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_8988844.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/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8988844.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8988844.pdb" } 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 3 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.76, per 1000 atoms: 0.26 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: 2.790 distance_ideal: 2.720 ideal - model: -0.070 slack: 0.000 delta_slack: -0.070 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: 2.662 distance_ideal: 2.710 ideal - model: 0.048 slack: 0.000 delta_slack: 0.048 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: 0.69 Conformation dependent library (CDL) restraints added in 157.6 milliseconds Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 884 1.03 - 1.25: 2379 1.25 - 1.47: 1375 1.47 - 1.68: 1251 1.68 - 1.90: 45 Bond restraints: 5934 Sorted by residual: bond pdb=" C THR A 20 " pdb=" O THR A 20 " ideal model delta sigma weight residual 1.236 1.011 0.224 1.16e-02 7.43e+03 3.75e+02 bond pdb=" CA ILE A 191 " pdb=" C ILE A 191 " ideal model delta sigma weight residual 1.523 1.738 -0.215 1.14e-02 7.69e+03 3.55e+02 bond pdb=" NZ LYS B 52 " pdb=" HZ3 LYS B 52 " ideal model delta sigma weight residual 0.890 1.265 -0.375 2.00e-02 2.50e+03 3.51e+02 bond pdb=" N GLU B 176 " pdb=" CA GLU B 176 " ideal model delta sigma weight residual 1.459 1.239 0.220 1.19e-02 7.06e+03 3.42e+02 bond pdb=" C THR B 21 " pdb=" O THR B 21 " ideal model delta sigma weight residual 1.236 1.448 -0.211 1.15e-02 7.56e+03 3.38e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 5308 3.86 - 7.73: 3547 7.73 - 11.59: 1505 11.59 - 15.46: 382 15.46 - 19.32: 68 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA B 57 " pdb=" C ALA B 57 " pdb=" N PRO B 58 " ideal model delta sigma weight residual 121.65 103.41 18.24 7.30e-01 1.88e+00 6.24e+02 angle pdb=" O ALA A 108 " pdb=" C ALA A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 120.38 133.48 -13.10 7.90e-01 1.60e+00 2.75e+02 angle pdb=" CA ALA B 57 " pdb=" C ALA B 57 " pdb=" O ALA B 57 " ideal model delta sigma weight residual 120.34 133.71 -13.37 9.20e-01 1.18e+00 2.11e+02 angle pdb=" C LYS A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta sigma weight residual 120.03 135.90 -15.87 1.12e+00 7.97e-01 2.01e+02 angle pdb=" O VAL A 69 " pdb=" C VAL A 69 " pdb=" N ILE A 70 " ideal model delta sigma weight residual 123.00 138.79 -15.79 1.14e+00 7.69e-01 1.92e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 1830 17.62 - 35.24: 154 35.24 - 52.86: 45 52.86 - 70.47: 16 70.47 - 88.09: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -152.36 -27.64 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual 180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.235: 216 0.235 - 0.468: 172 0.468 - 0.702: 75 0.702 - 0.935: 23 0.935 - 1.169: 6 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 92 " pdb=" N VAL A 92 " pdb=" C VAL A 92 " pdb=" CB VAL A 92 " both_signs ideal model delta sigma weight residual False 2.44 3.61 -1.17 2.00e-01 2.50e+01 3.42e+01 chirality pdb=" CA ILE B 45 " pdb=" N ILE B 45 " pdb=" C ILE B 45 " pdb=" CB ILE B 45 " both_signs ideal model delta sigma weight residual False 2.43 3.55 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" CB VAL B 19 " pdb=" CA VAL B 19 " pdb=" CG1 VAL B 19 " pdb=" CG2 VAL B 19 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.60e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.188 2.00e-02 2.50e+03 7.96e-02 1.90e+02 pdb=" CG PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.039 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.016 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.085 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.043 2.00e-02 2.50e+03 6.66e-02 1.77e+02 pdb=" CG TRP A 146 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.063 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.053 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.035 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.024 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.034 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.137 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.134 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.073 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.087 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 116 " -0.074 2.00e-02 2.50e+03 7.67e-02 1.32e+02 pdb=" CG HIS A 116 " 0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS A 116 " 0.166 2.00e-02 2.50e+03 pdb=" CD2 HIS A 116 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS A 116 " -0.071 2.00e-02 2.50e+03 pdb=" NE2 HIS A 116 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 HIS A 116 " -0.027 2.00e-02 2.50e+03 pdb=" HE1 HIS A 116 " -0.092 2.00e-02 2.50e+03 pdb=" HE2 HIS A 116 " 0.063 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.66: 37 1.66 - 2.40: 2955 2.40 - 3.13: 22594 3.13 - 3.87: 32854 3.87 - 4.60: 51946 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110386 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.930 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.965 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.984 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.080 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.204 2.620 ... (remaining 110381 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_8988844_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= 0.2034 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299872 | | target function (ml) not normalized (work): 805421.915908 | | target function (ml) not normalized (free): 16542.049859 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2127 0.1851 6.698 6.3068| | 2: 2.94 - 2.33 1.00 7339 128 0.1608 0.1543 5.529 5.5591| | 3: 2.33 - 2.04 0.96 6939 150 0.1646 0.1568 5.1342 5.1184| | 4: 2.04 - 1.85 1.00 7170 155 0.1753 0.1539 4.9572 5.0165| | 5: 1.85 - 1.72 0.99 7113 159 0.1916 0.1840 4.7915 4.8047| | 6: 1.72 - 1.62 0.99 7102 142 0.1966 0.1954 4.6559 4.7014| | 7: 1.62 - 1.54 0.99 7104 148 0.2001 0.1717 4.5583 4.567| | 8: 1.54 - 1.47 0.96 6798 152 0.2037 0.2252 4.4772 4.5254| | 9: 1.47 - 1.41 0.98 6938 155 0.2080 0.2151 4.3934 4.499| | 10: 1.41 - 1.36 0.99 7022 150 0.2171 0.2170 4.3115 4.3245| | 11: 1.36 - 1.32 0.99 6997 151 0.2121 0.2002 4.2347 4.2185| | 12: 1.32 - 1.28 0.98 6976 149 0.2121 0.2022 4.1926 4.2541| | 13: 1.28 - 1.25 0.98 6907 166 0.2042 0.2169 4.1276 4.1572| | 14: 1.25 - 1.22 0.98 7015 113 0.2091 0.2435 4.0742 4.3125| | 15: 1.22 - 1.19 0.98 6957 137 0.2113 0.1694 4.0428 3.9067| | 16: 1.19 - 1.17 0.93 6604 132 0.2096 0.2291 4.0011 4.078| | 17: 1.17 - 1.14 0.98 6941 135 0.2162 0.1893 3.9582 3.9726| | 18: 1.14 - 1.12 0.98 6875 142 0.2216 0.2413 3.9278 3.9127| | 19: 1.12 - 1.10 0.97 6949 106 0.2285 0.2432 3.8729 3.928| | 20: 1.10 - 1.08 0.97 6884 147 0.2309 0.2289 3.8178 3.84| | 21: 1.08 - 1.07 0.97 6852 152 0.2411 0.2882 3.7851 3.8899| | 22: 1.07 - 1.05 0.97 6838 135 0.2612 0.2608 3.762 3.7868| | 23: 1.05 - 1.03 0.97 6829 159 0.2706 0.2753 3.7289 3.8371| | 24: 1.03 - 1.02 0.96 6785 133 0.2883 0.2757 3.7041 3.7934| | 25: 1.02 - 1.01 0.93 6552 130 0.3082 0.3189 3.6724 