Starting phenix.refine on Sun Jan 12 15:15:40 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5035770.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5035770.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_5035770.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.21, per 1000 atoms: 0.33 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: 2.738 distance_ideal: 2.720 ideal - model: -0.018 slack: 0.000 delta_slack: -0.018 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: 2.710 distance_ideal: 2.710 ideal - model: -0.000 slack: 0.000 delta_slack: -0.000 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.17 Conformation dependent library (CDL) restraints added in 125.7 milliseconds Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.02: 711 1.02 - 1.25: 2590 1.25 - 1.49: 1482 1.49 - 1.72: 1131 1.72 - 1.95: 20 Bond restraints: 5934 Sorted by residual: bond pdb=" C PRO B 73 " pdb=" O PRO B 73 " ideal model delta sigma weight residual 1.233 1.474 -0.241 1.18e-02 7.18e+03 4.17e+02 bond pdb=" N LEU A 185 " pdb=" H LEU A 185 " ideal model delta sigma weight residual 0.860 1.250 -0.390 2.00e-02 2.50e+03 3.80e+02 bond pdb=" C GLY A 126 " pdb=" O GLY A 126 " ideal model delta sigma weight residual 1.232 1.434 -0.202 1.05e-02 9.07e+03 3.69e+02 bond pdb=" CA THR A 46 " pdb=" C THR A 46 " ideal model delta sigma weight residual 1.524 1.759 -0.235 1.23e-02 6.61e+03 3.64e+02 bond pdb=" CG LEU B 87 " pdb=" HG LEU B 87 " ideal model delta sigma weight residual 0.970 1.350 -0.380 2.00e-02 2.50e+03 3.60e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.18: 5692 4.18 - 8.36: 3513 8.36 - 12.54: 1310 12.54 - 16.72: 267 16.72 - 20.90: 28 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA CYS B 81 " pdb=" C CYS B 81 " pdb=" O CYS B 81 " ideal model delta sigma weight residual 120.82 137.69 -16.87 1.05e+00 9.07e-01 2.58e+02 angle pdb=" O THR B 16 " pdb=" C THR B 16 " pdb=" N GLU B 17 " ideal model delta sigma weight residual 122.12 138.29 -16.17 1.06e+00 8.90e-01 2.33e+02 angle pdb=" CA PHE B 164 " pdb=" CB PHE B 164 " pdb=" CG PHE B 164 " ideal model delta sigma weight residual 113.80 128.59 -14.79 1.00e+00 1.00e+00 2.19e+02 angle pdb=" CA LEU B 24 " pdb=" C LEU B 24 " pdb=" O LEU B 24 " ideal model delta sigma weight residual 120.42 104.78 15.64 1.06e+00 8.90e-01 2.18e+02 angle pdb=" CA SER B 4 " pdb=" C SER B 4 " pdb=" O SER B 4 " ideal model delta sigma weight residual 120.89 136.77 -15.88 1.10e+00 8.26e-01 2.08e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 1822 16.42 - 32.85: 161 32.85 - 49.27: 45 49.27 - 65.70: 17 65.70 - 82.12: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -149.64 -30.36 0 5.00e+00 4.00e-02 3.69e+01 dihedral pdb=" CA ARG B 100 " pdb=" C ARG B 100 " pdb=" N ILE B 101 " pdb=" CA ILE B 101 " ideal model delta harmonic sigma weight residual 180.00 -152.01 -27.99 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -152.06 -27.94 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 200 0.199 - 0.398: 119 0.398 - 0.596: 111 0.596 - 0.795: 41 0.795 - 0.994: 21 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA VAL B 89 " pdb=" N VAL B 89 " pdb=" C VAL B 89 " pdb=" CB VAL B 89 " both_signs ideal model delta sigma weight residual False 2.44 3.43 -0.99 2.00e-01 2.50e+01 2.47e+01 chirality pdb=" CA THR B 34 " pdb=" N THR B 34 " pdb=" C THR B 34 " pdb=" CB THR B 34 " both_signs ideal model delta sigma weight residual False 2.53 1.55 0.98 2.00e-01 2.50e+01 2.40e+01 chirality pdb=" CA VAL A 102 " pdb=" N VAL A 102 " pdb=" C VAL A 102 " pdb=" CB VAL A 102 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " -0.085 2.00e-02 2.50e+03 7.28e-02 2.12e+02 pdb=" CG TRP B 146 " 0.116 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.034 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.117 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.087 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.016 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.056 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.096 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.091 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.004 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " 0.040 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.138 2.00e-02 2.50e+03 7.17e-02 2.05e+02 pdb=" CG TRP A 146 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.068 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.097 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.085 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " -0.100 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.014 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.100 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.072 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.035 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.042 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.041 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.069 2.00e-02 2.50e+03 6.40e-02 1.64e+02 pdb=" CG TRP A 139 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.073 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.081 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.065 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " -0.050 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.113 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.060 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.069 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.056 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " 0.032 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.033 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.81 - 1.57: 22 1.57 - 2.33: 2032 2.33 - 3.09: 21911 3.09 - 3.84: 33079 3.84 - 4.60: 53273 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110317 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.813 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.037 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.047 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.057 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.098 2.620 ... (remaining 110312 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_5035770_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.2051 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303373 | | target function (ml) not normalized (work): 806077.631992 | | target function (ml) not normalized (free): 16641.170916 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2138 0.2018 6.6672 6.316| | 2: 2.94 - 2.33 1.00 7339 128 0.1629 0.1686 5.5478 5.6121| | 3: 2.33 - 2.04 0.96 6939 150 0.1645 0.1582 5.1452 5.0971| | 4: 2.04 - 1.85 1.00 7170 155 0.1749 0.1622 4.9591 5.0251| | 5: 1.85 - 1.72 0.99 7113 159 0.1932 0.1798 4.8045 4.8048| | 6: 1.72 - 1.62 0.99 7102 142 0.1993 0.2095 4.6828 4.7079| | 7: 1.62 - 1.54 0.99 7104 148 0.1984 0.1905 4.5529 4.6435| | 8: 1.54 - 1.47 0.96 6798 152 0.2046 0.2317 4.4785 4.5534| | 9: 1.47 - 1.41 0.98 6938 155 0.2114 0.2378 4.4086 4.5266| | 10: 1.41 - 1.36 0.99 7022 150 0.2143 0.2126 4.3201 4.3746| | 11: 1.36 - 1.32 0.99 6997 151 0.2107 0.2340 4.2368 4.3589| | 12: 1.32 - 1.28 0.98 6976 149 0.2087 0.1997 4.187 4.251| | 13: 1.28 - 1.25 0.98 6907 166 0.2024 0.2257 4.1295 4.263| | 14: 1.25 - 1.22 0.98 7015 113 0.2110 0.2488 4.0968 4.3552| | 15: 1.22 - 1.19 0.98 6957 137 0.2124 0.2014 4.0535 4.0439| | 16: 1.19 - 1.17 0.93 6604 132 0.2120 0.2101 4.0007 3.9952| | 17: 1.17 - 1.14 0.98 6941 135 0.2176 