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_2189413.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2189413.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_2189413.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.85, per 1000 atoms: 0.28 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: 2.648 distance_ideal: 2.720 ideal - model: 0.072 slack: 0.000 delta_slack: 0.072 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: 2.747 distance_ideal: 2.710 ideal - model: -0.037 slack: 0.000 delta_slack: -0.037 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 143.0 milliseconds Time building geometry restraints manager: 1.01 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: 565 1.00 - 1.23: 2509 1.23 - 1.45: 1418 1.45 - 1.67: 1383 1.67 - 1.89: 59 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA B 5 " pdb=" H ALA B 5 " ideal model delta sigma weight residual 0.860 1.288 -0.428 2.00e-02 2.50e+03 4.59e+02 bond pdb=" C ILE B 76 " pdb=" O ILE B 76 " ideal model delta sigma weight residual 1.237 0.995 0.242 1.13e-02 7.83e+03 4.58e+02 bond pdb=" C VAL A 37 " pdb=" O VAL A 37 " ideal model delta sigma weight residual 1.236 1.428 -0.192 9.90e-03 1.02e+04 3.78e+02 bond pdb=" N VAL A 114 " pdb=" H VAL A 114 " ideal model delta sigma weight residual 0.860 1.246 -0.386 2.00e-02 2.50e+03 3.73e+02 bond pdb=" N VAL B 37 " pdb=" H VAL B 37 " ideal model delta sigma weight residual 0.860 1.239 -0.379 2.00e-02 2.50e+03 3.59e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 6203 4.60 - 9.21: 3444 9.21 - 13.81: 1004 13.81 - 18.41: 148 18.41 - 23.01: 11 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA MET B 124 " pdb=" C MET B 124 " pdb=" O MET B 124 " ideal model delta sigma weight residual 121.23 138.59 -17.36 1.07e+00 8.73e-01 2.63e+02 angle pdb=" N PRO A 135 " pdb=" CA PRO A 135 " pdb=" CB PRO A 135 " ideal model delta sigma weight residual 103.35 89.35 14.00 8.70e-01 1.32e+00 2.59e+02 angle pdb=" O LEU A 54 " pdb=" C LEU A 54 " pdb=" N ALA A 55 " ideal model delta sigma weight residual 123.05 140.04 -16.99 1.19e+00 7.06e-01 2.04e+02 angle pdb=" O PRO B 120 " pdb=" C PRO B 120 " pdb=" N ILE B 121 " ideal model delta sigma weight residual 122.23 105.76 16.47 1.20e+00 6.94e-01 1.88e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" O ALA A 103 " ideal model delta sigma weight residual 120.40 106.09 14.31 1.05e+00 9.07e-01 1.86e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.21: 1843 17.21 - 34.41: 138 34.41 - 51.61: 51 51.61 - 68.80: 13 68.80 - 86.00: 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 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CG TRP B 146 " pdb=" CD2 TRP B 146 " pdb=" CE3 TRP B 146 " pdb=" HE3 TRP B 146 " ideal model delta harmonic sigma weight residual 0.00 26.66 -26.66 0 5.00e+00 4.00e-02 2.84e+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 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.229: 209 0.229 - 0.457: 155 0.457 - 0.685: 94 0.685 - 0.913: 30 0.913 - 1.142: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL A 114 " pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CB VAL A 114 " both_signs ideal model delta sigma weight residual False 2.44 1.30 1.14 2.00e-01 2.50e+01 3.26e+01 chirality pdb=" CA VAL A 37 " pdb=" N VAL A 37 " pdb=" C VAL A 37 " pdb=" CB VAL A 37 " both_signs ideal model delta sigma weight residual False 2.44 3.56 -1.12 2.00e-01 2.50e+01 3.15e+01 chirality pdb=" CA VAL A 60 " pdb=" N VAL A 60 " pdb=" C VAL A 60 " pdb=" CB VAL A 60 " both_signs ideal model delta sigma weight residual False 2.44 3.52 -1.08 2.00e-01 2.50e+01 2.89e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.060 2.00e-02 2.50e+03 6.87e-02 1.89e+02 pdb=" CG TRP B 146 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.056 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.076 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.091 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.113 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.048 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.112 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " 0.055 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.024 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " -0.009 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " -0.058 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.109 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.038 2.00e-02 2.50e+03 6.03e-02 1.45e+02 pdb=" CG TRP A 146 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.039 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.133 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.117 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.055 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.063 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.090 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.105 2.00e-02 2.50e+03 6.54e-02 1.28e+02 pdb=" CG PHE B 164 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.094 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.016 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.032 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.147 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.76 - 1.53: 17 1.53 - 2.29: 1715 2.29 - 3.06: 21432 3.06 - 3.83: 33253 3.83 - 4.60: 53870 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110287 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.758 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.901 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.926 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.018 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.148 2.620 ... (remaining 110282 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_2189413_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= 0.2024 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.295726 | | target function (ml) not normalized (work): 804645.378821 | | target function (ml) not normalized (free): 16589.905993 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2137 0.1846 6.7091 6.2849| | 2: 2.94 - 2.33 1.00 7339 128 0.1607 0.1761 5.5247 5.611| | 3: 2.33 - 2.04 0.96 6939 150 0.1621 0.1511 5.1301 5.1306| | 4: 2.04 - 1.85 1.00 7170 155 0.1750 0.1548 4.9547 4.9889| | 5: 1.85 - 1.72 0.99 7113 159 0.1889 0.1837 4.779 4.8769| | 6: 1.72 - 1.62 0.99 7102 142 0.1985 0.1983 4.6596 4.6903| | 7: 1.62 - 1.54 0.99 7104 148 0.1965 0.1974 4.5458 4.671| | 8: 1.54 - 1.47 0.96 6798 152 0.2060 0.2231 4.4767 4.4912| | 9: 1.47 - 1.41 0.98 6938 155 0.2061 0.2115 4.3882 4.4398| | 10: 1.41 - 1.36 0.99 7022 150 0.2106 0.2146 4.3037 4.3573| | 11: 1.36 - 1.32 0.99 6997 151 0.2083 0.2157 4.2192 4.2423| | 12: 1.32 - 1.28 0.98 6976 149 0.2056 0.1928 4.1623 4.1903| | 13: 1.28 - 1.25 0.98 6907 166 0.2014 0.2370 4.1124 4.2827| | 14: 1.25 - 1.22 0.98 7015 113 0.2088 0.2430 4.0879 4.3293| | 15: 1.22 - 1.19 0.98 6957 137 0.2111 0.1914 4.0517 4.0103| | 16: 1.19 - 1.17 0.93 6604 132 0.2130 0.2140 4.0193 4.0415| | 17: 1.17 - 1.14 0.98 6941 135 0.2149 0.2122 3.9488 4.0508| | 18: 1.14 - 1.12 0.98 6875 142 0.2188 0.2262 3.9087 3.8934| | 19: 1.12 - 1.10 0.97 6949 106 0.2265 0.2470 3.8732 3.9616| | 20: 1.10 - 1.08 0.97 6884 147 0.2318 0.2263 3.818 3.8274| | 21: 1.08 - 1.07 0.97 6852 152 0.2423 0.2572 3.7917 3.7918| | 22: 1.07 - 1.05 0.97 6838 135 0.2539 0.2579 3.7459 3.7764| | 23: 1.05 - 1.03 0.97 6829 159 0.2703 0.2783 3.7296 3.8298| | 24: 1.03 - 1.02 0.96 6785 133 0.2877 