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_3157372.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" 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_3157372.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3157372.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): 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6693 Apply specific restraints filenames to specific monomers "(chain A or chain B) and resseq 14" - /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif "(chain A or chain B) and resseq 23" - /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 174} Link IDs: {None: 174} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 2943 Classifications: {'peptide': 195} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain: "B" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1, 'water': 196} Link IDs: {None: 196} Chain: "S" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 435 Classifications: {'water': 435} Link IDs: {None: 434} Restraints for '(chain A or chain B) and resseq 14' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" Restraints for '(chain A or chain B) and resseq 23' were not modified by "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" Residues with excluded nonbonded symmetry interactions: 631 residue: pdb=" O HOH A 302 " occ=0.56 residue: pdb=" O HOH A 304 " occ=0.85 residue: pdb=" O HOH A 305 " occ=0.83 residue: pdb=" O HOH A 306 " occ=0.82 residue: pdb=" O HOH A 308 " occ=0.73 residue: pdb=" O HOH A 310 " occ=0.94 residue: pdb=" O HOH A 311 " occ=0.78 residue: pdb=" O HOH A 313 " occ=0.84 residue: pdb=" O HOH A 314 " occ=0.66 residue: pdb=" O HOH A 315 " occ=0.91 residue: pdb=" O HOH A 316 " occ=0.90 residue: pdb=" O HOH A 317 " occ=0.95 ... (remaining 619 not shown) Time building chain proxies: 2.23, per 1000 atoms: 0.33 Number of scatterers: 6693 At special positions: 0 Unit cell: (43.875, 78.313, 99.434, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 Mg 2 11.99 O 1357 8.00 N 488 7.00 C 1850 6.00 H 2984 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Custom bonds: bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3278 OE2 GLU B 14 .*. O " symmetry operation: x,y,z distance_model: 2.440 distance_ideal: 2.440 ideal - model: 0.000 slack: 0.000 delta_slack: 0.000 sigma: 10.0000 bond: atom 1: "ATOM 290 OD2 ASP A 23 .*. O " atom 2: "ATOM 3305 OG1 THR B 16 .*. O " symmetry operation: x,y,z distance_model: 2.652 distance_ideal: 2.720 ideal - model: 0.068 slack: 0.000 delta_slack: 0.068 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: 2.661 distance_ideal: 2.710 ideal - model: 0.049 slack: 0.000 delta_slack: 0.049 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: 1.25 Conformation dependent library (CDL) restraints added in 149.0 milliseconds Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.03: 857 1.03 - 1.26: 2499 1.26 - 1.49: 1496 1.49 - 1.72: 1067 1.72 - 1.95: 15 Bond restraints: 5934 Sorted by residual: bond pdb=" N VAL A 150 " pdb=" CA VAL A 150 " ideal model delta sigma weight residual 1.456 1.247 0.209 1.09e-02 8.42e+03 3.67e+02 bond pdb=" C ILE B 191 " pdb=" O ILE B 191 " ideal model delta sigma weight residual 1.237 1.029 0.208 1.11e-02 8.12e+03 3.52e+02 bond pdb=" NE2 GLN B 138 " pdb="HE21 GLN B 138 " ideal model delta sigma weight residual 0.860 1.234 -0.374 2.00e-02 2.50e+03 3.49e+02 bond pdb=" C LYS B 142 " pdb=" O LYS B 142 " ideal model delta sigma weight residual 1.234 1.004 0.231 1.26e-02 6.30e+03 3.35e+02 bond pdb=" N ILE B 118 " pdb=" H ILE B 118 " ideal model delta sigma weight residual 0.860 1.220 -0.360 2.00e-02 2.50e+03 3.24e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 6103 4.59 - 9.19: 3515 9.19 - 13.78: 1029 13.78 - 18.37: 151 18.37 - 22.96: 12 Bond angle restraints: 10810 Sorted by residual: angle pdb=" O ALA A 136 " pdb=" C ALA A 136 " pdb=" N GLU A 137 " ideal model delta sigma weight residual 122.22 140.79 -18.57 1.17e+00 7.31e-01 2.52e+02 angle pdb=" O ALA B 10 " pdb=" C ALA B 10 " pdb=" N PRO B 11 " ideal model delta sigma weight residual 121.71 112.01 9.70 6.40e-01 2.44e+00 2.30e+02 angle pdb=" OE1 GLN B 156 " pdb=" CD GLN B 156 " pdb=" NE2 GLN B 156 " ideal model delta sigma weight residual 122.60 137.23 -14.63 1.00e+00 1.00e+00 2.14e+02 angle pdb=" CA ALA B 10 " pdb=" C ALA B 10 " pdb=" O ALA B 10 " ideal model delta sigma weight residual 120.50 133.02 -12.52 9.20e-01 1.18e+00 1.85e+02 angle pdb=" CA PHE A 127 " pdb=" CB PHE A 127 " pdb=" CG PHE A 127 " ideal model delta sigma weight residual 113.80 101.07 12.73 1.00e+00 1.00e+00 1.62e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1858 17.60 - 35.19: 132 35.19 - 52.78: 40 52.78 - 70.37: 17 70.37 - 87.96: 3 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CB TRP A 139 " pdb=" CG TRP A 139 " pdb=" CD1 TRP A 139 " pdb=" HD1 TRP A 139 " ideal model delta harmonic sigma weight residual 0.00 26.69 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" N GLY B 75 " pdb=" CA