Starting phenix.refine on Sun Jan 12 15:15:39 2025 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7975575.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_7975575.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_7975575.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.18, 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: 2.622 distance_ideal: 2.720 ideal - model: 0.098 slack: 0.000 delta_slack: 0.098 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: 2.758 distance_ideal: 2.710 ideal - model: -0.048 slack: 0.000 delta_slack: -0.048 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 116.0 milliseconds Time building geometry restraints manager: 1.09 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: 758 1.02 - 1.25: 2522 1.25 - 1.48: 1504 1.48 - 1.72: 1127 1.72 - 1.95: 23 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL A 114 " pdb=" C VAL A 114 " ideal model delta sigma weight residual 1.524 1.756 -0.232 1.05e-02 9.07e+03 4.87e+02 bond pdb=" NE ARG A 149 " pdb=" CZ ARG A 149 " ideal model delta sigma weight residual 1.326 1.559 -0.233 1.10e-02 8.26e+03 4.47e+02 bond pdb=" C PHE B 119 " pdb=" N PRO B 120 " ideal model delta sigma weight residual 1.337 1.562 -0.225 1.11e-02 8.12e+03 4.11e+02 bond pdb=" N ILE A 191 " pdb=" CA ILE A 191 " ideal model delta sigma weight residual 1.458 1.701 -0.243 1.20e-02 6.94e+03 4.09e+02 bond pdb=" CB GLU B 137 " pdb=" HB2 GLU B 137 " ideal model delta sigma weight residual 0.970 1.355 -0.385 2.00e-02 2.50e+03 3.70e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 5883 4.35 - 8.71: 3483 8.71 - 13.06: 1220 13.06 - 17.42: 205 17.42 - 21.77: 19 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.45 133.15 -10.70 7.20e-01 1.93e+00 2.21e+02 angle pdb=" CA PHE A 82 " pdb=" CB PHE A 82 " pdb=" CG PHE A 82 " ideal model delta sigma weight residual 113.80 128.16 -14.36 1.00e+00 1.00e+00 2.06e+02 angle pdb=" CA ARG A 83 " pdb=" C ARG A 83 " pdb=" O ARG A 83 " ideal model delta sigma weight residual 120.63 135.34 -14.71 1.08e+00 8.57e-01 1.85e+02 angle pdb=" O ALA B 57 " pdb=" C ALA B 57 " pdb=" N PRO B 58 " ideal model delta sigma weight residual 121.83 132.39 -10.56 7.80e-01 1.64e+00 1.83e+02 angle pdb=" CA ASP A 170 " pdb=" CB ASP A 170 " pdb=" CG ASP A 170 " ideal model delta sigma weight residual 112.60 125.68 -13.08 1.00e+00 1.00e+00 1.71e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 1870 17.83 - 35.67: 119 35.67 - 53.50: 41 53.50 - 71.34: 16 71.34 - 89.17: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta harmonic sigma weight residual -180.00 -153.81 -26.19 0 5.00e+00 4.00e-02 2.74e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual -180.00 -154.35 -25.65 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ASP B 56 " pdb=" C ASP B 56 " pdb=" N ALA B 57 " pdb=" CA ALA B 57 " ideal model delta harmonic sigma weight residual -180.00 -155.72 -24.28 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.217: 217 0.217 - 0.433: 138 0.433 - 0.648: 87 0.648 - 0.864: 40 0.864 - 1.079: 10 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU A 25 " pdb=" CB LEU A 25 " pdb=" CD1 LEU A 25 " pdb=" CD2 LEU A 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.51 -1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" CA ASP B 84 " pdb=" N ASP B 84 " pdb=" C ASP B 84 " pdb=" CB ASP B 84 " both_signs ideal model delta sigma weight residual False 2.51 1.44 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CA THR B 91 " pdb=" N THR B 91 " pdb=" C THR B 91 " pdb=" CB THR B 91 " both_signs ideal model delta sigma weight residual False 2.53 3.55 -1.02 2.00e-01 2.50e+01 2.62e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 67 " 0.039 2.00e-02 2.50e+03 7.88e-02 1.86e+02 pdb=" CG TYR B 67 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 67 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 TYR B 67 " -0.160 2.00e-02 2.50e+03 pdb=" CE1 TYR B 67 " -0.135 2.00e-02 2.50e+03 pdb=" CE2 TYR B 67 " 0.112 2.00e-02 2.50e+03 pdb=" CZ TYR B 67 " 0.011 2.00e-02 2.50e+03 pdb=" OH TYR B 67 " 0.050 2.00e-02 2.50e+03 pdb=" HD1 TYR B 67 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 TYR B 67 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR B 67 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR B 67 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 146 " 0.043 2.00e-02 2.50e+03 5.71e-02 1.30e+02 pdb=" CG TRP B 146 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP B 146 " -0.076 2.00e-02 2.50e+03 pdb=" CD2 TRP B 146 " -0.021 2.00e-02 2.50e+03 pdb=" NE1 TRP B 146 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 146 " 0.059 2.00e-02 2.50e+03 pdb=" CE3 TRP B 146 " -0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 146 " 0.074 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 146 " 0.026 2.00e-02 2.50e+03 pdb=" CH2 TRP B 146 " -0.070 2.00e-02 2.50e+03 pdb=" HD1 TRP B 146 " -0.086 2.00e-02 2.50e+03 pdb=" HE1 TRP B 146 " 0.033 2.00e-02 2.50e+03 pdb=" HE3 TRP B 146 " 0.093 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 146 " 0.054 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 146 " -0.081 2.00e-02 2.50e+03 pdb=" HH2 TRP B 146 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 149 " 0.084 9.50e-02 1.11e+02 7.99e-02 1.27e+02 pdb=" NE ARG B 149 " -0.058 2.00e-02 2.50e+03 pdb=" CZ ARG B 149 " -0.056 2.00e-02 2.50e+03 pdb=" NH1 ARG B 149 " -0.069 2.00e-02 2.50e+03 pdb=" NH2 ARG B 149 " 0.061 2.00e-02 2.50e+03 pdb="HH11 ARG B 149 " 0.077 2.00e-02 2.50e+03 pdb="HH12 ARG B 149 " 0.059 2.00e-02 2.50e+03 pdb="HH21 ARG B 149 " 0.106 2.00e-02 2.50e+03 pdb="HH22 ARG B 149 " -0.123 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.93 - 1.67: 31 1.67 - 2.40: 3011 2.40 - 3.13: 22700 3.13 - 3.87: 32632 3.87 - 4.60: 51853 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110227 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.934 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.970 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.031 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.032 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.073 2.620 ... (remaining 110222 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_7975575_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= 0.2029 r_free= 0.2007 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.298586 | | target function (ml) not normalized (work): 805181.121965 | | target function (ml) not normalized (free): 16586.472003 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2146 0.2004 6.6678 6.32| | 2: 2.94 - 2.33 1.00 7339 128 0.1609 0.1609 5.5392 5.582| | 3: 2.33 - 2.04 0.96 6939 150 0.1622 0.1483 5.1308 5.1143| | 4: 2.04 - 1.85 1.00 7170 155 0.1744 0.1578 4.9633 4.9624| | 5: 1.85 - 1.72 0.99 7113 159 0.1926 0.1669 4.7885 4.8099| | 6: 1.72 - 1.62 0.99 7102 142 0.1972 0.1987 4.6524 4.6819| | 7: 1.62 - 1.54 0.99 7104 148 0.1997 0.1697 4.561 4.5592| | 8: 1.54 - 1.47 0.96 6798 152 0.2037 0.2488 4.4802 4.6053| | 9: 1.47 - 1.41 0.98 6938 155 0.2092 0.2469 4.4047 4.5528| | 10: 1.41 - 1.36 0.99 7022 150 0.2136 0.2369 4.3299 4.352| | 11: 1.36 - 1.32 0.99 6997 151 0.2083 0.2130 4.2371 4.2599| | 12: 1.32 - 1.28 0.98 6976 149 0.2107 0.2126 4.1844 4.2837| | 13: 1.28 - 1.25 0.98 6907 166 0.1998 0.2132 4.106 4.1416| | 14: 1.25 - 1.22 0.98 7015 113 0.2087 0.2121 4.0858 4.1937| | 15: 1.22 - 1.19 0.98 6957 137 0.2104 0.2160 4.0434 4.1006| | 16: 1.19 - 1.17 0.93 