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_9465109.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 { 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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9465109.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_9465109.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den } main { ordered_solvent = True number_of_macro_cycles = 10 max_number_of_iterations = 100 } pdb_interpretation { apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif residue_selection = (chain A or chain B) and resseq 14 } apply_cif_restraints { restraints_file_name = /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif residue_selection = (chain A or chain B) and resseq 23 } nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } geometry_restraints.edits { bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 14 and name OE2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 23 and name OD2 atom_selection_2 = chain B and resseq 16 and name OG1 distance_ideal = 2.72 sigma = 10.0 } bond { atom_selection_1 = chain A and resseq 14 and name OE2 atom_selection_2 = chain B and resseq 23 and name OD2 distance_ideal = 2.44 sigma = 10.0 } bond { atom_selection_1 = chain B and resseq 23 and name OD2 atom_selection_2 = chain A and resseq 16 and name OG1 distance_ideal = 2.71 sigma = 10.0 } } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 1.72, 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: 2.808 distance_ideal: 2.720 ideal - model: -0.088 slack: 0.000 delta_slack: -0.088 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: 2.745 distance_ideal: 2.710 ideal - model: -0.035 slack: 0.000 delta_slack: -0.035 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 130.7 milliseconds Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.77 - 1.01: 654 1.01 - 1.26: 2660 1.26 - 1.50: 1595 1.50 - 1.74: 1008 1.74 - 1.98: 17 Bond restraints: 5934 Sorted by residual: bond pdb=" C VAL B 7 " pdb=" O VAL B 7 " ideal model delta sigma weight residual 1.237 1.013 0.224 1.08e-02 8.57e+03 4.30e+02 bond pdb=" CG1 ILE B 70 " pdb="HG12 ILE B 70 " ideal model delta sigma weight residual 0.970 1.372 -0.402 2.00e-02 2.50e+03 4.04e+02 bond pdb=" N ILE B 22 " pdb=" CA ILE B 22 " ideal model delta sigma weight residual 1.461 1.688 -0.227 1.17e-02 7.31e+03 3.76e+02 bond pdb=" CB LYS B 151 " pdb=" HB2 LYS B 151 " ideal model delta sigma weight residual 0.970 1.335 -0.365 2.00e-02 2.50e+03 3.33e+02 bond pdb=" CA VAL A 150 " pdb=" CB VAL A 150 " ideal model delta sigma weight residual 1.544 1.330 0.214 1.19e-02 7.06e+03 3.23e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.37: 5874 4.37 - 8.75: 3519 8.75 - 13.12: 1204 13.12 - 17.49: 201 17.49 - 21.86: 12 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.71 133.59 -11.88 6.40e-01 2.44e+00 3.45e+02 angle pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " pdb=" CG ASP B 132 " ideal model delta sigma weight residual 112.60 128.03 -15.43 1.00e+00 1.00e+00 2.38e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.22 112.80 9.42 6.50e-01 2.37e+00 2.10e+02 angle pdb=" C PHE A 119 " pdb=" N PRO A 120 " pdb=" CA PRO A 120 " ideal model delta sigma weight residual 119.05 134.86 -15.81 1.11e+00 8.12e-01 2.03e+02 angle pdb=" O GLY A 190 " pdb=" C GLY A 190 " pdb=" N ILE A 191 " ideal model delta sigma weight residual 122.77 135.76 -12.99 9.40e-01 1.13e+00 1.91e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 1859 17.86 - 35.72: 130 35.72 - 53.59: 46 53.59 - 71.45: 12 71.45 - 89.31: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA LEU B 185 " pdb=" C LEU B 185 " pdb=" N VAL B 186 " pdb=" CA VAL B 186 " ideal model delta harmonic sigma weight residual 180.00 -151.63 -28.37 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N GLN A 156 " pdb=" CA GLN A 156 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual 180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.248: 235 0.248 - 0.494: 160 0.494 - 0.741: 76 0.741 - 0.987: 17 0.987 - 1.234: 4 Chirality restraints: 492 Sorted by residual: 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 -1.36 -1.23 2.00e-01 2.50e+01 3.81e+01 chirality pdb=" CG LEU B 130 " pdb=" CB LEU B 130 " pdb=" CD1 LEU B 130 " pdb=" CD2 LEU B 130 " both_signs ideal model delta sigma weight residual False -2.59 -1.53 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CB VAL B 186 " pdb=" CA VAL B 186 " pdb=" CG1 VAL B 186 " pdb=" CG2 VAL B 186 " both_signs ideal model delta sigma weight residual False -2.63 -3.65 1.02 2.00e-01 2.50e+01 2.62e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 119 " 0.077 2.00e-02 2.50e+03 8.92e-02 2.39e+02 pdb=" CG PHE B 119 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE B 119 " -0.131 2.00e-02 2.50e+03 pdb=" CD2 PHE B 119 " -0.084 2.00e-02 2.50e+03 pdb=" CE1 PHE B 119 " -0.121 2.00e-02 2.50e+03 pdb=" CE2 PHE B 119 " 0.070 2.00e-02 2.50e+03 pdb=" CZ PHE B 119 " 0.122 2.00e-02 2.50e+03 pdb=" HD1 PHE B 119 " 0.102 2.00e-02 2.50e+03 pdb=" HD2 PHE B 119 " -0.095 2.00e-02 2.50e+03 pdb=" HE1 PHE B 119 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 PHE B 119 " 0.084 2.00e-02 2.50e+03 pdb=" HZ PHE B 119 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 146 " 0.102 2.00e-02 2.50e+03 7.15e-02 2.04e+02 pdb=" CG TRP A 146 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TRP A 146 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 146 " -0.086 2.00e-02 2.50e+03 pdb=" NE1 TRP A 146 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP A 146 " -0.130 2.00e-02 2.50e+03 pdb=" CE3 TRP A 146 " 0.072 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 146 " -0.057 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 146 " 0.045 2.00e-02 2.50e+03 pdb=" CH2 TRP A 146 " -0.051 2.00e-02 2.50e+03 pdb=" HD1 TRP A 146 " -0.098 2.00e-02 2.50e+03 pdb=" HE1 TRP A 146 " 0.042 2.00e-02 2.50e+03 pdb=" HE3 TRP A 146 " -0.029 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 146 " 0.134 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 146 " -0.035 2.00e-02 2.50e+03 pdb=" HH2 TRP A 146 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 192 " -0.046 2.00e-02 2.50e+03 8.20e-02 2.02e+02 pdb=" CG TYR A 192 " -0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR A 192 " -0.118 2.00e-02 2.50e+03 pdb=" CD2 TYR A 192 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR A 192 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR A 192 " 0.055 2.00e-02 2.50e+03 pdb=" CZ TYR A 192 " -0.052 2.00e-02 2.50e+03 pdb=" OH TYR A 192 " 0.031 2.00e-02 2.50e+03 pdb=" HD1 TYR A 192 " 0.067 2.00e-02 2.50e+03 pdb=" HD2 TYR A 192 " 0.175 2.00e-02 2.50e+03 pdb=" HE1 TYR A 192 " 0.061 2.00e-02 2.50e+03 pdb=" HE2 TYR A 192 " -0.116 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 1.00 - 1.72: 50 1.72 - 2.44: 3700 2.44 - 3.16: 22826 3.16 - 3.88: 32586 3.88 - 4.60: 51165 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110327 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.995 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.006 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.012 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.048 2.620 nonbonded pdb=" HE3 LYS A 52 " pdb=" O HOH S1448 " model vdw 1.088 2.620 ... (remaining 110322 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_9465109_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Residue THR 16 is missing expected H atoms. Skipping. Residue THR 16 is missing expected H atoms. Skipping. Total: count: 2984 occupancy sum: 2984.00 (% of total atoms 46.96) Rotatable: count: 1008 occupancy sum: 1008.00 (% of total atoms 15.86) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.2020 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301649 | | target function (ml) not normalized (work): 805754.722158 | | target function (ml) not normalized (free): 