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_7309525.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7309525.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7309525.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 2 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: 2.50, per 1000 atoms: 0.37 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: 2.659 distance_ideal: 2.720 ideal - model: 0.061 slack: 0.000 delta_slack: 0.061 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: 2.690 distance_ideal: 2.710 ideal - model: 0.020 slack: 0.000 delta_slack: 0.020 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: 0.71 Conformation dependent library (CDL) restraints added in 146.7 milliseconds Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.72 - 0.95: 219 0.95 - 1.19: 2573 1.19 - 1.42: 1427 1.42 - 1.65: 1582 1.65 - 1.88: 133 Bond restraints: 5934 Sorted by residual: bond pdb=" N GLN B 156 " pdb=" H GLN B 156 " ideal model delta sigma weight residual 0.860 1.289 -0.429 2.00e-02 2.50e+03 4.61e+02 bond pdb=" CG HIS A 116 " pdb=" CD2 HIS A 116 " ideal model delta sigma weight residual 1.354 1.139 0.215 1.10e-02 8.26e+03 3.82e+02 bond pdb=" CA ILE A 101 " pdb=" C ILE A 101 " ideal model delta sigma weight residual 1.521 1.284 0.237 1.22e-02 6.72e+03 3.78e+02 bond pdb=" N ALA A 10 " pdb=" CA ALA A 10 " ideal model delta sigma weight residual 1.453 1.610 -0.157 8.30e-03 1.45e+04 3.57e+02 bond pdb=" C CYS B 47 " pdb=" N SER B 48 " ideal model delta sigma weight residual 1.335 1.577 -0.241 1.32e-02 5.74e+03 3.35e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.14: 5663 4.14 - 8.27: 3556 8.27 - 12.40: 1289 12.40 - 16.54: 275 16.54 - 20.67: 27 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA ILE A 169 " pdb=" C ILE A 169 " pdb=" N ASP A 170 " ideal model delta sigma weight residual 117.28 133.50 -16.22 1.16e+00 7.43e-01 1.96e+02 angle pdb=" O PHE B 127 " pdb=" C PHE B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 121.31 109.16 12.15 8.70e-01 1.32e+00 1.95e+02 angle pdb=" CA LYS B 177 " pdb=" C LYS B 177 " pdb=" O LYS B 177 " ideal model delta sigma weight residual 120.42 105.98 14.44 1.06e+00 8.90e-01 1.85e+02 angle pdb=" CA ASP B 147 " pdb=" CB ASP B 147 " pdb=" CG ASP B 147 " ideal model delta sigma weight residual 112.60 99.01 13.59 1.00e+00 1.00e+00 1.85e+02 angle pdb=" O ALA A 136 " pdb=" C ALA A 136 " pdb=" N GLU A 137 " ideal model delta sigma weight residual 122.12 136.19 -14.07 1.06e+00 8.90e-01 1.76e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 1866 17.97 - 35.95: 121 35.95 - 53.92: 43 53.92 - 71.89: 17 71.89 - 89.86: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 154.57 25.43 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA TYR B 192 " pdb=" C TYR B 192 " pdb=" N ASN B 193 " pdb=" CA ASN B 193 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ALA A 57 " pdb=" C ALA A 57 " pdb=" N PRO A 58 " pdb=" CA PRO A 58 " ideal model delta harmonic sigma weight residual 180.00 159.35 20.65 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.239: 234 0.239 - 0.478: 150 0.478 - 0.716: 85 0.716 - 0.954: 21 0.954 - 1.193: 2 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ALA B 35 " pdb=" N ALA B 35 " pdb=" C ALA B 35 " pdb=" CB ALA B 35 " both_signs ideal model delta sigma weight residual False 2.48 3.68 -1.19 2.00e-01 2.50e+01 3.56e+01 chirality pdb=" CA SER B 98 " pdb=" N SER B 98 " pdb=" C SER B 98 " pdb=" CB SER B 98 " both_signs ideal model delta sigma weight residual False 2.51 1.52 0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA ASP A 56 " pdb=" N ASP A 56 " pdb=" C ASP A 56 " pdb=" CB ASP A 56 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.25e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " 0.039 2.00e-02 2.50e+03 6.78e-02 1.84e+02 pdb=" CG TRP B 139 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " -0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.111 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " 0.090 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " 0.062 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " -0.108 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " 0.100 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.046 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " -0.075 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.087 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " -0.066 2.00e-02 2.50e+03 6.30e-02 1.59e+02 pdb=" CG TRP A 146 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.100 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.072 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.117 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.056 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.077 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.010 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " 0.064 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.053 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " 0.053 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 95 " -0.104 2.00e-02 2.50e+03 7.11e-02 1.51e+02 pdb=" CG PHE B 95 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE B 95 " 0.107 2.00e-02 2.50e+03 pdb=" CD2 PHE B 95 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 95 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 95 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 95 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE B 95 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE B 95 " 0.137 2.00e-02 2.50e+03 pdb=" HE1 PHE B 95 " 0.080 2.00e-02 2.50e+03 pdb=" HE2 PHE B 95 " -0.058 2.00e-02 2.50e+03 pdb=" HZ PHE B 95 " -0.079 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.60: 28 1.60 - 2.35: 2232 2.35 - 3.10: 22123 3.10 - 3.85: 33033 3.85 - 4.60: 52904 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110320 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.844 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.975 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.046 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.093 2.620 nonbonded pdb="HG22 VAL A 181 " pdb=" O HOH S1566 " model vdw 1.236 2.620 ... (remaining 110315 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_7309525_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= 0.2037 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.299731 | | target function (ml) not normalized (work): 805395.449476 | | target function (ml) not normalized (free): 16577.188784 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2147 0.1912 6.6957 6.3077| | 2: 2.94 - 2.33 1.00 7339 128 0.1608 0.1602 5.5309 5.5782| | 3: 2.33 - 2.04 0.96 6939 150 0.1627 0.1522 5.1375 5.1093| | 4: 2.04 - 1.85 1.00 7170 155 0.1756 0.1686 4.963 5.0797| | 5: 1.85 - 1.72 0.99 7113 159 0.1927 0.1808 4.8029 4.8724| | 6: 1.72 - 1.62 0.99 7102 142 0.2008 0.2046 4.6805 4.7485| | 7: 1.62 - 1.54 0.99 7104 148 0.2046 0.1849 4.5759 4.5806| | 8: 1.54 - 1.47 0.96 6798 152 0.2010 0.2443 4.4666 4.6099| | 9: 1.47 - 1.41 0.98 6938 155 0.2069 0.2064 4.3981 4.4492| | 10: 1.41 - 1.36 0.99 7022 150 0.2121 0.2090 4.3149 4.3415| | 11: 1.36 - 1.32 0.99 6997 151 0.2125 0.2417 4.2405 4.3649| | 12: 1.32 - 1.28 0.98 6976 149 0.2120 0.1868 4.1816 4.18| | 13: 1.28 - 1.25 0.98 6907 166 0.2037 0.2116 4.1171 4.2051| | 14: 1.25 - 1.22 0.98 7015 113 0.2074 0.2148 4.0673 4.1869| | 15: 1.22 - 1.19 0.98 6957 137 0.2095 0.1765 4.0261 3.9402| | 16: 1.19 - 1.17 0.93 6604 132 0.2105 0.2106 3.9919 4.0302| | 17: 1.17 - 1.14 