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_9606842.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9606842.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9606842.pdb" 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" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.79, per 1000 atoms: 0.27 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: 2.774 distance_ideal: 2.720 ideal - model: -0.054 slack: 0.000 delta_slack: -0.054 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: 2.636 distance_ideal: 2.710 ideal - model: 0.074 slack: 0.000 delta_slack: 0.074 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 226.0 milliseconds Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.01: 625 1.01 - 1.24: 2548 1.24 - 1.46: 1428 1.46 - 1.69: 1294 1.69 - 1.92: 39 Bond restraints: 5934 Sorted by residual: bond pdb=" N ILE B 22 " pdb=" CA ILE B 22 " ideal model delta sigma weight residual 1.460 1.694 -0.234 1.19e-02 7.06e+03 3.87e+02 bond pdb=" N THR B 21 " pdb=" H THR B 21 " ideal model delta sigma weight residual 0.860 1.248 -0.388 2.00e-02 2.50e+03 3.77e+02 bond pdb=" N LEU B 152 " pdb=" H LEU B 152 " ideal model delta sigma weight residual 0.860 1.248 -0.388 2.00e-02 2.50e+03 3.76e+02 bond pdb=" N GLY A 28 " pdb=" H GLY A 28 " ideal model delta sigma weight residual 0.860 1.230 -0.370 2.00e-02 2.50e+03 3.42e+02 bond pdb=" CA PHE A 119 " pdb=" CB PHE A 119 " ideal model delta sigma weight residual 1.526 1.325 0.201 1.09e-02 8.42e+03 3.41e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 6013 4.47 - 8.94: 3491 8.94 - 13.41: 1138 13.41 - 17.87: 156 17.87 - 22.34: 12 Bond angle restraints: 10810 Sorted by residual: angle pdb=" N VAL B 62 " pdb=" CA VAL B 62 " pdb=" C VAL B 62 " ideal model delta sigma weight residual 113.20 128.46 -15.26 9.60e-01 1.09e+00 2.53e+02 angle pdb=" NE ARG A 83 " pdb=" CZ ARG A 83 " pdb=" NH2 ARG A 83 " ideal model delta sigma weight residual 119.20 105.28 13.92 9.00e-01 1.23e+00 2.39e+02 angle pdb=" O PHE B 119 " pdb=" C PHE B 119 " pdb=" N PRO B 120 " ideal model delta sigma weight residual 121.34 134.91 -13.57 8.90e-01 1.26e+00 2.32e+02 angle pdb=" O GLY A 190 " pdb=" C GLY A 190 " pdb=" N ILE A 191 " ideal model delta sigma weight residual 122.71 134.57 -11.86 8.00e-01 1.56e+00 2.20e+02 angle pdb=" O ASP B 170 " pdb=" C ASP B 170 " pdb=" N LEU B 171 " ideal model delta sigma weight residual 122.11 105.13 16.98 1.15e+00 7.56e-01 2.18e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 1867 18.00 - 36.00: 123 36.00 - 54.00: 45 54.00 - 71.99: 11 71.99 - 89.99: 4 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP B 139 " pdb=" C TRP B 139 " pdb=" N LEU B 140 " pdb=" CA LEU B 140 " ideal model delta harmonic sigma weight residual 180.00 151.09 28.91 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA SER B 155 " pdb=" C SER B 155 " pdb=" N GLN B 156 " pdb=" CA GLN B 156 " ideal model delta harmonic sigma weight residual -180.00 -154.50 -25.50 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -154.68 -25.32 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.217: 204 0.217 - 0.433: 141 0.433 - 0.649: 95 0.649 - 0.866: 47 0.866 - 1.082: 5 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA ASP B 132 " pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CB ASP B 132 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" CB THR B 21 " pdb=" CA THR B 21 " pdb=" OG1 THR B 21 " pdb=" CG2 THR B 21 " both_signs ideal model delta sigma weight residual False 2.55 1.47 1.08 2.00e-01 2.50e+01 2.92e+01 chirality pdb=" CA VAL A 144 " pdb=" N VAL A 144 " pdb=" C VAL A 144 " pdb=" CB VAL A 144 " both_signs ideal model delta sigma weight residual False 2.44 3.47 -1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.032 2.00e-02 2.50e+03 6.35e-02 1.62e+02 pdb=" CG TRP A 146 " 0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.084 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " 0.050 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.034 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " -0.057 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.098 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " -0.061 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.067 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " -0.039 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.089 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.073 2.00e-02 2.50e+03 7.17e-02 1.54e+02 pdb=" CG PHE B 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.032 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.081 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.120 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.066 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 119 " -0.027 2.00e-02 2.50e+03 7.04e-02 1.49e+02 pdb=" CG PHE B 119 " 0.110 2.00e-02 2.50e+03 pdb=" CD1 PHE B 119 " 0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE B 119 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE B 119 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 PHE B 119 " -0.096 2.00e-02 2.50e+03 pdb=" CZ PHE B 119 " -0.087 2.00e-02 2.50e+03 pdb=" HD1 PHE B 119 " -0.036 2.00e-02 2.50e+03 pdb=" HD2 PHE B 119 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE B 119 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE B 119 " -0.018 2.00e-02 2.50e+03 pdb=" HZ PHE B 119 " 0.141 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.95 - 1.68: 39 1.68 - 2.41: 3148 2.41 - 3.14: 22662 3.14 - 3.87: 32706 3.87 - 4.60: 51742 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110297 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.946 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.004 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.016 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.133 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.170 2.620 ... (remaining 110292 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_9606842_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= 0.2033 r_free= 0.1972 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.301543 | | target function (ml) not normalized (work): 805734.897870 | | target function (ml) not normalized (free): 16539.657683 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2134 0.1846 6.7085 6.2964| | 2: 2.94 - 2.33 1.00 7339 128 0.1605 0.1622 5.5306 5.5727| | 3: 2.33 - 2.04 0.96 6939 150 0.1643 0.1598 5.1565 5.1588| | 4: 2.04 - 1.85 1.00 7170 155 0.1756 0.1733 4.976 5.0967| | 5: 1.85 - 1.72 0.99 7113 159 0.1928 0.1923 4.8047 4.8926| | 6: 1.72 - 1.62 0.99 7102 142 0.1977 0.2075 4.6643 4.7235| | 7: 1.62 - 1.54 0.99 7104 148 0.2000 0.1717 4.5616 4.5655| | 8: 1.54 - 1.47 0.96 6798 152 0.2037 0.2285 4.466 4.5664| | 9: 1.47 - 1.41 0.98 6938 155 0.2096 0.2121 4.3832 4.4383| | 10: 1.41 - 1.36 0.99 7022 150 0.2122 0.2237 4.3156 4.3921| | 11: 1.36 - 1.32 0.99 6997 151 0.2114 0.2240 4.245 4.3194| | 12: 1.32 - 1.28 0.98 6976 149 0.2063 0.1967 4.1738 4.2208| | 13: 1.28 - 1.25 0.98 6907 166 0.2023 0.1836 4.1297 4.0519| | 14: 1.25 - 1.22 0.98 7015 113 0.2088 0.2203 4.0736 4.2474| | 15: 1.22 - 1.19 0.98 6957 137 0.2128 0.1767 4.0432 3.9064| | 16: 1.19 - 1.17 0.93 6604 132 0.2136 0.2171 4.0056 4.0463| | 17: 1.17 - 1.14 0.98 6941 135 0.2160 0.1891 3.9497 4.0009| | 18: 1.14 - 1.12 0.98 6875 142 0.2205 0.2261 3.918 3.9518| | 19: 1.12 - 1.10 0.97 6949 106 0.2250 0.2400 3.8713 3.9295| | 20: 1.10 - 1.08 0.97 6884 147 0.2321 0.2127 3.8205 3.7987| | 21: 1.08 - 1.07 0.97 