0.2928 3.702 3.8111| | 25: 1.02 - 1.01 0.93 6552 130 0.3030 0.3111 3.6717 3.7661| | 26: 1.01 - 0.99 0.96 6767 158 0.3202 0.3275 3.6267 3.6447| | 27: 0.99 - 0.98 0.94 6648 131 0.3418 0.3347 3.6311 3.6318| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.04 0.91 0.98 34074.30| | 2: 2.94 - 2.33 7339 128 0.86 20.93 1.09 1.02 14617.84| | 3: 2.33 - 2.04 6939 150 0.93 12.43 1.11 1.06 4101.83| | 4: 2.04 - 1.85 7170 155 0.93 12.81 1.11 1.07 2579.36| | 5: 1.85 - 1.72 7113 159 0.91 15.49 1.11 1.08 2052.68| | 6: 1.72 - 1.62 7102 142 0.90 16.92 1.12 1.07 1677.74| | 7: 1.62 - 1.54 7104 148 0.88 18.40 1.11 1.07 1445.14| | 8: 1.54 - 1.47 6798 152 0.88 18.81 1.11 1.05 1176.42| | 9: 1.47 - 1.41 6938 155 0.88 18.96 1.10 1.05 986.99| | 10: 1.41 - 1.36 7022 150 0.88 19.42 1.09 1.05 806.19| | 11: 1.36 - 1.32 6997 151 0.88 19.42 1.08 1.05 698.50| | 12: 1.32 - 1.28 6976 149 0.88 19.32 1.07 1.04 623.67| | 13: 1.28 - 1.25 6907 166 0.87 20.69 1.07 1.03 640.08| | 14: 1.25 - 1.22 7015 113 0.86 21.74 1.08 1.04 630.44| | 15: 1.22 - 1.19 6957 137 0.85 22.25 1.08 1.04 604.78| | 16: 1.19 - 1.17 6604 132 0.87 20.89 1.07 1.03 512.08| | 17: 1.17 - 1.14 6941 135 0.86 21.24 1.09 1.03 450.81| | 18: 1.14 - 1.12 6875 142 0.86 21.05 1.08 1.00 390.68| | 19: 1.12 - 1.10 6949 106 0.86 21.87 1.07 0.99 372.71| | 20: 1.10 - 1.08 6884 147 0.85 22.85 1.06 0.98 346.42| | 21: 1.08 - 1.07 6852 152 0.84 24.10 1.05 0.97 340.20| | 22: 1.07 - 1.05 6838 135 0.81 26.13 1.05 0.96 339.90| | 23: 1.05 - 1.03 6829 159 0.79 28.80 1.05 0.95 353.71| | 24: 1.03 - 1.02 6785 133 0.76 31.08 1.05 0.96 361.07| | 25: 1.02 - 1.01 6552 130 0.75 32.27 1.03 0.91 338.64| | 26: 1.01 - 0.99 6767 158 0.73 33.92 1.03 0.90 315.91| | 27: 0.99 - 0.98 6648 131 0.73 34.32 1.04 0.90 302.78| |alpha: min = 0.90 max = 1.08 mean = 1.01| |beta: min = 302.78 max = 34074.30 mean = 2757.07| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.98| |phase err.(test): min = 0.00 max = 89.45 mean = 21.94| |-----------------------------------------------------------------------------| ----------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 0.293 2950 Z= 5.354 Angle : 5.225 19.108 4018 Z= 3.695 Chirality : 0.392 1.142 492 Planarity : 0.033 0.172 512 Dihedral : 12.720 86.003 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.40 % Favored : 95.08 % Rotamer: Outliers : 0.32 % Allowed : 4.52 % Favored : 95.16 % Cbeta Deviations : 31.74 % 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: -2.51 (0.40), residues: 386 helix: -2.71 (0.31), residues: 146 sheet: -1.50 (0.50), residues: 86 loop : -0.28 (0.54), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.086 0.014 ARG A 149 TYR 0.117 0.030 TYR A 192 PHE 0.114 0.034 PHE A 95 TRP 0.124 0.041 TRP A 146 HIS 0.090 0.025 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= 0.2024 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.295726 | | target function (ml) not normalized (work): 804645.378821 | | target function (ml) not normalized (free): 16589.905993 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2022 0.2024 0.1996 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2022 0.2024 0.1996 n_refl.: 191155 remove outliers: r(all,work,free)=0.2022 0.2024 0.1996 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2023 0.2024 0.1996 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1792 0.1789 0.1936 n_refl.: 191145 remove outliers: r(all,work,free)=0.1790 0.1787 0.1934 n_refl.: 191137 ======================== 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 0.4088 402.814 294.411 0.436 0.913 0.303 13.296-10.522 99.01 99 1 0.2430 528.187 522.521 0.793 0.914 0.255 10.503-8.327 98.90 177 3 0.2450 564.205 558.227 0.972 0.914 0.230 8.318-6.595 100.00 360 8 0.2474 414.736 404.522 0.972 0.913 0.165 6.588-5.215 100.00 711 7 0.2246 381.101 366.099 0.956 0.913 0.160 5.214-4.128 98.38 1367 28 0.1490 557.435 549.518 1.073 0.913 0.090 4.126-3.266 94.74 2603 46 0.1353 508.132 498.747 1.145 0.914 0.023 3.266-2.585 99.86 5447 97 0.1430 342.774 337.728 1.121 0.913 0.000 2.585-2.046 97.45 10613 204 0.1384 258.603 254.379 1.126 0.912 0.000 2.046-1.619 99.39 21536 464 0.1597 153.054 149.799 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1900 82.395 80.291 1.129 0.908 0.000 1.281-0.980 96.53 101826 2055 0.2314 44.202 41.683 1.113 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0021 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1787 r_free=0.1934 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1787 r_free=0.1934 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.806823 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 570.308509 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 0.1270 0.1502 0.0232 0.039 1.2 11.2 0.0 0.3 0 11.403 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 15.02 2.32 1.118 13.112 570.309 0.018 12.98 15.73 2.75 1.242 13.343 570.309 0.017 Individual atomic B min max mean iso aniso Overall: 5.17 73.04 15.02 1.40 435 3274 Protein: 5.17 40.32 11.00 1.40 0 2902 Water: 6.38 73.04 29.49 N/A 435 370 Other: 16.09 30.28 23.19 N/A 0 2 Chain A: 5.32 60.02 13.04 N/A 0 1626 Chain B: 5.17 73.04 12.77 N/A 0 1648 Chain S: 11.63 66.55 30.93 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2164 11.96 - 18.74 635 18.74 - 25.53 317 25.53 - 32.32 263 32.32 - 39.11 160 39.11 - 45.89 104 45.89 - 52.68 42 52.68 - 59.47 17 59.47 - 66.26 5 66.26 - 73.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1573 r_work=0.1297 r_free=0.1569 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1569 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1282 r_free = 0.1557 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1557 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015519 | | target function (ls_wunit_k1) not normalized (work): 2906.590177 | | target function (ls_wunit_k1) not normalized (free): 117.701332 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1282 0.1557 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1469 0.1466 0.1634 n_refl.: 191137 remove outliers: r(all,work,free)=0.1469 0.1466 0.1634 n_refl.: 191137 overall B=0.17 to atoms: r(all,work,free)=0.1492 0.1490 0.1643 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1548 n_refl.: 191137 remove outliers: r(all,work,free)=0.1280 0.1275 0.1548 n_refl.: 191137 ======================== 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 0.3626 402.814 378.943 0.489 0.963 0.281 13.296-10.522 99.01 99 1 0.2072 528.187 523.236 0.745 0.965 0.255 10.503-8.327 98.90 177 3 0.1712 564.205 562.088 0.885 0.965 0.203 8.318-6.595 100.00 360 8 0.1708 414.736 412.902 0.909 0.964 0.155 6.588-5.215 100.00 711 7 0.1543 381.101 373.351 0.887 0.965 0.150 5.214-4.128 98.38 1367 28 0.0907 557.435 554.285 0.976 0.965 0.080 4.126-3.266 94.74 2603 46 0.0827 508.132 504.361 1.043 0.965 0.014 3.266-2.585 99.86 5447 97 0.0920 342.774 340.443 1.026 0.965 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.421 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.390 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.397 1.047 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.150 1.024 0.965 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=0.1275 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1548 | n_water=805 | time (s): 2.450 (total time: 2.450) Filter (dist) r_work=0.1280 r_free=0.1553 | n_water=793 | time (s): 99.180 (total time: 101.630) Filter (q & B) r_work=0.1280 r_free=0.1553 | n_water=788 | time (s): 4.450 (total time: 106.080) Compute maps r_work=0.1280 r_free=0.1553 | n_water=788 | time (s): 1.900 (total time: 107.980) Filter (map) r_work=0.1307 r_free=0.1536 | n_water=650 | time (s): 4.490 (total time: 112.470) Find peaks r_work=0.1307 r_free=0.1536 | n_water=650 | time (s): 0.730 (total time: 113.200) Add new water r_work=0.1332 r_free=0.1566 | n_water=960 | time (s): 4.240 (total time: 117.440) Refine new water occ: r_work=0.1287 r_free=0.1521 adp: r_work=0.1273 r_free=0.1516 occ: r_work=0.1275 r_free=0.1514 adp: r_work=0.1268 r_free=0.1512 occ: r_work=0.1269 r_free=0.1510 adp: r_work=0.1267 r_free=0.1510 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1510 r_work=0.1267 r_free=0.1510 | n_water=960 | time (s): 86.250 (total time: 203.690) Filter (q & B) r_work=0.1270 r_free=0.1509 | n_water=893 | time (s): 4.670 (total time: 208.360) Filter (dist only) r_work=0.1271 r_free=0.1505 | n_water=891 | time (s): 111.980 (total time: 320.