0.98 6941 135 0.2161 0.2051 3.9542 4.0304| | 18: 1.14 - 1.12 0.98 6875 142 0.2207 0.2508 3.9179 3.9733| | 19: 1.12 - 1.10 0.97 6949 106 0.2248 0.2688 3.8659 3.9807| | 20: 1.10 - 1.08 0.97 6884 147 0.2346 0.2360 3.826 3.8669| | 21: 1.08 - 1.07 0.97 6852 152 0.2453 0.2627 3.7985 3.8032| | 22: 1.07 - 1.05 0.97 6838 135 0.2571 0.2494 3.7582 3.7151| | 23: 1.05 - 1.03 0.97 6829 159 0.2744 0.2779 3.7358 3.7918| | 24: 1.03 - 1.02 0.96 6785 133 0.2894 0.2987 3.6983 3.8049| | 25: 1.02 - 1.01 0.93 6552 130 0.3059 0.2917 3.6689 3.6805| | 26: 1.01 - 0.99 0.96 6767 158 0.3228 0.3080 3.6297 3.6281| | 27: 0.99 - 0.98 0.94 6648 131 0.3411 0.3305 3.6335 3.6337| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.39 0.91 0.98 35195.46| | 2: 2.94 - 2.33 7339 128 0.86 21.00 1.08 1.03 14850.47| | 3: 2.33 - 2.04 6939 150 0.93 12.42 1.10 1.06 4065.86| | 4: 2.04 - 1.85 7170 155 0.92 13.86 1.11 1.06 2880.90| | 5: 1.85 - 1.72 7113 159 0.90 16.41 1.12 1.07 2258.78| | 6: 1.72 - 1.62 7102 142 0.89 17.73 1.11 1.07 1806.02| | 7: 1.62 - 1.54 7104 148 0.88 18.53 1.11 1.07 1458.45| | 8: 1.54 - 1.47 6798 152 0.88 19.24 1.10 1.06 1239.77| | 9: 1.47 - 1.41 6938 155 0.88 19.64 1.10 1.06 1055.19| | 10: 1.41 - 1.36 7022 150 0.86 20.81 1.09 1.05 914.62| | 11: 1.36 - 1.32 6997 151 0.86 20.77 1.08 1.04 783.50| | 12: 1.32 - 1.28 6976 149 0.87 20.28 1.08 1.03 668.94| | 13: 1.28 - 1.25 6907 166 0.87 19.79 1.07 1.03 596.99| | 14: 1.25 - 1.22 7015 113 0.87 20.02 1.08 1.04 541.94| | 15: 1.22 - 1.19 6957 137 0.87 20.06 1.08 1.04 498.86| | 16: 1.19 - 1.17 6604 132 0.88 19.58 1.07 1.03 455.39| | 17: 1.17 - 1.14 6941 135 0.86 20.93 1.08 1.01 432.87| | 18: 1.14 - 1.12 6875 142 0.86 21.72 1.08 1.00 418.83| | 19: 1.12 - 1.10 6949 106 0.85 23.03 1.07 1.00 407.30| | 20: 1.10 - 1.08 6884 147 0.84 23.49 1.06 0.99 370.19| | 21: 1.08 - 1.07 6852 152 0.84 23.81 1.06 0.99 337.33| | 22: 1.07 - 1.05 6838 135 0.83 25.07 1.05 0.99 322.56| | 23: 1.05 - 1.03 6829 159 0.80 27.43 1.05 0.98 327.79| | 24: 1.03 - 1.02 6785 133 0.78 29.76 1.05 0.96 330.93| | 25: 1.02 - 1.01 6552 130 0.77 30.86 1.03 0.93 313.90| | 26: 1.01 - 0.99 6767 158 0.75 32.23 1.03 0.92 294.08| | 27: 0.99 - 0.98 6648 131 0.75 32.21 1.04 0.92 275.34| |alpha: min = 0.92 max = 1.07 mean = 1.02| |beta: min = 275.34 max = 35195.46 mean = 2833.99| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.97 mean = 21.81| |phase err.(test): min = 0.00 max = 89.50 mean = 21.87| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.247 2950 Z= 5.457 Angle : 5.197 18.138 4018 Z= 3.654 Chirality : 0.376 1.193 492 Planarity : 0.031 0.091 512 Dihedral : 12.764 89.862 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.37 % Favored : 96.11 % Rotamer: Outliers : 0.65 % Allowed : 4.84 % Favored : 94.52 % Cbeta Deviations : 31.46 % 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: -2.28 (0.37), residues: 386 helix: -2.65 (0.30), residues: 144 sheet: -0.75 (0.55), residues: 82 loop : -0.50 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.103 0.024 ARG A 149 TYR 0.117 0.039 TYR B 195 PHE 0.099 0.032 PHE B 95 TRP 0.120 0.047 TRP B 139 HIS 0.047 0.022 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.299731 | | target function (ml) not normalized (work): 805395.449476 | | target function (ml) not normalized (free): 16577.188784 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2035 0.2037 0.1995 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2035 0.2037 0.1995 n_refl.: 191155 remove outliers: r(all,work,free)=0.2035 0.2037 0.1995 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2035 0.2037 0.1995 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1802 0.1934 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1800 0.1933 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4061 402.814 292.622 0.437 0.912 0.303 13.296-10.522 99.01 99 1 0.2541 528.187 518.936 0.791 0.913 0.260 10.503-8.327 99.45 178 3 0.2490 565.118 556.541 0.972 0.913 0.240 8.318-6.595 100.00 360 8 0.2427 414.736 403.563 0.980 0.913 0.200 6.588-5.215 100.00 711 7 0.2263 381.101 365.573 0.959 0.913 0.140 5.214-4.128 98.38 1367 28 0.1494 557.435 550.721 1.078 0.913 0.080 4.126-3.266 94.74 2603 46 0.1363 508.132 498.100 1.147 0.914 0.014 3.266-2.585 99.86 5447 97 0.1443 342.774 337.554 1.120 0.913 0.000 2.585-2.046 97.45 10613 204 0.1391 258.603 254.081 1.125 0.912 0.000 2.046-1.619 99.39 21536 464 0.1625 153.054 149.857 1.145 0.911 0.000 1.619-1.281 98.00 42464 925 0.1921 82.395 80.212 1.129 0.909 0.000 1.281-0.980 96.53 101826 2055 0.2317 44.202 41.689 1.115 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0076 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1933 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1801 r_free=0.1936 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.825190 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 576.631658 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 0.1275 0.1505 0.0230 0.039 1.2 10.7 0.0 0.3 0 11.413 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.75 15.05 2.30 1.120 13.108 576.632 0.019 12.99 15.67 2.68 1.234 13.323 576.632 0.017 Individual atomic B min max mean iso aniso Overall: 5.16 73.04 14.99 1.40 435 3274 Protein: 5.16 40.31 10.99 1.40 0 2902 Water: 6.35 73.04 29.38 N/A 435 370 Other: 15.96 30.85 23.40 N/A 0 2 Chain A: 5.40 60.19 13.02 N/A 0 1626 Chain B: 5.16 73.04 12.75 N/A 0 1648 Chain S: 11.73 60.88 30.81 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.94 2156 11.94 - 18.73 645 18.73 - 25.52 325 25.52 - 32.31 256 32.31 - 39.10 159 39.10 - 45.89 105 45.89 - 52.68 42 52.68 - 59.46 16 59.46 - 66.25 4 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1567 r_work=0.1298 r_free=0.1563 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1563 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1284 r_free = 0.1553 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1284 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015655 | | target function (ls_wunit_k1) not normalized (work): 2932.093552 | | target function (ls_wunit_k1) not normalized (free): 115.202762 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1284 0.1553 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1469 0.1467 0.1633 n_refl.: 191138 remove outliers: r(all,work,free)=0.1469 0.1467 0.1633 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1493 0.1490 0.1643 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1545 n_refl.: 191138 remove outliers: r(all,work,free)=0.1281 0.1276 0.1545 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3620 402.814 374.899 0.470 1.001 0.287 13.296-10.522 99.01 99 1 0.2069 528.187 525.549 0.721 1.003 0.254 10.503-8.327 99.45 178 3 0.1766 565.118 561.080 0.855 1.003 0.203 8.318-6.595 100.00 360 8 0.1717 414.736 412.364 0.876 1.002 0.160 6.588-5.215 100.00 711 7 0.1537 381.101 373.504 0.854 1.003 0.150 5.214-4.128 98.38 1367 28 0.0898 557.435 555.177 0.940 1.003 0.054 4.126-3.266 94.74 2603 46 0.0834 508.132 504.166 1.004 1.004 0.014 3.266-2.585 99.86 5447 97 0.0926 342.774 340.197 0.986 1.003 0.000 2.585-2.046 97.45 10613 204 0.0953 258.603 256.370 0.997 1.004 0.000 2.046-1.619 99.39 21536 464 0.1090 153.054 151.364 1.015 1.004 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.415 1.006 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.169 0.984 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0382 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1545 | n_water=805 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1280 r_free=0.1551 | n_water=795 | time (s): 98.520 (total time: 100.880) Filter (q & B) r_work=0.1280 r_free=0.1550 | n_water=791 | time (s): 4.610 (total time: 105.490) Compute maps r_work=0.1280 r_free=0.1550 | n_water=791 | time (s): 1.660 (total time: 107.150) Filter (map) r_work=0.1306 r_free=0.1537 | n_water=659 | time (s): 4.090 (total time: 111.240) Find peaks r_work=0.1306 r_free=0.1537 | n_water=659 | time (s): 0.630 (total time: 111.870) Add new water r_work=0.1328 r_free=0.1564 | n_water=949 | time (s): 5.010 (total time: 116.880) Refine new water occ: r_work=0.1286 r_free=0.1513 adp: r_work=0.1273 r_free=0.1510 occ: r_work=0.1275 r_free=0.1507 adp: r_work=0.1268 r_free=0.1506 occ: r_work=0.1270 r_free=0.1504 adp: r_work=0.1267 r_free=0.1504 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1504 r_work=0.1267 r_free=0.1504 | n_water=949 | time (s): 78.910 (total time: 195.790) Filter (q & B) r_work=0.1271 r_free=0.1508 | n_water=883 | time (s): 4.550 (total time: 200.340) Filter (dist only) r_work=0.1271 r_free=0.1508 | n_water=882 | time (s): 110.480 (total time: 310.