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_4893068.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_4893068.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4893068.pdb" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.57, per 1000 atoms: 0.38 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.749 distance_ideal: 2.720 ideal - model: -0.029 slack: 0.000 delta_slack: -0.029 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: 2.654 distance_ideal: 2.710 ideal - model: 0.056 slack: 0.000 delta_slack: 0.056 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: 0.80 Conformation dependent library (CDL) restraints added in 194.7 milliseconds Time building geometry restraints manager: 1.13 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: 714 1.02 - 1.25: 2580 1.25 - 1.48: 1461 1.48 - 1.71: 1152 1.71 - 1.94: 27 Bond restraints: 5934 Sorted by residual: bond pdb=" C GLU A 180 " pdb=" O GLU A 180 " ideal model delta sigma weight residual 1.237 1.013 0.224 1.17e-02 7.31e+03 3.66e+02 bond pdb=" C VAL B 144 " pdb=" O VAL B 144 " ideal model delta sigma weight residual 1.236 1.424 -0.188 9.90e-03 1.02e+04 3.61e+02 bond pdb=" NE2 GLN B 138 " pdb="HE21 GLN B 138 " ideal model delta sigma weight residual 0.860 1.237 -0.377 2.00e-02 2.50e+03 3.55e+02 bond pdb=" N ALA B 79 " pdb=" H ALA B 79 " ideal model delta sigma weight residual 0.860 1.231 -0.371 2.00e-02 2.50e+03 3.43e+02 bond pdb=" CA GLY A 78 " pdb=" C GLY A 78 " ideal model delta sigma weight residual 1.516 1.717 -0.200 1.09e-02 8.42e+03 3.38e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.21: 5702 4.21 - 8.42: 3511 8.42 - 12.63: 1301 12.63 - 16.84: 264 16.84 - 21.04: 32 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA THR B 46 " pdb=" C THR B 46 " pdb=" O THR B 46 " ideal model delta sigma weight residual 120.32 137.59 -17.27 1.10e+00 8.26e-01 2.46e+02 angle pdb=" CA LEU B 153 " pdb=" C LEU B 153 " pdb=" O LEU B 153 " ideal model delta sigma weight residual 120.36 136.48 -16.12 1.08e+00 8.57e-01 2.23e+02 angle pdb=" CA ASP A 141 " pdb=" C ASP A 141 " pdb=" O ASP A 141 " ideal model delta sigma weight residual 121.11 139.36 -18.25 1.23e+00 6.61e-01 2.20e+02 angle pdb=" CA ARG B 149 " pdb=" C ARG B 149 " pdb=" O ARG B 149 " ideal model delta sigma weight residual 120.55 104.83 15.72 1.06e+00 8.90e-01 2.20e+02 angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 135.87 -13.69 9.60e-01 1.09e+00 2.03e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 1923 21.98 - 43.96: 91 43.96 - 65.94: 31 65.94 - 87.92: 4 87.92 - 109.90: 1 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -152.88 -27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CB TRP A 146 " pdb=" CG TRP A 146 " pdb=" CD1 TRP A 146 " pdb=" HD1 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 -24.69 24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA CYS A 47 " pdb=" C CYS A 47 " pdb=" N SER A 48 " pdb=" CA SER A 48 " ideal model delta harmonic sigma weight residual -180.00 -157.20 -22.80 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 204 0.217 - 0.434: 148 0.434 - 0.650: 92 0.650 - 0.867: 40 0.867 - 1.084: 8 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA LEU B 53 " pdb=" N LEU B 53 " pdb=" C LEU B 53 " pdb=" CB LEU B 53 " both_signs ideal model delta sigma weight residual False 2.51 3.59 -1.08 2.00e-01 2.50e+01 2.94e+01 chirality pdb=" CA ALA A 44 " pdb=" N ALA A 44 " pdb=" C ALA A 44 " pdb=" CB ALA A 44 " both_signs ideal model delta sigma weight residual False 2.48 3.52 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CA THR B 154 " pdb=" N THR B 154 " pdb=" C THR B 154 " pdb=" CB THR B 154 " both_signs ideal model delta sigma weight residual False 2.53 1.55 0.97 2.00e-01 2.50e+01 2.36e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.163 2.00e-02 2.50e+03 7.89e-02 1.87e+02 pdb=" CG PHE B 164 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.163 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.069 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.068 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " 0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.019 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.037 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " -0.024 2.00e-02 2.50e+03 6.59e-02 1.74e+02 pdb=" CG TRP A 139 " 0.112 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.012 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " 0.054 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.084 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " -0.115 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " -0.013 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " -0.088 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " 0.017 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " 0.091 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.045 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.055 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.127 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 164 " 0.140 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.050 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.013 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.047 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.88 - 1.62: 29 1.62 - 2.37: 2473 2.37 - 3.11: 22384 3.11 - 3.86: 32910 3.86 - 4.60: 52448 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110244 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.880 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.955 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.004 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.177 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.210 2.620 ... (remaining 110239 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_4893068_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= 0.2035 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.301645 | | target function (ml) not normalized (work): 805754.059170 | | target function (ml) not normalized (free): 16583.519353 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2132 0.1887 6.7059 6.2879| | 2: 2.94 - 2.33 1.00 7339 128 0.1614 0.1643 5.5309 5.5901| | 3: 2.33 - 2.04 0.96 6939 150 0.1634 0.1636 5.1365 5.2062| | 4: 2.04 - 1.85 1.00 7170 155 0.1764 0.1757 4.9681 5.0776| | 5: 1.85 - 1.72 0.99 7113 159 0.1904 0.1523 4.7894 4.704| | 6: 1.72 - 1.62 0.99 7102 142 0.1997 0.1973 4.672 4.6969| | 7: 1.62 - 1.54 0.99 7104 148 0.2018 0.1645 4.5543 4.5476| | 8: 1.54 - 1.47 0.96 6798 152 0.2049 0.2117 4.4651 4.4886| | 9: 1.47 - 1.41 0.98 6938 155 0.2105 0.2030 4.3915 4.394| | 10: 1.41 - 1.36 0.99 7022 150 0.2153 0.2429 4.3234 4.4434| | 11: 1.36 - 1.32 0.99 6997 151 0.2113 0.2138 4.2363 4.279| | 12: 1.32 - 1.28 0.98 6976 149 0.2093 0.2177 4.184 4.279| | 13: 1.28 - 1.25 0.98 6907 166 0.2001 0.2180 4.1311 4.1575| | 14: 1.25 - 1.22 0.98 7015 113 0.2102 0.2572 4.0899 4.3193| | 15: 1.22 - 1.19 0.98 6957 137 0.2103 0.1986 4.0472 4.0464| | 16: 1.19 - 1.17 0.93 6604 132 0.2158 0.2198 4.0154 4.0113| | 17: 1.17 - 1.14 0.98 6941 135 0.2182 0.1990 3.9624 4.0148| | 18: 1.14 - 1.12 0.98 6875 142 0.2213 0.2471 3.926 3.98| | 19: 1.12 - 1.10 0.97 6949 106 0.2257 0.2650 3.8703 4.021| | 20: 1.10 - 1.08 0.97 6884 147 0.2308 0.2282 3.8186 3.8204| | 21: 1.08 - 1.07 0.97 6852 152 0.2428 0.2590 3.7896 3.8174| | 22: 1.07 - 1.05 0.97 6838 135 0.2573 0.2511 3.7544 3.7498| | 23: 1.05 - 1.03 0.97 6829 159 0.2727 