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.401707 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 591.797567 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1255 0.1531 0.0276 0.041 1.1 18.5 0.0 0.3 0 11.701 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.31 2.76 2.041 15.251 591.798 0.014 12.32 15.18 2.87 2.426 15.320 591.798 0.014 Individual atomic B min max mean iso aniso Overall: 5.37 72.27 16.48 1.21 523 3272 Protein: 5.37 40.78 10.98 1.21 0 2902 Water: 6.62 72.27 34.38 N/A 523 368 Other: 16.39 32.43 24.41 N/A 0 2 Chain A: 5.50 56.34 13.01 N/A 0 1624 Chain B: 5.37 68.21 12.82 N/A 0 1648 Chain S: 13.42 72.27 38.79 N/A 523 0 Histogram: Values Number of atoms 5.37 - 12.06 2142 12.06 - 18.75 677 18.75 - 25.44 251 25.44 - 32.13 222 32.13 - 38.82 163 38.82 - 45.51 166 45.51 - 52.20 85 52.20 - 58.89 54 58.89 - 65.58 27 65.58 - 72.27 8 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1518 r_work=0.1232 r_free=0.1519 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1519 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1225 r_free = 0.1518 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1518 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013363 | | target function (ls_wunit_k1) not normalized (work): 2502.831153 | | target function (ls_wunit_k1) not normalized (free): 103.097930 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1225 0.1518 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1622 n_refl.: 191137 remove outliers: r(all,work,free)=0.1436 0.1433 0.1622 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1430 0.1620 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1238 0.1232 0.1525 n_refl.: 191137 remove outliers: r(all,work,free)=0.1238 0.1232 0.1525 n_refl.: 191137 ======================== 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 0.3187 402.814 381.351 0.486 0.962 0.265 13.296-10.522 99.01 99 1 0.1865 528.187 520.583 0.765 0.963 0.240 10.503-8.327 98.90 177 3 0.1408 564.205 567.725 0.919 0.963 0.186 8.318-6.595 100.00 360 8 0.1527 414.736 414.516 0.935 0.962 0.154 6.588-5.215 100.00 711 7 0.1339 381.101 376.564 0.913 0.962 0.136 5.214-4.128 98.38 1367 28 0.0829 557.435 556.120 0.996 0.963 0.090 4.126-3.266 94.74 2603 46 0.0758 508.132 505.345 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0864 342.774 341.426 1.048 0.961 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.725 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.610 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.347 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.216 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0554 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1232 r_free=0.1525 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1232 r_free=0.1525 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1232 r_free=0.1525 | n_water=891 | time (s): 3.640 (total time: 3.640) Filter (dist) r_work=0.1234 r_free=0.1527 | n_water=884 | time (s): 112.030 (total time: 115.670) Filter (q & B) r_work=0.1234 r_free=0.1527 | n_water=881 | time (s): 5.060 (total time: 120.730) Compute maps r_work=0.1234 r_free=0.1527 | n_water=881 | time (s): 2.230 (total time: 122.960) Filter (map) r_work=0.1273 r_free=0.1525 | n_water=682 | time (s): 5.200 (total time: 128.160) Find peaks r_work=0.1273 r_free=0.1525 | n_water=682 | time (s): 0.900 (total time: 129.060) Add new water r_work=0.1297 r_free=0.1549 | n_water=988 | time (s): 4.240 (total time: 133.300) Refine new water occ: r_work=0.1252 r_free=0.1521 adp: r_work=0.1253 r_free=0.1521 occ: r_work=0.1249 r_free=0.1520 adp: r_work=0.1248 r_free=0.1520 occ: r_work=0.1246 r_free=0.1519 adp: r_work=0.1245 r_free=0.1519 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1519 r_work=0.1245 r_free=0.1519 | n_water=988 | time (s): 261.880 (total time: 395.180) Filter (q & B) r_work=0.1250 r_free=0.1525 | n_water=873 | time (s): 5.830 (total time: 401.010) Filter (dist only) r_work=0.1250 r_free=0.1524 | n_water=872 | time (s): 118.490 (total time: 519.500) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.767001 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.296100 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1238 0.1447 0.0209 0.035 1.1 6.8 0.0 0.0 0 0.884 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.38 14.47 2.09 1.931 14.579 15.296 3.939 12.37 14.07 1.70 2.239 14.477 15.296 3.898 Individual atomic B min max mean iso aniso Overall: 5.55 67.81 15.25 1.04 506 3270 Protein: 5.55 36.69 10.73 1.04 0 2902 Water: 6.68 67.81 30.27 N/A 506 366 Other: 14.08 28.48 21.28 N/A 0 2 Chain A: 5.57 55.46 12.76 N/A 0 1624 Chain B: 5.55 67.81 12.52 N/A 0 1646 Chain S: 14.45 64.58 32.11 N/A 506 0 Histogram: Values Number of atoms 5.55 - 11.78 2142 11.78 - 18.00 686 18.00 - 24.23 288 24.23 - 30.46 229 30.46 - 36.68 180 36.68 - 42.91 141 42.91 - 49.13 77 49.13 - 55.36 22 55.36 - 61.58 8 61.58 - 67.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1407 r_work=0.1238 r_free=0.1408 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1408 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1395 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1232 r_free= 0.1395 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892459 | | target function (ml) not normalized (work): 729041.991596 | | target function (ml) not normalized (free): 15224.805283 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1232 0.1395 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1446 0.1446 0.1483 n_refl.: 191137 remove outliers: r(all,work,free)=0.1446 0.1446 0.1483 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1440 0.1439 0.1479 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1228 0.1390 n_refl.: 191137 remove outliers: r(all,work,free)=0.1231 0.1228 0.1390 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 94.06 92 3 0.3867 398.008 362.176 0.427 0.946 0.263 13.296-10.522 99.01 99 1 0.2430 528.187 511.020 0.711 0.948 0.229 10.503-8.327 97.80 175 3 0.1955 554.286 558.523 0.883 0.948 0.181 8.318-6.595 100.00 360 8 0.2089 414.736 409.369 0.894 0.947 0.131 6.588-5.215 100.00 711 7 0.1826 381.101 370.848 0.886 0.948 0.110 5.214-4.128 98.38 1367 28 0.1169 557.435 552.472 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1101 508.132 500.893 1.033 0.948 0.015 3.266-2.585 99.86 5447 97 0.1085 342.774 338.991 1.020 0.947 0.010 2.585-2.046 97.45 10613 204 0.0976 258.603 255.727 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0979 153.054 151.391 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.472 