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_9443647.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9443647.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9443647.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.51, per 1000 atoms: 0.38 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: 2.674 distance_ideal: 2.720 ideal - model: 0.046 slack: 0.000 delta_slack: 0.046 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: 2.746 distance_ideal: 2.710 ideal - model: -0.036 slack: 0.000 delta_slack: -0.036 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: 1.14 Conformation dependent library (CDL) restraints added in 200.9 milliseconds Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.00: 544 1.00 - 1.22: 2517 1.22 - 1.45: 1409 1.45 - 1.67: 1410 1.67 - 1.89: 54 Bond restraints: 5934 Sorted by residual: bond pdb=" CD2 HIS B 179 " pdb=" NE2 HIS B 179 " ideal model delta sigma weight residual 1.374 1.591 -0.217 1.10e-02 8.26e+03 3.89e+02 bond pdb=" N GLY A 74 " pdb=" H GLY A 74 " ideal model delta sigma weight residual 0.860 1.251 -0.391 2.00e-02 2.50e+03 3.81e+02 bond pdb=" N ARG B 100 " pdb=" CA ARG B 100 " ideal model delta sigma weight residual 1.452 1.688 -0.235 1.22e-02 6.72e+03 3.71e+02 bond pdb=" CE1 HIS B 96 " pdb=" HE1 HIS B 96 " ideal model delta sigma weight residual 0.930 1.309 -0.379 2.00e-02 2.50e+03 3.60e+02 bond pdb=" N VAL B 60 " pdb=" H VAL B 60 " ideal model delta sigma weight residual 0.860 1.237 -0.377 2.00e-02 2.50e+03 3.55e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.95: 5337 3.95 - 7.90: 3609 7.90 - 11.85: 1472 11.85 - 15.80: 341 15.80 - 19.75: 51 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O PHE B 127 " pdb=" C PHE B 127 " pdb=" N PRO B 128 " ideal model delta sigma weight residual 121.43 105.22 16.21 1.12e+00 7.97e-01 2.10e+02 angle pdb=" CA ILE A 134 " pdb=" C ILE A 134 " pdb=" O ILE A 134 " ideal model delta sigma weight residual 119.51 128.20 -8.69 6.20e-01 2.60e+00 1.97e+02 angle pdb=" CA ASP A 68 " pdb=" C ASP A 68 " pdb=" O ASP A 68 " ideal model delta sigma weight residual 119.27 103.03 16.24 1.17e+00 7.31e-01 1.93e+02 angle pdb=" O CYS A 81 " pdb=" C CYS A 81 " pdb=" N PHE A 82 " ideal model delta sigma weight residual 122.09 108.06 14.03 1.04e+00 9.25e-01 1.82e+02 angle pdb=" OE1 GLN B 156 " pdb=" CD GLN B 156 " pdb=" NE2 GLN B 156 " ideal model delta sigma weight residual 122.60 136.05 -13.45 1.00e+00 1.00e+00 1.81e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 1833 16.57 - 33.13: 144 33.13 - 49.69: 48 49.69 - 66.26: 20 66.26 - 82.82: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TYR B 194 " pdb=" C TYR B 194 " pdb=" N TYR B 195 " pdb=" CA TYR B 195 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA MET A 124 " pdb=" C MET A 124 " pdb=" N THR A 125 " pdb=" CA THR A 125 " ideal model delta harmonic sigma weight residual 180.00 157.10 22.90 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CG TRP B 139 " pdb=" CD2 TRP B 139 " pdb=" CE3 TRP B 139 " pdb=" HE3 TRP B 139 " ideal model delta harmonic sigma weight residual 0.00 -21.21 21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 215 0.227 - 0.453: 165 0.453 - 0.679: 82 0.679 - 0.905: 27 0.905 - 1.132: 3 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA GLU B 180 " pdb=" N GLU B 180 " pdb=" C GLU B 180 " pdb=" CB GLU B 180 " both_signs ideal model delta sigma weight residual False 2.51 3.64 -1.13 2.00e-01 2.50e+01 3.20e+01 chirality pdb=" CA LYS B 177 " pdb=" N LYS B 177 " pdb=" C LYS B 177 " pdb=" CB LYS B 177 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CA THR A 111 " pdb=" N THR A 111 " pdb=" C THR A 111 " pdb=" CB THR A 111 " both_signs ideal model delta sigma weight residual False 2.53 1.61 0.92 2.00e-01 2.50e+01 2.11e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.181 2.00e-02 2.50e+03 8.60e-02 2.22e+02 pdb=" CG PHE B 164 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.061 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.093 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.062 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.083 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.090 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.107 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.023 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.173 2.00e-02 2.50e+03 7.38e-02 1.63e+02 pdb=" CG TYR A 194 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " 0.055 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " 0.060 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " -0.029 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.126 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.031 2.00e-02 2.50e+03 5.79e-02 1.34e+02 pdb=" CG TRP A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.076 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.098 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.079 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.032 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.103 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.021 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.076 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.067 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.020 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.042 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " -0.040 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.82 - 1.58: 20 1.58 - 2.33: 2085 2.33 - 3.09: 21984 3.09 - 3.84: 33124 3.84 - 4.60: 53151 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110364 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.824 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.033 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.081 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.083 2.620 nonbonded pdb="HG22 VAL A 181 " pdb=" O HOH S1566 " model vdw 1.179 2.620 ... (remaining 110359 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_9443647_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= 0.2023 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.291064 | | target function (ml) not normalized (work): 803772.061359 | | target function (ml) not normalized (free): 16523.494357 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2133 0.1929 6.6842 6.3085| | 2: 2.94 - 2.33 1.00 7339 128 0.1612 0.1692 5.5329 5.5956| | 3: 2.33 - 2.04 0.96 6939 150 0.1644 0.1521 5.1444 5.1143| | 4: 2.04 - 1.85 1.00 7170 155 0.1760 0.1715 4.9574 5.0486| | 5: 1.85 - 1.72 0.99 7113 159 0.1896 0.1651 4.7861 4.8015| | 6: 1.72 - 1.62 0.99 7102 142 0.1956 0.1898 4.6473 4.6467| | 7: 1.62 - 1.54 0.99 7104 148 0.1982 0.1863 4.561 4.5835| | 8: 1.54 - 1.47 0.96 6798 152 0.2038 0.2400 4.4781 4.6182| | 9: 1.47 - 1.41 0.98 6938 155 0.2096 0.2187 4.3927 4.467| | 10: 1.41 - 1.36 0.99 7022 150 0.2105 0.2021 4.2968 4.2688| | 11: 1.36 - 1.32 0.99 6997 151 0.2068 0.1975 4.2202 4.1996| | 12: 1.32 - 1.28 0.98 6976 149 0.2071 0.1932 4.1587 4.2312| | 13: 1.28 - 1.25 0.98 6907 166 0.1988 0.2011 4.1037 4.1196| | 14: 1.25 - 1.22 0.98 7015 113 0.2069 0.2084 4.0662 4.1659| | 15: 1.22 - 1.19 0.98 6957 137 0.2084 0.2079 4.0225 4.0071| | 16: 1.19 - 1.17 0.93 6604 132 0.2098 0.2343 3.9932 4.1097| | 17: 1.17 - 1.14 0.98 6941 135 0.2166 0.1709 3.9487 3.8951| | 18: 1.14 - 1.12 0.98 6875 142 0.2186 0.2398 3.9068 3.9361| | 19: 1.12 - 1.10 0.97 6949 