6852 152 0.2419 0.2564 3.7879 3.7953| | 22: 1.07 - 1.05 0.97 6838 135 0.2554 0.2612 3.7465 3.7811| | 23: 1.05 - 1.03 0.97 6829 159 0.2750 0.2465 3.7387 3.7584| | 24: 1.03 - 1.02 0.96 6785 133 0.2904 0.2822 3.7035 3.7767| | 25: 1.02 - 1.01 0.93 6552 130 0.3061 0.3245 3.6753 3.797| | 26: 1.01 - 0.99 0.96 6767 158 0.3249 0.3093 3.6372 3.6011| | 27: 0.99 - 0.98 0.94 6648 131 0.3406 0.3053 3.6404 3.5779| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.00 0.91 0.97 34095.05| | 2: 2.94 - 2.33 7339 128 0.86 20.92 1.08 1.02 14730.44| | 3: 2.33 - 2.04 6939 150 0.93 12.89 1.11 1.05 4331.41| | 4: 2.04 - 1.85 7170 155 0.92 14.20 1.11 1.06 2990.03| | 5: 1.85 - 1.72 7113 159 0.90 16.20 1.11 1.08 2234.30| | 6: 1.72 - 1.62 7102 142 0.90 17.21 1.11 1.07 1719.66| | 7: 1.62 - 1.54 7104 148 0.89 17.51 1.10 1.07 1317.20| | 8: 1.54 - 1.47 6798 152 0.89 18.42 1.10 1.06 1136.88| | 9: 1.47 - 1.41 6938 155 0.88 19.01 1.11 1.07 978.66| | 10: 1.41 - 1.36 7022 150 0.87 20.52 1.09 1.06 896.88| | 11: 1.36 - 1.32 6997 151 0.87 20.50 1.08 1.06 774.37| | 12: 1.32 - 1.28 6976 149 0.87 20.05 1.07 1.04 668.24| | 13: 1.28 - 1.25 6907 166 0.88 19.15 1.06 1.05 578.72| | 14: 1.25 - 1.22 7015 113 0.88 19.62 1.07 1.04 517.41| | 15: 1.22 - 1.19 6957 137 0.88 19.61 1.07 1.04 478.93| | 16: 1.19 - 1.17 6604 132 0.88 19.49 1.07 1.03 444.95| | 17: 1.17 - 1.14 6941 135 0.87 20.47 1.08 1.02 420.54| | 18: 1.14 - 1.12 6875 142 0.87 20.91 1.08 0.99 385.45| | 19: 1.12 - 1.10 6949 106 0.86 21.41 1.07 1.00 362.06| | 20: 1.10 - 1.08 6884 147 0.86 22.09 1.06 0.98 329.11| | 21: 1.08 - 1.07 6852 152 0.84 23.27 1.05 0.98 322.91| | 22: 1.07 - 1.05 6838 135 0.83 25.09 1.06 0.97 313.30| | 23: 1.05 - 1.03 6829 159 0.80 27.61 1.05 0.98 328.03| | 24: 1.03 - 1.02 6785 133 0.78 29.64 1.06 0.98 332.93| | 25: 1.02 - 1.01 6552 130 0.76 30.99 1.03 0.95 325.28| | 26: 1.01 - 0.99 6767 158 0.75 32.47 1.03 0.94 297.53| | 27: 0.99 - 0.98 6648 131 0.76 31.08 1.04 0.92 261.20| |alpha: min = 0.92 max = 1.08 mean = 1.02| |beta: min = 261.20 max = 34095.05 mean = 2774.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.97 mean = 21.41| |phase err.(test): min = 0.00 max = 89.52 mean = 21.55| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.256 2950 Z= 5.609 Angle : 5.155 18.510 4018 Z= 3.677 Chirality : 0.389 1.082 492 Planarity : 0.033 0.119 512 Dihedral : 13.012 89.993 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.81 % Favored : 97.93 % Rotamer: Outliers : 1.94 % Allowed : 4.19 % Favored : 93.87 % Cbeta Deviations : 37.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.39), residues: 386 helix: -2.88 (0.28), residues: 146 sheet: -0.82 (0.52), residues: 86 loop : -0.16 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.027 ARG A 83 TYR 0.100 0.041 TYR A 192 PHE 0.104 0.037 PHE B 119 TRP 0.119 0.037 TRP B 139 HIS 0.063 0.019 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2033 r_free= 0.1972 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.301543 | | target function (ml) not normalized (work): 805734.897870 | | target function (ml) not normalized (free): 16539.657683 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2031 0.2033 0.1972 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2031 0.2033 0.1972 n_refl.: 191155 remove outliers: r(all,work,free)=0.2031 0.2033 0.1972 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2031 0.2033 0.1972 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1804 0.1802 0.1903 n_refl.: 191145 remove outliers: r(all,work,free)=0.1802 0.1800 0.1902 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 0.4070 402.814 292.751 0.435 0.912 0.299 13.296-10.522 99.01 99 1 0.2529 528.187 518.228 0.784 0.913 0.248 10.503-8.327 98.90 177 3 0.2468 564.205 559.764 0.971 0.913 0.223 8.318-6.595 100.00 360 8 0.2448 414.736 403.241 0.972 0.913 0.165 6.588-5.215 100.00 711 7 0.2302 381.101 365.084 0.956 0.913 0.129 5.214-4.128 98.38 1367 28 0.1463 557.435 551.255 1.082 0.913 0.100 4.126-3.266 94.74 2603 46 0.1333 508.132 499.243 1.148 0.913 0.023 3.266-2.585 99.86 5447 97 0.1442 342.774 337.638 1.120 0.913 0.000 2.585-2.046 97.45 10613 204 0.1407 258.603 254.212 1.126 0.912 0.000 2.046-1.619 99.39 21536 464 0.1626 153.054 149.709 1.144 0.911 0.000 1.619-1.281 98.00 42464 925 0.1914 82.395 80.154 1.128 0.909 0.000 1.281-0.980 96.53 101826 2055 0.2323 44.202 41.665 1.112 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0023 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1902 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1800 r_free=0.1902 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.090239 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.636284 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1504 0.0232 0.038 1.2 11.4 0.0 0.0 0 11.045 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 15.04 2.32 1.117 13.110 575.636 0.018 13.00 15.71 2.71 1.236 13.335 575.636 0.017 Individual atomic B min max mean iso aniso Overall: 5.20 73.04 15.01 1.40 435 3274 Protein: 5.20 40.60 10.99 1.40 0 2902 Water: 6.27 73.04 29.48 N/A 435 370 Other: 16.08 29.85 22.97 N/A 0 2 Chain A: 5.28 60.11 13.04 N/A 0 1626 Chain B: 5.20 73.04 12.76 N/A 0 1648 Chain S: 11.62 64.24 30.87 N/A 435 0 Histogram: Values Number of atoms 5.20 - 11.99 2172 11.99 - 18.77 636 18.77 - 25.55 314 25.55 - 32.34 254 32.34 - 39.12 162 39.12 - 45.91 106 45.91 - 52.69 43 52.69 - 59.47 16 59.47 - 66.26 5 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1571 r_work=0.1299 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1565 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 = 0.1284 r_free = 0.1556 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1284 r_free= 0.1556 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015570 | | target function (ls_wunit_k1) not normalized (work): 2916.176356 | | target function (ls_wunit_k1) not normalized (free): 116.521608 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1284 0.1556 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1467 0.1464 0.1632 n_refl.: 191137 remove outliers: r(all,work,free)=0.1467 0.1464 0.1632 n_refl.: 191137 overall B=0.18 to atoms: r(all,work,free)=0.1491 0.1488 0.1642 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1276 0.1547 n_refl.: 191137 remove outliers: r(all,work,free)=0.1281 0.1276 0.1546 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3599 402.814 381.688 0.487 0.964 0.275 13.296-10.522 99.01 99 1 0.2098 528.187 522.188 0.738 0.965 0.245 10.503-8.327 98.90 177 3 0.1726 564.205 562.461 0.886 0.965 0.193 8.318-6.595 100.00 360 8 0.1720 414.736 412.691 0.907 0.965 0.145 6.588-5.215 100.00 711 7 0.1548 381.101 373.357 0.886 0.965 0.140 5.214-4.128 98.38 1367 28 0.0904 557.435 554.332 0.977 0.965 0.070 4.126-3.266 94.74 2603 46 0.0831 508.132 504.284 1.043 0.966 0.014 3.266-2.585 99.86 5447 97 0.0920 342.774 340.421 1.025 0.966 0.000 2.585-2.046 97.45 10613 204 0.0951 258.603 256.390 1.036 0.966 0.000 2.046-1.619 99.39 21536 464 0.1088 153.054 151.411 1.054 0.966 0.000 1.619-1.281 98.00 42464 925 0.1282 82.395 81.403 1.046 0.966 0.000 1.281-0.980 96.52 101826 2054 0.1880 44.201 42.151 1.022 0.966 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0403 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1546 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1546 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1546 | n_water=805 | time (s): 2.770 (total time: 2.770) Filter (dist) r_work=0.1281 r_free=0.1549 | n_water=794 | time (s): 96.990 (total time: 99.760) Filter (q & B) r_work=0.1281 r_free=0.1548 | n_water=789 | time (s): 4.010 (total time: 103.770) Compute maps r_work=0.1281 r_free=0.1548 | n_water=789 | time (s): 1.970 (total time: 105.740) Filter (map) r_work=0.1305 r_free=0.1531 | n_water=655 | time (s): 4.850 (total time: 110.590) Find peaks r_work=0.1305 r_free=0.1531 | n_water=655 | time (s): 0.920 (total time: 111.510) Add new water r_work=0.1329 r_free=0.1561 | n_water=963 | time (s): 4.910 (total time: 116.420) Refine new water occ: r_work=0.1287 r_free=0.1513 adp: r_work=0.1274 r_free=0.1511 occ: r_work=0.1277 r_free=0.1506 adp: r_work=0.1269 r_free=0.1507 occ: r_work=0.1271 r_free=0.1505 adp: r_work=0.1268 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1506 r_work=0.1268 r_free=0.1506 | n_water=963 | time (s): 92.710 (total time: 209.130) Filter (q & B) r_work=0.1272 r_free=0.1506 | n_water=893 | time (s): 4.270 (total time: 213.400) Filter (dist only) r_work=0.1272 r_free=0.1504 | n_water=892 | time (s): 109.770 (total time: 323.