0.1974 3.9653 3.9774| | 18: 1.14 - 1.12 0.98 6875 142 0.2208 0.2482 3.9335 4.0021| | 19: 1.12 - 1.10 0.97 6949 106 0.2261 0.2704 3.8813 4.0629| | 20: 1.10 - 1.08 0.97 6884 147 0.2322 0.2520 3.8336 3.946| | 21: 1.08 - 1.07 0.97 6852 152 0.2465 0.2859 3.8012 3.8537| | 22: 1.07 - 1.05 0.97 6838 135 0.2533 0.2409 3.7475 3.6699| | 23: 1.05 - 1.03 0.97 6829 159 0.2695 0.2565 3.724 3.7873| | 24: 1.03 - 1.02 0.96 6785 133 0.2843 0.2798 3.6893 3.7699| | 25: 1.02 - 1.01 0.93 6552 130 0.3057 0.2835 3.6673 3.699| | 26: 1.01 - 0.99 0.96 6767 158 0.3179 0.3530 3.6269 3.6815| | 27: 0.99 - 0.98 0.94 6648 131 0.3380 0.3227 3.6365 3.5992| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.93 0.91 0.97 36965.50| | 2: 2.94 - 2.33 7339 128 0.85 21.51 1.09 1.02 15448.38| | 3: 2.33 - 2.04 6939 150 0.93 12.23 1.11 1.05 3958.02| | 4: 2.04 - 1.85 7170 155 0.93 13.30 1.11 1.06 2679.02| | 5: 1.85 - 1.72 7113 159 0.91 15.66 1.11 1.07 2071.61| | 6: 1.72 - 1.62 7102 142 0.90 17.18 1.11 1.06 1718.12| | 7: 1.62 - 1.54 7104 148 0.88 18.46 1.11 1.05 1439.37| | 8: 1.54 - 1.47 6798 152 0.88 19.46 1.10 1.04 1254.51| | 9: 1.47 - 1.41 6938 155 0.87 20.17 1.10 1.06 1101.27| | 10: 1.41 - 1.36 7022 150 0.85 21.65 1.09 1.06 969.60| | 11: 1.36 - 1.32 6997 151 0.86 21.33 1.09 1.04 826.35| | 12: 1.32 - 1.28 6976 149 0.86 21.49 1.08 1.02 737.87| | 13: 1.28 - 1.25 6907 166 0.85 21.81 1.07 1.01 693.90| | 14: 1.25 - 1.22 7015 113 0.85 22.46 1.07 1.02 657.25| | 15: 1.22 - 1.19 6957 137 0.85 21.95 1.08 1.03 586.34| | 16: 1.19 - 1.17 6604 132 0.87 20.87 1.08 1.02 497.21| | 17: 1.17 - 1.14 6941 135 0.86 21.36 1.08 1.01 453.33| | 18: 1.14 - 1.12 6875 142 0.85 22.31 1.08 0.97 423.73| | 19: 1.12 - 1.10 6949 106 0.84 24.03 1.08 0.99 436.03| | 20: 1.10 - 1.08 6884 147 0.83 24.33 1.07 0.98 394.62| | 21: 1.08 - 1.07 6852 152 0.83 25.05 1.07 0.99 369.34| | 22: 1.07 - 1.05 6838 135 0.82 25.25 1.06 0.97 322.47| | 23: 1.05 - 1.03 6829 159 0.81 26.97 1.05 0.98 319.14| | 24: 1.03 - 1.02 6785 133 0.79 28.88 1.05 0.98 319.55| | 25: 1.02 - 1.01 6552 130 0.76 31.03 1.04 0.94 317.11| | 26: 1.01 - 0.99 6767 158 0.74 32.65 1.03 0.91 298.11| | 27: 0.99 - 0.98 6648 131 0.75 32.00 1.03 0.88 266.44| |alpha: min = 0.88 max = 1.07 mean = 1.01| |beta: min = 266.44 max = 36965.50 mean = 2928.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.30| |phase err.(test): min = 0.00 max = 88.75 mean = 22.35| |-----------------------------------------------------------------------------| ----------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 0.251 2950 Z= 5.474 Angle : 5.219 18.507 4018 Z= 3.708 Chirality : 0.394 0.994 492 Planarity : 0.031 0.088 512 Dihedral : 12.718 82.120 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.29 % Allowed : 3.23 % Favored : 95.48 % Cbeta Deviations : 32.02 % 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: -2.73 (0.37), residues: 386 helix: -3.17 (0.27), residues: 146 sheet: -1.14 (0.52), residues: 82 loop : -0.46 (0.48), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.021 ARG B 49 TYR 0.132 0.035 TYR B 194 PHE 0.065 0.027 PHE A 95 TRP 0.137 0.049 TRP B 146 HIS 0.085 0.028 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.2051 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.303373 | | target function (ml) not normalized (work): 806077.631992 | | target function (ml) not normalized (free): 16641.170916 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2037 0.2051 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2037 0.2051 n_refl.: 191155 remove outliers: r(all,work,free)=0.2037 0.2037 0.2051 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2036 0.2037 0.2051 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1808 0.1805 0.1984 n_refl.: 191145 remove outliers: r(all,work,free)=0.1806 0.1803 0.1982 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4221 400.535 295.241 0.418 0.912 0.301 13.296-10.522 99.01 99 1 0.2491 528.187 521.564 0.761 0.913 0.255 10.503-8.327 99.45 178 3 0.2521 565.118 555.970 0.932 0.913 0.233 8.318-6.595 100.00 360 8 0.2507 414.736 403.384 0.930 0.913 0.164 6.588-5.215 100.00 711 7 0.2231 381.101 365.742 0.920 0.913 0.124 5.214-4.128 98.38 1367 28 0.1496 557.435 550.037 1.035 0.913 0.110 4.126-3.266 94.74 2603 46 0.1345 508.132 498.946 1.101 0.913 0.060 3.266-2.585 99.86 5447 97 0.1455 342.774 337.085 1.078 0.912 0.000 2.585-2.046 97.45 10613 204 0.1411 258.603 254.113 1.082 0.912 0.000 2.046-1.619 99.39 21536 464 0.1629 153.054 149.738 1.098 0.910 0.000 1.619-1.281 98.00 42464 925 0.1915 82.395 80.238 1.087 0.908 0.000 1.281-0.980 96.53 101826 2055 0.2317 44.202 41.699 1.071 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9745 b_overall=-0.0115 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1803 r_free=0.1982 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1803 r_free=0.1982 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.532952 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 564.050503 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 0.1272 0.1503 0.0231 0.039 1.2 10.9 0.0 0.3 0 11.266 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.03 2.31 1.119 13.108 564.051 0.018 13.01 15.76 2.75 1.255 13.353 564.051 0.017 Individual atomic B min max mean iso aniso Overall: 5.26 73.04 15.04 1.40 435 3274 Protein: 5.26 40.32 11.02 1.40 0 2902 Water: 6.36 73.04 29.49 N/A 435 370 Other: 16.13 30.25 23.19 N/A 0 2 Chain A: 5.32 59.55 13.08 N/A 0 1626 Chain B: 5.26 73.04 12.81 N/A 0 1648 Chain S: 11.31 63.54 30.84 N/A 435 0 Histogram: Values Number of atoms 5.26 - 12.03 2175 12.03 - 18.81 631 18.81 - 25.59 310 25.59 - 32.37 268 32.37 - 39.15 148 39.15 - 45.93 112 45.93 - 52.70 40 52.70 - 59.48 20 59.48 - 66.26 4 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1301 r_free=0.1576 r_work=0.1300 r_free=0.1570 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1300 r_free = 0.1570 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 = 0.1286 r_free = 0.1558 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1286 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015654 | | target function (ls_wunit_k1) not normalized (work): 2931.928438 | | target function (ls_wunit_k1) not normalized (free): 117.963731 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1286 0.1558 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1475 0.1473 0.1633 n_refl.: 191139 remove outliers: r(all,work,free)=0.1475 0.1473 0.1633 n_refl.: 191139 overall B=0.16 to atoms: r(all,work,free)=0.1498 0.1496 0.1642 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1283 0.1277 0.1549 n_refl.: 191139 remove outliers: r(all,work,free)=0.1282 0.1277 0.1549 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 0.3602 402.814 370.154 0.481 0.962 0.285 13.296-10.522 99.01 99 1 0.2071 528.187 519.953 0.738 0.964 0.240 10.503-8.327 99.45 178 3 0.1774 565.118 562.692 0.888 0.963 0.217 8.318-6.595 100.00 360 8 0.1713 414.736 412.895 0.910 0.963 0.150 6.588-5.215 100.00 711 7 0.1547 381.101 373.062 0.888 0.963 0.140 5.214-4.128 98.38 1367 28 0.0901 557.435 554.931 0.979 0.964 0.069 4.126-3.266 94.74 2603 46 0.0828 508.132 504.417 1.044 0.964 0.023 3.266-2.585 99.86 5447 97 0.0922 342.774 340.386 1.027 0.964 0.000 2.585-2.046 97.45 10613 204 0.0957 258.603 256.331 1.038 0.965 0.000 2.046-1.619 99.39 21536 464 0.1094 153.054 151.383 1.055 0.965 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.414 1.048 0.965 0.000 1.281-0.980 96.53 101826 2055 0.1876 44.202 42.166 1.024 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0356 