6604 132 0.2078 0.2305 3.9961 4.102| | 17: 1.17 - 1.14 0.98 6941 135 0.2122 0.2087 3.9471 4.0467| | 18: 1.14 - 1.12 0.98 6875 142 0.2182 0.2372 3.9188 3.9262| | 19: 1.12 - 1.10 0.97 6949 106 0.2280 0.2590 3.8756 4.0154| | 20: 1.10 - 1.08 0.97 6884 147 0.2310 0.2414 3.8252 3.893| | 21: 1.08 - 1.07 0.97 6852 152 0.2454 0.2657 3.7892 3.8085| | 22: 1.07 - 1.05 0.97 6838 135 0.2529 0.2469 3.7427 3.7272| | 23: 1.05 - 1.03 0.97 6829 159 0.2685 0.2700 3.725 3.8275| | 24: 1.03 - 1.02 0.96 6785 133 0.2917 0.2734 3.7102 3.7938| | 25: 1.02 - 1.01 0.93 6552 130 0.3079 0.2805 3.6751 3.7077| | 26: 1.01 - 0.99 0.96 6767 158 0.3191 0.3180 3.6293 3.6348| | 27: 0.99 - 0.98 0.94 6648 131 0.3407 0.3045 3.6408 3.5937| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 21.01 0.91 0.97 37232.80| | 2: 2.94 - 2.33 7339 128 0.85 21.34 1.09 1.02 15261.64| | 3: 2.33 - 2.04 6939 150 0.94 11.62 1.11 1.06 3689.95| | 4: 2.04 - 1.85 7170 155 0.93 12.70 1.11 1.07 2504.22| | 5: 1.85 - 1.72 7113 159 0.91 15.23 1.12 1.08 1982.45| | 6: 1.72 - 1.62 7102 142 0.90 16.49 1.12 1.07 1601.23| | 7: 1.62 - 1.54 7104 148 0.89 18.26 1.11 1.07 1420.57| | 8: 1.54 - 1.47 6798 152 0.88 19.37 1.10 1.07 1278.16| | 9: 1.47 - 1.41 6938 155 0.87 20.41 1.10 1.08 1134.60| | 10: 1.41 - 1.36 7022 150 0.86 21.33 1.09 1.07 970.24| | 11: 1.36 - 1.32 6997 151 0.86 21.13 1.08 1.04 814.29| | 12: 1.32 - 1.28 6976 149 0.86 20.76 1.08 1.04 694.40| | 13: 1.28 - 1.25 6907 166 0.87 20.14 1.07 1.04 619.15| | 14: 1.25 - 1.22 7015 113 0.87 20.34 1.07 1.05 566.76| | 15: 1.22 - 1.19 6957 137 0.86 21.36 1.07 1.04 556.52| | 16: 1.19 - 1.17 6604 132 0.87 20.87 1.07 1.03 514.45| | 17: 1.17 - 1.14 6941 135 0.85 22.04 1.08 1.01 478.42| | 18: 1.14 - 1.12 6875 142 0.85 21.97 1.08 0.98 424.01| | 19: 1.12 - 1.10 6949 106 0.84 23.13 1.07 0.98 403.36| | 20: 1.10 - 1.08 6884 147 0.84 23.29 1.07 0.97 364.27| | 21: 1.08 - 1.07 6852 152 0.83 24.30 1.06 0.98 341.09| | 22: 1.07 - 1.05 6838 135 0.82 25.51 1.05 0.98 324.98| | 23: 1.05 - 1.03 6829 159 0.80 27.17 1.06 0.98 326.08| | 24: 1.03 - 1.02 6785 133 0.78 29.17 1.05 0.99 327.76| | 25: 1.02 - 1.01 6552 130 0.78 30.00 1.04 0.95 302.95| | 26: 1.01 - 0.99 6767 158 0.76 31.08 1.03 0.93 278.82| | 27: 0.99 - 0.98 6648 131 0.77 30.40 1.04 0.93 253.36| |alpha: min = 0.93 max = 1.08 mean = 1.02| |beta: min = 253.36 max = 37232.80 mean = 2897.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.79| |phase err.(test): min = 0.00 max = 89.63 mean = 21.80| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.080 0.247 2950 Z= 5.375 Angle : 5.108 19.878 4018 Z= 3.640 Chirality : 0.386 1.079 492 Planarity : 0.035 0.131 512 Dihedral : 13.094 89.169 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.52 % Allowed : 4.15 % Favored : 95.34 % Rotamer: Outliers : 0.65 % Allowed : 3.55 % Favored : 95.81 % Cbeta Deviations : 28.93 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.37), residues: 386 helix: -1.78 (0.37), residues: 144 sheet: -1.16 (0.49), residues: 86 loop : -1.05 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.095 0.017 ARG A 97 TYR 0.170 0.035 TYR B 67 PHE 0.115 0.045 PHE A 164 TRP 0.086 0.031 TRP A 146 HIS 0.090 0.027 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2029 r_free= 0.2007 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.298586 | | target function (ml) not normalized (work): 805181.121965 | | target function (ml) not normalized (free): 16586.472003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2028 0.2029 0.2007 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2028 0.2029 0.2007 n_refl.: 191155 remove outliers: r(all,work,free)=0.2028 0.2029 0.2007 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2028 0.2029 0.2007 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1799 0.1796 0.1936 n_refl.: 191145 remove outliers: r(all,work,free)=0.1796 0.1794 0.1935 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 0.4082 402.814 294.313 0.438 0.909 0.301 13.296-10.522 100.00 100 1 0.2576 534.497 521.692 0.790 0.911 0.258 10.503-8.327 98.90 177 3 0.2434 564.205 560.232 0.973 0.911 0.240 8.318-6.595 100.00 360 8 0.2476 414.736 402.606 0.974 0.911 0.184 6.588-5.215 100.00 711 7 0.2301 381.101 364.769 0.963 0.911 0.160 5.214-4.128 98.38 1367 28 0.1523 557.435 549.589 1.077 0.911 0.090 4.126-3.266 94.74 2603 46 0.1336 508.132 498.929 1.150 0.911 0.025 3.266-2.585 99.86 5447 97 0.1442 342.774 337.683 1.122 0.911 0.020 2.585-2.046 97.45 10613 204 0.1386 258.603 254.455 1.128 0.911 0.000 2.046-1.619 99.39 21536 464 0.1610 153.054 149.717 1.146 0.910 0.000 1.619-1.281 98.00 42464 925 0.1919 82.395 80.136 1.129 0.908 0.000 1.281-0.980 96.53 101826 2055 0.2307 44.202 41.698 1.112 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0009 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1794 r_free=0.1935 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1794 r_free=0.1935 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.619920 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 578.622963 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 0.1271 0.1497 0.0226 0.038 1.2 11.0 0.0 0.3 0 11.310 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 14.97 2.26 1.118 13.111 578.623 0.018 12.94 15.58 2.64 1.204 13.276 578.623 0.017 Individual atomic B min max mean iso aniso Overall: 5.13 73.04 14.90 1.39 435 3274 Protein: 5.13 40.33 10.96 1.39 0 2902 Water: 6.40 73.04 29.08 N/A 435 370 Other: 15.84 30.39 23.12 N/A 0 2 Chain A: 5.36 60.55 12.98 N/A 0 1626 Chain B: 5.13 73.04 12.70 N/A 0 1648 Chain S: 11.17 60.40 30.42 N/A 435 0 Histogram: Values Number of atoms 5.13 - 11.92 2154 11.92 - 18.71 656 18.71 - 25.51 318 25.51 - 32.30 264 32.30 - 39.09 154 39.09 - 45.88 105 45.88 - 52.67 34 52.67 - 59.46 19 59.46 - 66.25 4 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1294 r_free=0.1558 r_work=0.1293 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1293 r_free = 0.1554 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 = 0.1279 r_free = 0.1545 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1279 r_free= 0.1545 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015563 | | target function (ls_wunit_k1) not normalized (work): 2914.996106 | | target function (ls_wunit_k1) not normalized (free): 114.895037 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1284 0.1279 0.1545 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1464 0.1461 0.1624 n_refl.: 191138 remove outliers: r(all,work,free)=0.1464 0.1461 0.1624 n_refl.: 191138 overall B=0.17 to atoms: r(all,work,free)=0.1487 0.1485 0.1633 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1276 0.1271 0.1538 n_refl.: 191138 remove outliers: r(all,work,free)=0.1276 0.1271 0.1538 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 0.3618 402.814 377.696 0.488 0.963 0.281 13.296-10.522 100.00 100 1 0.2120 534.497 530.348 0.751 0.964 0.249 10.503-8.327 98.90 177 3 0.1725 564.205 562.170 0.888 0.964 0.203 8.318-6.595 100.00 360 8 0.1710 414.736 412.340 0.910 0.964 0.165 6.588-5.215 100.00 711 7 0.1539 381.101 373.674 0.890 0.964 0.160 5.214-4.128 98.38 1367 28 0.0903 557.435 555.237 0.977 0.965 0.054 4.126-3.266 94.74 2603 46 0.0831 508.132 504.179 1.044 0.965 0.014 3.266-2.585 99.86 5447 97 0.0924 342.774 340.238 1.025 0.965 0.000 2.585-2.046 97.45 10613 204 0.0952 258.603 256.346 1.037 0.965 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.373 1.055 0.966 0.000 1.619-1.281 98.00 