GLY B 75 " ideal model delta harmonic sigma weight residual -180.00 -156.78 -23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA VAL A 112 " pdb=" C VAL A 112 " pdb=" N LEU A 113 " pdb=" CA LEU A 113 " ideal model delta harmonic sigma weight residual -180.00 -158.60 -21.40 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.254: 233 0.254 - 0.508: 165 0.508 - 0.762: 73 0.762 - 1.015: 20 1.015 - 1.269: 1 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 -1.32 -1.27 2.00e-01 2.50e+01 4.02e+01 chirality pdb=" CA LYS B 77 " pdb=" N LYS B 77 " pdb=" C LYS B 77 " pdb=" CB LYS B 77 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.50e+01 chirality pdb=" CA THR B 46 " pdb=" N THR B 46 " pdb=" C THR B 46 " pdb=" CB THR B 46 " both_signs ideal model delta sigma weight residual False 2.53 1.57 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 139 " 0.017 2.00e-02 2.50e+03 6.77e-02 1.83e+02 pdb=" CG TRP A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TRP A 139 " -0.124 2.00e-02 2.50e+03 pdb=" CD2 TRP A 139 " -0.052 2.00e-02 2.50e+03 pdb=" NE1 TRP A 139 " 0.110 2.00e-02 2.50e+03 pdb=" CE2 TRP A 139 " -0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP A 139 " 0.049 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 139 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 139 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TRP A 139 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 TRP A 139 " -0.100 2.00e-02 2.50e+03 pdb=" HE3 TRP A 139 " -0.027 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 139 " -0.009 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 139 " -0.105 2.00e-02 2.50e+03 pdb=" HH2 TRP A 139 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.111 2.00e-02 2.50e+03 7.00e-02 1.47e+02 pdb=" CG TYR A 194 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " -0.061 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " 0.056 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.079 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.102 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " -0.025 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.127 2.00e-02 2.50e+03 6.80e-02 1.39e+02 pdb=" CG PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.115 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.068 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.093 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.020 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.90 - 1.64: 28 1.64 - 2.38: 2625 2.38 - 3.12: 22431 3.12 - 3.86: 32882 3.86 - 4.60: 52273 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110239 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.897 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 1.020 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.058 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.070 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.192 2.620 ... (remaining 110234 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_3157372_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= 0.2031 r_free= 0.1999 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298870 | | target function (ml) not normalized (work): 805234.318823 | | target function (ml) not normalized (free): 16565.686759 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2141 0.1933 6.687 6.3019| | 2: 2.94 - 2.33 1.00 7339 128 0.1610 0.1605 5.5346 5.5806| | 3: 2.33 - 2.04 0.96 6939 150 0.1647 0.1668 5.1474 5.1516| | 4: 2.04 - 1.85 1.00 7170 155 0.1757 0.1642 4.9651 5.0445| | 5: 1.85 - 1.72 0.99 7113 159 0.1909 0.1740 4.7908 4.8054| | 6: 1.72 - 1.62 0.99 7102 142 0.1959 0.1961 4.6638 4.7285| | 7: 1.62 - 1.54 0.99 7104 148 0.1990 0.1778 4.5538 4.5604| | 8: 1.54 - 1.47 0.96 6798 152 0.2038 0.2185 4.4592 4.5147| | 9: 1.47 - 1.41 0.98 6938 155 0.2085 0.2312 4.3882 4.5354| | 10: 1.41 - 1.36 0.99 7022 150 0.2144 0.1941 4.3126 4.2803| | 11: 1.36 - 1.32 0.99 6997 151 0.2128 0.2132 4.2426 4.2757| | 12: 1.32 - 1.28 0.98 6976 149 0.2084 0.2136 4.1773 4.2922| | 13: 1.28 - 1.25 0.98 6907 166 0.2016 0.2355 4.1287 4.2527| | 14: 1.25 - 1.22 0.98 7015 113 0.2063 0.2366 4.0858 4.285| | 15: 1.22 - 1.19 0.98 6957 137 0.2076 0.1964 4.0484 4.0126| | 16: 1.19 - 1.17 0.93 6604 132 0.2121 0.2436 4.0083 4.1588| | 17: 1.17 - 1.14 0.98 6941 135 0.2204 0.2012 3.9735 4.0216| | 18: 1.14 - 1.12 0.98 6875 142 0.2232 0.2447 3.922 3.9186| | 19: 1.12 - 1.10 0.97 6949 106 0.2243 0.2429 3.8593 3.9961| | 20: 1.10 - 1.08 0.97 6884 147 0.2316 0.2136 3.814 3.7577| | 21: 1.08 - 1.07 0.97 6852 152 0.2445 0.2677 3.7924 3.822| | 22: 1.07 - 1.05 0.97 6838 135 0.2533 0.2431 3.7447 3.7041| | 23: 1.05 - 1.03 0.97 6829 159 0.2703 0.2585 3.7243 3.7563| | 24: 1.03 - 1.02 0.96 6785 133 0.2895 0.2749 3.7025 3.7481| | 25: 1.02 - 1.01 0.93 6552 130 0.2998 0.2828 3.6603 3.7219| | 26: 1.01 - 0.99 0.96 6767 158 0.3186 0.3335 3.6265 3.638| | 27: 0.99 - 0.98 0.94 6648 131 0.3400 0.3230 3.6425 3.587| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.43 