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.305 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=-0.1056 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1390 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1228 r_free=0.1390 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1390 | n_water=872 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1229 r_free=0.1391 | n_water=870 | time (s): 105.990 (total time: 108.270) Filter (q & B) r_work=0.1229 r_free=0.1386 | n_water=861 | time (s): 4.230 (total time: 112.500) Compute maps r_work=0.1229 r_free=0.1386 | n_water=861 | time (s): 1.690 (total time: 114.190) Filter (map) r_work=0.1250 r_free=0.1387 | n_water=715 | time (s): 4.660 (total time: 118.850) Find peaks r_work=0.1250 r_free=0.1387 | n_water=715 | time (s): 0.760 (total time: 119.610) Add new water r_work=0.1265 r_free=0.1402 | n_water=954 | time (s): 4.500 (total time: 124.110) Refine new water occ: r_work=0.1218 r_free=0.1370 adp: r_work=0.1210 r_free=0.1364 occ: r_work=0.1208 r_free=0.1365 adp: r_work=0.1208 r_free=0.1364 occ: r_work=0.1206 r_free=0.1366 adp: r_work=0.1205 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1364 r_work=0.1205 r_free=0.1364 | n_water=954 | time (s): 290.670 (total time: 414.780) Filter (q & B) r_work=0.1210 r_free=0.1364 | n_water=866 | time (s): 4.400 (total time: 419.180) Filter (dist only) r_work=0.1210 r_free=0.1363 | n_water=865 | time (s): 112.800 (total time: 531.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.534638 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.762267 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 0.1211 0.1361 0.0150 0.036 1.1 6.5 0.0 0.0 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 13.61 1.50 1.821 14.195 15.762 3.876 12.00 13.55 1.56 1.930 14.157 15.762 3.865 Individual atomic B min max mean iso aniso Overall: 5.52 67.34 14.98 1.00 499 3270 Protein: 5.52 33.42 10.65 1.00 0 2902 Water: 6.02 67.34 29.46 N/A 499 366 Other: 14.01 27.35 20.68 N/A 0 2 Chain A: 5.55 54.31 12.63 N/A 0 1624 Chain B: 5.52 67.34 12.42 N/A 0 1646 Chain S: 6.02 64.58 31.04 N/A 499 0 Histogram: Values Number of atoms 5.52 - 11.70 2119 11.70 - 17.88 731 17.88 - 24.06 290 24.06 - 30.25 227 30.25 - 36.43 176 36.43 - 42.61 128 42.61 - 48.79 68 48.79 - 54.97 23 54.97 - 61.16 4 61.16 - 67.34 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1355 r_work=0.1200 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1355 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1356 target_work(ml) = 3.863 | | 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.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1356 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863458 | | target function (ml) not normalized (work): 723598.551621 | | target function (ml) not normalized (free): 15132.091153 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1356 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1425 0.1425 0.1454 n_refl.: 191134 remove outliers: r(all,work,free)=0.1425 0.1425 0.1454 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1417 0.1417 0.1450 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1354 n_refl.: 191134 remove outliers: r(all,work,free)=0.1199 0.1196 0.1354 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3860 360.441 324.285 0.419 0.946 0.257 13.296-10.522 96.04 96 1 0.2304 480.490 449.370 0.701 0.948 0.197 10.503-8.327 97.80 175 3 0.2081 501.969 496.792 0.864 0.948 0.168 8.318-6.595 100.00 360 8 0.2151 375.591 370.534 0.889 0.947 0.100 6.588-5.215 100.00 711 7 0.1886 345.131 335.425 0.884 0.948 0.095 5.214-4.128 98.38 1367 28 0.1196 504.821 500.223 0.974 0.948 0.090 4.126-3.266 94.74 2603 46 0.1121 460.172 453.665 1.035 0.948 0.009 3.266-2.585 99.86 5447 97 0.1084 310.421 307.242 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0934 234.195 231.768 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0913 138.608 137.336 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0988 74.619 73.910 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.030 38.375 1.037 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1195 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1354 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1354 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1354 | n_water=865 | time (s): 2.990 (total time: 2.990) Filter (dist) r_work=0.1196 r_free=0.1354 | n_water=864 | time (s): 107.320 (total time: 110.310) Filter (q & B) r_work=0.1196 r_free=0.1356 | n_water=853 | time (s): 4.940 (total time: 115.250) Compute maps r_work=0.1196 r_free=0.1356 | n_water=853 | time (s): 2.010 (total time: 117.260) Filter (map) r_work=0.1217 r_free=0.1362 | n_water=737 | time (s): 4.800 (total time: 122.060) Find peaks r_work=0.1217 r_free=0.1362 | n_water=737 | time (s): 0.670 (total time: 122.730) Add new water r_work=0.1231 r_free=0.1380 | n_water=980 | time (s): 4.870 (total time: 127.600) Refine new water occ: r_work=0.1193 r_free=0.1339 adp: r_work=0.1193 r_free=0.1338 occ: r_work=0.1190 r_free=0.1337 adp: r_work=0.1190 r_free=0.1336 occ: r_work=0.1188 r_free=0.1336 adp: r_work=0.1188 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1336 r_work=0.1188 r_free=0.1336 | n_water=980 | time (s): 238.560 (total time: 366.160) Filter (q & B) r_work=0.1193 r_free=0.1348 | n_water=887 | time (s): 5.700 (total time: 371.860) Filter (dist only) r_work=0.1193 r_free=0.1347 | n_water=886 | time (s): 119.880 (total time: 491.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.563957 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.100545 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 0.1196 0.1356 0.0160 0.036 1.1 7.5 0.0 0.3 0 0.782 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.56 1.60 1.789 14.071 15.101 3.764 12.00 13.60 1.60 1.825 14.056 15.101 3.762 Individual atomic B min max mean iso aniso Overall: 5.58 67.13 14.87 0.96 521 3269 Protein: 5.58 32.50 10.60 0.96 0 2902 Water: 6.00 67.13 28.85 N/A 521 365 Other: 13.81 26.68 20.25 N/A 0 2 Chain A: 5.61 53.86 12.54 N/A 0 1623 Chain B: 5.58 67.13 12.36 N/A 0 1646 Chain S: 6.00 64.56 30.07 N/A 521 0 Histogram: Values Number of atoms 5.58 - 11.74 2143 11.74 - 17.89 714 17.89 - 24.05 308 24.05 - 30.20 246 30.20 - 36.36 173 36.36 - 42.51 116 42.51 - 48.67 65 48.67 - 54.82 19 54.82 - 60.98 3 60.98 - 67.13 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1360 r_work=0.1200 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1361 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761768 | | target function (ml) not normalized (work): 704541.542987 | | target function (ml) not normalized (free): 14751.873476 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1360 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1421 0.1420 0.1469 n_refl.: 191131 remove outliers: r(all,work,free)=0.1421 0.1420 0.1469 n_refl.: 191131 overall B=-0.04 to atoms: r(all,work,free)=0.1413 0.1413 0.1464 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1198 0.1359 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1197 0.1359 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3602 360.132 312.244 0.398 0.949 0.240 13.296-10.522 96.04 96 1 0.2368 480.490 461.911 0.707 0.950 0.173 10.503-8.327 97.80 175 3 0.2162 501.969 496.014 0.858 0.951 0.143 8.318-6.595 100.00 360 8 0.2180 375.591 370.817 0.880 0.950 0.080 6.588-5.215 100.00 711 7 0.1919 345.131 335.279 0.881 0.950 0.075 5.214-4.128 98.38 