42464 925 0.1271 82.395 81.422 1.046 0.966 0.000 1.281-0.980 96.53 101826 2055 0.1869 44.202 42.172 1.023 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0377 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1271 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1271 r_free=0.1538 | n_water=805 | time (s): 3.050 (total time: 3.050) Filter (dist) r_work=0.1276 r_free=0.1543 | n_water=794 | time (s): 100.050 (total time: 103.100) Filter (q & B) r_work=0.1276 r_free=0.1542 | n_water=791 | time (s): 4.390 (total time: 107.490) Compute maps r_work=0.1276 r_free=0.1542 | n_water=791 | time (s): 2.490 (total time: 109.980) Filter (map) r_work=0.1301 r_free=0.1523 | n_water=654 | time (s): 4.740 (total time: 114.720) Find peaks r_work=0.1301 r_free=0.1523 | n_water=654 | time (s): 0.660 (total time: 115.380) Add new water r_work=0.1324 r_free=0.1542 | n_water=955 | time (s): 4.240 (total time: 119.620) Refine new water occ: r_work=0.1281 r_free=0.1506 adp: r_work=0.1268 r_free=0.1503 occ: r_work=0.1271 r_free=0.1499 adp: r_work=0.1264 r_free=0.1498 occ: r_work=0.1266 r_free=0.1494 adp: r_work=0.1263 r_free=0.1495 ADP+occupancy (water only), MIN, final r_work=0.1263 r_free=0.1495 r_work=0.1263 r_free=0.1495 | n_water=955 | time (s): 78.810 (total time: 198.430) Filter (q & B) r_work=0.1266 r_free=0.1498 | n_water=885 | time (s): 4.330 (total time: 202.760) Filter (dist only) r_work=0.1267 r_free=0.1497 | n_water=883 | time (s): 113.790 (total time: 316.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.679523 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 590.351414 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 0.1252 0.1514 0.0262 0.042 1.1 19.2 0.0 0.3 0 11.840 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.14 2.62 2.030 15.051 590.351 0.015 12.34 15.06 2.72 2.381 15.130 590.351 0.014 Individual atomic B min max mean iso aniso Overall: 5.41 68.21 16.18 1.19 515 3272 Protein: 5.41 40.37 10.97 1.19 0 2902 Water: 6.70 68.21 33.30 N/A 515 368 Other: 16.49 33.30 24.90 N/A 0 2 Chain A: 5.49 56.86 12.96 N/A 0 1624 Chain B: 5.41 68.21 12.78 N/A 0 1648 Chain S: 9.58 67.68 37.21 N/A 515 0 Histogram: Values Number of atoms 5.41 - 11.69 2064 11.69 - 17.97 712 17.97 - 24.25 265 24.25 - 30.53 217 30.53 - 36.81 171 36.81 - 43.09 178 43.09 - 49.37 92 49.37 - 55.65 47 55.65 - 61.93 35 61.93 - 68.21 6 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1506 r_work=0.1234 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1507 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 = 0.1506 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1506 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013451 | | target function (ls_wunit_k1) not normalized (work): 2519.379587 | | target function (ls_wunit_k1) not normalized (free): 100.313722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1506 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1440 0.1438 0.1603 n_refl.: 191138 remove outliers: r(all,work,free)=0.1440 0.1438 0.1603 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1438 0.1435 0.1601 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1511 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1234 0.1511 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 0.3259 402.814 380.151 0.492 0.962 0.268 13.296-10.522 100.00 100 1 0.1877 534.497 526.065 0.763 0.963 0.218 10.503-8.327 98.90 177 3 0.1395 564.205 567.120 0.921 0.963 0.180 8.318-6.595 100.00 360 8 0.1557 414.736 414.368 0.938 0.962 0.170 6.588-5.215 100.00 711 7 0.1358 381.101 376.676 0.915 0.963 0.160 5.214-4.128 98.38 1367 28 0.0829 557.435 556.108 0.996 0.963 0.090 4.126-3.266 94.74 2603 46 0.0766 508.132 505.430 1.060 0.963 0.009 3.266-2.585 99.86 5447 97 0.0860 342.774 341.482 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0898 258.603 256.780 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.631 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.356 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.222 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0494 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1511 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1511 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1511 | n_water=883 | time (s): 3.390 (total time: 3.390) Filter (dist) r_work=0.1235 r_free=0.1514 | n_water=877 | time (s): 121.580 (total time: 124.970) Filter (q & B) r_work=0.1235 r_free=0.1514 | n_water=875 | time (s): 5.570 (total time: 130.540) Compute maps r_work=0.1235 r_free=0.1514 | n_water=875 | time (s): 2.230 (total time: 132.770) Filter (map) r_work=0.1273 r_free=0.1525 | n_water=689 | time (s): 5.100 (total time: 137.870) Find peaks r_work=0.1273 r_free=0.1525 | n_water=689 | time (s): 0.750 (total time: 138.620) Add new water r_work=0.1296 r_free=0.1552 | n_water=1000 | time (s): 4.810 (total time: 143.430) Refine new water occ: r_work=0.1252 r_free=0.1512 adp: r_work=0.1252 r_free=0.1514 occ: r_work=0.1248 r_free=0.1509 adp: r_work=0.1248 r_free=0.1511 occ: r_work=0.1245 r_free=0.1507 adp: r_work=0.1245 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1245 r_free=0.1509 r_work=0.1245 r_free=0.1509 | n_water=1000 | time (s): 230.630 (total time: 374.060) Filter (q & B) r_work=0.1249 r_free=0.1508 | n_water=868 | time (s): 6.050 (total time: 380.110) Filter (dist only) r_work=0.1250 r_free=0.1509 | n_water=867 | time (s): 122.570 (total time: 502.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.730248 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.600363 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 0.1433 0.0193 0.035 1.1 7.5 0.0 0.0 0 0.865 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.40 14.33 1.93 1.924 14.527 16.600 3.939 12.34 13.94 1.60 2.217 14.431 16.600 3.896 Individual atomic B min max mean iso aniso Overall: 5.52 67.77 15.18 1.06 500 3271 Protein: 5.52 36.62 10.73 1.06 0 2902 Water: 6.70 67.77 30.05 N/A 500 367 Other: 14.16 28.91 21.53 N/A 0 2 Chain A: 5.52 55.92 12.74 N/A 0 1624 Chain B: 5.55 67.77 12.50 N/A 0 1647 Chain S: 13.30 61.99 31.93 N/A 500 0 Histogram: Values Number of atoms 5.52 - 11.74 2133 11.74 - 17.97 690 17.97 - 24.19 291 24.19 - 30.42 238 30.42 - 36.65 177 36.65 - 42.87 145 42.87 - 49.10 64 49.10 - 55.32 22 55.32 - 61.55 9 61.55 - 67.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1394 r_work=0.1234 r_free=0.1395 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1395 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1229 r_free = 0.1384 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890371 | | target function (ml) not normalized (work): 728654.874291 | | target function (ml) not normalized (free): 15217.839999 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1229 0.1383 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1442 0.1442 0.1468 n_refl.: 191138 remove outliers: r(all,work,free)=0.1442 0.1442 0.1468 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1437 0.1465 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1380 n_refl.: 191138 remove outliers: r(all,work,free)=0.1227 0.1224 0.1380 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3830 398.008 362.533 0.425 0.946 0.253 13.296-10.522 98.02 98 1 0.2402 528.900 510.318 0.717 0.947 0.224 10.503-8.327 97.80 175 3 0.1946 554.286 557.800 0.884 0.947 0.179 8.318-6.595 100.00 360 8 0.2101 414.736 409.847 0.899 0.947 0.140 6.588-5.215 100.00 711 