0.91 0.97 35449.18| | 2: 2.94 - 2.33 7339 128 0.86 21.13 1.08 1.03 15012.61| | 3: 2.33 - 2.04 6939 150 0.93 12.31 1.11 1.06 4055.87| | 4: 2.04 - 1.85 7170 155 0.93 13.24 1.11 1.07 2729.06| | 5: 1.85 - 1.72 7113 159 0.91 15.41 1.12 1.08 2056.35| | 6: 1.72 - 1.62 7102 142 0.90 16.58 1.11 1.08 1647.05| | 7: 1.62 - 1.54 7104 148 0.89 17.82 1.11 1.07 1348.55| | 8: 1.54 - 1.47 6798 152 0.88 18.70 1.11 1.05 1158.23| | 9: 1.47 - 1.41 6938 155 0.88 19.32 1.10 1.05 993.11| | 10: 1.41 - 1.36 7022 150 0.87 20.30 1.10 1.04 859.05| | 11: 1.36 - 1.32 6997 151 0.87 20.25 1.08 1.04 755.26| | 12: 1.32 - 1.28 6976 149 0.87 20.75 1.09 1.03 696.98| | 13: 1.28 - 1.25 6907 166 0.86 21.34 1.07 1.03 680.96| | 14: 1.25 - 1.22 7015 113 0.85 22.72 1.08 1.01 663.11| | 15: 1.22 - 1.19 6957 137 0.85 22.72 1.08 1.00 614.61| | 16: 1.19 - 1.17 6604 132 0.86 21.98 1.07 1.00 540.25| | 17: 1.17 - 1.14 6941 135 0.86 21.83 1.08 1.02 474.91| | 18: 1.14 - 1.12 6875 142 0.86 21.42 1.08 1.01 416.13| | 19: 1.12 - 1.10 6949 106 0.85 22.10 1.08 1.01 382.32| | 20: 1.10 - 1.08 6884 147 0.85 22.21 1.07 0.99 332.40| | 21: 1.08 - 1.07 6852 152 0.84 23.26 1.06 0.98 318.29| | 22: 1.07 - 1.05 6838 135 0.83 24.31 1.06 0.98 303.44| | 23: 1.05 - 1.03 6829 159 0.81 26.65 1.05 0.98 312.65| | 24: 1.03 - 1.02 6785 133 0.79 28.73 1.04 0.98 317.55| | 25: 1.02 - 1.01 6552 130 0.77 30.32 1.03 0.94 308.57| | 26: 1.01 - 0.99 6767 158 0.75 31.79 1.02 0.91 288.57| | 27: 0.99 - 0.98 6648 131 0.76 31.40 1.03 0.89 256.55| |alpha: min = 0.89 max = 1.08 mean = 1.01| |beta: min = 256.55 max = 35449.18 mean = 2829.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 21.74| |phase err.(test): min = 0.00 max = 89.68 mean = 21.87| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.245 2950 Z= 5.327 Angle : 5.183 18.570 4018 Z= 3.688 Chirality : 0.381 1.269 492 Planarity : 0.033 0.174 512 Dihedral : 12.673 87.963 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.92 % Favored : 94.82 % Rotamer: Outliers : 0.65 % Allowed : 3.87 % Favored : 95.48 % 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: -2.48 (0.39), residues: 386 helix: -2.59 (0.33), residues: 146 sheet: -1.28 (0.49), residues: 96 loop : -0.45 (0.53), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.128 0.028 ARG A 149 TYR 0.107 0.041 TYR A 67 PHE 0.121 0.039 PHE A 164 TRP 0.118 0.046 TRP A 139 HIS 0.055 0.021 HIS A 96 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2031 r_free= 0.1999 coordinate error (max.-lik. estimate): 0.05 A | | | | normalized target function (ml) (work): 4.298870 | | target function (ml) not normalized (work): 805234.318823 | | target function (ml) not normalized (free): 16565.686759 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2030 0.2031 0.1999 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2030 0.2031 0.1999 n_refl.: 191155 remove outliers: r(all,work,free)=0.2030 0.2032 0.1999 n_refl.: 191145 overall B=0.00 to atoms: r(all,work,free)=0.2030 0.2032 0.1999 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1799 0.1796 0.1927 n_refl.: 191145 remove outliers: r(all,work,free)=0.1797 0.1794 0.1925 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.4068 402.814 291.956 0.435 0.910 0.298 13.296-10.522 98.02 98 1 0.2447 527.329 513.222 0.788 0.911 0.249 10.503-8.327 99.45 178 3 0.2513 565.118 556.532 0.972 0.911 0.227 8.318-6.595 100.00 360 8 0.2462 414.736 404.192 0.972 0.911 0.180 6.588-5.215 100.00 711 7 0.2242 381.101 366.339 0.962 0.911 0.170 5.214-4.128 98.38 1367 28 0.1490 557.435 549.852 1.075 0.911 0.090 4.126-3.266 94.74 2603 46 0.1365 508.132 499.213 1.146 0.912 0.020 3.266-2.585 99.86 5447 97 0.1437 342.774 337.172 1.119 0.911 0.010 2.585-2.046 97.45 10613 204 0.1396 258.603 254.195 1.128 0.910 0.000 2.046-1.619 99.39 21536 464 0.1610 153.054 149.938 1.146 0.909 0.000 1.619-1.281 98.00 42464 925 0.1912 82.395 80.149 1.133 0.906 0.000 1.281-0.980 96.53 101826 2055 0.2310 44.202 41.690 1.115 0.902 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0036 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1794 r_free=0.1925 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS B 123 ASN Total number of N/Q/H flips: 2 r_work=0.1798 r_free=0.1928 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.187616 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 575.811382 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 0.1275 0.1485 0.0210 0.035 1.2 12.4 0.0 0.3 0 11.594 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.75 14.85 2.10 1.117 13.113 575.811 0.019 13.03 15.51 2.49 1.246 13.327 575.811 0.018 Individual atomic B min max mean iso aniso Overall: 5.15 73.05 14.99 1.41 435 3274 Protein: 5.15 40.32 11.02 1.41 0 2902 Water: 6.33 73.05 29.28 N/A 435 370 Other: 16.02 31.29 23.66 N/A 0 2 Chain A: 5.40 60.05 13.06 N/A 0 1626 Chain B: 5.15 73.05 12.78 N/A 0 1648 Chain S: 12.00 65.15 30.57 N/A 435 0 Histogram: Values Number of atoms 5.15 - 11.94 2150 11.94 - 18.73 652 18.73 - 25.52 322 25.52 - 