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_4591434.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_4591434.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4591434.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/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): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.76, per 1000 atoms: 0.26 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: 2.755 distance_ideal: 2.720 ideal - model: -0.035 slack: 0.000 delta_slack: -0.035 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: 2.669 distance_ideal: 2.710 ideal - model: 0.041 slack: 0.000 delta_slack: 0.041 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 115.3 milliseconds Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.04: 945 1.04 - 1.25: 2355 1.25 - 1.47: 1364 1.47 - 1.68: 1219 1.68 - 1.90: 51 Bond restraints: 5934 Sorted by residual: bond pdb=" CG HIS B 96 " pdb=" CD2 HIS B 96 " ideal model delta sigma weight residual 1.354 1.134 0.220 1.10e-02 8.26e+03 4.00e+02 bond pdb=" N GLU A 137 " pdb=" CA GLU A 137 " ideal model delta sigma weight residual 1.456 1.715 -0.259 1.31e-02 5.83e+03 3.91e+02 bond pdb=" N ASP B 117 " pdb=" H ASP B 117 " ideal model delta sigma weight residual 0.860 1.237 -0.377 2.00e-02 2.50e+03 3.55e+02 bond pdb=" ND1 HIS A 96 " pdb=" CE1 HIS A 96 " ideal model delta sigma weight residual 1.321 1.134 0.187 1.00e-02 1.00e+04 3.51e+02 bond pdb=" N THR B 16 " pdb=" H THR B 16 " ideal model delta sigma weight residual 0.860 1.232 -0.372 2.00e-02 2.50e+03 3.46e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 5462 4.07 - 8.15: 3591 8.15 - 12.22: 1420 12.22 - 16.29: 307 16.29 - 20.37: 30 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O VAL A 89 " pdb=" C VAL A 89 " pdb=" N GLU A 90 " ideal model delta sigma weight residual 121.83 137.18 -15.35 1.03e+00 9.43e-01 2.22e+02 angle pdb=" O ALA A 10 " pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 121.85 111.52 10.33 7.00e-01 2.04e+00 2.18e+02 angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.65 132.24 -10.59 7.30e-01 1.88e+00 2.10e+02 angle pdb=" CA PHE B 82 " pdb=" CB PHE B 82 " pdb=" CG PHE B 82 " ideal model delta sigma weight residual 113.80 127.72 -13.92 1.00e+00 1.00e+00 1.94e+02 angle pdb=" O ALA A 18 " pdb=" C ALA A 18 " pdb=" N VAL A 19 " ideal model delta sigma weight residual 122.09 137.11 -15.02 1.08e+00 8.57e-01 1.93e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1841 16.33 - 32.65: 133 32.65 - 48.97: 44 48.97 - 65.30: 27 65.30 - 81.62: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CG TRP B 146 " pdb=" CD2 TRP B 146 " pdb=" CE3 TRP B 146 " pdb=" HE3 TRP B 146 " ideal model delta harmonic sigma weight residual 0.00 -28.57 28.57 0 5.00e+00 4.00e-02 3.27e+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 -156.72 -23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CG TRP A 146 " pdb=" CD2 TRP A 146 " pdb=" CE3 TRP A 146 " pdb=" HE3 TRP A 146 " ideal model delta harmonic sigma weight residual 0.00 22.96 -22.96 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 206 0.204 - 0.408: 146 0.408 - 0.612: 80 0.612 - 0.816: 49 0.816 - 1.020: 11 Chirality restraints: 492 Sorted by residual: chirality pdb=" CG LEU B 54 " pdb=" CB LEU B 54 " pdb=" CD1 LEU B 54 " pdb=" CD2 LEU B 54 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CG LEU B 25 " pdb=" CB LEU B 25 " pdb=" CD1 LEU B 25 " pdb=" CD2 LEU B 25 " both_signs ideal model delta sigma weight residual False -2.59 -1.59 -1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA VAL B 62 " pdb=" N VAL B 62 " pdb=" C VAL B 62 " pdb=" CB VAL B 62 " both_signs ideal model delta sigma weight residual False 2.44 1.45 0.99 2.00e-01 2.50e+01 2.47e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.174 2.00e-02 2.50e+03 8.01e-02 1.93e+02 pdb=" CG PHE B 164 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.059 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.053 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " 0.023 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.078 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.029 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.090 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.055 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.124 2.00e-02 2.50e+03 7.79e-02 1.82e+02 pdb=" CG PHE A 164 " -0.017 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.119 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.112 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.088 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.033 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 82 " -0.046 2.00e-02 2.50e+03 7.36e-02 1.63e+02 pdb=" CG PHE A 82 " -0.088 2.00e-02 2.50e+03 pdb=" CD1 PHE A 82 " 0.057 2.00e-02 2.50e+03 pdb=" CD2 PHE A 82 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE A 82 " 0.084 2.00e-02 2.50e+03 pdb=" CE2 PHE A 82 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 82 " -0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 82 " -0.085 2.00e-02 2.50e+03 pdb=" HD2 PHE A 82 " 0.109 2.00e-02 2.50e+03 pdb=" HE1 PHE A 82 " 0.104 2.00e-02 2.50e+03 pdb=" HE2 PHE A 82 " -0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 82 " -0.092 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.67: 33 1.67 - 2.41: 3056 2.41 - 3.14: 22701 3.14 - 3.87: 32778 3.87 - 4.60: 51603 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110171 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.942 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.031 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.051 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.122 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.160 2.620 ... (remaining 110166 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_4591434_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= 0.2042 r_free= 0.2006 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.305959 | | target function (ml) not normalized (work): 806562.159137 | | target function (ml) not normalized (free): 16592.254587 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2146 0.1950 6.6906 6.3148| | 2: 2.94 - 2.33 1.00 7339 128 0.1603 0.1675 5.5376 5.6061| | 3: 2.33 - 2.04 0.96 6939 150 0.1640 0.1499 5.1467 5.099| | 4: 2.04 - 1.85 1.00 7170 155 0.1782 0.1503 4.9642 4.9724| | 5: 1.85 - 1.72 0.99 7113 159 0.1917 0.1845 4.7984 4.892| | 6: 1.72 - 1.62 0.99 7102 142 0.1968 0.1901 4.6636 4.6706| | 7: 1.62 - 1.54 0.99 7104 148 0.2029 0.1948 4.573 4.609| | 8: 1.54 - 1.47 0.96 6798 152 0.2104 0.2151 4.4965 4.5014| | 9: 1.47 - 1.41 0.98 6938 155 0.2104 0.2104 4.4094 4.4593| | 10: 1.41 - 1.36 0.99 7022 150 0.2145 0.2561 4.3382 4.4763| | 11: 1.36 - 1.32 0.99 6997 151 0.2134 0.2269 4.2546 4.329| | 12: 1.32 - 1.28 0.98 6976 149 0.2085 0.1861 4.1827 4.176| | 13: 1.28 - 1.25 0.98 6907 166 0.2048 0.2133 4.1274 4.1763| | 14: 1.25 - 1.22 0.98 7015 113 0.2039 0.2258 4.0659 4.1615| | 15: 1.22 - 1.19 0.98 6957 137 0.2124 0.2231 4.0556 4.1362| | 16: 1.19 - 1.17 0.93 6604 132 0.2102 0.2264 4.0022 4.0921| | 17: 1.17 - 1.14 0.98 6941 135 0.2230 0.2026 3.9771 4.0368| | 18: 1.14 - 1.12 0.98 6875 142 0.2212 0.2443 3.9191 3.9114| | 19: 1.12 - 1.10 0.97 6949 106 0.2256 0.2491 3.8742 3.9908| | 20: 1.10 - 1.08 0.97 6884 147 0.2370 0.2560 3.846 3.8818| | 21: 1.08 - 1.07 0.97 6852 152 0.2456 0.2629 3.802 3.8181| | 22: 1.07 - 1.05 0.97 6838 135 0.2574 0.2655 3.7582 3.7651| | 23: 1.05 - 1.03 0.97 6829 159 0.2688 0.2624 3.7288 3.8051| | 24: 1.03 - 1.02 0.96 6785 133 0.2877 0.2875 3.6959 3.7995| | 25: 1.02 - 1.01 0.93 6552 130 0.3084 