0 1647 Chain S: 5.79 63.62 30.59 N/A 550 0 Histogram: Values Number of atoms 5.40 - 11.30 2090 11.30 - 17.21 789 17.21 - 23.11 282 23.11 - 29.02 225 29.02 - 34.92 190 34.92 - 40.82 116 40.82 - 46.73 87 46.73 - 52.63 30 52.63 - 58.53 8 58.53 - 64.44 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1355 r_work=0.1200 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1355 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1354 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1354 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756022 | | target function (ml) not normalized (work): 703469.092507 | | target function (ml) not normalized (free): 14734.596413 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1354 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1363 0.1361 0.1461 n_refl.: 191132 remove outliers: r(all,work,free)=0.1363 0.1361 0.1461 n_refl.: 191132 overall B=0.06 to atoms: r(all,work,free)=0.1371 0.1369 0.1466 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191132 remove outliers: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3674 361.012 332.281 0.449 0.910 0.219 13.296-10.522 98.02 98 1 0.2478 479.073 457.681 0.743 0.911 0.161 10.503-8.327 98.35 176 3 0.2186 502.955 496.043 0.933 0.912 0.137 8.318-6.595 100.00 360 8 0.2118 375.665 370.393 0.960 0.912 0.100 6.588-5.215 100.00 711 7 0.1913 345.198 334.990 0.954 0.912 0.100 5.214-4.128 98.38 1367 28 0.1221 504.920 499.347 1.049 0.913 0.070 4.126-3.266 94.74 2603 46 0.1147 460.262 452.753 1.114 0.914 0.009 3.266-2.585 99.86 5447 97 0.1119 310.482 306.799 1.096 0.914 0.000 2.585-2.046 97.45 10613 204 0.0956 234.241 231.564 1.105 0.916 0.000 2.046-1.619 99.39 21536 464 0.0905 138.635 137.262 1.122 0.918 0.000 1.619-1.281 98.00 42464 925 0.0948 74.633 73.974 1.111 0.922 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.037 38.348 1.074 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0581 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1342 | n_water=917 | time (s): 2.570 (total time: 2.570) Filter (dist) r_work=0.1188 r_free=0.1342 | n_water=917 | time (s): 122.020 (total time: 124.590) Filter (q & B) r_work=0.1189 r_free=0.1341 | n_water=910 | time (s): 4.750 (total time: 129.340) Compute maps r_work=0.1189 r_free=0.1341 | n_water=910 | time (s): 2.070 (total time: 131.410) Filter (map) r_work=0.1209 r_free=0.1344 | n_water=800 | time (s): 4.810 (total time: 136.220) Find peaks r_work=0.1209 r_free=0.1344 | n_water=800 | time (s): 0.570 (total time: 136.790) Add new water r_work=0.1218 r_free=0.1362 | n_water=998 | time (s): 5.070 (total time: 141.860) Refine new water occ: r_work=0.1188 r_free=0.1328 adp: r_work=0.1188 r_free=0.1328 occ: r_work=0.1186 r_free=0.1327 adp: r_work=0.1186 r_free=0.1327 occ: r_work=0.1184 r_free=0.1327 adp: r_work=0.1184 r_free=0.1328 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1328 r_work=0.1184 r_free=0.1328 | n_water=998 | time (s): 157.820 (total time: 299.680) Filter (q & B) r_work=0.1188 r_free=0.1338 | n_water=920 | time (s): 5.430 (total time: 305.110) Filter (dist only) r_work=0.1189 r_free=0.1336 | n_water=917 | time (s): 119.520 (total time: 424.