106 0.2223 0.2632 3.8535 4.0804| | 20: 1.10 - 1.08 0.97 6884 147 0.2283 0.2340 3.8119 3.9004| | 21: 1.08 - 1.07 0.97 6852 152 0.2431 0.2800 3.7955 3.8238| | 22: 1.07 - 1.05 0.97 6838 135 0.2530 0.2610 3.7439 3.7661| | 23: 1.05 - 1.03 0.97 6829 159 0.2682 0.2652 3.7243 3.8118| | 24: 1.03 - 1.02 0.96 6785 133 0.2872 0.2536 3.6934 3.7466| | 25: 1.02 - 1.01 0.93 6552 130 0.3053 0.2894 3.6709 3.7111| | 26: 1.01 - 0.99 0.96 6767 158 0.3200 0.3305 3.6216 3.6028| | 27: 0.99 - 0.98 0.94 6648 131 0.3378 0.3226 3.6299 3.6112| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.48 0.91 0.97 35554.56| | 2: 2.94 - 2.33 7339 128 0.86 21.09 1.09 1.03 14957.13| | 3: 2.33 - 2.04 6939 150 0.94 11.91 1.11 1.07 3916.43| | 4: 2.04 - 1.85 7170 155 0.93 12.80 1.12 1.07 2536.66| | 5: 1.85 - 1.72 7113 159 0.92 14.78 1.11 1.08 1899.91| | 6: 1.72 - 1.62 7102 142 0.90 16.18 1.11 1.08 1550.66| | 7: 1.62 - 1.54 7104 148 0.89 17.39 1.10 1.10 1335.31| | 8: 1.54 - 1.47 6798 152 0.89 18.30 1.11 1.09 1171.03| | 9: 1.47 - 1.41 6938 155 0.88 18.58 1.11 1.09 961.90| | 10: 1.41 - 1.36 7022 150 0.88 19.20 1.10 1.07 798.34| | 11: 1.36 - 1.32 6997 151 0.88 18.71 1.08 1.06 657.06| | 12: 1.32 - 1.28 6976 149 0.88 18.81 1.08 1.04 586.25| | 13: 1.28 - 1.25 6907 166 0.88 18.92 1.07 1.04 559.85| | 14: 1.25 - 1.22 7015 113 0.87 20.26 1.07 1.03 544.88| | 15: 1.22 - 1.19 6957 137 0.87 20.48 1.08 1.04 518.11| | 16: 1.19 - 1.17 6604 132 0.88 19.86 1.07 1.03 467.49| | 17: 1.17 - 1.14 6941 135 0.87 20.46 1.08 1.02 423.32| | 18: 1.14 - 1.12 6875 142 0.86 21.09 1.08 1.01 400.49| | 19: 1.12 - 1.10 6949 106 0.85 22.87 1.07 1.00 404.91| | 20: 1.10 - 1.08 6884 147 0.84 23.97 1.06 0.98 382.76| | 21: 1.08 - 1.07 6852 152 0.83 24.92 1.05 0.98 363.65| | 22: 1.07 - 1.05 6838 135 0.82 25.81 1.06 0.98 333.12| | 23: 1.05 - 1.03 6829 159 0.80 27.27 1.05 0.98 327.43| | 24: 1.03 - 1.02 6785 133 0.78 29.07 1.05 0.97 319.42| | 25: 1.02 - 1.01 6552 130 0.77 30.40 1.03 0.92 301.94| | 26: 1.01 - 0.99 6767 158 0.75 32.47 1.03 0.90 290.02| | 27: 0.99 - 0.98 6648 131 0.75 32.70 1.04 0.91 285.67| |alpha: min = 0.90 max = 1.10 mean = 1.02| |beta: min = 285.67 max = 35554.56 mean = 2787.52| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 21.35| |phase err.(test): min = 0.00 max = 89.22 mean = 21.41| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.270 2950 Z= 5.356 Angle : 5.180 17.404 4018 Z= 3.689 Chirality : 0.363 1.132 492 Planarity : 0.032 0.105 512 Dihedral : 12.680 82.818 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.29 % Allowed : 4.84 % Favored : 93.87 % Cbeta Deviations : 31.18 % 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: -2.22 (0.38), residues: 386 helix: -2.09 (0.34), residues: 146 sheet: -0.94 (0.54), residues: 86 loop : -0.86 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.111 0.015 ARG A 175 TYR 0.166 0.038 TYR A 194 PHE 0.135 0.038 PHE B 164 TRP 0.137 0.039 TRP A 139 HIS 0.075 0.021 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= 0.2023 r_free= 0.1978 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.291064 | | target function (ml) not normalized (work): 803772.061359 | | target function (ml) not normalized (free): 16523.494357 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2021 0.2023 0.1978 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2021 0.2023 0.1978 n_refl.: 191155 remove outliers: r(all,work,free)=0.2021 0.2023 0.1978 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2022 0.2023 0.1978 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1789 0.1786 0.1904 n_refl.: 191145 remove outliers: r(all,work,free)=0.1787 0.1784 0.1904 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4114 402.814 290.686 0.434 0.911 0.305 13.296-10.522 99.01 99 1 0.2505 528.187 520.415 0.797 0.912 0.263 10.503-8.327 99.45 178 3 0.2507 565.118 556.471 0.976 0.913 0.243 8.318-6.595 100.00 360 8 0.2445 414.736 405.118 0.973 0.913 0.179 6.588-5.215 100.00 711 7 0.2266 381.101 366.442 0.961 0.913 0.160 5.214-4.128 98.38 1367 28 0.1461 557.435 550.135 1.075 0.913 0.090 4.126-3.266 94.74 2603 46 0.1357 508.132 499.121 1.141 0.913 0.018 3.266-2.585 99.86 5447 97 0.1435 342.774 337.782 1.118 0.912 0.000 2.585-2.046 97.45 10613 204 0.1398 258.603 254.107 1.124 0.912 0.000 2.046-1.619 99.39 21536 464 0.1599 153.054 150.025 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1894 82.395 80.201 1.130 0.908 0.000 1.281-0.980 96.53 101826 2056 0.2297 44.203 41.712 1.112 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0057 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1784 r_free=0.1904 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=0.1785 r_free=0.1904 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.797304 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 580.075657 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 0.1274 0.1485 0.0212 0.035 1.2 11.7 0.0 0.6 0 11.899 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.74 14.85 2.12 1.119 13.114 580.076 0.019 13.03 15.54 2.51 1.293 13.387 580.076 0.018 Individual atomic B min max mean iso aniso Overall: 5.18 73.05 15.10 1.43 435 3274 Protein: 5.18 40.42 11.05 1.43 0 2902 Water: 6.38 73.05 29.68 N/A 435 370 Other: 16.14 31.21 23.67 N/A 0 2 Chain A: 5.33 60.18 13.12 N/A 0 1626 Chain B: 5.18 73.05 12.85 N/A 0 1648 Chain S: 11.57 63.24 30.99 N/A 435 0 Histogram: Values Number of atoms 5.18 - 11.97 2157 11.97 - 18.75 634 18.75 - 25.54 316 25.54 - 32.33 265 32.33 - 39.11 158 39.11 - 45.90 105 45.90 - 52.69 55 52.69 - 59.47 13 59.47 - 66.26 5 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1304 r_free=0.1554 r_work=0.1302 r_free=0.1550 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1302 r_free = 0.1550 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1287 r_free = 0.1538 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1287 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015817 | | target function (ls_wunit_k1) not normalized (work): 2962.549049 | | target function (ls_wunit_k1) not normalized (free): 113.958808 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1292 0.1287 0.1538 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1476 0.1474 0.1614 n_refl.: 191139 remove outliers: r(all,work,free)=0.1476 0.1474 0.1614 n_refl.: 191139 overall B=0.17 to atoms: r(all,work,free)=0.1501 0.1499 0.1625 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1284 0.1279 0.1530 n_refl.: 191139 remove outliers: r(all,work,free)=0.1284 0.1279 0.1529 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 0.3661 402.814 375.481 0.485 0.962 0.287 13.296-10.522 99.01 99 1 0.2092 528.187 521.791 0.747 0.964 0.270 10.503-8.327 99.45 178 3 0.1759 565.118 560.001 0.885 0.964 0.218 8.318-6.595 100.00 360 8 0.1749 414.736 411.437 0.910 0.964 0.165 6.588-5.215 100.00 711 7 0.1573 381.101 373.100 0.888 0.964 0.160 5.214-4.128 98.38 1367 28 0.0923 557.435 554.017 0.977 0.964 0.090 4.126-3.266 94.74 2603 46 0.0859 508.132 504.199 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0929 342.774 340.296 1.026 0.964 0.000 2.585-2.046 97.45 10613 204 0.0948 258.603 256.462 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1083 153.054 151.386 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.405 1.048 0.964 0.000 1.281-0.980 96.53 101826 2055 0.1881 44.202 42.138 1.026 0.963 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0379 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1279 