3.7576| | 26: 1.01 - 0.99 0.96 6767 158 0.3229 0.3290 3.6355 3.5903| | 27: 0.99 - 0.98 0.94 6648 131 0.3414 0.3362 3.6399 3.6296| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.20 0.91 0.98 34702.16| | 2: 2.94 - 2.33 7339 128 0.86 20.81 1.08 1.02 14623.01| | 3: 2.33 - 2.04 6939 150 0.93 12.14 1.11 1.06 3903.25| | 4: 2.04 - 1.85 7170 155 0.93 13.23 1.11 1.07 2698.51| | 5: 1.85 - 1.72 7113 159 0.91 15.33 1.12 1.08 2051.69| | 6: 1.72 - 1.62 7102 142 0.90 16.78 1.11 1.07 1639.09| | 7: 1.62 - 1.54 7104 148 0.89 17.68 1.11 1.06 1334.28| | 8: 1.54 - 1.47 6798 152 0.89 18.51 1.10 1.06 1170.28| | 9: 1.47 - 1.41 6938 155 0.88 19.05 1.10 1.06 991.30| | 10: 1.41 - 1.36 7022 150 0.87 19.87 1.10 1.05 829.21| | 11: 1.36 - 1.32 6997 151 0.88 19.38 1.09 1.05 693.36| | 12: 1.32 - 1.28 6976 149 0.88 19.62 1.07 1.04 637.04| | 13: 1.28 - 1.25 6907 166 0.87 19.80 1.07 1.04 601.35| | 14: 1.25 - 1.22 7015 113 0.87 20.45 1.08 1.03 558.48| | 15: 1.22 - 1.19 6957 137 0.87 20.49 1.08 1.03 516.64| | 16: 1.19 - 1.17 6604 132 0.88 19.76 1.07 1.02 460.60| | 17: 1.17 - 1.14 6941 135 0.87 20.40 1.08 1.01 423.23| | 18: 1.14 - 1.12 6875 142 0.87 20.70 1.08 0.99 380.27| | 19: 1.12 - 1.10 6949 106 0.85 22.11 1.07 0.99 374.57| | 20: 1.10 - 1.08 6884 147 0.84 23.30 1.06 0.98 359.18| | 21: 1.08 - 1.07 6852 152 0.82 25.18 1.06 0.98 367.80| | 22: 1.07 - 1.05 6838 135 0.80 26.98 1.06 0.97 352.43| | 23: 1.05 - 1.03 6829 159 0.79 28.77 1.05 0.97 356.34| | 24: 1.03 - 1.02 6785 133 0.77 30.14 1.05 0.95 339.54| | 25: 1.02 - 1.01 6552 130 0.76 31.60 1.03 0.91 321.52| | 26: 1.01 - 0.99 6767 158 0.74 32.76 1.03 0.89 293.32| | 27: 0.99 - 0.98 6648 131 0.75 32.43 1.04 0.91 277.16| |alpha: min = 0.89 max = 1.08 mean = 1.01| |beta: min = 277.16 max = 34702.16 mean = 2763.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 21.67| |phase err.(test): min = 0.00 max = 89.75 mean = 21.60| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.252 2950 Z= 5.417 Angle : 5.171 18.235 4018 Z= 3.664 Chirality : 0.373 1.169 492 Planarity : 0.030 0.138 512 Dihedral : 13.060 88.093 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.29 % Allowed : 3.23 % Favored : 95.48 % Cbeta Deviations : 32.87 % 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: -2.35 (0.38), residues: 386 helix: -2.46 (0.32), residues: 144 sheet: -1.24 (0.53), residues: 86 loop : -0.49 (0.47), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.015 ARG A 100 TYR 0.096 0.026 TYR B 67 PHE 0.119 0.034 PHE A 164 TRP 0.090 0.032 TRP B 146 HIS 0.087 0.041 HIS A 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2034 r_free= 0.1962 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.299872 | | target function (ml) not normalized (work): 805421.915908 | | target function (ml) not normalized (free): 16542.049859 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2032 0.2034 0.1962 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2032 0.2034 0.1962 n_refl.: 191155 remove outliers: r(all,work,free)=0.2032 0.2034 0.1962 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2032 0.2034 0.1962 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1804 0.1802 0.1889 n_refl.: 191145 remove outliers: r(all,work,free)=0.1802 0.1800 0.1888 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 95.05 93 3 0.4125 402.814 292.747 0.435 0.913 0.301 13.296-10.522 98.02 98 1 0.2466 527.329 514.018 0.789 0.914 0.255 10.503-8.327 98.90 177 3 0.2470 564.205 556.832 0.972 0.914 0.233 8.318-6.595 100.00 360 8 0.2466 414.736 402.807 0.974 0.914 0.190 6.588-5.215 100.00 711 7 0.2215 381.101 365.902 0.958 0.914 0.130 5.214-4.128 98.38 1367 28 0.1487 557.435 550.353 1.075 0.914 0.080 4.126-3.266 94.74 2603 46 0.1348 508.132 498.554 1.141 0.915 0.019 3.266-2.585 99.86 5447 97 0.1447 342.774 338.068 1.117 0.914 0.010 2.585-2.046 97.45 10613 204 0.1401 258.603 254.102 1.125 0.913 0.000 2.046-1.619 99.39 21536 464 0.1608 153.054 149.945 1.144 0.912 0.000 1.619-1.281 98.00 42464 925 0.1929 82.395 80.175 1.127 0.910 0.000 1.281-0.980 96.53 101826 2055 0.2323 44.202 41.678 1.111 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0004 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1888 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 r_work=0.1801 r_free=0.1888 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.338583 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.630321 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1273 0.1483 0.0210 0.035 1.2 11.7 0.0 0.3 0 11.669 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 14.83 2.10 1.119 13.110 575.630 0.019 12.99 15.50 2.50 1.265 13.364 575.630 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.04 15.06 1.42 435 3274 Protein: 5.16 40.49 11.03 1.42 0 2902 Water: 6.32 73.04 29.57 N/A 435 370 Other: 16.19 30.84 23.51 N/A 0 2 Chain A: 5.35 60.50 13.09 N/A 0 1626 Chain B: 5.16 73.04 12.82 N/A 0 1648 Chain S: 11.75 62.63 30.90 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2157 11.95 - 18.73 634 18.73 - 25.52 320 25.52 - 32.31 263 32.31 - 39.10 161 39.10 - 45.89 108 45.89 - 52.68 42 52.68 - 59.47 18 59.47 - 66.25 5 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1550 r_work=0.1299 r_free=0.1545 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1545 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1530 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1530 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015693 | | target function (ls_wunit_k1) not normalized (work): 2939.245050 | | target function (ls_wunit_k1) not normalized (free): 112.673823 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1530 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1470 0.1468 0.1603 n_refl.: 191136 remove outliers: r(all,work,free)=0.1470 0.1468 0.1603 n_refl.: 191136 overall B=0.16 to atoms: r(all,work,free)=0.1494 0.1492 0.1615 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1521 n_refl.: 191136 remove outliers: r(all,work,free)=0.1280 0.1275 0.1521 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 95.05 93 3 0.3661 402.814 368.211 0.458 0.998 0.287 13.296-10.522 98.02 98 1 0.2048 527.329 521.766 0.723 0.999 0.265 10.503-8.327 98.90 177 3 0.1727 564.205 564.990 0.860 0.999 0.213 8.318-6.595 100.00 360 8 0.1760 414.736 411.111 0.876 0.999 0.154 6.588-5.215 100.00 711 7 0.1582 381.101 373.553 0.857 0.999 0.140 5.214-4.128 98.38 1367 28 0.0928 557.435 554.255 0.942 1.000 0.059 4.126-3.266 94.74 2603 46 0.0856 508.132 504.106 1.007 1.000 0.024 3.266-2.585 99.86 5447 97 0.0928 342.774 340.423 0.990 1.000 0.010 2.585-2.046 97.45 10613 204 0.0945 258.603 256.370 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1078 153.054 151.379 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1276 82.395 81.346 1.011 0.999 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.180 0.990 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0367 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1521 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1521 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1521 | n_water=805 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1278 r_free=0.1527 | n_water=798 | time (s): 99.370 (total time: 102.600) Filter (q & B) r_work=0.1278 r_free=0.1527 | n_water=793 | time (s): 5.310 (total time: 107.910) Compute maps r_work=0.1278 r_free=0.1527 | n_water=793 | time (s): 2.340 (total time: 110.250) Filter (map) r_work=0.1300 r_free=0.1522 | n_water=666 | time (s): 5.260 (total time: 115.510) Find peaks r_work=0.1300 r_free=0.1522 | n_water=666 | time (s): 0.820 (total time: 116.330) Add new water r_work=0.1324 r_free=0.1563 | n_water=976 | time (s): 4.050 (total time: 120.380) Refine new water occ: r_work=0.1281 r_free=0.1513 adp: r_work=0.1270 r_free=0.1506 occ: r_work=0.1272 r_free=0.1504 adp: r_work=0.1265 r_free=0.1499 occ: r_work=0.1267 r_free=0.1497 adp: r_work=0.1264 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1264 r_free=0.1498 r_work=0.1264 r_free=0.1498 | n_water=976 | time (s): 84.650 (total time: 205.030) Filter (q & B) r_work=0.1267 r_free=0.1503 | n_water=905 | time (s): 5.540 (total time: 210.570) Filter (dist only) r_work=0.1267 r_free=0.1503 | n_water=904 | time (s): 113.190 (total time: 323.