7 0.1825 381.101 370.942 0.888 0.947 0.130 5.214-4.128 98.38 1367 28 0.1184 557.435 551.977 0.972 0.947 0.090 4.126-3.266 94.74 2603 46 0.1108 508.132 500.959 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1087 342.774 339.295 1.020 0.946 0.000 2.585-2.046 97.45 10613 204 0.0959 258.603 255.800 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0971 153.054 151.403 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1050 82.395 81.488 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1688 44.202 42.313 1.037 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0948 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1381 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1381 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1381 | n_water=867 | time (s): 2.300 (total time: 2.300) Filter (dist) r_work=0.1224 r_free=0.1381 | n_water=866 | time (s): 119.150 (total time: 121.450) Filter (q & B) r_work=0.1225 r_free=0.1381 | n_water=857 | time (s): 4.910 (total time: 126.360) Compute maps r_work=0.1225 r_free=0.1381 | n_water=857 | time (s): 2.250 (total time: 128.610) Filter (map) r_work=0.1247 r_free=0.1389 | n_water=720 | time (s): 4.880 (total time: 133.490) Find peaks r_work=0.1247 r_free=0.1389 | n_water=720 | time (s): 0.620 (total time: 134.110) Add new water r_work=0.1263 r_free=0.1407 | n_water=968 | time (s): 4.680 (total time: 138.790) Refine new water occ: r_work=0.1215 r_free=0.1371 adp: r_work=0.1207 r_free=0.1367 occ: r_work=0.1205 r_free=0.1366 adp: r_work=0.1205 r_free=0.1365 occ: r_work=0.1202 r_free=0.1364 adp: r_work=0.1202 r_free=0.1364 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1364 r_work=0.1202 r_free=0.1364 | n_water=968 | time (s): 256.810 (total time: 395.600) Filter (q & B) r_work=0.1206 r_free=0.1372 | n_water=865 | time (s): 4.170 (total time: 399.770) Filter (dist only) r_work=0.1207 r_free=0.1371 | n_water=864 | time (s): 109.220 (total time: 508.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.553229 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.257035 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 0.1206 0.1370 0.0163 0.035 1.1 6.0 0.0 0.0 0 0.777 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.70 1.63 1.828 14.117 16.257 3.874 11.98 13.66 1.67 1.925 14.085 16.257 3.864 Individual atomic B min max mean iso aniso Overall: 5.50 67.29 14.84 1.01 497 3271 Protein: 5.50 33.47 10.66 1.01 0 2902 Water: 5.90 67.29 28.88 N/A 497 367 Other: 13.97 27.85 20.91 N/A 0 2 Chain A: 5.55 54.83 12.61 N/A 0 1624 Chain B: 5.50 67.29 12.42 N/A 0 1647 Chain S: 5.90 62.08 30.18 N/A 497 0 Histogram: Values Number of atoms 5.50 - 11.68 2110 11.68 - 17.86 737 17.86 - 24.04 308 24.04 - 30.22 252 30.22 - 36.39 148 36.39 - 42.57 122 42.57 - 48.75 60 48.75 - 54.93 23 54.93 - 61.11 6 61.11 - 67.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1366 r_work=0.1199 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1366 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1366 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1366 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862331 | | target function (ml) not normalized (work): 723383.637613 | | target function (ml) not normalized (free): 15129.456634 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1366 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1422 0.1422 0.1472 n_refl.: 191133 remove outliers: r(all,work,free)=0.1422 0.1422 0.1472 n_refl.: 191133 overall B=-0.03 to atoms: r(all,work,free)=0.1415 0.1414 0.1468 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1363 n_refl.: 191133 remove outliers: r(all,work,free)=0.1198 0.1194 0.1363 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3849 352.023 320.800 0.404 0.946 0.239 13.296-10.522 96.04 96 1 0.2321 480.405 452.873 0.703 0.947 0.191 10.503-8.327 97.80 175 3 0.2119 501.880 495.527 0.861 0.948 0.170 8.318-6.595 100.00 360 8 0.2192 375.525 369.679 0.892 0.947 0.119 6.588-5.215 100.00 711 7 0.1909 345.069 335.500 0.883 0.948 0.089 5.214-4.128 98.38 1367 28 0.1211 504.732 499.521 0.973 0.948 0.070 4.126-3.266 94.74 2603 46 0.1121 460.090 453.392 1.035 0.948 0.005 3.266-2.585 99.86 5447 97 0.1083 310.366 307.202 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0928 234.153 231.786 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0911 138.583 137.307 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0985 74.605 73.887 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1661 40.022 38.359 1.037 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1182 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1363 | n_water=864 | time (s): 2.280 (total time: 2.280) Filter (dist) r_work=0.1194 r_free=0.1365 | n_water=863 | time (s): 122.960 (total time: 125.240) Filter (q & B) r_work=0.1195 r_free=0.1365 | n_water=852 | time (s): 4.400 (total time: 129.640) Compute maps r_work=0.1195 r_free=0.1365 | n_water=852 | time (s): 2.190 (total time: 131.830) Filter (map) r_work=0.1217 r_free=0.1364 | n_water=732 | time (s): 4.410 (total time: 136.240) Find peaks r_work=0.1217 r_free=0.1364 | n_water=732 | time (s): 0.560 (total time: 136.800) Add new water r_work=0.1229 r_free=0.1378 | n_water=973 | time (s): 3.960 (total time: 140.760) Refine new water occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1191 r_free=0.1339 occ: r_work=0.1188 r_free=0.1336 adp: r_work=0.1188 r_free=0.1337 occ: r_work=0.1186 r_free=0.1336 adp: r_work=0.1186 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1336 r_work=0.1186 r_free=0.1336 | n_water=973 | time (s): 220.060 (total time: 360.820) Filter (q & B) r_work=0.1190 r_free=0.1345 | n_water=894 | time (s): 4.460 (total time: 365.280) Filter (dist only) r_work=0.1190 r_free=0.1344 | n_water=893 | time (s): 112.050 (total time: 477.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.575158 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.138224 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1349 0.0157 0.036 1.1 6.6 0.0 0.3 0 0.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.49 1.57 1.793 14.100 15.138 3.762 11.98 13.54 1.57 1.834 14.084 15.138 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 67.05 14.91 0.97 526 3271 Protein: 5.58 32.60 10.61 0.97 0 2902 Water: 5.96 67.05 28.89 N/A 526 367 Other: 13.77 27.10 20.43 N/A 0 2 Chain A: 5.61 54.32 12.54 N/A 0 1624 Chain B: 5.58 67.05 12.35 N/A 0 1647 Chain S: 5.96 62.09 30.27 N/A 526 0 Histogram: Values Number of atoms 5.58 - 11.73 2144 11.73 - 17.88 717 17.88 - 24.02 308 24.02 - 30.17 245 30.17 - 36.32 164 36.32 - 42.46 126 42.46 - 48.61 67 48.61 - 54.76 20 54.76 - 60.90 4 60.90 - 67.