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.884801 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 595.578989 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1255 0.1525 0.0270 0.041 1.1 16.3 0.0 0.0 0 11.442 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.25 2.70 2.040 15.183 595.579 0.015 12.32 15.16 2.84 2.404 15.247 595.579 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 69.03 16.36 1.20 514 3272 Protein: 5.40 40.41 10.98 1.20 0 2902 Water: 6.64 69.03 34.06 N/A 514 368 Other: 16.47 33.46 24.97 N/A 0 2 Chain A: 5.58 57.19 12.98 N/A 0 1624 Chain B: 5.40 68.33 12.81 N/A 0 1648 Chain S: 13.21 69.03 38.44 N/A 514 0 Histogram: Values Number of atoms 5.40 - 11.76 2077 11.76 - 18.12 700 18.12 - 24.49 264 24.49 - 30.85 210 30.85 - 37.22 175 37.22 - 43.58 156 43.58 - 49.94 105 49.94 - 56.31 47 56.31 - 62.67 36 62.67 - 69.03 16 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1516 r_work=0.1233 r_free=0.1517 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1517 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1511 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1511 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013416 | | target function (ls_wunit_k1) not normalized (work): 2512.757400 | | target function (ls_wunit_k1) not normalized (free): 100.502869 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1226 0.1511 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1590 n_refl.: 191138 remove outliers: r(all,work,free)=0.1435 0.1432 0.1590 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1432 0.1430 0.1589 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1232 0.1517 n_refl.: 191138 remove outliers: r(all,work,free)=0.1238 0.1232 0.1517 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3261 402.814 377.345 0.495 0.963 0.272 13.296-10.522 99.01 99 1 0.1856 528.187 518.917 0.762 0.964 0.224 10.503-8.327 99.45 178 3 0.1394 565.118 566.307 0.923 0.964 0.174 8.318-6.595 100.00 360 8 0.1538 414.736 414.347 0.935 0.963 0.150 6.588-5.215 100.00 711 7 0.1334 381.101 376.528 0.911 0.963 0.150 5.214-4.128 98.38 1367 28 0.0828 557.435 556.190 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0758 508.132 505.485 1.058 0.963 0.009 3.266-2.585 99.86 5447 97 0.0856 342.774 341.416 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0902 258.603 256.825 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.642 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1257 82.395 81.351 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.217 1.057 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0467 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1517 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1517 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1517 | n_water=882 | time (s): 3.760 (total time: 3.760) Filter (dist) r_work=0.1235 r_free=0.1517 | n_water=877 | time (s): 108.940 (total time: 112.700) Filter (q & B) r_work=0.1235 r_free=0.1517 | n_water=875 | time (s): 4.520 (total time: 117.220) Compute maps r_work=0.1235 r_free=0.1517 | n_water=875 | time (s): 2.100 (total time: 119.320) Filter (map) r_work=0.1273 r_free=0.1524 | n_water=693 | time (s): 4.880 (total time: 124.200) Find peaks r_work=0.1273 r_free=0.1524 | n_water=693 | time (s): 0.810 (total time: 125.010) Add new water r_work=0.1296 r_free=0.1546 | n_water=1034 | time (s): 5.060 (total time: 130.070) Refine new water occ: r_work=0.1251 r_free=0.1506 adp: r_work=0.1251 r_free=0.1507 occ: r_work=0.1247 r_free=0.1505 adp: r_work=0.1246 r_free=0.1506 occ: r_work=0.1243 r_free=0.1506 adp: r_work=0.1242 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1506 r_work=0.1242 r_free=0.1506 | n_water=1034 | time (s): 264.820 (total time: 394.890) Filter (q & B) r_work=0.1247 r_free=0.1508 | n_water=894 | time (s): 6.120 (total time: 401.010) Filter (dist only) r_work=0.1247 r_free=0.1508 | n_water=893 | time (s): 117.780 (total time: 518.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.675350 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.052571 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 0.1234 0.1430 0.0196 0.035 1.1 7.5 0.0 0.0 0 0.838 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.34 14.30 1.96 1.931 14.657 16.053 3.937 12.29 13.90 1.61 2.188 14.574 16.053 3.897 Individual atomic B min max mean iso aniso Overall: 5.51 68.02 15.42 1.07 526 3271 Protein: 5.51 37.05 10.76 1.07 0 2902 Water: 6.67 68.02 30.53 N/A 526 367 Other: 14.22 29.26 21.74 N/A 0 2 Chain A: 5.52 56.44 12.78 N/A 0 1624 Chain B: 5.51 68.02 12.55 N/A 0 1647 Chain S: 14.07 64.41 32.54 N/A 526 0 Histogram: Values Number of atoms 5.51 - 11.76 2126 11.76 - 18.01 693 18.01 - 24.26 287 24.26 - 30.52 250 30.52 - 36.77 172 36.77 - 43.02 153 43.02 - 49.27 79 49.27 - 55.52 24 55.52 - 61.77 10 61.77 - 68.02 3 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1391 r_work=0.1230 r_free=0.1392 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1230 r_free = 0.1392 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1224 r_free = 0.1383 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1383 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891573 | | target function (ml) not normalized (work): 728879.861021 | | target function (ml) not normalized (free): 15224.719279 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1227 0.1224 0.1383 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1434 0.1433 0.1473 n_refl.: 191138 remove outliers: r(all,work,free)=0.1434 0.1433 0.1473 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1428 0.1428 0.1470 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1223 0.1220 0.1379 n_refl.: 191138 remove outliers: r(all,work,free)=0.1222 0.1219 0.1379 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3688 398.895 357.068 0.416 0.948 0.241 13.296-10.522 98.02 98 1 0.2334 530.665 505.640 0.703 0.949 0.204 10.503-8.327 98.90 177 3 0.1946 557.261 557.488 0.887 0.949 0.190 8.318-6.595 100.00 360 8 0.2017 414.736 411.448 0.894 0.949 0.100 6.588-5.215 100.00 711 7 0.1787 381.101 371.542 0.883 0.949 0.090 5.214-4.128 98.38 1367 28 0.1148 557.435 552.699 0.969 0.949 0.080 4.126-3.266 94.74 2603 46 0.1073 508.132 501.435 1.031 0.949 0.014 3.266-2.585 99.86 5447 97 0.1075 342.774 339.115 1.018 0.948 0.000 2.585-2.046 97.45 10613 204 0.0961 258.603 255.874 1.031 0.948 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.440 1.054 0.946 0.000 1.619-1.281 98.00 42464 925 0.1052 