16614.414520 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7412 127 0.2132 0.1948 6.6736 6.3159| | 2: 2.94 - 2.33 1.00 7339 128 0.1633 0.1573 5.5508 5.5977| | 3: 2.33 - 2.04 0.96 6939 150 0.1621 0.1782 5.1414 5.2446| | 4: 2.04 - 1.85 1.00 7170 155 0.1762 0.1724 4.9718 5.1081| | 5: 1.85 - 1.72 0.99 7113 159 0.1915 0.1781 4.8002 4.8153| | 6: 1.72 - 1.62 0.99 7102 142 0.2018 0.1994 4.6817 4.7398| | 7: 1.62 - 1.54 0.99 7104 148 0.2025 0.1736 4.5609 4.5752| | 8: 1.54 - 1.47 0.96 6798 152 0.2052 0.2408 4.4778 4.6178| | 9: 1.47 - 1.41 0.98 6938 155 0.2059 0.2232 4.3864 4.4871| | 10: 1.41 - 1.36 0.99 7022 150 0.2129 0.2256 4.3096 4.3462| | 11: 1.36 - 1.32 0.99 6997 151 0.2136 0.2129 4.2475 4.2921| | 12: 1.32 - 1.28 0.98 6976 149 0.2054 0.2024 4.1642 4.2499| | 13: 1.28 - 1.25 0.98 6907 166 0.2048 0.2094 4.1301 4.1324| | 14: 1.25 - 1.22 0.98 7015 113 0.2108 0.2622 4.0856 4.3233| | 15: 1.22 - 1.19 0.98 6957 137 0.2089 0.2022 4.0486 4.0024| | 16: 1.19 - 1.17 0.93 6604 132 0.2125 0.2237 4.0054 4.0753| | 17: 1.17 - 1.14 0.98 6941 135 0.2166 0.2097 3.9562 4.0659| | 18: 1.14 - 1.12 0.98 6875 142 0.2210 0.2102 3.9231 3.8754| | 19: 1.12 - 1.10 0.97 6949 106 0.2289 0.2370 3.8716 3.9634| | 20: 1.10 - 1.08 0.97 6884 147 0.2320 0.2195 3.816 3.825| | 21: 1.08 - 1.07 0.97 6852 152 0.2471 0.2401 3.8035 3.7861| | 22: 1.07 - 1.05 0.97 6838 135 0.2548 0.2361 3.7487 3.7113| | 23: 1.05 - 1.03 0.97 6829 159 0.2706 0.2443 3.724 3.7813| | 24: 1.03 - 1.02 0.96 6785 133 0.2890 0.2907 3.7071 3.7967| | 25: 1.02 - 1.01 0.93 6552 130 0.3059 0.3231 3.6717 3.7872| | 26: 1.01 - 0.99 0.96 6767 158 0.3183 0.3493 3.6265 3.6722| | 27: 0.99 - 0.98 0.94 6648 131 0.3405 0.3148 3.647 3.6125| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 20.75 0.91 0.97 36406.24| | 2: 2.94 - 2.33 7339 128 0.85 21.76 1.09 1.02 15742.86| | 3: 2.33 - 2.04 6939 150 0.93 13.24 1.11 1.06 4577.79| | 4: 2.04 - 1.85 7170 155 0.92 14.18 1.11 1.07 3066.81| | 5: 1.85 - 1.72 7113 159 0.90 16.19 1.11 1.08 2215.35| | 6: 1.72 - 1.62 7102 142 0.89 17.27 1.12 1.07 1731.75| | 7: 1.62 - 1.54 7104 148 0.88 18.38 1.11 1.06 1422.30| | 8: 1.54 - 1.47 6798 152 0.88 19.40 1.10 1.04 1236.99| | 9: 1.47 - 1.41 6938 155 0.87 19.71 1.10 1.05 1049.28| | 10: 1.41 - 1.36 7022 150 0.86 20.87 1.10 1.05 911.94| | 11: 1.36 - 1.32 6997 151 0.87 20.51 1.08 1.05 770.63| | 12: 1.32 - 1.28 6976 149 0.87 20.10 1.08 1.04 670.50| | 13: 1.28 - 1.25 6907 166 0.87 20.12 1.08 1.05 621.51| | 14: 1.25 - 1.22 7015 113 0.86 21.03 1.08 1.04 590.28| | 15: 1.22 - 1.19 6957 137 0.86 21.59 1.07 1.03 572.60| | 16: 1.19 - 1.17 6604 132 0.86 21.20 1.08 1.02 505.76| | 17: 1.17 - 1.14 6941 135 0.86 21.40 1.08 1.01 451.18| | 18: 1.14 - 1.12 6875 142 0.87 20.80 1.08 0.99 384.15| | 19: 1.12 - 1.10 6949 106 0.86 21.84 1.07 0.99 361.55| | 20: 1.10 - 1.08 6884 147 0.85 22.35 1.06 0.98 332.44| | 21: 1.08 - 1.07 6852 152 0.85 22.95 1.06 0.97 314.01| | 22: 1.07 - 1.05 6838 135 0.83 24.42 1.05 0.97 303.67| | 23: 1.05 - 1.03 6829 159 0.81 26.98 1.05 0.96 314.89| | 24: 1.03 - 1.02 6785 133 0.77 30.42 1.05 0.97 348.81| | 25: 1.02 - 1.01 6552 130 0.75 32.30 1.02 0.93 343.76| | 26: 1.01 - 0.99 6767 158 0.73 33.74 1.03 0.91 315.22| | 27: 0.99 - 0.98 6648 131 0.76 31.38 1.03 0.89 256.84| |alpha: min = 0.89 max = 1.08 mean = 1.01| |beta: min = 256.84 max = 36406.24 mean = 2939.60| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 21.95| |phase err.(test): min = 0.00 max = 88.31 mean = 22.04| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.287 2950 Z= 5.500 Angle : 5.262 17.723 4018 Z= 3.750 Chirality : 0.375 1.234 492 Planarity : 0.033 0.104 512 Dihedral : 12.754 89.309 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.52 % Allowed : 3.37 % Favored : 96.11 % Rotamer: Outliers : 1.61 % Allowed : 3.23 % Favored : 95.16 % Cbeta Deviations : 30.06 % 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: -2.50 (0.37), residues: 386 helix: -2.52 (0.30), residues: 146 sheet: -0.88 (0.55), residues: 86 loop : -0.93 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.022 ARG B 83 TYR 0.130 0.040 TYR B 194 PHE 0.138 0.040 PHE B 119 TRP 0.103 0.037 TRP A 146 HIS 0.060 0.029 HIS B 116 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2037 r_free= 0.2020 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.301649 | | target function (ml) not normalized (work): 805754.722158 | | target function (ml) not normalized (free): 16614.414520 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2036 0.2037 0.2020 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2036 0.2037 0.2020 n_refl.: 191155 remove outliers: r(all,work,free)=0.2036 0.2037 0.2020 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2036 0.2037 0.2020 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1805 0.1802 0.1952 n_refl.: 191145 remove outliers: r(all,work,free)=0.1803 0.1800 0.1952 n_refl.: 191141 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4183 400.535 296.619 0.434 0.913 0.299 13.296-10.522 100.00 100 1 0.2585 534.497 519.816 0.782 0.914 0.248 10.503-8.327 99.45 178 3 0.2522 565.118 556.516 0.968 0.915 0.223 8.318-6.595 100.00 360 8 0.2470 414.736 403.540 0.971 0.914 0.165 6.588-5.215 100.00 711 7 0.2246 381.101 366.201 0.957 0.914 0.160 5.214-4.128 98.38 1367 28 0.1476 557.435 550.150 1.074 0.915 0.090 4.126-3.266 94.74 2603 46 0.1335 508.132 499.307 1.142 0.915 0.024 3.266-2.585 99.86 5447 97 0.1436 342.774 337.723 1.119 0.914 0.010 2.585-2.046 97.45 10613 204 0.1400 258.603 254.127 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1628 153.054 149.788 1.143 0.911 0.000 1.619-1.281 98.00 42464 925 0.1915 82.395 80.227 1.128 0.909 0.000 1.281-0.980 96.53 101826 2056 0.2326 44.203 41.647 1.113 0.904 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0033 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1800 r_free=0.1952 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1800 r_free=0.1952 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.245234 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 577.657048 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1271 0.1494 0.0222 0.038 1.2 11.2 0.0 0.3 0 11.123 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.71 14.94 2.22 1.118 13.113 577.657 0.019 13.00 15.68 2.68 1.249 13.326 577.657 0.018 Individual atomic B min max mean iso aniso Overall: 5.16 73.05 14.99 1.41 435 3274 Protein: 5.16 40.32 11.00 1.41 0 2902 Water: 6.36 73.05 29.34 N/A 435 370 Other: 16.25 31.07 23.66 N/A 0 2 Chain A: 5.35 59.77 13.04 N/A 0 1626 Chain B: 5.16 73.05 12.76 N/A 0 1648 Chain S: 11.83 61.61 30.70 N/A 435 0 Histogram: Values Number of atoms 5.16 - 11.95 2162 11.95 - 18.74 643 18.74 - 25.53 316 25.53 - 32.32 264 32.32 - 39.11 158 39.11 - 45.89 101 45.89 - 52.68 42 52.68 - 59.47 18 59.47 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1300 r_free=0.1568 r_work=0.1299 r_free=0.1564 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1299 r_free = 0.1564 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 = 0.1285 r_free = 0.1553 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1285 r_free= 0.1553 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015725 | | target function (ls_wunit_k1) not normalized (work): 2945.272460 | | target function (ls_wunit_k1) not normalized (free): 115.432463 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1290 0.1285 0.1553 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1474 0.1471 0.1630 n_refl.: 191141 remove outliers: r(all,work,free)=0.1474 0.1471 0.1630 n_refl.: 191141 overall B=0.17 to atoms: r(all,work,free)=0.1498 0.1496 0.1641 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1282 0.1277 0.1546 n_refl.: 191141 remove outliers: r(all,work,free)=0.1282 0.1277 0.1545 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 0.3618 402.814 370.120 0.480 0.962 0.285 13.296-10.522 100.00 100 1 0.2091 534.497 526.686 0.742 0.964 