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.591988 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 581.803656 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 0.1253 0.1519 0.0265 0.039 1.1 18.9 0.0 0.3 0 11.296 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.19 2.65 2.055 15.325 581.804 0.014 12.33 15.07 2.74 2.399 15.343 581.804 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 68.27 16.49 1.21 535 3273 Protein: 5.42 39.85 11.03 1.21 0 2902 Water: 6.56 68.27 34.01 N/A 535 369 Other: 16.38 33.12 24.75 N/A 0 2 Chain A: 5.54 57.66 13.07 N/A 0 1625 Chain B: 5.42 68.27 12.85 N/A 0 1648 Chain S: 11.56 66.88 38.10 N/A 535 0 Histogram: Values Number of atoms 5.42 - 11.71 2052 11.71 - 17.99 716 17.99 - 24.27 275 24.27 - 30.56 225 30.56 - 36.84 169 36.84 - 43.13 163 43.13 - 49.41 83 49.41 - 55.70 57 55.70 - 61.98 55 61.98 - 68.27 13 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1507 r_work=0.1233 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 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 = 0.1228 r_free = 0.1501 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.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1501 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013340 | | target function (ls_wunit_k1) not normalized (work): 2498.530624 | | target function (ls_wunit_k1) not normalized (free): 100.533485 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1228 0.1501 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1594 n_refl.: 191136 remove outliers: r(all,work,free)=0.1435 0.1432 0.1594 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1429 0.1593 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1234 0.1508 n_refl.: 191136 remove outliers: r(all,work,free)=0.1240 0.1234 0.1508 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 95.05 93 3 0.3230 402.814 381.427 0.490 0.963 0.277 13.296-10.522 98.02 98 1 0.1848 527.329 519.407 0.760 0.964 0.228 10.503-8.327 98.90 177 3 0.1392 564.205 565.432 0.922 0.964 0.174 8.318-6.595 100.00 360 8 0.1537 414.736 413.297 0.932 0.964 0.145 6.588-5.215 100.00 711 7 0.1347 381.101 376.430 0.913 0.964 0.140 5.214-4.128 98.38 1367 28 0.0822 557.435 556.127 0.995 0.964 0.087 4.126-3.266 94.74 2603 46 0.0755 508.132 505.502 1.058 0.964 0.019 3.266-2.585 99.86 5447 97 0.0858 342.774 341.269 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0896 258.603 256.769 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.647 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1262 82.395 81.352 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.212 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0516 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1509 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1509 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1509 | n_water=904 | time (s): 3.220 (total time: 3.220) Filter (dist) r_work=0.1236 r_free=0.1508 | n_water=901 | time (s): 122.470 (total time: 125.690) Filter (q & B) r_work=0.1236 r_free=0.1509 | n_water=897 | time (s): 4.550 (total time: 130.240) Compute maps r_work=0.1236 r_free=0.1509 | n_water=897 | time (s): 2.140 (total time: 132.380) Filter (map) r_work=0.1275 r_free=0.1510 | n_water=703 | time (s): 4.470 (total time: 136.850) Find peaks r_work=0.1275 r_free=0.1510 | n_water=703 | time (s): 0.670 (total time: 137.520) Add new water r_work=0.1299 r_free=0.1547 | n_water=1020 | time (s): 4.640 (total time: 142.160) Refine new water occ: r_work=0.1255 r_free=0.1512 adp: r_work=0.1256 r_free=0.1514 occ: r_work=0.1252 r_free=0.1510 adp: r_work=0.1252 r_free=0.1511 occ: r_work=0.1249 r_free=0.1509 adp: r_work=0.1248 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1248 r_free=0.1510 r_work=0.1248 r_free=0.1510 | n_water=1020 | time (s): 231.590 (total time: 373.750) Filter (q & B) r_work=0.1253 r_free=0.1510 | n_water=878 | time (s): 4.530 (total time: 378.280) Filter (dist only) r_work=0.1253 r_free=0.1510 | n_water=877 | time (s): 118.970 (total time: 497.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.717226 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 17.128262 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 0.1243 0.1435 0.0192 0.034 1.1 7.0 0.0 0.0 0 0.859 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.43 14.35 1.92 1.945 14.627 17.128 3.942 12.34 13.93 1.59 2.278 14.521 17.128 3.895 Individual atomic B min max mean iso aniso Overall: 5.53 67.82 15.27 1.08 510 3271 Protein: 5.53 36.38 10.76 1.08 0 2902 Water: 6.71 67.82 30.19 N/A 510 367 Other: 13.96 28.55 21.25 N/A 0 2 Chain A: 5.53 56.57 12.80 N/A 0 1625 Chain B: 5.55 67.82 12.52 N/A 0 1646 Chain S: 14.71 62.66 32.02 N/A 510 0 Histogram: Values Number of atoms 5.53 - 11.76 2137 11.76 - 17.99 677 17.99 - 24.22 301 24.22 - 30.45 239 30.45 - 36.67 177 36.67 - 42.90 148 42.90 - 49.13 64 49.13 - 55.36 28 55.36 - 61.59 8 61.59 - 67.82 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1393 r_work=0.1235 r_free=0.1394 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1235 r_free = 0.1394 target_work(ml) = 3.895 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1392 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1392 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.889888 | | target function (ml) not normalized (work): 728556.602667 | | target function (ml) not normalized (free): 15217.682473 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1229 0.1392 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1443 0.1442 0.1491 n_refl.: 191136 remove outliers: r(all,work,free)=0.1443 0.1442 0.1491 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1436 0.1488 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1229 0.1226 0.1381 n_refl.: 191136 remove outliers: r(all,work,free)=0.1228 0.1225 0.1381 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3845 398.895 357.568 0.410 0.946 0.231 13.296-10.522 97.03 97 1 0.2353 529.824 506.120 0.713 0.947 0.210 10.503-8.327 97.80 175 3 0.1968 554.286 557.482 0.881 0.947 0.179 8.318-6.595 100.00 360 8 0.2135 414.736 409.402 0.899 0.947 0.135 6.588-5.215 100.00 711 7 0.1853 381.101 370.394 0.886 0.947 0.120 5.214-4.128 98.38 1367 28 0.1180 557.435 551.492 0.973 0.947 0.090 4.126-3.266 94.74 2603 46 0.1105 508.132 501.122 1.033 0.947 0.014 