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1549 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1549 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1549 | n_water=805 | time (s): 3.360 (total time: 3.360) Filter (dist) r_work=0.1282 r_free=0.1554 | n_water=793 | time (s): 98.290 (total time: 101.650) Filter (q & B) r_work=0.1283 r_free=0.1553 | n_water=789 | time (s): 4.420 (total time: 106.070) Compute maps r_work=0.1283 r_free=0.1553 | n_water=789 | time (s): 1.920 (total time: 107.990) Filter (map) r_work=0.1308 r_free=0.1530 | n_water=645 | time (s): 4.240 (total time: 112.230) Find peaks r_work=0.1308 r_free=0.1530 | n_water=645 | time (s): 0.630 (total time: 112.860) Add new water r_work=0.1331 r_free=0.1566 | n_water=956 | time (s): 4.190 (total time: 117.050) Refine new water occ: r_work=0.1286 r_free=0.1526 adp: r_work=0.1275 r_free=0.1519 occ: r_work=0.1279 r_free=0.1520 adp: r_work=0.1271 r_free=0.1518 occ: r_work=0.1273 r_free=0.1513 adp: r_work=0.1269 r_free=0.1514 ADP+occupancy (water only), MIN, final r_work=0.1269 r_free=0.1514 r_work=0.1269 r_free=0.1514 | n_water=956 | time (s): 76.500 (total time: 193.550) Filter (q & B) r_work=0.1273 r_free=0.1513 | n_water=884 | time (s): 4.310 (total time: 197.860) Filter (dist only) r_work=0.1273 r_free=0.1512 | n_water=883 | time (s): 109.350 (total time: 307.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.436790 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 580.619591 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 0.1257 0.1538 0.0281 0.040 1.1 18.7 0.0 0.0 0 11.718 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.57 15.38 2.81 2.048 15.143 580.620 0.015 12.33 15.21 2.87 2.437 15.175 580.620 0.014 Individual atomic B min max mean iso aniso Overall: 5.38 68.82 16.20 1.20 515 3272 Protein: 5.38 40.05 10.99 1.20 0 2902 Water: 6.61 68.82 33.33 N/A 515 368 Other: 16.42 33.09 24.76 N/A 0 2 Chain A: 5.46 55.70 13.01 N/A 0 1624 Chain B: 5.38 68.20 12.85 N/A 0 1648 Chain S: 10.11 68.82 36.98 N/A 515 0 Histogram: Values Number of atoms 5.38 - 11.72 2073 11.72 - 18.07 716 18.07 - 24.41 251 24.41 - 30.76 221 30.76 - 37.10 177 37.10 - 43.45 168 43.45 - 49.79 99 49.79 - 56.13 53 56.13 - 62.48 22 62.48 - 68.82 7 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1521 r_work=0.1234 r_free=0.1522 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1522 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 = 0.1227 r_free = 0.1520 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1520 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013524 | | target function (ls_wunit_k1) not normalized (work): 2533.027887 | | target function (ls_wunit_k1) not normalized (free): 104.149549 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1227 0.1520 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1441 0.1438 0.1616 n_refl.: 191138 remove outliers: r(all,work,free)=0.1441 0.1438 0.1616 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1438 0.1435 0.1614 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1234 0.1525 n_refl.: 191138 remove outliers: r(all,work,free)=0.1240 0.1234 0.1525 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 0.3307 402.814 376.244 0.485 0.962 0.270 13.296-10.522 99.01 99 1 0.1901 528.187 522.894 0.766 0.963 0.256 10.503-8.327 99.45 178 3 0.1504 565.118 567.800 0.919 0.963 0.184 8.318-6.595 100.00 360 8 0.1538 414.736 414.665 0.938 0.962 0.170 6.588-5.215 100.00 711 7 0.1362 381.101 376.309 0.912 0.962 0.140 5.214-4.128 98.38 1367 28 0.0835 557.435 555.683 0.997 0.962 0.090 4.126-3.266 94.74 2603 46 0.0757 508.132 505.747 1.060 0.962 0.014 3.266-2.585 99.86 5447 97 0.0861 342.774 341.295 1.047 0.961 0.000 2.585-2.046 97.45 10613 204 0.0900 258.603 256.737 1.059 0.960 0.000 2.046-1.619 99.39 21536 464 0.1047 153.054 151.615 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.347 1.075 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.213 1.061 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0562 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1525 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1525 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1525 | n_water=883 | time (s): 3.260 (total time: 3.260) Filter (dist) r_work=0.1236 r_free=0.1528 | n_water=876 | time (s): 110.770 (total time: 114.030) Filter (q & B) r_work=0.1236 r_free=0.1528 | n_water=873 | time (s): 4.190 (total time: 118.220) Compute maps r_work=0.1236 r_free=0.1528 | n_water=873 | time (s): 1.730 (total time: 119.950) Filter (map) r_work=0.1272 r_free=0.1525 | n_water=693 | time (s): 4.570 (total time: 124.520) Find peaks r_work=0.1272 r_free=0.1525 | n_water=693 | time (s): 0.870 (total time: 125.390) Add new water r_work=0.1294 r_free=0.1568 | n_water=1003 | time (s): 4.700 (total time: 130.090) Refine new water occ: r_work=0.1251 r_free=0.1520 adp: r_work=0.1251 r_free=0.1522 occ: r_work=0.1247 r_free=0.1517 adp: r_work=0.1247 r_free=0.1518 occ: r_work=0.1244 r_free=0.1515 adp: r_work=0.1244 r_free=0.1516 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1516 r_work=0.1244 r_free=0.1516 | n_water=1003 | time (s): 313.740 (total time: 443.830) Filter (q & B) r_work=0.1250 r_free=0.1522 | n_water=869 | time (s): 4.870 (total time: 448.700) Filter (dist only) r_work=0.1250 r_free=0.1522 | n_water=868 | time (s): 112.000 (total time: 560.700) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.721362 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.132071 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 0.1240 0.1442 0.0202 0.034 1.1 8.3 0.0 0.0 0 0.861 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.42 2.02 1.932 14.572 16.132 3.940 12.37 14.00 1.63 2.293 14.463 16.132 3.897 Individual atomic B min max mean iso aniso Overall: 5.52 67.64 15.21 1.04 501 3271 Protein: 5.52 35.60 10.71 1.04 0 2902 Water: 6.71 67.64 30.26 N/A 501 367 Other: 13.89 28.56 21.23 N/A 0 2 Chain A: 5.59 54.38 12.74 N/A 0 1624 Chain B: 5.52 67.64 12.52 N/A 0 1647 Chain S: 13.68 61.12 32.07 N/A 501 0 Histogram: Values Number of atoms 5.52 - 11.73 2128 11.73 - 17.95 700 17.95 - 24.16 287 24.16 - 30.37 238 30.37 - 36.58 172 36.58 - 42.79 137 42.79 - 49.01 74 49.01 - 55.22 22 55.22 - 61.43 13 61.43 - 67.64 1 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1401 r_work=0.1238 r_free=0.1401 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1401 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1393 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= 0.1231 r_free= 0.1393 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891701 | | target function (ml) not normalized (work): 728903.978433 | | target function (ml) not normalized (free): 15221.356274 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1393 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1452 0.1451 0.1492 n_refl.: 191138 remove outliers: r(all,work,free)=0.1452 0.1451 0.1492 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1445 0.1445 0.1488 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1231 0.1227 0.1385 n_refl.: 191138 remove outliers: r(all,work,free)=0.1230 0.1227 0.1385 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3822 398.008 361.447 0.431 0.945 0.251 13.296-10.522 98.02 98 1 0.2385 528.900 505.106 0.710 0.946 0.214 10.503-8.327 98.35 176 3 0.2035 555.265 558.902 0.885 0.946 0.181 8.318-6.595 100.00 360 8 0.2093 414.736 409.617 0.902 0.946 0.143 6.588-5.215 100.00 711 7 0.1823 381.101 