0.2780 3.7307 3.8444| | 24: 1.03 - 1.02 0.96 6785 133 0.2854 0.2884 3.6965 3.7818| | 25: 1.02 - 1.01 0.93 6552 130 0.3047 0.3190 3.6708 3.7563| | 26: 1.01 - 0.99 0.96 6767 158 0.3219 0.3405 3.6314 3.6559| | 27: 0.99 - 0.98 0.94 6648 131 0.3381 0.3168 3.6384 3.6357| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 19.94 0.91 0.97 33990.25| | 2: 2.94 - 2.33 7339 128 0.86 21.07 1.08 1.02 14826.34| | 3: 2.33 - 2.04 6939 150 0.93 12.85 1.11 1.06 4290.47| | 4: 2.04 - 1.85 7170 155 0.92 13.42 1.11 1.05 2715.08| | 5: 1.85 - 1.72 7113 159 0.92 14.72 1.11 1.07 1877.75| | 6: 1.72 - 1.62 7102 142 0.91 15.95 1.11 1.06 1506.02| | 7: 1.62 - 1.54 7104 148 0.90 16.86 1.11 1.07 1232.52| | 8: 1.54 - 1.47 6798 152 0.89 17.85 1.10 1.06 1076.38| | 9: 1.47 - 1.41 6938 155 0.88 18.56 1.10 1.06 940.38| | 10: 1.41 - 1.36 7022 150 0.87 20.26 1.09 1.05 873.29| | 11: 1.36 - 1.32 6997 151 0.86 20.75 1.08 1.04 780.08| | 12: 1.32 - 1.28 6976 149 0.87 20.59 1.08 1.04 697.19| | 13: 1.28 - 1.25 6907 166 0.87 20.36 1.06 1.05 643.19| | 14: 1.25 - 1.22 7015 113 0.86 21.15 1.07 1.04 596.64| | 15: 1.22 - 1.19 6957 137 0.86 21.38 1.08 1.04 565.86| | 16: 1.19 - 1.17 6604 132 0.87 21.01 1.08 1.03 508.46| | 17: 1.17 - 1.14 6941 135 0.85 21.90 1.08 1.02 474.34| | 18: 1.14 - 1.12 6875 142 0.85 22.00 1.08 0.99 425.34| | 19: 1.12 - 1.10 6949 106 0.85 22.70 1.07 0.99 396.36| | 20: 1.10 - 1.08 6884 147 0.85 22.98 1.06 0.97 349.79| | 21: 1.08 - 1.07 6852 152 0.84 24.09 1.06 0.98 340.85| | 22: 1.07 - 1.05 6838 135 0.82 25.71 1.05 0.99 336.76| | 23: 1.05 - 1.03 6829 159 0.79 28.38 1.05 0.98 350.52| | 24: 1.03 - 1.02 6785 133 0.76 30.81 1.05 0.96 353.14| | 25: 1.02 - 1.01 6552 130 0.75 32.38 1.03 0.91 336.06| | 26: 1.01 - 0.99 6767 158 0.73 33.92 1.03 0.88 310.55| | 27: 0.99 - 0.98 6648 131 0.74 33.21 1.04 0.87 279.76| |alpha: min = 0.87 max = 1.07 mean = 1.01| |beta: min = 279.76 max = 33990.25 mean = 2754.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.93| |phase err.(test): min = 0.00 max = 89.74 mean = 21.95| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.240 2950 Z= 5.472 Angle : 5.274 18.339 4018 Z= 3.723 Chirality : 0.394 1.084 492 Planarity : 0.032 0.113 512 Dihedral : 13.055 109.897 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.11 % Favored : 96.63 % Rotamer: Outliers : 0.97 % Allowed : 4.19 % Favored : 94.84 % Cbeta Deviations : 30.34 % 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: -1.84 (0.39), residues: 386 helix: -2.19 (0.34), residues: 144 sheet: -0.35 (0.59), residues: 66 loop : -0.47 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.080 0.019 ARG B 143 TYR 0.105 0.043 TYR A 192 PHE 0.166 0.044 PHE A 164 TRP 0.130 0.041 TRP A 146 HIS 0.085 0.037 HIS B 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2035 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 4.301645 | | target function (ml) not normalized (work): 805754.059170 | | target function (ml) not normalized (free): 16583.519353 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2034 0.2035 0.1995 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2034 0.2035 0.1995 n_refl.: 191155 remove outliers: r(all,work,free)=0.2034 0.2035 0.1995 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2034 0.2035 0.1995 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1807 0.1804 0.1936 n_refl.: 191145 remove outliers: r(all,work,free)=0.1805 0.1802 0.1934 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4049 402.814 293.276 0.438 0.911 0.301 13.296-10.522 99.01 99 1 0.2531 528.187 518.673 0.787 0.912 0.251 10.503-8.327 98.90 177 3 0.2492 564.205 558.708 0.976 0.912 0.227 8.318-6.595 100.00 360 8 0.2509 414.736 402.732 0.968 0.912 0.160 6.588-5.215 100.00 711 7 0.2243 381.101 366.283 0.961 0.912 0.150 5.214-4.128 98.38 1367 28 0.1490 557.435 549.206 1.079 0.912 0.100 4.126-3.266 94.74 2603 46 0.1354 508.132 500.097 1.146 0.913 0.029 3.266-2.585 99.86 5447 97 0.1449 342.774 337.680 1.121 0.912 0.020 2.585-2.046 97.45 10613 204 0.1389 258.603 254.062 1.128 0.911 0.000 2.046-1.619 99.39 21536 464 0.1623 153.054 149.871 1.144 0.910 0.000 1.619-1.281 98.00 42464 925 0.1928 82.395 80.177 1.130 0.909 0.000 1.281-0.980 96.53 101826 2055 0.2322 44.202 41.706 1.113 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0044 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1802 r_free=0.1934 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1802 r_free=0.1934 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.080952 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 572.565156 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 0.1508 0.0237 0.039 1.2 10.7 0.0 0.0 0 11.540 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 15.08 2.37 1.118 13.109 572.565 0.018 12.97 15.73 2.76 1.236 13.330 572.565 0.017 Individual atomic B min max mean iso aniso Overall: 5.20 73.04 15.00 1.40 435 3274 Protein: 5.20 40.32 10.99 1.40 0 2902 Water: 6.36 73.04 29.42 N/A 435 370 Other: 16.18 30.85 23.51 N/A 0 2 Chain A: 5.30 60.09 13.04 N/A 0 1626 Chain B: 5.20 73.04 12.76 N/A 0 1648 Chain S: 11.62 63.81 30.82 N/A 435 0 Histogram: Values Number of atoms 5.20 - 11.99 2171 11.99 - 18.77 633 18.77 - 25.55 317 25.55 - 32.34 265 32.34 - 39.12 156 39.12 - 45.91 99 45.91 - 52.69 47 52.69 - 59.47 17 59.47 - 66.26 3 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1573 r_work=0.1297 r_free=0.1569 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1569 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1282 r_free = 0.1558 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1558 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015536 | | target function (ls_wunit_k1) not normalized (work): 2909.838549 | | target function (ls_wunit_k1) not normalized (free): 116.962567 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1288 0.1282 0.1558 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1467 0.1464 0.1633 n_refl.: 191137 remove outliers: r(all,work,free)=0.1467 0.1464 0.1633 n_refl.: 191137 overall B=0.17 to atoms: r(all,work,free)=0.1490 0.1487 0.1643 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1275 0.1550 n_refl.: 191137 remove outliers: r(all,work,free)=0.1280 0.1275 0.1550 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3610 402.814 378.789 0.472 0.997 0.281 13.296-10.522 99.01 99 1 0.2061 528.187 524.410 0.718 0.998 0.249 10.503-8.327 98.90 177 3 0.1719 564.205 562.084 0.858 0.998 0.198 8.318-6.595 100.00 360 8 0.1720 414.736 412.821 0.878 0.998 0.150 6.588-5.215 100.00 711 7 0.1540 381.101 373.094 0.857 0.998 0.140 5.214-4.128 98.38 1367 28 0.0902 557.435 554.938 0.944 0.999 0.059 4.126-3.266 94.74 2603 46 0.0827 508.132 504.232 1.008 0.999 0.018 3.266-2.585 99.86 5447 97 0.0922 342.774 340.250 0.991 0.999 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.366 1.002 1.000 0.000 2.046-1.619 99.39 21536 464 0.1090 153.054 151.376 1.018 1.000 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.403 1.010 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.166 0.988 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0376 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1550 | n_water=805 | time (s): 2.950 (total time: 2.950) Filter (dist) r_work=0.1279 r_free=0.1556 | n_water=795 | time (s): 99.020 (total time: 101.970) Filter (q & B) r_work=0.1279 r_free=0.1556 | n_water=790 | time (s): 4.160 (total time: 106.130) Compute maps r_work=0.1279 r_free=0.1556 | n_water=790 | time (s): 2.130 (total time: 108.260) Filter (map) r_work=0.1307 r_free=0.1543 | n_water=648 | time (s): 5.320 (total time: 113.580) Find peaks r_work=0.1307 r_free=0.1543 | n_water=648 | time (s): 0.750 (total time: 114.330) Add new water r_work=0.1331 r_free=0.1576 | n_water=957 | time (s): 4.830 (total time: 119.160) Refine new water occ: r_work=0.1286 r_free=0.1523 adp: r_work=0.1272 r_free=0.1514 occ: r_work=0.1275 r_free=0.1512 adp: r_work=0.1267 r_free=0.1510 occ: r_work=0.1268 r_free=0.1507 adp: r_work=0.1266 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1266 r_free=0.1509 r_work=0.1266 r_free=0.1509 | n_water=957 | time (s): 84.940 (total time: 204.100) Filter (q & B) r_work=0.1270 r_free=0.1513 | n_water=884 | time (s): 4.860 (total time: 208.960) Filter (dist only) r_work=0.1270 r_free=0.1512 | n_water=883 | time (s): 111.400 (total time: 320.