3.266-2.585 99.86 5447 97 0.1083 342.774 339.122 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0970 258.603 255.642 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0967 153.054 151.447 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.483 1.053 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.318 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1040 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1225 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1381 | n_water=877 | time (s): 2.820 (total time: 2.820) Filter (dist) r_work=0.1226 r_free=0.1384 | n_water=875 | time (s): 105.580 (total time: 108.400) Filter (q & B) r_work=0.1226 r_free=0.1382 | n_water=865 | time (s): 4.090 (total time: 112.490) Compute maps r_work=0.1226 r_free=0.1382 | n_water=865 | time (s): 1.880 (total time: 114.370) Filter (map) r_work=0.1246 r_free=0.1370 | n_water=728 | time (s): 4.640 (total time: 119.010) Find peaks r_work=0.1246 r_free=0.1370 | n_water=728 | time (s): 0.870 (total time: 119.880) Add new water r_work=0.1263 r_free=0.1386 | n_water=975 | time (s): 4.230 (total time: 124.110) Refine new water occ: r_work=0.1215 r_free=0.1351 adp: r_work=0.1207 r_free=0.1346 occ: r_work=0.1205 r_free=0.1348 adp: r_work=0.1205 r_free=0.1347 occ: r_work=0.1203 r_free=0.1349 adp: r_work=0.1203 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1349 r_work=0.1203 r_free=0.1349 | n_water=975 | time (s): 337.140 (total time: 461.250) Filter (q & B) r_work=0.1208 r_free=0.1353 | n_water=869 | time (s): 5.110 (total time: 466.360) Filter (dist only) r_work=0.1209 r_free=0.1351 | n_water=867 | time (s): 115.440 (total time: 581.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.574225 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.139871 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 0.1206 0.1353 0.0147 0.035 1.1 6.3 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.53 1.47 1.842 14.166 15.140 3.871 12.00 13.52 1.52 1.926 14.135 15.140 3.865 Individual atomic B min max mean iso aniso Overall: 5.53 67.44 14.90 1.01 500 3271 Protein: 5.53 33.53 10.69 1.01 0 2902 Water: 5.90 67.44 28.97 N/A 500 367 Other: 13.95 27.68 20.82 N/A 0 2 Chain A: 5.53 55.65 12.69 N/A 0 1625 Chain B: 5.56 67.44 12.44 N/A 0 1646 Chain S: 5.90 60.33 30.18 N/A 500 0 Histogram: Values Number of atoms 5.53 - 11.72 2119 11.72 - 17.91 721 17.91 - 24.10 321 24.10 - 30.29 246 30.29 - 36.48 143 36.48 - 42.67 133 42.67 - 48.86 55 48.86 - 55.05 25 55.05 - 61.25 7 61.25 - 67.44 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1352 r_work=0.1201 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1352 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1346 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863526 | | target function (ml) not normalized (work): 723599.809423 | | target function (ml) not normalized (free): 15129.024222 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1346 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1408 0.1408 0.1465 n_refl.: 191131 remove outliers: r(all,work,free)=0.1408 0.1408 0.1465 n_refl.: 191131 overall B=-0.03 to atoms: r(all,work,free)=0.1401 0.1400 0.1460 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1345 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1345 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3760 357.190 323.893 0.409 0.950 0.241 13.296-10.522 96.04 96 1 0.2332 480.544 457.573 0.713 0.951 0.209 10.503-8.327 97.80 175 3 0.2007 502.025 497.791 0.863 0.952 0.174 8.318-6.595 100.00 360 8 0.2215 375.633 369.461 0.890 0.951 0.131 6.588-5.215 100.00 711 7 0.1940 345.169 334.757 0.881 0.952 0.113 5.214-4.128 98.38 1367 28 0.1210 504.877 499.591 0.969 0.952 0.090 4.126-3.266 94.74 2603 46 0.1123 460.223 453.486 1.030 0.952 0.000 3.266-2.585 99.86 5447 97 0.1080 310.455 307.253 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0933 234.221 231.792 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0914 138.623 137.339 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0990 74.627 73.906 1.048 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.034 38.373 1.035 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1216 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1345 | n_water=867 | time (s): 2.980 (total time: 2.980) Filter (dist) r_work=0.1197 r_free=0.1346 | n_water=866 | time (s): 106.200 (total time: 109.180) Filter (q & B) r_work=0.1197 r_free=0.1347 | n_water=861 | time (s): 4.210 (total time: 113.390) Compute maps r_work=0.1197 r_free=0.1347 | n_water=861 | time (s): 1.880 (total time: 115.270) Filter (map) r_work=0.1216 r_free=0.1352 | n_water=740 | time (s): 4.800 (total time: 120.070) Find peaks r_work=0.1216 r_free=0.1352 | n_water=740 | time (s): 0.720 (total time: 120.790) Add new water r_work=0.1232 r_free=0.1363 | n_water=979 | time (s): 4.610 (total time: 125.400) Refine new water occ: r_work=0.1194 r_free=0.1341 adp: r_work=0.1194 r_free=0.1340 occ: r_work=0.1191 r_free=0.1342 adp: r_work=0.1191 r_free=0.1341 occ: r_work=0.1189 r_free=0.1342 adp: r_work=0.1189 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1342 r_work=0.1189 r_free=0.1342 | n_water=979 | time (s): 257.580 (total time: 382.980) Filter (q & B) r_work=0.1193 r_free=0.1344 | n_water=905 | time (s): 4.450 (total time: 387.430) Filter (dist only) r_work=0.1193 r_free=0.1344 | n_water=904 | time (s): 113.440 (total time: 500.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.599696 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.295494 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 0.035 1.1 7.8 0.0 0.3 0 0.800 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.48 1.53 1.802 14.192 14.295 3.764 12.01 13.52 1.50 1.910 14.151 14.295 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 66.98 15.00 0.95 538 3270 Protein: 5.57 31.85 10.59 0.95 0 2902 Water: 6.03 66.98 29.12 N/A 538 366 Other: 13.87 26.32 20.10 N/A 0 2 Chain A: 5.59 54.55 12.54 N/A 0 1624 Chain B: 5.57 66.98 12.32 N/A 0 1646 Chain S: 6.03 60.27 30.59 N/A 538 0 Histogram: Values Number of atoms 5.57 - 11.71 2143 11.71 - 17.85 716 17.85 - 23.99 313 23.99 - 30.13 244 30.13 - 36.27 157 36.27 - 42.41 138 42.41 - 48.55 63 48.55 - 54.70 27 54.70 - 60.84 6 60.84 - 66.98 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1352 r_work=0.1201 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1352 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1350 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760577 | | target function (ml) not normalized (work): 704310.868509 | | target function (ml) not normalized (free): 14738.120360 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1400 0.1399 0.1475 n_refl.: 191129 remove outliers: r(all,work,free)=0.1400 0.1399 0.1475 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1392 0.1391 0.1470 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1351 n_refl.: 191129 remove outliers: r(all,work,free)=0.1201 0.1198 0.1351 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3636 356.839 309.893 0.394 0.950 0.230 13.296-10.522 96.04 96 1 0.2284 480.544 461.228 0.716 0.952 0.191 10.503-8.327 97.80 175 3 0.2024 502.025 498.155 0.863 0.952 0.170 8.318-6.595 100.00 360 8 0.2171 375.633 370.350 0.890 0.952 