32.31 263 32.31 - 39.10 154 39.10 - 45.89 102 45.89 - 52.68 46 52.68 - 59.47 15 59.47 - 66.26 4 66.26 - 73.05 1 =========================== Idealize ADP of riding H ========================== r_work=0.1303 r_free=0.1551 r_work=0.1302 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1302 r_free = 0.1546 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1287 r_free = 0.1536 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1287 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015804 | | target function (ls_wunit_k1) not normalized (work): 2960.039803 | | target function (ls_wunit_k1) not normalized (free): 111.848235 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1287 0.1536 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1475 0.1472 0.1616 n_refl.: 191137 remove outliers: r(all,work,free)=0.1475 0.1472 0.1616 n_refl.: 191137 overall B=0.16 to atoms: r(all,work,free)=0.1498 0.1496 0.1627 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1284 0.1279 0.1531 n_refl.: 191137 remove outliers: r(all,work,free)=0.1284 0.1279 0.1531 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3633 402.814 379.111 0.467 0.997 0.281 13.296-10.522 98.02 98 1 0.2064 527.329 521.694 0.723 0.999 0.260 10.503-8.327 99.45 178 3 0.1752 565.118 560.411 0.855 0.999 0.208 8.318-6.595 100.00 360 8 0.1762 414.736 411.423 0.876 0.999 0.155 6.588-5.215 100.00 711 7 0.1579 381.101 373.196 0.857 0.999 0.150 5.214-4.128 98.38 1367 28 0.0931 557.435 553.898 0.942 0.999 0.090 4.126-3.266 94.74 2603 46 0.0861 508.132 504.161 1.007 1.000 0.019 3.266-2.585 99.86 5447 97 0.0933 342.774 340.268 0.989 1.000 0.010 2.585-2.046 97.45 10613 204 0.0945 258.603 256.427 1.001 1.000 0.000 2.046-1.619 99.39 21536 464 0.1080 153.054 151.389 1.018 1.000 0.000 1.619-1.281 98.00 42464 925 0.1279 82.395 81.391 1.011 1.000 0.000 1.281-0.980 96.53 101826 2055 0.1881 44.202 42.142 0.989 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0366 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1279 r_free=0.1531 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.1279 r_free=0.1531 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1279 r_free=0.1531 | n_water=805 | time (s): 2.510 (total time: 2.510) Filter (dist) r_work=0.1281 r_free=0.1537 | n_water=800 | time (s): 106.630 (total time: 109.140) Filter (q & B) r_work=0.1282 r_free=0.1539 | n_water=795 | time (s): 4.880 (total time: 114.020) Compute maps r_work=0.1282 r_free=0.1539 | n_water=795 | time (s): 1.940 (total time: 115.960) Filter (map) r_work=0.1303 r_free=0.1530 | n_water=669 | time (s): 4.720 (total time: 120.680) Find peaks r_work=0.1303 r_free=0.1530 | n_water=669 | time (s): 0.830 (total time: 121.510) Add new water r_work=0.1328 r_free=0.1562 | n_water=988 | time (s): 3.990 (total time: 125.500) Refine new water occ: r_work=0.1283 r_free=0.1508 adp: r_work=0.1271 r_free=0.1506 occ: r_work=0.1273 r_free=0.1502 adp: r_work=0.1266 r_free=0.1504 occ: r_work=0.1267 r_free=0.1500 adp: r_work=0.1265 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1265 r_free=0.1503 r_work=0.1265 r_free=0.1503 | n_water=988 | time (s): 88.280 (total time: 213.780) Filter (q & B) r_work=0.1268 r_free=0.1508 | n_water=911 | time (s): 4.410 (total time: 218.190) Filter (dist only) r_work=0.1268 r_free=0.1508 | n_water=909 | time (s): 117.160 (total time: 335.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.661902 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 580.146394 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1252 0.1526 0.0274 0.039 1.2 20.6 0.0 0.3 0 11.831 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.52 15.26 2.74 2.048 15.306 580.146 0.014 12.28 15.04 2.76 2.417 15.337 580.146 0.014 Individual atomic B min max mean iso aniso Overall: 5.42 68.26 16.49 1.20 539 3274 Protein: 5.42 40.06 11.00 1.20 0 2902 Water: 6.62 68.26 34.00 N/A 539 370 Other: 16.19 31.49 23.84 N/A 0 2 Chain A: 5.58 56.29 13.05 N/A 0 1626 Chain B: 5.42 68.26 12.81 N/A 0 1648 Chain S: 11.90 66.20 38.10 N/A 539 0 Histogram: Values Number of atoms 5.42 - 11.71 2060 11.71 - 17.99 712 17.99 - 24.28 273 24.28 - 30.56 215 30.56 - 36.84 174 36.84 - 43.13 165 43.13 - 49.41 96 49.41 - 55.69 54 55.69 - 61.98 49 61.98 - 68.26 15 =========================== Idealize ADP of riding H ========================== r_work=0.1228 r_free=0.1504 r_work=0.1229 r_free=0.1505 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1229 r_free = 0.1505 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1223 r_free = 0.1499 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1223 r_free= 0.1499 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013307 | | target function (ls_wunit_k1) not normalized (work): 2492.266608 | | target function (ls_wunit_k1) not normalized (free): 102.852739 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1229 0.1223 0.1499 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1428 0.1424 0.1613 n_refl.: 191137 remove outliers: r(all,work,free)=0.1428 