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.337512 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 593.565150 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 0.1253 0.1524 0.0271 0.041 1.1 20.2 0.0 0.0 0 11.669 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.53 15.24 2.71 2.042 15.246 593.565 0.014 12.32 15.14 2.82 2.422 15.308 593.565 0.014 Individual atomic B min max mean iso aniso Overall: 5.39 68.22 16.46 1.20 524 3272 Protein: 5.39 40.02 10.98 1.20 0 2902 Water: 6.72 68.22 34.28 N/A 524 368 Other: 16.29 33.11 24.70 N/A 0 2 Chain A: 5.55 55.91 13.00 N/A 0 1624 Chain B: 5.39 68.22 12.83 N/A 0 1648 Chain S: 9.20 67.53 38.64 N/A 524 0 Histogram: Values Number of atoms 5.39 - 11.68 2052 11.68 - 17.96 724 17.96 - 24.24 258 24.24 - 30.52 203 30.52 - 36.81 179 36.81 - 43.09 155 43.09 - 49.37 106 49.37 - 55.65 65 55.65 - 61.94 30 61.94 - 68.22 24 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1514 r_work=0.1233 r_free=0.1515 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1515 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1512 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.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1512 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013350 | | target function (ls_wunit_k1) not normalized (work): 2500.430066 | | target function (ls_wunit_k1) not normalized (free): 103.742393 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1512 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1433 0.1430 0.1609 n_refl.: 191136 remove outliers: r(all,work,free)=0.1433 0.1430 0.1609 n_refl.: 191136 overall B=-0.02 to atoms: r(all,work,free)=0.1430 0.1427 0.1607 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1519 n_refl.: 191136 remove outliers: r(all,work,free)=0.1239 0.1233 0.1519 n_refl.: 191136 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3329 402.814 375.437 0.487 0.962 0.267 13.296-10.522 99.01 99 1 0.1916 528.187 520.015 0.754 0.963 0.223 10.503-8.327 98.90 177 3 0.1387 564.205 567.779 0.918 0.963 0.174 8.318-6.595 100.00 360 8 0.1537 414.736 415.217 0.935 0.963 0.145 6.588-5.215 100.00 711 7 0.1344 381.101 376.789 0.913 0.963 0.140 5.214-4.128 98.38 1367 28 0.0821 557.435 555.979 0.996 0.963 0.090 4.126-3.266 94.74 2603 46 0.0749 508.132 505.597 1.060 0.963 0.014 3.266-2.585 99.86 5447 97 0.0853 342.774 341.329 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0898 258.603 256.765 1.058 0.961 0.000 2.046-1.619 99.39 21536 464 0.1048 153.054 151.620 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1259 82.395 81.345 1.072 0.957 0.000 1.281-0.980 96.52 101826 2054 0.1876 44.201 42.214 1.058 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0478 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1519 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1519 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1519 | n_water=892 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1235 r_free=0.1520 | n_water=888 | time (s): 113.340 (total time: 116.580) Filter (q & B) r_work=0.1235 r_free=0.1520 | n_water=887 | time (s): 5.220 (total time: 121.800) Compute maps r_work=0.1235 r_free=0.1520 | n_water=887 | time (s): 1.620 (total time: 123.420) Filter (map) r_work=0.1276 r_free=0.1520 | n_water=685 | time (s): 5.380 (total time: 128.800) Find peaks r_work=0.1276 r_free=0.1520 | n_water=685 | time (s): 0.810 (total time: 129.610) Add new water r_work=0.1299 r_free=0.1550 | n_water=1013 | time (s): 5.410 (total time: 135.020) Refine new water occ: r_work=0.1253 r_free=0.1511 adp: r_work=0.1254 r_free=0.1514 occ: r_work=0.1250 r_free=0.1507 adp: r_work=0.1249 r_free=0.1509 occ: r_work=0.1247 r_free=0.1504 adp: r_work=0.1246 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1246 r_free=0.1505 r_work=0.1246 r_free=0.1505 | n_water=1013 | time (s): 191.240 (total time: 326.260) Filter (q & B) r_work=0.1250 r_free=0.1510 | n_water=880 | time (s): 4.960 (total time: 331.220) Filter (dist only) r_work=0.1251 r_free=0.1510 | n_water=879 | time (s): 129.120 (total time: 460.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.688600 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.196403 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 0.1241 0.1438 0.0197 0.035 1.1 8.3 0.0 0.0 0 0.844 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.38 1.97 1.931 14.591 16.196 3.941 12.33 13.98 1.64 2.214 14.499 16.196 3.896 Individual atomic B min max mean iso aniso Overall: 5.54 67.83 15.28 1.06 513 3270 Protein: 5.54 36.73 10.75 1.06 0 2902 Water: 6.70 67.83 30.24 N/A 513 366 Other: 13.99 28.89 21.44 N/A 0 2 Chain A: 5.54 55.08 12.78 N/A 0 1624 Chain B: 5.54 67.83 12.53 N/A 0 1646 Chain S: 12.95 62.36 32.05 N/A 513 0 Histogram: Values Number of atoms 5.54 - 11.77 2138 11.77 - 18.00 680 18.00 - 24.23 297 24.23 - 30.45 230 30.45 - 36.68 187 36.68 - 42.91 144 42.91 - 49.14 69 49.14 - 55.37 30 55.37 - 61.60 6 61.60 - 67.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1234 r_free=0.1398 r_work=0.1234 r_free=0.1399 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1399 target_work(ml) = 3.897 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1228 r_free = 0.1390 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191136 (all), 2.01 % free)-----------| | | | r_work= 0.1228 r_free= 0.1390 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890464 | | target function (ml) not normalized (work): 728668.429270 | | target function (ml) not normalized (free): 15208.897369 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1228 0.1390 n_refl.: 191136 re-set all scales: r(all,work,free)=0.1443 0.1443 0.1487 n_refl.: 191136 remove outliers: r(all,work,free)=0.1443 0.1443 0.1487 n_refl.: 191136 overall B=-0.03 to atoms: r(all,work,free)=0.1437 0.1437 0.1484 n_refl.: 191136 bulk-solvent and scaling: r(all,work,free)=0.1228 0.1225 0.1386 n_refl.: 191136 remove outliers: r(all,work,free)=0.1227 0.1224 0.1386 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3695 393.525 366.879 0.432 0.946 0.261 13.296-10.522 99.01 99 1 0.2523 528.187 508.441 0.710 0.947 0.240 10.503-8.327 97.80 175 3 0.1979 554.286 558.474 0.886 0.947 0.177 8.318-6.595 100.00 360 8 0.2113 414.736 409.269 0.897 0.947 0.137 6.588-5.215 100.00 711 7 0.1803 381.101 370.678 0.886 0.947 0.119 5.214-4.128 98.38 1367 28 0.1163 557.435 551.554 0.974 0.947 0.090 4.126-3.266 94.74 2603 46 0.1092 508.132 501.387 1.033 0.947 0.014 