371.003 0.889 0.946 0.123 5.214-4.128 98.38 1367 28 0.1169 557.435 552.023 0.974 0.946 0.080 4.126-3.266 94.74 2603 46 0.1093 508.132 501.536 1.034 0.946 0.009 3.266-2.585 99.86 5447 97 0.1100 342.774 338.995 1.022 0.946 0.000 2.585-2.046 97.45 10613 204 0.0972 258.603 255.732 1.035 0.945 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.409 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.488 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.317 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1078 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1386 | n_water=868 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1227 r_free=0.1385 | n_water=867 | time (s): 110.400 (total time: 112.980) Filter (q & B) r_work=0.1227 r_free=0.1382 | n_water=859 | time (s): 3.950 (total time: 116.930) Compute maps r_work=0.1227 r_free=0.1382 | n_water=859 | time (s): 2.370 (total time: 119.300) Filter (map) r_work=0.1248 r_free=0.1382 | n_water=718 | time (s): 4.990 (total time: 124.290) Find peaks r_work=0.1248 r_free=0.1382 | n_water=718 | time (s): 0.600 (total time: 124.890) Add new water r_work=0.1265 r_free=0.1399 | n_water=973 | time (s): 4.290 (total time: 129.180) Refine new water occ: r_work=0.1216 r_free=0.1355 adp: r_work=0.1208 r_free=0.1351 occ: r_work=0.1206 r_free=0.1352 adp: r_work=0.1206 r_free=0.1351 occ: r_work=0.1204 r_free=0.1353 adp: r_work=0.1203 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1352 r_work=0.1203 r_free=0.1352 | n_water=973 | time (s): 242.550 (total time: 371.730) Filter (q & B) r_work=0.1208 r_free=0.1360 | n_water=872 | time (s): 4.310 (total time: 376.040) Filter (dist only) r_work=0.1208 r_free=0.1360 | n_water=871 | time (s): 109.450 (total time: 485.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.603725 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.860106 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1207 0.1369 0.0163 0.035 1.1 6.6 0.0 0.3 0 0.802 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.07 13.69 1.63 1.815 14.177 14.860 3.874 12.00 13.68 1.68 1.894 14.146 14.860 3.866 Individual atomic B min max mean iso aniso Overall: 5.51 67.22 14.98 0.98 504 3271 Protein: 5.51 32.84 10.65 0.98 0 2902 Water: 5.92 67.22 29.39 N/A 504 367 Other: 13.96 27.43 20.69 N/A 0 2 Chain A: 5.56 53.30 12.63 N/A 0 1624 Chain B: 5.51 67.22 12.44 N/A 0 1647 Chain S: 5.92 61.13 30.83 N/A 504 0 Histogram: Values Number of atoms 5.51 - 11.68 2113 11.68 - 17.86 738 17.86 - 24.03 296 24.03 - 30.20 234 30.20 - 36.37 173 36.37 - 42.54 123 42.54 - 48.71 64 48.71 - 54.88 23 54.88 - 61.05 9 61.05 - 67.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1369 r_work=0.1200 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1369 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1367 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1367 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864248 | | target function (ml) not normalized (work): 723746.558476 | | target function (ml) not normalized (free): 15141.079626 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1198 0.1367 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1428 0.1428 0.1465 n_refl.: 191134 remove outliers: r(all,work,free)=0.1428 0.1428 0.1465 n_refl.: 191134 overall B=-0.04 to atoms: r(all,work,free)=0.1420 0.1420 0.1461 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1201 0.1197 0.1368 n_refl.: 191134 remove outliers: r(all,work,free)=0.1200 0.1197 0.1368 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3837 361.323 316.012 0.403 0.945 0.233 13.296-10.522 97.03 97 1 0.2350 481.357 456.592 0.712 0.947 0.204 10.503-8.327 98.35 176 3 0.2126 502.965 497.616 0.865 0.947 0.190 8.318-6.595 100.00 360 8 0.2164 375.672 371.160 0.895 0.947 0.105 6.588-5.215 100.00 711 7 0.1890 345.205 334.873 0.887 0.947 0.095 5.214-4.128 98.38 1367 28 0.1191 504.930 499.378 0.976 0.947 0.090 4.126-3.266 94.74 2603 46 0.1110 460.271 454.068 1.035 0.948 0.005 3.266-2.585 99.86 5447 97 0.1097 310.488 307.155 1.022 0.947 0.000 2.585-2.046 97.45 10613 204 0.0936 234.245 231.820 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0916 138.638 137.347 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0988 74.635 73.914 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.038 38.372 1.038 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1237 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1368 | n_water=871 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1197 r_free=0.1368 | n_water=871 | time (s): 106.260 (total time: 109.410) Filter (q & B) r_work=0.1197 r_free=0.1369 | n_water=860 | time (s): 5.070 (total time: 114.480) Compute maps r_work=0.1197 r_free=0.1369 | n_water=860 | time (s): 1.720 (total time: 116.200) Filter (map) r_work=0.1218 r_free=0.1360 | n_water=747 | time (s): 4.110 (total time: 120.310) Find peaks r_work=0.1218 r_free=0.1360 | n_water=747 | time (s): 0.670 (total time: 120.980) Add new water r_work=0.1231 r_free=0.1374 | n_water=954 | time (s): 4.750 (total time: 125.730) Refine new water occ: r_work=0.1197 r_free=0.1351 adp: r_work=0.1197 r_free=0.1351 occ: r_work=0.1197 r_free=0.1351 adp: r_work=0.1197 r_free=0.1351 occ: r_work=0.1197 r_free=0.1351 adp: r_work=0.1197 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1351 r_work=0.1197 r_free=0.1351 | n_water=954 | time (s): 126.540 (total time: 252.270) Filter (q & B) r_work=0.1203 r_free=0.1352 | n_water=833 | time (s): 5.400 (total time: 257.670) Filter (dist only) r_work=0.1203 r_free=0.1350 | n_water=831 | time (s): 108.670 (total time: 366.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.546888 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.209452 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 0.1205 0.1351 0.0146 0.035 1.1 5.8 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.51 1.46 1.782 13.938 15.209 3.766 12.07 13.55 1.48 1.877 13.900 15.209 3.762 Individual atomic B min max mean iso aniso Overall: 5.54 66.66 14.62 0.94 464 3271 Protein: 5.54 30.99 10.56 0.94 0 2902 Water: 6.07 66.66 28.77 N/A 464 367 Other: 13.86 25.79 19.83 N/A 0 2 Chain A: 5.59 51.83 12.50 N/A 0 1624 Chain B: 5.54 66.66 12.33 N/A 0 1647 Chain S: 6.07 61.15 30.14 N/A 464 0 Histogram: Values Number of atoms 5.54 - 11.65 2122 11.65 - 17.76 744 17.76 - 23.87 311 23.87 - 29.99 187 29.99 - 36.10 158 36.10 - 42.21 116 42.21 - 48.32 62 48.32 - 54.44 26 54.44 - 60.55 7 60.55 - 66.66 2 =========================== Idealize ADP of riding H ========================== r_work=0.1207 r_free=0.1355 r_work=0.1207 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1207 r_free = 0.1356 target_work(ml) = 3.763 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1357 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1206 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.761875 | | target function (ml) not normalized (work): 704565.327701 | | target function (ml) not normalized (free): 14743.584398 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1205 0.1358 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1424 0.1423 0.1476 n_refl.: 191132 remove outliers: r(all,work,free)=0.1424 0.1423 0.1476 n_refl.: 191132 overall B=-0.03 to atoms: r(all,work,free)=0.1418 0.1417 0.1472 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1352 n_refl.: 191132 remove outliers: r(all,work,free)=0.1203 0.1200 0.1352 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3584 361.020 313.584 0.393 0.972 0.231 13.296-10.522 96.04 