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.458386 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.431928 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 0.1340 0.0148 0.037 1.1 7.5 0.0 0.3 0 0.729 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.40 1.48 1.677 13.796 14.432 3.755 11.93 13.43 1.50 1.700 13.783 14.432 3.754 Individual atomic B min max mean iso aniso Overall: 5.49 63.48 14.74 0.87 550 3271 Protein: 5.49 28.11 10.31 0.87 0 2902 Water: 5.95 63.48 28.76 N/A 550 367 Other: 13.76 22.13 17.95 N/A 0 2 Chain A: 5.56 52.17 12.14 N/A 0 1624 Chain B: 5.49 63.47 11.99 N/A 0 1647 Chain S: 5.95 63.48 30.65 N/A 550 0 Histogram: Values Number of atoms 5.49 - 11.29 2059 11.29 - 17.09 820 17.09 - 22.89 270 22.89 - 28.69 225 28.69 - 34.49 187 34.49 - 40.29 124 40.29 - 46.09 90 46.09 - 51.88 29 51.88 - 57.68 13 57.68 - 63.48 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1343 r_work=0.1194 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1343 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 = 0.1344 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753990 | | target function (ml) not normalized (work): 703088.482377 | | target function (ml) not normalized (free): 14727.379804 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1380 0.1379 0.1470 n_refl.: 191132 remove outliers: r(all,work,free)=0.1380 0.1379 0.1470 n_refl.: 191132 overall B=0.01 to atoms: r(all,work,free)=0.1382 0.1381 0.1471 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1342 n_refl.: 191132 remove outliers: r(all,work,free)=0.1193 0.1190 0.1342 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3665 361.012 331.116 0.444 0.913 0.215 13.296-10.522 98.02 98 1 0.2469 479.073 458.529 0.735 0.915 0.149 10.503-8.327 98.35 176 3 0.2229 502.955 495.641 0.925 0.915 0.120 8.318-6.595 100.00 360 8 0.2122 375.665 370.083 0.953 0.915 0.100 6.588-5.215 100.00 711 7 0.1933 345.198 335.337 0.948 0.916 0.083 5.214-4.128 98.38 1367 28 0.1228 504.920 498.950 1.043 0.916 0.070 4.126-3.266 94.74 2603 46 0.1155 460.262 452.701 1.109 0.918 0.009 3.266-2.585 99.86 5447 97 0.1125 310.482 306.821 1.092 0.918 0.000 2.585-2.046 97.45 10613 204 0.0959 234.241 231.576 1.101 0.920 0.000 2.046-1.619 99.39 21536 464 0.0908 138.635 137.268 1.119 0.923 0.000 1.619-1.281 98.00 42464 925 0.0945 74.633 73.980 1.109 0.928 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.037 38.332 1.075 0.936 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1342 | n_water=917 | time (s): 2.920 (total time: 2.920) Filter (dist) r_work=0.1190 r_free=0.1342 | n_water=917 | time (s): 124.820 (total time: 127.740) Filter (q & B) r_work=0.1191 r_free=0.1341 | n_water=907 | time (s): 4.410 (total time: 132.150) Compute maps r_work=0.1191 r_free=0.1341 | n_water=907 | time (s): 1.700 (total time: 133.850) Filter (map) r_work=0.1213 r_free=0.1352 | n_water=796 | time (s): 4.480 (total time: 138.330) Find peaks r_work=0.1213 r_free=0.1352 | n_water=796 | time (s): 0.830 (total time: 139.160) Add new water r_work=0.1222 r_free=0.1363 | n_water=989 | time (s): 4.950 (total time: 144.110) Refine new water occ: r_work=0.1190 r_free=0.1332 adp: r_work=0.1190 r_free=0.1332 occ: r_work=0.1188 r_free=0.1330 adp: r_work=0.1188 r_free=0.1331 occ: r_work=0.1187 r_free=0.1330 adp: r_work=0.1186 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1331 r_work=0.1186 r_free=0.1331 | n_water=989 | time (s): 208.410 (total time: 352.520) Filter (q & B) r_work=0.1190 r_free=0.1338 | n_water=917 | time (s): 5.970 (total time: 358.490) Filter (dist only) r_work=0.1191 r_free=0.1338 | n_water=916 | time (s): 121.750 (total time: 480.