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_8586576.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_8586576.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_8586576.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.33, per 1000 atoms: 0.35 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: 2.613 distance_ideal: 2.720 ideal - model: 0.107 slack: 0.000 delta_slack: 0.107 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: 2.683 distance_ideal: 2.710 ideal - model: 0.027 slack: 0.000 delta_slack: 0.027 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: 0.95 Conformation dependent library (CDL) restraints added in 220.5 milliseconds Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 1.01: 589 1.01 - 1.24: 2621 1.24 - 1.47: 1508 1.47 - 1.71: 1190 1.71 - 1.94: 26 Bond restraints: 5934 Sorted by residual: bond pdb=" N ALA A 57 " pdb=" CA ALA A 57 " ideal model delta sigma weight residual 1.456 1.695 -0.240 1.04e-02 9.25e+03 5.31e+02 bond pdb=" C LYS B 133 " pdb=" N ILE B 134 " ideal model delta sigma weight residual 1.324 1.516 -0.192 8.60e-03 1.35e+04 4.98e+02 bond pdb=" C ILE A 162 " pdb=" N ASP A 163 " ideal model delta sigma weight residual 1.334 1.587 -0.253 1.20e-02 6.94e+03 4.43e+02 bond pdb=" C VAL B 32 " pdb=" O VAL B 32 " ideal model delta sigma weight residual 1.237 1.013 0.224 1.11e-02 8.12e+03 4.07e+02 bond pdb=" C GLY B 50 " pdb=" N VAL B 51 " ideal model delta sigma weight residual 1.335 1.089 0.246 1.22e-02 6.72e+03 4.06e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.01: 5607 4.01 - 8.03: 3438 8.03 - 12.04: 1428 12.04 - 16.06: 303 16.06 - 20.07: 34 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O PHE A 164 " pdb=" C PHE A 164 " pdb=" N GLY A 165 " ideal model delta sigma weight residual 122.08 139.00 -16.92 1.07e+00 8.73e-01 2.50e+02 angle pdb=" O VAL B 150 " pdb=" C VAL B 150 " pdb=" N LYS B 151 " ideal model delta sigma weight residual 121.78 137.60 -15.82 1.03e+00 9.43e-01 2.36e+02 angle pdb=" CA PHE A 82 " pdb=" CB PHE A 82 " pdb=" CG PHE A 82 " ideal model delta sigma weight residual 113.80 128.48 -14.68 1.00e+00 1.00e+00 2.15e+02 angle pdb=" OE1 GLN B 156 " pdb=" CD GLN B 156 " pdb=" NE2 GLN B 156 " ideal model delta sigma weight residual 122.60 136.90 -14.30 1.00e+00 1.00e+00 2.04e+02 angle pdb=" CA ILE A 162 " pdb=" C ILE A 162 " pdb=" O ILE A 162 " ideal model delta sigma weight residual 120.78 137.84 -17.06 1.25e+00 6.40e-01 1.86e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.10: 1830 16.10 - 32.19: 148 32.19 - 48.27: 47 48.27 - 64.36: 20 64.36 - 80.45: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 147.92 32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA VAL B 69 " pdb=" C VAL B 69 " pdb=" N ILE B 70 " pdb=" CA ILE B 70 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLY A 75 " pdb=" C GLY A 75 " pdb=" N ILE A 76 " pdb=" CA ILE A 76 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.264: 227 0.264 - 0.527: 176 0.527 - 0.790: 69 0.790 - 1.053: 18 1.053 - 1.316: 2 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB VAL A 186 " pdb=" CA VAL A 186 " pdb=" CG1 VAL A 186 " pdb=" CG2 VAL A 186 " both_signs ideal model delta sigma weight residual False -2.63 -3.95 1.32 2.00e-01 2.50e+01 4.33e+01 chirality pdb=" CA ILE A 121 " pdb=" N ILE A 121 " pdb=" C ILE A 121 " pdb=" CB ILE A 121 " both_signs ideal model delta sigma weight residual False 2.43 1.29 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CA PRO A 109 " pdb=" N PRO A 109 " pdb=" C PRO A 109 " pdb=" CB PRO A 109 " both_signs ideal model delta sigma weight residual False 2.72 1.67 1.05 2.00e-01 2.50e+01 2.73e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.119 2.00e-02 2.50e+03 6.60e-02 1.74e+02 pdb=" CG TRP A 146 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.118 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.056 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.047 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.059 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.068 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.112 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.053 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.013 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.054 2.00e-02 2.50e+03 5.97e-02 1.43e+02 pdb=" CG TRP B 146 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " 0.090 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " 0.028 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.048 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.100 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.102 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " -0.060 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " 0.033 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " -0.069 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.062 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.005 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.061 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.002 2.00e-02 2.50e+03 5.97e-02 1.43e+02 pdb=" CG TRP A 139 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.083 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.051 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.113 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.083 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.051 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.058 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " 0.058 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.024 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.028 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.014 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.084 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " -0.032 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.57: 23 1.57 - 2.33: 1999 2.33 - 3.08: 21870 3.08 - 3.84: 33107 3.84 - 4.60: 53351 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110350 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.811 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.886 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.057 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.098 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.209 2.620 ... (remaining 110345 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_8586576_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= 0.2044 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.304397 | | target function (ml) not normalized (work): 806269.578763 | | target function (ml) not normalized (free): 16544.931272 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2142 0.1910 6.6839 6.3237| | 2: 2.94 - 2.33 1.00 7339 128 0.1636 0.1654 5.5451 5.579| | 3: 2.33 - 2.04 0.96 6939 150 0.1636 0.1634 5.1441 5.1315| | 4: 2.04 - 1.85 1.00 7170 155 0.1748 0.1542 4.9663 4.993| | 5: 1.85 - 1.72 0.99 7113 159 0.1957 0.1759 4.8127 4.7982| | 6: 1.72 - 1.62 0.99 7102 142 0.1988 0.1833 4.6716 4.6155| | 7: 1.62 - 1.54 0.99 7104 148 0.2010 0.1785 4.5589 4.6137| | 8: 1.54 - 1.47 0.96 6798 152 0.2088 0.2071 4.4853 4.4877| | 9: 1.47 - 1.41 0.98 6938 155 0.2112 0.2168 4.4036 4.4928| | 10: 1.41 - 1.36 0.99 7022 150 0.2138 0.2045 4.3158 4.3265| | 11: 1.36 - 1.32 0.99 6997 151 0.2114 0.2122 4.2334 4.33| | 12: 1.32 - 1.28 0.98 6976 149 0.2117 0.2068 4.1952 4.2587| | 13: 1.28 - 1.25 0.98 6907 166 0.2063 0.2136 4.1413 4.2056| | 14: 1.25 - 1.22 0.98 7015 113 0.2086 0.2505 4.0861 4.3055| | 15: 1.22 - 1.19 0.98 