3.266-2.585 99.86 5447 97 0.1084 342.774 339.162 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0967 258.603 255.685 1.033 0.946 0.000 2.046-1.619 99.39 21536 464 0.0977 153.054 151.382 1.056 0.945 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.481 1.052 0.943 0.000 1.281-0.980 96.52 101826 2054 0.1686 44.201 42.313 1.037 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0968 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1386 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1224 r_free=0.1386 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1224 r_free=0.1386 | n_water=879 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1225 r_free=0.1387 | n_water=878 | time (s): 105.720 (total time: 108.310) Filter (q & B) r_work=0.1225 r_free=0.1384 | n_water=864 | time (s): 4.150 (total time: 112.460) Compute maps r_work=0.1225 r_free=0.1384 | n_water=864 | time (s): 1.690 (total time: 114.150) Filter (map) r_work=0.1247 r_free=0.1386 | n_water=722 | time (s): 5.110 (total time: 119.260) Find peaks r_work=0.1247 r_free=0.1386 | n_water=722 | time (s): 0.700 (total time: 119.960) Add new water r_work=0.1262 r_free=0.1398 | n_water=956 | time (s): 4.620 (total time: 124.580) Refine new water occ: r_work=0.1215 r_free=0.1357 adp: r_work=0.1207 r_free=0.1352 occ: r_work=0.1205 r_free=0.1353 adp: r_work=0.1205 r_free=0.1352 occ: r_work=0.1203 r_free=0.1353 adp: r_work=0.1203 r_free=0.1352 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1352 r_work=0.1203 r_free=0.1352 | n_water=956 | time (s): 262.440 (total time: 387.020) Filter (q & B) r_work=0.1207 r_free=0.1356 | n_water=874 | time (s): 5.690 (total time: 392.710) Filter (dist only) r_work=0.1207 r_free=0.1354 | n_water=872 | time (s): 114.220 (total time: 506.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.593997 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.899715 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 0.1204 0.1354 0.0150 0.036 1.1 6.5 0.0 0.0 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.04 13.54 1.50 1.836 14.229 15.900 3.873 11.96 13.49 1.53 1.979 14.180 15.900 3.864 Individual atomic B min max mean iso aniso Overall: 5.49 67.25 14.99 1.00 506 3270 Protein: 5.49 33.26 10.65 1.00 0 2902 Water: 5.91 67.25 29.40 N/A 506 366 Other: 13.95 27.64 20.79 N/A 0 2 Chain A: 5.57 53.60 12.62 N/A 0 1624 Chain B: 5.49 67.25 12.42 N/A 0 1646 Chain S: 5.91 62.46 30.95 N/A 506 0 Histogram: Values Number of atoms 5.49 - 11.67 2116 11.67 - 17.84 728 17.84 - 24.02 299 24.02 - 30.20 230 30.20 - 36.37 174 36.37 - 42.55 131 42.55 - 48.72 63 48.72 - 54.90 28 54.90 - 61.07 5 61.07 - 67.25 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1349 r_work=0.1196 r_free=0.1350 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1350 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1349 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862117 | | target function (ml) not normalized (work): 723343.559640 | | target function (ml) not normalized (free): 15111.976562 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1418 0.1418 0.1456 n_refl.: 191132 remove outliers: r(all,work,free)=0.1418 0.1418 0.1456 n_refl.: 191132 overall B=-0.03 to atoms: r(all,work,free)=0.1412 0.1411 0.1451 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1346 n_refl.: 191132 remove outliers: r(all,work,free)=0.1195 0.1192 0.1346 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3625 352.344 318.799 0.406 0.946 0.242 13.296-10.522 96.04 96 1 0.2403 480.239 446.681 0.692 0.948 0.183 10.503-8.327 97.80 175 3 0.2066 501.706 497.049 0.868 0.948 0.157 8.318-6.595 100.00 360 8 0.2159 375.394 370.868 0.893 0.947 0.110 6.588-5.215 100.00 711 7 0.1864 344.950 335.293 0.884 0.948 0.094 5.214-4.128 98.38 1367 28 0.1176 504.557 499.653 0.975 0.948 0.080 4.126-3.266 94.74 2603 46 0.1101 459.931 453.748 1.034 0.948 0.005 3.266-2.585 99.86 5447 97 0.1081 310.258 307.167 1.021 0.948 0.000 2.585-2.046 97.45 10613 204 0.0932 234.072 231.687 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0916 138.535 137.242 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0987 74.579 73.884 1.052 0.946 0.000 1.281-0.980 96.52 101826 2054 0.1662 40.008 38.355 1.036 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1136 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1346 | n_water=872 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1192 r_free=0.1346 | n_water=872 | time (s): 109.470 (total time: 112.130) Filter (q & B) r_work=0.1192 r_free=0.1346 | n_water=866 | time (s): 5.330 (total time: 117.460) Compute maps r_work=0.1192 r_free=0.1346 | n_water=866 | time (s): 2.150 (total time: 119.610) Filter (map) r_work=0.1211 r_free=0.1348 | n_water=752 | time (s): 4.420 (total time: 124.030) Find peaks r_work=0.1211 r_free=0.1348 | n_water=752 | time (s): 0.720 (total time: 124.750) Add new water r_work=0.1223 r_free=0.1358 | n_water=970 | time (s): 4.020 (total time: 128.770) Refine new water occ: r_work=0.1189 r_free=0.1332 adp: r_work=0.1189 r_free=0.1331 occ: r_work=0.1187 r_free=0.1333 adp: r_work=0.1187 r_free=0.1331 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1333 r_work=0.1185 r_free=0.1333 | n_water=970 | time (s): 288.460 (total time: 417.230) Filter (q & B) r_work=0.1188 r_free=0.1342 | n_water=897 | time (s): 4.200 (total time: 421.430) Filter (dist only) r_work=0.1189 r_free=0.1341 | n_water=896 | time (s): 117.060 (total time: 538.490) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.545530 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.244687 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1349 0.0157 0.037 1.1 6.8 0.0 0.3 0 0.773 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.49 1.57 1.789 14.146 15.245 3.762 11.95 13.53 1.57 1.834 14.128 15.245 3.760 Individual atomic B min max mean iso aniso Overall: 5.58 66.99 15.00 0.96 530 3270 Protein: 5.58 32.12 10.59 0.96 0 2902 Water: 5.91 66.99 29.25 N/A 530 366 Other: 13.80 26.77 20.28 N/A 0 2 Chain A: 5.59 52.94 12.54 N/A 0 1624 Chain B: 5.58 66.99 12.34 N/A 0 1646 Chain S: 5.91 62.46 30.77 N/A 530 0 Histogram: Values Number of atoms 5.58 - 11.72 2142 11.72 - 17.86 718 17.86 - 24.00 296 24.00 - 30.14 239 30.14 - 36.28 174 36.28 - 42.42 129 42.42 - 48.56 67 48.56 - 54.71 28 54.71 - 60.85 5 60.85 - 66.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1353 r_work=0.1196 r_free=0.1353 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1353 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1357 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758897 | | target function (ml) not normalized (work): 703992.635247 | | target function (ml) not normalized (free): 14731.727670 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1357 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1397 0.1396 0.1471 n_refl.: 191127 remove outliers: r(all,work,free)=0.1397 0.1396 0.1471 n_refl.: 191127 overall B=-0.04 to atoms: r(all,work,free)=0.1390 0.1389 0.1467 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1355 n_refl.: 191127 remove outliers: r(all,work,free)=0.1196 0.1193 0.1355 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3667 352.344 319.900 0.388 0.950 0.216 13.296-10.522 96.04 96 1 0.2424 480.239 460.000 0.701 0.951 0.163 10.503-8.327 97.80 175 3 0.2135 501.706 495.250 0.863 0.951 0.139 8.315-6.595 100.00 359 8 0.2098 374.449 370.610 0.889 0.951 0.110 6.588-5.215 100.00 711 7 0.1892 344.950 335.272 0.882 0.951 0.090 5.214-4.128 98.38 1367 28 0.1192 