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.046314 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 588.670144 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 0.1254 0.1531 0.0276 0.041 1.1 15.1 0.0 0.0 0 11.523 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.54 15.31 2.76 2.040 15.189 588.670 0.014 12.34 15.12 2.78 2.381 15.216 588.670 0.014 Individual atomic B min max mean iso aniso Overall: 5.44 68.21 16.31 1.20 515 3272 Protein: 5.44 40.16 11.00 1.20 0 2902 Water: 6.61 68.21 33.72 N/A 515 368 Other: 16.15 32.79 24.47 N/A 0 2 Chain A: 5.55 57.25 13.00 N/A 0 1624 Chain B: 5.44 68.21 12.82 N/A 0 1648 Chain S: 11.22 64.64 37.90 N/A 515 0 Histogram: Values Number of atoms 5.44 - 11.71 2059 11.71 - 17.99 711 17.99 - 24.27 263 24.27 - 30.54 227 30.54 - 36.82 168 36.82 - 43.10 160 43.10 - 49.38 90 49.38 - 55.65 53 55.65 - 61.93 44 61.93 - 68.21 12 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1512 r_work=0.1234 r_free=0.1514 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1514 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 = 0.1508 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1508 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013370 | | target function (ls_wunit_k1) not normalized (work): 2504.168385 | | target function (ls_wunit_k1) not normalized (free): 102.752951 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1233 0.1227 0.1508 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1435 0.1432 0.1612 n_refl.: 191137 remove outliers: r(all,work,free)=0.1435 0.1432 0.1612 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1429 0.1610 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1234 0.1517 n_refl.: 191137 remove outliers: r(all,work,free)=0.1239 0.1234 0.1517 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3182 402.814 378.474 0.499 0.963 0.280 13.296-10.522 99.01 99 1 0.1875 528.187 521.772 0.767 0.964 0.257 10.503-8.327 98.90 177 3 0.1407 564.205 565.485 0.920 0.964 0.176 8.318-6.595 100.00 360 8 0.1543 414.736 415.297 0.932 0.964 0.146 6.588-5.215 100.00 711 7 0.1370 381.101 375.582 0.910 0.964 0.130 5.214-4.128 98.38 1367 28 0.0817 557.435 555.959 0.994 0.964 0.090 4.126-3.266 94.74 2603 46 0.0760 508.132 505.649 1.057 0.964 0.014 3.266-2.585 99.86 5447 97 0.0851 342.774 341.378 1.045 0.963 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.800 1.057 0.962 0.000 2.046-1.619 99.39 21536 464 0.1046 153.054 151.644 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1261 82.395 81.342 1.072 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.213 1.058 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0484 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1234 r_free=0.1517 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1234 r_free=0.1517 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1234 r_free=0.1517 | n_water=883 | time (s): 3.400 (total time: 3.400) Filter (dist) r_work=0.1235 r_free=0.1517 | n_water=880 | time (s): 124.940 (total time: 128.340) Filter (q & B) r_work=0.1235 r_free=0.1517 | n_water=878 | time (s): 5.110 (total time: 133.450) Compute maps r_work=0.1235 r_free=0.1517 | n_water=878 | time (s): 1.880 (total time: 135.330) Filter (map) r_work=0.1277 r_free=0.1527 | n_water=680 | time (s): 4.450 (total time: 139.780) Find peaks r_work=0.1277 r_free=0.1527 | n_water=680 | time (s): 0.910 (total time: 140.690) Add new water r_work=0.1300 r_free=0.1567 | n_water=988 | time (s): 4.450 (total time: 145.140) Refine new water occ: r_work=0.1257 r_free=0.1520 adp: r_work=0.1258 r_free=0.1521 occ: r_work=0.1253 r_free=0.1516 adp: r_work=0.1253 r_free=0.1518 occ: r_work=0.1250 r_free=0.1513 adp: r_work=0.1250 r_free=0.1515 ADP+occupancy (water only), MIN, final r_work=0.1250 r_free=0.1515 r_work=0.1250 r_free=0.1515 | n_water=988 | time (s): 298.480 (total time: 443.620) Filter (q & B) r_work=0.1254 r_free=0.1515 | n_water=863 | time (s): 5.970 (total time: 449.590) Filter (dist only) r_work=0.1255 r_free=0.1515 | n_water=862 | time (s): 115.530 (total time: 565.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.686290 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.318477 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 0.1245 0.1440 0.0195 0.035 1.1 7.1 0.0 0.0 0 0.843 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.45 14.40 1.95 1.935 14.537 16.318 3.942 12.40 14.01 1.61 2.276 14.430 16.318 3.897 Individual atomic B min max mean iso aniso Overall: 5.55 67.71 15.14 1.06 495 3271 Protein: 5.55 36.17 10.73 1.06 0 2902 Water: 6.70 67.71 29.97 N/A 495 367 Other: 13.89 28.10 20.99 N/A 0 2 Chain A: 5.56 56.19 12.73 N/A 0 1624 Chain B: 5.55 67.71 12.50 N/A 0 1647 Chain S: 14.16 63.90 31.80 N/A 495 0 Histogram: Values Number of atoms 5.55 - 11.77 2141 11.77 - 17.99 681 17.99 - 24.20 299 24.20 - 30.42 233 30.42 - 36.63 170 36.63 - 42.85 149 42.85 - 49.07 60 49.07 - 55.28 22 55.28 - 61.50 8 61.50 - 67.71 3 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1401 r_work=0.1240 r_free=0.1402 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 r_free = 0.1402 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1234 r_free = 0.1398 target_work(ml) = 3.892 | | 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.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1234 r_free= 0.1398 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891688 | | target function (ml) not normalized (work): 728897.596543 | | target function (ml) not normalized (free): 15222.990788 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1234 0.1397 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1449 0.1448 0.1494 n_refl.: 191137 remove outliers: r(all,work,free)=0.1449 0.1448 0.1494 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1443 0.1442 0.1490 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1233 0.1230 0.1386 n_refl.: 191137 remove outliers: r(all,work,free)=0.1232 0.1229 0.1386 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3782 398.895 356.111 0.408 0.945 0.225 13.296-10.522 97.03 97 1 0.2439 531.410 498.519 0.703 0.947 0.195 10.503-8.327 97.80 175 3 0.1978 554.286 556.987 0.882 0.947 0.164 8.318-6.595 100.00 360 8 0.2117 414.736 409.831 0.900 0.946 0.135 6.588-5.215 100.00 711 7 0.1856 381.101 370.360 0.886 0.946 0.130 5.214-4.128 98.38 1367 28 0.1167 557.435 551.675 0.974 0.947 0.100 4.126-3.266 94.74 2603 46 0.1110 508.132 501.215 1.034 0.947 0.030 3.266-2.585 99.86 5447 97 0.1097 342.774 339.075 1.022 0.946 0.000 2.585-2.046 97.45 10613 204 0.0976 258.603 255.769 1.034 0.945 0.000 2.046-1.619 99.39 21536 464 0.0977 153.054 151.415 