0.240 10.503-8.327 99.45 178 3 0.1773 565.118 562.159 0.887 0.964 0.217 8.318-6.595 100.00 360 8 0.1732 414.736 411.902 0.911 0.963 0.155 6.588-5.215 100.00 711 7 0.1553 381.101 372.974 0.888 0.964 0.150 5.214-4.128 98.38 1367 28 0.0901 557.435 555.269 0.978 0.964 0.054 4.126-3.266 94.74 2603 46 0.0837 508.132 504.256 1.044 0.965 0.014 3.266-2.585 99.86 5447 97 0.0920 342.774 340.306 1.027 0.964 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.353 1.038 0.964 0.000 2.046-1.619 99.39 21536 464 0.1089 153.054 151.358 1.056 0.964 0.000 1.619-1.281 98.00 42464 925 0.1283 82.395 81.403 1.048 0.964 0.000 1.281-0.980 96.53 101826 2055 0.1879 44.202 42.181 1.026 0.963 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0379 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1277 r_free=0.1545 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1277 r_free=0.1545 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1277 r_free=0.1545 | n_water=805 | time (s): 2.800 (total time: 2.800) Filter (dist) r_work=0.1281 r_free=0.1549 | n_water=794 | time (s): 105.930 (total time: 108.730) Filter (q & B) r_work=0.1282 r_free=0.1549 | n_water=791 | time (s): 4.240 (total time: 112.970) Compute maps r_work=0.1282 r_free=0.1549 | n_water=791 | time (s): 2.090 (total time: 115.060) Filter (map) r_work=0.1307 r_free=0.1534 | n_water=657 | time (s): 4.090 (total time: 119.150) Find peaks r_work=0.1307 r_free=0.1534 | n_water=657 | time (s): 0.590 (total time: 119.740) Add new water r_work=0.1330 r_free=0.1567 | n_water=958 | time (s): 4.230 (total time: 123.970) Refine new water occ: r_work=0.1286 r_free=0.1517 adp: r_work=0.1273 r_free=0.1513 occ: r_work=0.1276 r_free=0.1509 adp: r_work=0.1269 r_free=0.1509 occ: r_work=0.1270 r_free=0.1504 adp: r_work=0.1267 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1267 r_free=0.1506 r_work=0.1267 r_free=0.1506 | n_water=958 | time (s): 92.010 (total time: 215.980) Filter (q & B) r_work=0.1271 r_free=0.1507 | n_water=895 | time (s): 4.560 (total time: 220.540) Filter (dist only) r_work=0.1271 r_free=0.1506 | n_water=894 | time (s): 111.820 (total time: 332.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.581332 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 588.600073 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 0.1527 0.0272 0.041 1.1 20.1 0.0 0.3 0 11.791 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.55 15.27 2.72 2.043 15.237 588.600 0.014 12.31 15.08 2.78 2.413 15.274 588.600 0.014 Individual atomic B min max mean iso aniso Overall: 5.45 68.21 16.40 1.20 526 3272 Protein: 5.45 40.33 10.98 1.20 0 2902 Water: 6.59 68.21 33.96 N/A 526 368 Other: 16.43 32.85 24.64 N/A 0 2 Chain A: 5.52 55.75 12.99 N/A 0 1624 Chain B: 5.45 68.21 12.80 N/A 0 1648 Chain S: 10.17 65.83 38.17 N/A 526 0 Histogram: Values Number of atoms 5.45 - 11.73 2068 11.73 - 18.01 703 18.01 - 24.28 270 24.28 - 30.56 204 30.56 - 36.83 184 36.83 - 43.11 153 43.11 - 49.38 101 49.38 - 55.66 61 55.66 - 61.94 45 61.94 - 68.21 9 =========================== Idealize ADP of riding H ========================== r_work=0.1231 r_free=0.1508 r_work=0.1231 r_free=0.1510 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1510 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 = 0.1225 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.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1225 r_free= 0.1502 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013393 | | target function (ls_wunit_k1) not normalized (work): 2508.415848 | | target function (ls_wunit_k1) not normalized (free): 101.813799 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1230 0.1225 0.1502 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1434 0.1431 0.1599 n_refl.: 191139 remove outliers: r(all,work,free)=0.1434 0.1431 0.1599 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1431 0.1428 0.1597 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1231 0.1509 n_refl.: 191139 remove outliers: r(all,work,free)=0.1237 0.1231 0.1509 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 0.3279 402.814 377.646 0.487 0.963 0.269 13.296-10.522 100.00 100 1 0.1892 534.497 528.615 0.768 0.964 0.230 10.503-8.327 99.45 178 3 0.1434 565.118 567.108 0.919 0.963 0.191 8.318-6.595 100.00 360 8 0.1522 414.736 414.355 0.938 0.963 0.153 6.588-5.215 100.00 711 7 0.1338 381.101 376.188 0.912 0.963 0.133 5.214-4.128 98.38 1367 28 0.0828 557.435 556.274 0.996 0.963 0.090 4.126-3.266 94.74 2603 46 0.0760 508.132 505.419 1.059 0.963 0.015 3.266-2.585 99.86 5447 97 0.0853 342.774 341.429 1.047 0.962 0.010 2.585-2.046 97.45 10613 204 0.0899 258.603 256.747 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1042 153.054 151.620 1.081 0.959 0.000 1.619-1.281 98.00 42464 925 0.1254 82.395 81.360 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1872 44.202 42.222 1.060 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0510 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1231 r_free=0.1508 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1231 r_free=0.1508 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1231 r_free=0.1508 | n_water=894 | time (s): 2.930 (total time: 2.930) Filter (dist) r_work=0.1232 r_free=0.1510 | n_water=889 | time (s): 115.230 (total time: 118.160) Filter (q & B) r_work=0.1233 r_free=0.1510 | n_water=885 | time (s): 4.770 (total time: 122.930) Compute maps r_work=0.1233 r_free=0.1510 | n_water=885 | time (s): 2.300 (total time: 125.230) Filter (map) r_work=0.1270 r_free=0.1517 | n_water=703 | time (s): 5.560 (total time: 130.790) Find peaks r_work=0.1270 r_free=0.1517 | n_water=703 | time (s): 0.600 (total time: 131.390) Add new water r_work=0.1293 r_free=0.1551 | n_water=1016 | time (s): 4.530 (total time: 135.920) Refine new water occ: r_work=0.1250 r_free=0.1512 adp: r_work=0.1251 r_free=0.1513 occ: r_work=0.1246 r_free=0.1510 adp: r_work=0.1246 r_free=0.1510 occ: r_work=0.1243 r_free=0.1509 adp: r_work=0.1242 r_free=0.1509 ADP+occupancy (water only), MIN, final r_work=0.1242 r_free=0.1509 r_work=0.1242 r_free=0.1509 | n_water=1016 | time (s): 350.240 (total time: 486.160) Filter (q & B) r_work=0.1245 r_free=0.1511 | n_water=885 | time (s): 5.430 (total time: 491.590) Filter (dist only) r_work=0.1246 r_free=0.1510 | n_water=883 | time (s): 108.320 (total time: 599.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.731485 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.296286 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 0.1235 0.1427 0.0192 0.035 1.1 8.3 0.0 0.0 0 0.866 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 14.27 1.92 1.930 14.608 16.296 3.937 12.28 13.90 1.62 2.193 14.523 16.296 3.896 Individual atomic B min max mean iso aniso Overall: 5.54 67.84 15.32 1.07 516 3271 Protein: 5.54 36.91 10.76 1.07 0 2902 Water: 6.65 67.84 30.29 N/A 516 367 Other: 14.23 28.74 21.49 N/A 0 2 Chain A: 5.55 54.98 12.79 N/A 0 1624 Chain B: 5.54 67.84 12.54 N/A 0 1647 Chain S: 12.76 61.85 32.19 N/A 516 0 Histogram: Values Number of atoms 5.54 - 11.77 2127 11.77 - 18.00 689 18.00 - 24.23 298 24.23 - 30.46 236 30.46 - 36.69 183 36.69 - 42.92 138 42.92 - 49.15 79 49.15 - 55.38 30 55.38 - 61.61 5 61.61 - 67.