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.473099 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.747891 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1342 0.0148 0.038 1.1 6.8 0.0 0.3 0 0.737 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.42 1.48 1.678 13.782 13.748 3.755 11.95 13.44 1.50 1.676 13.780 13.748 3.754 Individual atomic B min max mean iso aniso Overall: 5.51 63.43 14.72 0.86 549 3271 Protein: 5.51 28.01 10.33 0.86 0 2902 Water: 5.97 63.43 28.61 N/A 549 367 Other: 13.79 22.13 17.96 N/A 0 2 Chain A: 5.60 52.14 12.14 N/A 0 1624 Chain B: 5.51 63.17 12.00 N/A 0 1647 Chain S: 5.97 63.43 30.51 N/A 549 0 Histogram: Values Number of atoms 5.51 - 11.30 2056 11.30 - 17.10 825 17.10 - 22.89 274 22.89 - 28.68 221 28.68 - 34.47 186 34.47 - 40.26 124 40.26 - 46.05 89 46.05 - 51.85 29 51.85 - 57.64 12 57.64 - 63.43 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1344 r_work=0.1195 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1345 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1343 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754119 | | target function (ml) not normalized (work): 703112.688968 | | target function (ml) not normalized (free): 14728.998564 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1343 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1392 0.1390 0.1484 n_refl.: 191132 remove outliers: r(all,work,free)=0.1392 0.1390 0.1484 n_refl.: 191132 overall B=-0.00 to atoms: r(all,work,free)=0.1392 0.1390 0.1484 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1342 n_refl.: 191132 remove outliers: r(all,work,free)=0.1195 0.1192 0.1342 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3702 361.012 329.775 0.442 0.915 0.217 13.296-10.522 98.02 98 1 0.2461 479.073 459.866 0.734 0.917 0.154 10.503-8.327 98.35 176 3 0.2228 502.955 495.624 0.921 0.917 0.127 8.318-6.595 100.00 360 8 0.2147 375.665 370.057 0.951 0.917 0.101 6.588-5.215 100.00 711 7 0.1940 345.198 335.295 0.945 0.917 0.087 5.214-4.128 98.38 1367 28 0.1239 504.920 498.846 1.042 0.918 0.080 4.126-3.266 94.74 2603 46 0.1164 460.262 452.794 1.107 0.919 0.009 3.266-2.585 99.86 5447 97 0.1130 310.482 306.742 1.090 0.920 0.000 2.585-2.046 97.45 10613 204 0.0963 234.241 231.552 1.099 0.922 0.000 2.046-1.619 99.39 21536 464 0.0909 138.635 137.275 1.117 0.926 0.000 1.619-1.281 98.00 42464 925 0.0943 74.633 73.984 1.108 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.037 38.322 1.076 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0087 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1342 After: r_work=0.1193 r_free=0.1343 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1343 | n_water=916 | time (s): 2.910 (total time: 2.910) Filter (dist) r_work=0.1193 r_free=0.1343 | n_water=916 | time (s): 122.240 (total time: 125.150) Filter (q & B) r_work=0.1193 r_free=0.1342 | n_water=907 | time (s): 4.750 (total time: 129.900) Compute maps r_work=0.1193 r_free=0.1342 | n_water=907 | time (s): 1.950 (total time: 131.850) Filter (map) r_work=0.1213 r_free=0.1351 | n_water=802 | time (s): 5.300 (total time: 137.150) Find peaks r_work=0.1213 r_free=0.1351 | n_water=802 | time (s): 0.660 (total time: 137.810) Add new water r_work=0.1223 r_free=0.1367 | n_water=995 | time (s): 4.020 (total time: 141.830) Refine new water occ: r_work=0.1192 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1341 occ: r_work=0.1190 r_free=0.1341 adp: r_work=0.1190 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1341 r_work=0.1190 r_free=0.1341 | n_water=995 | time (s): 154.910 (total time: 296.740) Filter (q & B) r_work=0.1194 r_free=0.1346 | n_water=909 | time (s): 5.160 (total time: 301.900) Filter (dist only) r_work=0.1195 r_free=0.1347 | n_water=906 | time (s): 119.420 (total time: 421.320) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.476985 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.558830 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1348 0.0153 0.038 1.1 6.1 0.0 0.3 0 0.738 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.48 1.53 1.676 13.690 13.559 3.755 11.97 13.50 1.53 1.683 13.692 13.559 3.755 Individual atomic B min max mean iso aniso Overall: 5.57 63.19 14.56 0.85 539 3271 Protein: 5.57 27.75 10.34 0.85 0 2902 Water: 6.00 63.19 28.05 N/A 539 367 Other: 13.85 22.06 17.95 N/A 0 2 Chain A: 5.63 51.95 12.13 N/A 0 1624 Chain B: 5.57 62.17 11.98 N/A 0 1647 Chain S: 6.00 63.19 29.73 N/A 539 0 Histogram: Values Number of atoms 5.57 - 11.33 2061 11.33 - 17.09 830 17.09 - 22.85 292 22.85 - 28.62 227 28.62 - 34.38 157 34.38 - 40.14 108 40.14 - 45.90 88 45.90 - 51.67 31 51.67 - 57.43 11 57.43 - 63.19 5 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1350 r_work=0.1197 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1350 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1352 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755272 | | target function (ml) not normalized (work): 703328.628229 | | target function (ml) not normalized (free): 14732.832645 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7400 127 0.1374 0.1458 5.7013 5.789| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1328 5.0878 5.1776| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1158 4.6604 4.7428| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1091 4.3944 4.6008| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0976 4.1498 4.2469| | 6: 1.72 - 1.62 0.99 7102 142 0.0900 0.1064 3.948 4.0716| | 7: 1.62 - 1.54 0.99 7104 148 0.0891 0.0966 3.7974 3.9209| | 8: 1.54 - 1.47 0.96 6798 152 0.0890 0.1327 3.6967 3.9023| | 9: 1.47 - 1.41 0.98 6938 155 0.0925 0.1109 3.619 3.7363| | 10: 1.41 - 1.36 0.99 7022 150 0.0977 0.1201 3.5545 3.6732| | 11: 1.36 - 1.32 0.99 6997 151 0.0994 0.1127 3.485 3.5837| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1122 3.4581 3.5809| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1240 3.4353 3.5566| | 14: 1.25 - 1.22 0.98 7015 112 0.1108 0.1597 3.4326 3.6804| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1252 3.45 3.4988| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1576 3.4671 3.6708| | 17: 1.17 - 1.14 0.98 6940 135 0.1303 0.1235 3.436 3.4453| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1705 3.4397 3.5346| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1740 3.4201 3.5952| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1571 3.4107 3.4327| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2132 3.4188 3.5056| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1952 