96 1 0.2403 480.594 456.805 0.688 0.973 0.191 10.503-8.327 98.35 176 3 0.2198 502.965 494.545 0.829 0.973 0.170 8.315-6.595 100.00 359 8 0.2223 374.726 370.866 0.871 0.973 0.133 6.588-5.215 100.00 711 7 0.1966 345.205 334.373 0.860 0.972 0.112 5.214-4.128 98.38 1367 28 0.1234 504.930 498.863 0.948 0.972 0.110 4.126-3.266 94.74 2603 46 0.1153 460.271 453.724 1.007 0.970 0.000 3.266-2.585 99.86 5447 97 0.1111 310.488 307.070 0.996 0.968 0.000 2.585-2.046 97.45 10613 204 0.0954 234.245 231.739 1.011 0.964 0.000 2.046-1.619 99.39 21536 464 0.0916 138.638 137.328 1.040 0.957 0.000 1.619-1.281 98.00 42464 925 0.0971 74.635 73.945 1.048 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1644 40.038 38.368 1.052 0.929 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1009 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1352 | n_water=831 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1200 r_free=0.1352 | n_water=831 | time (s): 96.920 (total time: 99.250) Filter (q & B) r_work=0.1200 r_free=0.1351 | n_water=822 | time (s): 5.140 (total time: 104.390) Compute maps r_work=0.1200 r_free=0.1351 | n_water=822 | time (s): 1.630 (total time: 106.020) Filter (map) r_work=0.1215 r_free=0.1356 | n_water=744 | time (s): 5.090 (total time: 111.110) Find peaks r_work=0.1215 r_free=0.1356 | n_water=744 | time (s): 0.630 (total time: 111.740) Add new water r_work=0.1228 r_free=0.1370 | n_water=943 | time (s): 3.880 (total time: 115.620) Refine new water occ: r_work=0.1196 r_free=0.1347 adp: r_work=0.1196 r_free=0.1346 occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1193 r_free=0.1346 occ: r_work=0.1192 r_free=0.1348 adp: r_work=0.1191 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1347 r_work=0.1191 r_free=0.1347 | n_water=943 | time (s): 206.990 (total time: 322.610) Filter (q & B) r_work=0.1194 r_free=0.1352 | n_water=891 | time (s): 4.360 (total time: 326.970) Filter (dist only) r_work=0.1194 r_free=0.1352 | n_water=890 | time (s): 109.490 (total time: 436.460) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.577592 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.373217 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1361 0.0164 0.037 1.1 6.3 0.0 0.3 0 0.789 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.61 1.64 1.749 14.004 15.373 3.761 11.98 13.65 1.67 1.843 13.969 15.373 3.757 Individual atomic B min max mean iso aniso Overall: 5.57 65.53 14.83 0.91 523 3271 Protein: 5.57 29.18 10.48 0.91 0 2902 Water: 5.99 65.53 28.97 N/A 523 367 Other: 13.86 23.09 18.47 N/A 0 2 Chain A: 5.64 51.06 12.38 N/A 0 1624 Chain B: 5.57 65.53 12.23 N/A 0 1647 Chain S: 5.99 61.31 30.58 N/A 523 0 Histogram: Values Number of atoms 5.57 - 11.57 2105 11.57 - 17.56 783 17.56 - 23.56 276 23.56 - 29.56 215 29.56 - 35.55 177 35.55 - 41.55 124 41.55 - 47.54 76 47.54 - 53.54 27 53.54 - 59.53 8 59.53 - 65.53 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1365 r_work=0.1198 r_free=0.1365 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1370 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756926 | | target function (ml) not normalized (work): 703627.075881 | | target function (ml) not normalized (free): 14742.113431 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1370 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1403 0.1402 0.1493 n_refl.: 191129 remove outliers: r(all,work,free)=0.1403 0.1402 0.1493 n_refl.: 191129 overall B=-0.24 to atoms: r(all,work,free)=0.1365 0.1364 0.1470 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1372 n_refl.: 191129 remove outliers: r(all,work,free)=0.1202 0.1199 0.1372 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3643 361.020 331.081 0.432 0.950 0.225 13.296-10.522 96.04 96 1 0.2449 480.594 461.121 0.723 0.952 0.173 10.503-8.327 98.35 176 3 0.2209 502.965 495.430 0.881 0.952 0.150 8.315-6.595 100.00 359 8 0.2191 374.726 370.993 0.909 0.952 0.105 6.588-5.215 100.00 711 7 0.1939 345.205 334.952 0.907 0.952 0.100 5.214-4.128 98.38 1367 28 0.1229 504.930 498.973 0.997 0.952 0.090 4.126-3.266 94.74 2603 46 0.1139 460.271 453.687 1.057 0.953 0.000 3.266-2.585 99.86 5447 97 0.1120 310.488 307.019 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0951 234.245 231.709 1.046 0.953 0.000 2.046-1.619 99.39 21536 464 0.0910 138.638 137.341 1.063 0.954 0.000 1.619-1.281 98.00 42464 925 0.0969 74.635 73.935 1.049 0.954 0.000 1.281-0.980 96.53 101826 2055 0.1649 40.038 38.370 1.016 0.956 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0535 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1373 | n_water=890 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1199 r_free=0.1373 | n_water=889 | time (s): 119.370 (total time: 122.140) Filter (q & B) r_work=0.1200 r_free=0.1371 | n_water=877 | time (s): 5.350 (total time: 127.490) Compute maps r_work=0.1200 r_free=0.1371 | n_water=877 | time (s): 2.090 (total time: 129.580) Filter (map) r_work=0.1218 r_free=0.1355 | n_water=765 | time (s): 4.970 (total time: 134.550) Find peaks r_work=0.1218 r_free=0.1355 | n_water=765 | time (s): 0.770 (total time: 135.320) Add new water r_work=0.1229 r_free=0.1373 | n_water=970 | time (s): 4.080 (total time: 139.400) Refine new water occ: r_work=0.1196 r_free=0.1357 adp: r_work=0.1197 r_free=0.1357 occ: r_work=0.1195 r_free=0.1357 adp: r_work=0.1195 r_free=0.1356 occ: r_work=0.1194 r_free=0.1357 adp: r_work=0.1193 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1356 r_work=0.1193 r_free=0.1356 | n_water=970 | time (s): 202.350 (total time: 341.750) Filter (q & B) r_work=0.1197 r_free=0.1362 | n_water=899 | time (s): 4.240 (total time: 345.990) Filter (dist only) r_work=0.1197 r_free=0.1362 | n_water=898 | time (s): 113.590 (total time: 459.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.575215 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.622853 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1366 0.0165 0.037 1.1 6.1 0.0 0.3 0 0.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.66 1.65 1.719 13.698 14.623 3.759 12.03 13.69 1.66 1.753 13.684 14.623 3.758 Individual atomic B min max mean iso aniso Overall: 5.39 64.44 14.57 0.89 531 3271 Protein: 5.39 28.44 10.23 0.89 0 2902 Water: 5.77 64.44 28.57 N/A 531 367 Other: 13.68 22.13 17.91 N/A 0 2 Chain A: 5.45 50.42 12.09 N/A 0 1624 Chain B: 5.39 64.44 11.95 N/A 0 1647 Chain S: 5.77 61.22 30.25 N/A 531 0 Histogram: Values Number of atoms 5.39 - 11.30 2087 11.30 - 17.20 799 17.20 - 23.11 267 23.11 - 29.01 225 29.01 - 34.91 184 34.91 - 40.82 123 40.82 - 46.72 79 46.72 - 52.63 25 52.63 - 58.53 10 58.53 - 64.44 3 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1369 r_work=0.1203 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1369 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1372 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1372 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757333 | | target function (ml) not normalized (work): 703703.395049 | | target function (ml) not normalized (free): 14734.448071 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1372 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1373 0.1371 0.1472 n_refl.: 191129 remove outliers: r(all,work,free)=0.1373 0.1371 0.1472 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1381 0.1380 0.1476 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1192 0.1360 n_refl.: 191129 remove outliers: r(all,work,free)=0.1196 0.1192 0.1360 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3690 361.020 