r_free=0.1529 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1279 r_free=0.1529 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1529 | n_water=805 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1281 r_free=0.1531 | n_water=800 | time (s): 98.190 (total time: 100.640) Filter (q & B) r_work=0.1281 r_free=0.1532 | n_water=795 | time (s): 4.230 (total time: 104.870) Compute maps r_work=0.1281 r_free=0.1532 | n_water=795 | time (s): 2.310 (total time: 107.180) Filter (map) r_work=0.1305 r_free=0.1517 | n_water=668 | time (s): 4.990 (total time: 112.170) Find peaks r_work=0.1305 r_free=0.1517 | n_water=668 | time (s): 0.910 (total time: 113.080) Add new water r_work=0.1330 r_free=0.1548 | n_water=981 | time (s): 5.040 (total time: 118.120) Refine new water occ: r_work=0.1285 r_free=0.1503 adp: r_work=0.1272 r_free=0.1499 occ: r_work=0.1275 r_free=0.1495 adp: r_work=0.1268 r_free=0.1494 occ: r_work=0.1270 r_free=0.1493 adp: r_work=0.1267 r_free=0.1494 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1494 r_work=0.1267 r_free=0.1494 | n_water=981 | time (s): 85.340 (total time: 203.460) Filter (q & B) r_work=0.1270 r_free=0.1497 | n_water=907 | time (s): 5.060 (total time: 208.520) Filter (dist only) r_work=0.1270 r_free=0.1497 | n_water=906 | time (s): 115.190 (total time: 323.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.974723 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 578.854296 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1253 0.1516 0.0262 0.039 1.2 19.7 0.0 0.3 0 12.487 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.16 2.62 2.062 15.378 578.854 0.014 12.30 15.03 2.73 2.448 15.405 578.854 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 68.81 16.57 1.20 537 3273 Protein: 5.40 39.96 11.02 1.20 0 2902 Water: 6.61 68.81 34.33 N/A 537 369 Other: 16.27 33.05 24.66 N/A 0 2 Chain A: 5.54 56.09 13.08 N/A 0 1625 Chain B: 5.40 68.21 12.87 N/A 0 1648 Chain S: 13.88 68.81 38.50 N/A 537 0 Histogram: Values Number of atoms 5.40 - 11.74 2055 11.74 - 18.08 717 18.08 - 24.42 264 24.42 - 30.76 231 30.76 - 37.10 163 37.10 - 43.45 154 43.45 - 49.79 105 49.79 - 56.13 60 56.13 - 62.47 46 62.47 - 68.81 15 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1504 r_work=0.1231 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1505 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 = 0.1224 r_free = 0.1497 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1224 r_free= 0.1497 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013247 | | target function (ls_wunit_k1) not normalized (work): 2481.204642 | | target function (ls_wunit_k1) not normalized (free): 99.804332 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1224 0.1497 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1605 n_refl.: 191138 remove outliers: r(all,work,free)=0.1434 0.1431 0.1605 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1428 0.1602 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1507 n_refl.: 191138 remove outliers: r(all,work,free)=0.1237 0.1231 0.1507 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 0.3094 402.814 383.693 0.501 0.963 0.281 13.296-10.522 99.01 99 1 0.1881 528.187 519.876 0.769 0.964 0.260 10.503-8.327 99.45 178 3 0.1426 565.118 566.418 0.923 0.964 0.196 8.318-6.595 100.00 360 8 0.1495 414.736 414.359 0.937 0.964 0.151 6.588-5.215 100.00 711 7 0.1329 381.101 377.072 0.913 0.964 0.130 5.214-4.128 98.38 1367 28 0.0813 557.435 555.932 0.993 0.964 0.090 4.126-3.266 94.74 2603 46 0.0764 508.132 505.178 1.057 0.964 0.015 3.266-2.585 99.86 5447 97 0.0850 342.774 341.338 1.046 0.962 0.010 2.585-2.046 97.45 10613 204 0.0892 258.603 256.747 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1043 153.054 151.639 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1258 82.395 81.345 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.205 1.061 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0537 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1507 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1507 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1507 | n_water=906 | time (s): 3.260 (total time: 3.260) Filter (dist) r_work=0.1233 r_free=0.1509 | n_water=903 | time (s): 129.490 (total time: 132.750) Filter (q & B) r_work=0.1234 r_free=0.1509 | n_water=900 | time (s): 4.930 (total time: 137.680) Compute maps r_work=0.1234 r_free=0.1509 | n_water=900 | time (s): 2.090 (total time: 139.770) Filter (map) r_work=0.1269 r_free=0.1510 | n_water=713 | time (s): 5.740 (total time: 145.510) Find peaks r_work=0.1269 r_free=0.1510 | n_water=713 | time (s): 0.820 (total time: 146.330) Add new water r_work=0.1294 r_free=0.1542 | n_water=1015 | time (s): 4.900 (total time: 151.230) Refine new water occ: r_work=0.1251 r_free=0.1505 adp: r_work=0.1251 r_free=0.1505 occ: r_work=0.1247 r_free=0.1504 adp: r_work=0.1247 r_free=0.1504 occ: r_work=0.1244 r_free=0.1504 adp: r_work=0.1243 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1503 r_work=0.1243 r_free=0.1503 | n_water=1015 | time (s): 360.910 (total time: 512.140) Filter (q & B) r_work=0.1248 r_free=0.1506 | n_water=885 | time (s): 5.990 (total time: 518.130) Filter (dist only) r_work=0.1248 r_free=0.1506 | n_water=884 | time (s): 117.320 (total time: 635.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.793851 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.261360 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 0.1239 0.1434 0.0194 0.035 1.1 7.0 0.0 0.0 0 0.897 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.34 1.94 1.941 14.694 16.261 3.942 12.31 13.90 1.59 2.260 14.591 16.261 3.897 Individual atomic B min max mean iso aniso Overall: 5.51 67.76 15.40 1.06 518 3270 Protein: 5.51 36.39 10.76 1.06 0 2902 Water: 6.68 67.76 30.61 N/A 518 366 Other: 14.09 28.47 21.28 N/A 0 2 Chain A: 5.58 55.14 12.83 N/A 0 1625 Chain B: 5.51 67.76 12.52 N/A 0 1645 Chain S: 14.72 59.89 32.62 N/A 518 0 Histogram: Values Number of atoms 5.51 - 11.74 2122 11.74 - 17.96 682 17.96 - 24.19 301 24.19 - 30.41 238 30.41 - 36.64 183 36.64 - 42.86 137 42.86 - 49.08 82 49.08 - 55.31 32 55.31 - 61.53 10 61.53 - 67.76 1 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1390 r_work=0.1231 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1391 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1388 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= 0.1226 r_free= 0.1388 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891816 | | target function (ml) not normalized (work): 728925.538885 | | target function (ml) not normalized (free): 15229.162126 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1226 0.1387 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1439 0.1481 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1439 0.1481 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1433 0.1433 0.1477 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1225 0.1222 0.1382 n_refl.: 191138 remove outliers: r(all,work,free)=0.1225 0.1222 0.1382 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3817 398.008 366.535 0.449 0.947 0.287 13.296-10.522 99.01 99 1 0.2426 528.187 508.655 0.709 0.949 0.222 10.503-8.327 98.35 176 3 0.2035 555.265 555.770 0.887 0.949 0.159 8.318-6.595 100.00 360 8 0.2052 414.736 410.706 0.895 0.948 0.125 6.588-5.215 100.00 711 7 0.1798 381.101 371.142 0.885 0.948 0.110 