0.2849 3.6741 3.6963| | 26: 1.01 - 0.99 0.96 6767 158 0.3206 0.3389 3.6313 3.6414| | 27: 0.99 - 0.98 0.94 6648 131 0.3383 0.3043 3.6337 3.6025| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.54 0.91 0.98 35740.92| | 2: 2.94 - 2.33 7339 128 0.85 21.18 1.08 1.02 15050.71| | 3: 2.33 - 2.04 6939 150 0.93 12.19 1.11 1.06 4018.62| | 4: 2.04 - 1.85 7170 155 0.92 13.45 1.12 1.07 2728.85| | 5: 1.85 - 1.72 7113 159 0.91 15.77 1.11 1.08 2109.65| | 6: 1.72 - 1.62 7102 142 0.90 16.94 1.11 1.08 1677.89| | 7: 1.62 - 1.54 7104 148 0.89 17.73 1.11 1.07 1369.75| | 8: 1.54 - 1.47 6798 152 0.89 18.59 1.11 1.06 1179.68| | 9: 1.47 - 1.41 6938 155 0.87 19.68 1.10 1.06 1053.63| | 10: 1.41 - 1.36 7022 150 0.86 21.28 1.10 1.07 958.95| | 11: 1.36 - 1.32 6997 151 0.86 21.27 1.08 1.06 829.77| | 12: 1.32 - 1.28 6976 149 0.87 20.66 1.08 1.05 708.90| | 13: 1.28 - 1.25 6907 166 0.87 20.23 1.07 1.03 623.11| | 14: 1.25 - 1.22 7015 113 0.86 20.86 1.07 1.04 581.26| | 15: 1.22 - 1.19 6957 137 0.86 20.99 1.07 1.03 548.24| | 16: 1.19 - 1.17 6604 132 0.87 20.88 1.07 1.02 506.79| | 17: 1.17 - 1.14 6941 135 0.86 21.86 1.09 1.02 465.79| | 18: 1.14 - 1.12 6875 142 0.85 22.04 1.08 1.01 431.61| | 19: 1.12 - 1.10 6949 106 0.85 22.83 1.07 1.00 406.22| | 20: 1.10 - 1.08 6884 147 0.84 23.60 1.06 0.97 373.04| | 21: 1.08 - 1.07 6852 152 0.83 24.26 1.06 0.97 345.90| | 22: 1.07 - 1.05 6838 135 0.82 25.74 1.05 0.97 332.98| | 23: 1.05 - 1.03 6829 159 0.80 27.45 1.05 0.99 333.35| | 24: 1.03 - 1.02 6785 133 0.78 29.70 1.06 0.98 336.73| | 25: 1.02 - 1.01 6552 130 0.76 30.98 1.03 0.94 316.49| | 26: 1.01 - 0.99 6767 158 0.75 32.39 1.03 0.91 296.03| | 27: 0.99 - 0.98 6648 131 0.75 32.15 1.05 0.91 273.45| |alpha: min = 0.91 max = 1.08 mean = 1.02| |beta: min = 273.45 max = 35740.92 mean = 2853.64| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.96| |phase err.(test): min = 0.00 max = 90.00 mean = 22.15| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.265 2950 Z= 5.432 Angle : 5.226 19.073 4018 Z= 3.731 Chirality : 0.379 1.020 492 Planarity : 0.033 0.112 512 Dihedral : 12.813 81.620 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 20.92 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.11 % Favored : 96.37 % Rotamer: Outliers : 0.97 % Allowed : 4.52 % Favored : 94.52 % Cbeta Deviations : 32.30 % 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: -2.09 (0.41), residues: 386 helix: -2.51 (0.33), residues: 144 sheet: -1.21 (0.51), residues: 86 loop : 0.03 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.072 0.016 ARG A 27 TYR 0.113 0.027 TYR B 192 PHE 0.144 0.044 PHE A 164 TRP 0.144 0.042 TRP A 146 HIS 0.088 0.034 HIS A 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= 0.2042 r_free= 0.2006 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.305959 | | target function (ml) not normalized (work): 806562.159137 | | target function (ml) not normalized (free): 16592.254587 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2040 0.2042 0.2006 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2040 0.2042 0.2006 n_refl.: 191155 remove outliers: r(all,work,free)=0.2040 0.2042 0.2006 n_refl.: 191145 overall B=0.02 to atoms: r(all,work,free)=0.2042 0.2044 0.2007 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1812 0.1809 0.1936 n_refl.: 191145 remove outliers: r(all,work,free)=0.1810 0.1807 0.1936 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4079 402.814 291.587 0.424 0.933 0.301 13.296-10.522 100.00 100 1 0.2558 534.497 521.219 0.771 0.934 0.255 10.503-8.327 98.90 177 3 0.2471 564.205 558.906 0.942 0.934 0.233 8.318-6.595 100.00 360 8 0.2512 414.736 403.958 0.937 0.934 0.164 6.588-5.215 100.00 711 7 0.2281 381.101 366.360 0.932 0.933 0.140 5.214-4.128 98.38 1367 28 0.1499 557.435 549.974 1.049 0.933 0.080 4.126-3.266 94.74 2603 46 0.1359 508.132 498.895 1.117 0.932 0.014 3.266-2.585 99.86 5447 97 0.1447 342.774 337.098 1.093 0.929 0.000 2.585-2.046 97.45 10613 204 0.1400 258.603 254.521 1.103 0.926 0.000 2.046-1.619 99.39 21536 464 0.1622 153.054 149.742 1.130 0.920 0.000 1.619-1.281 98.00 42464 925 0.1944 82.395 80.209 1.124 0.911 0.000 1.281-0.980 96.53 101826 2056 0.2321 44.203 41.653 1.122 0.893 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0247 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1807 r_free=0.1936 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1807 r_free=0.1936 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.104670 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.358747 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 0.1268 0.1500 0.0232 0.038 1.1 11.4 0.0 0.0 0 11.052 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.68 15.00 2.32 1.117 13.126 575.359 0.018 12.97 15.70 2.73 1.263 13.398 575.359 0.017 Individual atomic B min max mean iso aniso Overall: 5.24 73.06 15.11 1.41 435 3274 Protein: 5.24 40.47 11.05 1.41 0 2902 Water: 6.36 73.06 29.73 N/A 435 370 Other: 16.17 30.12 23.15 N/A 0 2 Chain A: 5.30 59.83 13.11 N/A 0 1626 Chain B: 5.24 73.06 12.83 N/A 0 1648 Chain S: 11.80 65.88 31.20 N/A 435 0 Histogram: Values Number of atoms 5.24 - 12.02 2173 12.02 - 18.81 625 18.81 - 25.59 317 25.59 - 32.37 256 32.37 - 39.15 163 39.15 - 45.93 105 45.93 - 52.71 47 52.71 - 59.50 17 59.50 - 66.28 5 66.28 - 73.06 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1570 r_work=0.1296 r_free=0.1565 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 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 = 0.1281 r_free = 0.1554 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1554 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015545 | | target function (ls_wunit_k1) not normalized (work): 2911.559598 | | target function (ls_wunit_k1) not normalized (free): 116.682593 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1554 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1470 0.1468 0.1633 n_refl.: 191139 remove outliers: r(all,work,free)=0.1470 0.1468 0.1633 n_refl.: 191139 overall B=0.15 to atoms: r(all,work,free)=0.1493 0.1491 0.1643 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1281 0.1275 0.1549 n_refl.: 191139 remove outliers: r(all,work,free)=0.1281 0.1275 0.1548 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3612 402.814 378.660 0.471 0.997 0.281 13.296-10.522 100.00 100 1 0.2107 534.497 530.672 0.723 0.999 0.249 10.503-8.327 98.90 177 3 0.1721 564.205 562.578 0.855 0.999 0.198 8.318-6.595 100.00 360 8 0.1713 414.736 412.961 0.875 0.999 0.150 6.588-5.215 100.00 711 7 0.1537 381.101 373.526 0.855 0.999 0.140 5.214-4.128 98.38 1367 28 0.0906 557.435 554.376 0.942 0.999 0.070 4.126-3.266 94.74 2603 46 0.0831 508.132 504.213 1.006 1.000 0.009 3.266-2.585 99.86 5447 97 0.0920 342.774 340.402 0.989 0.999 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.381 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.388 1.019 1.000 0.000 1.619-1.281 98.00 42464 925 0.1281 82.395 81.391 1.012 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1878 44.202 42.157 0.990 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0351 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1548 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1548 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1548 | n_water=805 | time (s): 2.780 (total time: 2.780) Filter (dist) r_work=0.1280 r_free=0.1552 | n_water=794 | time (s): 101.560 (total time: 104.340) Filter (q & B) r_work=0.1280 r_free=0.1552 | n_water=790 | time (s): 4.190 (total time: 108.530) Compute maps r_work=0.1280 r_free=0.1552 | n_water=790 | time (s): 1.940 (total time: 110.470) Filter (map) r_work=0.1307 r_free=0.1535 | n_water=651 | time (s): 3.990 (total time: 114.460) Find peaks r_work=0.1307 r_free=0.1535 | n_water=651 | time (s): 0.570 (total time: 115.030) Add new water r_work=0.1329 r_free=0.1565 | n_water=964 | time (s): 4.130 (total time: 119.160) Refine new water occ: r_work=0.1286 r_free=0.1503 adp: r_work=0.1273 r_free=0.1503 occ: r_work=0.1277 r_free=0.1498 adp: r_work=0.1269 r_free=0.1503 occ: r_work=0.1270 r_free=0.1497 adp: r_work=0.1267 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1501 r_work=0.1267 r_free=0.1501 | n_water=964 | time (s): 79.940 (total time: 199.100) Filter (q & B) r_work=0.1271 r_free=0.1501 | n_water=884 | time (s): 4.270 (total time: 203.370) Filter (dist only) r_work=0.1271 r_free=0.1501 | n_water=883 | time (s): 110.420 (total time: 313.