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1391 r_work=0.1229 r_free=0.1391 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1391 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1223 r_free = 0.1382 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1223 r_free= 0.1382 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890112 | | target function (ml) not normalized (work): 728610.115027 | | target function (ml) not normalized (free): 15218.583398 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1226 0.1223 0.1381 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1438 0.1437 0.1477 n_refl.: 191139 remove outliers: r(all,work,free)=0.1438 0.1437 0.1477 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1432 0.1431 0.1473 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1223 0.1220 0.1376 n_refl.: 191139 remove outliers: r(all,work,free)=0.1222 0.1219 0.1376 n_refl.: 191134 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3841 398.895 353.279 0.414 0.947 0.238 13.296-10.522 99.01 99 1 0.2395 528.187 513.251 0.718 0.948 0.214 10.503-8.327 98.35 176 3 0.1974 555.265 556.396 0.884 0.948 0.170 8.318-6.595 100.00 360 8 0.2023 414.736 409.924 0.897 0.948 0.125 6.588-5.215 100.00 711 7 0.1822 381.101 370.886 0.885 0.948 0.107 5.214-4.128 98.38 1367 28 0.1157 557.435 552.326 0.971 0.948 0.090 4.126-3.266 94.74 2603 46 0.1071 508.132 501.464 1.032 0.948 0.015 3.266-2.585 99.86 5447 97 0.1079 342.774 339.227 1.019 0.947 0.010 2.585-2.046 97.45 10613 204 0.0959 258.603 255.765 1.032 0.947 0.000 2.046-1.619 99.39 21536 464 0.0971 153.054 151.412 1.055 0.945 0.000 1.619-1.281 98.00 42464 925 0.1048 82.395 81.492 1.052 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1689 44.202 42.315 1.038 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.0961 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1219 r_free=0.1376 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1219 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1219 r_free=0.1376 | n_water=883 | time (s): 2.270 (total time: 2.270) Filter (dist) r_work=0.1219 r_free=0.1376 | n_water=882 | time (s): 119.970 (total time: 122.240) Filter (q & B) r_work=0.1220 r_free=0.1372 | n_water=865 | time (s): 4.490 (total time: 126.730) Compute maps r_work=0.1220 r_free=0.1372 | n_water=865 | time (s): 1.820 (total time: 128.550) Filter (map) r_work=0.1238 r_free=0.1368 | n_water=738 | time (s): 4.590 (total time: 133.140) Find peaks r_work=0.1238 r_free=0.1368 | n_water=738 | time (s): 0.770 (total time: 133.910) Add new water r_work=0.1254 r_free=0.1386 | n_water=996 | time (s): 4.270 (total time: 138.180) Refine new water occ: r_work=0.1207 r_free=0.1344 adp: r_work=0.1199 r_free=0.1341 occ: r_work=0.1196 r_free=0.1341 adp: r_work=0.1196 r_free=0.1341 occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1194 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1341 r_work=0.1194 r_free=0.1341 | n_water=996 | time (s): 289.500 (total time: 427.680) Filter (q & B) r_work=0.1200 r_free=0.1347 | n_water=887 | time (s): 5.690 (total time: 433.370) Filter (dist only) r_work=0.1200 r_free=0.1347 | n_water=885 | time (s): 109.610 (total time: 542.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.602557 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.640370 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 0.1349 0.0151 0.035 1.1 6.3 0.0 0.3 0 0.801 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.98 13.49 1.51 1.840 14.316 15.640 3.872 11.92 13.44 1.52 1.960 14.271 15.640 3.864 Individual atomic B min max mean iso aniso Overall: 5.52 67.38 15.13 1.01 518 3271 Protein: 5.52 33.65 10.67 1.01 0 2902 Water: 5.90 67.38 29.74 N/A 518 367 Other: 14.00 27.74 20.87 N/A 0 2 Chain A: 5.53 53.91 12.64 N/A 0 1624 Chain B: 5.52 67.38 12.44 N/A 0 1647 Chain S: 5.90 61.78 31.51 N/A 518 0 Histogram: Values Number of atoms 5.52 - 11.70 2120 11.70 - 17.89 723 17.89 - 24.08 289 24.08 - 30.26 243 30.26 - 36.45 181 36.45 - 42.64 129 42.64 - 48.82 72 48.82 - 55.01 25 55.01 - 61.20 5 61.20 - 67.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1344 r_work=0.1192 r_free=0.1345 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1345 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1343 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191134 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1343 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.862080 | | target function (ml) not normalized (work): 723340.556089 | | target function (ml) not normalized (free): 15126.291294 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1344 n_refl.: 191134 re-set all scales: r(all,work,free)=0.1396 0.1396 0.1445 n_refl.: 191134 remove outliers: r(all,work,free)=0.1396 0.1396 0.1445 n_refl.: 191134 overall B=-0.03 to atoms: r(all,work,free)=0.1389 0.1388 0.1441 n_refl.: 191134 bulk-solvent and scaling: r(all,work,free)=0.1192 0.1189 0.1338 n_refl.: 191134 remove outliers: r(all,work,free)=0.1191 0.1188 0.1338 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 90.10 88 3 0.3645 355.989 313.844 0.351 0.951 0.140 13.296-10.522 97.03 97 1 0.2390 481.024 451.341 0.681 0.952 0.155 10.503-8.327 98.35 176 3 0.2085 502.616 496.111 0.869 0.952 0.147 8.318-6.595 100.00 360 8 0.2100 375.412 370.100 0.891 0.952 0.118 6.588-5.215 100.00 711 7 0.1851 344.966 335.407 0.884 0.952 0.100 5.214-4.128 98.38 1367 28 0.1152 504.581 500.174 0.970 0.953 0.080 4.126-3.266 94.74 2603 46 0.1077 459.953 453.906 1.029 0.953 0.009 3.266-2.585 99.86 5447 97 0.1080 310.273 307.138 1.016 0.952 0.000 2.585-2.046 97.45 10613 204 0.0929 234.083 231.734 1.029 0.952 0.000 2.046-1.619 99.39 21536 464 0.0912 138.542 137.286 1.052 0.951 0.000 1.619-1.281 98.00 42464 925 0.0987 74.583 73.896 1.048 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1664 40.010 38.361 1.034 0.947 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1187 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1338 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1338 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1338 | n_water=885 | time (s): 3.280 (total time: 3.280) Filter (dist) r_work=0.1188 r_free=0.1340 | n_water=884 | time (s): 120.300 (total time: 123.580) Filter (q & B) r_work=0.1189 r_free=0.1339 | n_water=873 | time (s): 3.980 (total time: 127.560) Compute maps r_work=0.1189 r_free=0.1339 | n_water=873 | time (s): 2.530 (total time: 130.090) Filter (map) r_work=0.1209 r_free=0.1346 | n_water=760 | time (s): 4.890 (total time: 134.980) Find peaks r_work=0.1209 r_free=0.1346 | n_water=760 | time (s): 0.550 (total time: 135.530) Add new water r_work=0.1221 r_free=0.1355 | n_water=1002 | time (s): 4.300 (total time: 139.830) Refine new water occ: r_work=0.1185 r_free=0.1337 adp: r_work=0.1185 r_free=0.1337 occ: r_work=0.1182 r_free=0.1338 adp: r_work=0.1182 r_free=0.1337 occ: r_work=0.1180 r_free=0.1339 adp: r_work=0.1179 r_free=0.1339 ADP+occupancy (water only), MIN, final r_work=0.1179 r_free=0.1339 r_work=0.1179 r_free=0.1339 | n_water=1002 | time (s): 236.730 (total time: 376.560) Filter (q & B) r_work=0.1185 r_free=0.1347 | n_water=910 | time (s): 4.730 (total time: 381.290) Filter (dist only) r_work=0.1185 r_free=0.1347 | n_water=909 | time (s): 115.990 (total time: 497.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.522120 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.577693 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1353 0.0164 0.036 1.1 8.7 0.0 0.3 0 0.761 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.53 1.64 1.796 14.249 15.578 3.763 11.94 13.56 1.63 1.892 14.214 15.578 3.759 Individual atomic B min max mean iso aniso Overall: 5.55 66.90 15.13 0.96 543 3270 Protein: 5.55 31.78 10.59 0.96 0 2902 Water: 6.00 66.90 29.61 N/A 543 366 Other: 13.90 26.07 19.99 N/A 0 2 Chain A: 5.58 52.72 12.51 N/A 0 1623 Chain B: 5.55 66.90 12.33 N/A 0 1647 Chain S: 6.00 61.74 31.44 N/A 543 0 Histogram: Values Number of atoms 5.55 - 11.69 2129 11.69 - 17.82 726 17.82 - 23.96 298 23.96 - 30.09 229 30.09 - 36.23 185 36.23 - 42.36 138 42.36 - 48.50 75 48.50 - 54.63 26 54.63 - 60.77 4 60.77 - 66.