1367 28 0.1211 504.821 499.538 0.971 0.951 0.070 4.126-3.266 94.74 2603 46 0.1141 460.172 453.396 1.033 0.951 0.005 3.266-2.585 99.86 5447 97 0.1097 310.421 307.168 1.019 0.950 0.000 2.585-2.046 97.45 10613 204 0.0942 234.195 231.779 1.032 0.949 0.000 2.046-1.619 99.39 21536 464 0.0914 138.608 137.334 1.055 0.948 0.000 1.619-1.281 98.00 42464 925 0.0979 74.619 73.920 1.053 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.030 38.368 1.041 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1291 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1359 | n_water=886 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1197 r_free=0.1359 | n_water=886 | time (s): 104.960 (total time: 107.560) Filter (q & B) r_work=0.1198 r_free=0.1358 | n_water=870 | time (s): 4.150 (total time: 111.710) Compute maps r_work=0.1198 r_free=0.1358 | n_water=870 | time (s): 1.870 (total time: 113.580) Filter (map) r_work=0.1219 r_free=0.1361 | n_water=755 | time (s): 4.390 (total time: 117.970) Find peaks r_work=0.1219 r_free=0.1361 | n_water=755 | time (s): 0.810 (total time: 118.780) Add new water r_work=0.1228 r_free=0.1373 | n_water=968 | time (s): 4.170 (total time: 122.950) Refine new water occ: r_work=0.1193 r_free=0.1344 adp: r_work=0.1193 r_free=0.1344 occ: r_work=0.1191 r_free=0.1343 adp: r_work=0.1191 r_free=0.1343 occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1189 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1343 r_work=0.1189 r_free=0.1343 | n_water=968 | time (s): 235.670 (total time: 358.620) Filter (q & B) r_work=0.1194 r_free=0.1349 | n_water=885 | time (s): 4.400 (total time: 363.020) Filter (dist only) r_work=0.1194 r_free=0.1349 | n_water=884 | time (s): 111.540 (total time: 474.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.538034 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.236340 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1357 0.0159 0.037 1.1 7.2 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.57 1.59 1.766 14.009 14.236 3.762 12.04 13.65 1.61 1.925 13.955 14.236 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 66.08 14.76 0.89 519 3269 Protein: 5.57 29.35 10.48 0.89 0 2902 Water: 5.99 66.08 28.79 N/A 519 365 Other: 13.86 23.87 18.86 N/A 0 2 Chain A: 5.63 52.58 12.38 N/A 0 1623 Chain B: 5.57 66.08 12.21 N/A 0 1646 Chain S: 5.99 64.64 30.25 N/A 519 0 Histogram: Values Number of atoms 5.57 - 11.62 2118 11.62 - 17.67 774 17.67 - 23.72 274 23.72 - 29.78 220 29.78 - 35.83 194 35.83 - 41.88 113 41.88 - 47.93 68 47.93 - 53.98 19 53.98 - 60.03 5 60.03 - 66.08 3 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1365 r_work=0.1205 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1366 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1362 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761122 | | target function (ml) not normalized (work): 704416.825013 | | target function (ml) not normalized (free): 14751.259590 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1362 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1416 0.1415 0.1466 n_refl.: 191130 remove outliers: r(all,work,free)=0.1416 0.1415 0.1466 n_refl.: 191130 overall B=-0.23 to atoms: r(all,work,free)=0.1379 0.1378 0.1446 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1202 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1204 0.1201 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3549 360.132 331.644 0.431 0.949 0.232 13.296-10.522 96.04 96 1 0.2345 480.490 462.523 0.719 0.951 0.158 10.503-8.327 97.80 175 3 0.2161 501.969 496.383 0.881 0.951 0.127 8.315-6.595 100.00 359 8 0.2147 374.645 370.785 0.906 0.951 0.093 6.588-5.215 100.00 711 7 0.1931 345.131 335.537 0.906 0.951 0.077 5.214-4.128 98.38 1367 28 0.1233 504.821 499.266 0.996 0.951 0.070 4.126-3.266 94.74 2603 46 0.1153 460.172 453.294 1.059 0.951 0.005 3.266-2.585 99.86 5447 97 0.1114 310.421 307.005 1.041 0.951 0.000 2.585-2.046 97.45 10613 204 0.0953 234.195 231.655 1.049 0.951 0.000 2.046-1.619 99.39 21536 464 0.0918 138.608 137.300 1.067 0.950 0.000 1.619-1.281 98.00 42464 925 0.0977 74.619 73.908 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.030 38.366 1.025 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0503 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1202 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1202 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1202 r_free=0.1359 | n_water=884 | time (s): 2.620 (total time: 2.620) Filter (dist) r_work=0.1202 r_free=0.1359 | n_water=884 | time (s): 112.000 (total time: 114.620) Filter (q & B) r_work=0.1203 r_free=0.1358 | n_water=871 | time (s): 4.810 (total time: 119.430) Compute maps r_work=0.1203 r_free=0.1358 | n_water=871 | time (s): 1.640 (total time: 121.070) Filter (map) r_work=0.1224 r_free=0.1355 | n_water=759 | time (s): 5.290 (total time: 126.360) Find peaks r_work=0.1224 r_free=0.1355 | n_water=759 | time (s): 0.820 (total time: 127.180) Add new water r_work=0.1233 r_free=0.1368 | n_water=982 | time (s): 4.590 (total time: 131.770) Refine new water occ: r_work=0.1199 r_free=0.1337 adp: r_work=0.1199 r_free=0.1337 occ: r_work=0.1197 r_free=0.1336 adp: r_work=0.1197 r_free=0.1335 occ: r_work=0.1195 r_free=0.1335 adp: r_work=0.1195 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1334 r_work=0.1195 r_free=0.1334 | n_water=982 | time (s): 263.600 (total time: 395.370) Filter (q & B) r_work=0.1200 r_free=0.1346 | n_water=892 | time (s): 5.250 (total time: 400.620) Filter (dist only) r_work=0.1200 r_free=0.1345 | n_water=891 | time (s): 113.750 (total time: 514.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568074 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.534339 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 0.1202 0.1349 0.0146 0.038 1.1 5.8 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.49 1.46 1.715 13.672 14.534 3.762 12.01 13.50 1.49 1.761 13.653 14.534 3.758 Individual atomic B min max mean iso aniso Overall: 5.40 64.70 14.51 0.88 526 3269 Protein: 5.40 28.53 10.24 0.88 0 2902 Water: 5.83 64.70 28.41 N/A 526 365 Other: 13.69 22.15 17.92 N/A 0 2 Chain A: 5.45 51.78 12.10 N/A 0 1623 Chain B: 5.40 64.70 11.94 N/A 0 1646 Chain S: 5.83 61.72 29.99 N/A 526 0 Histogram: Values Number of atoms 5.40 - 11.33 2098 11.33 - 17.26 788 17.26 - 23.19 277 23.19 - 29.12 214 29.12 - 35.05 195 35.05 - 40.98 120 40.98 - 46.91 69 46.91 - 52.84 27 52.84 - 58.77 4 58.77 - 64.70 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1351 r_work=0.1201 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1351 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1199 r_free = 0.1350 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1199 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757088 | | target function (ml) not normalized (work): 703657.570592 | | target function (ml) not normalized (free): 14734.405598 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1199 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1382 0.1381 0.1440 n_refl.: 191129 remove outliers: r(all,work,free)=0.1382 0.1381 0.1440 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1390 0.1389 0.1444 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1339 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1339 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3563 360.941 326.205 0.406 0.996 0.225 13.296-10.522 96.04 96 1 0.2371 480.490 461.596 0.690 0.997 0.155 10.503-8.327 97.80 175 3 0.2174 501.969 495.877 