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.804189 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 596.612427 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 0.1255 0.1518 0.0264 0.041 1.1 19.4 0.0 0.0 0 11.902 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.18 2.64 2.054 15.246 596.612 0.015 12.32 15.04 2.72 2.449 15.278 596.612 0.014 Individual atomic B min max mean iso aniso Overall: 5.40 68.21 16.36 1.21 515 3272 Protein: 5.40 41.28 10.99 1.21 0 2902 Water: 6.56 68.21 34.00 N/A 515 368 Other: 16.56 32.72 24.64 N/A 0 2 Chain A: 5.51 55.55 13.02 N/A 0 1624 Chain B: 5.40 68.21 12.87 N/A 0 1648 Chain S: 12.12 67.49 38.09 N/A 515 0 Histogram: Values Number of atoms 5.40 - 11.68 2057 11.68 - 17.96 712 17.96 - 24.25 258 24.25 - 30.53 207 30.53 - 36.81 178 36.81 - 43.09 173 43.09 - 49.37 99 49.37 - 55.65 51 55.65 - 61.93 45 61.93 - 68.21 7 =========================== Idealize ADP of riding H ========================== r_work=0.1232 r_free=0.1504 r_work=0.1232 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1505 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1502 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1226 r_free= 0.1502 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013437 | | target function (ls_wunit_k1) not normalized (work): 2516.702003 | | target function (ls_wunit_k1) not normalized (free): 100.254704 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1226 0.1502 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1439 0.1436 0.1593 n_refl.: 191138 remove outliers: r(all,work,free)=0.1439 0.1436 0.1593 n_refl.: 191138 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1433 0.1592 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1510 n_refl.: 191138 remove outliers: r(all,work,free)=0.1239 0.1233 0.1510 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3255 402.814 377.485 0.485 0.962 0.267 13.296-10.522 100.00 100 1 0.1854 534.497 530.140 0.773 0.963 0.250 10.503-8.327 98.90 177 3 0.1372 564.205 567.565 0.918 0.963 0.181 8.318-6.595 100.00 360 8 0.1542 414.736 413.388 0.933 0.963 0.143 6.588-5.215 100.00 711 7 0.1350 381.101 376.792 0.911 0.963 0.123 5.214-4.128 98.38 1367 28 0.0831 557.435 555.844 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0762 508.132 505.428 1.060 0.963 0.009 3.266-2.585 99.86 5447 97 0.0861 342.774 341.273 1.047 0.962 0.000 2.585-2.046 97.45 10613 204 0.0899 258.603 256.793 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1044 153.054 151.628 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1256 82.395 81.362 1.075 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1874 44.202 42.219 1.062 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0605 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1510 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1510 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1510 | n_water=883 | time (s): 3.700 (total time: 3.700) Filter (dist) r_work=0.1236 r_free=0.1511 | n_water=875 | time (s): 116.710 (total time: 120.410) Filter (q & B) r_work=0.1236 r_free=0.1511 | n_water=874 | time (s): 4.300 (total time: 124.710) Compute maps r_work=0.1236 r_free=0.1511 | n_water=874 | time (s): 2.570 (total time: 127.280) Filter (map) r_work=0.1274 r_free=0.1519 | n_water=693 | time (s): 5.040 (total time: 132.320) Find peaks r_work=0.1274 r_free=0.1519 | n_water=693 | time (s): 0.890 (total time: 133.210) Add new water r_work=0.1295 r_free=0.1541 | n_water=1006 | time (s): 4.740 (total time: 137.950) Refine new water occ: r_work=0.1251 r_free=0.1510 adp: r_work=0.1251 r_free=0.1511 occ: r_work=0.1247 r_free=0.1509 adp: r_work=0.1246 r_free=0.1509 occ: r_work=0.1243 r_free=0.1508 adp: r_work=0.1243 r_free=0.1507 ADP+occupancy (water only), MIN, final r_work=0.1243 r_free=0.1507 r_work=0.1243 r_free=0.1507 | n_water=1006 | time (s): 227.130 (total time: 365.080) Filter (q & B) r_work=0.1247 r_free=0.1515 | n_water=879 | time (s): 6.040 (total time: 371.120) Filter (dist only) r_work=0.1247 r_free=0.1515 | n_water=878 | time (s): 123.870 (total time: 494.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.655303 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.174683 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 0.1237 0.1446 0.0209 0.035 1.1 7.5 0.0 0.0 0 0.828 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.46 2.09 1.938 14.632 16.175 3.940 12.31 14.05 1.74 2.211 14.548 16.175 3.898 Individual atomic B min max mean iso aniso Overall: 5.54 67.84 15.35 1.06 511 3271 Protein: 5.54 37.61 10.77 1.06 0 2902 Water: 6.69 67.84 30.47 N/A 511 367 Other: 14.19 28.98 21.59 N/A 0 2 Chain A: 5.57 54.77 12.81 N/A 0 1624 Chain B: 5.54 67.84 12.60 N/A 0 1647 Chain S: 14.85 60.34 32.30 N/A 511 0 Histogram: Values Number of atoms 5.54 - 11.77 2124 11.77 - 18.00 691 18.00 - 24.23 300 24.23 - 30.46 236 30.46 - 36.69 177 36.69 - 42.92 135 42.92 - 49.15 75 49.15 - 55.38 33 55.38 - 61.61 10 61.61 - 67.84 1 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1405 r_work=0.1232 r_free=0.1406 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1232 r_free = 0.1406 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1227 r_free = 0.1401 target_work(ml) = 3.892 | | 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.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1401 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892392 | | target function (ml) not normalized (work): 729033.283591 | | target function (ml) not normalized (free): 15223.340097 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1231 0.1227 0.1400 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1445 0.1444 0.1482 n_refl.: 191138 remove outliers: r(all,work,free)=0.1445 0.1444 0.1482 n_refl.: 191138 overall B=-0.03 to atoms: r(all,work,free)=0.1438 0.1437 0.1478 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1227 0.1223 0.1395 n_refl.: 191138 remove outliers: r(all,work,free)=0.1227 0.1223 0.1395 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 94.06 92 3 0.3838 398.008 361.874 0.423 0.947 0.241 13.296-10.522 100.00 100 1 0.2440 534.497 514.234 0.713 0.948 0.215 10.503-8.327 98.90 177 3 0.1979 564.205 561.780 0.884 0.948 0.210 8.318-6.595 100.00 360 8 0.2085 414.736 410.735 0.891 0.948 0.120 6.588-5.215 100.00 711 7 0.1835 381.101 371.036 0.887 0.948 0.120 5.214-4.128 98.38 1367 28 0.1174 557.435 552.183 0.969 0.948 0.044 4.126-3.266 94.74 2603 46 0.1081 508.132 501.486 1.034 0.948 0.009 3.266-2.585 99.86 5447 97 0.1082 342.774 339.021 1.020 0.947 0.000 2.585-2.046 97.45 10613 204 0.0963 258.603 255.839 1.034 0.947 0.000 2.046-1.619 99.39 21536 464 0.0973 153.054 151.453 1.057 0.945 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.506 1.054 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.326 1.041 