82.395 81.498 1.050 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1691 44.202 42.322 1.035 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0898 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1219 r_free=0.1379 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1219 r_free=0.1379 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1219 r_free=0.1379 | n_water=893 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1219 r_free=0.1379 | n_water=893 | time (s): 109.480 (total time: 112.040) Filter (q & B) r_work=0.1220 r_free=0.1376 | n_water=882 | time (s): 4.460 (total time: 116.500) Compute maps r_work=0.1220 r_free=0.1376 | n_water=882 | time (s): 2.420 (total time: 118.920) Filter (map) r_work=0.1244 r_free=0.1375 | n_water=733 | time (s): 5.330 (total time: 124.250) Find peaks r_work=0.1244 r_free=0.1375 | n_water=733 | time (s): 0.560 (total time: 124.810) Add new water r_work=0.1258 r_free=0.1390 | n_water=973 | time (s): 4.570 (total time: 129.380) Refine new water occ: r_work=0.1211 r_free=0.1353 adp: r_work=0.1203 r_free=0.1348 occ: r_work=0.1200 r_free=0.1351 adp: r_work=0.1200 r_free=0.1349 occ: r_work=0.1198 r_free=0.1353 adp: r_work=0.1198 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1353 r_work=0.1198 r_free=0.1353 | n_water=973 | time (s): 285.230 (total time: 414.610) Filter (q & B) r_work=0.1202 r_free=0.1354 | n_water=887 | time (s): 4.440 (total time: 419.050) Filter (dist only) r_work=0.1203 r_free=0.1354 | n_water=885 | time (s): 111.210 (total time: 530.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.627714 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.200944 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 0.1352 0.0151 0.033 1.1 6.6 0.0 0.0 0 0.814 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.52 1.51 1.839 14.263 16.201 3.873 11.94 13.48 1.54 2.011 14.211 16.201 3.863 Individual atomic B min max mean iso aniso Overall: 5.49 67.44 15.03 1.00 518 3271 Protein: 5.49 33.29 10.64 1.00 0 2902 Water: 6.01 67.44 29.39 N/A 518 367 Other: 13.92 27.59 20.76 N/A 0 2 Chain A: 5.55 54.91 12.60 N/A 0 1624 Chain B: 5.49 67.44 12.42 N/A 0 1647 Chain S: 6.01 64.31 30.94 N/A 518 0 Histogram: Values Number of atoms 5.49 - 11.69 2117 11.69 - 17.88 730 17.88 - 24.07 292 24.07 - 30.27 255 30.27 - 36.46 167 36.46 - 42.66 131 42.66 - 48.85 68 48.85 - 55.05 20 55.05 - 61.24 7 61.24 - 67.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1348 r_work=0.1194 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1349 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1347 target_work(ml) = 3.861 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.860635 | | target function (ml) not normalized (work): 723069.840724 | | target function (ml) not normalized (free): 15119.138949 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1348 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1399 0.1398 0.1462 n_refl.: 191134 remove outliers: r(all,work,free)=0.1399 0.1398 0.1462 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1392 0.1391 0.1457 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1345 n_refl.: 191134 remove outliers: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3481 342.987 313.069 0.398 0.951 0.221 13.296-10.522 97.03 97 1 0.2391 480.810 454.230 0.696 0.952 0.190 10.503-8.327 97.80 175 3 0.2032 501.507 497.734 0.870 0.952 0.144 8.318-6.595 100.00 360 8 0.2152 375.245 370.056 0.888 0.952 0.105 6.588-5.215 100.00 711 7 0.1836 344.813 335.954 0.882 0.952 0.079 5.214-4.128 98.38 1367 28 0.1166 504.357 499.665 0.967 0.952 0.060 4.126-3.266 94.74 2603 46 0.1094 459.748 453.433 1.029 0.953 0.000 3.266-2.585 99.86 5447 97 0.1082 310.135 306.961 1.016 0.952 0.000 2.585-2.046 97.45 10613 204 0.0935 233.979 231.550 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0910 138.480 137.196 1.051 0.951 0.000 1.619-1.281 98.00 42464 925 0.0984 74.550 73.844 1.047 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1661 39.993 38.336 1.033 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1142 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1345 | n_water=885 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1189 r_free=0.1346 | n_water=884 | time (s): 109.810 (total time: 112.580) Filter (q & B) r_work=0.1190 r_free=0.1346 | n_water=871 | time (s): 4.910 (total time: 117.490) Compute maps r_work=0.1190 r_free=0.1346 | n_water=871 | time (s): 1.830 (total time: 119.320) Filter (map) r_work=0.1211 r_free=0.1362 | n_water=744 | time (s): 5.140 (total time: 124.460) Find peaks r_work=0.1211 r_free=0.1362 | n_water=744 | time (s): 0.870 (total time: 125.330) Add new water r_work=0.1222 r_free=0.1367 | n_water=986 | time (s): 4.560 (total time: 129.890) Refine new water occ: r_work=0.1185 r_free=0.1339 adp: r_work=0.1185 r_free=0.1338 occ: r_work=0.1182 r_free=0.1340 adp: r_work=0.1182 r_free=0.1338 occ: r_work=0.1181 r_free=0.1340 adp: r_work=0.1180 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1339 r_work=0.1180 r_free=0.1339 | n_water=986 | time (s): 293.020 (total time: 422.910) Filter (q & B) r_work=0.1185 r_free=0.1346 | n_water=905 | time (s): 4.830 (total time: 427.740) Filter (dist only) r_work=0.1186 r_free=0.1346 | n_water=903 | time (s): 111.010 (total time: 538.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.580426 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.364265 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 0.1189 0.1352 0.0163 0.035 1.1 7.8 0.0 0.3 0 0.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.52 1.63 1.788 14.196 15.364 3.760 11.93 13.56 1.62 1.824 14.181 15.364 3.758 Individual atomic B min max mean iso aniso Overall: 5.58 67.21 15.10 0.96 536 3271 Protein: 5.58 32.15 10.59 0.96 0 2902 Water: 5.99 67.21 29.57 N/A 536 367 Other: 13.75 26.80 20.27 N/A 0 2 Chain A: 5.58 54.37 12.53 N/A 0 1624 Chain B: 5.58 67.21 12.35 N/A 0 1647 Chain S: 5.99 64.26 31.33 N/A 536 0 Histogram: Values Number of atoms 5.58 - 11.74 2147 11.74 - 17.90 717 17.90 - 24.07 295 24.07 - 30.23 227 30.23 - 36.39 177 36.39 - 42.55 141 42.55 - 48.72 70 48.72 - 54.88 23 54.88 - 61.04 8 61.04 - 67.21 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1356 r_work=0.1194 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1356 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1358 target_work(ml) = 3.758 | | 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.