329.106 0.405 0.995 0.215 13.296-10.522 96.04 96 1 0.2452 480.594 460.064 0.691 0.997 0.163 10.503-8.327 98.35 176 3 0.2222 502.965 494.166 0.846 0.998 0.140 8.315-6.595 100.00 359 8 0.2207 374.726 370.216 0.871 0.998 0.100 6.588-5.215 100.00 711 7 0.1946 345.205 334.412 0.873 0.998 0.099 5.214-4.128 98.38 1367 28 0.1243 504.930 498.435 0.960 0.999 0.066 4.126-3.266 94.74 2603 46 0.1151 460.271 452.941 1.019 1.000 0.000 3.266-2.585 99.86 5447 97 0.1123 310.488 306.769 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0960 234.245 231.602 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0908 138.638 137.252 1.025 1.005 0.000 1.619-1.281 98.00 42464 925 0.0949 74.635 73.974 1.014 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.038 38.348 0.980 1.017 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0611 ============================ 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=898 | time (s): 3.060 (total time: 3.060) Filter (dist) r_work=0.1192 r_free=0.1360 | n_water=898 | time (s): 106.190 (total time: 109.250) Filter (q & B) r_work=0.1193 r_free=0.1360 | n_water=885 | time (s): 4.140 (total time: 113.390) Compute maps r_work=0.1193 r_free=0.1360 | n_water=885 | time (s): 1.800 (total time: 115.190) Filter (map) r_work=0.1213 r_free=0.1352 | n_water=773 | time (s): 5.260 (total time: 120.450) Find peaks r_work=0.1213 r_free=0.1352 | n_water=773 | time (s): 0.750 (total time: 121.200) Add new water r_work=0.1222 r_free=0.1367 | n_water=977 | time (s): 4.620 (total time: 125.820) Refine new water occ: r_work=0.1190 r_free=0.1356 adp: r_work=0.1191 r_free=0.1356 occ: r_work=0.1189 r_free=0.1357 adp: r_work=0.1189 r_free=0.1356 occ: r_work=0.1187 r_free=0.1357 adp: r_work=0.1187 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1357 r_work=0.1187 r_free=0.1357 | n_water=977 | time (s): 200.570 (total time: 326.390) Filter (q & B) r_work=0.1191 r_free=0.1362 | n_water=903 | time (s): 4.340 (total time: 330.730) Filter (dist only) r_work=0.1192 r_free=0.1362 | n_water=901 | time (s): 116.760 (total time: 447.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.495258 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.042674 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1367 0.0171 0.037 1.1 6.0 0.0 0.3 0 0.748 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.67 1.71 1.676 13.716 14.043 3.757 11.98 13.72 1.74 1.702 13.702 14.043 3.757 Individual atomic B min max mean iso aniso Overall: 5.49 63.53 14.60 0.87 534 3271 Protein: 5.49 27.94 10.30 0.87 0 2902 Water: 5.90 63.53 28.47 N/A 534 367 Other: 13.77 22.08 17.93 N/A 0 2 Chain A: 5.56 49.97 12.12 N/A 0 1624 Chain B: 5.49 63.53 11.99 N/A 0 1647 Chain S: 5.90 61.41 30.22 N/A 534 0 Histogram: Values Number of atoms 5.49 - 11.29 2068 11.29 - 17.10 822 17.10 - 22.90 266 22.90 - 28.71 219 28.71 - 34.51 181 34.51 - 40.32 126 40.32 - 46.12 82 46.12 - 51.92 26 51.92 - 57.73 11 57.73 - 63.53 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1372 r_work=0.1199 r_free=0.1372 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1372 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1375 target_work(ml) = 3.756 | | 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.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1375 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756221 | | target function (ml) not normalized (work): 703495.167710 | | target function (ml) not normalized (free): 14738.856498 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1375 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1392 0.1390 0.1500 n_refl.: 191129 remove outliers: r(all,work,free)=0.1392 0.1390 0.1500 n_refl.: 191129 overall B=0.01 to atoms: r(all,work,free)=0.1394 0.1392 0.1501 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1371 n_refl.: 191129 remove outliers: r(all,work,free)=0.1199 0.1196 0.1371 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3752 361.020 327.392 0.399 0.974 0.196 13.296-10.522 96.04 96 1 0.2400 480.594 461.291 0.699 0.976 0.145 10.503-8.327 98.35 176 3 0.2249 502.965 494.136 0.860 0.976 0.122 8.315-6.595 100.00 359 8 0.2208 374.726 370.005 0.888 0.976 0.107 6.588-5.215 100.00 711 7 0.1981 345.205 333.996 0.888 0.977 0.098 5.214-4.128 98.38 1367 28 0.1267 504.930 498.243 0.979 0.978 0.059 4.126-3.266 94.74 2603 46 0.1168 460.271 452.693 1.041 0.979 0.000 3.266-2.585 99.86 5447 97 0.1132 310.488 306.706 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0966 234.245 231.585 1.032 0.982 0.000 2.046-1.619 99.39 21536 464 0.0910 138.638 137.272 1.049 0.985 0.000 1.619-1.281 98.00 42464 925 0.0945 74.635 73.983 1.039 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.038 38.335 1.007 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0193 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1371 | n_water=901 | time (s): 3.100 (total time: 3.100) Filter (dist) r_work=0.1196 r_free=0.1371 | n_water=901 | time (s): 117.670 (total time: 120.770) Filter (q & B) r_work=0.1197 r_free=0.1370 | n_water=889 | time (s): 4.460 (total time: 125.230) Compute maps r_work=0.1197 r_free=0.1370 | n_water=889 | time (s): 2.280 (total time: 127.510) Filter (map) r_work=0.1220 r_free=0.1359 | n_water=764 | time (s): 4.240 (total time: 131.750) Find peaks r_work=0.1220 r_free=0.1359 | n_water=764 | time (s): 0.810 (total time: 132.560) Add new water r_work=0.1228 r_free=0.1371 | n_water=983 | time (s): 3.950 (total time: 136.510) Refine new water occ: r_work=0.1193 r_free=0.1347 adp: r_work=0.1194 r_free=0.1347 occ: r_work=0.1191 r_free=0.1347 adp: r_work=0.1191 r_free=0.1347 occ: r_work=0.1190 r_free=0.1346 adp: r_work=0.1190 r_free=0.1347 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1347 r_work=0.1190 r_free=0.1347 | n_water=983 | time (s): 191.190 (total time: 327.700) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=908 | time (s): 5.250 (total time: 332.950) Filter (dist only) r_work=0.1195 r_free=0.1356 | n_water=906 | time (s): 116.210 (total time: 449.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.554159 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.786515 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1356 0.0159 0.038 1.1 5.8 0.0 0.3 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.56 1.59 1.674 13.711 13.787 3.756 11.97 13.59 1.62 1.678 13.706 13.787 3.754 Individual atomic B min max mean iso aniso Overall: 5.51 62.96 14.60 0.86 540 3270 Protein: 5.51 27.93 10.32 0.86 0 2902 Water: 5.98 62.96 28.29 N/A 540 366 Other: 13.81 22.12 17.97 N/A 0 2 Chain A: 5.60 49.68 12.12 N/A 0 1624 Chain B: 5.51 62.96 11.97 N/A 0 1646 Chain S: 5.98 61.51 30.08 N/A 540 0 Histogram: Values Number of atoms 5.51 - 11.25 2054 11.25 - 17.00 833 17.00 - 22.74 272 22.74 - 28.49 218 28.49 - 34.24 188 34.24 - 39.98 119 39.98 - 45.73 76 45.73 - 51.47 35 51.47 - 57.22 11 57.22 - 62.96 4 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1359 r_work=0.1197 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1359 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1359 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1359 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754212 | | target function (ml) not normalized (work): 703118.933620 | | target function (ml) not normalized (free): 14730.393767 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1359 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1494 n_refl.: 191129 remove outliers: r(all,work,free)=0.1401 0.1400 0.1494 