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1126 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1223 r_free=0.1395 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1223 r_free=0.1395 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1223 r_free=0.1395 | n_water=878 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1223 r_free=0.1395 | n_water=878 | time (s): 109.590 (total time: 112.720) Filter (q & B) r_work=0.1224 r_free=0.1389 | n_water=861 | time (s): 4.730 (total time: 117.450) Compute maps r_work=0.1224 r_free=0.1389 | n_water=861 | time (s): 1.970 (total time: 119.420) Filter (map) r_work=0.1250 r_free=0.1389 | n_water=726 | time (s): 5.690 (total time: 125.110) Find peaks r_work=0.1250 r_free=0.1389 | n_water=726 | time (s): 0.720 (total time: 125.830) Add new water r_work=0.1264 r_free=0.1399 | n_water=975 | time (s): 5.020 (total time: 130.850) Refine new water occ: r_work=0.1215 r_free=0.1366 adp: r_work=0.1207 r_free=0.1362 occ: r_work=0.1204 r_free=0.1364 adp: r_work=0.1204 r_free=0.1363 occ: r_work=0.1202 r_free=0.1365 adp: r_work=0.1202 r_free=0.1363 ADP+occupancy (water only), MIN, final r_work=0.1202 r_free=0.1363 r_work=0.1202 r_free=0.1363 | n_water=975 | time (s): 298.580 (total time: 429.430) Filter (q & B) r_work=0.1207 r_free=0.1369 | n_water=884 | time (s): 4.280 (total time: 433.710) Filter (dist only) r_work=0.1208 r_free=0.1369 | n_water=882 | time (s): 113.470 (total time: 547.180) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.602172 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.899093 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1205 0.1375 0.0170 0.034 1.1 6.0 0.0 0.0 0 0.801 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 13.75 1.70 1.840 14.305 15.899 3.875 11.98 13.70 1.72 1.950 14.260 15.899 3.866 Individual atomic B min max mean iso aniso Overall: 5.51 67.41 15.11 1.01 515 3271 Protein: 5.51 34.25 10.68 1.01 0 2902 Water: 5.90 67.41 29.65 N/A 515 367 Other: 13.98 27.87 20.93 N/A 0 2 Chain A: 5.57 53.72 12.67 N/A 0 1624 Chain B: 5.51 67.41 12.49 N/A 0 1647 Chain S: 5.90 58.99 31.15 N/A 515 0 Histogram: Values Number of atoms 5.51 - 11.70 2116 11.70 - 17.89 723 17.89 - 24.08 296 24.08 - 30.27 239 30.27 - 36.46 185 36.46 - 42.65 130 42.65 - 48.84 61 48.84 - 55.03 27 55.03 - 61.22 8 61.22 - 67.41 1 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1370 r_work=0.1198 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1371 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1370 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1370 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864024 | | target function (ml) not normalized (work): 723716.283281 | | target function (ml) not normalized (free): 15137.916830 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1370 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1423 0.1423 0.1475 n_refl.: 191137 remove outliers: r(all,work,free)=0.1423 0.1423 0.1475 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1416 0.1415 0.1470 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1373 n_refl.: 191137 remove outliers: r(all,work,free)=0.1198 0.1194 0.1373 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 0.3919 361.248 316.405 0.407 0.947 0.248 13.296-10.522 98.02 98 1 0.2489 484.035 455.548 0.713 0.948 0.224 10.503-8.327 97.80 175 3 0.2040 501.973 504.719 0.880 0.948 0.210 8.318-6.595 100.00 360 8 0.2175 375.594 370.209 0.885 0.948 0.110 6.588-5.215 100.00 711 7 0.1881 345.133 335.919 0.884 0.948 0.090 5.214-4.128 98.38 1367 28 0.1203 504.825 499.948 0.973 0.948 0.080 4.126-3.266 94.74 2603 46 0.1116 460.175 453.676 1.034 0.948 0.009 3.266-2.585 99.86 5447 97 0.1081 310.423 307.217 1.020 0.948 0.000 2.585-2.046 97.45 10613 204 0.0929 234.196 231.733 1.033 0.948 0.000 2.046-1.619 99.39 21536 464 0.0909 138.609 137.307 1.056 0.947 0.000 1.619-1.281 98.00 42464 925 0.0988 74.619 73.893 1.053 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1664 40.030 38.354 1.039 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1220 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1194 r_free=0.1373 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1194 r_free=0.1373 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1373 | n_water=882 | time (s): 2.950 (total time: 2.950) Filter (dist) r_work=0.1195 r_free=0.1373 | n_water=881 | time (s): 114.450 (total time: 117.400) Filter (q & B) r_work=0.1195 r_free=0.1372 | n_water=873 | time (s): 4.810 (total time: 122.210) Compute maps r_work=0.1195 r_free=0.1372 | n_water=873 | time (s): 2.520 (total time: 124.730) Filter (map) r_work=0.1219 r_free=0.1360 | n_water=740 | time (s): 5.200 (total time: 129.930) Find peaks r_work=0.1219 r_free=0.1360 | n_water=740 | time (s): 0.660 (total time: 130.590) Add new water r_work=0.1232 r_free=0.1382 | n_water=972 | time (s): 4.790 (total time: 135.380) Refine new water occ: r_work=0.1195 r_free=0.1354 adp: r_work=0.1195 r_free=0.1354 occ: r_work=0.1192 r_free=0.1354 adp: r_work=0.1192 r_free=0.1354 occ: r_work=0.1190 r_free=0.1355 adp: r_work=0.1190 r_free=0.1354 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1354 r_work=0.1190 r_free=0.1354 | n_water=972 | time (s): 278.820 (total time: 414.200) Filter (q & B) r_work=0.1193 r_free=0.1359 | n_water=894 | time (s): 5.660 (total time: 419.860) Filter (dist only) r_work=0.1194 r_free=0.1359 | n_water=893 | time (s): 114.360 (total time: 534.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.607169 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.604564 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 0.1358 0.0162 0.034 1.1 6.3 0.0 0.0 0 0.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.58 1.62 1.801 14.198 15.605 3.764 12.01 13.63 1.61 1.909 14.154 15.605 3.761 Individual atomic B min max mean iso aniso Overall: 5.54 66.88 15.01 0.96 527 3270 Protein: 5.54 31.96 10.59 0.96 0 2902 Water: 6.05 66.88 29.37 N/A 527 366 Other: 13.88 26.04 19.96 N/A 0 2 Chain A: 5.59 52.96 12.54 N/A 0 1624 Chain B: 5.54 66.88 12.35 N/A 0 1646 Chain S: 6.05 58.76 30.91 N/A 527 0 Histogram: Values Number of atoms 5.54 - 11.67 2123 11.67 - 17.81 736 17.81 - 23.94 299 23.94 - 30.07 227 30.07 - 36.21 179 36.21 - 42.34 131 42.34 - 48.47 65 48.47 - 54.61 29 54.61 - 60.74 7 60.74 - 66.88 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1363 r_work=0.1201 r_free=0.1363 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1363 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1361 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760348 | | target function (ml) not normalized (work): 704279.357834 | | target function (ml) not normalized (free): 14735.830125 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1360 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1476 n_refl.: 191132 remove outliers: r(all,work,free)=0.1407 0.1406 0.1476 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1399 0.1398 0.1471 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1199 0.1353 n_refl.: 191132 remove outliers: r(all,work,free)=0.1201 0.1198 0.1353 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3768 356.395 318.696 0.349 0.950 0.140 13.296-10.522 97.03 97 1 0.2456 486.361 461.761 0.693 0.951 0.142 10.503-8.327 97.80 175 3 0.2124 501.973 495.418 0.864 0.952 0.141 8.318-6.595 100.00 360 8 0.2165 375.594 370.676 0.881 0.951 0.098 6.588-5.215 100.00 711 7 0.1887 345.133 335.380 0.882 0.952 0.097 5.214-4.128 98.38 1367 28 0.1226 504.825 500.223 0.970 0.952 0.067 4.126-3.266 94.74 2603 46 0.1140 460.175 453.440 1.032 0.952 0.005 3.266-2.585 99.86 5447 97 0.1107 310.423 