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1355 r_work=0.1198 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1353 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759331 | | target function (ml) not normalized (work): 704081.342626 | | target function (ml) not normalized (free): 14739.162533 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1353 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1414 0.1413 0.1479 n_refl.: 191130 remove outliers: r(all,work,free)=0.1414 0.1413 0.1479 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1407 0.1406 0.1474 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1352 n_refl.: 191130 remove outliers: r(all,work,free)=0.1197 0.1194 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 0.3748 352.746 310.456 0.384 0.949 0.229 13.296-10.522 96.04 96 1 0.2412 480.405 461.704 0.706 0.951 0.183 10.503-8.327 97.80 175 3 0.2123 501.880 496.320 0.855 0.951 0.163 8.318-6.595 100.00 360 8 0.2202 375.525 370.616 0.888 0.951 0.109 6.588-5.215 100.00 711 7 0.1880 345.069 335.374 0.881 0.951 0.080 5.214-4.128 98.38 1367 28 0.1205 504.732 499.363 0.972 0.951 0.070 4.126-3.266 94.74 2603 46 0.1125 460.090 453.282 1.033 0.951 0.009 3.266-2.585 99.86 5447 97 0.1093 310.366 307.175 1.018 0.950 0.000 2.585-2.046 97.45 10613 204 0.0941 234.153 231.727 1.031 0.950 0.000 2.046-1.619 99.39 21536 464 0.0911 138.583 137.301 1.054 0.949 0.000 1.619-1.281 98.00 42464 925 0.0977 74.605 73.888 1.052 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.022 38.347 1.040 0.943 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1266 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1352 | n_water=893 | time (s): 2.810 (total time: 2.810) Filter (dist) r_work=0.1195 r_free=0.1354 | n_water=890 | time (s): 121.940 (total time: 124.750) Filter (q & B) r_work=0.1195 r_free=0.1354 | n_water=877 | time (s): 4.490 (total time: 129.240) Compute maps r_work=0.1195 r_free=0.1354 | n_water=877 | time (s): 1.910 (total time: 131.150) Filter (map) r_work=0.1216 r_free=0.1355 | n_water=760 | time (s): 4.790 (total time: 135.940) Find peaks r_work=0.1216 r_free=0.1355 | n_water=760 | time (s): 0.660 (total time: 136.600) Add new water r_work=0.1226 r_free=0.1371 | n_water=983 | time (s): 4.790 (total time: 141.390) Refine new water occ: r_work=0.1191 r_free=0.1342 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1189 r_free=0.1340 adp: r_work=0.1189 r_free=0.1340 occ: r_work=0.1187 r_free=0.1338 adp: r_work=0.1187 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1339 r_work=0.1187 r_free=0.1339 | n_water=983 | time (s): 358.430 (total time: 499.820) Filter (q & B) r_work=0.1192 r_free=0.1347 | n_water=897 | time (s): 5.230 (total time: 505.050) Filter (dist only) r_work=0.1192 r_free=0.1347 | n_water=896 | time (s): 113.700 (total time: 618.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.549981 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.386500 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 0.1353 0.0157 0.037 1.1 5.6 0.0 0.3 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.53 1.57 1.768 14.031 14.386 3.760 12.02 13.58 1.57 1.939 13.978 14.386 3.759 Individual atomic B min max mean iso aniso Overall: 5.59 65.81 14.79 0.90 529 3271 Protein: 5.59 29.33 10.48 0.90 0 2902 Water: 6.03 65.81 28.75 N/A 529 367 Other: 13.87 23.86 18.87 N/A 0 2 Chain A: 5.62 52.92 12.37 N/A 0 1624 Chain B: 5.59 65.81 12.20 N/A 0 1647 Chain S: 6.03 62.31 30.27 N/A 529 0 Histogram: Values Number of atoms 5.59 - 11.61 2114 11.61 - 17.63 779 17.63 - 23.65 284 23.65 - 29.68 221 29.68 - 35.70 174 35.70 - 41.72 126 41.72 - 47.74 68 47.74 - 53.76 26 53.76 - 59.78 5 59.78 - 65.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1359 r_work=0.1202 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1359 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1360 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758310 | | target function (ml) not normalized (work): 703886.333680 | | target function (ml) not normalized (free): 14736.068730 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1487 n_refl.: 191129 remove outliers: r(all,work,free)=0.1404 0.1403 0.1487 n_refl.: 191129 overall B=-0.23 to atoms: r(all,work,free)=0.1368 0.1366 0.1463 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1358 n_refl.: 191129 remove outliers: r(all,work,free)=0.1202 0.1199 0.1358 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 0.3877 352.746 313.932 0.386 0.951 0.209 13.296-10.522 96.04 96 1 0.2383 480.405 463.469 0.720 0.953 0.170 10.503-8.327 97.80 175 3 0.2158 501.880 495.826 0.875 0.953 0.150 8.318-6.595 100.00 360 8 0.2190 375.525 371.135 0.904 0.953 0.095 6.588-5.215 100.00 711 7 0.1919 345.069 335.456 0.902 0.953 0.085 5.214-4.128 98.38 1367 28 0.1215 504.732 499.441 0.993 0.954 0.049 4.126-3.266 94.74 2603 46 0.1150 460.090 453.040 1.056 0.954 0.009 3.266-2.585 99.86 5447 97 0.1111 310.366 307.174 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0953 234.153 231.653 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0913 138.583 137.302 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0972 74.605 73.896 1.052 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.022 38.348 1.024 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0504 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1358 | n_water=896 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1199 r_free=0.1358 | n_water=896 | time (s): 117.690 (total time: 120.180) Filter (q & B) r_work=0.1200 r_free=0.1359 | n_water=887 | time (s): 5.160 (total time: 125.340) Compute maps r_work=0.1200 r_free=0.1359 | n_water=887 | time (s): 1.610 (total time: 126.950) Filter (map) r_work=0.1223 r_free=0.1362 | n_water=772 | time (s): 4.280 (total time: 131.230) Find peaks r_work=0.1223 r_free=0.1362 | n_water=772 | time (s): 0.550 (total time: 131.780) Add new water r_work=0.1231 r_free=0.1377 | n_water=978 | time (s): 4.540 (total time: 136.320) Refine new water occ: r_work=0.1198 r_free=0.1346 adp: r_work=0.1198 r_free=0.1346 occ: r_work=0.1196 r_free=0.1345 adp: r_work=0.1196 r_free=0.1346 occ: r_work=0.1194 r_free=0.1345 adp: r_work=0.1194 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1345 r_work=0.1194 r_free=0.1345 | n_water=978 | time (s): 266.000 (total time: 402.320) Filter (q & B) r_work=0.1198 r_free=0.1347 | n_water=904 | time (s): 4.330 (total time: 406.650) Filter (dist only) r_work=0.1198 r_free=0.1347 | n_water=903 | time (s): 114.200 (total time: 520.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.592975 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.905530 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1352 0.0150 0.038 1.1 6.5 0.0 0.3 0 0.796 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.52 1.50 1.715 13.684 14.906 3.759 12.00 13.54 1.54 1.746 13.669 14.906 3.755 Individual atomic B min max mean iso aniso Overall: 5.41 64.58 14.54 0.89 536 3271 Protein: 5.41 28.66 10.25 0.89 0 2902 Water: 5.82 64.58 28.31 N/A 536 367 Other: 13.69 22.42 18.06 N/A 0 2 Chain A: 5.46 52.29 12.10 N/A 0 1624 Chain B: 5.41 64.58 11.95 N/A 0 1647 Chain S: 5.82 62.27 29.88 N/A 536 0 Histogram: Values Number of atoms 5.41 - 11.33 2100 11.33 - 17.25 787 17.25 - 23.17 286 23.17 - 29.08 220 29.08 - 35.00 179 35.00 - 40.92 123 40.92 - 46.83 75 46.83 - 52.75 30 52.75 - 58.67 4 58.67 - 64.58 3 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1354 r_work=0.1200 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1354 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1355 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.754776 | | target function (ml) not normalized (work): 703224.507758 | | target function (ml) not normalized (free): 14727.482267 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1372 0.1370 0.1467 n_refl.: 191129 remove outliers: r(all,work,free)=0.1372 0.1370 0.1467 n_refl.: 191129 overall B=0.06 to atoms: r(all,work,free)=0.1380 0.1378 0.1472 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191129 remove outliers: r(all,work,free)=0.1192 0.1189 0.1345 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3844 348.078 312.700 0.369 0.975 0.195 13.296-10.522 