504.557 499.327 0.971 0.952 0.034 4.126-3.266 94.74 2603 46 0.1120 459.931 453.459 1.031 0.952 0.000 3.266-2.585 99.86 5447 97 0.1096 310.258 307.033 1.018 0.952 0.000 2.585-2.046 97.45 10613 204 0.0940 234.072 231.578 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0914 138.535 137.226 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0978 74.579 73.869 1.047 0.951 0.000 1.281-0.980 96.52 101826 2054 0.1654 40.008 38.341 1.032 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1269 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1355 | n_water=896 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1194 r_free=0.1356 | n_water=894 | time (s): 122.520 (total time: 125.180) Filter (q & B) r_work=0.1194 r_free=0.1356 | n_water=881 | time (s): 5.160 (total time: 130.340) Compute maps r_work=0.1194 r_free=0.1356 | n_water=881 | time (s): 1.960 (total time: 132.300) Filter (map) r_work=0.1218 r_free=0.1357 | n_water=758 | time (s): 4.600 (total time: 136.900) Find peaks r_work=0.1218 r_free=0.1357 | n_water=758 | time (s): 0.700 (total time: 137.600) Add new water r_work=0.1227 r_free=0.1365 | n_water=969 | time (s): 4.360 (total time: 141.960) Refine new water occ: r_work=0.1193 r_free=0.1341 adp: r_work=0.1193 r_free=0.1340 occ: r_work=0.1191 r_free=0.1340 adp: r_work=0.1191 r_free=0.1340 occ: r_work=0.1189 r_free=0.1340 adp: r_work=0.1189 r_free=0.1340 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1340 r_work=0.1189 r_free=0.1340 | n_water=969 | time (s): 181.490 (total time: 323.450) Filter (q & B) r_work=0.1193 r_free=0.1344 | n_water=894 | time (s): 4.160 (total time: 327.610) Filter (dist only) r_work=0.1194 r_free=0.1343 | n_water=893 | time (s): 111.980 (total time: 439.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.530643 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.089790 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 0.1346 0.0149 0.037 1.1 8.5 0.0 0.3 0 0.765 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.46 1.49 1.765 14.049 15.090 3.760 12.00 13.47 1.47 1.902 14.006 15.090 3.757 Individual atomic B min max mean iso aniso Overall: 5.56 65.88 14.85 0.91 527 3270 Protein: 5.56 29.68 10.49 0.91 0 2902 Water: 5.98 65.88 29.02 N/A 527 366 Other: 13.88 23.88 18.88 N/A 0 2 Chain A: 5.64 51.43 12.40 N/A 0 1624 Chain B: 5.56 65.88 12.22 N/A 0 1646 Chain S: 5.98 62.55 30.64 N/A 527 0 Histogram: Values Number of atoms 5.56 - 11.60 2110 11.60 - 17.63 776 17.63 - 23.66 278 23.66 - 29.69 212 29.69 - 35.72 183 35.72 - 41.75 130 41.75 - 47.78 73 47.78 - 53.81 27 53.81 - 59.84 6 59.84 - 65.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1347 r_work=0.1200 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1348 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1346 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756250 | | target function (ml) not normalized (work): 703493.015252 | | target function (ml) not normalized (free): 14715.173847 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1346 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1467 n_refl.: 191126 remove outliers: r(all,work,free)=0.1402 0.1401 0.1467 n_refl.: 191126 overall B=-0.22 to atoms: r(all,work,free)=0.1367 0.1366 0.1447 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1344 n_refl.: 191126 remove outliers: r(all,work,free)=0.1200 0.1197 0.1344 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3766 352.344 319.397 0.386 0.951 0.202 13.296-10.522 96.04 96 1 0.2422 480.239 460.818 0.717 0.953 0.153 10.503-8.327 97.80 175 3 0.2139 501.706 495.454 0.880 0.953 0.131 8.315-6.595 100.00 359 8 0.2120 374.449 370.519 0.905 0.953 0.100 6.588-5.215 100.00 711 7 0.1919 344.950 335.175 0.900 0.953 0.080 5.214-4.128 98.38 1367 28 0.1220 504.557 499.099 0.995 0.953 0.060 4.126-3.266 94.74 2603 46 0.1144 459.931 453.206 1.055 0.954 0.000 3.266-2.585 99.86 5447 97 0.1113 310.258 307.020 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0949 234.072 231.565 1.047 0.953 0.000 2.046-1.619 99.39 21536 464 0.0911 138.535 137.242 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0971 74.579 73.882 1.053 0.951 0.000 1.281-0.980 96.52 101826 2054 0.1649 40.008 38.348 1.024 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0477 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1345 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1345 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1345 | n_water=893 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1197 r_free=0.1345 | n_water=893 | time (s): 107.770 (total time: 110.260) Filter (q & B) r_work=0.1198 r_free=0.1344 | n_water=883 | time (s): 4.280 (total time: 114.540) Compute maps r_work=0.1198 r_free=0.1344 | n_water=883 | time (s): 1.770 (total time: 116.310) Filter (map) r_work=0.1220 r_free=0.1346 | n_water=767 | time (s): 5.140 (total time: 121.450) Find peaks r_work=0.1220 r_free=0.1346 | n_water=767 | time (s): 0.600 (total time: 122.050) Add new water r_work=0.1229 r_free=0.1353 | n_water=977 | time (s): 5.160 (total time: 127.210) Refine new water occ: r_work=0.1194 r_free=0.1334 adp: r_work=0.1194 r_free=0.1334 occ: r_work=0.1192 r_free=0.1334 adp: r_work=0.1192 r_free=0.1333 occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1190 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1333 r_work=0.1190 r_free=0.1333 | n_water=977 | time (s): 182.770 (total time: 309.980) Filter (q & B) r_work=0.1194 r_free=0.1336 | n_water=905 | time (s): 4.450 (total time: 314.430) Filter (dist only) r_work=0.1195 r_free=0.1338 | n_water=902 | time (s): 117.160 (total time: 431.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.613236 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.443391 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 0.1342 0.0144 0.038 1.1 6.5 0.0 0.3 0 0.807 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.42 1.44 1.723 13.760 14.443 3.757 11.99 13.44 1.45 1.767 13.739 14.443 3.755 Individual atomic B min max mean iso aniso Overall: 5.41 64.72 14.64 0.89 536 3270 Protein: 5.41 28.69 10.26 0.89 0 2902 Water: 5.83 64.72 28.72 N/A 536 366 Other: 13.71 22.52 18.12 N/A 0 2 Chain A: 5.47 50.99 12.13 N/A 0 1624 Chain B: 5.41 64.72 11.96 N/A 0 1646 Chain S: 5.83 62.45 30.45 N/A 536 0 Histogram: Values Number of atoms 5.41 - 11.34 2097 11.34 - 17.27 787 17.27 - 23.20 273 23.20 - 29.14 214 29.14 - 35.07 194 35.07 - 41.00 123 41.00 - 46.93 80 46.93 - 52.86 30 52.86 - 58.79 6 58.79 - 64.