307.115 1.018 0.952 0.000 2.585-2.046 97.45 10613 204 0.0947 234.196 231.757 1.030 0.952 0.000 2.046-1.619 99.39 21536 464 0.0914 138.609 137.323 1.053 0.952 0.000 1.619-1.281 98.00 42464 925 0.0977 74.619 73.924 1.049 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1654 40.030 38.369 1.035 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1382 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1198 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1198 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1198 r_free=0.1353 | n_water=893 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1199 r_free=0.1353 | n_water=892 | time (s): 119.660 (total time: 122.030) Filter (q & B) r_work=0.1199 r_free=0.1353 | n_water=885 | time (s): 4.450 (total time: 126.480) Compute maps r_work=0.1199 r_free=0.1353 | n_water=885 | time (s): 1.690 (total time: 128.170) Filter (map) r_work=0.1220 r_free=0.1352 | n_water=772 | time (s): 4.940 (total time: 133.110) Find peaks r_work=0.1220 r_free=0.1352 | n_water=772 | time (s): 0.950 (total time: 134.060) Add new water r_work=0.1229 r_free=0.1365 | n_water=975 | time (s): 4.740 (total time: 138.800) Refine new water occ: r_work=0.1196 r_free=0.1334 adp: r_work=0.1196 r_free=0.1334 occ: r_work=0.1194 r_free=0.1333 adp: r_work=0.1194 r_free=0.1333 occ: r_work=0.1192 r_free=0.1333 adp: r_work=0.1192 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1333 r_work=0.1192 r_free=0.1333 | n_water=975 | time (s): 240.090 (total time: 378.890) Filter (q & B) r_work=0.1195 r_free=0.1341 | n_water=910 | time (s): 4.710 (total time: 383.600) Filter (dist only) r_work=0.1196 r_free=0.1340 | n_water=909 | time (s): 119.390 (total time: 502.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.500181 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.327783 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1344 0.0145 0.036 1.1 6.6 0.0 0.3 0 0.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.44 1.45 1.760 14.093 15.328 3.761 11.99 13.44 1.45 1.871 14.059 15.328 3.757 Individual atomic B min max mean iso aniso Overall: 5.58 65.66 14.96 0.91 543 3270 Protein: 5.58 29.72 10.49 0.91 0 2902 Water: 5.91 65.66 29.20 N/A 543 366 Other: 13.84 23.30 18.57 N/A 0 2 Chain A: 5.61 52.60 12.41 N/A 0 1624 Chain B: 5.58 65.66 12.23 N/A 0 1646 Chain S: 5.91 58.36 30.85 N/A 543 0 Histogram: Values Number of atoms 5.58 - 11.59 2108 11.59 - 17.60 774 17.60 - 23.61 282 23.61 - 29.61 213 29.61 - 35.62 198 35.62 - 41.63 126 41.63 - 47.64 73 47.64 - 53.65 31 53.65 - 59.66 7 59.66 - 65.66 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1345 r_work=0.1200 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1345 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1342 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1342 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756603 | | target function (ml) not normalized (work): 703566.629305 | | target function (ml) not normalized (free): 14718.686643 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1343 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1389 0.1388 0.1473 n_refl.: 191129 remove outliers: r(all,work,free)=0.1389 0.1388 0.1473 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1382 0.1380 0.1468 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1339 n_refl.: 191129 remove outliers: r(all,work,free)=0.1198 0.1196 0.1339 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 90.10 88 3 0.3680 356.162 322.331 0.335 0.955 0.100 13.296-10.522 96.04 96 1 0.2384 485.533 459.405 0.681 0.956 0.110 10.503-8.327 97.80 175 3 0.2169 501.973 494.413 0.858 0.956 0.114 8.318-6.595 100.00 360 8 0.2150 375.594 370.817 0.876 0.956 0.095 6.588-5.215 100.00 711 7 0.1908 345.133 335.565 0.876 0.956 0.085 5.214-4.128 98.38 1367 28 0.1225 504.825 500.273 0.965 0.956 0.039 4.126-3.266 94.74 2603 46 0.1141 460.175 453.484 1.029 0.956 0.000 3.266-2.585 99.86 5447 97 0.1109 310.423 307.235 1.015 0.955 0.000 2.585-2.046 97.45 10613 204 0.0946 234.196 231.732 1.026 0.955 0.000 2.046-1.619 99.39 21536 464 0.0909 138.609 137.333 1.049 0.954 0.000 1.619-1.281 98.00 42464 925 0.0970 74.619 73.933 1.047 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.030 38.365 1.035 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1356 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1339 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1339 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1339 | n_water=909 | time (s): 2.360 (total time: 2.360) Filter (dist) r_work=0.1196 r_free=0.1340 | n_water=908 | time (s): 109.280 (total time: 111.640) Filter (q & B) r_work=0.1196 r_free=0.1341 | n_water=899 | time (s): 4.410 (total time: 116.050) Compute maps r_work=0.1196 r_free=0.1341 | n_water=899 | time (s): 2.340 (total time: 118.390) Filter (map) r_work=0.1217 r_free=0.1351 | n_water=786 | time (s): 5.270 (total time: 123.660) Find peaks r_work=0.1217 r_free=0.1351 | n_water=786 | time (s): 0.880 (total time: 124.540) Add new water r_work=0.1224 r_free=0.1363 | n_water=985 | time (s): 4.890 (total time: 129.430) Refine new water occ: r_work=0.1193 r_free=0.1338 adp: r_work=0.1193 r_free=0.1338 occ: r_work=0.1191 r_free=0.1337 adp: r_work=0.1191 r_free=0.1337 occ: r_work=0.1190 r_free=0.1338 adp: r_work=0.1190 r_free=0.1337 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1337 r_work=0.1190 r_free=0.1337 | n_water=985 | time (s): 228.650 (total time: 358.080) Filter (q & B) r_work=0.1194 r_free=0.1346 | n_water=909 | time (s): 5.160 (total time: 363.240) Filter (dist only) r_work=0.1194 r_free=0.1345 | n_water=908 | time (s): 116.510 (total time: 479.750) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.555282 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.702133 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1198 0.1351 0.0153 0.036 1.1 7.3 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.51 1.53 1.724 13.969 13.702 3.758 12.01 13.55 1.54 1.737 13.961 13.702 3.759 Individual atomic B min max mean iso aniso Overall: 5.56 65.37 14.89 0.89 542 3270 Protein: 5.56 29.36 10.46 0.89 0 2902 Water: 5.95 65.37 29.04 N/A 542 366 Other: 13.84 22.96 18.40 N/A 0 2 Chain A: 5.60 52.48 12.35 N/A 0 1624 Chain B: 5.56 65.37 12.18 N/A 0 1646 Chain S: 5.95 58.27 30.73 N/A 542 0 Histogram: Values Number of atoms 5.56 - 11.54 2103 11.54 - 17.52 780 17.52 - 23.50 282 23.50 - 29.48 210 29.48 - 35.46 194 35.46 - 41.45 129 41.45 - 47.43 75 47.43 - 53.41 31 53.41 - 59.39 7 59.39 - 65.37 1 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1355 r_work=0.1201 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1355 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758124 | | target function (ml) not normalized (work): 703844.009256 | | target function (ml) not normalized (free): 14732.400664 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1355 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1384 0.1382 0.1493 n_refl.: 191127 remove outliers: r(all,work,free)=0.1384 0.1382 0.1493 n_refl.: 191127 overall B=-0.01 to atoms: r(all,work,free)=0.1382 0.1380 0.1492 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1346 n_refl.: 191127 remove outliers: r(all,work,free)=0.1193 0.1190 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 90.10 88 3 0.3695 356.162 327.166 0.357 0.920 0.090 13.296-10.522 96.04 96 1 0.2362 485.533 467.848 0.737 0.921 0.109 10.503-8.327 97.80 175 3 0.2197 501.973 492.786 0.907 0.921 0.109 8.318-6.595 100.00 360 8 0.2167 375.594 369.782 0.927 0.921 0.093 6.588-5.215 100.00 711 7 0.1929 345.133 334.917 0.929 0.921 0.082 