96.04 96 1 0.2380 480.405 461.877 0.702 0.977 0.151 10.503-8.327 97.80 175 3 0.2194 501.880 494.482 0.858 0.978 0.130 8.318-6.595 100.00 360 8 0.2210 375.525 370.457 0.887 0.978 0.078 6.588-5.215 100.00 711 7 0.1941 345.069 334.893 0.885 0.978 0.065 5.214-4.128 98.38 1367 28 0.1246 504.732 498.747 0.979 0.979 0.053 4.126-3.266 94.74 2603 46 0.1154 460.090 452.414 1.040 0.980 0.005 3.266-2.585 99.86 5447 97 0.1114 310.366 306.823 1.023 0.981 0.000 2.585-2.046 97.45 10613 204 0.0953 234.153 231.549 1.030 0.982 0.000 2.046-1.619 99.39 21536 464 0.0905 138.583 137.222 1.047 0.985 0.000 1.619-1.281 98.00 42464 925 0.0945 74.605 73.938 1.035 0.989 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.022 38.324 1.000 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0582 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1345 | n_water=903 | time (s): 3.150 (total time: 3.150) Filter (dist) r_work=0.1189 r_free=0.1345 | n_water=901 | time (s): 119.950 (total time: 123.100) Filter (q & B) r_work=0.1189 r_free=0.1346 | n_water=894 | time (s): 4.380 (total time: 127.480) Compute maps r_work=0.1189 r_free=0.1346 | n_water=894 | time (s): 1.910 (total time: 129.390) Filter (map) r_work=0.1214 r_free=0.1353 | n_water=775 | time (s): 4.780 (total time: 134.170) Find peaks r_work=0.1214 r_free=0.1353 | n_water=775 | time (s): 0.690 (total time: 134.860) Add new water r_work=0.1221 r_free=0.1369 | n_water=985 | time (s): 4.460 (total time: 139.320) Refine new water occ: r_work=0.1188 r_free=0.1336 adp: r_work=0.1188 r_free=0.1336 occ: r_work=0.1186 r_free=0.1334 adp: r_work=0.1186 r_free=0.1334 occ: r_work=0.1184 r_free=0.1333 adp: r_work=0.1184 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1333 r_work=0.1184 r_free=0.1333 | n_water=985 | time (s): 240.470 (total time: 379.790) Filter (q & B) r_work=0.1189 r_free=0.1338 | n_water=905 | time (s): 4.560 (total time: 384.350) Filter (dist only) r_work=0.1189 r_free=0.1338 | n_water=904 | time (s): 112.810 (total time: 497.160) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.576176 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.736658 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1345 0.0153 0.038 1.1 5.6 0.0 0.3 0 0.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.45 1.53 1.680 13.708 14.737 3.754 11.93 13.49 1.57 1.688 13.702 14.737 3.752 Individual atomic B min max mean iso aniso Overall: 5.47 64.08 14.59 0.88 537 3271 Protein: 5.47 28.44 10.32 0.88 0 2902 Water: 5.91 64.08 28.28 N/A 537 367 Other: 13.76 22.30 18.03 N/A 0 2 Chain A: 5.57 52.15 12.14 N/A 0 1624 Chain B: 5.47 64.08 12.00 N/A 0 1647 Chain S: 5.91 62.39 29.96 N/A 537 0 Histogram: Values Number of atoms 5.47 - 11.33 2072 11.33 - 17.19 815 17.19 - 23.05 280 23.05 - 28.92 229 28.92 - 34.78 174 34.78 - 40.64 117 40.64 - 46.50 75 46.50 - 52.36 39 52.36 - 58.22 3 58.22 - 64.08 4 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1349 r_work=0.1193 r_free=0.1349 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1349 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1346 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751604 | | target function (ml) not normalized (work): 702626.575617 | | target function (ml) not normalized (free): 14715.856674 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1346 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1389 0.1387 0.1477 n_refl.: 191128 remove outliers: r(all,work,free)=0.1389 0.1387 0.1477 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1391 0.1389 0.1478 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1345 n_refl.: 191128 remove outliers: r(all,work,free)=0.1193 0.1190 0.1345 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3869 348.078 308.250 0.358 0.994 0.201 13.296-10.522 96.04 96 1 0.2392 480.405 462.605 0.685 0.996 0.149 10.503-8.327 97.80 175 3 0.2228 501.880 493.367 0.838 0.997 0.123 8.318-6.595 100.00 360 8 0.2186 375.525 370.449 0.869 0.997 0.088 6.588-5.215 100.00 711 7 0.1952 345.069 335.033 0.867 0.997 0.070 5.214-4.128 98.38 1367 28 0.1249 504.732 498.632 0.958 0.998 0.039 4.126-3.266 94.74 2603 46 0.1171 460.090 452.458 1.020 0.999 0.005 3.266-2.585 99.86 5447 97 0.1119 310.366 306.783 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0956 234.153 231.519 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0905 138.583 137.234 1.028 1.006 0.000 1.619-1.281 98.00 42464 925 0.0940 74.605 73.954 1.018 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.022 38.315 0.987 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0189 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1345 | n_water=904 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1190 r_free=0.1345 | n_water=904 | time (s): 113.820 (total time: 116.500) Filter (q & B) r_work=0.1190 r_free=0.1344 | n_water=895 | time (s): 5.180 (total time: 121.680) Compute maps r_work=0.1190 r_free=0.1344 | n_water=895 | time (s): 2.500 (total time: 124.180) Filter (map) r_work=0.1213 r_free=0.1359 | n_water=785 | time (s): 4.100 (total time: 128.280) Find peaks r_work=0.1213 r_free=0.1359 | n_water=785 | time (s): 0.710 (total time: 128.990) Add new water r_work=0.1219 r_free=0.1374 | n_water=986 | time (s): 4.040 (total time: 133.030) Refine new water occ: r_work=0.1187 r_free=0.1335 adp: r_work=0.1187 r_free=0.1336 occ: r_work=0.1185 r_free=0.1335 adp: r_work=0.1185 r_free=0.1335 occ: r_work=0.1184 r_free=0.1334 adp: r_work=0.1184 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1334 r_work=0.1184 r_free=0.1334 | n_water=986 | time (s): 270.900 (total time: 403.930) Filter (q & B) r_work=0.1188 r_free=0.1343 | n_water=913 | time (s): 5.160 (total time: 409.090) Filter (dist only) r_work=0.1188 r_free=0.1343 | n_water=910 | time (s): 112.420 (total time: 521.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.565656 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.795400 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1350 0.0157 0.039 1.1 5.1 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.50 1.57 1.683 13.718 14.795 3.753 11.92 13.53 1.60 1.693 13.713 14.795 3.751 Individual atomic B min max mean iso aniso Overall: 5.55 63.19 14.58 0.87 543 3271 Protein: 5.55 28.20 10.34 0.87 0 2902 Water: 5.95 63.19 28.09 N/A 543 367 Other: 13.82 22.22 18.02 N/A 0 2 Chain A: 5.61 51.85 12.13 N/A 0 1624 Chain B: 5.55 63.19 11.99 N/A 0 1647 Chain S: 5.95 62.50 29.76 N/A 543 0 Histogram: Values Number of atoms 5.55 - 11.31 2061 11.31 - 17.08 828 17.08 - 22.84 277 22.84 - 28.61 222 28.61 - 34.37 186 34.37 - 40.14 116 40.14 - 45.90 79 45.90 - 51.67 36 51.67 - 57.43 4 57.43 - 63.19 5 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1353 r_work=0.1192 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1353 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1349 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.750952 | | target function (ml) not normalized (work): 702504.541474 | | target function (ml) not normalized (free): 14719.093837 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1350 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1485 n_refl.: 191128 remove outliers: r(all,work,free)=0.1401 0.1399 0.1485 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1400 0.1399 0.1485 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191128 remove outliers: r(all,work,free)=0.1193 0.1190 0.1348 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3839 