0.846 0.998 0.123 8.315-6.595 100.00 359 8 0.2164 374.645 369.300 0.867 0.998 0.092 6.588-5.215 100.00 711 7 0.1939 345.131 335.191 0.871 0.998 0.074 5.214-4.128 98.38 1367 28 0.1234 504.821 498.722 0.958 0.999 0.060 4.126-3.266 94.74 2603 46 0.1156 460.172 452.659 1.019 1.000 0.000 3.266-2.585 99.86 5447 97 0.1109 310.421 306.827 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0955 234.195 231.592 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.608 137.238 1.025 1.005 0.000 1.619-1.281 98.00 42464 925 0.0952 74.619 73.957 1.013 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.030 38.343 0.980 1.017 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0633 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1339 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1339 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1339 | n_water=891 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1190 r_free=0.1339 | n_water=891 | time (s): 116.880 (total time: 119.360) Filter (q & B) r_work=0.1190 r_free=0.1338 | n_water=882 | time (s): 5.350 (total time: 124.710) Compute maps r_work=0.1190 r_free=0.1338 | n_water=882 | time (s): 2.330 (total time: 127.040) Filter (map) r_work=0.1212 r_free=0.1348 | n_water=772 | time (s): 4.160 (total time: 131.200) Find peaks r_work=0.1212 r_free=0.1348 | n_water=772 | time (s): 0.600 (total time: 131.800) Add new water r_work=0.1220 r_free=0.1359 | n_water=982 | time (s): 4.440 (total time: 136.240) Refine new water occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1334 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1333 occ: r_work=0.1184 r_free=0.1333 adp: r_work=0.1184 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1333 r_work=0.1184 r_free=0.1333 | n_water=982 | time (s): 235.160 (total time: 371.400) Filter (q & B) r_work=0.1188 r_free=0.1343 | n_water=900 | time (s): 4.430 (total time: 375.830) Filter (dist only) r_work=0.1189 r_free=0.1343 | n_water=898 | time (s): 114.030 (total time: 489.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.480723 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.458831 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1346 0.0154 0.038 1.1 6.0 0.0 0.3 0 0.740 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.46 1.54 1.677 13.689 14.459 3.757 11.93 13.47 1.54 1.684 13.683 14.459 3.755 Individual atomic B min max mean iso aniso Overall: 5.45 64.27 14.57 0.87 533 3269 Protein: 5.45 28.29 10.31 0.87 0 2902 Water: 5.91 64.27 28.33 N/A 533 365 Other: 13.75 22.22 17.99 N/A 0 2 Chain A: 5.55 51.60 12.14 N/A 0 1623 Chain B: 5.45 64.27 11.99 N/A 0 1646 Chain S: 5.91 61.81 29.97 N/A 533 0 Histogram: Values Number of atoms 5.45 - 11.33 2073 11.33 - 17.21 813 17.21 - 23.10 275 23.10 - 28.98 216 28.98 - 34.86 195 34.86 - 40.74 121 40.74 - 46.63 74 46.63 - 52.51 28 52.51 - 58.39 4 58.39 - 64.27 3 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1348 r_work=0.1193 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1348 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1349 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754282 | | target function (ml) not normalized (work): 703128.153402 | | target function (ml) not normalized (free): 14724.817798 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1349 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1382 0.1381 0.1461 n_refl.: 191128 remove outliers: r(all,work,free)=0.1382 0.1381 0.1461 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1384 0.1383 0.1463 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191128 remove outliers: r(all,work,free)=0.1194 0.1191 0.1344 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3695 360.941 329.355 0.397 0.995 0.205 13.296-10.522 96.04 96 1 0.2367 480.490 461.348 0.682 0.997 0.137 10.503-8.327 97.80 175 3 0.2219 501.969 495.098 0.843 0.997 0.107 8.315-6.595 100.00 359 8 0.2154 374.645 369.454 0.866 0.997 0.085 6.588-5.215 100.00 711 7 0.1954 345.131 334.992 0.869 0.997 0.070 5.214-4.128 98.38 1367 28 0.1245 504.821 498.800 0.956 0.998 0.034 4.126-3.266 94.74 2603 46 0.1162 460.172 452.611 1.020 1.000 0.005 3.266-2.585 99.86 5447 97 0.1114 310.421 306.814 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0957 234.195 231.544 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.608 137.241 1.027 1.006 0.000 1.619-1.281 98.00 42464 925 0.0948 74.619 73.964 1.017 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.030 38.329 0.986 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0206 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1344 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1344 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1344 | n_water=898 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1191 r_free=0.1344 | n_water=897 | time (s): 123.350 (total time: 125.860) Filter (q & B) r_work=0.1191 r_free=0.1344 | n_water=889 | time (s): 5.160 (total time: 131.020) Compute maps r_work=0.1191 r_free=0.1344 | n_water=889 | time (s): 2.150 (total time: 133.170) Filter (map) r_work=0.1214 r_free=0.1350 | n_water=778 | time (s): 5.110 (total time: 138.280) Find peaks r_work=0.1214 r_free=0.1350 | n_water=778 | time (s): 0.530 (total time: 138.810) Add new water r_work=0.1221 r_free=0.1355 | n_water=990 | time (s): 3.980 (total time: 142.790) Refine new water occ: r_work=0.1189 r_free=0.1334 adp: r_work=0.1189 r_free=0.1334 occ: r_work=0.1187 r_free=0.1333 adp: r_work=0.1187 r_free=0.1334 occ: r_work=0.1185 r_free=0.1332 adp: r_work=0.1185 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1332 r_work=0.1185 r_free=0.1332 | n_water=990 | time (s): 217.650 (total time: 360.440) Filter (q & B) r_work=0.1189 r_free=0.1341 | n_water=905 | time (s): 4.540 (total time: 364.980) Filter (dist only) r_work=0.1190 r_free=0.1340 | n_water=904 | time (s): 114.320 (total time: 479.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.536503 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.716445 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1346 0.0153 0.039 1.1 6.0 0.0 0.3 0 0.768 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.46 1.53 1.680 13.726 14.716 3.755 11.92 13.48 1.56 1.690 13.720 14.716 3.753 Individual atomic B min max mean iso aniso Overall: 5.54 63.28 14.61 0.87 539 3269 Protein: 5.54 28.14 10.33 0.87 0 2902 Water: 5.96 63.28 28.32 N/A 539 365 Other: 13.80 22.16 17.98 N/A 0 2 Chain A: 5.60 51.17 12.13 N/A 0 1623 Chain B: 5.54 63.28 11.99 N/A 0 1646 Chain S: 5.96 61.96 30.08 N/A 539 0 Histogram: Values Number of atoms 5.54 - 11.31 2061 11.31 - 17.09 826 17.09 - 22.86 266 22.86 - 28.63 217 28.63 - 34.41 197 34.41 - 40.18 118 40.18 - 45.96 79 45.96 - 51.73 33 51.73 - 57.50 8 57.50 - 63.28 3 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1348 r_work=0.1193 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1348 target_work(ml) = 3.753 | | 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) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (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): 3.752623 | | target function (ml) not normalized (work): 702817.442416 | | target function (ml) not normalized (free): 14727.583450 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1348 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1394 0.1393 0.1476 n_refl.: 191128 remove outliers: r(all,work,free)=0.1394 0.1393 0.1476 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1394 0.1392 0.1475 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1347 