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1401 0.1399 0.1494 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191129 remove outliers: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3750 361.020 327.347 0.394 0.994 0.203 13.296-10.522 96.04 96 1 0.2391 480.594 461.351 0.682 0.996 0.146 10.503-8.327 98.35 176 3 0.2234 502.965 494.470 0.840 0.997 0.117 8.315-6.595 100.00 359 8 0.2219 374.726 369.820 0.868 0.997 0.105 6.588-5.215 100.00 711 7 0.1975 345.205 334.028 0.869 0.997 0.096 5.214-4.128 98.38 1367 28 0.1256 504.930 498.283 0.959 0.998 0.061 4.126-3.266 94.74 2603 46 0.1173 460.271 452.841 1.020 1.000 0.005 3.266-2.585 99.86 5447 97 0.1138 310.488 306.682 1.003 1.001 0.000 2.585-2.046 97.45 10613 204 0.0965 234.245 231.563 1.011 1.003 0.000 2.046-1.619 99.39 21536 464 0.0908 138.638 137.264 1.027 1.007 0.000 1.619-1.281 98.00 42464 925 0.0941 74.635 73.988 1.019 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.038 38.325 0.989 1.024 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0083 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1359 After: r_work=0.1196 r_free=0.1359 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1359 | n_water=906 | time (s): 3.170 (total time: 3.170) Filter (dist) r_work=0.1196 r_free=0.1359 | n_water=906 | time (s): 119.700 (total time: 122.870) Filter (q & B) r_work=0.1196 r_free=0.1360 | n_water=896 | time (s): 4.700 (total time: 127.570) Compute maps r_work=0.1196 r_free=0.1360 | n_water=896 | time (s): 2.230 (total time: 129.800) Filter (map) r_work=0.1218 r_free=0.1357 | n_water=775 | time (s): 4.640 (total time: 134.440) Find peaks r_work=0.1218 r_free=0.1357 | n_water=775 | time (s): 0.640 (total time: 135.080) Add new water r_work=0.1225 r_free=0.1367 | n_water=986 | time (s): 5.260 (total time: 140.340) Refine new water occ: r_work=0.1193 r_free=0.1351 adp: r_work=0.1193 r_free=0.1351 occ: r_work=0.1191 r_free=0.1352 adp: r_work=0.1191 r_free=0.1352 occ: r_work=0.1190 r_free=0.1353 adp: r_work=0.1190 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1353 r_work=0.1190 r_free=0.1353 | n_water=986 | time (s): 348.830 (total time: 489.170) Filter (q & B) r_work=0.1194 r_free=0.1363 | n_water=908 | time (s): 5.890 (total time: 495.060) Filter (dist only) r_work=0.1195 r_free=0.1363 | n_water=906 | time (s): 114.480 (total time: 609.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.505487 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.391707 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1367 0.0171 0.038 1.1 7.0 0.0 0.3 0 0.753 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.67 1.71 1.673 13.707 14.392 3.756 11.96 13.69 1.73 1.669 13.708 14.392 3.754 Individual atomic B min max mean iso aniso Overall: 5.56 61.89 14.60 0.86 540 3270 Protein: 5.56 27.96 10.34 0.86 0 2902 Water: 6.01 61.89 28.21 N/A 540 366 Other: 13.86 22.06 17.96 N/A 0 2 Chain A: 5.66 49.11 12.11 N/A 0 1624 Chain B: 5.56 61.89 11.97 N/A 0 1646 Chain S: 6.01 61.63 30.08 N/A 540 0 Histogram: Values Number of atoms 5.56 - 11.19 2029 11.19 - 16.82 853 16.82 - 22.46 275 22.46 - 28.09 199 28.09 - 33.72 194 33.72 - 39.36 123 39.36 - 44.99 78 44.99 - 50.62 42 50.62 - 56.25 11 56.25 - 61.89 6 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1369 r_work=0.1196 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1369 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1369 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753575 | | target function (ml) not normalized (work): 702999.474081 | | target function (ml) not normalized (free): 14728.023052 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1375 0.1567 5.7006 5.7965| | 2: 2.94 - 2.33 1.00 7339 128 0.1081 0.1334 5.0915 5.1842| | 3: 2.33 - 2.04 0.96 6939 150 0.0902 0.1179 4.6558 4.7437| | 4: 2.04 - 1.85 1.00 7170 155 0.0894 0.1052 4.3856 4.5551| | 5: 1.85 - 1.72 0.99 7113 159 0.0930 0.0982 4.1458 4.2409| | 6: 1.72 - 1.62 0.99 7102 142 0.0891 0.1067 3.9386 4.0617| | 7: 1.62 - 1.54 0.99 7104 148 0.0885 0.0956 3.792 3.9148| | 8: 1.54 - 1.47 0.96 6798 152 0.0886 0.1321 3.6943 3.9022| | 9: 1.47 - 1.41 0.98 6938 155 0.0922 0.1126 3.6164 3.7522| | 10: 1.41 - 1.36 0.99 7022 150 0.0974 0.1172 3.5524 3.671| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1109 3.4806 3.578| | 12: 1.32 - 1.28 0.98 6975 149 0.1032 0.1141 3.4577 3.5903| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1251 3.4377 3.5684| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1583 3.4336 3.6797| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1250 3.4499 3.4951| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1558 3.4658 3.6627| | 17: 1.17 - 1.14 0.98 6940 135 0.1299 0.1226 3.4336 3.4436| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1701 3.4382 3.532| | 19: 1.12 - 1.10 0.97 6948 106 0.1468 0.1768 3.4193 3.5994| | 20: 1.10 - 1.08 0.97 6884 147 0.1582 0.1581 3.4104 3.4367| | 21: 1.08 - 1.07 0.97 6852 152 0.1728 0.2144 3.4187 3.5073| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1960 3.4135 3.4177| | 23: 1.05 - 1.03 0.97 6827 159 0.2117 0.2024 3.433 3.4867| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2257 3.4357 3.5116| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2515 3.4489 3.5236| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2866 3.4157 3.4249| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2792 3.4696 3.3937| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7397 127 0.93 12.10 1.00 0.95 11787.85| | 2: 2.94 - 2.33 7339 128 0.92 13.10 0.99 0.95 5330.73| | 3: 2.33 - 2.04 6939 150 0.96 7.65 1.01 0.95 1701.70| | 4: 2.04 - 1.85 7170 155 0.96 7.56 1.00 0.96 988.79| | 5: 1.85 - 1.72 7113 159 0.96 7.96 1.00 0.96 622.08| | 6: 1.72 - 1.62 7102 142 0.96 7.86 1.00 0.96 432.91| | 7: 1.62 - 1.54 7104 148 0.96 7.98 1.01 0.97 329.69| | 8: 1.54 - 1.47 6798 152 0.96 8.19 1.01 0.97 275.36| | 9: 1.47 - 1.41 6938 155 0.96 8.38 1.00 0.98 228.31| | 10: 1.41 - 1.36 7022 150 0.96 8.84 1.00 0.97 200.54| | 11: 1.36 - 1.32 6997 151 0.96 8.87 0.99 0.96 173.16| | 12: 1.32 - 1.28 6975 149 0.96 8.98 0.98 0.95 160.78| | 13: 1.28 - 1.25 6907 166 0.96 9.58 1.01 0.96 159.23| | 14: 1.25 - 1.22 7015 112 0.95 10.79 1.01 0.97 165.00| | 15: 1.22 - 1.19 6956 137 0.95 11.31 1.01 0.98 168.14| | 16: 1.19 - 1.17 6604 132 0.95 11.48 1.01 0.96 161.38| | 17: 1.17 - 1.14 6940 135 0.94 12.26 1.01 0.96 154.34| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.95 147.95| | 19: 1.12 - 1.10 6948 106 0.93 14.18 1.00 0.95 151.63| | 20: 1.10 - 1.08 6884 147 0.92 15.27 1.00 0.94 151.17| | 21: 1.08 - 1.07 6852 152 0.91 16.72 1.00 0.93 154.38| | 22: 1.07 - 1.05 6836 135 0.89 18.36 0.99 0.93 155.90| | 23: 1.05 - 1.03 6827 159 0.87 20.54 0.99 0.92 165.49| | 24: 1.03 - 1.02 6784 133 0.85 23.21 0.99 0.93 179.65| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.90 182.46| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.88 176.57| | 27: 0.99 - 0.98 6647 131 0.82 26.23 0.99 0.87 160.31| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.95 max = 11787.85 mean = 954.98| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.31| |phase err.