6957 137 0.2118 0.1884 4.055 4.0156| | 16: 1.19 - 1.17 0.93 6604 132 0.2104 0.2036 4.0015 4.0434| | 17: 1.17 - 1.14 0.98 6941 135 0.2176 0.1990 3.9659 4.0127| | 18: 1.14 - 1.12 0.98 6875 142 0.2197 0.2253 3.9107 3.8678| | 19: 1.12 - 1.10 0.97 6949 106 0.2275 0.2310 3.8718 3.932| | 20: 1.10 - 1.08 0.97 6884 147 0.2325 0.2041 3.8252 3.7862| | 21: 1.08 - 1.07 0.97 6852 152 0.2439 0.2398 3.7987 3.7318| | 22: 1.07 - 1.05 0.97 6838 135 0.2568 0.2658 3.7587 3.7685| | 23: 1.05 - 1.03 0.97 6829 159 0.2720 0.2860 3.7331 3.9042| | 24: 1.03 - 1.02 0.96 6785 133 0.2873 0.2773 3.6979 3.7632| | 25: 1.02 - 1.01 0.93 6552 130 0.3074 0.2903 3.6682 3.7144| | 26: 1.01 - 0.99 0.96 6767 158 0.3225 0.3446 3.6315 3.6846| | 27: 0.99 - 0.98 0.94 6648 131 0.3436 0.3203 3.6432 3.6027| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.57 0.91 0.98 36024.44| | 2: 2.94 - 2.33 7339 128 0.86 21.15 1.09 1.03 15213.76| | 3: 2.33 - 2.04 6939 150 0.93 12.26 1.11 1.06 4032.90| | 4: 2.04 - 1.85 7170 155 0.93 12.84 1.11 1.06 2569.94| | 5: 1.85 - 1.72 7113 159 0.92 14.77 1.12 1.08 1912.55| | 6: 1.72 - 1.62 7102 142 0.91 15.79 1.11 1.08 1501.72| | 7: 1.62 - 1.54 7104 148 0.90 17.14 1.11 1.08 1292.50| | 8: 1.54 - 1.47 6798 152 0.89 18.06 1.11 1.07 1116.84| | 9: 1.47 - 1.41 6938 155 0.88 18.91 1.10 1.07 985.70| | 10: 1.41 - 1.36 7022 150 0.87 20.39 1.09 1.04 870.79| | 11: 1.36 - 1.32 6997 151 0.87 20.58 1.09 1.03 764.29| | 12: 1.32 - 1.28 6976 149 0.86 20.92 1.07 1.02 695.53| | 13: 1.28 - 1.25 6907 166 0.86 20.78 1.07 1.03 653.68| | 14: 1.25 - 1.22 7015 113 0.86 21.63 1.08 1.03 618.46| | 15: 1.22 - 1.19 6957 137 0.86 21.33 1.08 1.03 561.02| | 16: 1.19 - 1.17 6604 132 0.87 20.38 1.07 1.03 489.15| | 17: 1.17 - 1.14 6941 135 0.87 20.62 1.07 1.03 427.14| | 18: 1.14 - 1.12 6875 142 0.87 20.26 1.08 1.02 377.62| | 19: 1.12 - 1.10 6949 106 0.87 20.68 1.07 1.01 341.97| | 20: 1.10 - 1.08 6884 147 0.86 21.19 1.06 0.98 308.95| | 21: 1.08 - 1.07 6852 152 0.85 22.86 1.05 0.98 310.51| | 22: 1.07 - 1.05 6838 135 0.82 25.73 1.05 0.96 329.15| | 23: 1.05 - 1.03 6829 159 0.79 28.60 1.05 0.96 349.38| | 24: 1.03 - 1.02 6785 133 0.77 30.63 1.05 0.97 353.66| | 25: 1.02 - 1.01 6552 130 0.75 31.82 1.03 0.94 330.47| | 26: 1.01 - 0.99 6767 158 0.74 32.75 1.03 0.91 301.47| | 27: 0.99 - 0.98 6648 131 0.75 32.08 1.03 0.89 264.70| |alpha: min = 0.89 max = 1.08 mean = 1.01| |beta: min = 264.70 max = 36024.44 mean = 2831.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.57| |phase err.(test): min = 0.00 max = 89.92 mean = 21.56| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.253 2950 Z= 5.527 Angle : 5.123 17.059 4018 Z= 3.609 Chirality : 0.397 1.316 492 Planarity : 0.032 0.107 512 Dihedral : 12.951 80.451 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.97 % Allowed : 4.84 % Favored : 94.19 % Cbeta Deviations : 33.99 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.39), residues: 386 helix: -2.79 (0.31), residues: 140 sheet: -0.98 (0.57), residues: 82 loop : -0.29 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.077 0.021 ARG A 175 TYR 0.101 0.042 TYR A 67 PHE 0.132 0.042 PHE A 164 TRP 0.123 0.036 TRP B 146 HIS 0.071 0.025 HIS A 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2044 r_free= 0.1961 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.304397 | | target function (ml) not normalized (work): 806269.578763 | | target function (ml) not normalized (free): 16544.931272 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2042 0.2044 0.1961 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2042 0.2044 0.1961 n_refl.: 191155 remove outliers: r(all,work,free)=0.2042 0.2044 0.1961 n_refl.: 191145 overall B=-0.02 to atoms: r(all,work,free)=0.2040 0.2042 0.1960 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1814 0.1812 0.1906 n_refl.: 191145 remove outliers: r(all,work,free)=0.1811 0.1810 0.1904 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4069 402.814 292.108 0.429 0.916 0.301 13.296-10.522 99.01 99 1 0.2485 528.187 519.091 0.780 0.917 0.253 10.503-8.327 99.45 178 3 0.2540 565.118 556.443 0.961 0.917 0.230 8.318-6.595 100.00 360 8 0.2478 414.736 404.693 0.963 0.917 0.170 6.588-5.215 100.00 711 7 0.2293 381.101 364.748 0.947 0.918 0.160 5.214-4.128 98.38 1367 28 0.1486 557.435 549.605 1.061 0.919 0.080 4.126-3.266 94.74 2603 46 0.1342 508.132 498.697 1.130 0.920 0.023 3.266-2.585 99.86 5447 97 0.1451 342.774 337.480 1.102 0.921 0.000 2.585-2.046 97.45 10613 204 0.1400 258.603 254.390 1.105 0.923 0.000 2.046-1.619 99.39 21536 464 0.1637 153.054 149.955 1.118 0.926 0.000 1.619-1.281 98.00 42464 925 0.1936 82.395 80.494 1.099 0.931 0.000 1.281-0.980 96.53 101826 2055 0.2332 44.202 41.996 1.071 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0508 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1810 r_free=0.1904 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1810 r_free=0.1905 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.868995 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 563.787679 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1273 0.1499 0.0226 0.038 1.2 11.7 0.0 0.3 0 11.434 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.73 14.99 2.26 1.117 13.092 563.788 0.019 12.99 15.67 2.68 1.246 13.362 563.788 0.018 Individual atomic B min max mean iso aniso Overall: 5.27 73.02 15.07 1.41 435 3274 Protein: 5.27 40.32 11.04 1.41 0 2902 Water: 6.38 73.02 29.57 N/A 435 370 Other: 15.95 30.13 23.04 N/A 0 2 Chain A: 5.39 59.96 13.09 N/A 0 1626 Chain B: 5.27 73.02 12.83 N/A 0 1648 Chain S: 11.24 63.12 30.93 N/A 435 0 Histogram: Values Number of atoms 5.27 - 12.05 2173 12.05 - 18.82 633 18.82 - 25.60 312 25.60 - 32.37 260 32.37 - 39.15 160 39.15 - 45.92 106 45.92 - 52.70 44 52.70 - 59.47 17 59.47 - 66.25 3 66.25 - 73.02 1 =========================== Idealize ADP of riding H ========================== r_work=0.1299 r_free=0.1567 r_work=0.1298 r_free=0.1562 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1298 r_free = 0.1562 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1283 r_free = 0.1550 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1283 r_free= 0.1550 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015698 | | target function (ls_wunit_k1) not normalized (work): 2940.274545 | | target function (ls_wunit_k1) not normalized (free): 116.191912 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1283 0.1550 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1472 0.1469 0.1627 n_refl.: 191138 remove outliers: r(all,work,free)=0.1472 0.1469 0.1627 n_refl.: 191138 overall B=0.14 to atoms: r(all,work,free)=0.1493 0.1491 0.1637 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1274 0.1537 n_refl.: 191138 remove outliers: r(all,work,free)=0.1279 0.1274 0.1537 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3604 402.814 383.797 0.487 0.963 0.270 13.296-10.522 99.01 99 1 0.2114 528.187 519.528 0.733 0.964 0.240 10.503-8.327 99.45 178 3 0.1767 565.118 561.814 0.887 0.964 0.198 8.318-6.595 100.00 360 8 0.1741 414.736 410.915 0.907 0.964 0.160 6.588-5.215 100.00 711 7 0.1559 381.101 372.827 0.887 0.964 0.160 5.214-4.128 98.38 1367 28 0.0911 557.435 554.591 0.975 0.965 0.055 4.126-3.266 94.74 2603 46 0.0841 508.132 504.009 1.043 0.966 0.018 3.266-2.585 99.86 5447 97 0.0928 342.774 340.176 1.024 0.965 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.380 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1087 153.054 151.395 1.054 0.966 0.000 1.619-1.281 98.00 42464 925 0.1271 82.395 81.431 1.046 0.967 