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1357 r_work=0.1194 r_free=0.1357 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1357 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1361 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1361 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758724 | | target function (ml) not normalized (work): 703963.830532 | | target function (ml) not normalized (free): 14743.461355 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1191 0.1361 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1376 0.1374 0.1483 n_refl.: 191129 remove outliers: r(all,work,free)=0.1376 0.1374 0.1483 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1369 0.1367 0.1478 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1193 0.1190 0.1359 n_refl.: 191129 remove outliers: r(all,work,free)=0.1193 0.1190 0.1359 n_refl.: 191129 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3619 355.989 327.771 0.346 0.957 0.110 13.296-10.522 97.03 97 1 0.2420 481.024 460.677 0.678 0.959 0.137 10.503-8.327 98.35 176 3 0.2121 502.616 496.132 0.863 0.959 0.140 8.318-6.595 100.00 360 8 0.2072 375.412 371.276 0.881 0.958 0.111 6.588-5.215 100.00 711 7 0.1858 344.966 335.822 0.878 0.958 0.090 5.214-4.128 98.38 1367 28 0.1167 504.581 499.648 0.964 0.959 0.070 4.126-3.266 94.74 2603 46 0.1101 459.953 453.360 1.023 0.959 0.005 3.266-2.585 99.86 5447 97 0.1100 310.273 306.981 1.010 0.958 0.000 2.585-2.046 97.45 10613 204 0.0943 234.083 231.604 1.023 0.957 0.000 2.046-1.619 99.39 21536 464 0.0914 138.542 137.230 1.047 0.955 0.000 1.619-1.281 98.00 42464 925 0.0976 74.583 73.872 1.045 0.953 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.010 38.335 1.034 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1236 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1359 | n_water=909 | time (s): 3.250 (total time: 3.250) Filter (dist) r_work=0.1191 r_free=0.1358 | n_water=908 | time (s): 122.460 (total time: 125.710) Filter (q & B) r_work=0.1191 r_free=0.1359 | n_water=897 | time (s): 5.240 (total time: 130.950) Compute maps r_work=0.1191 r_free=0.1359 | n_water=897 | time (s): 1.670 (total time: 132.620) Filter (map) r_work=0.1212 r_free=0.1350 | n_water=785 | time (s): 4.390 (total time: 137.010) Find peaks r_work=0.1212 r_free=0.1350 | n_water=785 | time (s): 0.800 (total time: 137.810) Add new water r_work=0.1222 r_free=0.1360 | n_water=1001 | time (s): 5.190 (total time: 143.000) Refine new water occ: r_work=0.1189 r_free=0.1338 adp: r_work=0.1189 r_free=0.1338 occ: r_work=0.1187 r_free=0.1338 adp: r_work=0.1187 r_free=0.1338 occ: r_work=0.1185 r_free=0.1337 adp: r_work=0.1185 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1185 r_free=0.1338 r_work=0.1185 r_free=0.1338 | n_water=1001 | time (s): 170.550 (total time: 313.550) Filter (q & B) r_work=0.1190 r_free=0.1348 | n_water=915 | time (s): 5.120 (total time: 318.670) Filter (dist only) r_work=0.1190 r_free=0.1348 | n_water=914 | time (s): 114.810 (total time: 433.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.501101 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.335605 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1349 0.0155 0.036 1.1 5.6 0.0 0.3 0 0.751 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 13.49 1.55 1.760 14.124 15.336 3.759 11.94 13.50 1.56 1.872 14.086 15.336 3.756 Individual atomic B min max mean iso aniso Overall: 5.56 65.83 15.00 0.91 548 3270 Protein: 5.56 29.56 10.49 0.91 0 2902 Water: 6.00 65.83 29.31 N/A 548 366 Other: 13.86 23.43 18.64 N/A 0 2 Chain A: 5.64 51.31 12.38 N/A 0 1623 Chain B: 5.56 65.83 12.21 N/A 0 1647 Chain S: 6.00 61.76 31.16 N/A 548 0 Histogram: Values Number of atoms 5.56 - 11.59 2109 11.59 - 17.61 773 17.61 - 23.64 275 23.64 - 29.67 219 29.67 - 35.69 196 35.69 - 41.72 134 41.72 - 47.75 75 47.75 - 53.78 27 53.78 - 59.80 7 59.80 - 65.83 3 =========================== Idealize ADP of riding H ========================== r_work=0.1194 r_free=0.1350 r_work=0.1194 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1194 r_free = 0.1351 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1351 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.754979 | | target function (ml) not normalized (work): 703262.581993 | | target function (ml) not normalized (free): 14724.461697 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1352 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1377 0.1375 0.1475 n_refl.: 191129 remove outliers: r(all,work,free)=0.1377 0.1375 0.1475 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1370 0.1368 0.1470 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1350 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 90.10 88 3 0.3671 355.989 326.748 0.340 0.957 0.100 13.296-10.522 97.03 97 1 0.2441 481.024 461.092 0.669 0.958 0.113 10.503-8.327 98.35 176 3 0.2153 502.616 494.945 0.861 0.959 0.120 8.318-6.595 100.00 360 8 0.2097 375.412 371.275 0.878 0.958 0.099 6.588-5.215 100.00 711 7 0.1881 344.966 336.034 0.876 0.958 0.087 5.214-4.128 98.38 1367 28 0.1184 504.581 499.598 0.965 0.959 0.070 4.126-3.266 94.74 2603 46 0.1118 459.953 453.219 1.025 0.959 0.005 3.266-2.585 99.86 5447 97 0.1105 310.273 306.989 1.011 0.958 0.000 2.585-2.046 97.45 10613 204 0.0949 234.083 231.579 1.023 0.957 0.000 2.046-1.619 99.39 21536 464 0.0910 138.542 137.249 1.047 0.956 0.000 1.619-1.281 98.00 42464 925 0.0966 74.583 73.885 1.045 0.954 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.010 38.335 1.034 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1319 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1350 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1350 | n_water=914 | time (s): 3.130 (total time: 3.130) Filter (dist) r_work=0.1191 r_free=0.1349 | n_water=913 | time (s): 123.020 (total time: 126.150) Filter (q & B) r_work=0.1192 r_free=0.1349 | n_water=907 | time (s): 5.410 (total time: 131.560) Compute maps r_work=0.1192 r_free=0.1349 | n_water=907 | time (s): 2.150 (total time: 133.710) Filter (map) r_work=0.1213 r_free=0.1345 | n_water=794 | time (s): 5.920 (total time: 139.630) Find peaks r_work=0.1213 r_free=0.1345 | n_water=794 | time (s): 0.780 (total time: 140.410) Add new water r_work=0.1221 r_free=0.1352 | n_water=999 | time (s): 4.000 (total time: 144.410) Refine new water occ: r_work=0.1190 r_free=0.1334 adp: r_work=0.1190 r_free=0.1334 occ: r_work=0.1188 r_free=0.1334 adp: r_work=0.1188 r_free=0.1334 occ: r_work=0.1187 r_free=0.1333 adp: r_work=0.1187 r_free=0.1333 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1333 r_work=0.1187 r_free=0.1333 | n_water=999 | time (s): 167.430 (total time: 311.840) Filter (q & B) r_work=0.1190 r_free=0.1342 | n_water=919 | time (s): 5.500 (total time: 317.340) Filter (dist only) r_work=0.1191 r_free=0.1342 | n_water=918 | time (s): 113.960 (total time: 431.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.585335 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.095395 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1349 0.0156 0.038 1.1 7.3 0.0 0.3 0 0.793 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.49 1.56 1.724 13.960 14.095 3.756 11.97 13.53 1.56 1.752 13.947 14.095 3.756 Individual atomic B min max mean iso aniso Overall: 5.55 65.26 14.86 0.89 552 3270 Protein: 5.55 28.97 10.45 0.89 0 2902 Water: 6.01 65.26 28.78 N/A 552 366 Other: 13.82 22.76 18.29 N/A 0 2 Chain A: 5.64 51.11 12.30 N/A 0 1623 Chain B: 5.55 65.26 12.15 N/A 0 1647 Chain S: 6.01 61.76 30.46 N/A 552 0 Histogram: Values Number of atoms 5.55 - 11.52 2102 11.52 - 17.49 784 17.49 - 23.46 282 23.46 - 29.43 233 29.43 - 35.41 191 35.41 - 41.38 121 41.38 - 47.35 70 47.35 - 53.32 29 53.32 - 59.29 7 59.29 - 65.