3.4132 3.4136| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2028 3.4332 3.4868| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2250 3.4362 3.5085| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2525 3.4492 3.5275| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2862 3.4163 3.4262| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2819 3.4684 3.3959| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7400 127 0.93 12.03 1.00 0.95 11714.09| | 2: 2.94 - 2.33 7339 128 0.92 13.08 0.99 0.95 5308.96| | 3: 2.33 - 2.04 6939 150 0.96 7.68 1.01 0.95 1711.29| | 4: 2.04 - 1.85 7170 155 0.96 7.71 1.00 0.95 1019.27| | 5: 1.85 - 1.72 7113 159 0.96 8.03 1.00 0.96 633.71| | 6: 1.72 - 1.62 7102 142 0.96 7.93 1.00 0.96 438.36| | 7: 1.62 - 1.54 7104 148 0.96 8.01 1.01 0.97 330.66| | 8: 1.54 - 1.47 6798 152 0.96 8.16 1.01 0.97 274.42| | 9: 1.47 - 1.41 6938 155 0.96 8.35 1.00 0.98 226.62| | 10: 1.41 - 1.36 7022 150 0.96 8.81 1.00 0.97 199.32| | 11: 1.36 - 1.32 6997 151 0.96 8.85 0.99 0.96 172.64| | 12: 1.32 - 1.28 6975 149 0.96 8.91 0.98 0.95 159.34| | 13: 1.28 - 1.25 6907 166 0.96 9.46 1.01 0.96 157.13| | 14: 1.25 - 1.22 7015 112 0.95 10.67 1.01 0.97 162.69| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.01 0.98 167.61| | 16: 1.19 - 1.17 6604 132 0.95 11.50 1.01 0.96 162.12| | 17: 1.17 - 1.14 6940 135 0.94 12.35 1.01 0.96 155.72| | 18: 1.14 - 1.12 6875 142 0.94 12.78 1.01 0.95 148.34| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.95 151.17| | 20: 1.10 - 1.08 6884 147 0.92 15.19 1.00 0.94 149.96| | 21: 1.08 - 1.07 6852 152 0.91 16.64 1.00 0.93 153.05| | 22: 1.07 - 1.05 6836 135 0.89 18.25 0.99 0.93 154.42| | 23: 1.05 - 1.03 6827 159 0.87 20.46 0.99 0.92 164.40| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.93 179.04| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.90 182.52| | 26: 1.01 - 0.99 6767 158 0.81 26.68 0.98 0.89 177.27| | 27: 0.99 - 0.98 6647 131 0.82 26.35 0.99 0.87 161.72| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.34 max = 11714.09 mean = 953.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.30| |phase err.(test): min = 0.00 max = 89.50 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1352 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1506 n_refl.: 191132 remove outliers: r(all,work,free)=0.1404 0.1402 0.1506 n_refl.: 191132 overall B=-0.06 to atoms: r(all,work,free)=0.1394 0.1392 0.1498 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1350 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1195 0.1350 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3753 361.012 327.840 0.391 0.994 0.213 13.296-10.522 98.02 98 1 0.2496 479.073 457.865 0.652 0.996 0.146 10.503-8.327 98.35 176 3 0.2279 502.955 494.885 0.824 0.996 0.117 8.318-6.595 100.00 360 8 0.2190 375.665 370.095 0.850 0.996 0.086 6.588-5.215 100.00 711 7 0.1981 345.198 334.654 0.845 0.997 0.070 5.214-4.128 98.38 1367 28 0.1253 504.920 498.521 0.934 0.998 0.050 4.126-3.266 94.74 2603 46 0.1169 460.262 452.814 0.995 0.999 0.005 3.266-2.585 99.86 5447 97 0.1126 310.482 306.850 0.979 1.000 0.000 2.585-2.046 97.45 10613 204 0.0965 234.241 231.556 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0911 138.635 137.277 1.001 1.007 0.000 1.619-1.281 98.00 42464 925 0.0945 74.633 73.984 0.991 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.037 