0.105 6.588-5.215 100.00 711 7 0.1924 345.169 334.964 0.882 0.952 0.090 5.214-4.128 98.38 1367 28 0.1198 504.877 499.689 0.969 0.952 0.044 4.126-3.266 94.74 2603 46 0.1135 460.223 453.239 1.031 0.953 0.005 3.266-2.585 99.86 5447 97 0.1100 310.455 307.287 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0948 234.221 231.766 1.029 0.953 0.000 2.046-1.619 99.39 21536 464 0.0917 138.623 137.354 1.052 0.953 0.000 1.619-1.281 98.00 42464 925 0.0982 74.627 73.920 1.048 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1656 40.034 38.372 1.033 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1419 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1351 | n_water=904 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1198 r_free=0.1351 | n_water=904 | time (s): 111.590 (total time: 114.100) Filter (q & B) r_work=0.1198 r_free=0.1351 | n_water=894 | time (s): 4.760 (total time: 118.860) Compute maps r_work=0.1198 r_free=0.1351 | n_water=894 | time (s): 1.860 (total time: 120.720) Filter (map) r_work=0.1221 r_free=0.1351 | n_water=758 | time (s): 5.270 (total time: 125.990) Find peaks r_work=0.1221 r_free=0.1351 | n_water=758 | time (s): 0.580 (total time: 126.570) Add new water r_work=0.1231 r_free=0.1364 | n_water=978 | time (s): 4.170 (total time: 130.740) Refine new water occ: r_work=0.1197 r_free=0.1344 adp: r_work=0.1197 r_free=0.1343 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=0.1342 adp: r_work=0.1193 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1342 r_work=0.1193 r_free=0.1342 | n_water=978 | time (s): 204.660 (total time: 335.400) Filter (q & B) r_work=0.1197 r_free=0.1342 | n_water=905 | time (s): 5.120 (total time: 340.520) Filter (dist only) r_work=0.1197 r_free=0.1342 | n_water=904 | time (s): 114.480 (total time: 455.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.488038 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.236678 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1354 0.0153 0.036 1.1 6.5 0.0 0.3 0 0.744 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.54 1.53 1.760 14.039 15.237 3.763 12.00 13.54 1.54 1.879 13.999 15.237 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 65.81 14.85 0.91 538 3270 Protein: 5.59 29.58 10.50 0.91 0 2902 Water: 5.99 65.81 28.80 N/A 538 366 Other: 13.89 23.60 18.75 N/A 0 2 Chain A: 5.61 52.13 12.41 N/A 0 1624 Chain B: 5.59 65.81 12.20 N/A 0 1646 Chain S: 5.99 60.18 30.30 N/A 538 0 Histogram: Values Number of atoms 5.59 - 11.61 2117 11.61 - 17.64 767 17.64 - 23.66 288 23.66 - 29.68 235 29.68 - 35.70 164 35.70 - 41.72 131 41.72 - 47.74 68 47.74 - 53.77 29 53.77 - 59.79 6 59.79 - 65.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1354 r_work=0.1201 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757202 | | target function (ml) not normalized (work): 703675.051897 | | target function (ml) not normalized (free): 14736.910305 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1392 0.1390 0.1483 n_refl.: 191128 remove outliers: r(all,work,free)=0.1392 0.1390 0.1483 n_refl.: 191128 overall B=-0.23 to atoms: r(all,work,free)=0.1357 0.1355 0.1460 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1353 n_refl.: 191128 remove outliers: r(all,work,free)=0.1200 0.1197 0.1353 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3672 356.839 328.959 0.418 0.953 0.218 13.296-10.522 96.04 96 1 0.2305 480.544 461.764 0.727 0.954 0.177 10.503-8.327 97.80 175 3 0.2089 502.025 497.955 0.883 0.955 0.156 8.318-6.595 100.00 360 8 0.2165 375.633 370.526 0.906 0.954 0.095 6.588-5.215 100.00 711 7 0.1946 345.169 335.017 0.900 0.954 0.080 5.214-4.128 98.38 1367 28 0.1217 504.877 499.515 0.993 0.955 0.070 4.126-3.266 94.74 2603 46 0.1151 460.223 453.033 1.054 0.955 0.000 3.266-2.585 99.86 5447 97 0.1110 310.455 307.184 1.038 0.954 0.000 2.585-2.046 97.45 10613 204 0.0952 234.221 231.675 1.045 0.954 0.000 2.046-1.619 99.39 21536 464 0.0912 138.623 137.324 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0969 74.627 73.923 1.051 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1648 40.034 38.378 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=0.0509 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1353 | n_water=904 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1197 r_free=0.1354 | n_water=903 | time (s): 113.100 (total time: 115.760) Filter (q & B) r_work=0.1198 r_free=0.1354 | n_water=890 | time (s): 5.260 (total time: 121.020) Compute maps r_work=0.1198 r_free=0.1354 | n_water=890 | time (s): 1.770 (total time: 122.790) Filter (map) r_work=0.1221 r_free=0.1358 | n_water=765 | time (s): 4.810 (total time: 127.600) Find peaks r_work=0.1221 r_free=0.1358 | n_water=765 | time (s): 0.650 (total time: 128.250) Add new water r_work=0.1232 r_free=0.1372 | n_water=993 | time (s): 4.370 (total time: 132.620) Refine new water occ: r_work=0.1196 r_free=0.1342 adp: r_work=0.1196 r_free=0.1342 occ: r_work=0.1194 r_free=0.1342 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1343 adp: r_work=0.1192 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1343 r_work=0.1192 r_free=0.1343 | n_water=993 | time (s): 231.540 (total time: 364.160) Filter (q & B) r_work=0.1196 r_free=0.1349 | n_water=913 | time (s): 4.540 (total time: 368.700) Filter (dist only) r_work=0.1196 r_free=0.1349 | n_water=912 | time (s): 120.650 (total time: 489.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.546105 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.285624 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 0.1354 0.0155 0.037 1.1 6.6 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.54 1.55 1.724 13.725 14.286 3.759 12.02 13.57 1.55 1.774 13.704 14.286 3.758 Individual atomic B min max mean iso aniso Overall: 5.39 64.61 14.58 0.88 546 3270 Protein: 5.39 28.48 10.25 0.88 0 2902 Water: 5.84 64.61 28.34 N/A 546 366 Other: 13.70 22.21 17.96 N/A 0 2 Chain A: 5.44 51.53 12.12 N/A 0 1624 Chain B: 5.39 64.61 11.93 N/A 0 1646 Chain S: 5.84 59.88 29.86 N/A 546 0 Histogram: Values Number of atoms 5.39 - 11.32 2096 11.32 - 17.24 788 17.24 - 23.16 285 23.16 - 29.08 233 29.08 - 35.00 178 35.00 - 40.92 126 40.92 - 46.85 68 46.85 - 52.77 33 52.77 - 58.69 6 58.69 - 64.61 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1357 r_work=0.1202 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1357 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1359 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757033 | | target function (ml) not normalized (work): 703643.516613 | | target function (ml) not normalized (free): 14740.298422 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1359 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1365 0.1363 0.1473 n_refl.: 191128 remove outliers: r(all,work,free)=0.1365 0.1363 0.1473 n_refl.: 191128 overall B=0.06 to atoms: r(all,work,free)=0.1372 0.1370 0.1478 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1350 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1350 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3529 356.839 329.551 0.414 0.995 0.231 13.296-10.522 96.04 96 1 0.2341 480.544 461.026 0.694 0.997 0.160 10.503-8.327 97.80 175 3 0.2138 502.025 496.640 0.849 0.997 0.130 8.318-6.595 100.00 360 8 0.2172 375.633 369.628 0.873 0.997 0.096 