n_refl.: 191128 remove outliers: r(all,work,free)=0.1193 0.1190 0.1347 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3679 360.941 328.881 0.429 0.914 0.202 13.296-10.522 96.04 96 1 0.2392 480.490 462.460 0.744 0.916 0.139 10.503-8.327 97.80 175 3 0.2201 501.969 495.810 0.915 0.916 0.111 8.315-6.595 100.00 359 8 0.2163 374.645 369.347 0.941 0.916 0.092 6.588-5.215 100.00 711 7 0.1956 345.131 334.853 0.946 0.917 0.077 5.214-4.128 98.38 1367 28 0.1260 504.821 498.750 1.040 0.918 0.039 4.126-3.266 94.74 2603 46 0.1174 460.172 452.374 1.110 0.919 0.005 3.266-2.585 99.86 5447 97 0.1122 310.421 306.815 1.091 0.920 0.000 2.585-2.046 97.45 10613 204 0.0955 234.195 231.552 1.100 0.922 0.000 2.046-1.619 99.39 21536 464 0.0906 138.608 137.232 1.118 0.926 0.000 1.619-1.281 98.00 42464 925 0.0943 74.619 73.969 1.107 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.030 38.322 1.075 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0096 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1347 After: r_work=0.1191 r_free=0.1347 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1347 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1347 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1347 | n_water=904 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1192 r_free=0.1347 | n_water=902 | time (s): 124.830 (total time: 127.510) Filter (q & B) r_work=0.1192 r_free=0.1348 | n_water=891 | time (s): 4.640 (total time: 132.150) Compute maps r_work=0.1192 r_free=0.1348 | n_water=891 | time (s): 2.010 (total time: 134.160) Filter (map) r_work=0.1214 r_free=0.1357 | n_water=779 | time (s): 5.520 (total time: 139.680) Find peaks r_work=0.1214 r_free=0.1357 | n_water=779 | time (s): 0.680 (total time: 140.360) Add new water r_work=0.1221 r_free=0.1369 | n_water=983 | time (s): 4.850 (total time: 145.210) Refine new water occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1190 r_free=0.1338 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1336 occ: r_work=0.1186 r_free=0.1333 adp: r_work=0.1186 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1335 r_work=0.1186 r_free=0.1335 | n_water=983 | time (s): 239.460 (total time: 384.670) Filter (q & B) r_work=0.1190 r_free=0.1344 | n_water=904 | time (s): 4.470 (total time: 389.140) Filter (dist only) r_work=0.1190 r_free=0.1344 | n_water=903 | time (s): 117.330 (total time: 506.470) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.486679 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.514766 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1346 0.0154 0.039 1.1 7.5 0.0 0.3 0 0.743 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.46 1.54 1.679 13.719 13.515 3.755 11.95 13.49 1.55 1.674 13.719 13.515 3.755 Individual atomic B min max mean iso aniso Overall: 5.57 63.13 14.60 0.85 538 3269 Protein: 5.57 28.03 10.35 0.85 0 2902 Water: 6.05 63.13 28.27 N/A 538 365 Other: 13.82 22.17 18.00 N/A 0 2 Chain A: 5.64 51.11 12.12 N/A 0 1623 Chain B: 5.57 63.13 11.99 N/A 0 1646 Chain S: 6.05 59.74 30.08 N/A 538 0 Histogram: Values Number of atoms 5.57 - 11.33 2061 11.33 - 17.08 833 17.08 - 22.84 267 22.84 - 28.60 217 28.60 - 34.35 187 34.35 - 40.11 117 40.11 - 45.86 80 45.86 - 51.62 35 51.62 - 57.38 8 57.38 - 63.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1349 r_work=0.1195 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1349 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1349 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.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755175 | | target function (ml) not normalized (work): 703295.483400 | | target function (ml) not normalized (free): 14727.727789 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1362 0.1434 5.6907 5.7623| | 2: 2.94 - 2.33 1.00 7339 128 0.1069 0.1352 5.0765 5.1848| | 3: 2.33 - 2.04 0.96 6939 150 0.0902 0.1157 4.6528 4.7252| | 4: 2.04 - 1.85 1.00 7170 155 0.0899 0.1060 4.3943 4.5668| | 5: 1.85 - 1.72 0.99 7113 159 0.0938 0.1008 4.1577 4.2584| | 6: 1.72 - 1.62 0.99 7102 142 0.0901 0.1113 3.9535 4.0907| | 7: 1.62 - 1.54 0.99 7104 148 0.0895 0.0953 3.8048 3.933| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1307 3.7025 3.9076| | 9: 1.47 - 1.41 0.98 6938 155 0.0927 0.1110 3.6216 3.7448| | 10: 1.41 - 1.36 0.99 7022 150 0.0979 0.1199 3.5585 3.6795| | 11: 1.36 - 1.32 0.99 6997 151 0.0995 0.1116 3.4865 3.5902| | 12: 1.32 - 1.28 0.98 6975 149 0.1035 0.1136 3.4609 3.5837| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1236 3.4364 3.5588| | 14: 1.25 - 1.22 0.98 7015 112 0.1107 0.1580 3.4316 3.6744| | 15: 1.22 - 1.19 0.98 6956 137 0.1168 0.1249 3.4477 3.4916| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1554 3.4652 3.6607| | 17: 1.17 - 1.14 0.98 6940 135 0.1301 0.1218 3.434 3.437| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1700 3.4379 3.531| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1746 3.4196 3.5933| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1580 3.41 3.4327| | 21: 1.08 - 1.07 0.97 6852 152 0.1730 0.2123 3.4186 3.5006| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1955 3.4132 3.4155| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2025 3.4337 3.4867| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2248 3.4359 3.5105| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2508 3.449 3.5252| | 26: 1.01 - 0.99 0.96 6767 158 0.2759 0.2862 3.4161 3.4231| | 27: 0.99 - 0.98 0.94 6647 131 0.3045 0.2812 3.4691 3.3957| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.58 1.00 0.96 11140.42| | 2: 2.94 - 2.33 7339 128 0.93 12.67 0.99 0.95 5073.96| | 3: 2.33 - 2.04 6939 150 0.96 7.55 1.01 0.95 1667.61| | 4: 2.04 - 1.85 7170 155 0.96 7.65 1.00 0.95 1007.05| | 5: 1.85 - 1.72 7113 159 0.96 8.18 1.00 0.96 644.42| | 6: 1.72 - 1.62 7102 142 0.96 8.16 1.00 0.96 452.32| | 7: 1.62 - 1.54 7104 148 0.96 8.21 1.01 0.97 341.28| | 8: 1.54 - 1.47 6798 152 0.96 8.33 1.01 0.97 281.37| | 9: 1.47 - 1.41 6938 155 0.96 8.51 1.00 0.98 231.41| | 10: 1.41 - 1.36 7022 150 0.96 8.95 1.00 0.97 203.34| | 11: 1.36 - 1.32 6997 151 0.96 8.97 0.99 0.96 175.50| | 12: 1.32 - 1.28 6975 149 0.96 9.01 0.98 0.95 161.30| | 13: 1.28 - 1.25 6907 166 0.96 9.49 1.01 0.96 157.61| | 14: 1.25 - 1.22 7015 112 0.95 10.64 1.01 0.97 162.00| | 15: 1.22 - 1.19 6956 137 0.95 11.17 1.01 0.98 165.53| | 16: 1.19 - 1.17 6604 132 0.95 11.40 1.01 0.96 159.68| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.96 153.44| | 18: 1.14 - 1.12 6875 142 0.94 12.72 1.01 0.95 147.18| | 19: 1.12 - 1.10 6948 106 0.93 14.10 1.00 0.95 150.50| | 20: 1.10 - 1.08 6884 147 0.92 15.20 1.00 0.94 149.91| | 21: 1.08 - 1.07 6852 152 0.91 16.63 1.00 0.93 153.05| | 22: 1.07 - 1.05 6836 135 0.89 18.29 0.99 0.93 155.03| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 165.02| | 24: 1.03 - 1.02 6784 133 0.85 23.19 0.99 0.93 179.42| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.90 182.35| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.88 176.79| | 27: 0.99 - 0.98 6647 131 0.82 26.30 0.99 0.87 161.22| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.18 max = 11140.42 mean = 920.75| |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 = 88.76 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1477 n_refl.: 191128 remove outliers: r(all,work,free)=0.1404 0.1403 0.1477 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1396 0.1394 0.1472 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1348 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1348 