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.500 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1686 44.202 42.324 1.040 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1022 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1229 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1229 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1386 | n_water=862 | time (s): 3.280 (total time: 3.280) Filter (dist) r_work=0.1229 r_free=0.1384 | n_water=858 | time (s): 117.680 (total time: 120.960) Filter (q & B) r_work=0.1230 r_free=0.1382 | n_water=845 | time (s): 4.570 (total time: 125.530) Compute maps r_work=0.1230 r_free=0.1382 | n_water=845 | time (s): 1.760 (total time: 127.290) Filter (map) r_work=0.1250 r_free=0.1393 | n_water=712 | time (s): 5.310 (total time: 132.600) Find peaks r_work=0.1250 r_free=0.1393 | n_water=712 | time (s): 0.660 (total time: 133.260) Add new water r_work=0.1267 r_free=0.1404 | n_water=960 | time (s): 3.970 (total time: 137.230) Refine new water occ: r_work=0.1216 r_free=0.1367 adp: r_work=0.1208 r_free=0.1363 occ: r_work=0.1206 r_free=0.1361 adp: r_work=0.1206 r_free=0.1361 occ: r_work=0.1206 r_free=0.1361 adp: r_work=0.1206 r_free=0.1361 ADP+occupancy (water only), MIN, final r_work=0.1206 r_free=0.1361 r_work=0.1206 r_free=0.1361 | n_water=960 | time (s): 171.770 (total time: 309.000) Filter (q & B) r_work=0.1211 r_free=0.1371 | n_water=849 | time (s): 4.670 (total time: 313.670) Filter (dist only) r_work=0.1212 r_free=0.1370 | n_water=848 | time (s): 107.110 (total time: 420.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.550210 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.157527 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 0.1210 0.1369 0.0159 0.035 1.1 6.1 0.0 0.0 0 0.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 13.69 1.59 1.829 14.054 16.158 3.873 12.00 13.65 1.65 1.911 14.030 16.158 3.864 Individual atomic B min max mean iso aniso Overall: 5.50 67.25 14.75 1.01 481 3271 Protein: 5.50 33.25 10.67 1.01 0 2902 Water: 6.09 67.25 28.68 N/A 481 367 Other: 14.00 27.27 20.63 N/A 0 2 Chain A: 5.52 55.09 12.62 N/A 0 1624 Chain B: 5.50 67.25 12.43 N/A 0 1647 Chain S: 6.09 61.82 29.85 N/A 481 0 Histogram: Values Number of atoms 5.50 - 11.68 2107 11.68 - 17.85 734 17.85 - 24.03 346 24.03 - 30.20 202 30.20 - 36.38 152 36.38 - 42.55 124 42.55 - 48.73 58 48.73 - 54.90 20 54.90 - 61.08 5 61.08 - 67.25 4 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1365 r_work=0.1200 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1366 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1362 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861743 | | target function (ml) not normalized (work): 723265.866593 | | target function (ml) not normalized (free): 15120.995308 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1362 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1409 0.1407 0.1492 n_refl.: 191131 remove outliers: r(all,work,free)=0.1409 0.1407 0.1492 n_refl.: 191131 overall B=-0.03 to atoms: r(all,work,free)=0.1402 0.1400 0.1487 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1362 n_refl.: 191131 remove outliers: r(all,work,free)=0.1200 0.1196 0.1362 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 0.3814 361.229 323.402 0.404 0.949 0.231 13.296-10.522 96.04 96 1 0.2422 480.468 454.124 0.704 0.950 0.186 10.503-8.327 97.80 175 3 0.2127 501.946 495.907 0.856 0.951 0.167 8.318-6.595 100.00 360 8 0.2206 375.574 369.683 0.888 0.950 0.120 6.588-5.215 100.00 711 7 0.1922 345.115 335.690 0.879 0.950 0.094 5.214-4.128 98.38 1367 28 0.1204 504.798 499.490 0.969 0.951 0.049 4.126-3.266 94.74 2603 46 0.1126 460.151 453.728 1.031 0.951 0.009 3.266-2.585 99.86 5447 97 0.1082 310.407 307.181 1.018 0.951 0.000 2.585-2.046 97.45 10613 204 0.0936 234.184 231.771 1.030 0.950 0.000 2.046-1.619 99.39 21536 464 0.0911 138.602 137.315 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0985 74.615 73.899 1.049 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1662 40.028 38.359 1.034 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1168 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1362 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1362 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1362 | n_water=848 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1196 r_free=0.1362 | n_water=847 | time (s): 107.460 (total time: 109.940) Filter (q & B) r_work=0.1197 r_free=0.1364 | n_water=837 | time (s): 5.500 (total time: 115.440) Compute maps r_work=0.1197 r_free=0.1364 | n_water=837 | time (s): 2.420 (total time: 117.860) Filter (map) r_work=0.1220 r_free=0.1357 | n_water=721 | time (s): 4.620 (total time: 122.480) Find peaks r_work=0.1220 r_free=0.1357 | n_water=721 | time (s): 0.570 (total time: 123.050) Add new water r_work=0.1231 r_free=0.1372 | n_water=955 | time (s): 3.980 (total time: 127.030) Refine new water occ: r_work=0.1190 r_free=0.1343 adp: r_work=0.1190 r_free=0.1344 occ: r_work=0.1188 r_free=0.1341 adp: r_work=0.1188 r_free=0.1341 occ: r_work=0.1186 r_free=0.1339 adp: r_work=0.1186 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1339 r_work=0.1186 r_free=0.1339 | n_water=955 | time (s): 196.230 (total time: 323.260) Filter (q & B) r_work=0.1190 r_free=0.1345 | n_water=882 | time (s): 5.390 (total time: 328.650) Filter (dist only) r_work=0.1190 r_free=0.1344 | n_water=881 | time (s): 115.270 (total time: 443.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.495782 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.387898 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 0.0156 0.036 1.1 5.6 0.0 0.3 0 0.748 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.49 1.56 1.797 14.100 15.388 3.762 11.98 13.55 1.57 1.858 14.075 15.388 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 66.93 14.88 0.97 514 3271 Protein: 5.58 32.29 10.60 0.97 0 2902 Water: 5.93 66.93 28.97 N/A 514 367 Other: 13.83 26.21 20.02 N/A 0 2 Chain A: 5.61 54.38 12.53 N/A 0 1624 Chain B: 5.58 66.93 12.34 N/A 0 1647 Chain S: 5.93 61.72 30.44 N/A 514 0 Histogram: Values Number of atoms 5.58 - 11.72 2137 11.72 - 17.85 723 17.85 - 23.99 310 23.99 - 30.12 220 30.12 - 36.26 177 36.26 - 42.39 131 42.39 - 48.53 60 48.53 - 54.66 19 54.66 - 60.80 4 60.80 - 66.93 4 =========================== 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: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1358 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758998 | | target function (ml) not normalized (work): 704018.971706 | | target function (ml) not normalized (free): 14733.477178 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1358 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1490 n_refl.: 191130 remove outliers: r(all,work,free)=0.1403 0.1401 0.1490 n_refl.: 191130 overall B=-0.04 to atoms: r(all,work,free)=0.1395 0.1394 0.1484 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191130 remove outliers: r(all,work,free)=0.1198 0.1195 0.1359 n_refl.: 191130 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3829 361.229 322.851 0.393 0.952 0.217 13.296-10.522 96.04 96 1 0.2426 480.468 461.067 0.713 0.954 0.195 10.503-8.327 97.80 175 3 0.2089 501.946 496.172 0.856 0.954 0.158 8.318-6.595 100.00 360 8 0.2159 375.574 370.699 0.883 0.954 0.105 6.588-5.215 100.00 711 7 0.1880 345.115 335.866 0.878 0.954 0.083 5.214-4.128 98.38 1367 28 0.1206 504.798 499.735 0.967 0.954 0.034 4.126-3.266 94.74 2603 46 0.1125 460.151 453.587 