5.214-4.128 98.38 1367 28 0.1242 504.825 499.170 1.024 0.922 0.034 4.126-3.266 94.74 2603 46 0.1155 460.175 452.700 1.091 0.923 0.000 3.266-2.585 99.86 5447 97 0.1114 310.423 306.807 1.075 0.924 0.000 2.585-2.046 97.45 10613 204 0.0954 234.196 231.523 1.085 0.925 0.000 2.046-1.619 99.39 21536 464 0.0907 138.609 137.197 1.105 0.928 0.000 1.619-1.281 98.00 42464 925 0.0949 74.619 73.959 1.098 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.030 38.323 1.070 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0226 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1346 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1346 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1346 | n_water=908 | time (s): 2.650 (total time: 2.650) Filter (dist) r_work=0.1190 r_free=0.1345 | n_water=906 | time (s): 113.260 (total time: 115.910) Filter (q & B) r_work=0.1191 r_free=0.1345 | n_water=893 | time (s): 4.150 (total time: 120.060) Compute maps r_work=0.1191 r_free=0.1345 | n_water=893 | time (s): 1.910 (total time: 121.970) Filter (map) r_work=0.1213 r_free=0.1345 | n_water=786 | time (s): 4.120 (total time: 126.090) Find peaks r_work=0.1213 r_free=0.1345 | n_water=786 | time (s): 0.610 (total time: 126.700) Add new water r_work=0.1219 r_free=0.1359 | n_water=993 | time (s): 3.890 (total time: 130.590) Refine new water occ: r_work=0.1187 r_free=0.1335 adp: r_work=0.1187 r_free=0.1336 occ: r_work=0.1185 r_free=0.1334 adp: r_work=0.1185 r_free=0.1335 occ: r_work=0.1184 r_free=0.1334 adp: r_work=0.1184 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1335 r_work=0.1184 r_free=0.1335 | n_water=993 | time (s): 218.400 (total time: 348.990) Filter (q & B) r_work=0.1189 r_free=0.1340 | n_water=910 | time (s): 5.060 (total time: 354.050) Filter (dist only) r_work=0.1189 r_free=0.1339 | n_water=908 | time (s): 116.790 (total time: 470.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.586552 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.847572 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 0.1343 0.0151 0.037 1.1 6.8 0.0 0.3 0 0.793 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.43 1.51 1.709 13.932 14.848 3.756 11.90 13.43 1.52 1.722 13.924 14.848 3.752 Individual atomic B min max mean iso aniso Overall: 5.60 64.77 14.84 0.89 542 3270 Protein: 5.60 29.05 10.46 0.89 0 2902 Water: 6.04 64.77 28.83 N/A 542 366 Other: 13.88 22.44 18.16 N/A 0 2 Chain A: 5.67 52.27 12.32 N/A 0 1624 Chain B: 5.60 64.77 12.16 N/A 0 1646 Chain S: 6.04 58.18 30.54 N/A 542 0 Histogram: Values Number of atoms 5.60 - 11.51 2091 11.51 - 17.43 793 17.43 - 23.35 284 23.35 - 29.26 203 29.26 - 35.18 196 35.18 - 41.10 130 41.10 - 47.01 74 47.01 - 52.93 33 52.93 - 58.85 7 58.85 - 64.77 1 =========================== Idealize ADP of riding H ========================== r_work=0.1190 r_free=0.1343 r_work=0.1191 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1343 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1342 target_work(ml) = 3.752 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1189 r_free= 0.1342 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751889 | | target function (ml) not normalized (work): 702676.288727 | | target function (ml) not normalized (free): 14712.171348 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1192 0.1189 0.1342 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1391 0.1389 0.1502 n_refl.: 191127 remove outliers: r(all,work,free)=0.1391 0.1389 0.1502 n_refl.: 191127 overall B=-0.02 to atoms: r(all,work,free)=0.1388 0.1386 0.1499 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1340 n_refl.: 191127 remove outliers: r(all,work,free)=0.1191 0.1188 0.1340 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 90.10 88 3 0.3711 356.162 326.857 0.325 0.995 0.080 13.296-10.522 96.04 96 1 0.2355 485.533 467.465 0.674 0.996 0.090 10.503-8.327 97.80 175 3 0.2221 501.973 492.181 0.836 0.997 0.097 8.318-6.595 100.00 360 8 0.2174 375.594 369.794 0.855 0.997 0.088 6.588-5.215 100.00 711 7 0.1944 345.133 335.095 0.856 0.997 0.080 5.214-4.128 98.38 1367 28 0.1258 504.825 499.037 0.946 0.998 0.034 4.126-3.266 94.74 2603 46 0.1162 460.175 452.740 1.009 0.999 0.000 3.266-2.585 99.86 5447 97 0.1121 310.423 306.821 0.994 1.000 0.000 2.585-2.046 97.45 10613 204 0.0953 234.196 231.512 1.003 1.002 0.000 2.046-1.619 99.39 21536 464 0.0905 138.609 137.220 1.022 1.005 0.000 1.619-1.281 98.00 42464 925 0.0942 74.619 73.971 1.016 1.010 0.000 1.281-0.980 96.53 101826 2055 0.1622 40.030 38.318 0.991 1.019 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0447 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1340 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1340 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1340 | n_water=908 | time (s): 3.090 (total time: 3.090) Filter (dist) r_work=0.1188 r_free=0.1340 | n_water=907 | time (s): 113.480 (total time: 116.570) Filter (q & B) r_work=0.1189 r_free=0.1339 | n_water=897 | time (s): 5.260 (total time: 121.830) Compute maps r_work=0.1189 r_free=0.1339 | n_water=897 | time (s): 2.220 (total time: 124.050) Filter (map) r_work=0.1210 r_free=0.1339 | n_water=795 | time (s): 4.130 (total time: 128.180) Find peaks r_work=0.1210 r_free=0.1339 | n_water=795 | time (s): 0.550 (total time: 128.730) Add new water r_work=0.1216 r_free=0.1352 | n_water=995 | time (s): 3.980 (total time: 132.710) Refine new water occ: r_work=0.1185 r_free=0.1331 adp: r_work=0.1185 r_free=0.1331 occ: r_work=0.1183 r_free=0.1330 adp: r_work=0.1183 r_free=0.1330 occ: r_work=0.1182 r_free=0.1329 adp: r_work=0.1182 r_free=0.1329 ADP+occupancy (water only), MIN, final r_work=0.1182 r_free=0.1329 r_work=0.1182 r_free=0.1329 | n_water=995 | time (s): 159.470 (total time: 292.180) Filter (q & B) r_work=0.1186 r_free=0.1335 | n_water=915 | time (s): 4.690 (total time: 296.870) Filter (dist only) r_work=0.1187 r_free=0.1334 | n_water=913 | time (s): 117.940 (total time: 414.810) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.467706 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.000677 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 0.1191 0.1344 0.0153 0.037 1.1 6.6 0.0 0.3 0 0.734 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.44 1.53 1.706 13.922 14.001 3.754 11.94 13.48 1.55 1.713 13.917 14.001 3.754 Individual atomic B min max mean iso aniso Overall: 5.61 64.41 14.83 0.87 547 3270 Protein: 5.61 28.77 10.45 0.87 0 2902 Water: 6.04 64.41 28.75 N/A 547 366 Other: 13.88 22.34 18.11 N/A 0 2 Chain A: 5.69 52.17 12.29 N/A 0 1624 Chain B: 5.61 64.41 12.14 N/A 0 1646 Chain S: 6.04 58.16 30.51 N/A 547 0 Histogram: Values Number of atoms 5.61 - 11.49 2084 11.49 - 17.37 805 17.37 - 23.25 282 23.25 - 29.13 207 29.13 - 35.01 191 35.01 - 40.89 128 40.89 - 46.77 77 46.77 - 52.65 33 52.65 - 58.53 9 58.53 - 64.41 1 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1348 r_work=0.1194 r_free=0.1348 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1348 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1350 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.