348.078 308.058 0.361 0.974 0.194 13.296-10.522 96.04 96 1 0.2410 480.405 462.597 0.696 0.976 0.146 10.503-8.327 97.80 175 3 0.2226 501.880 493.647 0.854 0.977 0.113 8.318-6.595 100.00 360 8 0.2192 375.525 370.078 0.889 0.976 0.098 6.588-5.215 100.00 711 7 0.1958 345.069 334.883 0.886 0.977 0.090 5.214-4.128 98.38 1367 28 0.1254 504.732 498.639 0.978 0.978 0.049 4.126-3.266 94.74 2603 46 0.1178 460.090 452.420 1.041 0.979 0.005 3.266-2.585 99.86 5447 97 0.1127 310.366 306.739 1.024 0.980 0.000 2.585-2.046 97.45 10613 204 0.0958 234.153 231.522 1.032 0.983 0.000 2.046-1.619 99.39 21536 464 0.0904 138.583 137.233 1.049 0.986 0.000 1.619-1.281 98.00 42464 925 0.0937 74.605 73.956 1.041 0.992 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.022 38.306 1.010 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0095 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1190 r_free=0.1348 After: r_work=0.1191 r_free=0.1348 ================================== NQH flips ================================== r_work=0.1191 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1348 | n_water=910 | time (s): 2.890 (total time: 2.890) Filter (dist) r_work=0.1191 r_free=0.1348 | n_water=910 | time (s): 120.710 (total time: 123.600) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=900 | time (s): 5.370 (total time: 128.970) Compute maps r_work=0.1192 r_free=0.1349 | n_water=900 | time (s): 2.230 (total time: 131.200) Filter (map) r_work=0.1215 r_free=0.1354 | n_water=782 | time (s): 5.010 (total time: 136.210) Find peaks r_work=0.1215 r_free=0.1354 | n_water=782 | time (s): 0.660 (total time: 136.870) Add new water r_work=0.1222 r_free=0.1368 | n_water=983 | time (s): 4.900 (total time: 141.770) Refine new water occ: r_work=0.1190 r_free=0.1336 adp: r_work=0.1190 r_free=0.1336 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1335 occ: r_work=0.1186 r_free=0.1336 adp: r_work=0.1186 r_free=0.1336 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1336 r_work=0.1186 r_free=0.1336 | n_water=983 | time (s): 243.790 (total time: 385.560) Filter (q & B) r_work=0.1191 r_free=0.1343 | n_water=906 | time (s): 4.940 (total time: 390.500) Filter (dist only) r_work=0.1191 r_free=0.1343 | n_water=904 | time (s): 114.550 (total time: 505.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.537796 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.377919 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1348 0.0154 0.039 1.2 6.6 0.0 0.3 0 0.769 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.48 1.54 1.681 13.695 14.378 3.753 11.95 13.50 1.55 1.674 13.698 14.378 3.753 Individual atomic B min max mean iso aniso Overall: 5.58 63.02 14.55 0.87 537 3271 Protein: 5.58 28.18 10.36 0.87 0 2902 Water: 6.03 63.02 28.00 N/A 537 367 Other: 13.85 22.26 18.06 N/A 0 2 Chain A: 5.65 51.79 12.13 N/A 0 1624 Chain B: 5.58 63.02 12.00 N/A 0 1647 Chain S: 6.03 62.51 29.71 N/A 537 0 Histogram: Values Number of atoms 5.58 - 11.32 2058 11.32 - 17.07 835 17.07 - 22.81 272 22.81 - 28.55 224 28.55 - 34.30 184 34.30 - 40.04 108 40.04 - 45.79 81 45.79 - 51.53 37 51.53 - 57.27 4 57.27 - 63.02 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1350 r_work=0.1195 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1350 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1351 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752767 | | target function (ml) not normalized (work): 702844.503329 | | target function (ml) not normalized (free): 14719.864414 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1370 0.1474 5.6931 5.7649| | 2: 2.94 - 2.33 1.00 7339 128 0.1077 0.1296 5.0783 5.161| | 3: 2.33 - 2.04 0.96 6939 150 0.0903 0.1180 4.6519 4.7354| | 4: 2.04 - 1.85 1.00 7170 155 0.0898 0.1040 4.3905 4.5545| | 5: 1.85 - 1.72 0.99 7113 159 0.0932 0.0999 4.1525 4.2509| | 6: 1.72 - 1.62 0.99 7102 142 0.0894 0.1109 3.9473 4.0858| | 7: 1.62 - 1.54 0.99 7104 148 0.0887 0.0968 3.7963 3.9274| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1307 3.6976 3.898| | 9: 1.47 - 1.41 0.98 6938 155 0.0921 0.1135 3.6187 3.7545| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1197 3.5534 3.6746| | 11: 1.36 - 1.32 0.99 6997 151 0.0987 0.1132 3.4813 3.5895| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1118 3.4564 3.5786| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1244 3.4337 3.5643| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1576 3.4295 3.671| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1236 3.4455 3.482| | 16: 1.19 - 1.17 0.93 6604 132 0.1246 0.1550 3.4615 3.6589| | 17: 1.17 - 1.14 0.98 6940 135 0.1297 0.1216 3.4307 3.4375| | 18: 1.14 - 1.12 0.98 6875 142 0.1383 0.1704 3.437 3.5306| | 19: 1.12 - 1.10 0.97 6948 106 0.1469 0.1751 3.4185 3.5951| | 20: 1.10 - 1.08 0.97 6884 147 0.1581 0.1578 3.4087 3.4294| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2134 3.4176 3.5053| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1951 3.4124 3.4174| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2018 3.4328 3.4883| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2256 3.435 3.5108| | 25: 1.02 - 1.01 0.93 6552 130 0.2613 0.2512 3.4493 3.5225| | 26: 1.01 - 0.99 0.96 6767 158 0.2758 0.2841 3.4158 3.4217| | 27: 0.99 - 0.98 0.94 6647 131 0.3043 0.2808 3.4684 3.3964| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.64 1.00 0.95 11114.01| | 2: 2.94 - 2.33 7339 128 0.93 12.68 0.99 0.95 5074.11| | 3: 2.33 - 2.04 6939 150 0.96 7.57 1.01 0.95 1675.68| | 4: 2.04 - 1.85 7170 155 0.96 7.64 1.00 0.95 1001.87| | 5: 1.85 - 1.72 7113 159 0.96 8.14 1.00 0.96 641.50| | 6: 1.72 - 1.62 7102 142 0.96 8.10 1.00 0.96 448.70| | 7: 1.62 - 1.54 7104 148 0.96 8.14 1.01 0.97 337.69| | 8: 1.54 - 1.47 6798 152 0.96 8.26 1.01 0.97 279.24| | 9: 1.47 - 1.41 6938 155 0.96 8.47 1.00 0.98 231.24| | 10: 1.41 - 1.36 7022 150 0.96 8.93 1.00 0.97 203.03| | 11: 1.36 - 1.32 6997 151 0.96 8.93 0.99 0.96 174.91| | 12: 1.32 - 1.28 6975 149 0.96 8.98 0.98 0.95 160.16| | 13: 1.28 - 1.25 6907 166 0.96 9.50 1.01 0.96 157.26| | 14: 1.25 - 1.22 7015 112 0.95 10.65 1.01 0.96 162.01| | 15: 1.22 - 1.19 6956 137 0.95 11.17 1.01 0.98 165.36| | 16: 1.19 - 1.17 6604 132 0.95 11.38 1.01 0.96 159.16| | 17: 1.17 - 1.14 6940 135 0.94 12.19 1.01 0.96 152.79| | 18: 1.14 - 1.12 6875 142 0.94 12.69 1.01 0.95 146.71| | 19: 1.12 - 1.10 6948 106 0.93 14.10 1.00 0.95 150.26| | 20: 1.10 - 1.08 6884 147 0.92 15.20 1.00 0.94 149.80| | 21: 1.08 - 1.07 6852 152 0.91 16.65 1.00 0.93 153.40| | 22: 1.07 - 1.05 6836 135 0.89 18.36 0.99 0.93 155.53| | 23: 1.05 - 1.03 6827 159 0.87 20.56 0.99 0.92 165.38| | 24: 1.03 - 1.02 6784 133 0.85 23.20 0.99 0.93 179.40| | 25: 1.02 - 1.01 6552 130 0.83 25.15 0.98 0.90 181.95| | 26: 1.01 - 0.99 6767 158 0.81 26.62 0.98 0.89 176.52| | 27: 0.99 - 0.98 6647 131 0.82 26.33 0.99 0.87 161.41| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.71 max = 11114.01 mean = 919.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.93 mean = 13.28| |phase err.