1.028 0.954 0.005 3.266-2.585 99.86 5447 97 0.1094 310.407 307.177 1.016 0.953 0.000 2.585-2.046 97.45 10613 204 0.0948 234.184 231.709 1.028 0.953 0.000 2.046-1.619 99.39 21536 464 0.0913 138.602 137.284 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0976 74.615 73.895 1.049 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.028 38.352 1.038 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1283 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1359 | n_water=881 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1195 r_free=0.1359 | n_water=880 | time (s): 109.170 (total time: 111.730) Filter (q & B) r_work=0.1195 r_free=0.1358 | n_water=867 | time (s): 4.060 (total time: 115.790) Compute maps r_work=0.1195 r_free=0.1358 | n_water=867 | time (s): 2.190 (total time: 117.980) Filter (map) r_work=0.1221 r_free=0.1360 | n_water=746 | time (s): 4.640 (total time: 122.620) Find peaks r_work=0.1221 r_free=0.1360 | n_water=746 | time (s): 0.620 (total time: 123.240) Add new water r_work=0.1231 r_free=0.1365 | n_water=964 | time (s): 4.090 (total time: 127.330) Refine new water occ: r_work=0.1194 r_free=0.1339 adp: r_work=0.1194 r_free=0.1340 occ: r_work=0.1192 r_free=0.1339 adp: r_work=0.1192 r_free=0.1340 occ: r_work=0.1191 r_free=0.1339 adp: r_work=0.1190 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1340 r_work=0.1190 r_free=0.1340 | n_water=964 | time (s): 188.500 (total time: 315.830) Filter (q & B) r_work=0.1194 r_free=0.1346 | n_water=897 | time (s): 5.970 (total time: 321.800) Filter (dist only) r_work=0.1194 r_free=0.1346 | n_water=896 | time (s): 123.290 (total time: 445.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.552514 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.931976 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 0.1195 0.1352 0.0157 0.037 1.1 5.8 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.52 1.57 1.768 14.053 14.932 3.759 11.99 13.54 1.56 1.913 14.003 14.932 3.758 Individual atomic B min max mean iso aniso Overall: 5.60 65.72 14.84 0.91 531 3269 Protein: 5.60 29.40 10.49 0.91 0 2902 Water: 6.01 65.72 28.91 N/A 531 365 Other: 13.88 23.29 18.59 N/A 0 2 Chain A: 5.64 51.53 12.37 N/A 0 1623 Chain B: 5.60 65.72 12.20 N/A 0 1646 Chain S: 6.01 61.70 30.57 N/A 531 0 Histogram: Values Number of atoms 5.60 - 11.61 2116 11.61 - 17.62 771 17.62 - 23.64 282 23.64 - 29.65 213 29.65 - 35.66 179 35.66 - 41.67 137 41.67 - 47.69 68 47.69 - 53.70 25 53.70 - 59.71 5 59.71 - 65.72 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1355 r_work=0.1199 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1357 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191130 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756864 | | target function (ml) not normalized (work): 703619.380480 | | target function (ml) not normalized (free): 14730.126256 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1357 n_refl.: 191130 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1488 n_refl.: 191130 remove outliers: r(all,work,free)=0.1402 0.1401 0.1488 n_refl.: 191130 overall B=-0.22 to atoms: r(all,work,free)=0.1367 0.1365 0.1464 n_refl.: 191130 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1196 0.1356 n_refl.: 191130 remove outliers: r(all,work,free)=0.1199 0.1196 0.1356 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3601 360.925 315.191 0.400 0.952 0.211 13.296-10.522 95.05 95 1 0.2319 479.571 454.828 0.716 0.953 0.154 10.503-8.327 97.80 175 3 0.2165 501.946 495.474 0.878 0.954 0.130 8.318-6.595 100.00 360 8 0.2148 375.574 371.446 0.907 0.954 0.103 6.588-5.215 100.00 711 7 0.1878 345.115 336.178 0.902 0.954 0.083 5.214-4.128 98.38 1367 28 0.1217 504.798 499.825 0.992 0.954 0.041 4.126-3.266 94.74 2603 46 0.1137 460.151 453.570 1.055 0.954 0.013 3.266-2.585 99.86 5447 97 0.1108 310.407 307.335 1.038 0.953 0.003 2.585-2.046 97.45 10613 204 0.0952 234.184 231.808 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0913 138.602 137.331 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0970 74.615 73.929 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.028 38.362 1.025 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0484 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1356 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1356 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1356 | n_water=896 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1196 r_free=0.1356 | n_water=896 | time (s): 106.550 (total time: 109.110) Filter (q & B) r_work=0.1197 r_free=0.1357 | n_water=886 | time (s): 4.070 (total time: 113.180) Compute maps r_work=0.1197 r_free=0.1357 | n_water=886 | time (s): 1.690 (total time: 114.870) Filter (map) r_work=0.1218 r_free=0.1366 | n_water=764 | time (s): 4.580 (total time: 119.450) Find peaks r_work=0.1218 r_free=0.1366 | n_water=764 | time (s): 0.830 (total time: 120.280) Add new water r_work=0.1227 r_free=0.1373 | n_water=969 | time (s): 4.120 (total time: 124.400) Refine new water occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1195 r_free=0.1341 occ: r_work=0.1193 r_free=0.1340 adp: r_work=0.1193 r_free=0.1341 occ: r_work=0.1191 r_free=0.1339 adp: r_work=0.1191 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1340 r_work=0.1191 r_free=0.1340 | n_water=969 | time (s): 226.680 (total time: 351.080) Filter (q & B) r_work=0.1195 r_free=0.1350 | n_water=897 | time (s): 5.720 (total time: 356.800) Filter (dist only) r_work=0.1195 r_free=0.1350 | n_water=896 | time (s): 114.100 (total time: 470.900) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566246 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.218982 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1356 0.0159 0.037 1.1 6.3 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.56 1.59 1.722 13.716 14.219 3.758 11.99 13.58 1.58 1.764 13.703 14.219 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 64.57 14.58 0.88 531 3269 Protein: 5.39 28.48 10.26 0.88 0 2902 Water: 5.80 64.57 28.55 N/A 531 365 Other: 13.72 22.26 17.99 N/A 0 2 Chain A: 5.47 50.94 12.10 N/A 0 1623 Chain B: 5.39 64.57 11.94 N/A 0 1646 Chain S: 5.80 61.65 30.32 N/A 531 0 Histogram: Values Number of atoms 5.39 - 11.31 2092 11.31 - 17.22 793 17.22 - 23.14 270 23.14 - 29.06 222 29.06 - 34.98 174 34.98 - 40.90 139 40.90 - 46.81 73 46.81 - 52.73 28 52.73 - 58.65 5 58.65 - 64.57 4 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1358 r_work=0.1199 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1358 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1358 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756401 | | target function (ml) not normalized (work): 703525.123322 | | target function (ml) not normalized (free): 14726.033229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1358 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1365 0.1363 0.1478 n_refl.: 191128 remove outliers: r(all,work,free)=0.1365 0.1363 0.1478 n_refl.: 191128 overall B=0.05 to atoms: r(all,work,free)=0.1372 0.1370 0.1483 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1348 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1348 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3627 360.925 332.677 0.404 0.995 0.207 13.296-10.522 95.05 95 1 0.2311 479.571 465.397 0.700 0.997 0.146 10.503-8.327 97.80 175 3 0.2191 501.946 494.346 0.849 0.997 0.120 8.318-6.595 100.00 360 8 0.2154 375.574 370.573 0.874 0.997 0.098 6.588-5.215 100.00 711 7 0.1894 345.115 