6.588-5.215 100.00 711 7 0.1983 345.169 334.220 0.869 0.998 0.077 5.214-4.128 98.38 1367 28 0.1225 504.877 498.829 0.959 0.999 0.060 4.126-3.266 94.74 2603 46 0.1169 460.223 452.468 1.018 1.000 0.000 3.266-2.585 99.86 5447 97 0.1117 310.455 306.916 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0958 234.221 231.529 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0908 138.623 137.255 1.025 1.005 0.000 1.619-1.281 98.00 42464 925 0.0949 74.627 73.965 1.014 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.034 38.347 0.980 1.017 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0616 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1350 | n_water=912 | time (s): 3.320 (total time: 3.320) Filter (dist) r_work=0.1191 r_free=0.1350 | n_water=912 | time (s): 111.310 (total time: 114.630) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=900 | time (s): 4.310 (total time: 118.940) Compute maps r_work=0.1192 r_free=0.1349 | n_water=900 | time (s): 1.800 (total time: 120.740) Filter (map) r_work=0.1214 r_free=0.1350 | n_water=777 | time (s): 4.180 (total time: 124.920) Find peaks r_work=0.1214 r_free=0.1350 | n_water=777 | time (s): 0.610 (total time: 125.530) Add new water r_work=0.1222 r_free=0.1362 | n_water=984 | time (s): 4.090 (total time: 129.620) Refine new water occ: r_work=0.1190 r_free=0.1335 adp: r_work=0.1190 r_free=0.1335 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1335 occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1186 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1335 r_work=0.1186 r_free=0.1335 | n_water=984 | time (s): 238.350 (total time: 367.970) Filter (q & B) r_work=0.1191 r_free=0.1347 | n_water=909 | time (s): 5.020 (total time: 372.990) Filter (dist only) r_work=0.1191 r_free=0.1346 | n_water=908 | time (s): 117.150 (total time: 490.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.475705 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.526340 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 0.0154 0.038 1.1 5.5 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 1.54 1.678 13.675 13.526 3.757 11.97 13.53 1.56 1.716 13.665 13.526 3.756 Individual atomic B min max mean iso aniso Overall: 5.49 63.54 14.53 0.86 542 3270 Protein: 5.49 27.83 10.29 0.86 0 2902 Water: 5.93 63.54 28.06 N/A 542 366 Other: 13.76 21.87 17.82 N/A 0 2 Chain A: 5.54 51.15 12.13 N/A 0 1624 Chain B: 5.49 63.54 11.96 N/A 0 1646 Chain S: 5.93 59.86 29.54 N/A 542 0 Histogram: Values Number of atoms 5.49 - 11.30 2067 11.30 - 17.10 818 17.10 - 22.91 282 22.91 - 28.71 228 28.71 - 34.52 185 34.52 - 40.32 117 40.32 - 46.13 70 46.13 - 51.93 36 51.93 - 57.73 6 57.73 - 63.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1353 r_work=0.1197 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1353 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1353 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755885 | | target function (ml) not normalized (work): 703428.448831 | | target function (ml) not normalized (free): 14733.304784 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1353 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1384 0.1382 0.1486 n_refl.: 191128 remove outliers: r(all,work,free)=0.1384 0.1382 0.1486 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1386 0.1384 0.1487 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191128 remove outliers: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3618 356.839 327.871 0.415 0.974 0.223 13.296-10.522 96.04 96 1 0.2345 480.544 461.413 0.706 0.975 0.155 10.503-8.327 97.80 175 3 0.2178 502.025 496.199 0.864 0.976 0.127 8.318-6.595 100.00 360 8 0.2211 375.633 369.302 0.888 0.976 0.095 6.588-5.215 100.00 711 7 0.1993 345.169 334.114 0.885 0.976 0.077 5.214-4.128 98.38 1367 28 0.1241 504.877 498.892 0.978 0.977 0.029 4.126-3.266 94.74 2603 46 0.1179 460.223 452.265 1.041 0.978 0.000 3.266-2.585 99.86 5447 97 0.1124 310.455 306.925 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0964 234.221 231.513 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0912 138.623 137.263 1.049 0.984 0.000 1.619-1.281 98.00 42464 925 0.0947 74.627 73.972 1.039 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.034 38.331 1.008 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0189 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1351 | n_water=908 | time (s): 3.220 (total time: 3.220) Filter (dist) r_work=0.1195 r_free=0.1351 | n_water=907 | time (s): 114.770 (total time: 117.990) Filter (q & B) r_work=0.1196 r_free=0.1347 | n_water=897 | time (s): 4.530 (total time: 122.520) Compute maps r_work=0.1196 r_free=0.1347 | n_water=897 | time (s): 1.940 (total time: 124.460) Filter (map) r_work=0.1218 r_free=0.1350 | n_water=774 | time (s): 4.980 (total time: 129.440) Find peaks r_work=0.1218 r_free=0.1350 | n_water=774 | time (s): 0.530 (total time: 129.970) Add new water r_work=0.1226 r_free=0.1361 | n_water=1000 | time (s): 3.690 (total time: 133.660) Refine new water occ: r_work=0.1192 r_free=0.1335 adp: r_work=0.1192 r_free=0.1335 occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1190 r_free=0.1335 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1335 r_work=0.1188 r_free=0.1335 | n_water=1000 | time (s): 173.840 (total time: 307.500) Filter (q & B) r_work=0.1193 r_free=0.1345 | n_water=919 | time (s): 4.550 (total time: 312.050) Filter (dist only) r_work=0.1193 r_free=0.1345 | n_water=917 | time (s): 115.740 (total time: 427.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.556200 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.294272 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 0.1350 0.0155 0.039 1.1 6.7 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.50 1.55 1.672 13.711 14.294 3.756 11.93 13.52 1.59 1.677 13.707 14.294 3.753 Individual atomic B min max mean iso aniso Overall: 5.55 62.42 14.60 0.87 551 3270 Protein: 5.55 28.02 10.32 0.87 0 2902 Water: 5.97 62.42 28.13 N/A 551 366 Other: 13.82 22.06 17.94 N/A 0 2 Chain A: 5.60 50.85 12.13 N/A 0 1624 Chain B: 5.55 62.42 11.96 N/A 0 1646 Chain S: 5.97 59.74 29.79 N/A 551 0 Histogram: Values Number of atoms 5.55 - 11.24 2044 11.24 - 16.93 834 16.93 - 22.61 282 22.61 - 28.30 217 28.30 - 33.99 186 33.99 - 39.67 124 39.67 - 45.36 84 45.36 - 51.05 37 51.05 - 56.73 9 56.73 - 62.42 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1352 r_work=0.1194 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1352 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752555 | | target function (ml) not normalized (work): 702804.724216 | | target function (ml) not normalized (free): 14728.204547 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1494 n_refl.: 191128 remove outliers: r(all,work,free)=0.1391 0.1389 0.1494 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1390 0.1388 0.1494 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1349 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1349 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3669 356.839 326.350 0.394 0.994 0.205 13.296-10.522 96.04 96 1 0.2357 480.544 461.096 0.685 0.996 0.139 10.503-8.327 97.80 175 3 0.2175 502.025 496.791 0.844 0.996 0.110 8.318-6.595 100.00 360 8 0.2193 375.633 369.228 0.868 0.996 0.085 6.588-5.215 100.00 