(test): min = 0.00 max = 89.16 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1410 0.1409 0.1494 n_refl.: 191128 remove outliers: r(all,work,free)=0.1410 0.1409 0.1494 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1401 0.1400 0.1488 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1349 n_refl.: 191128 remove outliers: r(all,work,free)=0.1196 0.1193 0.1349 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3829 348.078 308.620 0.346 0.994 0.195 13.296-10.522 96.04 96 1 0.2435 480.405 462.437 0.661 0.995 0.139 10.503-8.327 97.80 175 3 0.2239 501.880 492.928 0.817 0.996 0.106 8.318-6.595 100.00 360 8 0.2188 375.525 370.182 0.850 0.996 0.095 6.588-5.215 100.00 711 7 0.1940 345.069 334.817 0.847 0.997 0.090 5.214-4.128 98.38 1367 28 0.1249 504.732 498.675 0.936 0.998 0.049 4.126-3.266 94.74 2603 46 0.1178 460.090 452.343 0.997 0.999 0.005 3.266-2.585 99.86 5447 97 0.1127 310.366 306.841 0.980 1.000 0.000 2.585-2.046 97.45 10613 204 0.0964 234.153 231.517 0.986 1.003 0.000 2.046-1.619 99.39 21536 464 0.0909 138.583 137.229 1.001 1.007 0.000 1.619-1.281 98.00 42464 925 0.0942 74.605 73.953 0.991 1.014 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.022 38.297 0.960 1.027 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0122 ================= 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 : 0.2029 0.2007 0.080 5.108 5.2 78.0 14.6 805 0.000 1_bss: 0.1794 0.1935 0.080 5.108 5.2 78.0 14.6 805 0.000 1_settarget: 0.1794 0.1935 0.080 5.108 5.2 78.0 14.6 805 0.000 1_nqh: 0.1794 0.1935 0.080 5.108 5.2 78.0 14.6 805 0.000 1_weight: 0.1794 0.1935 0.080 5.108 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1497 0.038 1.162 5.2 78.0 14.6 805 0.155 1_adp: 0.1294 0.1558 0.038 1.162 5.1 73.0 14.9 805 0.155 1_regHadp: 0.1293 0.1554 0.038 1.162 5.1 73.0 14.9 805 0.155 1_occ: 0.1279 0.1545 0.038 1.162 5.1 73.0 14.9 805 0.155 2_bss: 0.1271 0.1538 0.038 1.162 5.3 73.2 15.1 805 0.155 2_settarget: 0.1271 0.1538 0.038 1.162 5.3 73.2 15.1 805 0.155 2_updatecdl: 0.1271 0.1538 0.038 1.169 5.3 73.2 15.1 805 0.155 2_nqh: 0.1271 0.1538 0.038 1.169 5.3 73.2 15.1 805 0.155 2_sol: 0.1267 0.1497 0.038 1.169 5.3 73.2 16.0 883 n/a 2_weight: 0.1267 0.1497 0.038 1.169 5.3 73.2 16.0 883 n/a 2_xyzrec: 0.1252 0.1514 0.042 1.138 5.3 73.2 16.0 883 n/a 2_adp: 0.1234 0.1506 0.042 1.138 5.4 68.2 16.2 883 n/a 2_regHadp: 0.1234 0.1507 0.042 1.138 5.4 68.2 16.2 883 n/a 2_occ: 0.1227 0.1506 0.042 1.138 5.4 68.2 16.2 883 n/a 3_bss: 0.1234 0.1511 0.042 1.138 5.4 68.2 16.2 883 n/a 3_settarget: 0.1234 0.1511 0.042 1.138 5.4 68.2 16.2 883 n/a 3_updatecdl: 0.1234 0.1511 0.042 1.146 5.4 68.2 16.2 883 n/a 3_nqh: 0.1234 0.1511 0.042 1.146 5.4 68.2 16.2 883 n/a 3_sol: 0.1250 0.1509 0.042 1.146 5.4 68.2 15.3 867 n/a 3_weight: 0.1250 0.1509 0.042 1.146 5.4 68.2 15.3 867 n/a 3_xyzrec: 0.1240 0.1433 0.035 1.107 5.4 68.2 15.3 867 n/a 3_adp: 0.1234 0.1394 0.035 1.107 5.5 67.8 15.2 867 n/a 3_regHadp: 0.1234 0.1395 0.035 1.107 5.5 67.8 15.2 867 n/a 3_occ: 0.1229 0.1384 0.035 1.107 5.5 67.8 15.2 867 n/a 4_bss: 0.1224 0.1381 0.035 1.107 5.5 67.7 15.2 867 n/a 4_settarget: 0.1224 0.1381 0.035 1.107 5.5 67.7 15.2 867 n/a 4_updatecdl: 0.1224 0.1381 0.035 1.113 5.5 67.7 15.2 867 n/a 4_nqh: 0.1224 0.1381 0.035 1.113 5.5 67.7 15.2 867 n/a 4_sol: 0.1207 0.1371 0.035 1.113 5.5 67.7 14.9 864 n/a 4_weight: 0.1207 0.1371 0.035 1.113 5.5 67.7 14.9 864 n/a 4_xyzrec: 0.1206 0.1370 0.035 1.122 5.5 67.7 14.9 864 n/a 4_adp: 0.1199 0.1366 0.035 1.122 5.5 67.3 14.8 864 n/a 4_regHadp: 0.1199 0.1366 0.035 1.122 5.5 67.3 14.8 864 n/a 4_occ: 0.1196 0.1366 0.035 1.122 5.5 67.3 14.8 864 n/a 5_bss: 0.1194 0.1363 0.035 1.122 5.5 67.3 14.8 864 n/a 5_settarget: 0.1194 0.1363 0.035 1.122 5.5 67.3 14.8 864 n/a 5_updatecdl: 0.1194 0.1363 0.035 1.123 5.5 67.3 14.8 864 n/a 5_nqh: 0.1194 0.1363 0.035 1.123 5.5 67.3 14.8 864 n/a 5_sol: 0.1190 0.1344 0.035 1.123 5.5 67.3 14.9 893 n/a 5_weight: 0.1190 0.1344 0.035 1.123 5.5 67.3 14.9 893 n/a 5_xyzrec: 0.1193 0.1349 0.036 1.130 5.5 67.3 14.9 893 n/a 5_adp: 0.1198 0.1355 0.036 1.130 5.6 67.1 14.9 893 n/a 5_regHadp: 0.1198 0.1355 0.036 1.130 5.6 67.1 14.9 893 n/a 5_occ: 0.1195 0.1353 0.036 1.130 5.6 67.1 14.9 893 n/a 6_bss: 0.1194 0.1352 0.036 1.130 5.5 67.0 14.9 893 n/a 6_settarget: 0.1194 0.1352 0.036 1.130 5.5 67.0 14.9 893 n/a 6_updatecdl: 0.1194 0.1352 0.036 1.130 5.5 67.0 14.9 893 n/a 6_nqh: 0.1194 0.1352 0.036 1.130 5.5 67.0 14.9 893 n/a 6_sol: 0.1192 0.1347 0.036 1.130 5.5 67.0 14.9 896 n/a 6_weight: 0.1192 0.1347 0.036 1.130 5.5 67.0 14.9 896 n/a 6_xyzrec: 0.1196 0.1353 0.037 1.123 5.5 67.0 14.9 896 n/a 6_adp: 0.1202 0.1359 0.037 1.123 5.6 65.8 14.8 896 n/a 6_regHadp: 0.1202 0.1359 0.037 1.123 5.6 65.8 14.8 896 n/a 6_occ: 0.1200 0.1360 0.037 1.123 5.6 65.8 14.8 896 n/a 7_bss: 0.1199 0.1358 0.037 1.123 5.4 65.6 14.6 896 n/a 7_settarget: 0.1199 0.1358 0.037 1.123 5.4 65.6 14.6 896 n/a 7_updatecdl: 0.1199 0.1358 0.037 1.123 5.4 65.6 14.6 896 n/a 7_nqh: 0.1199 0.1358 0.037 1.123 5.4 65.6 14.6 896 n/a 7_sol: 0.1198 0.1347 0.037 1.123 5.4 65.6 14.6 903 n/a 7_weight: 0.1198 0.1347 0.037 1.123 5.4 65.6 14.6 903 n/a 7_xyzrec: 0.1201 0.1352 0.038 1.129 5.4 65.6 14.6 903 n/a 7_adp: 0.1200 0.1354 0.038 1.129 5.4 64.6 14.5 903 n/a 7_regHadp: 0.1200 0.1354 0.038 1.129 5.4 64.6 14.5 903 n/a 7_occ: 0.1198 0.1355 0.038 1.129 5.4 64.6 14.5 903 n/a 8_bss: 0.1189 0.1345 0.038 1.129 5.5 64.6 14.6 903 n/a 8_settarget: 0.1189 0.1345 0.038 1.129 5.5 64.6 14.6 903 n/a 8_updatecdl: 0.1189 0.1345 0.038 1.129 5.5 64.6 14.6 903 n/a 8_nqh: 0.1189 0.1345 0.038 1.129 5.5 64.6 14.6 903 n/a 8_sol: 0.1189 0.1338 0.038 1.129 5.5 64.6 14.6 904 n/a 8_weight: 0.1189 0.1338 0.038 1.129 5.5 64.6 14.6 904 n/a 8_xyzrec: 0.1192 0.1345 0.038 1.119 5.5 64.6 14.6 904 n/a 8_adp: 0.1193 0.1349 0.038 1.119 5.5 64.1 14.6 904 n/a 8_regHadp: 0.1193 0.1349 0.038 1.119 5.5 64.1 14.6 904 n/a 8_occ: 0.1191 0.1346 0.038 1.119 5.5 64.1 14.6 904 n/a 9_bss: 0.1190 0.1345 0.038 1.119 5.5 64.1 14.6 904 n/a 9_settarget: 0.1190 0.1345 0.038 1.119 5.5 64.1 14.6 904 n/a 9_updatecdl: 0.1190 0.1345 0.038 1.119 5.5 64.1 14.6 904 n/a 9_nqh: 0.1190 0.1345 0.038 1.119 5.5 64.1 14.6 904 n/a 9_sol: 0.1188 0.1343 0.038 1.119 5.5 64.1 14.6 910 n/a 9_weight: 0.1188 0.1343 0.038 1.119 5.5 64.1 14.6 910 n/a 9_xyzrec: 0.1192 0.1350 0.039 1.121 5.5 64.1 14.6 910 n/a 9_adp: 0.1192 0.1353 0.039 1.121 5.5 63.2 14.6 910 n/a 9_regHadp: 0.1192 0.1353 0.039 1.121 5.5 63.2 14.6 910 n/a 9_occ: 0.1191 0.1349 0.039 1.121 5.5 63.2 14.6 910 n/a 10_bss: 0.1190 0.1348 0.039 1.121 5.5 63.2 14.6 910 n/a 10_settarget: 0.1190 0.1348 0.039 1.121 5.5 63.2 14.6 910 n/a 10_updatecdl: 0.1190 0.1348 0.039 1.121 5.5 63.2 14.6 910 n/a 10_setrh: 0.1191 0.1348 0.039 1.121 5.5 63.2 14.6 910 n/a 10_nqh: 0.1191 0.1348 0.039 1.121 5.5 63.2 14.6 910 n/a 10_sol: 0.1191 0.1343 0.039 1.121 5.5 63.2 14.5 904 n/a 10_weight: 0.1191 0.1343 0.039 1.121 5.5 63.2 14.5 904 n/a 10_xyzrec: 0.1194 0.1348 0.039 1.159 5.5 63.2 14.5 904 n/a 10_adp: 0.1195 0.1350 0.039 1.159 5.6 63.0 14.6 904 n/a 10_regHadp: 0.1195 0.1350 0.039 1.159 5.6 63.0 14.6 904 n/a 10_occ: 0.1194 0.1351 0.039 1.159 5.6 63.0 14.6 904 n/a end: 0.1193 0.1349 0.039 1.159 5.5 63.0 14.5 904 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7975575_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_7975575_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.9200 Refinement macro-cycles (run) : 12142.8900 Write final files (write_after_run_outputs) : 153.1200 Total : 12302.9300 Total CPU time: 3.43 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:12 PST -0800 (1736736132.08 s) Start R-work = 0.1794, R-free = 0.1935 Final R-work = 0.1193, R-free = 0.1349 =============================================================================== Job complete usr+sys time: 12573.57 seconds wall clock time: 210 minutes 31.67 seconds (12631.67 seconds total)