5.214-4.128 98.38 1367 28 0.1165 557.435 551.702 0.971 0.948 0.080 4.126-3.266 94.74 2603 46 0.1093 508.132 501.246 1.030 0.949 0.019 3.266-2.585 99.86 5447 97 0.1077 342.774 339.152 1.019 0.948 0.010 2.585-2.046 97.45 10613 204 0.0962 258.603 255.735 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0965 153.054 151.421 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1054 82.395 81.473 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1690 44.202 42.307 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1041 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1222 r_free=0.1382 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1222 r_free=0.1382 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1222 r_free=0.1382 | n_water=884 | time (s): 3.030 (total time: 3.030) Filter (dist) r_work=0.1223 r_free=0.1384 | n_water=883 | time (s): 116.930 (total time: 119.960) Filter (q & B) r_work=0.1223 r_free=0.1380 | n_water=874 | time (s): 4.360 (total time: 124.320) Compute maps r_work=0.1223 r_free=0.1380 | n_water=874 | time (s): 2.540 (total time: 126.860) Filter (map) r_work=0.1249 r_free=0.1380 | n_water=725 | time (s): 5.340 (total time: 132.200) Find peaks r_work=0.1249 r_free=0.1380 | n_water=725 | time (s): 0.590 (total time: 132.790) Add new water r_work=0.1264 r_free=0.1404 | n_water=959 | time (s): 4.170 (total time: 136.960) Refine new water occ: r_work=0.1215 r_free=0.1358 adp: r_work=0.1207 r_free=0.1355 occ: r_work=0.1205 r_free=0.1356 adp: r_work=0.1205 r_free=0.1355 occ: r_work=0.1203 r_free=0.1356 adp: r_work=0.1202 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1355 r_work=0.1202 r_free=0.1355 | n_water=959 | time (s): 319.970 (total time: 456.930) Filter (q & B) r_work=0.1207 r_free=0.1361 | n_water=867 | time (s): 5.920 (total time: 462.850) Filter (dist only) r_work=0.1208 r_free=0.1362 | n_water=865 | time (s): 112.050 (total time: 574.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.564416 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.043877 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 0.1207 0.1363 0.0155 0.036 1.1 6.1 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.63 1.55 1.838 14.230 16.044 3.875 11.99 13.60 1.61 1.925 14.194 16.044 3.866 Individual atomic B min max mean iso aniso Overall: 5.51 67.35 15.00 1.02 499 3270 Protein: 5.51 33.55 10.70 1.02 0 2902 Water: 5.92 67.35 29.42 N/A 499 366 Other: 14.02 27.63 20.82 N/A 0 2 Chain A: 5.53 54.18 12.71 N/A 0 1625 Chain B: 5.51 67.35 12.44 N/A 0 1645 Chain S: 5.92 59.92 30.90 N/A 499 0 Histogram: Values Number of atoms 5.51 - 11.70 2116 11.70 - 17.88 718 17.88 - 24.06 302 24.06 - 30.25 241 30.25 - 36.43 170 36.43 - 42.62 115 42.62 - 48.80 69 48.80 - 54.98 30 54.98 - 61.17 7 61.17 - 67.35 1 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1361 r_work=0.1200 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1361 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864055 | | target function (ml) not normalized (work): 723714.383848 | | target function (ml) not normalized (free): 15143.464348 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1430 0.1429 0.1474 n_refl.: 191135 remove outliers: r(all,work,free)=0.1430 0.1429 0.1474 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1422 0.1421 0.1469 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191135 remove outliers: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3752 360.258 325.082 0.422 0.945 0.248 13.296-10.522 99.01 99 1 0.2409 478.091 458.855 0.700 0.947 0.199 10.503-8.327 98.35 176 3 0.2151 502.600 495.857 0.869 0.947 0.190 8.318-6.595 100.00 360 8 0.2173 375.400 369.783 0.895 0.947 0.120 6.588-5.215 100.00 711 7 0.1908 344.955 334.788 0.885 0.947 0.100 5.214-4.128 98.38 1367 28 0.1202 504.564 499.238 0.974 0.947 0.090 4.126-3.266 94.74 2603 46 0.1119 459.938 453.219 1.034 0.947 0.005 3.266-2.585 99.86 5447 97 0.1090 310.263 306.816 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0929 234.076 231.640 1.034 0.946 0.000 2.046-1.619 99.39 21536 464 0.0909 138.537 137.226 1.058 0.946 0.000 1.619-1.281 98.00 42464 925 0.0988 74.581 73.849 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.009 38.345 1.041 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1218 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1196 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1351 | n_water=865 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1196 r_free=0.1351 | n_water=865 | time (s): 105.970 (total time: 108.560) Filter (q & B) r_work=0.1197 r_free=0.1351 | n_water=856 | time (s): 4.540 (total time: 113.100) Compute maps r_work=0.1197 r_free=0.1351 | n_water=856 | time (s): 1.840 (total time: 114.940) Filter (map) r_work=0.1218 r_free=0.1362 | n_water=734 | time (s): 4.370 (total time: 119.310) Find peaks r_work=0.1218 r_free=0.1362 | n_water=734 | time (s): 0.590 (total time: 119.900) Add new water r_work=0.1231 r_free=0.1387 | n_water=970 | time (s): 3.910 (total time: 123.810) Refine new water occ: r_work=0.1195 r_free=0.1352 adp: r_work=0.1195 r_free=0.1352 occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1192 r_free=0.1350 occ: r_work=0.1191 r_free=0.1350 adp: r_work=0.1190 r_free=0.1350 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1350 r_work=0.1190 r_free=0.1350 | n_water=970 | time (s): 232.300 (total time: 356.110) Filter (q & B) r_work=0.1195 r_free=0.1354 | n_water=875 | time (s): 4.350 (total time: 360.460) Filter (dist only) r_work=0.1195 r_free=0.1355 | n_water=873 | time (s): 114.840 (total time: 475.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.578619 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.643590 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 0.036 1.1 6.5 0.0 0.3 0 0.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.55 1.57 1.805 14.153 15.644 3.764 12.01 13.56 1.56 1.870 14.125 15.644 3.761 Individual atomic B min max mean iso aniso Overall: 5.58 67.02 14.95 0.97 508 3269 Protein: 5.58 32.56 10.63 0.97 0 2902 Water: 6.04 67.02 29.30 N/A 508 365 Other: 13.83 26.57 20.20 N/A 0 2 Chain A: 5.58 53.45 12.60 N/A 0 1624 Chain B: 5.58 67.02 12.35 N/A 0 1645 Chain S: 6.04 59.94 30.87 N/A 508 0 Histogram: Values Number of atoms 5.58 - 11.73 2137 11.73 - 17.87 710 17.87 - 24.01 309 24.01 - 30.16 226 30.16 - 36.30 166 36.30 - 42.44 121 42.44 - 48.59 70 48.59 - 54.73 31 54.73 - 60.87 6 60.87 - 67.