335.899 0.871 0.997 0.081 5.214-4.128 98.38 1367 28 0.1217 504.798 499.202 0.958 0.998 0.034 4.126-3.266 94.74 2603 46 0.1154 460.151 452.791 1.019 0.999 0.005 3.266-2.585 99.86 5447 97 0.1108 310.407 306.974 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0959 234.184 231.599 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.602 137.199 1.025 1.005 0.000 1.619-1.281 98.00 42464 925 0.0950 74.615 73.951 1.014 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1630 40.028 38.339 0.980 1.017 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0637 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1348 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1348 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1348 | n_water=896 | time (s): 2.980 (total time: 2.980) Filter (dist) r_work=0.1189 r_free=0.1348 | n_water=896 | time (s): 106.970 (total time: 109.950) Filter (q & B) r_work=0.1189 r_free=0.1348 | n_water=885 | time (s): 4.260 (total time: 114.210) Compute maps r_work=0.1189 r_free=0.1348 | n_water=885 | time (s): 1.860 (total time: 116.070) Filter (map) r_work=0.1211 r_free=0.1349 | n_water=778 | time (s): 4.170 (total time: 120.240) Find peaks r_work=0.1211 r_free=0.1349 | n_water=778 | time (s): 0.620 (total time: 120.860) Add new water r_work=0.1218 r_free=0.1355 | n_water=977 | time (s): 3.960 (total time: 124.820) Refine new water occ: r_work=0.1186 r_free=0.1332 adp: r_work=0.1187 r_free=0.1332 occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1185 r_free=0.1332 occ: r_work=0.1184 r_free=0.1330 adp: r_work=0.1183 r_free=0.1331 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1331 r_work=0.1183 r_free=0.1331 | n_water=977 | time (s): 283.090 (total time: 407.910) Filter (q & B) r_work=0.1188 r_free=0.1342 | n_water=899 | time (s): 4.340 (total time: 412.250) Filter (dist only) r_work=0.1188 r_free=0.1342 | n_water=898 | time (s): 112.730 (total time: 524.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.568490 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.768273 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 0.1190 0.1348 0.0158 0.038 1.1 5.3 0.0 0.3 0 0.784 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.48 1.58 1.680 13.720 14.768 3.755 11.90 13.52 1.62 1.702 13.711 14.768 3.752 Individual atomic B min max mean iso aniso Overall: 5.50 63.60 14.61 0.88 533 3269 Protein: 5.50 28.30 10.31 0.88 0 2902 Water: 5.88 63.60 28.48 N/A 533 365 Other: 13.77 22.04 17.90 N/A 0 2 Chain A: 5.57 50.56 12.12 N/A 0 1623 Chain B: 5.50 63.60 11.97 N/A 0 1646 Chain S: 5.88 61.91 30.34 N/A 533 0 Histogram: Values Number of atoms 5.50 - 11.31 2066 11.31 - 17.12 824 17.12 - 22.93 265 22.93 - 28.74 212 28.74 - 34.55 182 34.55 - 40.36 130 40.36 - 46.17 82 46.17 - 51.98 30 51.98 - 57.79 7 57.79 - 63.60 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1352 r_work=0.1190 r_free=0.1352 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1352 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1351 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751619 | | target function (ml) not normalized (work): 702629.551047 | | target function (ml) not normalized (free): 14720.477670 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1351 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1380 0.1379 0.1484 n_refl.: 191128 remove outliers: r(all,work,free)=0.1380 0.1379 0.1484 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1382 0.1380 0.1485 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1350 n_refl.: 191128 remove outliers: r(all,work,free)=0.1190 0.1187 0.1350 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3603 360.925 332.858 0.411 0.974 0.207 13.296-10.522 95.05 95 1 0.2284 479.571 467.889 0.715 0.976 0.146 10.503-8.327 97.80 175 3 0.2171 501.946 495.447 0.863 0.976 0.115 8.318-6.595 100.00 360 8 0.2171 375.574 370.449 0.888 0.976 0.094 6.588-5.215 100.00 711 7 0.1904 345.115 336.024 0.888 0.976 0.078 5.214-4.128 98.38 1367 28 0.1233 504.798 499.050 0.978 0.977 0.034 4.126-3.266 94.74 2603 46 0.1160 460.151 452.541 1.041 0.978 0.005 3.266-2.585 99.86 5447 97 0.1122 310.407 306.819 1.024 0.979 0.000 2.585-2.046 97.45 10613 204 0.0959 234.184 231.555 1.032 0.981 0.000 2.046-1.619 99.39 21536 464 0.0905 138.602 137.232 1.049 0.985 0.000 1.619-1.281 98.00 42464 925 0.0941 74.615 73.968 1.039 0.990 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.028 38.326 1.007 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1350 | n_water=898 | time (s): 2.180 (total time: 2.180) Filter (dist) r_work=0.1187 r_free=0.1352 | n_water=897 | time (s): 111.090 (total time: 113.270) Filter (q & B) r_work=0.1189 r_free=0.1353 | n_water=884 | time (s): 5.260 (total time: 118.530) Compute maps r_work=0.1189 r_free=0.1353 | n_water=884 | time (s): 1.790 (total time: 120.320) Filter (map) r_work=0.1210 r_free=0.1349 | n_water=778 | time (s): 3.960 (total time: 124.280) Find peaks r_work=0.1210 r_free=0.1349 | n_water=778 | time (s): 0.740 (total time: 125.020) Add new water r_work=0.1217 r_free=0.1358 | n_water=983 | time (s): 4.320 (total time: 129.340) Refine new water occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1333 occ: r_work=0.1183 r_free=0.1334 adp: r_work=0.1183 r_free=0.1334 occ: r_work=0.1182 r_free=0.1334 adp: r_work=0.1182 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1334 r_work=0.1182 r_free=0.1334 | n_water=983 | time (s): 234.020 (total time: 363.360) Filter (q & B) r_work=0.1186 r_free=0.1345 | n_water=900 | time (s): 4.790 (total time: 368.150) Filter (dist only) r_work=0.1186 r_free=0.1345 | n_water=898 | time (s): 115.860 (total time: 484.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.573705 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.292859 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 0.1189 0.1352 0.0163 0.039 1.1 4.4 0.0 0.3 0 0.787 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.52 1.63 1.682 13.693 14.293 3.753 11.90 13.56 1.66 1.681 13.692 14.293 3.753 Individual atomic B min max mean iso aniso Overall: 5.53 63.31 14.56 0.87 533 3269 Protein: 5.53 28.16 10.34 0.87 0 2902 Water: 6.00 63.31 28.17 N/A 533 365 Other: 13.79 22.08 17.93 N/A 0 2 Chain A: 5.60 50.50 12.12 N/A 0 1623 Chain B: 5.53 63.31 11.98 N/A 0 1646 Chain S: 6.00 61.97 29.94 N/A 533 0 Histogram: Values Number of atoms 5.53 - 11.31 2056 11.31 - 17.09 832 17.09 - 22.86 274 22.86 - 28.64 218 28.64 - 34.42 191 34.42 - 40.20 110 40.20 - 45.98 78 45.98 - 51.76 31 51.76 - 57.53 8 57.53 - 63.31 4 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1356 r_work=0.1190 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1190 r_free = 0.1356 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1358 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.752572 | | target function (ml) not normalized (work): 702807.887464 | | target function (ml) not normalized (free): 14729.974341 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1358 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1392 0.1390 0.1502 n_refl.: 191128 remove outliers: r(all,work,free)=0.1392 0.1390 0.1502 n_refl.: 191128 overall B=-0.00 to atoms: r(all,work,free)=0.1391 0.1389 0.1502 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1357 n_refl.: 191128 remove outliers: r(all,work,free)=0.1192 0.1189 0.1357 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3650 360.925 330.938 0.411 0.973 0.211 13.296-10.522 95.05 95 1 0.2309 479.571 466.936 0.717 