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1354 r_work=0.1197 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1354 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1355 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.755750 | | target function (ml) not normalized (work): 703406.888497 | | target function (ml) not normalized (free): 14732.069773 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1355 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1383 0.1381 0.1485 n_refl.: 191129 remove outliers: r(all,work,free)=0.1383 0.1381 0.1485 n_refl.: 191129 overall B=-0.01 to atoms: r(all,work,free)=0.1382 0.1380 0.1484 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1189 0.1186 0.1343 n_refl.: 191129 remove outliers: r(all,work,free)=0.1189 0.1186 0.1343 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 90.10 88 3 0.3716 355.989 325.833 0.355 0.919 0.090 13.296-10.522 97.03 97 1 0.2479 481.024 459.620 0.708 0.920 0.109 10.503-8.327 98.35 176 3 0.2210 502.616 493.203 0.912 0.921 0.118 8.318-6.595 100.00 360 8 0.2147 375.412 370.243 0.933 0.920 0.100 6.588-5.215 100.00 711 7 0.1932 344.966 335.170 0.930 0.921 0.083 5.214-4.128 98.38 1367 28 0.1212 504.581 498.775 1.025 0.922 0.044 4.126-3.266 94.74 2603 46 0.1132 459.953 452.423 1.091 0.923 0.009 3.266-2.585 99.86 5447 97 0.1117 310.273 306.632 1.075 0.923 0.000 2.585-2.046 97.45 10613 204 0.0953 234.083 231.434 1.085 0.925 0.000 2.046-1.619 99.39 21536 464 0.0908 138.542 137.152 1.106 0.927 0.000 1.619-1.281 98.00 42464 925 0.0945 74.583 73.931 1.100 0.931 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.010 38.303 1.072 0.938 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0243 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1342 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1186 r_free=0.1342 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1342 | n_water=918 | time (s): 2.330 (total time: 2.330) Filter (dist) r_work=0.1186 r_free=0.1342 | n_water=918 | time (s): 109.510 (total time: 111.840) Filter (q & B) r_work=0.1187 r_free=0.1343 | n_water=904 | time (s): 4.700 (total time: 116.540) Compute maps r_work=0.1187 r_free=0.1343 | n_water=904 | time (s): 2.070 (total time: 118.610) Filter (map) r_work=0.1209 r_free=0.1343 | n_water=792 | time (s): 4.100 (total time: 122.710) Find peaks r_work=0.1209 r_free=0.1343 | n_water=792 | time (s): 0.550 (total time: 123.260) Add new water r_work=0.1216 r_free=0.1347 | n_water=986 | time (s): 4.950 (total time: 128.210) Refine new water occ: r_work=0.1184 r_free=0.1323 adp: r_work=0.1185 r_free=0.1323 occ: r_work=0.1183 r_free=0.1323 adp: r_work=0.1183 r_free=0.1323 occ: r_work=0.1182 r_free=0.1322 adp: r_work=0.1181 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1323 r_work=0.1181 r_free=0.1323 | n_water=986 | time (s): 141.340 (total time: 269.550) Filter (q & B) r_work=0.1184 r_free=0.1336 | n_water=926 | time (s): 5.410 (total time: 274.960) Filter (dist only) r_work=0.1185 r_free=0.1336 | n_water=924 | time (s): 114.620 (total time: 389.580) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.502062 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.559757 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 0.1188 0.1339 0.0151 0.038 1.1 7.7 0.0 0.3 0 0.751 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.88 13.39 1.51 1.705 13.963 14.560 3.754 11.87 13.40 1.53 1.726 13.954 14.560 3.751 Individual atomic B min max mean iso aniso Overall: 5.60 64.35 14.90 0.88 558 3270 Protein: 5.60 28.58 10.45 0.88 0 2902 Water: 6.02 64.35 28.88 N/A 558 366 Other: 13.87 22.35 18.11 N/A 0 2 Chain A: 5.68 50.82 12.26 N/A 0 1623 Chain B: 5.60 64.35 12.12 N/A 0 1647 Chain S: 6.02 61.83 30.76 N/A 558 0 Histogram: Values Number of atoms 5.60 - 11.47 2074 11.47 - 17.35 811 17.35 - 23.22 274 23.22 - 29.10 219 29.10 - 34.97 195 34.97 - 40.85 135 40.85 - 46.72 78 46.72 - 52.60 31 52.60 - 58.47 6 58.47 - 64.35 5 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1340 r_work=0.1187 r_free=0.1340 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1340 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1186 r_free = 0.1341 target_work(ml) = 3.751 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1186 r_free= 0.1341 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.751044 | | target function (ml) not normalized (work): 702525.438330 | | target function (ml) not normalized (free): 14715.765878 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1189 0.1186 0.1341 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1387 0.1385 0.1497 n_refl.: 191129 remove outliers: r(all,work,free)=0.1387 0.1385 0.1497 n_refl.: 191129 overall B=-0.02 to atoms: r(all,work,free)=0.1384 0.1382 0.1495 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1188 0.1185 0.1340 n_refl.: 191129 remove outliers: r(all,work,free)=0.1188 0.1185 0.1340 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 90.10 88 3 0.3724 355.989 325.761 0.326 0.985 0.080 13.296-10.522 97.03 97 1 0.2493 481.024 459.951 0.656 0.987 0.100 10.503-8.327 98.35 176 3 0.2208 502.616 493.236 0.848 0.987 0.103 8.318-6.595 100.00 360 8 0.2130 375.412 370.446 0.868 0.987 0.091 6.588-5.215 100.00 711 7 0.1921 344.966 335.411 0.867 0.988 0.080 5.214-4.128 98.38 1367 28 0.1211 504.581 498.837 0.956 0.989 0.046 4.126-3.266 94.74 2603 46 0.1138 459.953 452.354 1.018 0.990 0.009 3.266-2.585 99.86 5447 97 0.1120 310.273 306.642 1.002 0.991 0.000 2.585-2.046 97.45 10613 204 0.0956 234.083 231.455 1.012 0.992 0.000 2.046-1.619 99.39 21536 464 0.0905 138.542 137.187 1.032 0.995 0.000 1.619-1.281 98.00 42464 925 0.0940 74.583 73.937 1.026 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1624 40.010 38.290 1.002 1.008 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0439 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1340 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1340 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1340 | n_water=924 | time (s): 2.640 (total time: 2.640) Filter (dist) r_work=0.1186 r_free=0.1340 | n_water=922 | time (s): 111.760 (total time: 114.400) Filter (q & B) r_work=0.1186 r_free=0.1340 | n_water=912 | time (s): 4.510 (total time: 118.910) Compute maps r_work=0.1186 r_free=0.1340 | n_water=912 | time (s): 2.130 (total time: 121.040) Filter (map) r_work=0.1206 r_free=0.1336 | n_water=802 | time (s): 4.480 (total time: 125.520) Find peaks r_work=0.1206 r_free=0.1336 | n_water=802 | time (s): 0.660 (total time: 126.180) Add new water r_work=0.1213 r_free=0.1341 | n_water=991 | time (s): 4.280 (total time: 130.460) Refine new water occ: r_work=0.1185 r_free=0.1322 adp: r_work=0.1185 r_free=0.1322 occ: r_work=0.1183 r_free=0.1322 adp: r_work=0.1183 r_free=0.1322 occ: r_work=0.1183 r_free=0.1322 adp: r_work=0.1183 r_free=0.1322 ADP+occupancy (water only), MIN, final r_work=0.1183 r_free=0.1322 r_work=0.1183 r_free=0.1322 | n_water=991 | time (s): 219.100 (total time: 349.560) Filter (q & B) r_work=0.1187 r_free=0.1336 | n_water=908 | time (s): 5.720 (total time: 355.280) Filter (dist only) r_work=0.1188 r_free=0.1336 | n_water=906 | time (s): 116.290 (total time: 471.570) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.551157 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.043223 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1189 0.1342 0.0153 0.038 1.1 5.6 0.0 0.3 0 0.776 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.89 13.42 1.53 1.700 13.827 15.043 3.752 11.89 13.42 1.54 1.707 13.833 15.043 3.750 Individual atomic B min max mean iso aniso Overall: 5.62 63.31 14.70 0.88 540 3270 Protein: 5.62 28.48 10.45 0.88 0 2902 Water: 6.04 63.31 28.33 N/A 540 366 Other: 13.89 22.32 18.10 N/A 0 2 Chain A: 5.71 50.46 12.23 N/A 0 1623 Chain B: 5.62 63.31 12.10 N/A 0 1647 Chain S: 6.04 61.93 30.07 N/A 540 0 Histogram: Values Number of atoms 5.62 - 11.39 2054 11.39 - 17.16 826 17.16 - 22.93 287 22.93 - 28.70 224 28.70 - 34.46 170 34.46 - 40.23 121 40.23 - 46.00 82 46.00 - 51.77 34 51.77 - 57.54 6 57.54 - 63.31 6 =========================== Idealize ADP of riding H ========================== r_work=0.1189 r_free=0.1342 r_work=0.1189 r_free=0.1343 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1189 r_free = 0.1343 target_work(ml) = 3.750 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1188 r_free = 0.1342 target_work(ml) = 3.750 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1188 