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1344 r_work=0.1199 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1344 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1346 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1346 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755120 | | target function (ml) not normalized (work): 703281.377034 | | target function (ml) not normalized (free): 14714.740492 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1198 0.1346 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1373 0.1372 0.1460 n_refl.: 191126 remove outliers: r(all,work,free)=0.1373 0.1372 0.1460 n_refl.: 191126 overall B=0.11 to atoms: r(all,work,free)=0.1390 0.1388 0.1470 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1335 n_refl.: 191126 remove outliers: r(all,work,free)=0.1190 0.1187 0.1335 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3787 352.344 317.536 0.391 0.925 0.197 13.296-10.522 96.04 96 1 0.2412 480.239 461.620 0.728 0.926 0.142 10.503-8.327 97.80 175 3 0.2158 501.706 493.536 0.898 0.926 0.117 8.315-6.595 100.00 359 8 0.2127 374.449 370.236 0.923 0.926 0.091 6.588-5.215 100.00 711 7 0.1923 344.950 335.353 0.922 0.926 0.073 5.214-4.128 98.38 1367 28 0.1226 504.557 498.694 1.018 0.926 0.034 4.126-3.266 94.74 2603 46 0.1153 459.931 452.320 1.082 0.926 0.000 3.266-2.585 99.86 5447 97 0.1115 310.258 306.642 1.068 0.925 0.000 2.585-2.046 97.45 10613 204 0.0954 234.072 231.440 1.081 0.924 0.000 2.046-1.619 99.39 21536 464 0.0906 138.535 137.135 1.104 0.922 0.000 1.619-1.281 98.00 42464 925 0.0948 74.579 73.925 1.103 0.920 0.000 1.281-0.980 96.52 101826 2054 0.1625 40.008 38.320 1.084 0.915 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0260 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1335 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1335 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1335 | n_water=902 | time (s): 2.780 (total time: 2.780) Filter (dist) r_work=0.1188 r_free=0.1334 | n_water=901 | time (s): 113.360 (total time: 116.140) Filter (q & B) r_work=0.1188 r_free=0.1334 | n_water=893 | time (s): 5.450 (total time: 121.590) Compute maps r_work=0.1188 r_free=0.1334 | n_water=893 | time (s): 2.560 (total time: 124.150) Filter (map) r_work=0.1213 r_free=0.1336 | n_water=771 | time (s): 5.280 (total time: 129.430) Find peaks r_work=0.1213 r_free=0.1336 | n_water=771 | time (s): 0.610 (total time: 130.040) Add new water r_work=0.1221 r_free=0.1345 | n_water=988 | time (s): 5.110 (total time: 135.150) Refine new water occ: r_work=0.1185 r_free=0.1323 adp: r_work=0.1185 r_free=0.1322 occ: r_work=0.1183 r_free=0.1324 adp: r_work=0.1183 r_free=0.1323 occ: r_work=0.1182 r_free=0.1324 adp: r_work=0.1182 r_free=0.1324 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1324 r_work=0.1182 r_free=0.1324 | n_water=988 | time (s): 251.240 (total time: 386.390) Filter (q & B) r_work=0.1186 r_free=0.1330 | n_water=910 | time (s): 4.720 (total time: 391.110) Filter (dist only) r_work=0.1187 r_free=0.1330 | n_water=908 | time (s): 118.280 (total time: 509.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.500854 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.584157 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 0.1340 0.0150 0.039 1.1 7.2 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.40 1.50 1.681 13.783 13.584 3.754 11.93 13.44 1.51 1.698 13.771 13.584 3.754 Individual atomic B min max mean iso aniso Overall: 5.53 64.22 14.66 0.87 543 3269 Protein: 5.53 28.32 10.38 0.87 0 2902 Water: 5.97 64.22 28.35 N/A 543 365 Other: 13.83 22.33 18.08 N/A 0 2 Chain A: 5.65 50.94 12.21 N/A 0 1624 Chain B: 5.53 64.22 12.04 N/A 0 1645 Chain S: 5.97 62.60 29.92 N/A 543 0 Histogram: Values Number of atoms 5.53 - 11.40 2076 11.40 - 17.27 813 17.27 - 23.13 269 23.13 - 29.00 235 29.00 - 34.87 192 34.87 - 40.74 114 40.74 - 46.61 72 46.61 - 52.48 31 52.48 - 58.35 8 58.35 - 64.22 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1344 r_work=0.1193 r_free=0.1344 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1344 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1345 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753939 | | target function (ml) not normalized (work): 703060.231876 | | target function (ml) not normalized (free): 14713.643137 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1345 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1487 n_refl.: 191126 remove outliers: r(all,work,free)=0.1402 0.1401 0.1487 n_refl.: 191126 overall B=-0.01 to atoms: r(all,work,free)=0.1401 0.1400 0.1486 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1343 n_refl.: 191126 remove outliers: r(all,work,free)=0.1195 0.1192 0.1343 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3812 352.344 316.359 0.363 0.995 0.193 13.296-10.522 96.04 96 1 0.2437 480.239 462.251 0.681 0.996 0.137 10.503-8.327 97.80 175 3 0.2226 501.706 492.668 0.843 0.997 0.113 8.315-6.595 100.00 359 8 0.2164 374.449 370.022 0.867 0.997 0.088 6.588-5.215 100.00 711 7 0.1940 344.950 335.088 0.867 0.997 0.073 5.214-4.128 98.38 1367 28 0.1247 504.557 498.490 0.958 0.998 0.034 4.126-3.266 94.74 2603 46 0.1162 459.931 452.279 1.019 0.999 0.000 3.266-2.585 99.86 5447 97 0.1126 310.258 306.626 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0957 234.072 231.467 1.012 1.002 0.000 2.046-1.619 99.39 21536 464 0.0910 138.535 137.169 1.029 1.006 0.000 1.619-1.281 98.00 42464 925 0.0947 74.579 73.930 1.022 1.011 0.000 1.281-0.980 96.52 101826 2054 0.1625 40.008 38.304 0.993 1.021 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0157 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1343 | n_water=908 | time (s): 3.180 (total time: 3.180) Filter (dist) r_work=0.1192 r_free=0.1343 | n_water=907 | time (s): 113.940 (total time: 117.120) Filter (q & B) r_work=0.1193 r_free=0.1343 | n_water=893 | time (s): 3.920 (total time: 121.040) Compute maps r_work=0.1193 r_free=0.1343 | n_water=893 | time (s): 1.770 (total time: 122.810) Filter (map) r_work=0.1216 r_free=0.1342 | n_water=776 | time (s): 4.600 (total time: 127.410) Find peaks r_work=0.1216 r_free=0.1342 | n_water=776 | time (s): 0.700 (total time: 128.110) Add new water r_work=0.1222 r_free=0.1353 | n_water=991 | time (s): 5.100 (total time: 133.210) Refine new water occ: r_work=0.1187 r_free=0.1327 adp: r_work=0.1187 r_free=0.1327 occ: r_work=0.1185 r_free=0.1327 adp: r_work=0.1185 r_free=0.1326 occ: r_work=0.1184 r_free=0.1326 adp: r_work=0.1184 r_free=0.1326 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1326 r_work=0.1184 r_free=0.1326 | n_water=991 | time (s): 236.780 (total time: 369.990) Filter (q & B) r_work=0.1188 r_free=0.1334 | n_water=913 | time (s): 4.840 (total time: 374.830) Filter (dist only) r_work=0.1189 r_free=0.1333 | n_water=911 | time (s): 114.860 (total time: 489.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524651 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.162714 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1338 0.0146 0.039 1.1 6.1 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.38 1.46 1.686 13.793 13.163 3.754 11.94 13.42 1.48 1.708 13.781 13.163 3.754 Individual atomic B min max mean iso aniso Overall: 5.60 63.25 14.67 0.85 546 3269 Protein: 5.60 27.88 10.37 0.85 0 2902 Water: 5.99 63.25 28.35 N/A 546 365 Other: 13.88 22.16 18.02 N/A 0 2 Chain A: 5.67 50.62 12.18 N/A 0 1624 Chain B: 5.60 63.25 12.02 N/A 0 1645 Chain S: 5.99 62.56 30.06 N/A 546 0 Histogram: Values Number of atoms 5.60 - 11.36 2065 11.36 - 17.13 830 17.13 - 22.89 264 22.89 - 28.66 220 28.66 - 34.42 191 34.42 - 40.19 118 40.19 - 45.95 81 45.95 - 51.72 34 51.72 - 57.49 7 57.49 - 63.25 5 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1342 r_work=0.1194 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1342 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1343 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1193 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753527 | | target function (ml) not normalized (work): 702983.053664 | | target function (ml) not normalized (free): 14715.670003 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1343 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1408 0.1407 0.1490 n_refl.: 191126 remove outliers: r(all,work,free)=0.1408 0.1407 0.1490 n_refl.: 191126 overall B=-0.07 to atoms: r(all,work,free)=0.1397 0.1396 0.1483 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1341 n_refl.: 191126 remove outliers: r(all,work,free)=0.1195 0.1192 0.1341 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3735 352.344 316.916 0.363 0.975 0.196 13.296-10.522 96.04 96 1 0.2428 480.239 462.039 0.676 0.976 0.134 10.503-8.327 97.80 175 3 0.2205 501.706 493.457 0.841 0.977 0.110 8.315-6.595 100.00 359 8 0.2141 374.449 370.166 0.864 0.977 0.080 6.588-5.215 100.00 711 7 0.1945 344.950 335.172 0.864 0.977 0.080 5.214-4.128 98.38 1367 28 0.1246 504.557 498.382 0.954 0.978 0.034 4.126-3.266 94.74 2603 46 0.1167 459.931 452.304 1.014 0.980 0.000 3.266-2.585 99.86 5447 97 0.1126 310.258 306.607 0.998 0.981 0.000 2.585-2.046 97.45 10613 204 0.0960 234.072 231.459 1.006 0.983 0.000 2.046-1.619 99.39 21536 464 0.0910 138.535 137.172 1.021 0.987 0.000 1.619-1.281 98.00 42464 925 0.0945 74.579 73.932 1.012 0.993 0.000 1.281-0.980 96.52 101826 2054 0.1625 40.008 38.292 0.980 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0145 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1342 After: r_work=0.1193 r_free=0.1342 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1342 | n_water=911 | time (s): 3.250 (total time: 3.250) Filter (dist) r_work=0.1193 r_free=0.1341 | n_water=910 | time (s): 118.420 (total time: 121.670) Filter (q & B) r_work=0.1194 r_free=0.1341 | n_water=900 | time (s): 4.360 (total time: 126.030) Compute maps r_work=0.1194 r_free=0.1341 | n_water=900 | time (s): 1.940 (total time: 127.970) Filter (map) r_work=0.1215 r_free=0.1346 | n_water=789 | time (s): 5.790 (total time: 133.760) Find peaks r_work=0.1215 r_free=0.1346 | n_water=789 | time (s): 0.630 (total time: 134.390) Add new water r_work=0.1222 r_free=0.1359 | n_water=1002 | time (s): 4.040 (total time: 138.430) Refine new water occ: r_work=0.1189 r_free=0.1338 adp: r_work=0.1189 r_free=0.1337 occ: r_work=0.1187 r_free=0.1335 adp: r_work=0.1187 r_free=0.1336 occ: r_work=0.1186 r_free=0.1333 adp: r_work=0.1186 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1333 r_work=0.1186 r_free=0.1333 | n_water=1002 | time (s): 222.840 (total time: 361.270) Filter (q & B) r_work=0.1190 r_free=0.1338 | n_water=925 | time (s): 5.490 (total time: 366.760) Filter (dist only) r_work=0.1191 r_free=0.1337 | n_water=923 | time (s): 117.950 (total time: 484.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.566412 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.871499 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1345 0.0149 0.039 1.2 9.2 0.0 0.3 0 0.783 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.45 1.49 1.677 13.743 13.871 3.757 11.95 13.47 1.52 1.674 13.744 13.871 3.755 Individual atomic B min max mean iso aniso Overall: 5.55 62.38 14.66 0.85 558 3269 Protein: 5.55 27.92 10.33 0.85 0 2902 Water: 5.96 62.38 28.28 N/A 558 365 Other: 13.82 22.21 18.01 N/A 0 2 Chain A: 5.64 50.28 12.10 N/A 0 1624 Chain B: 5.55 62.20 11.95 N/A 0 1645 Chain S: 5.96 62.38 30.08 N/A 558 0 Histogram: Values Number of atoms 5.55 - 11.24 2042 11.24 - 16.92 846 16.92 - 22.60 270 22.60 - 28.29 218 28.29 - 33.97 196 33.97 - 39.65 120 39.65 - 45.33 84 45.33 - 51.02 35 51.02 - 56.70 11 56.70 - 62.38 5 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1347 r_work=0.1195 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1347 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1345 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1345 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754909 | | target function (ml) not normalized (work): 703241.869409 | | target function (ml) not normalized (free): 14720.615153 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7395 127 0.1361 0.1413 5.686 5.755| | 2: 2.94 - 2.33 1.00 7339 128 0.1073 0.1305 5.0739 5.1563| | 3: 2.33 - 2.04 0.96 6939 150 0.0902 0.1172 4.6494 4.7351| | 4: 2.04 - 1.85 1.00 7170 155 0.0900 0.1045 4.3901 4.5571| | 5: 1.85 - 1.72 0.99 7113 159 0.0934 0.1004 4.1526 4.2488| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1089 3.9493 4.0713| | 7: 1.62 - 1.54 0.99 7104 148 0.0891 0.0983 3.8036 3.9463| | 8: 1.54 - 1.47 0.96 6798 152 0.0898 0.1323 3.7087 3.9147| | 9: 1.47 - 1.41 0.98 6938 155 0.0930 0.1154 3.63 3.7717| | 10: 1.41 - 1.36 0.99 7022 150 0.0979 0.1205 3.5637 3.6808| | 11: 1.36 - 1.32 0.99 6997 151 0.0997 0.1148 3.4912 3.5975| | 12: 1.32 - 1.28 0.98 6975 149 0.1038 0.1140 3.4641 3.5905| | 13: 1.28 - 1.25 0.98 6907 166 0.1044 0.1247 3.4395 3.5695| | 14: 1.25 - 1.22 0.98 7015 112 0.1105 0.1584 3.4318 3.6793| | 15: 1.22 - 1.19 0.98 6956 137 0.1166 0.1241 3.4434 3.4785| | 16: 1.19 - 1.17 0.93 6604 131 0.1247 0.1497 3.4595 3.5954| | 17: 1.17 - 1.14 0.98 6940 135 0.1295 0.1225 3.4289 3.4389| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1709 3.4374 3.5336| | 19: 1.12 - 1.10 0.97 6948 106 0.1473 0.1773 3.4215 3.6018| | 20: 1.10 - 1.08 0.97 6884 147 0.1586 0.1591 3.4116 3.4392| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2166 3.4185 3.5104| | 22: 1.07 - 1.05 0.97 6836 135 0.1906 0.1943 3.4138 3.4137| | 23: 1.05 - 1.03 0.97 6827 159 0.2121 0.2016 3.433 3.487| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2259 3.4358 3.5129| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2515 3.4496 3.5236| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2861 3.4154 3.4239| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2794 3.4697 3.395| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7395 127 0.93 11.51 1.00 0.97 10922.45| | 2: 2.94 - 2.33 7339 128 0.93 12.58 0.99 0.98 5001.72| | 3: 2.33 - 2.04 6939 150 0.96 7.51 1.01 0.98 1664.45| | 4: 2.04 - 1.85 7170 155 0.96 7.60 1.00 0.98 995.30| | 5: 1.85 - 1.72 7113 159 0.96 8.11 1.00 0.98 637.16| | 6: 1.72 - 1.62 7102 142 0.96 8.12 1.00 0.99 448.89| | 7: 1.62 - 1.54 7104 148 0.96 8.24 1.01 1.00 343.06| | 8: 1.54 - 1.47 6798 152 0.96 8.42 1.01 1.00 285.73| | 9: 1.47 - 1.41 6938 155 0.96 8.65 1.00 1.00 237.52| | 10: 1.41 - 1.36 7022 150 0.96 9.09 1.00 1.00 207.85| | 11: 1.36 - 1.32 6997 151 0.96 9.08 0.99 0.98 178.51| | 12: 1.32 - 1.28 6975 149 0.96 9.10 0.98 0.97 162.92| | 13: 1.28 - 1.25 6907 166 0.96 9.60 1.01 0.98 159.69| | 14: 1.25 - 1.22 7015 112 0.95 10.65 1.01 0.99 162.21| | 15: 1.22 - 1.19 6956 137 0.95 11.07 1.01 1.00 162.52| | 16: 1.19 - 1.17 6604 131 0.95 11.15 1.01 0.98 154.22| | 17: 1.17 - 1.14 6940 135 0.94 12.02 1.01 0.98 149.54| | 18: 1.14 - 1.12 6875 142 0.94 12.68 1.01 0.97 146.59| | 19: 1.12 - 1.10 6948 106 0.93 14.22 1.00 0.97 152.32| | 20: 1.10 - 1.08 6884 147 0.92 15.34 1.00 0.96 151.72| | 21: 1.08 - 1.07 6852 152 0.91 16.73 1.00 0.95 154.47| | 22: 1.07 - 1.05 6836 135 0.89 18.36 0.99 0.95 155.42| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.94 164.93| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.99 0.95 179.13| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.92 182.12| | 26: 1.01 - 0.99 6767 158 0.81 26.63 0.98 0.91 176.49| | 27: 0.99 - 0.98 6647 131 0.82 26.26 0.99 0.90 160.37| |alpha: min = 0.90 max = 1.00 mean = 0.97| |beta: min = 146.59 max = 10922.45 mean = 908.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.96 mean = 13.29| |phase err.