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757518 | | target function (ml) not normalized (work): 703730.591179 | | target function (ml) not normalized (free): 14738.452121 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1358 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1388 0.1387 0.1482 n_refl.: 191127 remove outliers: r(all,work,free)=0.1388 0.1387 0.1482 n_refl.: 191127 overall B=-0.03 to atoms: r(all,work,free)=0.1382 0.1380 0.1478 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1354 n_refl.: 191127 remove outliers: r(all,work,free)=0.1193 0.1190 0.1354 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3423 342.987 317.680 0.399 0.953 0.217 13.296-10.522 97.03 97 1 0.2331 480.810 461.590 0.694 0.954 0.170 10.503-8.327 97.80 175 3 0.2074 501.507 495.097 0.863 0.954 0.150 8.318-6.595 100.00 360 8 0.2121 375.245 370.791 0.889 0.954 0.120 6.588-5.215 100.00 711 7 0.1869 344.813 335.338 0.883 0.954 0.119 5.214-4.128 98.38 1367 28 0.1184 504.357 499.393 0.964 0.954 0.039 4.126-3.266 94.74 2603 46 0.1125 459.748 452.913 1.027 0.955 0.000 3.266-2.585 99.86 5447 97 0.1087 310.135 306.984 1.014 0.954 0.000 2.585-2.046 97.45 10613 204 0.0942 233.979 231.491 1.027 0.953 0.000 2.046-1.619 99.39 21536 464 0.0912 138.480 137.172 1.050 0.952 0.000 1.619-1.281 98.00 42464 925 0.0976 74.550 73.838 1.048 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1652 39.993 38.328 1.036 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1230 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1355 | n_water=903 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1190 r_free=0.1355 | n_water=903 | time (s): 109.730 (total time: 112.270) Filter (q & B) r_work=0.1190 r_free=0.1356 | n_water=890 | time (s): 5.330 (total time: 117.600) Compute maps r_work=0.1190 r_free=0.1356 | n_water=890 | time (s): 1.860 (total time: 119.460) Filter (map) r_work=0.1211 r_free=0.1360 | n_water=773 | time (s): 5.500 (total time: 124.960) Find peaks r_work=0.1211 r_free=0.1360 | n_water=773 | time (s): 0.780 (total time: 125.740) Add new water r_work=0.1222 r_free=0.1370 | n_water=995 | time (s): 5.300 (total time: 131.040) Refine new water occ: r_work=0.1188 r_free=0.1342 adp: r_work=0.1188 r_free=0.1342 occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1186 r_free=0.1342 occ: r_work=0.1184 r_free=0.1342 adp: r_work=0.1184 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1342 r_work=0.1184 r_free=0.1342 | n_water=995 | time (s): 287.310 (total time: 418.350) Filter (q & B) r_work=0.1188 r_free=0.1348 | n_water=920 | time (s): 4.910 (total time: 423.260) Filter (dist only) r_work=0.1188 r_free=0.1347 | n_water=919 | time (s): 112.020 (total time: 535.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.563539 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.514563 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1356 0.0164 0.036 1.1 9.7 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.56 1.64 1.764 14.164 14.515 3.759 11.96 13.60 1.64 1.912 14.116 14.515 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 66.04 15.04 0.90 552 3271 Protein: 5.59 29.27 10.48 0.90 0 2902 Water: 6.00 66.04 29.44 N/A 552 367 Other: 13.86 23.78 18.82 N/A 0 2 Chain A: 5.63 51.40 12.38 N/A 0 1624 Chain B: 5.59 66.04 12.22 N/A 0 1647 Chain S: 6.00 64.04 31.31 N/A 552 0 Histogram: Values Number of atoms 5.59 - 11.63 2123 11.63 - 17.68 767 17.68 - 23.72 268 23.72 - 29.77 219 29.77 - 35.82 190 35.82 - 41.86 141 41.86 - 47.91 82 47.91 - 53.95 24 53.95 - 60.00 5 60.00 - 66.04 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1360 r_work=0.1196 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1361 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1362 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756978 | | target function (ml) not normalized (work): 703629.404168 | | target function (ml) not normalized (free): 14737.761001 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1362 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1389 0.1388 0.1492 n_refl.: 191127 remove outliers: r(all,work,free)=0.1389 0.1388 0.1492 n_refl.: 191127 overall B=-0.04 to atoms: r(all,work,free)=0.1382 0.1380 0.1486 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1361 n_refl.: 191127 remove outliers: r(all,work,free)=0.1197 0.1194 0.1361 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3508 342.987 316.898 0.386 0.952 0.199 13.296-10.522 97.03 97 1 0.2348 480.810 461.966 0.691 0.953 0.153 10.503-8.327 97.80 175 3 0.2071 501.507 494.982 0.862 0.953 0.133 8.318-6.595 100.00 360 8 0.2127 375.245 370.725 0.885 0.953 0.105 6.588-5.215 100.00 711 7 0.1875 344.813 335.417 0.883 0.953 0.087 5.214-4.128 98.38 1367 28 0.1183 504.357 499.783 0.967 0.954 0.029 4.126-3.266 94.74 2603 46 0.1134 459.748 452.786 1.030 0.954 0.000 3.266-2.585 99.86 5447 97 0.1106 310.135 307.101 1.016 0.954 0.000 2.585-2.046 97.45 10613 204 0.0949 233.979 231.523 1.027 0.954 0.000 2.046-1.619 99.39 21536 464 0.0913 138.480 137.189 1.049 0.955 0.000 1.619-1.281 98.00 42464 925 0.0974 74.550 73.839 1.044 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1653 39.993 38.323 1.029 0.957 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1406 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1361 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1361 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1361 | n_water=919 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1194 r_free=0.1361 | n_water=919 | time (s): 107.470 (total time: 110.070) Filter (q & B) r_work=0.1194 r_free=0.1361 | n_water=908 | time (s): 4.310 (total time: 114.380) Compute maps r_work=0.1194 r_free=0.1361 | n_water=908 | time (s): 1.960 (total time: 116.340) Filter (map) r_work=0.1217 r_free=0.1361 | n_water=784 | time (s): 4.760 (total time: 121.100) Find peaks r_work=0.1217 r_free=0.1361 | n_water=784 | time (s): 0.540 (total time: 121.640) Add new water r_work=0.1224 r_free=0.1371 | n_water=1002 | time (s): 4.070 (total time: 125.710) Refine new water occ: r_work=0.1192 r_free=0.1347 adp: r_work=0.1192 r_free=0.1347 occ: r_work=0.1190 r_free=0.1348 adp: r_work=0.1190 r_free=0.1347 occ: r_work=0.1188 r_free=0.1349 adp: r_work=0.1188 r_free=0.1348 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1348 r_work=0.1188 r_free=0.1348 | n_water=1002 | time (s): 228.750 (total time: 354.460) Filter (q & B) r_work=0.1193 r_free=0.1352 | n_water=920 | time (s): 5.180 (total time: 359.640) Filter (dist only) r_work=0.1193 r_free=0.1352 | n_water=918 | time (s): 119.830 (total time: 479.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.584493 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.884711 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1358 0.0161 0.037 1.1 6.8 0.0 0.3 0 0.792 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.58 1.61 1.717 13.985 13.885 3.758 11.99 13.60 1.61 1.777 13.965 13.885 3.757 Individual atomic B min max mean iso aniso Overall: 5.59 64.76 14.91 0.87 551 3271 Protein: 5.59 28.39 10.42 0.87 0 2902 Water: 5.97 64.76 29.09 N/A 551 367 Other: 13.90 22.13 18.01 N/A 0 2 Chain A: 5.63 49.92 12.28 N/A 0 1624 Chain B: 5.59 64.76 12.13 N/A 0 1647 Chain S: 5.97 63.95 30.98 N/A 551 0 Histogram: Values Number of atoms 5.59 - 11.51 2099 11.51 - 17.43 788 17.43 - 23.34 265 23.34 - 29.26 220 29.26 - 35.18 194 35.18 - 41.09 133 41.09 - 47.01 87 47.01 - 52.92 24 52.92 - 58.84 7 58.84 - 64.76 5 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1360 r_work=0.1199 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1360 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1358 target_work(ml) = 3.756 | | 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.