711 7 0.1994 345.169 334.046 0.865 0.997 0.067 5.214-4.128 98.38 1367 28 0.1240 504.877 498.893 0.958 0.998 0.024 4.126-3.266 94.74 2603 46 0.1178 460.223 452.275 1.020 0.999 0.000 3.266-2.585 99.86 5447 97 0.1128 310.455 306.912 1.004 1.000 0.000 2.585-2.046 97.45 10613 204 0.0959 234.221 231.534 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0906 138.623 137.265 1.028 1.007 0.000 1.619-1.281 98.00 42464 925 0.0939 74.627 73.982 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.034 38.326 0.989 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0103 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1349 After: r_work=0.1192 r_free=0.1350 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1350 | n_water=917 | time (s): 3.140 (total time: 3.140) Filter (dist) r_work=0.1192 r_free=0.1350 | n_water=917 | time (s): 118.140 (total time: 121.280) Filter (q & B) r_work=0.1193 r_free=0.1348 | n_water=905 | time (s): 4.770 (total time: 126.050) Compute maps r_work=0.1193 r_free=0.1348 | n_water=905 | time (s): 2.280 (total time: 128.330) Filter (map) r_work=0.1217 r_free=0.1360 | n_water=784 | time (s): 5.190 (total time: 133.520) Find peaks r_work=0.1217 r_free=0.1360 | n_water=784 | time (s): 0.680 (total time: 134.200) Add new water r_work=0.1223 r_free=0.1368 | n_water=993 | time (s): 4.730 (total time: 138.930) Refine new water occ: r_work=0.1190 r_free=0.1337 adp: r_work=0.1190 r_free=0.1337 occ: r_work=0.1188 r_free=0.1337 adp: r_work=0.1188 r_free=0.1337 occ: r_work=0.1187 r_free=0.1338 adp: r_work=0.1187 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1338 r_work=0.1187 r_free=0.1338 | n_water=993 | time (s): 234.080 (total time: 373.010) Filter (q & B) r_work=0.1191 r_free=0.1345 | n_water=917 | time (s): 5.010 (total time: 378.020) Filter (dist only) r_work=0.1192 r_free=0.1344 | n_water=915 | time (s): 117.590 (total time: 495.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.511605 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.053926 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1349 0.0154 0.039 1.1 8.7 0.0 0.3 0 0.756 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.49 1.54 1.675 13.705 14.054 3.755 11.95 13.51 1.56 1.669 13.707 14.054 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 62.14 14.59 0.86 549 3270 Protein: 5.56 27.92 10.34 0.86 0 2902 Water: 6.00 62.14 28.05 N/A 549 366 Other: 13.83 22.07 17.95 N/A 0 2 Chain A: 5.63 50.79 12.12 N/A 0 1624 Chain B: 5.56 62.14 11.96 N/A 0 1646 Chain S: 6.00 59.68 29.76 N/A 549 0 Histogram: Values Number of atoms 5.56 - 11.22 2034 11.22 - 16.88 840 16.88 - 22.53 288 22.53 - 28.19 218 28.19 - 33.85 184 33.85 - 39.51 121 39.51 - 45.17 84 45.17 - 50.82 36 50.82 - 56.48 10 56.48 - 62.14 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1351 r_work=0.1195 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1351 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1351 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754290 | | target function (ml) not normalized (work): 703129.778644 | | target function (ml) not normalized (free): 14729.770612 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1367 0.1454 5.6918 5.7775| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1346 5.0831 5.1831| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1184 4.6596 4.7435| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1036 4.3941 4.5628| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0993 4.1513 4.2532| | 6: 1.72 - 1.62 0.99 7102 142 0.0895 0.1067 3.9459 4.0674| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0965 3.8001 3.9371| | 8: 1.54 - 1.47 0.96 6798 152 0.0889 0.1305 3.6995 3.9054| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1131 3.6191 3.7534| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1180 3.5547 3.6729| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1124 3.4821 3.5846| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1131 3.4564 3.5757| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1248 3.4341 3.5621| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1580 3.4303 3.6686| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1244 3.4468 3.4911| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1549 3.4645 3.659| | 17: 1.17 - 1.14 0.98 6940 135 0.1300 0.1228 3.434 3.4441| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1700 3.4389 3.5329| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1767 3.4209 3.6018| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1578 3.4112 3.439| | 21: 1.08 - 1.07 0.97 6852 152 0.1731 0.2140 3.419 3.5059| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1954 3.4134 3.4149| | 23: 1.05 - 1.03 0.97 6827 159 0.2122 0.2021 3.4339 3.4853| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2268 3.4361 3.5136| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2517 3.4493 3.5251| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2878 3.416 3.424| | 27: 0.99 - 0.98 0.94 6647 131 0.3041 0.2811 3.4683 3.3962| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.71 1.00 0.96 11333.14| | 2: 2.94 - 2.33 7339 128 0.93 12.88 0.99 0.95 5188.46| | 3: 2.33 - 2.04 6939 150 0.96 7.71 1.01 0.95 1716.56| | 4: 2.04 - 1.85 7170 155 0.96 7.66 1.00 0.95 1008.43| | 5: 1.85 - 1.72 7113 159 0.96 8.10 1.00 0.96 635.18| | 6: 1.72 - 1.62 7102 142 0.96 8.01 1.00 0.96 443.23| | 7: 1.62 - 1.54 7104 148 0.96 8.17 1.01 0.97 337.88| | 8: 1.54 - 1.47 6798 152 0.96 8.27 1.01 0.97 279.41| | 9: 1.47 - 1.41 6938 155 0.96 8.45 1.00 0.98 230.21| | 10: 1.41 - 1.36 7022 150 0.96 8.85 1.00 0.97 201.25| | 11: 1.36 - 1.32 6997 151 0.96 8.85 0.99 0.96 173.30| | 12: 1.32 - 1.28 6975 149 0.96 8.90 0.98 0.95 158.88| | 13: 1.28 - 1.25 6907 166 0.96 9.44 1.01 0.96 156.27| | 14: 1.25 - 1.22 7015 112 0.95 10.59 1.01 0.97 161.24| | 15: 1.22 - 1.19 6956 137 0.95 11.17 1.01 0.98 165.42| | 16: 1.19 - 1.17 6604 132 0.95 11.39 1.01 0.96 159.79| | 17: 1.17 - 1.14 6940 135 0.94 12.27 1.01 0.96 154.19| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.95 148.36| | 19: 1.12 - 1.10 6948 106 0.93 14.21 1.00 0.95 152.18| | 20: 1.10 - 1.08 6884 147 0.92 15.29 1.00 0.94 151.39| | 21: 1.08 - 1.07 6852 152 0.91 16.71 1.00 0.93 154.19| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.93 155.42| | 23: 1.05 - 1.03 6827 159 0.87 20.53 0.99 0.92 165.19| | 24: 1.03 - 1.02 6784 133 0.85 23.21 0.99 0.93 179.76| | 25: 1.02 - 1.01 6552 130 0.83 25.20 0.98 0.90 182.73| | 26: 1.01 - 0.99 6767 158 0.81 26.66 0.98 0.88 177.22| | 27: 0.99 - 0.98 6647 131 0.82 26.34 0.99 0.87 161.69| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.36 max = 11333.14 mean = 933.75| |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 = 88.27 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1499 n_refl.: 191128 remove outliers: r(all,work,free)=0.1400 0.1398 0.1499 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1391 0.1389 0.1493 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1350 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1350 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3631 356.839 326.063 0.393 0.975 0.209 13.296-10.522 96.04 96 1 0.2359 480.544 460.960 0.678 0.976 0.137 10.503-8.327 97.80 175 3 0.2168 502.025 496.465 0.838 0.976 0.107 8.318-6.595 100.00 360 