38.321 0.959 1.027 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0139 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2038 0.2025 0.081 5.264 5.2 78.0 14.6 805 0.000 1_bss: 0.1803 0.1970 0.081 5.264 5.2 78.0 14.6 805 0.000 1_settarget: 0.1803 0.1970 0.081 5.264 5.2 78.0 14.6 805 0.000 1_nqh: 0.1803 0.1970 0.081 5.264 5.2 78.0 14.6 805 0.000 1_weight: 0.1803 0.1970 0.081 5.264 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1276 0.1488 0.036 1.173 5.2 78.0 14.6 805 0.142 1_adp: 0.1305 0.1561 0.036 1.173 5.1 73.0 15.0 805 0.142 1_regHadp: 0.1304 0.1556 0.036 1.173 5.1 73.0 15.0 805 0.142 1_occ: 0.1288 0.1543 0.036 1.173 5.1 73.0 15.0 805 0.142 2_bss: 0.1281 0.1534 0.036 1.173 5.3 73.2 15.2 805 0.142 2_settarget: 0.1281 0.1534 0.036 1.173 5.3 73.2 15.2 805 0.142 2_updatecdl: 0.1281 0.1534 0.036 1.197 5.3 73.2 15.2 805 0.142 2_nqh: 0.1281 0.1534 0.036 1.197 5.3 73.2 15.2 805 0.142 2_sol: 0.1272 0.1514 0.036 1.197 5.3 73.2 16.3 902 n/a 2_weight: 0.1272 0.1514 0.036 1.197 5.3 73.2 16.3 902 n/a 2_xyzrec: 0.1255 0.1524 0.039 1.143 5.3 73.2 16.3 902 n/a 2_adp: 0.1231 0.1508 0.039 1.143 5.4 68.2 16.4 902 n/a 2_regHadp: 0.1231 0.1509 0.039 1.143 5.4 68.2 16.4 902 n/a 2_occ: 0.1225 0.1503 0.039 1.143 5.4 68.2 16.4 902 n/a 3_bss: 0.1231 0.1512 0.039 1.143 5.4 68.2 16.3 902 n/a 3_settarget: 0.1231 0.1512 0.039 1.143 5.4 68.2 16.3 902 n/a 3_updatecdl: 0.1231 0.1512 0.039 1.151 5.4 68.2 16.3 902 n/a 3_nqh: 0.1231 0.1512 0.039 1.151 5.4 68.2 16.3 902 n/a 3_sol: 0.1251 0.1497 0.039 1.151 5.4 68.2 15.5 879 n/a 3_weight: 0.1251 0.1497 0.039 1.151 5.4 68.2 15.5 879 n/a 3_xyzrec: 0.1240 0.1433 0.034 1.108 5.4 68.2 15.5 879 n/a 3_adp: 0.1236 0.1395 0.034 1.108 5.5 67.8 15.3 879 n/a 3_regHadp: 0.1237 0.1395 0.034 1.108 5.5 67.8 15.3 879 n/a 3_occ: 0.1231 0.1393 0.034 1.108 5.5 67.8 15.3 879 n/a 4_bss: 0.1227 0.1387 0.034 1.108 5.5 67.8 15.3 879 n/a 4_settarget: 0.1227 0.1387 0.034 1.108 5.5 67.8 15.3 879 n/a 4_updatecdl: 0.1227 0.1387 0.034 1.104 5.5 67.8 15.3 879 n/a 4_nqh: 0.1227 0.1387 0.034 1.104 5.5 67.8 15.3 879 n/a 4_sol: 0.1210 0.1364 0.034 1.104 5.5 67.8 15.0 873 n/a 4_weight: 0.1210 0.1364 0.034 1.104 5.5 67.8 15.0 873 n/a 4_xyzrec: 0.1208 0.1362 0.034 1.121 5.5 67.8 15.0 873 n/a 4_adp: 0.1201 0.1361 0.034 1.121 5.5 67.2 14.9 873 n/a 4_regHadp: 0.1201 0.1361 0.034 1.121 5.5 67.2 14.9 873 n/a 4_occ: 0.1199 0.1357 0.034 1.121 5.5 67.2 14.9 873 n/a 5_bss: 0.1197 0.1354 0.034 1.121 5.4 67.2 14.9 873 n/a 5_settarget: 0.1197 0.1354 0.034 1.121 5.4 67.2 14.9 873 n/a 5_updatecdl: 0.1197 0.1354 0.034 1.121 5.4 67.2 14.9 873 n/a 5_nqh: 0.1197 0.1354 0.034 1.121 5.4 67.2 14.9 873 n/a 5_sol: 0.1196 0.1354 0.034 1.121 5.4 67.2 15.0 881 n/a 5_weight: 0.1196 0.1354 0.034 1.121 5.4 67.2 15.0 881 n/a 5_xyzrec: 0.1198 0.1354 0.034 1.129 5.4 67.2 15.0 881 n/a 5_adp: 0.1202 0.1356 0.034 1.129 5.6 66.9 15.0 881 n/a 5_regHadp: 0.1202 0.1357 0.034 1.129 5.6 66.9 15.0 881 n/a 5_occ: 0.1200 0.1355 0.034 1.129 5.6 66.9 15.0 881 n/a 6_bss: 0.1199 0.1353 0.034 1.129 5.5 66.8 14.9 881 n/a 6_settarget: 0.1199 0.1353 0.034 1.129 5.5 66.8 14.9 881 n/a 6_updatecdl: 0.1199 0.1353 0.034 1.129 5.5 66.8 14.9 881 n/a 6_nqh: 0.1199 0.1353 0.034 1.129 5.5 66.8 14.9 881 n/a 6_sol: 0.1196 0.1347 0.034 1.129 5.5 66.8 15.0 905 n/a 6_weight: 0.1196 0.1347 0.034 1.129 5.5 66.8 