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756250 | | target function (ml) not normalized (work): 703492.962913 | | target function (ml) not normalized (free): 14733.576438 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1358 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1393 0.1391 0.1485 n_refl.: 191127 remove outliers: r(all,work,free)=0.1393 0.1391 0.1485 n_refl.: 191127 overall B=-0.01 to atoms: r(all,work,free)=0.1391 0.1390 0.1484 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1346 n_refl.: 191127 remove outliers: r(all,work,free)=0.1190 0.1187 0.1346 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 89.11 87 3 0.3523 342.987 314.864 0.403 0.916 0.193 13.296-10.522 97.03 97 1 0.2364 480.810 461.265 0.725 0.918 0.141 10.503-8.327 97.80 175 3 0.2112 501.507 493.504 0.910 0.918 0.120 8.318-6.595 100.00 360 8 0.2159 375.245 369.946 0.934 0.918 0.090 6.588-5.215 100.00 711 7 0.1898 344.813 335.227 0.936 0.918 0.090 5.214-4.128 98.38 1367 28 0.1207 504.357 498.805 1.027 0.919 0.024 4.126-3.266 94.74 2603 46 0.1149 459.748 452.249 1.093 0.920 0.000 3.266-2.585 99.86 5447 97 0.1114 310.135 306.678 1.077 0.921 0.000 2.585-2.046 97.45 10613 204 0.0956 233.979 231.360 1.088 0.923 0.000 2.046-1.619 99.39 21536 464 0.0908 138.480 137.088 1.107 0.926 0.000 1.619-1.281 98.00 42464 925 0.0950 74.550 73.889 1.101 0.930 0.000 1.281-0.980 96.53 101826 2055 0.1628 39.993 38.294 1.072 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0260 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1346 | n_water=918 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1187 r_free=0.1346 | n_water=918 | time (s): 110.190 (total time: 112.850) Filter (q & B) r_work=0.1187 r_free=0.1345 | n_water=907 | time (s): 4.070 (total time: 116.920) Compute maps r_work=0.1187 r_free=0.1345 | n_water=907 | time (s): 1.820 (total time: 118.740) Filter (map) r_work=0.1212 r_free=0.1352 | n_water=783 | time (s): 6.010 (total time: 124.750) Find peaks r_work=0.1212 r_free=0.1352 | n_water=783 | time (s): 0.840 (total time: 125.590) Add new water r_work=0.1218 r_free=0.1359 | n_water=1000 | time (s): 5.310 (total time: 130.900) Refine new water occ: r_work=0.1184 r_free=0.1331 adp: r_work=0.1184 r_free=0.1331 occ: r_work=0.1182 r_free=0.1334 adp: r_work=0.1182 r_free=0.1333 occ: r_work=0.1180 r_free=0.1335 adp: r_work=0.1180 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1336 r_work=0.1180 r_free=0.1336 | n_water=1000 | time (s): 270.770 (total time: 401.670) Filter (q & B) r_work=0.1184 r_free=0.1339 | n_water=921 | time (s): 4.200 (total time: 405.870) Filter (dist only) r_work=0.1185 r_free=0.1338 | n_water=920 | time (s): 115.100 (total time: 520.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565599 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.039216 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 0.1188 0.1349 0.0161 0.037 1.1 6.0 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.49 1.61 1.694 13.919 14.039 3.754 11.88 13.49 1.61 1.707 13.910 14.039 3.752 Individual atomic B min max mean iso aniso Overall: 5.62 63.96 14.86 0.87 554 3270 Protein: 5.62 28.22 10.42 0.87 0 2902 Water: 6.05 63.96 28.84 N/A 554 366 Other: 13.91 22.36 18.14 N/A 0 2 Chain A: 5.71 49.67 12.24 N/A 0 1624 Chain B: 5.62 63.83 12.09 N/A 0 1646 Chain S: 6.05 63.96 30.78 N/A 554 0 Histogram: Values Number of atoms 5.62 - 11.45 2074 11.45 - 17.28 817 17.28 - 23.12 271 23.12 - 28.95 213 28.95 - 34.79 189 34.79 - 40.62 128 40.62 - 46.45 89 46.45 - 52.29 29 52.29 - 58.12 9 58.12 - 63.96 5 =========================== Idealize ADP of riding H ========================== r_work=0.1188 r_free=0.1350 r_work=0.1188 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1350 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1350 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1186 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751339 | | target function (ml) not normalized (work): 702573.193314 | | target function (ml) not normalized (free): 14722.126068 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1186 0.1350 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1488 n_refl.: 191127 remove outliers: r(all,work,free)=0.1400 0.1398 0.1488 n_refl.: 191127 overall B=-0.02 to atoms: r(all,work,free)=0.1396 0.1395 0.1486 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1185 0.1349 n_refl.: 191127 remove outliers: r(all,work,free)=0.1188 0.1185 0.1349 n_refl.: 191126 ======================== 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 89.11 87 3 0.3496 342.987 315.223 0.373 0.976 0.185 13.296-10.522 96.04 96 1 0.2284 479.930 455.989 0.677 0.977 0.135 10.503-8.327 97.80 175 3 0.2114 501.507 493.878 0.851 0.978 0.113 8.318-6.595 100.00 360 8 0.2166 375.245 370.182 0.875 0.978 0.080 6.588-5.215 100.00 711 7 0.1907 344.813 335.671 0.876 0.978 0.080 5.214-4.128 98.38 1367 28 0.1196 504.357 499.067 0.964 0.979 0.030 4.126-3.266 94.74 2603 46 0.1161 459.748 452.456 1.027 0.981 0.005 3.266-2.585 99.86 5447 97 0.1117 310.135 306.691 1.012 0.981 0.000 2.585-2.046 97.45 10613 204 0.0957 233.979 231.378 1.021 0.984 0.000 2.046-1.619 99.39 21536 464 0.0905 138.480 137.151 1.040 0.987 0.000 1.619-1.281 98.00 42464 925 0.0944 74.550 73.911 1.034 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1623 39.993 38.284 1.009 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0500 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1349 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1186 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1352 | n_water=920 | time (s): 2.520 (total time: 2.520) Filter (dist) r_work=0.1186 r_free=0.1353 | n_water=919 | time (s): 116.070 (total time: 118.590) Filter (q & B) r_work=0.1186 r_free=0.1353 | n_water=909 | time (s): 4.850 (total time: 123.440) Compute maps r_work=0.1186 r_free=0.1353 | n_water=909 | time (s): 2.190 (total time: 125.630) Filter (map) r_work=0.1209 r_free=0.1360 | n_water=794 | time (s): 5.240 (total time: 130.870) Find peaks r_work=0.1209 r_free=0.1360 | n_water=794 | time (s): 0.570 (total time: 131.440) Add new water r_work=0.1215 r_free=0.1364 | n_water=1011 | time (s): 5.190 (total time: 136.630) Refine new water occ: r_work=0.1182 r_free=0.1336 adp: r_work=0.1182 r_free=0.1337 occ: r_work=0.1180 r_free=0.1337 adp: r_work=0.1180 r_free=0.1338 occ: r_work=0.1178 r_free=0.1338 adp: r_work=0.1178 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1178 r_free=0.1339 r_work=0.1178 r_free=0.1339 | n_water=1011 | time (s): 389.510 (total time: 526.140) Filter (q & B) r_work=0.1183 r_free=0.1346 | n_water=929 | time (s): 4.270 (total time: 530.410) Filter (dist only) r_work=0.1183 r_free=0.1345 | n_water=927 | time (s): 114.050 (total time: 644.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.514902 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.747374 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 0.1187 0.1350 0.0163 0.038 1.1 9.5 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 13.50 1.63 1.690 13.909 13.747 3.753 11.87 13.50 1.63 1.687 13.908 13.747 3.752 Individual atomic B min max mean iso aniso Overall: 5.59 63.94 14.86 0.86 561 3270 Protein: 5.59 28.10 10.42 0.86 0 2902 Water: 6.08 63.94 28.76 N/A 561 366 Other: 13.91 22.28 18.09 N/A 0 2 Chain A: 5.70 49.58 12.21 N/A 0 1624 Chain B: 5.59 63.49 12.07 N/A 0 1646 Chain S: 6.08 63.94 30.75 N/A 561 0 Histogram: Values Number of atoms 5.59 - 11.42 2074 11.42 - 17.26 819 17.26 - 23.09 275 23.09 - 28.93 219 28.93 - 34.76 190 34.76 - 40.60 121 40.60 - 46.43 90 46.43 - 52.27 29 52.27 - 58.10 9 58.10 - 63.94 5 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1350 r_work=0.1188 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1188 r_free = 0.1350 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1352 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1186 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751728 | | target function (ml) not normalized (work): 702642.310929 | | target function (ml) not normalized (free): 14728.532384 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1190 0.1186 0.1352 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1493 n_refl.: 191126 remove outliers: r(all,work,free)=0.1401 0.1400 0.1493 n_refl.: 191126 overall B=-0.02 to atoms: r(all,work,free)=0.1397 0.1395 0.1491 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1186 0.1352 n_refl.: 191126 remove outliers: r(all,work,free)=0.1189 