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1356 r_work=0.1201 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1357 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1357 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759771 | | target function (ml) not normalized (work): 704182.493004 | | target function (ml) not normalized (free): 14740.149641 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1357 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1428 0.1427 0.1487 n_refl.: 191135 remove outliers: r(all,work,free)=0.1428 0.1427 0.1487 n_refl.: 191135 overall B=-0.04 to atoms: r(all,work,free)=0.1420 0.1419 0.1481 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1356 n_refl.: 191135 remove outliers: r(all,work,free)=0.1200 0.1197 0.1356 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 0.3432 359.949 317.175 0.415 0.947 0.241 13.296-10.522 99.01 99 1 0.2486 478.091 456.405 0.692 0.948 0.190 10.503-8.327 98.35 176 3 0.2144 502.600 496.614 0.866 0.948 0.148 8.318-6.595 100.00 360 8 0.2147 375.400 369.989 0.891 0.948 0.105 6.588-5.215 100.00 711 7 0.1914 344.955 334.783 0.885 0.948 0.090 5.214-4.128 98.38 1367 28 0.1209 504.564 499.116 0.973 0.948 0.080 4.126-3.266 94.74 2603 46 0.1143 459.938 453.074 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1108 310.263 306.743 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0944 234.076 231.665 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0909 138.537 137.238 1.058 0.946 0.000 1.619-1.281 98.00 42464 925 0.0978 74.581 73.876 1.056 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.009 38.345 1.045 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1300 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1356 | n_water=873 | time (s): 3.230 (total time: 3.230) Filter (dist) r_work=0.1197 r_free=0.1356 | n_water=873 | time (s): 105.560 (total time: 108.790) Filter (q & B) r_work=0.1197 r_free=0.1354 | n_water=862 | time (s): 5.330 (total time: 114.120) Compute maps r_work=0.1197 r_free=0.1354 | n_water=862 | time (s): 2.190 (total time: 116.310) Filter (map) r_work=0.1216 r_free=0.1348 | n_water=755 | time (s): 5.120 (total time: 121.430) Find peaks r_work=0.1216 r_free=0.1348 | n_water=755 | time (s): 0.560 (total time: 121.990) Add new water r_work=0.1226 r_free=0.1362 | n_water=975 | time (s): 4.330 (total time: 126.320) Refine new water occ: r_work=0.1195 r_free=0.1346 adp: r_work=0.1195 r_free=0.1346 occ: r_work=0.1193 r_free=0.1344 adp: r_work=0.1192 r_free=0.1344 occ: r_work=0.1192 r_free=0.1344 adp: r_work=0.1192 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1345 r_work=0.1192 r_free=0.1345 | n_water=975 | time (s): 293.840 (total time: 420.160) Filter (q & B) r_work=0.1198 r_free=0.1356 | n_water=871 | time (s): 4.440 (total time: 424.600) Filter (dist only) r_work=0.1198 r_free=0.1356 | n_water=868 | time (s): 112.410 (total time: 537.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.612818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.529949 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 0.1360 0.0159 0.037 1.1 5.3 0.0 0.3 0 0.806 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.60 1.59 1.775 13.994 14.530 3.761 12.06 13.65 1.59 1.933 13.938 14.530 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 65.90 14.70 0.91 503 3269 Protein: 5.58 29.50 10.51 0.91 0 2902 Water: 5.97 65.90 28.71 N/A 503 365 Other: 13.88 23.92 18.90 N/A 0 2 Chain A: 5.63 52.43 12.43 N/A 0 1624 Chain B: 5.58 65.90 12.21 N/A 0 1645 Chain S: 5.97 60.06 30.16 N/A 503 0 Histogram: Values Number of atoms 5.58 - 11.61 2114 11.61 - 17.65 763 17.65 - 23.68 304 23.68 - 29.71 208 29.71 - 35.74 162 35.74 - 41.77 113 41.77 - 47.80 64 47.80 - 53.83 37 53.83 - 59.87 5 59.87 - 65.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1365 r_work=0.1206 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1366 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1365 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758654 | | target function (ml) not normalized (work): 703969.622364 | | target function (ml) not normalized (free): 14741.024736 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1365 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1425 0.1424 0.1498 n_refl.: 191134 remove outliers: r(all,work,free)=0.1425 0.1424 0.1498 n_refl.: 191134 overall B=-0.24 to atoms: r(all,work,free)=0.1383 0.1381 0.1471 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1203 0.1366 n_refl.: 191134 remove outliers: r(all,work,free)=0.1207 0.1203 0.1366 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 0.3654 359.949 333.600 0.445 0.946 0.245 13.296-10.522 99.01 99 1 0.2497 478.091 457.463 0.709 0.947 0.189 10.503-8.327 98.35 176 3 0.2204 502.600 496.449 0.887 0.947 0.163 8.318-6.595 100.00 360 8 0.2212 375.400 369.628 0.914 0.947 0.100 6.588-5.215 100.00 711 7 0.1943 344.955 334.547 0.909 0.947 0.090 5.214-4.128 98.38 1367 28 0.1231 504.564 498.827 0.999 0.948 0.080 4.126-3.266 94.74 2603 46 0.1165 459.938 452.649 1.061 0.948 0.005 3.266-2.585 99.86 5447 97 0.1125 310.263 306.731 1.044 0.948 0.000 2.585-2.046 97.45 10613 204 0.0955 234.076 231.569 1.052 0.948 0.000 2.046-1.619 99.39 21536 464 0.0912 138.537 137.222 1.069 0.949 0.000 1.619-1.281 98.00 42464 925 0.0972 74.581 73.870 1.054 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.009 38.350 1.022 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0537 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1204 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1366 | n_water=868 | time (s): 3.200 (total time: 3.200) Filter (dist) r_work=0.1204 r_free=0.1367 | n_water=867 | time (s): 123.650 (total time: 126.850) Filter (q & B) r_work=0.1204 r_free=0.1366 | n_water=858 | time (s): 5.740 (total time: 132.590) Compute maps r_work=0.1204 r_free=0.1366 | n_water=858 | time (s): 2.590 (total time: 135.180) Filter (map) r_work=0.1224 r_free=0.1356 | n_water=751 | time (s): 4.380 (total time: 139.560) Find peaks r_work=0.1224 r_free=0.1356 | n_water=751 | time (s): 0.790 (total time: 140.350) Add new water r_work=0.1235 r_free=0.1368 | n_water=975 | time (s): 5.060 (total time: 145.410) Refine new water occ: r_work=0.1201 r_free=0.1354 adp: r_work=0.1201 r_free=0.1354 occ: r_work=0.1198 r_free=0.1353 adp: r_work=0.1198 r_free=0.1353 occ: r_work=0.1196 r_free=0.1354 adp: r_work=0.1196 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1353 r_work=0.1196 r_free=0.1353 | n_water=975 | time (s): 241.540 (total time: 386.950) Filter (q & B) r_work=0.1200 r_free=0.1362 | n_water=899 | time (s): 4.320 (total time: 391.270) Filter (dist only) r_work=0.1201 r_free=0.1361 | n_water=897 | time (s): 117.440 (total time: 508.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.556067 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.674714 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 0.1204 0.1364 0.0160 0.037 1.1 8.4 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.64 1.60 1.724 13.733 14.675 3.760 12.04 13.66 1.62 1.783 13.710 14.675 3.757 Individual atomic B min max mean iso aniso Overall: 5.40 64.34 14.59 0.89 532 3269 Protein: 5.40 28.47 10.24 0.89 0 2902 Water: 5.84 64.34 28.65 N/A 532 365 Other: 13.67 22.06 17.87 N/A 0 2 Chain A: 5.41 52.04 12.12 N/A 0 1624 Chain B: 5.40 64.34 11.92 N/A 0 1645 Chain S: 5.84 59.98 30.38 N/A 532 0 Histogram: Values Number of atoms 5.40 - 11.30 2093 11.30 - 17.19 784 17.19 - 23.08 290 23.08 - 28.98 212 28.98 - 34.87 177 34.87 - 40.77 119 40.77 - 46.66 80 46.66 - 52.55 35 52.55 - 58.45 8 58.45 - 64.