0.1424 0.1613 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1425 0.1421 0.1611 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1230 0.1507 n_refl.: 191137 remove outliers: r(all,work,free)=0.1235 0.1230 0.1507 n_refl.: 191137 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3225 402.814 381.115 0.490 0.963 0.271 13.296-10.522 98.02 98 1 0.1854 527.329 520.053 0.763 0.964 0.223 10.503-8.327 99.45 178 3 0.1417 565.118 567.470 0.920 0.964 0.179 8.318-6.595 100.00 360 8 0.1566 414.736 413.452 0.934 0.964 0.154 6.588-5.215 100.00 711 7 0.1349 381.101 376.896 0.913 0.964 0.149 5.214-4.128 98.38 1367 28 0.0825 557.435 555.592 0.994 0.964 0.100 4.126-3.266 94.74 2603 46 0.0760 508.132 505.477 1.058 0.964 0.014 3.266-2.585 99.86 5447 97 0.0855 342.774 341.272 1.045 0.963 0.000 2.585-2.046 97.45 10613 204 0.0892 258.603 256.740 1.058 0.962 0.000 2.046-1.619 99.39 21536 464 0.1038 153.054 151.639 1.079 0.960 0.000 1.619-1.281 98.00 42464 925 0.1253 82.395 81.359 1.073 0.957 0.000 1.281-0.980 96.53 101826 2055 0.1873 44.202 42.214 1.059 0.951 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0560 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1230 r_free=0.1507 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.1230 r_free=0.1507 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1507 | n_water=909 | time (s): 3.760 (total time: 3.760) Filter (dist) r_work=0.1231 r_free=0.1508 | n_water=905 | time (s): 108.910 (total time: 112.670) Filter (q & B) r_work=0.1231 r_free=0.1508 | n_water=902 | time (s): 4.520 (total time: 117.190) Compute maps r_work=0.1231 r_free=0.1508 | n_water=902 | time (s): 2.260 (total time: 119.450) Filter (map) r_work=0.1267 r_free=0.1503 | n_water=717 | time (s): 5.240 (total time: 124.690) Find peaks r_work=0.1267 r_free=0.1503 | n_water=717 | time (s): 0.560 (total time: 125.250) Add new water r_work=0.1291 r_free=0.1545 | n_water=1033 | time (s): 4.120 (total time: 129.370) Refine new water occ: r_work=0.1250 r_free=0.1503 adp: r_work=0.1250 r_free=0.1504 occ: r_work=0.1245 r_free=0.1500 adp: r_work=0.1245 r_free=0.1502 occ: r_work=0.1242 r_free=0.1499 adp: r_work=0.1241 r_free=0.1500 ADP+occupancy (water only), MIN, final r_work=0.1241 r_free=0.1500 r_work=0.1241 r_free=0.1500 | n_water=1033 | time (s): 308.020 (total time: 437.390) Filter (q & B) r_work=0.1247 r_free=0.1499 | n_water=899 | time (s): 5.030 (total time: 442.420) Filter (dist only) r_work=0.1248 r_free=0.1501 | n_water=897 | time (s): 116.830 (total time: 559.250) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.688247 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.318369 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 0.1239 0.1431 0.0192 0.034 1.1 7.0 0.0 0.0 0 0.844 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.31 1.92 1.934 14.677 16.318 3.938 12.36 13.92 1.56 2.292 14.565 16.318 3.896 Individual atomic B min max mean iso aniso Overall: 5.57 67.69 15.38 1.05 528 3273 Protein: 5.57 35.73 10.71 1.05 0 2902 Water: 6.72 67.69 30.49 N/A 528 369 Other: 13.80 27.48 20.64 N/A 0 2 Chain A: 5.58 55.04 12.74 N/A 0 1625 Chain B: 5.57 67.69 12.51 N/A 0 1648 Chain S: 14.14 62.72 32.48 N/A 528 0 Histogram: Values Number of atoms 5.57 - 11.78 2139 11.78 - 17.99 683 17.99 - 24.20 292 24.20 - 30.42 242 30.42 - 36.63 183 36.63 - 42.84 152 42.84 - 49.05 70 49.05 - 55.27 24 55.27 - 61.48 14 61.48 - 67.69 2 =========================== Idealize ADP of riding H ========================== r_work=0.1236 r_free=0.1393 r_work=0.1237 r_free=0.1394 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1394 target_work(ml) = 3.896 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1384 target_work(ml) = 3.890 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1231 r_free= 0.1384 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.890090 | | target function (ml) not normalized (work): 728598.360837 | | target function (ml) not normalized (free): 15216.152840 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1231 0.1384 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1439 0.1439 0.1480 n_refl.: 191137 remove outliers: r(all,work,free)=0.1439 0.1439 0.1480 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1433 0.1432 0.1476 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1227 0.1375 n_refl.: 191137 remove outliers: r(all,work,free)=0.1229 0.1226 0.1375 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3930 398.895 354.438 0.404 0.947 0.228 13.296-10.522 97.03 97 1 0.2322 529.824 506.043 0.709 0.948 0.198 10.503-8.327 98.35 176 3 0.2054 555.265 555.870 0.888 0.948 0.161 8.318-6.595 100.00 360 8 0.2115 414.736 409.251 0.896 0.948 0.130 6.588-5.215 100.00 711 7 0.1846 381.101 370.500 0.884 0.948 0.117 5.214-4.128 98.38 1367 28 0.1179 557.435 551.826 0.973 0.948 0.100 4.126-3.266 94.74 2603 46 0.1095 508.132 501.283 1.031 0.948 0.009 3.266-2.585 99.86 5447 97 0.1092 342.774 339.062 1.019 0.948 0.000 2.585-2.046 97.45 10613 204 0.0971 