r_free= 0.1342 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.749572 | | target function (ml) not normalized (work): 702249.854786 | | target function (ml) not normalized (free): 14707.416389 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1191 0.1188 0.1342 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1501 n_refl.: 191129 remove outliers: r(all,work,free)=0.1397 0.1395 0.1501 n_refl.: 191129 overall B=-0.02 to atoms: r(all,work,free)=0.1393 0.1391 0.1497 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1187 0.1340 n_refl.: 191129 remove outliers: r(all,work,free)=0.1190 0.1187 0.1340 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 90.10 88 3 0.3744 355.989 325.403 0.342 0.921 0.070 13.296-10.522 97.03 97 1 0.2495 481.024 459.122 0.697 0.922 0.095 10.503-8.327 98.35 176 3 0.2250 502.616 493.154 0.903 0.922 0.105 8.318-6.595 100.00 360 8 0.2195 375.412 369.842 0.925 0.922 0.091 6.588-5.215 100.00 711 7 0.1945 344.966 335.144 0.926 0.923 0.080 5.214-4.128 98.38 1367 28 0.1235 504.581 498.891 1.022 0.924 0.034 4.126-3.266 94.74 2603 46 0.1151 459.953 452.308 1.090 0.925 0.000 3.266-2.585 99.86 5447 97 0.1124 310.273 306.688 1.074 0.926 0.000 2.585-2.046 97.45 10613 204 0.0956 234.083 231.446 1.084 0.928 0.000 2.046-1.619 99.39 21536 464 0.0905 138.542 137.193 1.104 0.931 0.000 1.619-1.281 98.00 42464 925 0.0935 74.583 73.946 1.099 0.936 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.010 38.289 1.073 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0624 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1187 r_free=0.1340 After: r_work=0.1188 r_free=0.1341 ================================== NQH flips ================================== r_work=0.1188 r_free=0.1341 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1341 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1341 | n_water=906 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1188 r_free=0.1341 | n_water=906 | time (s): 111.650 (total time: 114.310) Filter (q & B) r_work=0.1189 r_free=0.1342 | n_water=895 | time (s): 4.250 (total time: 118.560) Compute maps r_work=0.1189 r_free=0.1342 | n_water=895 | time (s): 1.810 (total time: 120.370) Filter (map) r_work=0.1208 r_free=0.1336 | n_water=796 | time (s): 5.010 (total time: 125.380) Find peaks r_work=0.1208 r_free=0.1336 | n_water=796 | time (s): 0.560 (total time: 125.940) Add new water r_work=0.1214 r_free=0.1339 | n_water=995 | time (s): 4.340 (total time: 130.280) Refine new water occ: r_work=0.1184 r_free=0.1322 adp: r_work=0.1184 r_free=0.1322 occ: r_work=0.1183 r_free=0.1322 adp: r_work=0.1183 r_free=0.1322 occ: r_work=0.1182 r_free=0.1323 adp: r_work=0.1181 r_free=0.1323 ADP+occupancy (water only), MIN, final r_work=0.1181 r_free=0.1323 r_work=0.1181 r_free=0.1323 | n_water=995 | time (s): 200.570 (total time: 330.850) Filter (q & B) r_work=0.1185 r_free=0.1338 | n_water=924 | time (s): 5.390 (total time: 336.240) Filter (dist only) r_work=0.1185 r_free=0.1338 | n_water=921 | time (s): 121.820 (total time: 458.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.491211 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.034808 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1190 0.1344 0.0154 0.038 1.2 11.4 0.0 0.3 0 0.746 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.90 13.44 1.54 1.696 13.889 14.035 3.753 11.92 13.47 1.55 1.691 13.890 14.035 3.754 Individual atomic B min max mean iso aniso Overall: 5.62 63.01 14.81 0.86 555 3270 Protein: 5.62 28.32 10.44 0.86 0 2902 Water: 6.10 63.01 28.57 N/A 555 366 Other: 13.90 22.29 18.10 N/A 0 2 Chain A: 5.72 50.39 12.21 N/A 0 1623 Chain B: 5.62 63.01 12.08 N/A 0 1647 Chain S: 6.10 61.93 30.52 N/A 555 0 Histogram: Values Number of atoms 5.62 - 11.36 2048 11.36 - 17.10 832 17.10 - 22.84 279 22.84 - 28.57 214 28.57 - 34.31 192 34.31 - 40.05 128 40.05 - 45.79 84 45.79 - 51.53 35 51.53 - 57.27 7 57.27 - 63.01 6 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1347 r_work=0.1192 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1347 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1350 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1191 r_free= 0.1350 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753748 | | target function (ml) not normalized (work): 703031.869979 | | target function (ml) not normalized (free): 14723.381216 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7397 127 0.1353 0.1444 5.6826 5.7537| | 2: 2.94 - 2.33 1.00 7339 128 0.1071 0.1382 5.076 5.189| | 3: 2.33 - 2.04 0.96 6939 150 0.0907 0.1146 4.6576 4.7416| | 4: 2.04 - 1.85 1.00 7170 155 0.0902 0.1041 4.3954 4.5726| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.0985 4.1494 4.2284| | 6: 1.72 - 1.62 0.99 7102 142 0.0898 0.1094 3.9474 4.0845| | 7: 1.62 - 1.54 0.99 7104 148 0.0887 0.0973 3.7996 3.939| | 8: 1.54 - 1.47 0.96 6798 152 0.0891 0.1310 3.6996 3.8986| | 9: 1.47 - 1.41 0.98 6938 155 0.0922 0.1119 3.6191 3.7519| | 10: 1.41 - 1.36 0.99 7022 150 0.0975 0.1179 3.5554 3.6677| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1123 3.4833 3.5833| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1122 3.4585 3.5802| | 13: 1.28 - 1.25 0.98 6907 166 0.1041 0.1233 3.4366 3.5625| | 14: 1.25 - 1.22 0.98 7015 112 0.1106 0.1586 3.4333 3.6849| | 15: 1.22 - 1.19 0.98 6956 137 0.1167 0.1241 3.4485 3.4912| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1544 3.4646 3.6531| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1233 3.4326 3.4422| | 18: 1.14 - 1.12 0.98 6875 142 0.1384 0.1699 3.4382 3.531| | 19: 1.12 - 1.10 0.97 6948 106 0.1471 0.1751 3.4194 3.5879| | 20: 1.10 - 1.08 0.97 6884 147 0.1585 0.1590 3.4099 3.4372| | 21: 1.08 - 1.07 0.97 6852 152 0.1729 0.2139 3.418 3.5031| | 22: 1.07 - 1.05 0.97 6836 135 0.1905 0.1948 3.4131 3.4136| | 23: 1.05 - 1.03 0.97 6827 159 0.2122 0.2023 3.4333 3.4855| | 24: 1.03 - 1.02 0.96 6784 133 0.2334 0.2258 3.4357 3.5112| | 25: 1.02 - 1.01 0.93 6552 130 0.2612 0.2512 3.4493 3.522| | 26: 1.01 - 0.99 0.96 6767 158 0.2756 0.2855 3.4157 3.4226| | 27: 0.99 - 0.98 0.94 6647 131 0.3044 0.2806 3.4685 3.397| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7397 127 0.93 11.46 1.00 0.97 11023.86| | 2: 2.94 - 2.33 7339 128 0.93 12.71 0.99 0.97 5076.27| | 3: 2.33 - 2.04 6939 150 0.96 7.67 1.01 0.97 1699.76| | 4: 2.04 - 1.85 7170 155 0.96 7.66 1.00 0.97 1007.08| | 5: 1.85 - 1.72 7113 159 0.96 8.03 1.00 0.97 629.45| | 6: 1.72 - 1.62 7102 142 0.96 8.05 1.00 0.97 445.61| | 7: 1.62 - 1.54 7104 148 0.96 8.16 1.01 0.98 338.39| | 8: 1.54 - 1.47 6798 152 0.96 8.25 1.01 0.98 278.84| | 9: 1.47 - 1.41 6938 155 0.96 8.41 1.00 0.99 229.30| | 10: 1.41 - 1.36 7022 150 0.96 8.83 1.00 0.98 200.89| | 11: 1.36 - 1.32 6997 151 0.96 8.88 0.99 0.97 173.99| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.98 0.96 160.24| | 13: 1.28 - 1.25 6907 166 0.96 9.52 1.00 0.97 158.13| | 14: 1.25 - 1.22 7015 112 0.95 10.73 1.01 0.98 163.37| | 15: 1.22 - 1.19 6956 137 0.95 11.27 1.01 0.99 166.91| | 16: 1.19 - 1.17 6604 132 0.95 11.44 1.00 0.97 160.26| | 17: 1.17 - 1.14 6940 135 0.94 12.24 1.01 0.97 153.62| | 18: 1.14 - 1.12 6875 142 0.94 12.74 1.01 0.96 147.32| | 19: 1.12 - 1.10 6948 106 0.93 14.14 1.00 0.96 151.00| | 20: 1.10 - 1.08 6884 147 0.92 15.25 1.00 0.95 150.45| | 21: 1.08 - 1.07 6852 152 0.91 16.66 1.00 0.95 153.56| | 22: 1.07 - 1.05 6836 135 0.89 18.32 1.00 0.94 155.18| | 23: 1.05 - 1.03 6827 159 0.87 20.53 1.00 0.94 164.81| | 24: 1.03 - 1.02 6784 133 0.85 23.19 1.00 0.94 179.10| | 25: 1.02 - 1.01 6552 130 0.83 25.17 0.98 0.91 182.10| | 26: 1.01 - 0.99 6767 158 0.81 26.68 0.99 0.90 176.88| | 27: 0.99 - 0.98 6647 131 0.82 26.40 0.99 0.89 161.78| |alpha: min = 0.89 max = 0.99 mean = 0.96| |beta: min = 147.32 max = 11023.86 mean = 916.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 13.28| |phase err.