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.153 1.022 0.968 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0329 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1537 | n_water=805 | time (s): 2.530 (total time: 2.530) Filter (dist) r_work=0.1278 r_free=0.1540 | n_water=796 | time (s): 98.780 (total time: 101.310) Filter (q & B) r_work=0.1279 r_free=0.1541 | n_water=790 | time (s): 4.170 (total time: 105.480) Compute maps r_work=0.1279 r_free=0.1541 | n_water=790 | time (s): 1.920 (total time: 107.400) Filter (map) r_work=0.1303 r_free=0.1533 | n_water=656 | time (s): 4.300 (total time: 111.700) Find peaks r_work=0.1303 r_free=0.1533 | n_water=656 | time (s): 0.560 (total time: 112.260) Add new water r_work=0.1327 r_free=0.1568 | n_water=964 | time (s): 4.230 (total time: 116.490) Refine new water occ: r_work=0.1283 r_free=0.1502 adp: r_work=0.1270 r_free=0.1501 occ: r_work=0.1273 r_free=0.1497 adp: r_work=0.1266 r_free=0.1498 occ: r_work=0.1267 r_free=0.1494 adp: r_work=0.1264 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1264 r_free=0.1495 r_work=0.1264 r_free=0.1495 | n_water=964 | time (s): 89.200 (total time: 205.690) Filter (q & B) r_work=0.1268 r_free=0.1503 | n_water=900 | time (s): 4.670 (total time: 210.360) Filter (dist only) r_work=0.1268 r_free=0.1502 | n_water=899 | time (s): 112.730 (total time: 323.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.915962 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 600.223036 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 0.1251 0.1512 0.0261 0.040 1.1 20.1 0.0 0.3 0 11.958 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.51 15.12 2.61 2.052 15.320 600.223 0.014 12.32 15.03 2.71 2.412 15.357 600.223 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 68.25 16.52 1.21 531 3272 Protein: 5.40 40.25 11.01 1.21 0 2902 Water: 6.59 68.25 34.28 N/A 531 368 Other: 16.21 31.78 24.00 N/A 0 2 Chain A: 5.49 56.37 13.03 N/A 0 1624 Chain B: 5.40 68.25 12.85 N/A 0 1648 Chain S: 12.45 67.69 38.57 N/A 531 0 Histogram: Values Number of atoms 5.40 - 11.68 2050 11.68 - 17.97 714 17.97 - 24.26 266 24.26 - 30.54 215 30.54 - 36.83 181 36.83 - 43.11 156 43.11 - 49.40 100 49.40 - 55.68 62 55.68 - 61.97 44 61.97 - 68.25 15 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1504 r_work=0.1233 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1505 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1499 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1499 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013385 | | target function (ls_wunit_k1) not normalized (work): 2506.968805 | | target function (ls_wunit_k1) not normalized (free): 101.355408 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1499 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1433 0.1430 0.1603 n_refl.: 191138 remove outliers: r(all,work,free)=0.1433 0.1430 0.1603 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1601 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1509 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1234 0.1509 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3200 402.814 377.682 0.486 0.963 0.265 13.296-10.522 99.01 99 1 0.1919 528.187 517.195 0.752 0.964 0.213 10.503-8.327 99.45 178 3 0.1415 565.118 567.415 0.921 0.964 0.178 8.318-6.595 100.00 360 8 0.1523 414.736 413.424 0.938 0.963 0.144 6.588-5.215 100.00 711 7 0.1371 381.101 376.455 0.910 0.963 0.123 5.214-4.128 98.38 1367 28 0.0819 557.435 556.304 0.994 0.963 0.060 4.126-3.266 94.74 2603 46 0.0757 508.132 505.545 1.059 0.963 0.015 3.266-2.585 99.86 5447 97 0.0857 342.774 341.270 1.046 0.962 0.005 2.585-2.046 97.45 10613 204 0.0895 258.603 256.703 1.059 0.962 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.611 1.080 0.960 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.334 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.210 1.059 0.952 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0600 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1509 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1509 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1509 | n_water=899 | time (s): 3.660 (total time: 3.660) Filter (dist) r_work=0.1235 r_free=0.1514 | n_water=895 | time (s): 116.580 (total time: 120.240) Filter (q & B) r_work=0.1235 r_free=0.1515 | n_water=892 | time (s): 5.140 (total time: 125.380) Compute maps r_work=0.1235 r_free=0.1515 | n_water=892 | time (s): 1.840 (total time: 127.220) Filter (map) r_work=0.1279 r_free=0.1528 | n_water=687 | time (s): 5.540 (total time: 132.760) Find peaks r_work=0.1279 r_free=0.1528 | n_water=687 | time (s): 0.870 (total time: 133.630) Add new water r_work=0.1301 r_free=0.1561 | n_water=999 | time (s): 5.010 (total time: 138.640) Refine new water occ: r_work=0.1257 r_free=0.1524 adp: r_work=0.1257 r_free=0.1525 occ: r_work=0.1252 r_free=0.1519 adp: r_work=0.1252 r_free=0.1520 occ: r_work=0.1249 r_free=0.1515 adp: r_work=0.1249 r_free=0.1516 ADP+occupancy (water only), MIN, final r_work=0.1249 r_free=0.1516 r_work=0.1249 r_free=0.1516 | n_water=999 | time (s): 251.590 (total time: 390.230) Filter (q & B) r_work=0.1253 r_free=0.1521 | n_water=875 | time (s): 5.920 (total time: 396.150) Filter (dist only) r_work=0.1253 r_free=0.1521 | n_water=874 | time (s): 120.200 (total time: 516.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.740075 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.799871 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 0.1244 0.1444 0.0201 0.035 1.1 7.7 0.0 0.0 0 0.870 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.44 14.44 2.01 1.938 14.612 16.800 3.942 12.33 14.04 1.71 2.218 14.520 16.800 3.897 Individual atomic B min max mean iso aniso Overall: 5.54 67.89 15.29 1.07 507 3271 Protein: 5.54 36.85 10.77 1.07 0 2902 Water: 6.68 67.89 30.28 N/A 507 367 Other: 14.10 28.17 21.14 N/A 0 2 Chain A: 5.55 55.56 12.80 N/A 0 1624 Chain B: 5.54 67.89 12.57 N/A 0 1647 Chain S: 15.00 62.19 32.11 N/A 507 0 Histogram: Values Number of atoms 5.54 - 11.78 2131 11.78 - 18.01 684 18.01 - 24.25 298 24.25 - 30.48 242 30.48 - 36.72 175 36.72 - 42.95 141 42.95 - 49.18 67 49.18 - 55.42 26 55.42 - 61.65 12 61.65 - 67.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1405 r_work=0.1234 r_free=0.1405 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1405 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1401 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1401 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891553 | | target function (ml) not normalized (work): 728876.161599 | | target function (ml) not normalized (free): 15228.346509 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1401 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1441 0.1505 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1441 0.1505 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1436 0.1435 0.1501 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1396 n_refl.: 191138 remove outliers: r(all,work,free)=0.1228 0.1224 0.1396 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3769 398.008 361.755 0.417 0.947 0.247 13.296-10.522 99.01 99 1 0.2448 528.187 507.576 0.697 0.948 0.203 10.503-8.327 98.90 177 3 0.2054 557.261 558.311 0.884 0.948 0.180 8.318-6.595 100.00 360 8 0.2115 414.736 409.137 0.893 0.948 0.110 6.588-5.215 100.00 711 7 0.1863 381.101 370.670 0.880 0.948 0.100 5.214-4.128 98.38 1367 28 0.1183 557.435 552.127 0.972 0.948 0.080 4.126-3.266 94.74 2603 46 0.1102 508.132 501.076 1.033 0.948 0.019 3.266-2.585 99.86 5447 