8 0.2187 375.633 369.282 0.865 0.976 0.083 6.588-5.215 100.00 711 7 0.1986 345.169 334.344 0.861 0.977 0.067 5.214-4.128 98.38 1367 28 0.1247 504.877 498.857 0.953 0.978 0.024 4.126-3.266 94.74 2603 46 0.1177 460.223 452.149 1.016 0.979 0.000 3.266-2.585 99.86 5447 97 0.1123 310.455 306.988 1.000 0.981 0.000 2.585-2.046 97.45 10613 204 0.0965 234.221 231.538 1.005 0.983 0.000 2.046-1.619 99.39 21536 464 0.0910 138.623 137.265 1.021 0.988 0.000 1.619-1.281 98.00 42464 925 0.0944 74.627 73.980 1.010 0.995 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.034 38.319 0.977 1.009 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0125 ================= 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 : 0.2034 0.1962 0.080 5.171 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1888 0.080 5.171 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1888 0.080 5.171 5.2 78.0 14.6 805 0.000 1_nqh: 0.1801 0.1888 0.080 5.171 5.2 78.0 14.6 805 0.002 1_weight: 0.1801 0.1888 0.080 5.171 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1273 0.1483 0.035 1.169 5.2 78.0 14.6 805 0.142 1_adp: 0.1300 0.1550 0.035 1.169 5.2 73.0 15.1 805 0.142 1_regHadp: 0.1299 0.1545 0.035 1.169 5.2 73.0 15.1 805 0.142 1_occ: 0.1283 0.1530 0.035 1.169 5.2 73.0 15.1 805 0.142 2_bss: 0.1275 0.1521 0.035 1.169 5.3 73.2 15.2 805 0.142 2_settarget: 0.1275 0.1521 0.035 1.169 5.3 73.2 15.2 805 0.142 2_updatecdl: 0.1275 0.1521 0.035 1.184 5.3 73.2 15.2 805 0.142 2_nqh: 0.1275 0.1521 0.035 1.184 5.3 73.2 15.2 805 0.142 2_sol: 0.1267 0.1503 0.035 1.184 5.3 73.2 16.5 904 n/a 2_weight: 0.1267 0.1503 0.035 1.184 5.3 73.2 16.5 904 n/a 2_xyzrec: 0.1253 0.1519 0.039 1.135 5.3 73.2 16.5 904 n/a 2_adp: 0.1233 0.1507 0.039 1.135 5.4 68.3 16.5 904 n/a 2_regHadp: 0.1233 0.1509 0.039 1.135 5.4 68.3 16.5 904 n/a 2_occ: 0.1228 0.1501 0.039 1.135 5.4 68.3 16.5 904 n/a 3_bss: 0.1234 0.1509 0.039 1.135 5.4 68.2 16.5 904 n/a 3_settarget: 0.1234 0.1509 0.039 1.135 5.4 68.2 16.5 904 n/a 3_updatecdl: 0.1234 0.1509 0.039 1.141 5.4 68.2 16.5 904 n/a 3_nqh: 0.1234 0.1509 0.039 1.141 5.4 68.2 16.5 904 n/a 3_sol: 0.1253 0.1510 0.039 1.141 5.4 68.2 15.5 877 n/a 3_weight: 0.1253 0.1510 0.039 1.141 5.4 68.2 15.5 877 n/a 3_xyzrec: 0.1243 0.1435 0.034 1.097 5.4 68.2 15.5 877 n/a 3_adp: 0.1234 0.1393 0.034 1.097 5.5 67.8 15.3 877 n/a 3_regHadp: 0.1235 0.1394 0.034 1.097 5.5 67.8 15.3 877 n/a 3_occ: 0.1229 0.1392 0.034 1.097 5.5 67.8 15.3 877 n/a 4_bss: 0.1225 0.1381 0.034 1.097 5.5 67.8 15.2 877 n/a 4_settarget: 0.1225 0.1381 0.034 1.097 5.5 67.8 15.2 877 n/a 4_updatecdl: 0.1225 0.1381 0.034 1.099 5.5 67.8 15.2 877 n/a 4_nqh: 0.1225 0.1381 0.034 1.099 5.5 67.8 15.2 877 n/a 4_sol: 0.1209 0.1351 0.034 1.099 5.5 67.8 15.0 867 n/a 4_weight: 0.1209 0.1351 0.034 1.099 5.5 67.8 15.0 867 n/a 4_xyzrec: 0.1206 0.1353 0.035 1.117 5.5 67.8 15.0 867 n/a 4_adp: 0.1200 0.1352 0.035 1.117 5.5 67.4 14.9 867 n/a 4_regHadp: 0.1201 0.1352 0.035 1.117 5.5 67.4 14.9 867 n/a 4_occ: 0.1198 0.1346 0.035 1.117 5.5 67.4 14.9 867 n/a 5_bss: 0.1197 0.1345 0.035 1.117 5.5 67.4 14.9 867 n/a 5_settarget: 0.1197 0.1345 0.035 1.117 5.5 67.4 14.9 867 n/a 5_updatecdl: 0.1197 0.1345 0.035 1.117 5.5 67.4 14.9 867 n/a 5_nqh: 0.1197 0.1345 0.035 1.117 5.5 67.4 14.9 867 n/a 5_sol: 0.1193 0.1344 0.035 1.117 5.5 67.4 15.1 904 n/a 5_weight: 0.1193 0.1344 0.035 1.117 5.5 67.4 15.1 904 n/a 5_xyzrec: 0.1195 0.1348 0.035 1.125 5.5 67.4 15.1 904 n/a 5_adp: 0.1201 0.1352 0.035 1.125 5.6 67.0 15.0 904 n/a 5_regHadp: 0.1201 0.1352 0.035 1.125 5.6 67.0 15.0 904 n/a 5_occ: 0.1199 0.1350 0.035 1.125 5.6 67.0 15.0 904 n/a 6_bss: 0.1198 0.1351 0.035 1.125 5.5 66.9 15.0 904 n/a 6_settarget: 0.1198 0.1351 0.035 1.125 5.5 66.9 15.0 904 n/a 6_updatecdl: 0.1198 0.1351 0.035 1.125 5.5 66.9 15.0 904 n/a 6_nqh: 0.1198 0.1351 0.035 1.125 5.5 66.9 15.0 904 n/a 6_sol: 0.1197 0.1342 0.035 1.125 5.5 66.9 14.9 904 n/a 6_weight: 0.1197 0.1342 0.035 1.125 5.5 66.9 14.9 904 n/a 6_xyzrec: 0.1201 0.1354 0.036 1.119 5.5 66.9 14.9 904 n/a 6_adp: 0.1200 0.1354 0.036 1.119 5.6 65.8 14.8 904 n/a 6_regHadp: 0.1201 0.1355 0.036 1.119 5.6 65.8 14.8 904 n/a 6_occ: 0.1198 0.1355 0.036 1.119 5.6 65.8 14.8 904 n/a 7_bss: 0.1197 0.1353 0.036 1.119 5.4 65.6 14.6 904 n/a 7_settarget: 0.1197 0.1353 0.036 1.119 5.4 65.6 14.6 904 n/a 7_updatecdl: 0.1197 0.1353 0.036 1.119 5.4 65.6 14.6 904 n/a 7_nqh: 0.1197 0.1353 0.036 1.119 5.4 65.6 14.6 904 n/a 7_sol: 0.1196 0.1349 0.036 1.119 5.4 65.6 14.6 912 n/a 7_weight: 0.1196 0.1349 0.036 1.119 5.4 65.6 14.6 912 n/a 7_xyzrec: 0.1199 0.1354 0.037 1.118 5.4 65.6 14.6 912 n/a 7_adp: 0.1202 0.1357 0.037 1.118 5.4 64.6 14.6 912 n/a 7_regHadp: 0.1202 0.1357 0.037 1.118 5.4 64.6 14.6 912 n/a 7_occ: 0.1200 0.1359 0.037 1.118 5.4 64.6 14.6 912 n/a 8_bss: 0.1191 0.1350 0.037 1.118 5.5 64.7 14.6 912 n/a 8_settarget: 0.1191 0.1350 0.037 1.118 5.5 64.7 14.6 912 n/a 8_updatecdl: 0.1191 0.1350 0.037 1.118 5.5 64.7 14.6 912 n/a 8_nqh: 0.1191 0.1350 0.037 1.118 5.5 64.7 14.6 912 n/a 8_sol: 0.1191 0.1346 0.037 1.118 5.5 64.7 14.5 908 n/a 8_weight: 0.1191 0.1346 0.037 1.118 5.5 64.7 14.5 908 n/a 8_xyzrec: 0.1195 0.1348 0.038 1.112 5.5 64.7 14.5 908 n/a 8_adp: 0.1197 0.1353 0.038 1.112 5.5 63.5 14.5 908 n/a 8_regHadp: 0.1197 0.1353 0.038 1.112 5.5 63.5 14.5 908 n/a 8_occ: 0.1196 0.1353 0.038 1.112 5.5 63.5 14.5 908 n/a 9_bss: 0.1195 0.1351 0.038 1.112 5.5 63.6 14.5 908 n/a 9_settarget: 0.1195 0.1351 0.038 1.112 5.5 63.6 14.5 908 n/a 9_updatecdl: 0.1195 0.1351 0.038 1.112 5.5 63.6 14.5 908 n/a 9_nqh: 0.1195 0.1351 0.038 1.112 5.5 63.6 14.5 908 n/a 9_sol: 0.1193 0.1345 0.038 1.112 5.5 63.6 14.6 917 n/a 9_weight: 0.1193 0.1345 0.038 1.112 5.5 63.6 14.6 917 n/a 9_xyzrec: 0.1195 0.1350 0.039 1.108 5.5 63.6 14.6 917 n/a 9_adp: 0.1193 0.1352 0.039 1.108 5.6 62.4 14.6 917 n/a 9_regHadp: 0.1194 0.1352 0.039 1.108 5.6 62.4 14.6 917 n/a 9_occ: 0.1192 0.1350 0.039 1.108 5.6 62.4 14.6 917 n/a 10_bss: 0.1191 0.1349 0.039 1.108 5.5 62.4 14.6 917 n/a 10_settarget: 0.1191 0.1349 0.039 1.108 5.5 62.4 14.6 917 n/a 10_updatecdl: 0.1191 0.1349 0.039 1.108 5.5 62.4 14.6 917 n/a 10_setrh: 0.1192 0.1350 0.039 1.108 5.5 62.4 14.6 917 n/a 10_nqh: 0.1192 0.1350 0.039 1.108 5.5 62.4 14.6 917 n/a 10_sol: 0.1192 0.1344 0.039 1.108 5.5 62.4 14.6 915 n/a 10_weight: 0.1192 0.1344 0.039 1.108 5.5 62.4 14.6 915 n/a 10_xyzrec: 0.1194 0.1349 0.039 1.144 5.5 62.4 14.6 915 n/a 10_adp: 0.1195 0.1351 0.039 1.144 5.6 62.1 14.6 915 n/a 10_regHadp: 0.1195 0.1351 0.039 1.144 5.6 62.1 14.6 915 n/a 10_occ: 0.1194 0.1351 0.039 1.144 5.6 62.1 14.6 915 n/a end: 0.1194 0.1350 0.039 1.144 5.5 62.1 14.5 915 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8988844_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8988844_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3400 Refinement macro-cycles (run) : 11999.8400 Write final files (write_after_run_outputs) : 152.4100 Total : 12158.5900 Total CPU time: 3.39 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:39:45 PST -0800 (1736735985.16 s) Start R-work = 0.1800, R-free = 0.1888 Final R-work = 0.1194, R-free = 0.1350 =============================================================================== Job complete usr+sys time: 12443.94 seconds wall clock time: 208 minutes 21.57 seconds (12501.57 seconds total)