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753998 | | target function (ml) not normalized (work): 703071.257688 | | target function (ml) not normalized (free): 14725.886577 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1196 0.1193 0.1350 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1516 n_refl.: 191127 remove outliers: r(all,work,free)=0.1397 0.1395 0.1516 n_refl.: 191127 overall B=-0.02 to atoms: r(all,work,free)=0.1393 0.1391 0.1512 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1350 n_refl.: 191127 remove outliers: r(all,work,free)=0.1195 0.1192 0.1350 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 90.10 88 3 0.3717 356.162 326.739 0.323 0.986 0.070 13.296-10.522 96.04 96 1 0.2350 485.533 468.116 0.681 0.987 0.090 10.503-8.327 97.80 175 3 0.2218 501.973 492.890 0.843 0.988 0.100 8.318-6.595 100.00 360 8 0.2164 375.594 369.748 0.862 0.988 0.089 6.588-5.215 100.00 711 7 0.1949 345.133 335.165 0.864 0.988 0.083 5.214-4.128 98.38 1367 28 0.1261 504.825 498.871 0.956 0.989 0.039 4.126-3.266 94.74 2603 46 0.1169 460.175 452.588 1.019 0.990 0.000 3.266-2.585 99.86 5447 97 0.1129 310.423 306.765 1.003 0.991 0.000 2.585-2.046 97.45 10613 204 0.0958 234.196 231.493 1.012 0.994 0.000 2.046-1.619 99.39 21536 464 0.0908 138.609 137.217 1.031 0.997 0.000 1.619-1.281 98.00 42464 925 0.0943 74.619 73.970 1.025 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.030 38.305 1.000 1.013 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0601 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1192 r_free=0.1350 After: r_work=0.1193 r_free=0.1350 ================================== NQH flips ================================== r_work=0.1193 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1193 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1350 | n_water=913 | time (s): 2.860 (total time: 2.860) Filter (dist) r_work=0.1193 r_free=0.1350 | n_water=911 | time (s): 115.510 (total time: 118.370) Filter (q & B) r_work=0.1194 r_free=0.1350 | n_water=899 | time (s): 5.030 (total time: 123.400) Compute maps r_work=0.1194 r_free=0.1350 | n_water=899 | time (s): 1.590 (total time: 124.990) Filter (map) r_work=0.1214 r_free=0.1348 | n_water=795 | time (s): 4.000 (total time: 128.990) Find peaks r_work=0.1214 r_free=0.1348 | n_water=795 | time (s): 0.760 (total time: 129.750) Add new water r_work=0.1220 r_free=0.1361 | n_water=1006 | time (s): 5.010 (total time: 134.760) Refine new water occ: r_work=0.1189 r_free=0.1337 adp: r_work=0.1190 r_free=0.1337 occ: r_work=0.1188 r_free=0.1335 adp: r_work=0.1188 r_free=0.1336 occ: r_work=0.1186 r_free=0.1334 adp: r_work=0.1186 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1335 r_work=0.1186 r_free=0.1335 | n_water=1006 | time (s): 215.620 (total time: 350.380) Filter (q & B) r_work=0.1190 r_free=0.1344 | n_water=922 | time (s): 4.100 (total time: 354.480) Filter (dist only) r_work=0.1191 r_free=0.1343 | n_water=920 | time (s): 121.940 (total time: 476.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.547038 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.510797 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1347 0.0155 0.037 1.2 9.5 0.0 0.3 0 0.774 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.47 1.55 1.698 13.906 13.511 3.755 11.96 13.51 1.55 1.726 13.889 13.511 3.756 Individual atomic B min max mean iso aniso Overall: 5.63 63.26 14.80 0.85 554 3270 Protein: 5.63 28.10 10.43 0.85 0 2902 Water: 6.07 63.26 28.58 N/A 554 366 Other: 13.90 22.11 18.01 N/A 0 2 Chain A: 5.70 51.84 12.24 N/A 0 1624 Chain B: 5.63 63.26 12.09 N/A 0 1646 Chain S: 6.07 58.15 30.36 N/A 554 0 Histogram: Values Number of atoms 5.63 - 11.39 2059 11.39 - 17.15 832 17.15 - 22.92 271 22.92 - 28.68 210 28.68 - 34.44 195 34.44 - 40.21 125 40.21 - 45.97 84 45.97 - 51.73 35 51.73 - 57.50 10 57.50 - 63.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1351 r_work=0.1196 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1351 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1349 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1349 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755832 | | target function (ml) not normalized (work): 703414.770230 | | target function (ml) not normalized (free): 14732.690466 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1369 0.1459 5.6941 5.7834| | 2: 2.94 - 2.33 1.00 7339 128 0.1068 0.1286 5.0864 5.173| | 3: 2.33 - 2.04 0.96 6939 150 0.0904 0.1194 4.6589 4.7583| | 4: 2.04 - 1.85 1.00 7170 155 0.0901 0.1057 4.3925 4.5723| | 5: 1.85 - 1.72 0.99 7113 159 0.0934 0.0980 4.1524 4.2312| | 6: 1.72 - 1.62 0.99 7102 142 0.0900 0.1107 3.9484 4.0877| | 7: 1.62 - 1.54 0.99 7104 148 0.0889 0.0959 3.8002 3.9279| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1306 3.7027 3.8995| | 9: 1.47 - 1.41 0.98 6938 155 0.0929 0.1128 3.6251 3.7562| | 10: 1.41 - 1.36 0.99 7022 150 0.0981 0.1199 3.5613 3.6861| | 11: 1.36 - 1.32 0.99 6997 151 0.0998 0.1141 3.4905 3.5904| | 12: 1.32 - 1.28 0.98 6975 149 0.1032 0.1116 3.4617 3.5767| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1251 3.4386 3.5699| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1590 3.4333 3.6843| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1246 3.4493 3.4906| | 16: 1.19 - 1.17 0.93 6604 132 0.1251 0.1546 3.4658 3.6525| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1227 3.4333 3.4414| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1712 3.4382 3.5315| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1751 3.42 3.5978| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1582 3.4102 3.4334| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2135 3.418 3.5051| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1956 3.4128 3.4153| | 23: 1.05 - 1.03 0.97 6827 159 0.2119 0.2015 3.433 3.4827| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2250 3.4355 3.5111| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2524 3.4496 3.5228| | 26: 1.01 - 0.99 0.96 6767 158 0.2755 0.2843 3.416 3.4224| | 27: 0.99 - 0.98 0.94 6647 131 0.3042 0.2801 3.4684 3.3981| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.03 1.00 0.96 11696.72| | 2: 2.94 - 2.33 7339 128 0.92 13.06 0.99 0.96 5299.14| | 3: 2.33 - 2.04 6939 150 0.96 7.67 1.01 0.96 1704.23| | 4: 2.04 - 1.85 7170 155 0.96 7.70 1.00 0.96 1006.37| | 5: 1.85 - 1.72 7113 159 0.96 8.08 1.00 0.97 633.35| | 6: 1.72 - 1.62 7102 142 0.96 8.01 1.00 0.97 442.50| | 7: 1.62 - 1.54 7104 148 0.96 8.11 1.01 0.98 336.03| | 8: 1.54 - 1.47 6798 152 0.96 8.26 1.01 0.98 279.29| | 9: 1.47 - 1.41 6938 155 0.96 8.52 1.00 0.99 232.32| | 10: 1.41 - 1.36 7022 150 0.96 8.98 1.00 0.98 204.59| | 11: 1.36 - 1.32 6997 151 0.96 8.99 0.99 0.97 176.65| | 12: 1.32 - 1.28 6975 149 0.96 9.02 0.98 0.96 161.52| | 13: 1.28 - 1.25 6907 166 0.96 9.54 1.01 0.97 159.01| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.97 163.70| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.01 0.99 167.19| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.97 160.38| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.97 153.96| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.96 147.70| | 19: 1.12 - 1.10 6948 106 0.93 14.16 1.00 0.96 151.25| | 20: 1.10 - 1.08 6884 147 0.92 15.22 1.00 0.95 150.31| | 21: 1.08 - 1.07 6852 152 0.91 16.62 1.00 0.94 153.16| | 22: 1.07 - 1.05 6836 135 0.89 18.26 1.00 0.94 154.55| | 23: 1.05 - 1.03 6827 159 0.87 20.44 1.00 0.93 164.11| | 24: 1.03 - 1.02 6784 133 0.85 23.11 1.00 0.94 178.52| | 25: 1.02 - 1.01 6552 130 0.83 25.13 0.98 0.91 181.78| | 26: 1.01 - 0.99 6767 158 0.81 26.68 0.99 0.90 177.06| | 27: 0.99 - 0.98 6647 131 0.82 26.44 0.99 0.89 162.44| |alpha: min = 0.89 max = 0.99 mean = 0.96| |beta: min = 147.70 max = 11696.72 mean = 952.12| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.33| |phase err.