97 0.1089 342.774 339.026 1.020 0.947 0.005 2.585-2.046 97.45 10613 204 0.0954 258.603 255.790 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0968 153.054 151.423 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.478 1.052 0.945 0.000 1.281-0.980 96.53 101826 2055 0.1690 44.202 42.315 1.037 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1051 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1396 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1396 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1396 | n_water=874 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1224 r_free=0.1395 | n_water=873 | time (s): 108.400 (total time: 110.730) Filter (q & B) r_work=0.1225 r_free=0.1394 | n_water=867 | time (s): 4.310 (total time: 115.040) Compute maps r_work=0.1225 r_free=0.1394 | n_water=867 | time (s): 2.020 (total time: 117.060) Filter (map) r_work=0.1248 r_free=0.1386 | n_water=724 | time (s): 4.880 (total time: 121.940) Find peaks r_work=0.1248 r_free=0.1386 | n_water=724 | time (s): 0.550 (total time: 122.490) Add new water r_work=0.1262 r_free=0.1410 | n_water=959 | time (s): 4.320 (total time: 126.810) Refine new water occ: r_work=0.1215 r_free=0.1373 adp: r_work=0.1208 r_free=0.1368 occ: r_work=0.1205 r_free=0.1370 adp: r_work=0.1205 r_free=0.1369 occ: r_work=0.1203 r_free=0.1370 adp: r_work=0.1203 r_free=0.1370 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1370 r_work=0.1203 r_free=0.1370 | n_water=959 | time (s): 230.590 (total time: 357.400) Filter (q & B) r_work=0.1208 r_free=0.1380 | n_water=866 | time (s): 4.600 (total time: 362.000) Filter (dist only) r_work=0.1209 r_free=0.1380 | n_water=864 | time (s): 111.620 (total time: 473.620) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.610323 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.880768 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1383 0.0175 0.036 1.1 5.8 0.0 0.0 0 0.805 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.83 1.75 1.843 14.215 15.881 3.876 12.04 13.81 1.77 1.994 14.160 15.881 3.868 Individual atomic B min max mean iso aniso Overall: 5.54 67.38 14.93 1.00 497 3271 Protein: 5.54 33.34 10.66 1.00 0 2902 Water: 5.91 67.38 29.26 N/A 497 367 Other: 13.97 26.84 20.40 N/A 0 2 Chain A: 5.54 54.25 12.63 N/A 0 1624 Chain B: 5.54 67.38 12.44 N/A 0 1647 Chain S: 5.91 62.05 30.70 N/A 497 0 Histogram: Values Number of atoms 5.54 - 11.72 2128 11.72 - 17.90 719 17.90 - 24.09 306 24.09 - 30.27 248 30.27 - 36.46 148 36.46 - 42.64 121 42.64 - 48.83 60 48.83 - 55.01 27 55.01 - 61.19 9 61.19 - 67.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1381 r_work=0.1204 r_free=0.1381 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1381 target_work(ml) = 3.868 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1376 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1376 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.865649 | | target function (ml) not normalized (work): 724016.695206 | | target function (ml) not normalized (free): 15150.613716 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1376 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1430 0.1429 0.1493 n_refl.: 191136 remove outliers: r(all,work,free)=0.1430 0.1429 0.1493 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1423 0.1422 0.1488 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1200 0.1373 n_refl.: 191136 remove outliers: r(all,work,free)=0.1203 0.1200 0.1373 n_refl.: 191133 ======================== 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 0.3897 360.682 320.328 0.401 0.947 0.236 13.296-10.522 96.04 96 1 0.2364 480.811 447.096 0.695 0.949 0.206 10.503-8.327 98.90 177 3 0.2196 505.000 497.089 0.866 0.949 0.169 8.318-6.595 100.00 360 8 0.2228 375.842 368.736 0.887 0.948 0.117 6.588-5.215 100.00 711 7 0.1948 345.361 335.056 0.880 0.949 0.097 5.214-4.128 98.38 1367 28 0.1220 505.158 499.863 0.972 0.949 0.080 4.126-3.266 94.74 2603 46 0.1136 460.479 453.641 1.032 0.949 0.000 3.266-2.585 99.86 5447 97 0.1100 310.628 307.286 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0928 234.351 231.927 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0912 138.700 137.416 1.057 0.946 0.000 1.619-1.281 98.00 42464 925 0.0987 74.668 73.961 1.055 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.056 38.396 1.043 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1192 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1373 | n_water=864 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1200 r_free=0.1373 | n_water=864 | time (s): 100.020 (total time: 102.410) Filter (q & B) r_work=0.1200 r_free=0.1373 | n_water=851 | time (s): 4.910 (total time: 107.320) Compute maps r_work=0.1200 r_free=0.1373 | n_water=851 | time (s): 1.720 (total time: 109.040) Filter (map) r_work=0.1222 r_free=0.1367 | n_water=731 | time (s): 4.310 (total time: 113.350) Find peaks r_work=0.1222 r_free=0.1367 | n_water=731 | time (s): 0.620 (total time: 113.970) Add new water r_work=0.1236 r_free=0.1386 | n_water=959 | time (s): 4.180 (total time: 118.150) Refine new water occ: r_work=0.1197 r_free=0.1355 adp: r_work=0.1197 r_free=0.1354 occ: r_work=0.1194 r_free=0.1355 adp: r_work=0.1194 r_free=0.1354 occ: r_work=0.1192 r_free=0.1354 adp: r_work=0.1192 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1354 r_work=0.1192 r_free=0.1354 | n_water=959 | time (s): 204.410 (total time: 322.560) Filter (q & B) r_work=0.1197 r_free=0.1363 | n_water=880 | time (s): 4.800 (total time: 327.360) Filter (dist only) r_work=0.1197 r_free=0.1362 | n_water=879 | time (s): 117.570 (total time: 444.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.581284 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.684239 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 0.1200 0.1372 0.0172 0.037 1.1 5.4 0.0 0.3 0 0.791 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.72 1.72 1.790 14.124 14.684 3.766 12.04 13.74 1.71 1.823 14.110 14.684 3.764 Individual atomic B min max mean iso aniso Overall: 5.59 67.19 14.96 0.96 513 3270 Protein: 5.59 32.49 10.61 0.96 0 2902 Water: 5.97 67.19 29.32 N/A 513 366 Other: 13.76 26.20 19.98 N/A 0 2 Chain A: 5.60 53.80 12.55 N/A 0 1623 Chain B: 5.59 67.19 12.38 N/A 0 1647 Chain S: 5.97 61.99 30.91 N/A 513 0 Histogram: Values Number of atoms 5.59 - 11.75 2147 11.75 - 17.91 717 17.91 - 24.07 295 24.07 - 30.23 236 30.23 - 36.39 165 36.39 - 42.55 127 42.55 - 48.71 62 48.71 - 54.87 22 54.87 - 61.03 10 61.03 - 67.