258.603 255.744 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0969 153.054 151.436 1.056 0.946 0.000 1.619-1.281 98.00 42464 925 0.1051 82.395 81.492 1.053 0.944 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.314 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1082 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1226 r_free=0.1375 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS Total number of N/Q/H flips: 1 r_work=0.1230 r_free=0.1380 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1380 | n_water=897 | time (s): 2.790 (total time: 2.790) Filter (dist) r_work=0.1231 r_free=0.1383 | n_water=895 | time (s): 110.570 (total time: 113.360) Filter (q & B) r_work=0.1231 r_free=0.1380 | n_water=885 | time (s): 4.350 (total time: 117.710) Compute maps r_work=0.1231 r_free=0.1380 | n_water=885 | time (s): 2.250 (total time: 119.960) Filter (map) r_work=0.1251 r_free=0.1390 | n_water=744 | time (s): 4.720 (total time: 124.680) Find peaks r_work=0.1251 r_free=0.1390 | n_water=744 | time (s): 0.750 (total time: 125.430) Add new water r_work=0.1267 r_free=0.1416 | n_water=977 | time (s): 4.360 (total time: 129.790) Refine new water occ: r_work=0.1222 r_free=0.1364 adp: r_work=0.1214 r_free=0.1360 occ: r_work=0.1212 r_free=0.1359 adp: r_work=0.1212 r_free=0.1359 occ: r_work=0.1212 r_free=0.1359 adp: r_work=0.1212 r_free=0.1359 ADP+occupancy (water only), MIN, final r_work=0.1212 r_free=0.1359 r_work=0.1212 r_free=0.1359 | n_water=977 | time (s): 164.130 (total time: 293.920) Filter (q & B) r_work=0.1217 r_free=0.1367 | n_water=847 | time (s): 4.730 (total time: 298.650) Filter (dist only) r_work=0.1218 r_free=0.1368 | n_water=845 | time (s): 112.310 (total time: 410.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.640562 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.155243 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 0.1211 0.1366 0.0155 0.036 1.1 6.1 0.0 0.3 0 0.820 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 13.66 1.55 1.820 14.102 15.155 3.874 12.04 13.65 1.61 1.914 14.068 15.155 3.866 Individual atomic B min max mean iso aniso Overall: 5.50 67.18 14.84 0.98 476 3273 Protein: 5.50 32.79 10.64 0.98 0 2902 Water: 5.99 67.18 29.23 N/A 476 369 Other: 13.93 26.48 20.21 N/A 0 2 Chain A: 5.57 53.87 12.62 N/A 0 1625 Chain B: 5.50 67.18 12.42 N/A 0 1648 Chain S: 5.99 59.78 30.76 N/A 476 0 Histogram: Values Number of atoms 5.50 - 11.66 2101 11.66 - 17.83 741 17.83 - 24.00 334 24.00 - 30.17 193 30.17 - 36.34 148 36.34 - 42.51 133 42.51 - 48.67 64 48.67 - 54.84 24 54.84 - 61.01 10 61.01 - 67.18 1 =========================== Idealize ADP of riding H ========================== r_work=0.1204 r_free=0.1365 r_work=0.1204 r_free=0.1366 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1204 r_free = 0.1366 target_work(ml) = 3.866 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1202 r_free = 0.1360 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1202 r_free= 0.1360 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.864081 | | target function (ml) not normalized (work): 723707.541928 | | target function (ml) not normalized (free): 15141.879636 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1205 0.1202 0.1360 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1414 0.1413 0.1491 n_refl.: 191132 remove outliers: r(all,work,free)=0.1414 0.1413 0.1491 n_refl.: 191132 overall B=-0.03 to atoms: r(all,work,free)=0.1407 0.1406 0.1485 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1357 n_refl.: 191132 remove outliers: r(all,work,free)=0.1203 0.1200 0.1357 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3788 361.440 327.970 0.418 0.949 0.243 13.296-10.522 97.03 97 1 0.2397 480.076 461.564 0.708 0.951 0.188 10.503-8.327 98.35 176 3 0.2184 503.127 495.411 0.864 0.951 0.158 8.318-6.595 100.00 360 8 0.2236 375.794 368.402 0.887 0.951 0.132 6.588-5.215 100.00 711 7 0.1933 345.317 335.343 0.878 0.951 0.113 5.214-4.128 98.38 1367 28 0.1230 505.094 499.524 0.969 0.951 0.080 4.126-3.266 94.74 2603 46 0.1134 460.420 453.496 1.030 0.951 0.009 3.266-2.585 99.86 5447 97 0.1095 310.588 307.258 1.017 0.950 0.000 2.585-2.046 97.45 10613 204 0.0938 234.321 231.850 1.030 0.950 0.000 2.046-1.619 99.39 21536 464 0.0913 138.683 137.372 1.054 0.948 0.000 1.619-1.281 98.00 42464 925 0.0986 74.659 73.931 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1659 40.051 38.379 1.041 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1195 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1357 | n_water=845 | time (s): 3.240 (total time: 3.240) Filter (dist) r_work=0.1201 r_free=0.1356 | n_water=844 | time (s): 102.710 (total time: 105.950) Filter (q & B) r_work=0.1201 r_free=0.1356 | n_water=840 | time (s): 4.190 (total time: 110.140) Compute maps r_work=0.1201 r_free=0.1356 | n_water=840 | time (s): 1.760 (total time: 111.900) Filter (map) r_work=0.1217 r_free=0.1355 | n_water=739 | time (s): 4.790 (total time: 116.690) Find peaks r_work=0.1217 r_free=0.1355 | n_water=739 | time (s): 0.800 (total time: 117.490) Add new water r_work=0.1232 r_free=0.1375 | n_water=970 | time (s): 3.940 (total time: 121.430) Refine new water occ: r_work=0.1195 r_free=0.1342 adp: r_work=0.1195 r_free=0.1342 occ: r_work=0.1192 r_free=0.1343 adp: r_work=0.1192 r_free=0.1343 occ: r_work=0.1190 r_free=0.1344 adp: r_work=0.1190 r_free=0.1344 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1344 r_work=0.1190 r_free=0.1344 | n_water=970 | time (s): 293.280 (total time: 414.710) Filter (q & B) r_work=0.1194 r_free=0.1349 | n_water=890 | time (s): 4.140 (total time: 418.850) Filter (dist only) r_work=0.1194 r_free=0.1348 | n_water=889 | time (s): 115.170 (total time: 534.