15.0 905 n/a 6_xyzrec: 0.1198 0.1349 0.036 1.131 5.5 66.8 15.0 905 n/a 6_adp: 0.1201 0.1351 0.036 1.131 5.6 65.8 14.9 905 n/a 6_regHadp: 0.1201 0.1352 0.036 1.131 5.6 65.8 14.9 905 n/a 6_occ: 0.1198 0.1351 0.036 1.131 5.6 65.8 14.9 905 n/a 7_bss: 0.1197 0.1350 0.036 1.131 5.3 65.5 14.7 905 n/a 7_settarget: 0.1197 0.1350 0.036 1.131 5.3 65.5 14.7 905 n/a 7_updatecdl: 0.1197 0.1350 0.036 1.131 5.3 65.5 14.7 905 n/a 7_nqh: 0.1197 0.1350 0.036 1.131 5.3 65.5 14.7 905 n/a 7_sol: 0.1196 0.1347 0.036 1.131 5.3 65.5 14.7 917 n/a 7_weight: 0.1196 0.1347 0.036 1.131 5.3 65.5 14.7 917 n/a 7_xyzrec: 0.1199 0.1353 0.037 1.117 5.3 65.5 14.7 917 n/a 7_adp: 0.1199 0.1355 0.037 1.117 5.4 64.4 14.7 917 n/a 7_regHadp: 0.1200 0.1355 0.037 1.117 5.4 64.4 14.7 917 n/a 7_occ: 0.1197 0.1354 0.037 1.117 5.4 64.4 14.7 917 n/a 8_bss: 0.1188 0.1342 0.037 1.117 5.5 64.5 14.8 917 n/a 8_settarget: 0.1188 0.1342 0.037 1.117 5.5 64.5 14.8 917 n/a 8_updatecdl: 0.1188 0.1342 0.037 1.116 5.5 64.5 14.8 917 n/a 8_nqh: 0.1188 0.1342 0.037 1.116 5.5 64.5 14.8 917 n/a 8_sol: 0.1189 0.1336 0.037 1.116 5.5 64.5 14.8 917 n/a 8_weight: 0.1189 0.1336 0.037 1.116 5.5 64.5 14.8 917 n/a 8_xyzrec: 0.1192 0.1340 0.037 1.116 5.5 64.5 14.8 917 n/a 8_adp: 0.1193 0.1343 0.037 1.116 5.5 63.5 14.7 917 n/a 8_regHadp: 0.1194 0.1343 0.037 1.116 5.5 63.5 14.7 917 n/a 8_occ: 0.1191 0.1344 0.037 1.116 5.5 63.5 14.7 917 n/a 9_bss: 0.1190 0.1342 0.037 1.116 5.5 63.5 14.8 917 n/a 9_settarget: 0.1190 0.1342 0.037 1.116 5.5 63.5 14.8 917 n/a 9_updatecdl: 0.1190 0.1342 0.037 1.117 5.5 63.5 14.8 917 n/a 9_nqh: 0.1190 0.1342 0.037 1.117 5.5 63.5 14.8 917 n/a 9_sol: 0.1191 0.1338 0.037 1.117 5.5 63.5 14.7 916 n/a 9_weight: 0.1191 0.1338 0.037 1.117 5.5 63.5 14.7 916 n/a 9_xyzrec: 0.1193 0.1342 0.038 1.112 5.5 63.5 14.7 916 n/a 9_adp: 0.1195 0.1344 0.038 1.112 5.5 63.4 14.7 916 n/a 9_regHadp: 0.1195 0.1345 0.038 1.112 5.5 63.4 14.7 916 n/a 9_occ: 0.1193 0.1343 0.038 1.112 5.5 63.4 14.7 916 n/a 10_bss: 0.1192 0.1342 0.038 1.112 5.5 63.4 14.7 916 n/a 10_settarget: 0.1192 0.1342 0.038 1.112 5.5 63.4 14.7 916 n/a 10_updatecdl: 0.1192 0.1342 0.038 1.112 5.5 63.4 14.7 916 n/a 10_setrh: 0.1193 0.1343 0.038 1.112 5.5 63.4 14.7 916 n/a 10_nqh: 0.1193 0.1343 0.038 1.112 5.5 63.4 14.7 916 n/a 10_sol: 0.1195 0.1347 0.038 1.112 5.5 63.4 14.6 906 n/a 10_weight: 0.1195 0.1347 0.038 1.112 5.5 63.4 14.6 906 n/a 10_xyzrec: 0.1195 0.1348 0.038 1.121 5.5 63.4 14.6 906 n/a 10_adp: 0.1197 0.1350 0.038 1.121 5.6 63.2 14.6 906 n/a 10_regHadp: 0.1197 0.1350 0.038 1.121 5.6 63.2 14.6 906 n/a 10_occ: 0.1196 0.1352 0.038 1.121 5.6 63.2 14.6 906 n/a end: 0.1195 0.1350 0.038 1.121 5.5 63.1 14.5 906 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2738015_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2738015_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.8700 Refinement macro-cycles (run) : 11891.6000 Write final files (write_after_run_outputs) : 167.3500 Total : 12064.8200 Total CPU time: 3.36 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:38:19 PST -0800 (1736735899.61 s) Start R-work = 0.1803, R-free = 0.1970 Final R-work = 0.1195, R-free = 0.1350 =============================================================================== Job complete usr+sys time: 12381.63 seconds wall clock time: 207 minutes 23.82 seconds (12443.82 seconds total)