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1375 r_work=0.1204 r_free=0.1375 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1375 target_work(ml) = 3.764 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1377 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1377 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.763301 | | target function (ml) not normalized (work): 704836.255005 | | target function (ml) not normalized (free): 14766.481210 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1201 0.1377 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1427 0.1425 0.1507 n_refl.: 191133 remove outliers: r(all,work,free)=0.1427 0.1425 0.1507 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1419 0.1418 0.1502 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1377 n_refl.: 191133 remove outliers: r(all,work,free)=0.1204 0.1200 0.1377 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3833 361.486 317.379 0.395 0.948 0.225 13.296-10.522 96.04 96 1 0.2285 480.811 463.882 0.706 0.949 0.176 10.503-8.327 98.35 176 3 0.2212 503.191 497.892 0.866 0.950 0.150 8.318-6.595 100.00 360 8 0.2172 375.842 369.960 0.885 0.949 0.111 6.588-5.215 100.00 711 7 0.1935 345.361 335.424 0.883 0.950 0.090 5.214-4.128 98.38 1367 28 0.1217 505.158 499.990 0.973 0.950 0.080 4.126-3.266 94.74 2603 46 0.1144 460.479 453.495 1.033 0.950 0.005 3.266-2.585 99.86 5447 97 0.1118 310.628 307.131 1.020 0.949 0.000 2.585-2.046 97.45 10613 204 0.0944 234.351 231.778 1.032 0.949 0.000 2.046-1.619 99.39 21536 464 0.0914 138.700 137.381 1.056 0.948 0.000 1.619-1.281 98.00 42464 925 0.0978 74.668 73.946 1.054 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.056 38.380 1.042 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1299 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1377 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1377 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1377 | n_water=879 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1200 r_free=0.1379 | n_water=877 | time (s): 125.440 (total time: 127.840) Filter (q & B) r_work=0.1201 r_free=0.1379 | n_water=868 | time (s): 4.640 (total time: 132.480) Compute maps r_work=0.1201 r_free=0.1379 | n_water=868 | time (s): 2.360 (total time: 134.840) Filter (map) r_work=0.1221 r_free=0.1366 | n_water=745 | time (s): 4.620 (total time: 139.460) Find peaks r_work=0.1221 r_free=0.1366 | n_water=745 | time (s): 0.800 (total time: 140.260) Add new water r_work=0.1234 r_free=0.1380 | n_water=957 | time (s): 5.020 (total time: 145.280) Refine new water occ: r_work=0.1199 r_free=0.1353 adp: r_work=0.1200 r_free=0.1352 occ: r_work=0.1197 r_free=0.1354 adp: r_work=0.1197 r_free=0.1353 occ: r_work=0.1195 r_free=0.1355 adp: r_work=0.1195 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1354 r_work=0.1195 r_free=0.1354 | n_water=957 | time (s): 182.780 (total time: 328.060) Filter (q & B) r_work=0.1199 r_free=0.1360 | n_water=890 | time (s): 5.700 (total time: 333.760) Filter (dist only) r_work=0.1199 r_free=0.1359 | n_water=888 | time (s): 112.270 (total time: 446.030) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.521189 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.938542 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 0.1364 0.0162 0.037 1.1 6.0 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.64 1.62 1.768 14.058 14.939 3.764 12.05 13.68 1.63 1.932 14.008 14.939 3.761 Individual atomic B min max mean iso aniso Overall: 5.60 66.06 14.84 0.90 523 3269 Protein: 5.60 29.56 10.49 0.90 0 2902 Water: 5.97 66.06 29.05 N/A 523 365 Other: 13.85 23.19 18.52 N/A 0 2 Chain A: 5.60 51.48 12.39 N/A 0 1623 Chain B: 5.60 66.06 12.22 N/A 0 1646 Chain S: 5.97 61.95 30.71 N/A 523 0 Histogram: Values Number of atoms 5.60 - 11.64 2128 11.64 - 17.69 759 17.69 - 23.74 279 23.74 - 29.78 227 29.78 - 35.83 168 35.83 - 41.88 124 41.88 - 47.92 66 47.92 - 53.97 31 53.97 - 60.02 8 60.02 - 66.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1368 r_work=0.1206 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1369 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1203 r_free = 0.1366 target_work(ml) = 3.760 | | 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.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1203 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760082 | | target function (ml) not normalized (work): 704225.817821 | | target function (ml) not normalized (free): 14748.188211 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1206 0.1203 0.1367 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1489 n_refl.: 191131 remove outliers: r(all,work,free)=0.1407 0.1406 0.1489 n_refl.: 191131 overall B=-0.19 to atoms: r(all,work,free)=0.1377 0.1375 0.1469 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1359 n_refl.: 191131 remove outliers: r(all,work,free)=0.1201 0.1198 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 92.08 90 3 0.3606 361.182 316.192 0.391 0.973 0.211 13.296-10.522 96.04 96 1 0.2321 480.811 463.445 0.695 0.974 0.152 10.503-8.327 98.35 176 3 0.2239 503.191 496.482 0.860 0.975 0.127 8.318-6.595 100.00 360 8 0.2172 375.842 369.912 0.882 0.974 0.115 6.588-5.215 100.00 711 7 0.1923 345.361 336.208 0.883 0.974 0.107 5.214-4.128 98.38 1367 28 0.1234 505.158 499.717 0.971 0.973 0.066 4.126-3.266 94.74 2603 46 0.1153 460.479 453.259 1.031 0.972 0.000 3.266-2.585 99.86 5447 97 0.1123 310.628 307.174 1.018 0.970 0.000 2.585-2.046 97.45 10613 204 0.0957 234.351 231.796 1.030 0.966 0.000 2.046-1.619 99.39 21536 464 0.0914 138.700 137.380 1.054 0.961 0.000 1.619-1.281 98.00 42464 925 0.0965 74.668 73.976 1.053 0.952 0.000 1.281-0.980 96.53 101826 2055 0.1642 40.056 38.379 1.043 0.935 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0411 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1359 | n_water=888 | time (s): 2.830 (total time: 2.830) Filter (dist) r_work=0.1199 r_free=0.1359 | n_water=888 | time (s): 106.560 (total time: 109.390) Filter (q & B) r_work=0.1199 r_free=0.1360 | n_water=881 | time (s): 4.220 (total time: 113.610) Compute maps r_work=0.1199 r_free=0.1360 | n_water=881 | time (s): 1.900 (total time: 115.510) Filter (map) r_work=0.1221 r_free=0.1352 | n_water=760 | time (s): 5.200 (total time: 120.710) Find peaks r_work=0.1221 r_free=0.1352 | n_water=760 | time (s): 0.610 (total time: 121.320) Add new water r_work=0.1231 r_free=0.1366 | n_water=958 | time (s): 4.680 (total time: 126.000) Refine new water occ: r_work=0.1198 r_free=0.1347 adp: r_work=0.1198 r_free=0.1346 occ: r_work=0.1195 r_free=0.1348 adp: r_work=0.1195 r_free=0.1347 occ: r_work=0.1193 r_free=0.1348 adp: r_work=0.1193 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1347 r_work=0.1193 r_free=0.1347 | n_water=958 | time (s): 199.980 (total time: 325.980) Filter (q & B) r_work=0.1197 r_free=0.1356 | n_water=900 | time (s): 4.240 (total time: 330.220) Filter (dist only) r_work=0.1197 r_free=0.1355 | n_water=899 | time (s): 119.530 (total time: 449.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.623578 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.938605 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1357 0.0159 0.038 1.1 6.0 0.0 0.3 0 0.812 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.57 1.59 1.720 13.780 13.939 3.759 12.01 13.63 1.62 1.766 13.758 13.939 3.759 Individual atomic B min max mean iso aniso Overall: 5.43 65.10 14.65 0.88 534 3269 Protein: 5.43 28.40 10.29 0.88 0 2902 Water: 5.79 65.10 28.72 N/A 534 365 Other: 13.71 22.09 17.90 N/A 0 2 Chain A: 5.48 51.02 12.14 N/A 0 1623 Chain B: 5.43 65.10 11.99 N/A 0 1646 Chain S: 5.79 61.83 30.48 N/A 534 0 Histogram: Values Number of atoms 5.43 - 11.39 2109 11.39 - 17.36 778 17.36 - 23.33 280 23.33 - 29.29 226 29.29 - 35.26 166 35.26 - 41.23 128 41.23 - 47.20 73 47.20 - 53.16 33 53.16 - 59.13 6 59.13 - 65.10 4 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1364 r_work=0.1202 r_free=0.1364 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1364 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758112 | | target function (ml) not normalized (work): 703853.131092 | | target function (ml) not normalized (free): 14745.929857 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1366 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1377 0.1375 0.1480 n_refl.: 191130 remove outliers: r(all,work,free)=0.1377 0.1375 0.1480 n_refl.: 191130 overall B=0.04 to atoms: r(all,work,free)=0.1383 0.1381 0.1484 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1192 0.1360 n_refl.: 191130 remove outliers: r(all,work,free)=0.1196 0.1192 0.1360 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 92.08 90 3 0.3605 361.182 333.860 0.404 1.013 0.219 13.296-10.522 96.04 96 1 0.2361 480.811 463.112 0.675 1.015 0.157 10.503-8.327 98.35 176 3 0.2230 503.191 496.216 0.832 1.015 0.130 8.318-6.595 100.00 360 8 0.2166 375.842 369.422 0.853 1.015 0.110 6.588-5.215 100.00 711 7 0.1939 345.361 335.738 0.854 1.015 0.092 5.214-4.128 98.38 1367 28 0.1238 505.158 498.906 0.943 1.015 0.090 4.126-3.266 94.74 2603 46 0.1155 460.479 452.587 0.999 1.015 0.000 3.266-2.585 99.86 5447 97 0.1127 310.628 306.817 0.985 1.014 0.000 2.585-2.046 97.45 10613 204 0.0963 234.351 231.584 0.996 1.013 0.000 2.046-1.619 99.39 21536 464 0.0912 138.700 137.256 1.016 1.012 0.000 1.619-1.281 98.00 42464 925 0.0947 74.668 74.000 1.013 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.056 38.357 0.993 1.005 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0637 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1360 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1360 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1360 | n_water=899 | time (s): 3.350 (total time: 3.350) Filter (dist) r_work=0.1192 r_free=0.1360 | n_water=899 | time (s): 107.710 (total time: 111.060) Filter (q & B) r_work=0.1193 r_free=0.1361 | n_water=890 | time (s): 5.200 (total time: 116.260) Compute maps r_work=0.1193 r_free=0.1361 | n_water=890 | time (s): 1.810 (total time: 118.070) Filter (map) r_work=0.1213 r_free=0.1348 | n_water=765 | time (s): 5.340 (total time: 123.410) Find peaks r_work=0.1213 r_free=0.1348 | n_water=765 | time (s): 0.650 (total time: 124.060) Add new water r_work=0.1224 r_free=0.1363 | n_water=962 | time (s): 4.250 (total time: 128.310) Refine new water occ: r_work=0.1192 r_free=0.1352 adp: r_work=0.1192 r_free=0.1351 occ: r_work=0.1190 r_free=0.1351 adp: r_work=0.1189 r_free=0.1350 occ: r_work=0.1188 r_free=0.1351 adp: r_work=0.1188 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1351 r_work=0.1188 r_free=0.1351 | n_water=962 | time (s): 185.220 (total time: 313.530) Filter (q & B) r_work=0.1191 r_free=0.1358 | n_water=906 | time (s): 4.540 (total time: 318.070) Filter (dist only) r_work=0.1192 r_free=0.1358 | n_water=905 | time (s): 115.720 (total time: 433.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554690 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.653974 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1364 0.0170 0.038 1.1 5.3 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.64 1.70 1.681 13.725 14.654 3.758 11.93 13.65 1.71 1.704 13.720 14.654 3.754 Individual atomic B min max mean iso aniso Overall: 5.51 64.04 14.60 0.88 540 3269 Protein: 5.51 28.23 10.33 0.88 0 2902 Water: 5.91 64.04 28.29 N/A 540 365 Other: 13.77 21.95 17.86 N/A 0 2 Chain A: 5.57 50.68 12.15 N/A 0 1623 Chain B: 5.51 64.04 12.01 N/A 0 1646 Chain S: 5.91 61.97 29.90 N/A 540 0 Histogram: Values Number of atoms 5.51 - 11.37 2073 11.37 - 17.22 818 17.22 - 23.07 278 23.07 - 28.92 232 28.92 - 34.78 177 34.78 - 40.63 112 40.63 - 46.48 73 46.48 - 52.34 33 52.34 - 58.19 9 58.19 - 64.04 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1365 r_work=0.1194 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1365 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1365 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.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753949 | | target function (ml) not normalized (work): 703073.296291 | | target function (ml) not normalized (free): 14736.392365 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1365 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1390 0.1388 0.1489 n_refl.: 191130 remove outliers: r(all,work,free)=0.1390 0.1388 0.1489 n_refl.: 191130 overall B=0.01 to atoms: r(all,work,free)=0.1392 0.1390 0.1490 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1191 0.1363 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1191 0.1363 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 92.08 90 3 0.3663 361.182 333.266 0.428 0.931 0.207 13.296-10.522 96.04 96 1 0.2380 480.811 461.957 0.729 0.932 0.146 10.503-8.327 98.35 176 3 0.2278 503.191 495.215 0.902 0.932 0.120 8.318-6.595 100.00 360 8 0.2164 375.842 369.823 0.923 0.932 0.098 6.588-5.215 100.00 711 7 0.1967 345.361 335.190 0.927 0.932 0.083 5.214-4.128 98.38 1367 28 0.1248 505.158 498.900 1.026 0.932 0.080 4.126-3.266 94.74 2603 46 0.1166 460.479 452.636 1.088 0.933 0.000 3.266-2.585 99.86 5447 97 0.1130 310.628 306.843 1.073 0.932 0.000 2.585-2.046 97.45 10613 204 0.0966 234.351 231.595 1.085 0.932 0.000 2.046-1.619 99.39 21536 464 0.0908 138.700 137.280 1.108 0.931 0.000 1.619-1.281 98.00 42464 925 0.0938 74.668 74.015 1.106 0.930 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.056 38.346 1.087 0.928 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0192 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1363 | n_water=905 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1191 r_free=0.1363 | n_water=905 | time (s): 108.220 (total time: 110.890) Filter (q & B) r_work=0.1192 r_free=0.1365 | n_water=896 | time (s): 4.260 (total time: 115.150) Compute maps r_work=0.1192 r_free=0.1365 | n_water=896 | time (s): 1.530 (total time: 116.680) Filter (map) r_work=0.1214 r_free=0.1353 | n_water=776 | time (s): 4.560 (total time: 121.240) Find peaks r_work=0.1214 r_free=0.1353 | n_water=776 | time (s): 0.620 (total time: 121.860) Add new water r_work=0.1222 r_free=0.1366 | n_water=970 | time (s): 4.020 (total time: 125.880) Refine new water occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1190 r_free=0.1342 occ: r_work=0.1188 r_free=0.1343 adp: r_work=0.1188 r_free=0.1343 occ: r_work=0.1187 r_free=0.1344 adp: r_work=0.1186 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1343 r_work=0.1186 r_free=0.1343 | n_water=970 | time (s): 235.420 (total time: 361.300) Filter (q & B) r_work=0.1190 r_free=0.1353 | n_water=909 | time (s): 4.850 (total time: 366.150) Filter (dist only) r_work=0.1190 r_free=0.1353 | n_water=908 | time (s): 120.840 (total time: 486.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.589316 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.987074 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1357 0.0164 0.039 1.1 6.0 0.0 0.3 0 0.795 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.57 1.64 1.683 13.763 13.987 3.754 11.94 13.61 1.66 1.681 13.763 13.987 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 63.82 14.66 0.86 543 3269 Protein: 5.56 28.01 10.36 0.86 0 2902 Water: 5.95 63.82 28.40 N/A 543 365 Other: 13.82 22.02 17.92 N/A 0 2 Chain A: 5.61 50.62 12.16 N/A 0 1623 Chain B: 5.56 63.82 12.02 N/A 0 1646 Chain S: 5.95 62.02 30.17 N/A 543 0 Histogram: Values Number of atoms 5.56 - 11.39 2074 11.39 - 17.21 818 17.21 - 23.04 280 23.04 - 28.86 218 28.86 - 34.69 179 34.69 - 40.52 121 40.52 - 46.34 75 46.34 - 52.17 33 52.17 - 57.99 10 57.99 - 63.82 4 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1361 r_work=0.1195 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1365 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753758 | | target function (ml) not normalized (work): 703037.597978 | | target function (ml) not normalized (free): 14737.782861 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1365 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1400 0.1398 0.1500 n_refl.: 191130 remove outliers: r(all,work,free)=0.1400 0.1398 0.1500 n_refl.: 191130 overall B=-0.00 to atoms: r(all,work,free)=0.1400 