(test): min = 0.00 max = 89.86 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1369 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1408 0.1406 0.1504 n_refl.: 191129 remove outliers: r(all,work,free)=0.1408 0.1406 0.1504 n_refl.: 191129 overall B=-0.06 to atoms: r(all,work,free)=0.1399 0.1397 0.1499 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1368 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1368 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3709 361.020 327.989 0.380 0.994 0.195 13.296-10.522 96.04 96 1 0.2423 480.594 460.779 0.661 0.995 0.134 10.503-8.327 98.35 176 3 0.2242 502.965 494.669 0.820 0.996 0.108 8.315-6.595 100.00 359 8 0.2209 374.726 369.655 0.844 0.996 0.095 6.588-5.215 100.00 711 7 0.1985 345.205 334.109 0.846 0.996 0.083 5.214-4.128 98.38 1367 28 0.1259 504.930 498.164 0.937 0.997 0.080 4.126-3.266 94.74 2603 46 0.1175 460.271 452.717 0.997 0.999 0.000 3.266-2.585 99.86 5447 97 0.1128 310.488 306.779 0.980 1.000 0.000 2.585-2.046 97.45 10613 204 0.0965 234.245 231.576 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0906 138.638 137.279 1.001 1.008 0.000 1.619-1.281 98.00 42464 925 0.0942 74.635 73.989 0.990 1.015 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.038 38.321 0.958 1.029 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0127 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2037 0.2051 0.082 5.219 5.2 78.0 14.6 805 0.000 1_bss: 0.1803 0.1982 0.082 5.219 5.2 78.0 14.6 805 0.000 1_settarget: 0.1803 0.1982 0.082 5.219 5.2 78.0 14.6 805 0.000 1_nqh: 0.1803 0.1982 0.082 5.219 5.2 78.0 14.6 805 0.000 1_weight: 0.1803 0.1982 0.082 5.219 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1272 0.1503 0.039 1.151 5.2 78.0 14.6 805 0.157 1_adp: 0.1301 0.1576 0.039 1.151 5.3 73.0 15.0 805 0.157 1_regHadp: 0.1300 0.1570 0.039 1.151 5.3 73.0 15.0 805 0.157 1_occ: 0.1286 0.1558 0.039 1.151 5.3 73.0 15.0 805 0.157 2_bss: 0.1277 0.1549 0.039 1.151 5.4 73.2 15.2 805 0.157 2_settarget: 0.1277 0.1549 0.039 1.151 5.4 73.2 15.2 805 0.157 2_updatecdl: 0.1277 0.1549 0.039 1.171 5.4 73.2 15.2 805 0.157 2_nqh: 0.1277 0.1549 0.039 1.171 5.4 73.2 15.2 805 0.157 2_sol: 0.1273 0.1512 0.039 1.171 5.4 73.2 16.1 883 n/a 2_weight: 0.1273 0.1512 0.039 1.171 5.4 73.2 16.1 883 n/a 2_xyzrec: 0.1257 0.1538 0.040 1.146 5.4 73.2 16.1 883 n/a 2_adp: 0.1234 0.1521 0.040 1.146 5.4 68.8 16.2 883 n/a 2_regHadp: 0.1234 0.1522 0.040 1.146 5.4 68.8 16.2 883 n/a 2_occ: 0.1227 0.1520 0.040 1.146 5.4 68.8 16.2 883 n/a 3_bss: 0.1234 0.1525 0.040 1.146 5.4 68.8 16.2 883 n/a 3_settarget: 0.1234 0.1525 0.040 1.146 5.4 68.8 16.2 883 n/a 3_updatecdl: 0.1234 0.1525 0.040 1.151 5.4 68.8 16.2 883 n/a 3_nqh: 0.1234 0.1525 0.040 1.151 5.4 68.8 16.2 883 n/a 3_sol: 0.1250 0.1522 0.040 1.151 5.4 68.2 15.4 868 n/a 3_weight: 0.1250 0.1522 0.040 1.151 5.4 68.2 15.4 868 n/a 3_xyzrec: 0.1240 0.1442 0.034 1.116 5.4 68.2 15.4 868 n/a 3_adp: 0.1237 0.1401 0.034 1.116 5.5 67.6 15.2 868 n/a 3_regHadp: 0.1238 0.1401 0.034 1.116 5.5 67.6 15.2 868 n/a 3_occ: 0.1231 0.1393 0.034 1.116 5.5 67.6 15.2 868 n/a 4_bss: 0.1227 0.1386 0.034 1.116 5.5 67.6 15.2 868 n/a 4_settarget: 0.1227 0.1386 0.034 1.116 5.5 67.6 15.2 868 n/a 4_updatecdl: 0.1227 0.1386 0.034 1.121 5.5 67.6 15.2 868 n/a 4_nqh: 0.1227 0.1386 0.034 1.121 5.5 67.6 15.2 868 n/a 4_sol: 0.1208 0.1360 0.034 1.121 5.5 67.6 15.0 871 n/a 4_weight: 0.1208 0.1360 0.034 1.121 5.5 67.6 15.0 871 n/a 4_xyzrec: 0.1207 0.1369 0.035 1.145 5.5 67.6 15.0 871 n/a 4_adp: 0.1200 0.1369 0.035 1.145 5.5 67.2 15.0 871 n/a 4_regHadp: 0.1200 0.1369 0.035 1.145 5.5 67.2 15.0 871 n/a 4_occ: 0.1198 0.1367 0.035 1.145 5.5 67.2 15.0 871 n/a 5_bss: 0.1197 0.1368 0.035 1.145 5.5 67.2 14.9 871 n/a 5_settarget: 0.1197 0.1368 0.035 1.145 5.5 67.2 14.9 871 n/a 5_updatecdl: 0.1197 0.1368 0.035 1.145 5.5 67.2 14.9 871 n/a 5_nqh: 0.1197 0.1368 0.035 1.145 5.5 67.2 14.9 871 n/a 5_sol: 0.1203 0.1350 0.035 1.145 5.5 67.2 14.7 831 n/a 5_weight: 0.1203 0.1350 0.035 1.145 5.5 67.2 14.7 831 n/a 5_xyzrec: 0.1205 0.1351 0.035 1.132 5.5 67.2 14.7 831 n/a 5_adp: 0.1207 0.1355 0.035 1.132 5.5 66.7 14.6 831 n/a 5_regHadp: 0.1207 0.1356 0.035 1.132 5.5 66.7 14.6 831 n/a 5_occ: 0.1206 0.1357 0.035 1.132 5.5 66.7 14.6 831 n/a 6_bss: 0.1200 0.1352 0.035 1.132 5.5 66.6 14.6 831 n/a 6_settarget: 0.1200 0.1352 0.035 1.132 5.5 66.6 14.6 831 n/a 6_updatecdl: 0.1200 0.1352 0.035 1.133 5.5 66.6 14.6 831 n/a 6_nqh: 0.1200 0.1352 0.035 1.133 5.5 66.6 14.6 831 n/a 6_sol: 0.1194 0.1352 0.035 1.133 5.5 66.6 14.9 890 n/a 6_weight: 0.1194 0.1352 0.035 1.133 5.5 66.6 14.9 890 n/a 6_xyzrec: 0.1197 0.1361 0.037 1.131 5.5 66.6 14.9 890 n/a 6_adp: 0.1198 0.1365 0.037 1.131 5.6 65.5 14.8 890 n/a 6_regHadp: 0.1198 0.1365 0.037 1.131 5.6 65.5 14.8 890 n/a 6_occ: 0.1195 0.1370 0.037 1.131 5.6 65.5 14.8 890 n/a 7_bss: 0.1199 0.1373 0.037 1.131 5.3 65.3 14.6 890 n/a 7_settarget: 0.1199 0.1373 0.037 1.131 5.3 65.3 14.6 890 n/a 7_updatecdl: 0.1199 0.1373 0.037 1.130 5.3 65.3 14.6 890 n/a 7_nqh: 0.1199 0.1373 0.037 1.130 5.3 65.3 14.6 890 n/a 7_sol: 0.1197 0.1362 0.037 1.130 5.3 65.3 14.6 898 n/a 7_weight: 0.1197 0.1362 0.037 1.130 5.3 65.3 14.6 898 n/a 7_xyzrec: 0.1201 0.1366 0.037 1.138 5.3 65.3 14.6 898 n/a 7_adp: 0.1203 0.1369 0.037 1.138 5.4 64.4 14.6 898 n/a 7_regHadp: 0.1203 0.1369 0.037 1.138 5.4 64.4 14.6 898 n/a 7_occ: 0.1202 0.1372 0.037 1.138 5.4 64.4 14.6 898 n/a 8_bss: 0.1192 0.1360 0.037 1.138 5.5 64.5 14.6 898 n/a 8_settarget: 0.1192 0.1360 0.037 1.138 5.5 64.5 14.6 898 n/a 8_updatecdl: 0.1192 0.1360 0.037 1.138 5.5 64.5 14.6 898 n/a 8_nqh: 0.1192 0.1360 0.037 1.138 5.5 64.5 14.6 898 n/a 8_sol: 0.1192 0.1362 0.037 1.138 5.5 64.5 14.6 901 n/a 8_weight: 0.1192 0.1362 0.037 1.138 5.5 64.5 14.6 901 n/a 8_xyzrec: 0.1196 0.1367 0.037 1.113 5.5 64.5 14.6 901 n/a 8_adp: 0.1199 0.1372 0.037 1.113 5.5 63.5 14.6 901 n/a 8_regHadp: 0.1199 0.1372 0.037 1.113 5.5 63.5 14.6 901 n/a 8_occ: 0.1197 0.1375 0.037 1.113 5.5 63.5 14.6 901 n/a 9_bss: 0.1196 0.1371 0.037 1.113 5.5 63.5 14.6 901 n/a 9_settarget: 0.1196 0.1371 0.037 1.113 5.5 63.5 14.6 901 n/a 9_updatecdl: 0.1196 0.1371 0.037 1.114 5.5 63.5 14.6 901 n/a 9_nqh: 0.1196 0.1371 0.037 1.114 5.5 63.5 14.6 901 n/a 9_sol: 0.1195 0.1356 0.037 1.114 5.5 63.5 14.6 906 n/a 9_weight: 0.1195 0.1356 0.037 1.114 5.5 63.5 14.6 906 n/a 9_xyzrec: 0.1197 0.1356 0.038 1.121 5.5 63.5 14.6 906 n/a 9_adp: 0.1197 0.1359 0.038 1.121 5.5 63.0 14.6 906 n/a 9_regHadp: 0.1197 0.1359 0.038 1.121 5.5 63.0 14.6 906 n/a 9_occ: 0.1196 0.1359 0.038 1.121 5.5 63.0 14.6 906 n/a 10_bss: 0.1195 0.1359 0.038 1.121 5.5 63.0 14.6 906 n/a 10_settarget: 0.1195 0.1359 0.038 1.121 5.5 63.0 14.6 906 n/a 10_updatecdl: 0.1195 0.1359 0.038 1.122 5.5 63.0 14.6 906 n/a 10_setrh: 0.1196 0.1359 0.038 1.122 5.5 63.0 14.6 906 n/a 10_nqh: 0.1196 0.1359 0.038 1.122 5.5 63.0 14.6 906 n/a 10_sol: 0.1195 0.1363 0.038 1.122 5.5 63.0 14.6 906 n/a 10_weight: 0.1195 0.1363 0.038 1.122 5.5 63.0 14.6 906 n/a 10_xyzrec: 0.1196 0.1367 0.038 1.149 5.5 63.0 14.6 906 n/a 10_adp: 0.1196 0.1369 0.038 1.149 5.6 61.9 14.6 906 n/a 10_regHadp: 0.1196 0.1369 0.038 1.149 5.6 61.9 14.6 906 n/a 10_occ: 0.1195 0.1369 0.038 1.149 5.6 61.9 14.6 906 n/a end: 0.1194 0.1368 0.038 1.149 5.5 61.8 14.5 906 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5035770_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_5035770_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.9900 Refinement macro-cycles (run) : 11847.5700 Write final files (write_after_run_outputs) : 150.0400 Total : 12003.6000 Total CPU time: 3.35 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:37:23 PST -0800 (1736735843.02 s) Start R-work = 0.1803, R-free = 0.1982 Final R-work = 0.1194, R-free = 0.1368 =============================================================================== Job complete usr+sys time: 12311.42 seconds wall clock time: 206 minutes 15.86 seconds (12375.86 seconds total)