0.1186 0.1352 n_refl.: 191126 ======================== 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 89.11 87 3 0.3479 342.987 314.531 0.364 0.994 0.180 13.296-10.522 96.04 96 1 0.2266 479.930 463.659 0.673 0.996 0.122 10.503-8.327 97.80 175 3 0.2114 501.507 493.688 0.835 0.996 0.097 8.318-6.595 100.00 360 8 0.2141 375.245 369.911 0.859 0.996 0.082 6.588-5.215 100.00 711 7 0.1926 344.813 335.470 0.858 0.997 0.067 5.214-4.128 98.38 1367 28 0.1196 504.357 499.120 0.947 0.998 0.025 4.126-3.266 94.74 2603 46 0.1165 459.748 452.311 1.009 0.999 0.005 3.266-2.585 99.86 5447 97 0.1123 310.135 306.703 0.994 1.000 0.000 2.585-2.046 97.45 10613 204 0.0958 233.979 231.342 1.003 1.003 0.000 2.046-1.619 99.39 21536 464 0.0907 138.480 137.123 1.021 1.007 0.000 1.619-1.281 98.00 42464 925 0.0943 74.550 73.907 1.015 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1623 39.993 38.276 0.991 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0648 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1186 r_free=0.1352 After: r_work=0.1187 r_free=0.1352 ================================== NQH flips ================================== r_work=0.1187 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1352 | n_water=927 | time (s): 3.300 (total time: 3.300) Filter (dist) r_work=0.1187 r_free=0.1352 | n_water=926 | time (s): 135.140 (total time: 138.440) Filter (q & B) r_work=0.1188 r_free=0.1352 | n_water=913 | time (s): 5.220 (total time: 143.660) Compute maps r_work=0.1188 r_free=0.1352 | n_water=913 | time (s): 1.920 (total time: 145.580) Filter (map) r_work=0.1210 r_free=0.1355 | n_water=803 | time (s): 4.920 (total time: 150.500) Find peaks r_work=0.1210 r_free=0.1355 | n_water=803 | time (s): 0.900 (total time: 151.400) Add new water r_work=0.1215 r_free=0.1357 | n_water=1020 | time (s): 4.890 (total time: 156.290) Refine new water occ: r_work=0.1183 r_free=0.1328 adp: r_work=0.1183 r_free=0.1329 occ: r_work=0.1181 r_free=0.1329 adp: r_work=0.1181 r_free=0.1330 occ: r_work=0.1179 r_free=0.1331 adp: r_work=0.1179 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1331 r_work=0.1179 r_free=0.1331 | n_water=1020 | time (s): 241.180 (total time: 397.470) Filter (q & B) r_work=0.1184 r_free=0.1342 | n_water=932 | time (s): 5.040 (total time: 402.510) Filter (dist only) r_work=0.1185 r_free=0.1341 | n_water=930 | time (s): 121.160 (total time: 523.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.442673 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.344998 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1355 0.0157 0.039 1.2 12.4 0.0 0.3 0 0.721 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.55 1.57 1.685 13.856 14.345 3.761 11.96 13.56 1.60 1.678 13.869 14.345 3.759 Individual atomic B min max mean iso aniso Overall: 5.64 64.00 14.80 0.86 564 3270 Protein: 5.64 28.14 10.42 0.86 0 2902 Water: 6.07 64.00 28.46 N/A 564 366 Other: 13.94 22.21 18.07 N/A 0 2 Chain A: 5.74 49.33 12.18 N/A 0 1624 Chain B: 5.64 62.59 12.05 N/A 0 1646 Chain S: 6.07 64.00 30.37 N/A 564 0 Histogram: Values Number of atoms 5.64 - 11.47 2078 11.47 - 17.31 831 17.31 - 23.15 262 23.15 - 28.98 230 28.98 - 34.82 201 34.82 - 40.66 106 40.66 - 46.49 81 46.49 - 52.33 32 52.33 - 58.17 8 58.17 - 64.00 5 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1356 r_work=0.1196 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1356 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1356 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.758886 | | target function (ml) not normalized (work): 703982.983967 | | target function (ml) not normalized (free): 14748.540865 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7394 127 0.1340 0.1394 5.6718 5.7099| | 2: 2.94 - 2.33 1.00 7339 128 0.1075 0.1422 5.0635 5.1884| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1164 4.655 4.723| | 4: 2.04 - 1.85 1.00 7170 155 0.0903 0.1043 4.3934 4.5605| | 5: 1.85 - 1.72 0.99 7113 159 0.0946 0.1021 4.1624 4.254| | 6: 1.72 - 1.62 0.99 7102 142 0.0906 0.1112 3.9602 4.1021| | 7: 1.62 - 1.54 0.99 7104 148 0.0910 0.0949 3.8197 3.9433| | 8: 1.54 - 1.47 0.96 6798 152 0.0908 0.1371 3.7209 3.9393| | 9: 1.47 - 1.41 0.98 6938 155 0.0940 0.1150 3.6381 3.7785| | 10: 1.41 - 1.36 0.99 7022 150 0.0988 0.1205 3.5716 3.6894| | 11: 1.36 - 1.32 0.99 6997 151 0.1005 0.1128 3.4971 3.5947| | 12: 1.32 - 1.28 0.98 6975 149 0.1039 0.1131 3.4665 3.6018| | 13: 1.28 - 1.25 0.98 6907 166 0.1048 0.1234 3.4437 3.5667| | 14: 1.25 - 1.22 0.98 7015 112 0.1110 0.1595 3.4377 3.691| | 15: 1.22 - 1.19 0.98 6956 137 0.1175 0.1247 3.4543 3.4944| | 16: 1.19 - 1.17 0.93 6604 132 0.1255 0.1544 3.4687 3.6521| | 17: 1.17 - 1.14 0.98 6940 135 0.1303 0.1222 3.4364 3.4446| | 18: 1.14 - 1.12 0.98 6875 142 0.1390 0.1736 3.4421 3.542| | 19: 1.12 - 1.10 0.97 6948 106 0.1477 0.1791 3.4235 3.6037| | 20: 1.10 - 1.08 0.97 6884 147 0.1590 0.1612 3.4137 3.4463| | 21: 1.08 - 1.07 0.97 6852 152 0.1734 0.2171 3.4206 3.5099| | 22: 1.07 - 1.05 0.97 6836 135 0.1910 0.1966 3.4154 3.4198| | 23: 1.05 - 1.03 0.97 6827 159 0.2126 0.2029 3.4347 3.4902| | 24: 1.03 - 1.02 0.96 6784 133 0.2337 0.2273 3.4368 3.5177| | 25: 1.02 - 1.01 0.93 6552 130 0.2616 0.2506 3.4499 3.5207| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2849 3.4152 3.422| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2794 3.4682 3.3964| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7394 127 0.94 10.77 1.00 0.97 10061.10| | 2: 2.94 - 2.33 7339 128 0.93 12.10 0.99 0.97 4718.17| | 3: 2.33 - 2.04 6939 150 0.96 7.54 1.01 0.97 1667.45| | 4: 2.04 - 1.85 7170 155 0.96 7.64 1.00 0.96 998.36| | 5: 1.85 - 1.72 7113 159 0.96 8.19 1.00 0.97 643.39| | 6: 1.72 - 1.62 7102 142 0.96 8.24 1.00 0.97 459.26| | 7: 1.62 - 1.54 7104 148 0.96 8.41 1.01 0.98 350.95| | 8: 1.54 - 1.47 6798 152 0.96 8.59 1.01 0.98 292.87| | 9: 1.47 - 1.41 6938 155 0.96 8.79 1.00 0.99 241.68| | 10: 1.41 - 1.36 7022 150 0.96 9.20 1.00 0.98 210.92| | 11: 1.36 - 1.32 6997 151 0.96 9.17 0.99 0.97 180.64| | 12: 1.32 - 1.28 6975 149 0.96 9.19 0.98 0.96 164.97| | 13: 1.28 - 1.25 6907 166 0.95 9.71 1.01 0.97 161.55| | 14: 1.25 - 1.22 7015 112 0.95 10.83 1.01 0.97 165.50| | 15: 1.22 - 1.19 6956 137 0.94 11.36 1.01 0.99 168.44| | 16: 1.19 - 1.17 6604 132 0.95 11.51 1.00 0.97 161.67| | 17: 1.17 - 1.14 6940 135 0.94 12.35 1.01 0.97 155.57| | 18: 1.14 - 1.12 6875 142 0.94 12.91 1.01 0.96 150.22| | 19: 1.12 - 1.10 6948 106 0.93 14.35 1.00 0.96 154.34| | 20: 1.10 - 1.08 6884 147 0.92 15.48 1.00 0.95 153.66| | 21: 1.08 - 1.07 6852 152 0.91 16.86 1.00 0.94 156.07| | 22: 1.07 - 1.05 6836 135 0.89 18.50 1.00 0.94 157.19| | 23: 1.05 - 1.03 6827 159 0.87 20.67 1.00 0.93 166.65| | 24: 1.03 - 1.02 6784 133 0.85 23.27 1.00 0.94 180.34| | 25: 1.02 - 1.01 6552 130 0.83 25.20 0.98 0.91 182.39| | 26: 1.01 - 0.99 6767 158 0.81 26.60 0.99 0.90 176.32| | 27: 0.99 - 0.98 6647 131 0.82 26.26 0.99 0.89 160.80| |alpha: min = 0.89 max = 0.99 mean = 0.96| |beta: min = 150.22 max = 10061.10 mean = 866.93| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.97 mean = 13.37| |phase err.