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1367 r_work=0.1205 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1367 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1367 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756517 | | target function (ml) not normalized (work): 703569.314164 | | target function (ml) not normalized (free): 14735.497843 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1367 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1386 0.1384 0.1476 n_refl.: 191134 remove outliers: r(all,work,free)=0.1386 0.1384 0.1476 n_refl.: 191134 overall B=0.10 to atoms: r(all,work,free)=0.1402 0.1400 0.1486 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1355 n_refl.: 191134 remove outliers: r(all,work,free)=0.1195 0.1192 0.1355 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3649 360.758 328.009 0.418 0.970 0.229 13.296-10.522 98.02 98 1 0.2447 478.735 454.927 0.678 0.972 0.165 10.503-8.327 98.35 176 3 0.2221 502.600 495.111 0.863 0.972 0.136 8.318-6.595 100.00 360 8 0.2174 375.400 369.520 0.887 0.972 0.101 6.588-5.215 100.00 711 7 0.1938 344.955 334.376 0.882 0.972 0.083 5.214-4.128 98.38 1367 28 0.1227 504.564 498.755 0.972 0.973 0.070 4.126-3.266 94.74 2603 46 0.1165 459.938 452.264 1.033 0.974 0.009 3.266-2.585 99.86 5447 97 0.1131 310.263 306.564 1.016 0.974 0.000 2.585-2.046 97.45 10613 204 0.0957 234.076 231.495 1.025 0.976 0.000 2.046-1.619 99.39 21536 464 0.0907 138.537 137.154 1.043 0.978 0.000 1.619-1.281 98.00 42464 925 0.0947 74.581 73.924 1.034 0.982 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.009 38.328 1.003 0.988 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0235 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1355 | n_water=897 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1192 r_free=0.1355 | n_water=897 | time (s): 120.640 (total time: 123.230) Filter (q & B) r_work=0.1193 r_free=0.1353 | n_water=884 | time (s): 5.400 (total time: 128.630) Compute maps r_work=0.1193 r_free=0.1353 | n_water=884 | time (s): 1.810 (total time: 130.440) Filter (map) r_work=0.1213 r_free=0.1346 | n_water=770 | time (s): 4.430 (total time: 134.870) Find peaks r_work=0.1213 r_free=0.1346 | n_water=770 | time (s): 0.660 (total time: 135.530) Add new water r_work=0.1223 r_free=0.1358 | n_water=989 | time (s): 5.110 (total time: 140.640) Refine new water occ: r_work=0.1190 r_free=0.1346 adp: r_work=0.1190 r_free=0.1347 occ: r_work=0.1188 r_free=0.1343 adp: r_work=0.1188 r_free=0.1344 occ: r_work=0.1186 r_free=0.1341 adp: r_work=0.1186 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1343 r_work=0.1186 r_free=0.1343 | n_water=989 | time (s): 232.890 (total time: 373.530) Filter (q & B) r_work=0.1191 r_free=0.1346 | n_water=901 | time (s): 4.720 (total time: 378.250) Filter (dist only) r_work=0.1191 r_free=0.1345 | n_water=899 | time (s): 114.240 (total time: 492.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.486225 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.146192 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1350 0.0156 0.038 1.1 5.6 0.0 0.3 0 0.743 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.50 1.56 1.679 13.775 15.146 3.755 11.94 13.52 1.58 1.682 13.770 15.146 3.752 Individual atomic B min max mean iso aniso Overall: 5.48 63.91 14.68 0.89 534 3269 Protein: 5.48 28.42 10.37 0.89 0 2902 Water: 5.91 63.91 28.61 N/A 534 365 Other: 13.80 22.29 18.05 N/A 0 2 Chain A: 5.59 52.06 12.21 N/A 0 1624 Chain B: 5.48 63.91 12.02 N/A 0 1645 Chain S: 5.91 60.16 30.43 N/A 534 0 Histogram: Values Number of atoms 5.48 - 11.33 2057 11.33 - 17.17 823 17.17 - 23.01 286 23.01 - 28.85 211 28.85 - 34.70 177 34.70 - 40.54 120 40.54 - 46.38 86 46.38 - 52.23 29 52.23 - 58.07 11 58.07 - 63.91 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1352 r_work=0.1194 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1352 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1351 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751906 | | target function (ml) not normalized (work): 702698.247891 | | target function (ml) not normalized (free): 14720.694676 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1351 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1390 0.1389 0.1481 n_refl.: 191132 remove outliers: r(all,work,free)=0.1390 0.1389 0.1481 n_refl.: 191132 overall B=-0.00 to atoms: r(all,work,free)=0.1390 0.1389 0.1481 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191132 remove outliers: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3694 360.758 330.842 0.419 0.973 0.215 13.296-10.522 98.02 98 1 0.2450 478.735 459.351 0.683 0.974 0.147 10.503-8.327 98.35 176 3 0.2256 502.600 494.371 0.868 0.975 0.114 8.318-6.595 100.00 360 8 0.2163 375.400 369.758 0.891 0.974 0.093 6.588-5.215 100.00 711 7 0.1944 344.955 334.529 0.888 0.975 0.075 5.214-4.128 98.38 1367 28 0.1227 504.564 498.708 0.979 0.976 0.040 4.126-3.266 94.74 2603 46 0.1166 459.938 451.936 1.042 0.977 0.009 3.266-2.585 99.86 5447 97 0.1129 310.263 306.508 1.025 0.978 0.000 2.585-2.046 97.45 10613 204 0.0958 234.076 231.451 1.034 0.980 0.000 2.046-1.619 99.39 21536 464 0.0906 138.537 137.149 1.052 0.983 0.000 1.619-1.281 98.00 42464 925 0.0941 74.581 73.931 1.044 0.988 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.009 38.309 1.014 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0002 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1348 | n_water=899 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1190 r_free=0.1347 | n_water=898 | time (s): 121.690 (total time: 124.120) Filter (q & B) r_work=0.1190 r_free=0.1347 | n_water=891 | time (s): 4.480 (total time: 128.600) Compute maps r_work=0.1190 r_free=0.1347 | n_water=891 | time (s): 2.020 (total time: 130.620) Filter (map) r_work=0.1211 r_free=0.1346 | n_water=779 | time (s): 4.770 (total time: 135.390) Find peaks r_work=0.1211 r_free=0.1346 | n_water=779 | time (s): 0.750 (total time: 136.140) Add new water r_work=0.1219 r_free=0.1353 | n_water=994 | time (s): 4.100 (total time: 140.240) Refine new water occ: r_work=0.1187 r_free=0.1340 adp: r_work=0.1187 r_free=0.1340 occ: r_work=0.1185 r_free=0.1338 adp: r_work=0.1185 r_free=0.1338 occ: r_work=0.1184 r_free=0.1337 adp: r_work=0.1184 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1337 r_work=0.1184 r_free=0.1337 | n_water=994 | time (s): 293.800 (total time: 434.040) Filter (q & B) r_work=0.1188 r_free=0.1343 | n_water=908 | time (s): 4.550 (total time: 438.590) Filter (dist only) r_work=0.1189 r_free=0.1341 | n_water=906 | time (s): 118.390 (total time: 556.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.539193 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.308877 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 0.1345 0.0155 0.038 1.1 7.0 0.0 0.3 0 0.770 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.45 1.55 1.691 13.797 14.309 3.752 11.93 13.48 1.56 1.690 13.796 14.309 3.752 Individual atomic B min max mean iso aniso Overall: 5.56 63.68 14.70 0.87 541 3269 Protein: 5.56 28.29 10.38 0.87 0 2902 Water: 5.95 63.68 28.52 N/A 541 365 Other: 13.82 22.29 18.06 N/A 0 2 Chain A: 5.60 52.03 12.20 N/A 0 1624 Chain B: 5.56 63.68 12.02 N/A 0 1645 Chain S: 5.95 60.19 30.34 N/A 541 0 Histogram: Values Number of atoms 5.56 - 11.37 2070 11.37 - 17.18 814 17.18 - 22.99 289 22.99 - 28.81 210 28.81 - 34.62 179 34.62 - 40.43 119 40.43 - 46.24 85 46.24 - 52.05 30 52.05 - 57.87 11 57.87 - 63.68 3 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1348 r_work=0.1193 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1349 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1348 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1348 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751856 | | target function (ml) not normalized (work): 702688.823226 | | target function (ml) not normalized (free): 14722.393295 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1348 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1497 n_refl.: 191132 remove outliers: r(all,work,free)=0.1397 0.1395 0.1497 n_refl.: 191132 overall B=-0.01 to atoms: r(all,work,free)=0.1395 0.1394 0.1496 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191132 