0.1398 0.1500 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1363 n_refl.: 191130 remove outliers: r(all,work,free)=0.1195 0.1192 0.1363 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 92.08 90 3 0.3695 361.182 331.628 0.422 0.932 0.199 13.296-10.522 96.04 96 1 0.2385 480.811 461.760 0.727 0.933 0.141 10.503-8.327 98.35 176 3 0.2270 503.191 495.686 0.899 0.934 0.117 8.318-6.595 100.00 360 8 0.2166 375.842 369.352 0.922 0.934 0.100 6.588-5.215 100.00 711 7 0.1983 345.361 334.900 0.924 0.934 0.087 5.214-4.128 98.38 1367 28 0.1253 505.158 499.007 1.024 0.934 0.080 4.126-3.266 94.74 2603 46 0.1169 460.479 452.517 1.087 0.934 0.000 3.266-2.585 99.86 5447 97 0.1135 310.628 306.812 1.071 0.934 0.000 2.585-2.046 97.45 10613 204 0.0965 234.351 231.579 1.084 0.934 0.000 2.046-1.619 99.39 21536 464 0.0909 138.700 137.283 1.106 0.934 0.000 1.619-1.281 98.00 42464 925 0.0936 74.668 74.016 1.106 0.933 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.056 38.336 1.087 0.933 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0097 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1363 After: r_work=0.1193 r_free=0.1363 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1363 | n_water=908 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1193 r_free=0.1363 | n_water=907 | time (s): 117.930 (total time: 120.590) Filter (q & B) r_work=0.1194 r_free=0.1361 | n_water=896 | time (s): 4.920 (total time: 125.510) Compute maps r_work=0.1194 r_free=0.1361 | n_water=896 | time (s): 1.720 (total time: 127.230) Filter (map) r_work=0.1214 r_free=0.1358 | n_water=779 | time (s): 4.540 (total time: 131.770) Find peaks r_work=0.1214 r_free=0.1358 | n_water=779 | time (s): 0.540 (total time: 132.310) Add new water r_work=0.1223 r_free=0.1375 | n_water=969 | time (s): 3.780 (total time: 136.090) Refine new water occ: r_work=0.1191 r_free=0.1348 adp: r_work=0.1191 r_free=0.1348 occ: r_work=0.1189 r_free=0.1348 adp: r_work=0.1189 r_free=0.1348 occ: r_work=0.1188 r_free=0.1349 adp: r_work=0.1188 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1188 r_free=0.1349 r_work=0.1188 r_free=0.1349 | n_water=969 | time (s): 196.980 (total time: 333.070) Filter (q & B) r_work=0.1192 r_free=0.1357 | n_water=909 | time (s): 5.210 (total time: 338.280) Filter (dist only) r_work=0.1192 r_free=0.1356 | n_water=907 | time (s): 121.280 (total time: 459.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.567115 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.911311 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 0.1363 0.0165 0.039 1.2 8.0 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.63 1.65 1.680 13.765 13.911 3.758 11.99 13.66 1.67 1.686 13.765 13.911 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 63.01 14.66 0.85 542 3269 Protein: 5.59 27.80 10.37 0.85 0 2902 Water: 6.02 63.01 28.36 N/A 542 365 Other: 13.85 22.04 17.94 N/A 0 2 Chain A: 5.68 50.36 12.14 N/A 0 1623 Chain B: 5.59 63.01 12.01 N/A 0 1646 Chain S: 6.02 62.15 30.23 N/A 542 0 Histogram: Values Number of atoms 5.59 - 11.33 2058 11.33 - 17.08 829 17.08 - 22.82 283 22.82 - 28.56 212 28.56 - 34.30 182 34.30 - 40.04 116 40.04 - 45.78 78 45.78 - 51.53 36 51.53 - 57.27 12 57.27 - 63.01 5 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1366 r_work=0.1199 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1366 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1367 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757690 | | target function (ml) not normalized (work): 703774.033513 | | target function (ml) not normalized (free): 14747.197967 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7398 127 0.1369 0.1474 5.6951 5.778| | 2: 2.94 - 2.33 1.00 7339 128 0.1084 0.1379 5.0918 5.2098| | 3: 2.33 - 2.04 0.96 6939 150 0.0913 0.1219 4.6699 4.7655| | 4: 2.04 - 1.85 1.00 7170 155 0.0907 0.1073 4.3998 4.5817| | 5: 1.85 - 1.72 0.99 7113 159 0.0934 0.0991 4.1541 4.2486| | 6: 1.72 - 1.62 0.99 7102 142 0.0904 0.1102 3.9539 4.0891| | 7: 1.62 - 1.54 0.99 7104 148 0.0892 0.0985 3.8066 3.9484| | 8: 1.54 - 1.47 0.96 6798 152 0.0896 0.1324 3.7069 3.9054| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1147 3.6223 3.7573| | 10: 1.41 - 1.36 0.99 7022 150 0.0980 0.1184 3.5574 3.668| | 11: 1.36 - 1.32 0.99 6997 151 0.0993 0.1133 3.4876 3.5907| | 12: 1.32 - 1.28 0.98 6975 149 0.1033 0.1122 3.4629 3.5875| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1242 3.4391 3.5667| | 14: 1.25 - 1.22 0.98 7015 112 0.1102 0.1596 3.4343 3.6868| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1245 3.4501 3.493| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1533 3.4664 3.6459| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1221 3.4338 3.4383| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1720 3.4391 3.5379| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1765 3.4206 3.6| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1586 3.4114 3.4376| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2141 3.4195 3.506| | 22: 1.07 - 1.05 0.97 6836 135 0.1902 0.1948 3.4141 3.4146| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2023 3.4343 3.4892| | 24: 1.03 - 1.02 0.96 6784 133 0.2332 0.2256 3.4368 3.5124| | 25: 1.02 - 1.01 0.93 6552 130 0.2607 0.2536 3.45 3.5234| | 26: 1.01 - 0.99 0.96 6767 158 0.2752 0.2847 3.4163 3.425| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2787 3.4705 3.3954| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7398 127 0.93 11.94 1.00 0.95 11537.50| | 2: 2.94 - 2.33 7339 128 0.92 13.07 0.99 0.95 5300.61| | 3: 2.33 - 2.04 6939 150 0.96 7.84 1.01 0.96 1758.13| | 4: 2.04 - 1.85 7170 155 0.96 7.73 1.00 0.96 1021.97| | 5: 1.85 - 1.72 7113 159 0.96 8.11 1.00 0.96 638.81| | 6: 1.72 - 1.62 7102 142 0.96 8.15 1.00 0.97 451.45| | 7: 1.62 - 1.54 7104 148 0.96 8.22 1.01 0.97 343.26| | 8: 1.54 - 1.47 6798 152 0.96 8.32 1.01 0.97 282.06| | 9: 1.47 - 1.41 6938 155 0.96 8.48 1.00 0.98 231.08| | 10: 1.41 - 1.36 7022 150 0.96 8.90 1.00 0.97 202.78| | 11: 1.36 - 1.32 6997 151 0.96 8.96 0.99 0.96 175.83| | 12: 1.32 - 1.28 6975 149 0.96 9.07 0.99 0.95 162.65| | 13: 1.28 - 1.25 6907 166 0.96 9.56 1.00 0.96 159.92| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.97 164.48| | 15: 1.22 - 1.19 6956 137 0.95 11.23 1.01 0.98 166.65| | 16: 1.19 - 1.17 6604 132 0.95 11.39 1.00 0.96 159.88| | 17: 1.17 - 1.14 6940 135 0.94 12.20 1.01 0.96 153.37| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.95 148.17| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.95 152.11| | 20: 1.10 - 1.08 6884 147 0.92 15.28 1.00 0.94 151.29| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.94 154.02| | 22: 1.07 - 1.05 6836 135 0.89 18.31 1.00 0.93 155.44| | 23: 1.05 - 1.03 6827 159 0.87 20.51 1.00 0.93 165.39| | 24: 1.03 - 1.02 6784 133 0.85 23.18 1.00 0.94 179.62| | 25: 1.02 - 1.01 6552 130 0.83 25.15 0.98 0.91 182.66| | 26: 1.01 - 0.99 6767 158 0.81 26.61 0.99 0.90 176.77| | 27: 0.99 - 0.98 6647 131 0.82 26.22 1.00 0.88 160.61| |alpha: min = 0.88 max = 0.98 mean = 0.95| |beta: min = 148.17 max = 11537.50 mean = 949.67| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.34| |phase err.