(test): min = 0.00 max = 89.62 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1194 0.1191 0.1350 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1404 0.1402 0.1513 n_refl.: 191129 remove outliers: r(all,work,free)=0.1404 0.1402 0.1513 n_refl.: 191129 overall B=-0.13 to atoms: r(all,work,free)=0.1382 0.1380 0.1495 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1349 n_refl.: 191129 remove outliers: r(all,work,free)=0.1194 0.1191 0.1349 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 90.10 88 3 0.3736 355.989 325.794 0.311 0.986 0.060 13.296-10.522 97.03 97 1 0.2448 481.024 460.635 0.642 0.988 0.093 10.503-8.327 98.35 176 3 0.2213 502.616 492.848 0.832 0.988 0.097 8.318-6.595 100.00 360 8 0.2151 375.412 370.210 0.853 0.988 0.090 6.588-5.215 100.00 711 7 0.1932 344.966 334.815 0.852 0.989 0.083 5.214-4.128 98.38 1367 28 0.1226 504.581 499.017 0.941 0.990 0.044 4.126-3.266 94.74 2603 46 0.1156 459.953 452.056 1.003 0.991 0.005 3.266-2.585 99.86 5447 97 0.1123 310.273 306.821 0.986 0.992 0.000 2.585-2.046 97.45 10613 204 0.0963 234.083 231.464 0.993 0.994 0.000 2.046-1.619 99.39 21536 464 0.0912 138.542 137.169 1.008 0.998 0.000 1.619-1.281 98.00 42464 925 0.0943 74.583 73.941 0.999 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.010 38.278 0.967 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0280 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2037 0.2020 0.082 5.262 5.2 78.0 14.6 805 0.000 1_bss: 0.1800 0.1952 0.082 5.262 5.2 78.0 14.6 805 0.000 1_settarget: 0.1800 0.1952 0.082 5.262 5.2 78.0 14.6 805 0.000 1_nqh: 0.1800 0.1952 0.082 5.262 5.2 78.0 14.6 805 0.000 1_weight: 0.1800 0.1952 0.082 5.262 5.2 78.0 14.6 805 0.000 1_xyzrec: 0.1271 0.1494 0.038 1.153 5.2 78.0 14.6 805 0.153 1_adp: 0.1300 0.1568 0.038 1.153 5.2 73.0 15.0 805 0.153 1_regHadp: 0.1299 0.1564 0.038 1.153 5.2 73.0 15.0 805 0.153 1_occ: 0.1285 0.1553 0.038 1.153 5.2 73.0 15.0 805 0.153 2_bss: 0.1277 0.1545 0.038 1.153 5.3 73.2 15.2 805 0.153 2_settarget: 0.1277 0.1545 0.038 1.153 5.3 73.2 15.2 805 0.153 2_updatecdl: 0.1277 0.1545 0.038 1.174 5.3 73.2 15.2 805 0.153 2_nqh: 0.1277 0.1545 0.038 1.174 5.3 73.2 15.2 805 0.153 2_sol: 0.1271 0.1506 0.038 1.174 5.3 73.2 16.3 894 n/a 2_weight: 0.1271 0.1506 0.038 1.174 5.3 73.2 16.3 894 n/a 2_xyzrec: 0.1255 0.1527 0.041 1.133 5.3 73.2 16.3 894 n/a 2_adp: 0.1231 0.1508 0.041 1.133 5.5 68.2 16.4 894 n/a 2_regHadp: 0.1231 0.1510 0.041 1.133 5.5 68.2 16.4 894 n/a 2_occ: 0.1225 0.1502 0.041 1.133 5.5 68.2 16.4 894 n/a 3_bss: 0.1231 0.1508 0.041 1.133 5.4 68.2 16.4 894 n/a 3_settarget: 0.1231 0.1508 0.041 1.133 5.4 68.2 16.4 894 n/a 3_updatecdl: 0.1231 0.1508 0.041 1.136 5.4 68.2 16.4 894 n/a 3_nqh: 0.1231 0.1508 0.041 1.136 5.4 68.2 16.4 894 n/a 3_sol: 0.1246 0.1510 0.041 1.136 5.4 68.2 15.5 883 n/a 3_weight: 0.1246 0.1510 0.041 1.136 5.4 68.2 15.5 883 n/a 3_xyzrec: 0.1235 0.1427 0.035 1.102 5.4 68.2 15.5 883 n/a 3_adp: 0.1228 0.1391 0.035 1.102 5.5 67.8 15.3 883 n/a 3_regHadp: 0.1229 0.1391 0.035 1.102 5.5 67.8 15.3 883 n/a 3_occ: 0.1223 0.1382 0.035 1.102 5.5 67.8 15.3 883 n/a 4_bss: 0.1219 0.1376 0.035 1.102 5.5 67.8 15.3 883 n/a 4_settarget: 0.1219 0.1376 0.035 1.102 5.5 67.8 15.3 883 n/a 4_updatecdl: 0.1219 0.1376 0.035 1.103 5.5 67.8 15.3 883 n/a 4_nqh: 0.1219 0.1376 0.035 1.103 5.5 67.8 15.3 883 n/a 4_sol: 0.1200 0.1347 0.035 1.103 5.5 67.8 15.2 885 n/a 4_weight: 0.1200 0.1347 0.035 1.103 5.5 67.8 15.2 885 n/a 4_xyzrec: 0.1198 0.1349 0.035 1.120 5.5 67.8 15.2 885 n/a 4_adp: 0.1192 0.1344 0.035 1.120 5.5 67.4 15.1 885 n/a 4_regHadp: 0.1192 0.1345 0.035 1.120 5.5 67.4 15.1 885 n/a 4_occ: 0.1190 0.1343 0.035 1.120 5.5 67.4 15.1 885 n/a 5_bss: 0.1188 0.1338 0.035 1.120 5.5 67.4 15.1 885 n/a 5_settarget: 0.1188 0.1338 0.035 1.120 5.5 67.4 15.1 885 n/a 5_updatecdl: 0.1188 0.1338 0.035 1.120 5.5 67.4 15.1 885 n/a 5_nqh: 0.1188 0.1338 0.035 1.120 5.5 67.4 15.1 885 n/a 5_sol: 0.1185 0.1347 0.035 1.120 5.5 67.4 15.2 909 n/a 5_weight: 0.1185 0.1347 0.035 1.120 5.5 67.4 15.2 909 n/a 5_xyzrec: 0.1189 0.1353 0.036 1.121 5.5 67.4 15.2 909 n/a 5_adp: 0.1194 0.1357 0.036 1.121 5.6 66.9 15.1 909 n/a 5_regHadp: 0.1194 0.1357 0.036 1.121 5.6 66.9 15.1 909 n/a 5_occ: 0.1191 0.1361 0.036 1.121 5.6 66.9 15.1 909 n/a 6_bss: 0.1190 0.1359 0.036 1.121 5.5 66.9 15.1 909 n/a 6_settarget: 0.1190 0.1359 0.036 1.121 5.5 66.9 15.1 909 n/a 6_updatecdl: 0.1190 0.1359 0.036 1.122 5.5 66.9 15.1 909 n/a 6_nqh: 0.1190 0.1359 0.036 1.122 5.5 66.9 15.1 909 n/a 6_sol: 0.1190 0.1348 0.036 1.122 5.5 66.9 15.1 914 n/a 6_weight: 0.1190 0.1348 0.036 1.122 5.5 66.9 15.1 914 n/a 6_xyzrec: 0.1193 0.1349 0.036 1.125 5.5 66.9 15.1 914 n/a 6_adp: 0.1194 0.1350 0.036 1.125 5.6 65.8 15.0 914 n/a 6_regHadp: 0.1194 0.1351 0.036 1.125 5.6 65.8 15.0 914 n/a 6_occ: 0.1192 0.1351 0.036 1.125 5.6 65.8 15.0 914 n/a 7_bss: 0.1191 0.1350 0.036 1.125 5.5 65.8 15.0 914 n/a 7_settarget: 0.1191 0.1350 0.036 1.125 5.5 65.8 15.0 914 n/a 7_updatecdl: 0.1191 0.1350 0.036 1.125 5.5 65.8 15.0 914 n/a 7_nqh: 0.1191 0.1350 0.036 1.125 5.5 65.8 15.0 914 n/a 7_sol: 0.1191 0.1342 0.036 1.125 5.5 65.8 14.9 918 n/a 7_weight: 0.1191 0.1342 0.036 1.125 5.5 65.8 14.9 918 n/a 7_xyzrec: 0.1194 0.1349 0.038 1.124 5.5 65.8 14.9 918 n/a 7_adp: 0.1197 0.1354 0.038 1.124 5.5 65.3 14.9 918 n/a 7_regHadp: 0.1197 0.1354 0.038 1.124 5.5 65.3 14.9 918 n/a 7_occ: 0.1196 0.1355 0.038 1.124 5.5 65.3 14.9 918 n/a 8_bss: 0.1186 0.1342 0.038 1.124 5.5 65.3 14.9 918 n/a 8_settarget: 0.1186 0.1342 0.038 1.124 5.5 65.3 14.9 918 n/a 8_updatecdl: 0.1186 0.1342 0.038 1.124 5.5 65.3 14.9 918 n/a 8_nqh: 0.1186 0.1342 0.038 1.124 5.5 65.3 14.9 918 n/a 8_sol: 0.1185 0.1336 0.038 1.124 5.5 65.3 14.9 924 n/a 8_weight: 0.1185 0.1336 0.038 1.124 5.5 65.3 14.9 924 n/a 8_xyzrec: 0.1188 0.1339 0.038 1.112 5.5 65.3 14.9 924 n/a 8_adp: 0.1187 0.1340 0.038 1.112 5.6 64.4 14.9 924 n/a 8_regHadp: 0.1187 0.1340 0.038 1.112 5.6 64.4 14.9 924 n/a 8_occ: 0.1186 0.1341 0.038 1.112 5.6 64.4 14.9 924 n/a 9_bss: 0.1185 0.1340 0.038 1.112 5.6 64.3 14.9 924 n/a 9_settarget: 0.1185 0.1340 0.038 1.112 5.6 64.3 14.9 924 n/a 9_updatecdl: 0.1185 0.1340 0.038 1.113 5.6 64.3 14.9 924 n/a 9_nqh: 0.1185 0.1340 0.038 1.113 5.6 64.3 14.9 924 n/a 9_sol: 0.1188 0.1336 0.038 1.113 5.6 64.3 14.7 906 n/a 9_weight: 0.1188 0.1336 0.038 1.113 5.6 64.3 14.7 906 n/a 9_xyzrec: 0.1189 0.1342 0.038 1.120 5.6 64.3 14.7 906 n/a 9_adp: 0.1189 0.1342 0.038 1.120 5.6 63.3 14.7 906 n/a 9_regHadp: 0.1189 0.1343 0.038 1.120 5.6 63.3 14.7 906 n/a 9_occ: 0.1188 0.1342 0.038 1.120 5.6 63.3 14.7 906 n/a 10_bss: 0.1187 0.1340 0.038 1.120 5.6 63.3 14.7 906 n/a 10_settarget: 0.1187 0.1340 0.038 1.120 5.6 63.3 14.7 906 n/a 10_updatecdl: 0.1187 0.1340 0.038 1.120 5.6 63.3 14.7 906 n/a 10_setrh: 0.1188 0.1341 0.038 1.120 5.6 63.3 14.7 906 n/a 10_nqh: 0.1188 0.1341 0.038 1.120 5.6 63.3 14.7 906 n/a 10_sol: 0.1185 0.1338 0.038 1.120 5.6 63.3 14.8 921 n/a 10_weight: 0.1185 0.1338 0.038 1.120 5.6 63.3 14.8 921 n/a 10_xyzrec: 0.1190 0.1344 0.038 1.159 5.6 63.3 14.8 921 n/a 10_adp: 0.1192 0.1347 0.038 1.159 5.6 63.0 14.8 921 n/a 10_regHadp: 0.1192 0.1347 0.038 1.159 5.6 63.0 14.8 921 n/a 10_occ: 0.1191 0.1350 0.038 1.159 5.6 63.0 14.8 921 n/a end: 0.1191 0.1349 0.038 1.159 5.5 62.9 14.7 921 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9465109_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_9465109_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.5900 Refinement macro-cycles (run) : 11916.6400 Write final files (write_after_run_outputs) : 166.6300 Total : 12088.8600 Total CPU time: 3.37 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:38:43 PST -0800 (1736735923.49 s) Start R-work = 0.1800, R-free = 0.1952 Final R-work = 0.1191, R-free = 0.1349 =============================================================================== Job complete usr+sys time: 12410.38 seconds wall clock time: 207 minutes 52.62 seconds (12472.62 seconds total)