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.593488 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.290351 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1355 0.0158 0.036 1.1 6.6 0.0 0.3 0 0.797 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.55 1.58 1.781 14.124 15.290 3.765 12.00 13.58 1.58 1.848 14.097 15.290 3.761 Individual atomic B min max mean iso aniso Overall: 5.58 66.77 14.96 0.95 521 3272 Protein: 5.58 31.28 10.57 0.95 0 2902 Water: 6.04 66.77 29.26 N/A 521 368 Other: 13.81 25.28 19.55 N/A 0 2 Chain A: 5.59 52.94 12.50 N/A 0 1624 Chain B: 5.58 66.77 12.34 N/A 0 1648 Chain S: 6.04 59.81 30.91 N/A 521 0 Histogram: Values Number of atoms 5.58 - 11.70 2133 11.70 - 17.82 730 17.82 - 23.94 297 23.94 - 30.06 231 30.06 - 36.18 167 36.18 - 42.30 131 42.30 - 48.41 70 48.41 - 54.53 23 54.53 - 60.65 10 60.65 - 66.77 1 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1358 r_work=0.1200 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1357 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759630 | | target function (ml) not normalized (work): 704144.883556 | | target function (ml) not normalized (free): 14737.803874 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1404 0.1403 0.1487 n_refl.: 191132 remove outliers: r(all,work,free)=0.1404 0.1403 0.1487 n_refl.: 191132 overall B=-0.04 to atoms: r(all,work,free)=0.1396 0.1395 0.1481 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1352 n_refl.: 191132 remove outliers: r(all,work,free)=0.1200 0.1197 0.1352 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3863 361.440 323.166 0.394 0.950 0.214 13.296-10.522 96.04 96 1 0.2358 480.750 456.173 0.701 0.952 0.180 10.503-8.327 98.35 176 3 0.2166 503.127 494.745 0.864 0.952 0.157 8.318-6.595 100.00 360 8 0.2156 375.794 369.774 0.887 0.952 0.120 6.588-5.215 100.00 711 7 0.1894 345.317 335.348 0.882 0.952 0.103 5.214-4.128 98.38 1367 28 0.1220 505.094 499.287 0.968 0.952 0.049 4.126-3.266 94.74 2603 46 0.1138 460.420 453.213 1.031 0.952 0.009 3.266-2.585 99.86 5447 97 0.1104 310.588 307.293 1.017 0.952 0.000 2.585-2.046 97.45 10613 204 0.0945 234.321 231.867 1.030 0.951 0.000 2.046-1.619 99.39 21536 464 0.0912 138.683 137.391 1.054 0.950 0.000 1.619-1.281 98.00 42464 925 0.0974 74.659 73.949 1.052 0.949 0.000 1.281-0.980 96.53 101826 2055 0.1652 40.051 38.378 1.040 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1379 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1352 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1352 | n_water=889 | time (s): 2.950 (total time: 2.950) Filter (dist) r_work=0.1197 r_free=0.1352 | n_water=889 | time (s): 105.900 (total time: 108.850) Filter (q & B) r_work=0.1197 r_free=0.1352 | n_water=879 | time (s): 5.620 (total time: 114.470) Compute maps r_work=0.1197 r_free=0.1352 | n_water=879 | time (s): 2.440 (total time: 116.910) Filter (map) r_work=0.1218 r_free=0.1356 | n_water=762 | time (s): 5.130 (total time: 122.040) Find peaks r_work=0.1218 r_free=0.1356 | n_water=762 | time (s): 0.730 (total time: 122.770) Add new water r_work=0.1229 r_free=0.1366 | n_water=982 | time (s): 4.240 (total time: 127.010) Refine new water occ: r_work=0.1195 r_free=0.1334 adp: r_work=0.1196 r_free=0.1334 occ: r_work=0.1193 r_free=0.1334 adp: r_work=0.1193 r_free=0.1334 occ: r_work=0.1192 r_free=0.1334 adp: r_work=0.1191 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1334 r_work=0.1191 r_free=0.1334 | n_water=982 | time (s): 210.130 (total time: 337.140) Filter (q & B) r_work=0.1196 r_free=0.1344 | n_water=903 | time (s): 5.100 (total time: 342.240) Filter (dist only) r_work=0.1197 r_free=0.1343 | n_water=901 | time (s): 112.100 (total time: 454.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.514097 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.242855 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 0.1200 0.1355 0.0156 0.036 1.1 7.8 0.0 0.3 0 0.757 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 13.55 1.56 1.754 14.043 14.243 3.761 12.03 13.59 1.56 1.855 14.006 14.243 3.760 Individual atomic B min max mean iso aniso Overall: 5.59 65.83 14.88 0.90 534 3271 Protein: 5.59 29.13 10.49 0.90 0 2902 Water: 5.97 65.83 29.03 N/A 534 367 Other: 13.84 23.40 18.62 N/A 0 2 Chain A: 5.64 51.80 12.38 N/A 0 1624 Chain B: 5.59 65.83 12.21 N/A 0 1647 Chain S: 5.97 59.86 30.72 N/A 534 0 Histogram: Values Number of atoms 5.59 - 11.61 2117 11.61 - 17.64 767 17.64 - 23.66 284 23.66 - 29.69 222 29.69 - 35.71 179 35.71 - 41.73 135 41.73 - 47.76 63 47.76 - 53.78 27 53.78 - 59.81 9 59.81 - 65.