(test): min = 0.00 max = 89.75 mean = 13.49| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1349 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1523 n_refl.: 191127 remove outliers: r(all,work,free)=0.1403 0.1401 0.1523 n_refl.: 191127 overall B=-0.13 to atoms: r(all,work,free)=0.1382 0.1380 0.1504 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1350 n_refl.: 191127 remove outliers: r(all,work,free)=0.1197 0.1194 0.1350 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 90.10 88 3 0.3690 356.162 328.150 0.312 0.994 0.060 13.296-10.522 96.04 96 1 0.2379 485.533 468.738 0.673 0.995 0.110 10.503-8.327 97.80 175 3 0.2194 501.973 493.602 0.823 0.996 0.107 8.318-6.595 100.00 360 8 0.2157 375.594 370.049 0.844 0.996 0.093 6.588-5.215 100.00 711 7 0.1948 345.133 334.997 0.843 0.997 0.080 5.214-4.128 98.38 1367 28 0.1263 504.825 499.023 0.933 0.998 0.029 4.126-3.266 94.74 2603 46 0.1175 460.175 452.422 0.995 0.999 0.000 3.266-2.585 99.86 5447 97 0.1122 310.423 306.823 0.979 1.000 0.000 2.585-2.046 97.45 10613 204 0.0962 234.196 231.494 0.985 1.003 0.000 2.046-1.619 99.39 21536 464 0.0912 138.609 137.204 1.000 1.007 0.000 1.619-1.281 98.00 42464 925 0.0947 74.619 73.963 0.990 1.013 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.030 38.301 0.958 1.025 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0277 ================= 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 : 0.2042 0.2006 0.081 5.226 5.2 78.0 14.6 805 0.000 1_bss: 0.1807 0.1936 0.081 5.226 5.2 78.1 14.6 805 0.000 1_settarget: 0.1807 0.1936 0.081 5.226 5.2 78.1 14.6 805 0.000 1_nqh: 0.1807 0.1936 0.081 5.226 5.2 78.1 14.6 805 0.000 1_weight: 0.1807 0.1936 0.081 5.226 5.2 78.1 14.6 805 0.000 1_xyzrec: 0.1268 0.1500 0.038 1.146 5.2 78.1 14.6 805 0.156 1_adp: 0.1297 0.1570 0.038 1.146 5.2 73.1 15.1 805 0.156 1_regHadp: 0.1296 0.1565 0.038 1.146 5.2 73.1 15.1 805 0.156 1_occ: 0.1281 0.1554 0.038 1.146 5.2 73.1 15.1 805 0.156 2_bss: 0.1275 0.1548 0.038 1.146 5.4 73.2 15.3 805 0.156 2_settarget: 0.1275 0.1548 0.038 1.146 5.4 73.2 15.3 805 0.156 2_updatecdl: 0.1275 0.1548 0.038 1.160 5.4 73.2 15.3 805 0.156 2_nqh: 0.1275 0.1548 0.038 1.160 5.4 73.2 15.3 805 0.156 2_sol: 0.1271 0.1501 0.038 1.160 5.4 73.2 16.3 883 n/a 2_weight: 0.1271 0.1501 0.038 1.160 5.4 73.2 16.3 883 n/a 2_xyzrec: 0.1255 0.1518 0.041 1.141 5.4 73.2 16.3 883 n/a 2_adp: 0.1232 0.1504 0.041 1.141 5.4 68.2 16.4 883 n/a 2_regHadp: 0.1232 0.1505 0.041 1.141 5.4 68.2 16.4 883 n/a 2_occ: 0.1226 0.1502 0.041 1.141 5.4 68.2 16.4 883 n/a 3_bss: 0.1233 0.1510 0.041 1.141 5.4 68.2 16.3 883 n/a 3_settarget: 0.1233 0.1510 0.041 1.141 5.4 68.2 16.3 883 n/a 3_updatecdl: 0.1233 0.1510 0.041 1.148 5.4 68.2 16.3 883 n/a 3_nqh: 0.1233 0.1510 0.041 1.148 5.4 68.2 16.3 883 n/a 3_sol: 0.1247 0.1515 0.041 1.148 5.4 68.2 15.5 878 n/a 3_weight: 0.1247 0.1515 0.041 1.148 5.4 68.2 15.5 878 n/a 3_xyzrec: 0.1237 0.1446 0.035 1.102 5.4 68.2 15.5 878 n/a 3_adp: 0.1231 0.1405 0.035 1.102 5.5 67.8 15.4 878 n/a 3_regHadp: 0.1232 0.1406 0.035 1.102 5.5 67.8 15.4 878 n/a 3_occ: 0.1227 0.1401 0.035 1.102 5.5 67.8 15.4 878 n/a 4_bss: 0.1223 0.1395 0.035 1.102 5.5 67.8 15.3 878 n/a 4_settarget: 0.1223 0.1395 0.035 1.102 5.5 67.8 15.3 878 n/a 4_updatecdl: 0.1223 0.1395 0.035 1.105 5.5 67.8 15.3 878 n/a 4_nqh: 0.1223 0.1395 0.035 1.105 5.5 67.8 15.3 878 n/a 4_sol: 0.1208 0.1369 0.035 1.105 5.5 67.8 15.2 882 n/a 4_weight: 0.1208 0.1369 0.035 1.105 5.5 67.8 15.2 882 n/a 4_xyzrec: 0.1205 0.1375 0.034 1.119 5.5 67.8 15.2 882 n/a 4_adp: 0.1198 0.1370 0.034 1.119 5.5 67.4 15.1 882 n/a 4_regHadp: 0.1198 0.1371 0.034 1.119 5.5 67.4 15.1 882 n/a 4_occ: 0.1196 0.1370 0.034 1.119 5.5 67.4 15.1 882 n/a 5_bss: 0.1194 0.1373 0.034 1.119 5.5 67.4 15.1 882 n/a 5_settarget: 0.1194 0.1373 0.034 1.119 5.5 67.4 15.1 882 n/a 5_updatecdl: 0.1194 0.1373 0.034 1.119 5.5 67.4 15.1 882 n/a 5_nqh: 0.1194 0.1373 0.034 1.119 5.5 67.4 15.1 882 n/a 5_sol: 0.1194 0.1359 0.034 1.119 5.5 67.4 15.1 893 n/a 5_weight: 0.1194 0.1359 0.034 1.119 5.5 67.4 15.1 893 n/a 5_xyzrec: 0.1197 0.1358 0.034 1.129 5.5 67.4 15.1 893 n/a 5_adp: 0.1201 0.1363 0.034 1.129 5.5 66.9 15.0 893 n/a 5_regHadp: 0.1201 0.1363 0.034 1.129 5.5 66.9 15.0 893 n/a 5_occ: 0.1200 0.1361 0.034 1.129 5.5 66.9 15.0 893 n/a 6_bss: 0.1198 0.1353 0.034 1.129 5.5 66.8 15.0 893 n/a 6_settarget: 0.1198 0.1353 0.034 1.129 5.5 66.8 15.0 893 n/a 6_updatecdl: 0.1198 0.1353 0.034 1.129 5.5 66.8 15.0 893 n/a 6_nqh: 0.1198 0.1353 0.034 1.129 5.5 66.8 15.0 893 n/a 6_sol: 0.1196 0.1340 0.034 1.129 5.5 66.8 15.0 909 n/a 6_weight: 0.1196 0.1340 0.034 1.129 5.5 66.8 15.0 909 n/a 6_xyzrec: 0.1199 0.1344 0.036 1.123 5.5 66.8 15.0 909 n/a 6_adp: 0.1200 0.1345 0.036 1.123 5.6 65.7 15.0 909 n/a 6_regHadp: 0.1200 0.1345 0.036 1.123 5.6 65.7 15.0 909 n/a 6_occ: 0.1197 0.1342 0.036 1.123 5.6 65.7 15.0 909 n/a 7_bss: 0.1196 0.1339 0.036 1.123 5.5 65.6 14.9 909 n/a 7_settarget: 0.1196 0.1339 0.036 1.123 5.5 65.6 14.9 909 n/a 7_updatecdl: 0.1196 0.1339 0.036 1.123 5.5 65.6 14.9 909 n/a 7_nqh: 0.1196 0.1339 0.036 1.123 5.5 65.6 14.9 909 n/a 7_sol: 0.1194 0.1345 0.036 1.123 5.5 65.6 14.9 908 n/a 7_weight: 0.1194 0.1345 0.036 1.123 5.5 65.6 14.9 908 n/a 7_xyzrec: 0.1198 0.1351 0.036 1.128 5.5 65.6 14.9 908 n/a 7_adp: 0.1201 0.1355 0.036 1.128 5.6 65.4 14.9 908 n/a 7_regHadp: 0.1201 0.1355 0.036 1.128 5.6 65.4 14.9 908 n/a 7_occ: 0.1200 0.1355 0.036 1.128 5.6 65.4 14.9 908 n/a 8_bss: 0.1190 0.1346 0.036 1.128 5.5 65.4 14.9 908 n/a 8_settarget: 0.1190 0.1346 0.036 1.128 5.5 65.4 14.9 908 n/a 8_updatecdl: 0.1190 0.1346 0.036 1.129 5.5 65.4 14.9 908 n/a 8_nqh: 0.1190 0.1346 0.036 1.129 5.5 65.4 14.9 908 n/a 8_sol: 0.1189 0.1339 0.036 1.129 5.5 65.4 14.9 908 n/a 8_weight: 0.1189 0.1339 0.036 1.129 5.5 65.4 14.9 908 n/a 8_xyzrec: 0.1192 0.1343 0.037 1.130 5.5 65.4 14.9 908 n/a 8_adp: 0.1190 0.1343 0.037 1.130 5.6 64.8 14.8 908 n/a 8_regHadp: 0.1191 0.1343 0.037 1.130 5.6 64.8 14.8 908 n/a 8_occ: 0.1189 0.1342 0.037 1.130 5.6 64.8 14.8 908 n/a 9_bss: 0.1188 0.1340 0.037 1.130 5.6 64.7 14.8 908 n/a 9_settarget: 0.1188 0.1340 0.037 1.130 5.6 64.7 14.8 908 n/a 9_updatecdl: 0.1188 0.1340 0.037 1.130 5.6 64.7 14.8 908 n/a 9_nqh: 0.1188 0.1340 0.037 1.130 5.6 64.7 14.8 908 n/a 9_sol: 0.1187 0.1334 0.037 1.130 5.6 64.7 14.8 913 n/a 9_weight: 0.1187 0.1334 0.037 1.130 5.6 64.7 14.8 913 n/a 9_xyzrec: 0.1191 0.1344 0.037 1.111 5.6 64.7 14.8 913 n/a 9_adp: 0.1194 0.1348 0.037 1.111 5.6 64.4 14.8 913 n/a 9_regHadp: 0.1194 0.1348 0.037 1.111 5.6 64.4 14.8 913 n/a 9_occ: 0.1192 0.1350 0.037 1.111 5.6 64.4 14.8 913 n/a 10_bss: 0.1192 0.1350 0.037 1.111 5.6 64.4 14.8 913 n/a 10_settarget: 0.1192 0.1350 0.037 1.111 5.6 64.4 14.8 913 n/a 10_updatecdl: 0.1192 0.1350 0.037 1.111 5.6 64.4 14.8 913 n/a 10_setrh: 0.1193 0.1350 0.037 1.111 5.6 64.4 14.8 913 n/a 10_nqh: 0.1193 0.1350 0.037 1.111 5.6 64.4 14.8 913 n/a 10_sol: 0.1191 0.1343 0.037 1.111 5.6 64.4 14.8 920 n/a 10_weight: 0.1191 0.1343 0.037 1.111 5.6 64.4 14.8 920 n/a 10_xyzrec: 0.1193 0.1347 0.037 1.161 5.6 64.4 14.8 920 n/a 10_adp: 0.1196 0.1351 0.037 1.161 5.6 63.3 14.8 920 n/a 10_regHadp: 0.1196 0.1351 0.037 1.161 5.6 63.3 14.8 920 n/a 10_occ: 0.1194 0.1349 0.037 1.161 5.6 63.3 14.8 920 n/a end: 0.1194 0.1350 0.037 1.161 5.5 63.1 14.7 920 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4591434_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4591434_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.8000 Refinement macro-cycles (run) : 11862.0000 Write final files (write_after_run_outputs) : 166.1400 Total : 12033.9400 Total CPU time: 3.35 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:37:50 PST -0800 (1736735870.01 s) Start R-work = 0.1807, R-free = 0.1936 Final R-work = 0.1194, R-free = 0.1350 =============================================================================== Job complete usr+sys time: 12349.18 seconds wall clock time: 206 minutes 52.84 seconds (12412.84 seconds total)