(test): min = 0.00 max = 88.80 mean = 13.53| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1356 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1413 0.1412 0.1500 n_refl.: 191126 remove outliers: r(all,work,free)=0.1413 0.1412 0.1500 n_refl.: 191126 overall B=-0.13 to atoms: r(all,work,free)=0.1392 0.1390 0.1486 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1355 n_refl.: 191126 remove outliers: r(all,work,free)=0.1197 0.1194 0.1355 n_refl.: 191126 ======================== 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 89.11 87 3 0.3454 342.987 315.749 0.387 0.919 0.180 13.296-10.522 96.04 96 1 0.2292 479.930 464.294 0.713 0.920 0.114 10.503-8.327 97.80 175 3 0.2139 501.507 492.691 0.889 0.921 0.090 8.318-6.595 100.00 360 8 0.2154 375.245 370.138 0.914 0.921 0.078 6.588-5.215 100.00 711 7 0.1930 344.813 335.158 0.914 0.921 0.067 5.214-4.128 98.38 1367 28 0.1203 504.357 498.974 1.008 0.922 0.020 4.126-3.266 94.74 2603 46 0.1168 459.748 452.050 1.076 0.924 0.000 3.266-2.585 99.86 5447 97 0.1120 310.135 306.739 1.059 0.925 0.000 2.585-2.046 97.45 10613 204 0.0966 233.979 231.313 1.064 0.928 0.000 2.046-1.619 99.39 21536 464 0.0918 138.480 137.102 1.080 0.932 0.000 1.619-1.281 98.00 42464 925 0.0960 74.550 73.887 1.069 0.939 0.000 1.281-0.980 96.53 101826 2055 0.1630 39.993 38.269 1.033 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0292 ================= 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 : 0.2037 0.1995 0.082 5.197 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1933 0.082 5.197 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1933 0.082 5.197 5.2 78.0 14.6 805 0.000 1_nqh: 0.1801 0.1936 0.082 5.197 5.2 78.0 14.6 805 0.002 1_weight: 0.1801 0.1936 0.082 5.197 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1275 0.1505 0.039 1.175 5.2 78.0 14.6 805 0.157 1_adp: 0.1299 0.1567 0.039 1.175 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1298 0.1563 0.039 1.175 5.2 73.0 15.0 805 0.157 1_occ: 0.1284 0.1553 0.039 1.175 5.2 73.0 15.0 805 0.157 2_bss: 0.1276 0.1545 0.039 1.175 5.3 73.2 15.2 805 0.157 2_settarget: 0.1276 0.1545 0.039 1.175 5.3 73.2 15.2 805 0.157 2_updatecdl: 0.1276 0.1545 0.039 1.188 5.3 73.2 15.2 805 0.157 2_nqh: 0.1276 0.1545 0.039 1.188 5.3 73.2 15.2 805 0.157 2_sol: 0.1271 0.1508 0.039 1.188 5.3 73.2 16.2 882 n/a 2_weight: 0.1271 0.1508 0.039 1.188 5.3 73.2 16.2 882 n/a 2_xyzrec: 0.1255 0.1525 0.041 1.146 5.3 73.2 16.2 882 n/a 2_adp: 0.1232 0.1516 0.041 1.146 5.4 69.0 16.4 882 n/a 2_regHadp: 0.1233 0.1517 0.041 1.146 5.4 69.0 16.4 882 n/a 2_occ: 0.1226 0.1511 0.041 1.146 5.4 69.0 16.4 882 n/a 3_bss: 0.1232 0.1517 0.041 1.146 5.4 69.0 16.3 882 n/a 3_settarget: 0.1232 0.1517 0.041 1.146 5.4 69.0 16.3 882 n/a 3_updatecdl: 0.1232 0.1517 0.041 1.145 5.4 69.0 16.3 882 n/a 3_nqh: 0.1232 0.1517 0.041 1.145 5.4 69.0 16.3 882 n/a 3_sol: 0.1247 0.1508 0.041 1.145 5.4 68.3 15.6 893 n/a 3_weight: 0.1247 0.1508 0.041 1.145 5.4 68.3 15.6 893 n/a 3_xyzrec: 0.1234 0.1430 0.035 1.105 5.4 68.3 15.6 893 n/a 3_adp: 0.1229 0.1391 0.035 1.105 5.5 68.0 15.4 893 n/a 3_regHadp: 0.1230 0.1392 0.035 1.105 5.5 68.0 15.4 893 n/a 3_occ: 0.1224 0.1383 0.035 1.105 5.5 68.0 15.4 893 n/a 4_bss: 0.1219 0.1379 0.035 1.105 5.5 68.0 15.4 893 n/a 4_settarget: 0.1219 0.1379 0.035 1.105 5.5 68.0 15.4 893 n/a 4_updatecdl: 0.1219 0.1379 0.035 1.105 5.5 68.0 15.4 893 n/a 4_nqh: 0.1219 0.1379 0.035 1.105 5.5 68.0 15.4 893 n/a 4_sol: 0.1203 0.1354 0.035 1.105 5.5 68.0 15.1 885 n/a 4_weight: 0.1203 0.1354 0.035 1.105 5.5 68.0 15.1 885 n/a 4_xyzrec: 0.1201 0.1352 0.033 1.130 5.5 68.0 15.1 885 n/a 4_adp: 0.1194 0.1348 0.033 1.130 5.5 67.4 15.0 885 n/a 4_regHadp: 0.1194 0.1349 0.033 1.130 5.5 67.4 15.0 885 n/a 4_occ: 0.1192 0.1347 0.033 1.130 5.5 67.4 15.0 885 n/a 5_bss: 0.1189 0.1345 0.033 1.130 5.5 67.4 15.0 885 n/a 5_settarget: 0.1189 0.1345 0.033 1.130 5.5 67.4 15.0 885 n/a 5_updatecdl: 0.1189 0.1345 0.033 1.131 5.5 67.4 15.0 885 n/a 5_nqh: 0.1189 0.1345 0.033 1.131 5.5 67.4 15.0 885 n/a 5_sol: 0.1186 0.1346 0.033 1.131 5.5 67.4 15.1 903 n/a 5_weight: 0.1186 0.1346 0.033 1.131 5.5 67.4 15.1 903 n/a 5_xyzrec: 0.1189 0.1352 0.035 1.128 5.5 67.4 15.1 903 n/a 5_adp: 0.1193 0.1356 0.035 1.128 5.6 67.2 15.1 903 n/a 5_regHadp: 0.1194 0.1356 0.035 1.128 5.6 67.2 15.1 903 n/a 5_occ: 0.1192 0.1358 0.035 1.128 5.6 67.2 15.1 903 n/a 6_bss: 0.1190 0.1355 0.035 1.128 5.5 67.2 15.1 903 n/a 6_settarget: 0.1190 0.1355 0.035 1.128 5.5 67.2 15.1 903 n/a 6_updatecdl: 0.1190 0.1355 0.035 1.127 5.5 67.2 15.1 903 n/a 6_nqh: 0.1190 0.1355 0.035 1.127 5.5 67.2 15.1 903 n/a 6_sol: 0.1188 0.1347 0.035 1.127 5.5 67.2 15.1 919 n/a 6_weight: 0.1188 0.1347 0.035 1.127 5.5 67.2 15.1 919 n/a 6_xyzrec: 0.1191 0.1356 0.036 1.125 5.5 67.2 15.1 919 n/a 6_adp: 0.1196 0.1360 0.036 1.125 5.6 66.0 15.0 919 n/a 6_regHadp: 0.1196 0.1361 0.036 1.125 5.6 66.0 15.0 919 n/a 6_occ: 0.1194 0.1362 0.036 1.125 5.6 66.0 15.0 919 n/a 7_bss: 0.1194 0.1361 0.036 1.125 5.5 66.0 15.0 919 n/a 7_settarget: 0.1194 0.1361 0.036 1.125 5.5 66.0 15.0 919 n/a 7_updatecdl: 0.1194 0.1361 0.036 1.126 5.5 66.0 15.0 919 n/a 7_nqh: 0.1194 0.1361 0.036 1.126 5.5 66.0 15.0 919 n/a 7_sol: 0.1193 0.1352 0.036 1.126 5.5 66.0 14.9 918 n/a 7_weight: 0.1193 0.1352 0.036 1.126 5.5 66.0 14.9 918 n/a 7_xyzrec: 0.1197 0.1358 0.037 1.128 5.5 66.0 14.9 918 n/a 7_adp: 0.1199 0.1360 0.037 1.128 5.6 64.8 14.9 918 n/a 7_regHadp: 0.1199 0.1360 0.037 1.128 5.6 64.8 14.9 918 n/a 7_occ: 0.1197 0.1358 0.037 1.128 5.6 64.8 14.9 918 n/a 8_bss: 0.1187 0.1346 0.037 1.128 5.6 64.7 14.9 918 n/a 8_settarget: 0.1187 0.1346 0.037 1.128 5.6 64.7 14.9 918 n/a 8_updatecdl: 0.1187 0.1346 0.037 1.128 5.6 64.7 14.9 918 n/a 8_nqh: 0.1187 0.1346 0.037 1.128 5.6 64.7 14.9 918 n/a 8_sol: 0.1185 0.1338 0.037 1.128 5.6 64.7 14.9 920 n/a 8_weight: 0.1185 0.1338 0.037 1.128 5.6 64.7 14.9 920 n/a 8_xyzrec: 0.1188 0.1349 0.037 1.114 5.6 64.7 14.9 920 n/a 8_adp: 0.1188 0.1350 0.037 1.114 5.6 64.0 14.9 920 n/a 8_regHadp: 0.1188 0.1350 0.037 1.114 5.6 64.0 14.9 920 n/a 8_occ: 0.1186 0.1350 0.037 1.114 5.6 64.0 14.9 920 n/a 9_bss: 0.1185 0.1349 0.037 1.114 5.6 63.9 14.8 920 n/a 9_settarget: 0.1185 0.1349 0.037 1.114 5.6 63.9 14.8 920 n/a 9_updatecdl: 0.1185 0.1349 0.037 1.114 5.6 63.9 14.8 920 n/a 9_nqh: 0.1186 0.1352 0.037 1.114 5.6 63.9 14.8 920 n/a 9_sol: 0.1183 0.1345 0.037 1.114 5.6 63.9 14.9 927 n/a 9_weight: 0.1183 0.1345 0.037 1.114 5.6 63.9 14.9 927 n/a 9_xyzrec: 0.1187 0.1350 0.038 1.106 5.6 63.9 14.9 927 n/a 9_adp: 0.1187 0.1350 0.038 1.106 5.6 63.9 14.9 927 n/a 9_regHadp: 0.1188 0.1350 0.038 1.106 5.6 63.9 14.9 927 n/a 9_occ: 0.1186 0.1352 0.038 1.106 5.6 63.9 14.9 927 n/a 10_bss: 0.1186 0.1352 0.038 1.106 5.6 63.9 14.8 927 n/a 10_settarget: 0.1186 0.1352 0.038 1.106 5.6 63.9 14.8 927 n/a 10_updatecdl: 0.1186 0.1352 0.038 1.108 5.6 63.9 14.8 927 n/a 10_setrh: 0.1187 0.1352 0.038 1.108 5.6 63.9 14.8 927 n/a 10_nqh: 0.1187 0.1352 0.038 1.108 5.6 63.9 14.8 927 n/a 10_sol: 0.1185 0.1341 0.038 1.108 5.6 63.9 14.8 930 n/a 10_weight: 0.1185 0.1341 0.038 1.108 5.6 63.9 14.8 930 n/a 10_xyzrec: 0.1197 0.1355 0.039 1.167 5.6 63.9 14.8 930 n/a 10_adp: 0.1196 0.1356 0.039 1.167 5.6 64.0 14.8 930 n/a 10_regHadp: 0.1196 0.1356 0.039 1.167 5.6 64.0 14.8 930 n/a 10_occ: 0.1195 0.1356 0.039 1.167 5.6 64.0 14.8 930 n/a end: 0.1195 0.1355 0.039 1.167 5.5 63.9 14.7 930 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7309525_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7309525_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.7500 Refinement macro-cycles (run) : 12479.8500 Write final files (write_after_run_outputs) : 129.8200 Total : 12615.4200 Total CPU time: 3.51 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:47:31 PST -0800 (1736736451.36 s) Start R-work = 0.1800, R-free = 0.1933 Final R-work = 0.1195, R-free = 0.1355 =============================================================================== Job complete usr+sys time: 12862.34 seconds wall clock time: 215 minutes 24.80 seconds (12924.80 seconds total)