(test): min = 0.00 max = 89.43 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1345 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1405 0.1404 0.1486 n_refl.: 191126 remove outliers: r(all,work,free)=0.1405 0.1404 0.1486 n_refl.: 191126 overall B=-0.01 to atoms: r(all,work,free)=0.1404 0.1402 0.1485 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1342 n_refl.: 191126 remove outliers: r(all,work,free)=0.1196 0.1193 0.1342 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3744 352.344 316.770 0.345 0.994 0.180 13.296-10.522 96.04 96 1 0.2415 480.239 462.166 0.652 0.995 0.112 10.503-8.327 97.80 175 3 0.2206 501.706 492.546 0.824 0.996 0.085 8.315-6.595 100.00 359 8 0.2119 374.449 370.232 0.846 0.996 0.075 6.588-5.215 100.00 711 7 0.1931 344.950 334.787 0.844 0.996 0.067 5.214-4.128 98.38 1367 28 0.1253 504.557 498.360 0.935 0.996 0.029 4.126-3.266 94.74 2603 46 0.1166 459.931 452.197 0.997 0.996 0.000 3.266-2.585 99.86 5447 97 0.1126 310.258 306.613 0.982 0.996 0.000 2.585-2.046 97.45 10613 204 0.0963 234.072 231.440 0.992 0.996 0.000 2.046-1.619 99.39 21536 464 0.0912 138.535 137.140 1.012 0.996 0.000 1.619-1.281 98.00 42464 925 0.0948 74.579 73.927 1.010 0.996 0.000 1.281-0.980 96.52 101826 2054 0.1623 40.008 38.293 0.991 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0021 ================= 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 : 0.2033 0.1972 0.083 5.155 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1902 0.083 5.155 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1902 0.083 5.155 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1902 0.083 5.155 5.2 78.0 14.6 805 0.000 1_weight: 0.1800 0.1902 0.083 5.155 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1272 0.1504 0.038 1.162 5.2 78.0 14.6 805 0.156 1_adp: 0.1300 0.1571 0.038 1.162 5.2 73.0 15.0 805 0.156 1_regHadp: 0.1299 0.1565 0.038 1.162 5.2 73.0 15.0 805 0.156 1_occ: 0.1284 0.1556 0.038 1.162 5.2 73.0 15.0 805 0.156 2_bss: 0.1276 0.1546 0.038 1.162 5.4 73.2 15.2 805 0.156 2_settarget: 0.1276 0.1546 0.038 1.162 5.4 73.2 15.2 805 0.156 2_updatecdl: 0.1276 0.1546 0.038 1.170 5.4 73.2 15.2 805 0.156 2_nqh: 0.1276 0.1546 0.038 1.170 5.4 73.2 15.2 805 0.156 2_sol: 0.1272 0.1504 0.038 1.170 5.4 73.2 16.4 892 n/a 2_weight: 0.1272 0.1504 0.038 1.170 5.4 73.2 16.4 892 n/a 2_xyzrec: 0.1253 0.1524 0.041 1.146 5.4 73.2 16.4 892 n/a 2_adp: 0.1232 0.1514 0.041 1.146 5.4 68.2 16.5 892 n/a 2_regHadp: 0.1233 0.1515 0.041 1.146 5.4 68.2 16.5 892 n/a 2_occ: 0.1226 0.1512 0.041 1.146 5.4 68.2 16.5 892 n/a 3_bss: 0.1233 0.1519 0.041 1.146 5.4 68.2 16.4 892 n/a 3_settarget: 0.1233 0.1519 0.041 1.146 5.4 68.2 16.4 892 n/a 3_updatecdl: 0.1233 0.1519 0.041 1.145 5.4 68.2 16.4 892 n/a 3_nqh: 0.1233 0.1519 0.041 1.145 5.4 68.2 16.4 892 n/a 3_sol: 0.1251 0.1510 0.041 1.145 5.4 68.2 15.4 879 n/a 3_weight: 0.1251 0.1510 0.041 1.145 5.4 68.2 15.4 879 n/a 3_xyzrec: 0.1241 0.1438 0.035 1.099 5.4 68.2 15.4 879 n/a 3_adp: 0.1234 0.1398 0.035 1.099 5.5 67.8 15.3 879 n/a 3_regHadp: 0.1234 0.1399 0.035 1.099 5.5 67.8 15.3 879 n/a 3_occ: 0.1228 0.1390 0.035 1.099 5.5 67.8 15.3 879 n/a 4_bss: 0.1224 0.1386 0.035 1.099 5.5 67.8 15.3 879 n/a 4_settarget: 0.1224 0.1386 0.035 1.099 5.5 67.8 15.3 879 n/a 4_updatecdl: 0.1224 0.1386 0.035 1.104 5.5 67.8 15.3 879 n/a 4_nqh: 0.1224 0.1386 0.035 1.104 5.5 67.8 15.3 879 n/a 4_sol: 0.1207 0.1354 0.035 1.104 5.5 67.8 15.1 872 n/a 4_weight: 0.1207 0.1354 0.035 1.104 5.5 67.8 15.1 872 n/a 4_xyzrec: 0.1204 0.1354 0.036 1.133 5.5 67.8 15.1 872 n/a 4_adp: 0.1196 0.1349 0.036 1.133 5.5 67.2 15.0 872 n/a 4_regHadp: 0.1196 0.1350 0.036 1.133 5.5 67.2 15.0 872 n/a 4_occ: 0.1194 0.1349 0.036 1.133 5.5 67.2 15.0 872 n/a 5_bss: 0.1192 0.1346 0.036 1.133 5.5 67.2 15.0 872 n/a 5_settarget: 0.1192 0.1346 0.036 1.133 5.5 67.2 15.0 872 n/a 5_updatecdl: 0.1192 0.1346 0.036 1.134 5.5 67.2 15.0 872 n/a 5_nqh: 0.1192 0.1346 0.036 1.134 5.5 67.2 15.0 872 n/a 5_sol: 0.1189 0.1341 0.036 1.134 5.5 67.2 15.0 896 n/a 5_weight: 0.1189 0.1341 0.036 1.134 5.5 67.2 15.0 896 n/a 5_xyzrec: 0.1192 0.1349 0.037 1.129 5.5 67.2 15.0 896 n/a 5_adp: 0.1195 0.1353 0.037 1.129 5.6 67.0 15.0 896 n/a 5_regHadp: 0.1196 0.1353 0.037 1.129 5.6 67.0 15.0 896 n/a 5_occ: 0.1194 0.1357 0.037 1.129 5.6 67.0 15.0 896 n/a 6_bss: 0.1193 0.1355 0.037 1.129 5.5 67.0 15.0 896 n/a 6_settarget: 0.1193 0.1355 0.037 1.129 5.5 67.0 15.0 896 n/a 6_updatecdl: 0.1193 0.1355 0.037 1.129 5.5 67.0 15.0 896 n/a 6_nqh: 0.1193 0.1355 0.037 1.129 5.5 67.0 15.0 896 n/a 6_sol: 0.1194 0.1343 0.037 1.129 5.5 67.0 14.9 893 n/a 6_weight: 0.1194 0.1343 0.037 1.129 5.5 67.0 14.9 893 n/a 6_xyzrec: 0.1197 0.1346 0.037 1.124 5.5 67.0 14.9 893 n/a 6_adp: 0.1200 0.1347 0.037 1.124 5.6 65.9 14.9 893 n/a 6_regHadp: 0.1200 0.1348 0.037 1.124 5.6 65.9 14.9 893 n/a 6_occ: 0.1198 0.1346 0.037 1.124 5.6 65.9 14.9 893 n/a 7_bss: 0.1197 0.1345 0.037 1.124 5.3 65.7 14.6 893 n/a 7_settarget: 0.1197 0.1345 0.037 1.124 5.3 65.7 14.6 893 n/a 7_updatecdl: 0.1197 0.1345 0.037 1.125 5.3 65.7 14.6 893 n/a 7_nqh: 0.1197 0.1345 0.037 1.125 5.3 65.7 14.6 893 n/a 7_sol: 0.1195 0.1338 0.037 1.125 5.3 65.7 14.7 902 n/a 7_weight: 0.1195 0.1338 0.037 1.125 5.3 65.7 14.7 902 n/a 7_xyzrec: 0.1197 0.1342 0.038 1.131 5.3 65.7 14.7 902 n/a 7_adp: 0.1199 0.1344 0.038 1.131 5.4 64.7 14.6 902 n/a 7_regHadp: 0.1199 0.1344 0.038 1.131 5.4 64.7 14.6 902 n/a 7_occ: 0.1198 0.1346 0.038 1.131 5.4 64.7 14.6 902 n/a 8_bss: 0.1187 0.1335 0.038 1.131 5.5 64.8 14.8 902 n/a 8_settarget: 0.1187 0.1335 0.038 1.131 5.5 64.8 14.8 902 n/a 8_updatecdl: 0.1187 0.1335 0.038 1.131 5.5 64.8 14.8 902 n/a 8_nqh: 0.1187 0.1335 0.038 1.131 5.5 64.8 14.8 902 n/a 8_sol: 0.1187 0.1330 0.038 1.131 5.5 64.8 14.7 908 n/a 8_weight: 0.1187 0.1330 0.038 1.131 5.5 64.8 14.7 908 n/a 8_xyzrec: 0.1190 0.1340 0.039 1.115 5.5 64.8 14.7 908 n/a 8_adp: 0.1193 0.1344 0.039 1.115 5.5 64.2 14.7 908 n/a 8_regHadp: 0.1193 0.1344 0.039 1.115 5.5 64.2 14.7 908 n/a 8_occ: 0.1193 0.1345 0.039 1.115 5.5 64.2 14.7 908 n/a 9_bss: 0.1192 0.1343 0.039 1.115 5.5 64.2 14.7 908 n/a 9_settarget: 0.1192 0.1343 0.039 1.115 5.5 64.2 14.7 908 n/a 9_updatecdl: 0.1192 0.1343 0.039 1.115 5.5 64.2 14.7 908 n/a 9_nqh: 0.1192 0.1343 0.039 1.115 5.5 64.2 14.7 908 n/a 9_sol: 0.1189 0.1333 0.039 1.115 5.5 64.2 14.7 911 n/a 9_weight: 0.1189 0.1333 0.039 1.115 5.5 64.2 14.7 911 n/a 9_xyzrec: 0.1192 0.1338 0.039 1.114 5.5 64.2 14.7 911 n/a 9_adp: 0.1194 0.1342 0.039 1.114 5.6 63.3 14.7 911 n/a 9_regHadp: 0.1194 0.1342 0.039 1.114 5.6 63.3 14.7 911 n/a 9_occ: 0.1193 0.1343 0.039 1.114 5.6 63.3 14.7 911 n/a 10_bss: 0.1192 0.1342 0.039 1.114 5.5 63.2 14.6 911 n/a 10_settarget: 0.1192 0.1342 0.039 1.114 5.5 63.2 14.6 911 n/a 10_updatecdl: 0.1192 0.1342 0.039 1.114 5.5 63.2 14.6 911 n/a 10_setrh: 0.1193 0.1342 0.039 1.114 5.5 63.2 14.6 911 n/a 10_nqh: 0.1193 0.1342 0.039 1.114 5.5 63.2 14.6 911 n/a 10_sol: 0.1191 0.1337 0.039 1.114 5.5 63.2 14.7 923 n/a 10_weight: 0.1191 0.1337 0.039 1.114 5.5 63.2 14.7 923 n/a 10_xyzrec: 0.1196 0.1345 0.039 1.182 5.5 63.2 14.7 923 n/a 10_adp: 0.1195 0.1347 0.039 1.182 5.6 62.4 14.7 923 n/a 10_regHadp: 0.1195 0.1347 0.039 1.182 5.6 62.4 14.7 923 n/a 10_occ: 0.1194 0.1345 0.039 1.182 5.6 62.4 14.7 923 n/a end: 0.1193 0.1342 0.039 1.182 5.5 62.4 14.7 923 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9606842_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9606842_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.6500 Refinement macro-cycles (run) : 12123.8800 Write final files (write_after_run_outputs) : 163.1500 Total : 12292.6800 Total CPU time: 3.43 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:42:06 PST -0800 (1736736126.18 s) Start R-work = 0.1800, R-free = 0.1902 Final R-work = 0.1193, R-free = 0.1342 =============================================================================== Job complete usr+sys time: 12573.02 seconds wall clock time: 210 minutes 32.55 seconds (12632.55 seconds total)