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3641 360.941 329.773 0.399 0.973 0.210 13.296-10.522 96.04 96 1 0.2386 480.490 463.001 0.678 0.975 0.133 10.503-8.327 97.80 175 3 0.2197 501.969 495.385 0.840 0.975 0.097 8.315-6.595 100.00 359 8 0.2150 374.645 369.397 0.861 0.975 0.088 6.588-5.215 100.00 711 7 0.1935 345.131 334.828 0.867 0.976 0.082 5.214-4.128 98.38 1367 28 0.1265 504.821 498.451 0.954 0.977 0.051 4.126-3.266 94.74 2603 46 0.1166 460.172 452.576 1.018 0.978 0.000 3.266-2.585 99.86 5447 97 0.1119 310.421 307.010 1.000 0.980 0.000 2.585-2.046 97.45 10613 204 0.0962 234.195 231.530 1.007 0.982 0.000 2.046-1.619 99.39 21536 464 0.0913 138.608 137.235 1.022 0.987 0.000 1.619-1.281 98.00 42464 925 0.0948 74.619 73.964 1.011 0.994 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.030 38.310 0.978 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0124 ================= 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 : 0.2024 0.1996 0.080 5.225 5.2 78.0 14.6 805 0.000 1_bss: 0.1787 0.1934 0.080 5.225 5.2 78.0 14.6 805 0.000 1_settarget: 0.1787 0.1934 0.080 5.225 5.2 78.0 14.6 805 0.000 1_nqh: 0.1787 0.1934 0.080 5.225 5.2 78.0 14.6 805 0.000 1_weight: 0.1787 0.1934 0.080 5.225 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1270 0.1502 0.039 1.166 5.2 78.0 14.6 805 0.155 1_adp: 0.1298 0.1573 0.039 1.166 5.2 73.0 15.0 805 0.155 1_regHadp: 0.1297 0.1569 0.039 1.166 5.2 73.0 15.0 805 0.155 1_occ: 0.1282 0.1557 0.039 1.166 5.2 73.0 15.0 805 0.155 2_bss: 0.1275 0.1548 0.039 1.166 5.3 73.2 15.2 805 0.155 2_settarget: 0.1275 0.1548 0.039 1.166 5.3 73.2 15.2 805 0.155 2_updatecdl: 0.1275 0.1548 0.039 1.176 5.3 73.2 15.2 805 0.155 2_nqh: 0.1275 0.1548 0.039 1.176 5.3 73.2 15.2 805 0.155 2_sol: 0.1271 0.1505 0.039 1.176 5.3 73.2 16.4 891 n/a 2_weight: 0.1271 0.1505 0.039 1.176 5.3 73.2 16.4 891 n/a 2_xyzrec: 0.1255 0.1531 0.041 1.150 5.3 73.2 16.4 891 n/a 2_adp: 0.1232 0.1518 0.041 1.150 5.4 72.3 16.5 891 n/a 2_regHadp: 0.1232 0.1519 0.041 1.150 5.4 72.3 16.5 891 n/a 2_occ: 0.1225 0.1518 0.041 1.150 5.4 72.3 16.5 891 n/a 3_bss: 0.1232 0.1525 0.041 1.150 5.4 72.2 16.5 891 n/a 3_settarget: 0.1232 0.1525 0.041 1.150 5.4 72.2 16.5 891 n/a 3_updatecdl: 0.1232 0.1525 0.041 1.153 5.4 72.2 16.5 891 n/a 3_nqh: 0.1232 0.1525 0.041 1.153 5.4 72.2 16.5 891 n/a 3_sol: 0.1250 0.1524 0.041 1.153 5.4 68.2 15.4 872 n/a 3_weight: 0.1250 0.1524 0.041 1.153 5.4 68.2 15.4 872 n/a 3_xyzrec: 0.1238 0.1447 0.035 1.109 5.4 68.2 15.4 872 n/a 3_adp: 0.1237 0.1407 0.035 1.109 5.6 67.8 15.2 872 n/a 3_regHadp: 0.1238 0.1408 0.035 1.109 5.6 67.8 15.2 872 n/a 3_occ: 0.1232 0.1395 0.035 1.109 5.6 67.8 15.2 872 n/a 4_bss: 0.1228 0.1390 0.035 1.109 5.5 67.8 15.2 872 n/a 4_settarget: 0.1228 0.1390 0.035 1.109 5.5 67.8 15.2 872 n/a 4_updatecdl: 0.1228 0.1390 0.035 1.114 5.5 67.8 15.2 872 n/a 4_nqh: 0.1228 0.1390 0.035 1.114 5.5 67.8 15.2 872 n/a 4_sol: 0.1210 0.1363 0.035 1.114 5.5 67.8 15.0 865 n/a 4_weight: 0.1210 0.1363 0.035 1.114 5.5 67.8 15.0 865 n/a 4_xyzrec: 0.1211 0.1361 0.036 1.119 5.5 67.8 15.0 865 n/a 4_adp: 0.1200 0.1355 0.036 1.119 5.5 67.3 15.0 865 n/a 4_regHadp: 0.1200 0.1355 0.036 1.119 5.5 67.3 15.0 865 n/a 4_occ: 0.1197 0.1356 0.036 1.119 5.5 67.3 15.0 865 n/a 5_bss: 0.1196 0.1354 0.036 1.119 5.5 67.3 14.9 865 n/a 5_settarget: 0.1196 0.1354 0.036 1.119 5.5 67.3 14.9 865 n/a 5_updatecdl: 0.1196 0.1354 0.036 1.119 5.5 67.3 14.9 865 n/a 5_nqh: 0.1196 0.1354 0.036 1.119 5.5 67.3 14.9 865 n/a 5_sol: 0.1193 0.1347 0.036 1.119 5.5 67.3 14.9 886 n/a 5_weight: 0.1193 0.1347 0.036 1.119 5.5 67.3 14.9 886 n/a 5_xyzrec: 0.1196 0.1356 0.036 1.130 5.5 67.3 14.9 886 n/a 5_adp: 0.1200 0.1360 0.036 1.130 5.6 67.1 14.9 886 n/a 5_regHadp: 0.1200 0.1360 0.036 1.130 5.6 67.1 14.9 886 n/a 5_occ: 0.1199 0.1361 0.036 1.130 5.6 67.1 14.9 886 n/a 6_bss: 0.1197 0.1359 0.036 1.130 5.5 67.1 14.8 886 n/a 6_settarget: 0.1197 0.1359 0.036 1.130 5.5 67.1 14.8 886 n/a 6_updatecdl: 0.1197 0.1359 0.036 1.130 5.5 67.1 14.8 886 n/a 6_nqh: 0.1197 0.1359 0.036 1.130 5.5 67.1 14.8 886 n/a 6_sol: 0.1194 0.1349 0.036 1.130 5.5 67.1 14.9 884 n/a 6_weight: 0.1194 0.1349 0.036 1.130 5.5 67.1 14.9 884 n/a 6_xyzrec: 0.1198 0.1357 0.037 1.130 5.5 67.1 14.9 884 n/a 6_adp: 0.1204 0.1365 0.037 1.130 5.6 66.1 14.8 884 n/a 6_regHadp: 0.1205 0.1366 0.037 1.130 5.6 66.1 14.8 884 n/a 6_occ: 0.1203 0.1362 0.037 1.130 5.6 66.1 14.8 884 n/a 7_bss: 0.1202 0.1359 0.037 1.130 5.3 65.9 14.5 884 n/a 7_settarget: 0.1202 0.1359 0.037 1.130 5.3 65.9 14.5 884 n/a 7_updatecdl: 0.1202 0.1359 0.037 1.130 5.3 65.9 14.5 884 n/a 7_nqh: 0.1202 0.1359 0.037 1.130 5.3 65.9 14.5 884 n/a 7_sol: 0.1200 0.1345 0.037 1.130 5.3 65.9 14.5 891 n/a 7_weight: 0.1200 0.1345 0.037 1.130 5.3 65.9 14.5 891 n/a 7_xyzrec: 0.1202 0.1349 0.038 1.129 5.3 65.9 14.5 891 n/a 7_adp: 0.1201 0.1351 0.038 1.129 5.4 64.7 14.5 891 n/a 7_regHadp: 0.1201 0.1351 0.038 1.129 5.4 64.7 14.5 891 n/a 7_occ: 0.1199 0.1350 0.038 1.129 5.4 64.7 14.5 891 n/a 8_bss: 0.1190 0.1339 0.038 1.129 5.5 64.8 14.6 891 n/a 8_settarget: 0.1190 0.1339 0.038 1.129 5.5 64.8 14.6 891 n/a 8_updatecdl: 0.1190 0.1339 0.038 1.129 5.5 64.8 14.6 891 n/a 8_nqh: 0.1190 0.1339 0.038 1.129 5.5 64.8 14.6 891 n/a 8_sol: 0.1189 0.1343 0.038 1.129 5.5 64.8 14.6 898 n/a 8_weight: 0.1189 0.1343 0.038 1.129 5.5 64.8 14.6 898 n/a 8_xyzrec: 0.1192 0.1346 0.038 1.118 5.5 64.8 14.6 898 n/a 8_adp: 0.1193 0.1348 0.038 1.118 5.4 64.3 14.6 898 n/a 8_regHadp: 0.1193 0.1348 0.038 1.118 5.4 64.3 14.6 898 n/a 8_occ: 0.1192 0.1349 0.038 1.118 5.4 64.3 14.6 898 n/a 9_bss: 0.1191 0.1344 0.038 1.118 5.5 64.3 14.6 898 n/a 9_settarget: 0.1191 0.1344 0.038 1.118 5.5 64.3 14.6 898 n/a 9_updatecdl: 0.1191 0.1344 0.038 1.118 5.5 64.3 14.6 898 n/a 9_nqh: 0.1191 0.1344 0.038 1.118 5.5 64.3 14.6 898 n/a 9_sol: 0.1190 0.1340 0.038 1.118 5.5 64.3 14.6 904 n/a 9_weight: 0.1190 0.1340 0.038 1.118 5.5 64.3 14.6 904 n/a 9_xyzrec: 0.1192 0.1346 0.039 1.119 5.5 64.3 14.6 904 n/a 9_adp: 0.1192 0.1348 0.039 1.119 5.5 63.3 14.6 904 n/a 9_regHadp: 0.1193 0.1348 0.039 1.119 5.5 63.3 14.6 904 n/a 9_occ: 0.1191 0.1348 0.039 1.119 5.5 63.3 14.6 904 n/a 10_bss: 0.1190 0.1347 0.039 1.119 5.5 63.3 14.6 904 n/a 10_settarget: 0.1190 0.1347 0.039 1.119 5.5 63.3 14.6 904 n/a 10_updatecdl: 0.1190 0.1347 0.039 1.119 5.5 63.3 14.6 904 n/a 10_setrh: 0.1191 0.1347 0.039 1.119 5.5 63.3 14.6 904 n/a 10_nqh: 0.1191 0.1347 0.039 1.119 5.5 63.3 14.6 904 n/a 10_sol: 0.1190 0.1344 0.039 1.119 5.5 63.3 14.6 903 n/a 10_weight: 0.1190 0.1344 0.039 1.119 5.5 63.3 14.6 903 n/a 10_xyzrec: 0.1192 0.1346 0.039 1.146 5.5 63.3 14.6 903 n/a 10_adp: 0.1195 0.1349 0.039 1.146 5.6 63.1 14.6 903 n/a 10_regHadp: 0.1195 0.1349 0.039 1.146 5.6 63.1 14.6 903 n/a 10_occ: 0.1194 0.1349 0.039 1.146 5.6 63.1 14.6 903 n/a end: 0.1193 0.1348 0.039 1.146 5.5 63.1 14.5 903 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2189413_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_2189413_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.3800 Refinement macro-cycles (run) : 11975.3300 Write final files (write_after_run_outputs) : 175.6000 Total : 12157.3100 Total CPU time: 3.39 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:39:50 PST -0800 (1736735990.44 s) Start R-work = 0.1787, R-free = 0.1934 Final R-work = 0.1193, R-free = 0.1348 =============================================================================== Job complete usr+sys time: 12464.34 seconds wall clock time: 208 minutes 45.82 seconds (12525.82 seconds total)