(test): min = 0.00 max = 89.56 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1367 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1412 0.1410 0.1503 n_refl.: 191130 remove outliers: r(all,work,free)=0.1412 0.1410 0.1503 n_refl.: 191130 overall B=-0.06 to atoms: r(all,work,free)=0.1402 0.1401 0.1496 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1366 n_refl.: 191130 remove outliers: r(all,work,free)=0.1200 0.1197 0.1366 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 92.08 90 3 0.3660 361.182 330.663 0.409 0.933 0.197 13.296-10.522 96.04 96 1 0.2399 480.811 461.149 0.705 0.934 0.136 10.503-8.327 98.35 176 3 0.2248 503.191 496.004 0.878 0.934 0.110 8.318-6.595 100.00 360 8 0.2146 375.842 369.421 0.899 0.934 0.091 6.588-5.215 100.00 711 7 0.1975 345.361 335.287 0.900 0.934 0.077 5.214-4.128 98.38 1367 28 0.1254 505.158 499.003 0.996 0.935 0.034 4.126-3.266 94.74 2603 46 0.1169 460.479 452.535 1.061 0.935 0.000 3.266-2.585 99.86 5447 97 0.1137 310.628 306.856 1.045 0.935 0.000 2.585-2.046 97.45 10613 204 0.0971 234.351 231.575 1.055 0.935 0.000 2.046-1.619 99.39 21536 464 0.0916 138.700 137.275 1.076 0.936 0.000 1.619-1.281 98.00 42464 925 0.0948 74.668 74.005 1.073 0.937 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.056 38.332 1.052 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0131 ================= 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 : 0.2044 0.1961 0.082 5.123 5.2 78.0 14.6 805 0.000 1_bss: 0.1810 0.1904 0.082 5.123 5.2 78.0 14.6 805 0.000 1_settarget: 0.1810 0.1904 0.082 5.123 5.2 78.0 14.6 805 0.000 1_nqh: 0.1810 0.1905 0.082 5.123 5.2 78.0 14.6 805 0.002 1_weight: 0.1810 0.1905 0.082 5.123 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1273 0.1499 0.038 1.157 5.2 78.0 14.6 805 0.154 1_adp: 0.1299 0.1567 0.038 1.157 5.3 73.0 15.1 805 0.154 1_regHadp: 0.1298 0.1562 0.038 1.157 5.3 73.0 15.1 805 0.154 1_occ: 0.1283 0.1550 0.038 1.157 5.3 73.0 15.1 805 0.154 2_bss: 0.1274 0.1537 0.038 1.157 5.4 73.2 15.2 805 0.154 2_settarget: 0.1274 0.1537 0.038 1.157 5.4 73.2 15.2 805 0.154 2_updatecdl: 0.1274 0.1537 0.038 1.176 5.4 73.2 15.2 805 0.154 2_nqh: 0.1274 0.1537 0.038 1.176 5.4 73.2 15.2 805 0.154 2_sol: 0.1268 0.1502 0.038 1.176 5.4 73.2 16.5 899 n/a 2_weight: 0.1268 0.1502 0.038 1.176 5.4 73.2 16.5 899 n/a 2_xyzrec: 0.1251 0.1512 0.040 1.118 5.4 73.2 16.5 899 n/a 2_adp: 0.1232 0.1504 0.040 1.118 5.4 68.3 16.5 899 n/a 2_regHadp: 0.1233 0.1505 0.040 1.118 5.4 68.3 16.5 899 n/a 2_occ: 0.1226 0.1499 0.040 1.118 5.4 68.3 16.5 899 n/a 3_bss: 0.1234 0.1509 0.040 1.118 5.4 68.2 16.5 899 n/a 3_settarget: 0.1234 0.1509 0.040 1.118 5.4 68.2 16.5 899 n/a 3_updatecdl: 0.1234 0.1509 0.040 1.123 5.4 68.2 16.5 899 n/a 3_nqh: 0.1234 0.1509 0.040 1.123 5.4 68.2 16.5 899 n/a 3_sol: 0.1253 0.1521 0.040 1.123 5.4 68.2 15.5 874 n/a 3_weight: 0.1253 0.1521 0.040 1.123 5.4 68.2 15.5 874 n/a 3_xyzrec: 0.1244 0.1444 0.035 1.101 5.4 68.2 15.5 874 n/a 3_adp: 0.1234 0.1405 0.035 1.101 5.5 67.9 15.3 874 n/a 3_regHadp: 0.1234 0.1405 0.035 1.101 5.5 67.9 15.3 874 n/a 3_occ: 0.1229 0.1401 0.035 1.101 5.5 67.9 15.3 874 n/a 4_bss: 0.1224 0.1396 0.035 1.101 5.5 67.9 15.3 874 n/a 4_settarget: 0.1224 0.1396 0.035 1.101 5.5 67.9 15.3 874 n/a 4_updatecdl: 0.1224 0.1396 0.035 1.106 5.5 67.9 15.3 874 n/a 4_nqh: 0.1224 0.1396 0.035 1.106 5.5 67.9 15.3 874 n/a 4_sol: 0.1209 0.1380 0.035 1.106 5.5 67.9 15.0 864 n/a 4_weight: 0.1209 0.1380 0.035 1.106 5.5 67.9 15.0 864 n/a 4_xyzrec: 0.1208 0.1383 0.036 1.120 5.5 67.9 15.0 864 n/a 4_adp: 0.1204 0.1381 0.036 1.120 5.5 67.4 14.9 864 n/a 4_regHadp: 0.1204 0.1381 0.036 1.120 5.5 67.4 14.9 864 n/a 4_occ: 0.1202 0.1376 0.036 1.120 5.5 67.4 14.9 864 n/a 5_bss: 0.1200 0.1373 0.036 1.120 5.5 67.3 14.9 864 n/a 5_settarget: 0.1200 0.1373 0.036 1.120 5.5 67.3 14.9 864 n/a 5_updatecdl: 0.1200 0.1373 0.036 1.120 5.5 67.3 14.9 864 n/a 5_nqh: 0.1200 0.1373 0.036 1.120 5.5 67.3 14.9 864 n/a 5_sol: 0.1197 0.1362 0.036 1.120 5.5 67.3 15.0 879 n/a 5_weight: 0.1197 0.1362 0.036 1.120 5.5 67.3 15.0 879 n/a 5_xyzrec: 0.1200 0.1372 0.037 1.130 5.5 67.3 15.0 879 n/a 5_adp: 0.1204 0.1375 0.037 1.130 5.6 67.2 15.0 879 n/a 5_regHadp: 0.1204 0.1375 0.037 1.130 5.6 67.2 15.0 879 n/a 5_occ: 0.1201 0.1377 0.037 1.130 5.6 67.2 15.0 879 n/a 6_bss: 0.1200 0.1377 0.037 1.130 5.6 67.2 14.9 879 n/a 6_settarget: 0.1200 0.1377 0.037 1.130 5.6 67.2 14.9 879 n/a 6_updatecdl: 0.1200 0.1377 0.037 1.130 5.6 67.2 14.9 879 n/a 6_nqh: 0.1200 0.1377 0.037 1.130 5.6 67.2 14.9 879 n/a 6_sol: 0.1199 0.1359 0.037 1.130 5.6 67.2 14.9 888 n/a 6_weight: 0.1199 0.1359 0.037 1.130 5.6 67.2 14.9 888 n/a 6_xyzrec: 0.1202 0.1364 0.037 1.130 5.6 67.2 14.9 888 n/a 6_adp: 0.1205 0.1368 0.037 1.130 5.6 66.1 14.8 888 n/a 6_regHadp: 0.1206 0.1369 0.037 1.130 5.6 66.1 14.8 888 n/a 6_occ: 0.1203 0.1366 0.037 1.130 5.6 66.1 14.8 888 n/a 7_bss: 0.1199 0.1359 0.037 1.130 5.4 65.9 14.7 888 n/a 7_settarget: 0.1199 0.1359 0.037 1.130 5.4 65.9 14.7 888 n/a 7_updatecdl: 0.1199 0.1359 0.037 1.130 5.4 65.9 14.7 888 n/a 7_nqh: 0.1199 0.1359 0.037 1.130 5.4 65.9 14.7 888 n/a 7_sol: 0.1197 0.1355 0.037 1.130 5.4 65.9 14.7 899 n/a 7_weight: 0.1197 0.1355 0.037 1.130 5.4 65.9 14.7 899 n/a 7_xyzrec: 0.1199 0.1357 0.038 1.134 5.4 65.9 14.7 899 n/a 7_adp: 0.1202 0.1364 0.038 1.134 5.4 65.1 14.7 899 n/a 7_regHadp: 0.1202 0.1364 0.038 1.134 5.4 65.1 14.7 899 n/a 7_occ: 0.1200 0.1366 0.038 1.134 5.4 65.1 14.7 899 n/a 8_bss: 0.1192 0.1360 0.038 1.134 5.5 65.1 14.7 899 n/a 8_settarget: 0.1192 0.1360 0.038 1.134 5.5 65.1 14.7 899 n/a 8_updatecdl: 0.1192 0.1360 0.038 1.134 5.5 65.1 14.7 899 n/a 8_nqh: 0.1192 0.1360 0.038 1.134 5.5 65.1 14.7 899 n/a 8_sol: 0.1192 0.1358 0.038 1.134 5.5 65.1 14.6 905 n/a 8_weight: 0.1192 0.1358 0.038 1.134 5.5 65.1 14.6 905 n/a 8_xyzrec: 0.1194 0.1364 0.038 1.126 5.5 65.1 14.6 905 n/a 8_adp: 0.1194 0.1365 0.038 1.126 5.5 64.0 14.6 905 n/a 8_regHadp: 0.1194 0.1365 0.038 1.126 5.5 64.0 14.6 905 n/a 8_occ: 0.1193 0.1365 0.038 1.126 5.5 64.0 14.6 905 n/a 9_bss: 0.1191 0.1363 0.038 1.126 5.5 64.1 14.6 905 n/a 9_settarget: 0.1191 0.1363 0.038 1.126 5.5 64.1 14.6 905 n/a 9_updatecdl: 0.1191 0.1363 0.038 1.126 5.5 64.1 14.6 905 n/a 9_nqh: 0.1191 0.1363 0.038 1.126 5.5 64.1 14.6 905 n/a 9_sol: 0.1190 0.1353 0.038 1.126 5.5 64.1 14.7 908 n/a 9_weight: 0.1190 0.1353 0.038 1.126 5.5 64.1 14.7 908 n/a 9_xyzrec: 0.1193 0.1357 0.039 1.121 5.5 64.1 14.7 908 n/a 9_adp: 0.1194 0.1361 0.039 1.121 5.6 63.8 14.7 908 n/a 9_regHadp: 0.1195 0.1361 0.039 1.121 5.6 63.8 14.7 908 n/a 9_occ: 0.1193 0.1365 0.039 1.121 5.6 63.8 14.7 908 n/a 10_bss: 0.1192 0.1363 0.039 1.121 5.6 63.8 14.7 908 n/a 10_settarget: 0.1192 0.1363 0.039 1.121 5.6 63.8 14.7 908 n/a 10_updatecdl: 0.1192 0.1363 0.039 1.120 5.6 63.8 14.7 908 n/a 10_setrh: 0.1193 0.1363 0.039 1.120 5.6 63.8 14.7 908 n/a 10_nqh: 0.1193 0.1363 0.039 1.120 5.6 63.8 14.7 908 n/a 10_sol: 0.1192 0.1356 0.039 1.120 5.6 63.8 14.7 907 n/a 10_weight: 0.1192 0.1356 0.039 1.120 5.6 63.8 14.7 907 n/a 10_xyzrec: 0.1198 0.1363 0.039 1.175 5.6 63.8 14.7 907 n/a 10_adp: 0.1199 0.1366 0.039 1.175 5.6 63.0 14.7 907 n/a 10_regHadp: 0.1199 0.1366 0.039 1.175 5.6 63.0 14.7 907 n/a 10_occ: 0.1198 0.1367 0.039 1.175 5.6 63.0 14.7 907 n/a end: 0.1197 0.1366 0.039 1.175 5.5 62.9 14.6 907 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8586576_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_8586576_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1700 Refinement macro-cycles (run) : 11782.6300 Write final files (write_after_run_outputs) : 173.2700 Total : 11963.0700 Total CPU time: 3.33 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:36:37 PST -0800 (1736735797.68 s) Start R-work = 0.1810, R-free = 0.1904 Final R-work = 0.1197, R-free = 0.1366 =============================================================================== Job complete usr+sys time: 12285.69 seconds wall clock time: 205 minutes 48.64 seconds (12348.64 seconds total)