remove outliers: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3668 360.758 330.637 0.403 0.994 0.213 13.296-10.522 98.02 98 1 0.2476 478.735 459.369 0.660 0.996 0.144 10.503-8.327 98.35 176 3 0.2224 502.600 494.641 0.841 0.996 0.108 8.318-6.595 100.00 360 8 0.2152 375.400 369.660 0.861 0.996 0.085 6.588-5.215 100.00 711 7 0.1941 344.955 334.623 0.860 0.997 0.067 5.214-4.128 98.38 1367 28 0.1228 504.564 498.669 0.948 0.998 0.035 4.126-3.266 94.74 2603 46 0.1167 459.938 452.011 1.009 0.999 0.009 3.266-2.585 99.86 5447 97 0.1128 310.263 306.552 0.993 1.000 0.000 2.585-2.046 97.45 10613 204 0.0962 234.076 231.404 1.002 1.002 0.000 2.046-1.619 99.39 21536 464 0.0908 138.537 137.149 1.019 1.006 0.000 1.619-1.281 98.00 42464 925 0.0940 74.581 73.928 1.012 1.012 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.009 38.298 0.984 1.023 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0252 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1348 After: r_work=0.1191 r_free=0.1348 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1348 | n_water=906 | time (s): 3.160 (total time: 3.160) Filter (dist) r_work=0.1191 r_free=0.1348 | n_water=906 | time (s): 115.090 (total time: 118.250) Filter (q & B) r_work=0.1192 r_free=0.1347 | n_water=895 | time (s): 6.150 (total time: 124.400) Compute maps r_work=0.1192 r_free=0.1347 | n_water=895 | time (s): 1.820 (total time: 126.220) Filter (map) r_work=0.1211 r_free=0.1352 | n_water=790 | time (s): 4.260 (total time: 130.480) Find peaks r_work=0.1211 r_free=0.1352 | n_water=790 | time (s): 0.630 (total time: 131.110) Add new water r_work=0.1218 r_free=0.1358 | n_water=997 | time (s): 5.000 (total time: 136.110) Refine new water occ: r_work=0.1188 r_free=0.1337 adp: r_work=0.1188 r_free=0.1338 occ: r_work=0.1186 r_free=0.1335 adp: r_work=0.1186 r_free=0.1336 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1336 r_work=0.1185 r_free=0.1336 | n_water=997 | time (s): 225.370 (total time: 361.480) Filter (q & B) r_work=0.1189 r_free=0.1344 | n_water=921 | time (s): 4.320 (total time: 365.800) Filter (dist only) r_work=0.1190 r_free=0.1342 | n_water=919 | time (s): 116.150 (total time: 481.950) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.526328 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.215485 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1347 0.0155 0.038 1.2 8.7 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.47 1.55 1.687 13.814 13.215 3.754 11.96 13.51 1.55 1.683 13.816 13.215 3.755 Individual atomic B min max mean iso aniso Overall: 5.61 63.50 14.73 0.85 554 3269 Protein: 5.61 28.16 10.39 0.85 0 2902 Water: 6.01 63.50 28.43 N/A 554 365 Other: 13.86 22.28 18.07 N/A 0 2 Chain A: 5.67 52.00 12.20 N/A 0 1624 Chain B: 5.61 63.50 12.02 N/A 0 1645 Chain S: 6.01 60.21 30.22 N/A 554 0 Histogram: Values Number of atoms 5.61 - 11.39 2073 11.39 - 17.18 816 17.18 - 22.97 291 22.97 - 28.76 213 28.76 - 34.55 183 34.55 - 40.34 118 40.34 - 46.13 85 46.13 - 51.92 28 51.92 - 57.71 13 57.71 - 63.50 3 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1351 r_work=0.1196 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1351 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1350 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755091 | | target function (ml) not normalized (work): 703294.718423 | | target function (ml) not normalized (free): 14726.223730 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7400 127 0.1356 0.1427 5.6853 5.7504| | 2: 2.94 - 2.33 1.00 7339 128 0.1076 0.1339 5.0716 5.1749| | 3: 2.33 - 2.04 0.96 6939 150 0.0908 0.1189 4.6619 4.7402| | 4: 2.04 - 1.85 1.00 7170 155 0.0905 0.1050 4.3977 4.5734| | 5: 1.85 - 1.72 0.99 7113 159 0.0938 0.1027 4.1564 4.2663| | 6: 1.72 - 1.62 0.99 7102 142 0.0902 0.1091 3.9518 4.08| | 7: 1.62 - 1.54 0.99 7104 148 0.0893 0.0948 3.8028 3.9284| | 8: 1.54 - 1.47 0.96 6798 152 0.0895 0.1318 3.7031 3.9065| | 9: 1.47 - 1.41 0.98 6938 155 0.0931 0.1134 3.6248 3.7554| | 10: 1.41 - 1.36 0.99 7022 150 0.0981 0.1191 3.5593 3.6705| | 11: 1.36 - 1.32 0.99 6997 151 0.0996 0.1134 3.4879 3.5921| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1120 3.4577 3.5729| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1238 3.4345 3.5632| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1571 3.4303 3.668| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1243 3.447 3.4874| | 16: 1.19 - 1.17 0.93 6604 132 0.1253 0.1546 3.4656 3.6583| | 17: 1.17 - 1.14 0.98 6940 135 0.1303 0.1241 3.4346 3.447| | 18: 1.14 - 1.12 0.98 6875 142 0.1386 0.1705 3.4392 3.5323| | 19: 1.12 - 1.10 0.97 6948 106 0.1472 0.1751 3.4199 3.5928| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1579 3.4094 3.4328| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2139 3.4188 3.5039| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1956 3.4133 3.4147| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2019 3.4336 3.4885| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2252 3.4358 3.5083| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2511 3.4487 3.5216| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2850 3.4154 3.4207| | 27: 0.99 - 0.98 0.94 6647 131 0.3045 0.2806 3.4692 3.3955| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7400 127 0.93 11.36 1.00 0.96 10736.98| | 2: 2.94 - 2.33 7339 128 0.93 12.60 0.99 0.96 4976.46| | 3: 2.33 - 2.04 6939 150 0.96 7.69 1.01 0.96 1707.02| | 4: 2.04 - 1.85 7170 155 0.96 7.74 1.00 0.96 1018.40| | 5: 1.85 - 1.72 7113 159 0.96 8.19 1.00 0.97 644.64| | 6: 1.72 - 1.62 7102 142 0.96 8.12 1.00 0.97 448.86| | 7: 1.62 - 1.54 7104 148 0.96 8.17 1.01 0.98 338.72| | 8: 1.54 - 1.47 6798 152 0.96 8.30 1.01 0.98 280.30| | 9: 1.47 - 1.41 6938 155 0.96 8.51 1.00 0.99 232.01| | 10: 1.41 - 1.36 7022 150 0.96 8.95 1.00 0.98 203.49| | 11: 1.36 - 1.32 6997 151 0.96 8.93 0.99 0.97 174.96| | 12: 1.32 - 1.28 6975 149 0.96 8.95 0.98 0.96 159.78| | 13: 1.28 - 1.25 6907 166 0.96 9.43 1.01 0.97 156.17| | 14: 1.25 - 1.22 7015 112 0.95 10.59 1.01 0.97 160.92| | 15: 1.22 - 1.19 6956 137 0.95 11.15 1.01 0.99 165.19| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.01 0.97 160.15| | 17: 1.17 - 1.14 6940 135 0.94 12.29 1.01 0.97 154.47| | 18: 1.14 - 1.12 6875 142 0.94 12.79 1.01 0.96 148.15| | 19: 1.12 - 1.10 6948 106 0.93 14.17 1.00 0.95 151.26| | 20: 1.10 - 1.08 6884 147 0.92 15.24 1.00 0.95 150.21| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.94 153.45| | 22: 1.07 - 1.05 6836 135 0.89 18.33 0.99 0.94 155.17| | 23: 1.05 - 1.03 6827 159 0.87 20.54 0.99 0.93 164.92| | 24: 1.03 - 1.02 6784 133 0.85 23.16 0.99 0.94 178.79| | 25: 1.02 - 1.01 6552 130 0.83 25.12 0.98 0.91 181.61| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.89 176.21| | 27: 0.99 - 0.98 6647 131 0.82 26.34 0.99 0.88 161.06| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 148.15 max = 10736.98 mean = 902.76| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.29| |phase err.