0.975 0.152 10.503-8.327 97.80 175 3 0.2197 501.946 494.578 0.861 0.975 0.121 8.318-6.595 100.00 360 8 0.2175 375.574 369.737 0.887 0.975 0.094 6.588-5.215 100.00 711 7 0.1921 345.115 335.683 0.888 0.976 0.073 5.214-4.128 98.38 1367 28 0.1239 504.798 498.979 0.978 0.977 0.030 4.126-3.266 94.74 2603 46 0.1165 460.151 452.593 1.042 0.978 0.005 3.266-2.585 99.86 5447 97 0.1123 310.407 306.853 1.025 0.979 0.000 2.585-2.046 97.45 10613 204 0.0960 234.184 231.551 1.033 0.981 0.000 2.046-1.619 99.39 21536 464 0.0908 138.602 137.225 1.050 0.985 0.000 1.619-1.281 98.00 42464 925 0.0939 74.615 73.968 1.041 0.991 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.028 38.316 1.011 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0103 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1189 r_free=0.1357 After: r_work=0.1190 r_free=0.1358 ================================== NQH flips ================================== r_work=0.1190 r_free=0.1358 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1358 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1358 | n_water=898 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1190 r_free=0.1358 | n_water=898 | time (s): 109.830 (total time: 113.070) Filter (q & B) r_work=0.1190 r_free=0.1357 | n_water=891 | time (s): 5.070 (total time: 118.140) Compute maps r_work=0.1190 r_free=0.1357 | n_water=891 | time (s): 1.870 (total time: 120.010) Filter (map) r_work=0.1211 r_free=0.1353 | n_water=783 | time (s): 5.270 (total time: 125.280) Find peaks r_work=0.1211 r_free=0.1353 | n_water=783 | time (s): 0.610 (total time: 125.890) Add new water r_work=0.1217 r_free=0.1365 | n_water=987 | time (s): 3.670 (total time: 129.560) Refine new water occ: r_work=0.1187 r_free=0.1344 adp: r_work=0.1187 r_free=0.1344 occ: r_work=0.1186 r_free=0.1343 adp: r_work=0.1186 r_free=0.1343 occ: r_work=0.1184 r_free=0.1343 adp: r_work=0.1184 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1343 r_work=0.1184 r_free=0.1343 | n_water=987 | time (s): 161.690 (total time: 291.250) Filter (q & B) r_work=0.1189 r_free=0.1352 | n_water=901 | time (s): 4.880 (total time: 296.130) Filter (dist only) r_work=0.1189 r_free=0.1353 | n_water=899 | time (s): 117.210 (total time: 413.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.529575 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.633384 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 0.1360 0.0167 0.039 1.2 7.2 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.60 1.67 1.679 13.707 14.633 3.756 11.93 13.61 1.68 1.679 13.708 14.633 3.754 Individual atomic B min max mean iso aniso Overall: 5.55 62.49 14.57 0.87 535 3268 Protein: 5.55 28.05 10.36 0.87 0 2902 Water: 6.02 62.49 28.18 N/A 535 364 Other: 13.81 22.06 17.94 N/A 0 2 Chain A: 5.66 50.27 12.11 N/A 0 1623 Chain B: 5.55 62.49 11.96 N/A 0 1645 Chain S: 6.02 62.00 30.09 N/A 535 0 Histogram: Values Number of atoms 5.55 - 11.24 2036 11.24 - 16.93 842 16.93 - 22.63 277 22.63 - 28.32 211 28.32 - 34.02 197 34.02 - 39.71 114 39.71 - 45.41 80 45.41 - 51.10 33 51.10 - 56.80 6 56.80 - 62.49 7 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1361 r_work=0.1193 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1361 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1362 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1362 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754236 | | target function (ml) not normalized (work): 703119.544525 | | target function (ml) not normalized (free): 14734.101122 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1357 0.1472 5.6868 5.7622| | 2: 2.94 - 2.33 1.00 7339 128 0.1069 0.1391 5.08 5.1908| | 3: 2.33 - 2.04 0.96 6939 150 0.0911 0.1191 4.6613 4.7555| | 4: 2.04 - 1.85 1.00 7170 155 0.0900 0.1034 4.3958 4.5676| | 5: 1.85 - 1.72 0.99 7113 159 0.0933 0.1005 4.1544 4.2636| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1087 3.9511 4.0761| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0972 3.7996 3.9296| | 8: 1.54 - 1.47 0.96 6798 152 0.0892 0.1319 3.7002 3.9042| | 9: 1.47 - 1.41 0.98 6938 155 0.0928 0.1148 3.6219 3.758| | 10: 1.41 - 1.36 0.99 7022 150 0.0973 0.1185 3.5543 3.6728| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1131 3.4814 3.5862| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1107 3.4555 3.575| | 13: 1.28 - 1.25 0.98 6907 166 0.1040 0.1254 3.4352 3.5698| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1598 3.4318 3.6843| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1241 3.4484 3.4878| | 16: 1.19 - 1.17 0.93 6604 132 0.1249 0.1540 3.4636 3.654| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1222 3.4317 3.441| | 18: 1.14 - 1.12 0.98 6875 142 0.1382 0.1716 3.4372 3.5344| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1766 3.4198 3.5996| | 20: 1.10 - 1.08 0.97 6884 147 0.1583 0.1581 3.4101 3.4374| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2139 3.4179 3.5028| | 22: 1.07 - 1.05 0.97 6836 135 0.1904 0.1957 3.4128 3.4157| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2012 3.4334 3.4857| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2245 3.4355 3.5081| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2526 3.4494 3.5265| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2851 3.4156 3.4224| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2809 3.4687 3.3972| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 11216.10| | 2: 2.94 - 2.33 7339 128 0.93 12.82 0.99 0.95 5162.69| | 3: 2.33 - 2.04 6939 150 0.96 7.76 1.01 0.95 1736.70| | 4: 2.04 - 1.85 7170 155 0.96 7.77 1.00 0.95 1026.74| | 5: 1.85 - 1.72 7113 159 0.96 8.21 1.00 0.96 646.96| | 6: 1.72 - 1.62 7102 142 0.96 8.09 1.00 0.96 448.05| | 7: 1.62 - 1.54 7104 148 0.96 8.15 1.01 0.97 338.18| | 8: 1.54 - 1.47 6798 152 0.96 8.27 1.01 0.97 279.36| | 9: 1.47 - 1.41 6938 155 0.96 8.47 1.00 0.98 230.48| | 10: 1.41 - 1.36 7022 150 0.96 8.88 1.00 0.97 201.74| | 11: 1.36 - 1.32 6997 151 0.96 8.88 0.99 0.96 173.42| | 12: 1.32 - 1.28 6975 149 0.96 8.93 0.98 0.95 159.33| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.01 0.96 157.98| | 14: 1.25 - 1.22 7015 112 0.95 10.72 1.01 0.97 163.55| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.01 0.98 167.00| | 16: 1.19 - 1.17 6604 132 0.95 11.42 1.01 0.96 159.86| | 17: 1.17 - 1.14 6940 135 0.94 12.23 1.01 0.96 153.52| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.95 147.74| | 19: 1.12 - 1.10 6948 106 0.93 14.19 1.00 0.95 151.73| | 20: 1.10 - 1.08 6884 147 0.92 15.27 1.00 0.94 150.91| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.68| | 22: 1.07 - 1.05 6836 135 0.89 18.31 0.99 0.93 154.93| | 23: 1.05 - 1.03 6827 159 0.87 20.49 0.99 0.92 164.59| | 24: 1.03 - 1.02 6784 133 0.85 23.15 0.99 0.93 178.93| | 25: 1.02 - 1.01 6552 130 0.83 25.18 0.98 0.90 182.30| | 26: 1.01 - 0.99 6767 158 0.81 26.67 0.98 0.88 177.06| | 27: 0.99 - 0.98 6647 131 0.82 26.37 0.99 0.87 161.65| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 147.74 max = 11216.10 mean = 930.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.90 mean = 13.31| |phase err.(test): min = 0.00 max = 88.58 mean = 13.