(test): min = 0.00 max = 88.08 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1350 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1499 n_refl.: 191132 remove outliers: r(all,work,free)=0.1404 0.1402 0.1499 n_refl.: 191132 overall B=-0.08 to atoms: r(all,work,free)=0.1391 0.1389 0.1489 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191132 remove outliers: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3716 360.758 328.808 0.390 0.974 0.195 13.296-10.522 98.02 98 1 0.2494 478.735 458.876 0.659 0.976 0.129 10.503-8.327 98.35 176 3 0.2222 502.600 494.270 0.846 0.976 0.098 8.318-6.595 100.00 360 8 0.2133 375.400 369.648 0.865 0.976 0.073 6.588-5.215 100.00 711 7 0.1931 344.955 334.490 0.864 0.977 0.050 5.214-4.128 98.38 1367 28 0.1222 504.564 498.698 0.953 0.978 0.020 4.126-3.266 94.74 2603 46 0.1167 459.938 452.184 1.015 0.979 0.002 3.266-2.585 99.86 5447 97 0.1126 310.263 306.584 0.999 0.980 0.000 2.585-2.046 97.45 10613 204 0.0968 234.076 231.426 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0916 138.537 137.155 1.021 0.987 0.000 1.619-1.281 98.00 42464 925 0.0948 74.581 73.923 1.011 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.009 38.291 0.978 1.006 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0181 ================= 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 : 0.2023 0.1978 0.080 5.180 5.2 78.0 14.6 805 0.000 1_bss: 0.1784 0.1904 0.080 5.180 5.2 78.0 14.6 805 0.000 1_settarget: 0.1784 0.1904 0.080 5.180 5.2 78.0 14.6 805 0.000 1_nqh: 0.1785 0.1904 0.080 5.180 5.2 78.0 14.6 805 0.002 1_weight: 0.1785 0.1904 0.080 5.180 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1274 0.1485 0.035 1.177 5.2 78.0 14.6 805 0.142 1_adp: 0.1304 0.1554 0.035 1.177 5.2 73.0 15.1 805 0.142 1_regHadp: 0.1302 0.1550 0.035 1.177 5.2 73.0 15.1 805 0.142 1_occ: 0.1287 0.1538 0.035 1.177 5.2 73.0 15.1 805 0.142 2_bss: 0.1279 0.1529 0.035 1.177 5.3 73.2 15.3 805 0.142 2_settarget: 0.1279 0.1529 0.035 1.177 5.3 73.2 15.3 805 0.142 2_updatecdl: 0.1279 0.1529 0.035 1.186 5.3 73.2 15.3 805 0.142 2_nqh: 0.1279 0.1529 0.035 1.186 5.3 73.2 15.3 805 0.142 2_sol: 0.1270 0.1497 0.035 1.186 5.3 73.2 16.5 906 n/a 2_weight: 0.1270 0.1497 0.035 1.186 5.3 73.2 16.5 906 n/a 2_xyzrec: 0.1253 0.1516 0.039 1.158 5.3 73.2 16.5 906 n/a 2_adp: 0.1230 0.1504 0.039 1.158 5.4 68.8 16.6 906 n/a 2_regHadp: 0.1231 0.1505 0.039 1.158 5.4 68.8 16.6 906 n/a 2_occ: 0.1224 0.1497 0.039 1.158 5.4 68.8 16.6 906 n/a 3_bss: 0.1231 0.1507 0.039 1.158 5.4 68.8 16.6 906 n/a 3_settarget: 0.1231 0.1507 0.039 1.158 5.4 68.8 16.6 906 n/a 3_updatecdl: 0.1231 0.1507 0.039 1.158 5.4 68.8 16.6 906 n/a 3_nqh: 0.1231 0.1507 0.039 1.158 5.4 68.8 16.6 906 n/a 3_sol: 0.1248 0.1506 0.039 1.158 5.4 68.2 15.6 884 n/a 3_weight: 0.1248 0.1506 0.039 1.158 5.4 68.2 15.6 884 n/a 3_xyzrec: 0.1239 0.1434 0.035 1.109 5.4 68.2 15.6 884 n/a 3_adp: 0.1231 0.1390 0.035 1.109 5.5 67.8 15.4 884 n/a 3_regHadp: 0.1231 0.1391 0.035 1.109 5.5 67.8 15.4 884 n/a 3_occ: 0.1226 0.1388 0.035 1.109 5.5 67.8 15.4 884 n/a 4_bss: 0.1222 0.1382 0.035 1.109 5.5 67.7 15.4 884 n/a 4_settarget: 0.1222 0.1382 0.035 1.109 5.5 67.7 15.4 884 n/a 4_updatecdl: 0.1222 0.1382 0.035 1.109 5.5 67.7 15.4 884 n/a 4_nqh: 0.1222 0.1382 0.035 1.109 5.5 67.7 15.4 884 n/a 4_sol: 0.1208 0.1362 0.035 1.109 5.5 67.7 15.1 865 n/a 4_weight: 0.1208 0.1362 0.035 1.109 5.5 67.7 15.1 865 n/a 4_xyzrec: 0.1207 0.1363 0.036 1.114 5.5 67.7 15.1 865 n/a 4_adp: 0.1199 0.1361 0.036 1.114 5.5 67.4 15.0 865 n/a 4_regHadp: 0.1200 0.1361 0.036 1.114 5.5 67.4 15.0 865 n/a 4_occ: 0.1197 0.1357 0.036 1.114 5.5 67.4 15.0 865 n/a 5_bss: 0.1195 0.1350 0.036 1.114 5.5 67.3 15.0 865 n/a 5_settarget: 0.1195 0.1350 0.036 1.114 5.5 67.3 15.0 865 n/a 5_updatecdl: 0.1195 0.1350 0.036 1.114 5.5 67.3 15.0 865 n/a 5_nqh: 0.1196 0.1351 0.036 1.114 5.5 67.3 15.0 865 n/a 5_sol: 0.1195 0.1355 0.036 1.114 5.5 67.3 15.0 873 n/a 5_weight: 0.1195 0.1355 0.036 1.114 5.5 67.3 15.0 873 n/a 5_xyzrec: 0.1197 0.1355 0.036 1.128 5.5 67.3 15.0 873 n/a 5_adp: 0.1201 0.1356 0.036 1.128 5.6 67.0 14.9 873 n/a 5_regHadp: 0.1201 0.1357 0.036 1.128 5.6 67.0 14.9 873 n/a 5_occ: 0.1199 0.1357 0.036 1.128 5.6 67.0 14.9 873 n/a 6_bss: 0.1197 0.1356 0.036 1.128 5.5 67.0 14.9 873 n/a 6_settarget: 0.1197 0.1356 0.036 1.128 5.5 67.0 14.9 873 n/a 6_updatecdl: 0.1197 0.1356 0.036 1.128 5.5 67.0 14.9 873 n/a 6_nqh: 0.1197 0.1356 0.036 1.128 5.5 67.0 14.9 873 n/a 6_sol: 0.1198 0.1356 0.036 1.128 5.5 67.0 14.8 868 n/a 6_weight: 0.1198 0.1356 0.036 1.128 5.5 67.0 14.8 868 n/a 6_xyzrec: 0.1201 0.1360 0.037 1.127 5.5 67.0 14.8 868 n/a 6_adp: 0.1206 0.1365 0.037 1.127 5.6 65.9 14.7 868 n/a 6_regHadp: 0.1206 0.1366 0.037 1.127 5.6 65.9 14.7 868 n/a 6_occ: 0.1203 0.1365 0.037 1.127 5.6 65.9 14.7 868 n/a 7_bss: 0.1204 0.1366 0.037 1.127 5.3 65.7 14.5 868 n/a 7_settarget: 0.1204 0.1366 0.037 1.127 5.3 65.7 14.5 868 n/a 7_updatecdl: 0.1204 0.1366 0.037 1.127 5.3 65.7 14.5 868 n/a 7_nqh: 0.1204 0.1366 0.037 1.127 5.3 65.7 14.5 868 n/a 7_sol: 0.1201 0.1361 0.037 1.127 5.3 65.7 14.6 897 n/a 7_weight: 0.1201 0.1361 0.037 1.127 5.3 65.7 14.6 897 n/a 7_xyzrec: 0.1204 0.1364 0.037 1.131 5.3 65.7 14.6 897 n/a 7_adp: 0.1204 0.1367 0.037 1.131 5.4 64.3 14.6 897 n/a 7_regHadp: 0.1205 0.1367 0.037 1.131 5.4 64.3 14.6 897 n/a 7_occ: 0.1202 0.1367 0.037 1.131 5.4 64.3 14.6 897 n/a 8_bss: 0.1192 0.1355 0.037 1.131 5.5 64.4 14.7 897 n/a 8_settarget: 0.1192 0.1355 0.037 1.131 5.5 64.4 14.7 897 n/a 8_updatecdl: 0.1192 0.1355 0.037 1.131 5.5 64.4 14.7 897 n/a 8_nqh: 0.1192 0.1355 0.037 1.131 5.5 64.4 14.7 897 n/a 8_sol: 0.1191 0.1345 0.037 1.131 5.5 64.4 14.7 899 n/a 8_weight: 0.1191 0.1345 0.037 1.131 5.5 64.4 14.7 899 n/a 8_xyzrec: 0.1194 0.1350 0.038 1.111 5.5 64.4 14.7 899 n/a 8_adp: 0.1194 0.1352 0.038 1.111 5.5 63.9 14.7 899 n/a 8_regHadp: 0.1194 0.1352 0.038 1.111 5.5 63.9 14.7 899 n/a 8_occ: 0.1192 0.1351 0.038 1.111 5.5 63.9 14.7 899 n/a 9_bss: 0.1190 0.1348 0.038 1.111 5.5 63.9 14.7 899 n/a 9_settarget: 0.1190 0.1348 0.038 1.111 5.5 63.9 14.7 899 n/a 9_updatecdl: 0.1190 0.1348 0.038 1.111 5.5 63.9 14.7 899 n/a 9_nqh: 0.1190 0.1348 0.038 1.111 5.5 63.9 14.7 899 n/a 9_sol: 0.1189 0.1341 0.038 1.111 5.5 63.9 14.7 906 n/a 9_weight: 0.1189 0.1341 0.038 1.111 5.5 63.9 14.7 906 n/a 9_xyzrec: 0.1191 0.1345 0.038 1.124 5.5 63.9 14.7 906 n/a 9_adp: 0.1193 0.1348 0.038 1.124 5.6 63.7 14.7 906 n/a 9_regHadp: 0.1193 0.1349 0.038 1.124 5.6 63.7 14.7 906 n/a 9_occ: 0.1191 0.1348 0.038 1.124 5.6 63.7 14.7 906 n/a 10_bss: 0.1190 0.1348 0.038 1.124 5.5 63.7 14.7 906 n/a 10_settarget: 0.1190 0.1348 0.038 1.124 5.5 63.7 14.7 906 n/a 10_updatecdl: 0.1190 0.1348 0.038 1.125 5.5 63.7 14.7 906 n/a 10_setrh: 0.1191 0.1348 0.038 1.125 5.5 63.7 14.7 906 n/a 10_nqh: 0.1191 0.1348 0.038 1.125 5.5 63.7 14.7 906 n/a 10_sol: 0.1190 0.1342 0.038 1.125 5.5 63.7 14.7 919 n/a 10_weight: 0.1190 0.1342 0.038 1.125 5.5 63.7 14.7 919 n/a 10_xyzrec: 0.1193 0.1347 0.038 1.163 5.5 63.7 14.7 919 n/a 10_adp: 0.1196 0.1351 0.038 1.163 5.6 63.5 14.7 919 n/a 10_regHadp: 0.1196 0.1351 0.038 1.163 5.6 63.5 14.7 919 n/a 10_occ: 0.1195 0.1350 0.038 1.163 5.6 63.5 14.7 919 n/a end: 0.1194 0.1349 0.038 1.163 5.5 63.4 14.6 919 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9443647_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9443647_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.3600 Refinement macro-cycles (run) : 12241.4000 Write final files (write_after_run_outputs) : 148.9200 Total : 12395.6800 Total CPU time: 3.45 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:43:54 PST -0800 (1736736234.66 s) Start R-work = 0.1784, R-free = 0.1904 Final R-work = 0.1194, R-free = 0.1349 =============================================================================== Job complete usr+sys time: 12658.34 seconds wall clock time: 212 minutes 0.78 seconds (12720.78 seconds total)