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1362 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1511 n_refl.: 191128 remove outliers: r(all,work,free)=0.1401 0.1399 0.1511 n_refl.: 191128 overall B=-0.06 to atoms: r(all,work,free)=0.1392 0.1390 0.1504 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1191 0.1360 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1191 0.1360 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3573 360.925 332.044 0.427 0.916 0.210 13.296-10.522 95.05 95 1 0.2322 479.571 467.123 0.737 0.918 0.139 10.503-8.327 97.80 175 3 0.2183 501.946 494.959 0.892 0.918 0.109 8.318-6.595 100.00 360 8 0.2159 375.574 370.303 0.918 0.918 0.089 6.588-5.215 100.00 711 7 0.1930 345.115 335.644 0.919 0.918 0.072 5.214-4.128 98.38 1367 28 0.1241 504.798 498.949 1.013 0.919 0.024 4.126-3.266 94.74 2603 46 0.1167 460.151 452.596 1.081 0.921 0.000 3.266-2.585 99.86 5447 97 0.1122 310.407 306.901 1.063 0.922 0.000 2.585-2.046 97.45 10613 204 0.0965 234.184 231.558 1.070 0.924 0.000 2.046-1.619 99.39 21536 464 0.0911 138.602 137.223 1.086 0.929 0.000 1.619-1.281 98.00 42464 925 0.0945 74.615 73.963 1.075 0.935 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.028 38.309 1.040 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0131 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2035 0.1995 0.081 5.274 5.2 78.0 14.6 805 0.000 1_bss: 0.1802 0.1934 0.081 5.274 5.2 78.0 14.6 805 0.000 1_settarget: 0.1802 0.1934 0.081 5.274 5.2 78.0 14.6 805 0.000 1_nqh: 0.1802 0.1934 0.081 5.274 5.2 78.0 14.6 805 0.000 1_weight: 0.1802 0.1934 0.081 5.274 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1508 0.039 1.153 5.2 78.0 14.6 805 0.157 1_adp: 0.1298 0.1573 0.039 1.153 5.2 73.0 15.0 805 0.157 1_regHadp: 0.1297 0.1569 0.039 1.153 5.2 73.0 15.0 805 0.157 1_occ: 0.1282 0.1558 0.039 1.153 5.2 73.0 15.0 805 0.157 2_bss: 0.1275 0.1550 0.039 1.153 5.4 73.2 15.2 805 0.157 2_settarget: 0.1275 0.1550 0.039 1.153 5.4 73.2 15.2 805 0.157 2_updatecdl: 0.1275 0.1550 0.039 1.170 5.4 73.2 15.2 805 0.157 2_nqh: 0.1275 0.1550 0.039 1.170 5.4 73.2 15.2 805 0.157 2_sol: 0.1270 0.1512 0.039 1.170 5.4 73.2 16.3 883 n/a 2_weight: 0.1270 0.1512 0.039 1.170 5.4 73.2 16.3 883 n/a 2_xyzrec: 0.1254 0.1531 0.041 1.136 5.4 73.2 16.3 883 n/a 2_adp: 0.1234 0.1512 0.041 1.136 5.4 68.2 16.3 883 n/a 2_regHadp: 0.1234 0.1514 0.041 1.136 5.4 68.2 16.3 883 n/a 2_occ: 0.1227 0.1508 0.041 1.136 5.4 68.2 16.3 883 n/a 3_bss: 0.1234 0.1517 0.041 1.136 5.4 68.2 16.3 883 n/a 3_settarget: 0.1234 0.1517 0.041 1.136 5.4 68.2 16.3 883 n/a 3_updatecdl: 0.1234 0.1517 0.041 1.143 5.4 68.2 16.3 883 n/a 3_nqh: 0.1234 0.1517 0.041 1.143 5.4 68.2 16.3 883 n/a 3_sol: 0.1255 0.1515 0.041 1.143 5.4 68.2 15.3 862 n/a 3_weight: 0.1255 0.1515 0.041 1.143 5.4 68.2 15.3 862 n/a 3_xyzrec: 0.1245 0.1440 0.035 1.103 5.4 68.2 15.3 862 n/a 3_adp: 0.1240 0.1401 0.035 1.103 5.6 67.7 15.1 862 n/a 3_regHadp: 0.1240 0.1402 0.035 1.103 5.6 67.7 15.1 862 n/a 3_occ: 0.1234 0.1398 0.035 1.103 5.6 67.7 15.1 862 n/a 4_bss: 0.1229 0.1386 0.035 1.103 5.5 67.7 15.1 862 n/a 4_settarget: 0.1229 0.1386 0.035 1.103 5.5 67.7 15.1 862 n/a 4_updatecdl: 0.1229 0.1386 0.035 1.103 5.5 67.7 15.1 862 n/a 4_nqh: 0.1229 0.1386 0.035 1.103 5.5 67.7 15.1 862 n/a 4_sol: 0.1212 0.1370 0.035 1.103 5.5 67.7 14.8 848 n/a 4_weight: 0.1212 0.1370 0.035 1.103 5.5 67.7 14.8 848 n/a 4_xyzrec: 0.1210 0.1369 0.035 1.126 5.5 67.7 14.8 848 n/a 4_adp: 0.1200 0.1365 0.035 1.126 5.5 67.3 14.7 848 n/a 4_regHadp: 0.1200 0.1366 0.035 1.126 5.5 67.3 14.7 848 n/a 4_occ: 0.1198 0.1362 0.035 1.126 5.5 67.3 14.7 848 n/a 5_bss: 0.1197 0.1362 0.035 1.126 5.5 67.2 14.7 848 n/a 5_settarget: 0.1197 0.1362 0.035 1.126 5.5 67.2 14.7 848 n/a 5_updatecdl: 0.1197 0.1362 0.035 1.127 5.5 67.2 14.7 848 n/a 5_nqh: 0.1197 0.1362 0.035 1.127 5.5 67.2 14.7 848 n/a 5_sol: 0.1190 0.1344 0.035 1.127 5.5 67.2 14.9 881 n/a 5_weight: 0.1190 0.1344 0.035 1.127 5.5 67.2 14.9 881 n/a 5_xyzrec: 0.1193 0.1349 0.036 1.123 5.5 67.2 14.9 881 n/a 5_adp: 0.1198 0.1355 0.036 1.123 5.6 66.9 14.9 881 n/a 5_regHadp: 0.1198 0.1355 0.036 1.123 5.6 66.9 14.9 881 n/a 5_occ: 0.1196 0.1358 0.036 1.123 5.6 66.9 14.9 881 n/a 6_bss: 0.1195 0.1359 0.036 1.123 5.5 66.9 14.8 881 n/a 6_settarget: 0.1195 0.1359 0.036 1.123 5.5 66.9 14.8 881 n/a 6_updatecdl: 0.1195 0.1359 0.036 1.123 5.5 66.9 14.8 881 n/a 6_nqh: 0.1195 0.1359 0.036 1.123 5.5 66.9 14.8 881 n/a 6_sol: 0.1194 0.1346 0.036 1.123 5.5 66.9 14.9 896 n/a 6_weight: 0.1194 0.1346 0.036 1.123 5.5 66.9 14.9 896 n/a 6_xyzrec: 0.1195 0.1352 0.037 1.125 5.5 66.9 14.9 896 n/a 6_adp: 0.1199 0.1355 0.037 1.125 5.6 65.7 14.8 896 n/a 6_regHadp: 0.1199 0.1355 0.037 1.125 5.6 65.7 14.8 896 n/a 6_occ: 0.1197 0.1357 0.037 1.125 5.6 65.7 14.8 896 n/a 7_bss: 0.1196 0.1356 0.037 1.125 5.4 65.5 14.6 896 n/a 7_settarget: 0.1196 0.1356 0.037 1.125 5.4 65.5 14.6 896 n/a 7_updatecdl: 0.1196 0.1356 0.037 1.126 5.4 65.5 14.6 896 n/a 7_nqh: 0.1196 0.1356 0.037 1.126 5.4 65.5 14.6 896 n/a 7_sol: 0.1195 0.1350 0.037 1.126 5.4 65.5 14.6 896 n/a 7_weight: 0.1195 0.1350 0.037 1.126 5.4 65.5 14.6 896 n/a 7_xyzrec: 0.1197 0.1356 0.037 1.142 5.4 65.5 14.6 896 n/a 7_adp: 0.1199 0.1358 0.037 1.142 5.4 64.6 14.6 896 n/a 7_regHadp: 0.1199 0.1358 0.037 1.142 5.4 64.6 14.6 896 n/a 7_occ: 0.1198 0.1358 0.037 1.142 5.4 64.6 14.6 896 n/a 8_bss: 0.1189 0.1348 0.037 1.142 5.4 64.6 14.6 896 n/a 8_settarget: 0.1189 0.1348 0.037 1.142 5.4 64.6 14.6 896 n/a 8_updatecdl: 0.1189 0.1348 0.037 1.142 5.4 64.6 14.6 896 n/a 8_nqh: 0.1189 0.1348 0.037 1.142 5.4 64.6 14.6 896 n/a 8_sol: 0.1188 0.1342 0.037 1.142 5.4 64.6 14.6 898 n/a 8_weight: 0.1188 0.1342 0.037 1.142 5.4 64.6 14.6 898 n/a 8_xyzrec: 0.1190 0.1348 0.038 1.120 5.4 64.6 14.6 898 n/a 8_adp: 0.1190 0.1352 0.038 1.120 5.5 63.6 14.6 898 n/a 8_regHadp: 0.1190 0.1352 0.038 1.120 5.5 63.6 14.6 898 n/a 8_occ: 0.1189 0.1351 0.038 1.120 5.5 63.6 14.6 898 n/a 9_bss: 0.1187 0.1350 0.038 1.120 5.5 63.6 14.6 898 n/a 9_settarget: 0.1187 0.1350 0.038 1.120 5.5 63.6 14.6 898 n/a 9_updatecdl: 0.1187 0.1350 0.038 1.120 5.5 63.6 14.6 898 n/a 9_nqh: 0.1187 0.1350 0.038 1.120 5.5 63.6 14.6 898 n/a 9_sol: 0.1186 0.1345 0.038 1.120 5.5 63.6 14.6 898 n/a 9_weight: 0.1186 0.1345 0.038 1.120 5.5 63.6 14.6 898 n/a 9_xyzrec: 0.1189 0.1352 0.039 1.118 5.5 63.6 14.6 898 n/a 9_adp: 0.1190 0.1356 0.039 1.118 5.5 63.3 14.6 898 n/a 9_regHadp: 0.1190 0.1356 0.039 1.118 5.5 63.3 14.6 898 n/a 9_occ: 0.1190 0.1358 0.039 1.118 5.5 63.3 14.6 898 n/a 10_bss: 0.1189 0.1357 0.039 1.118 5.5 63.3 14.6 898 n/a 10_settarget: 0.1189 0.1357 0.039 1.118 5.5 63.3 14.6 898 n/a 10_updatecdl: 0.1189 0.1357 0.039 1.118 5.5 63.3 14.6 898 n/a 10_setrh: 0.1190 0.1358 0.039 1.118 5.5 63.3 14.6 898 n/a 10_nqh: 0.1190 0.1358 0.039 1.118 5.5 63.3 14.6 898 n/a 10_sol: 0.1189 0.1353 0.039 1.118 5.5 63.3 14.6 899 n/a 10_weight: 0.1189 0.1353 0.039 1.118 5.5 63.3 14.6 899 n/a 10_xyzrec: 0.1193 0.1360 0.039 1.157 5.5 63.3 14.6 899 n/a 10_adp: 0.1193 0.1361 0.039 1.157 5.5 62.5 14.6 899 n/a 10_regHadp: 0.1193 0.1361 0.039 1.157 5.5 62.5 14.6 899 n/a 10_occ: 0.1192 0.1362 0.039 1.157 5.5 62.5 14.6 899 n/a end: 0.1191 0.1360 0.039 1.157 5.5 62.4 14.5 899 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4893068_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4893068_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.7800 Refinement macro-cycles (run) : 11665.3400 Write final files (write_after_run_outputs) : 163.5900 Total : 11834.7100 Total CPU time: 3.30 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:34:24 PST -0800 (1736735664.24 s) Start R-work = 0.1802, R-free = 0.1934 Final R-work = 0.1191, R-free = 0.1360 =============================================================================== Job complete usr+sys time: 12154.11 seconds wall clock time: 203 minutes 32.03 seconds (12212.03 seconds total)