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1360 r_work=0.1203 r_free=0.1360 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1360 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1358 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759033 | | target function (ml) not normalized (work): 704029.201856 | | target function (ml) not normalized (free): 14741.429488 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1358 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1405 0.1403 0.1486 n_refl.: 191131 remove outliers: r(all,work,free)=0.1405 0.1403 0.1486 n_refl.: 191131 overall B=-0.24 to atoms: r(all,work,free)=0.1367 0.1365 0.1462 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1204 0.1201 0.1357 n_refl.: 191131 remove outliers: r(all,work,free)=0.1204 0.1201 0.1357 n_refl.: 191131 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3991 361.440 320.776 0.392 0.951 0.203 13.296-10.522 96.04 96 1 0.2307 480.750 461.946 0.714 0.952 0.149 10.503-8.327 98.35 176 3 0.2247 503.127 493.745 0.884 0.953 0.127 8.318-6.595 100.00 360 8 0.2136 375.794 369.941 0.908 0.953 0.105 6.588-5.215 100.00 711 7 0.1902 345.317 335.901 0.904 0.953 0.090 5.214-4.128 98.38 1367 28 0.1231 505.094 499.379 0.993 0.953 0.045 4.126-3.266 94.74 2603 46 0.1155 460.420 452.974 1.056 0.953 0.009 3.266-2.585 99.86 5447 97 0.1122 310.588 307.233 1.039 0.953 0.000 2.585-2.046 97.45 10613 204 0.0951 234.321 231.799 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0913 138.683 137.397 1.065 0.952 0.000 1.619-1.281 98.00 42464 925 0.0970 74.659 73.950 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1651 40.051 38.374 1.024 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0517 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1357 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1201 r_free=0.1357 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1201 r_free=0.1357 | n_water=901 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1201 r_free=0.1357 | n_water=901 | time (s): 117.390 (total time: 120.400) Filter (q & B) r_work=0.1202 r_free=0.1357 | n_water=890 | time (s): 4.250 (total time: 124.650) Compute maps r_work=0.1202 r_free=0.1357 | n_water=890 | time (s): 2.120 (total time: 126.770) Filter (map) r_work=0.1222 r_free=0.1362 | n_water=768 | time (s): 5.600 (total time: 132.370) Find peaks r_work=0.1222 r_free=0.1362 | n_water=768 | time (s): 0.640 (total time: 133.010) Add new water r_work=0.1231 r_free=0.1373 | n_water=983 | time (s): 4.460 (total time: 137.470) Refine new water occ: r_work=0.1199 r_free=0.1338 adp: r_work=0.1199 r_free=0.1339 occ: r_work=0.1197 r_free=0.1337 adp: r_work=0.1197 r_free=0.1338 occ: r_work=0.1195 r_free=0.1337 adp: r_work=0.1195 r_free=0.1338 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1338 r_work=0.1195 r_free=0.1338 | n_water=983 | time (s): 348.470 (total time: 485.940) Filter (q & B) r_work=0.1200 r_free=0.1348 | n_water=900 | time (s): 5.660 (total time: 491.600) Filter (dist only) r_work=0.1200 r_free=0.1347 | n_water=899 | time (s): 113.480 (total time: 605.080) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.650985 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.181383 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1201 0.1353 0.0151 0.036 1.1 6.3 0.0 0.3 0 0.825 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.53 1.51 1.717 13.728 14.181 3.759 12.02 13.54 1.51 1.776 13.711 14.181 3.757 Individual atomic B min max mean iso aniso Overall: 5.39 64.30 14.61 0.88 532 3271 Protein: 5.39 28.15 10.23 0.88 0 2902 Water: 5.82 64.30 28.74 N/A 532 367 Other: 13.69 21.93 17.81 N/A 0 2 Chain A: 5.45 51.41 12.08 N/A 0 1624 Chain B: 5.39 64.30 11.93 N/A 0 1647 Chain S: 5.82 59.81 30.61 N/A 532 0 Histogram: Values Number of atoms 5.39 - 11.28 2086 11.28 - 17.17 795 17.17 - 23.06 272 23.06 - 28.96 214 28.96 - 34.85 187 34.85 - 40.74 126 40.74 - 46.63 79 46.63 - 52.52 32 52.52 - 58.41 8 58.41 - 64.30 4 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1354 r_work=0.1203 r_free=0.1354 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1354 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1352 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191131 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.756797 | | target function (ml) not normalized (work): 703610.467008 | | target function (ml) not normalized (free): 14730.885770 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1200 0.1352 n_refl.: 191131 re-set all scales: r(all,work,free)=0.1372 0.1371 0.1461 n_refl.: 191131 remove outliers: r(all,work,free)=0.1372 0.1371 0.1461 n_refl.: 191131 overall B=0.11 to atoms: r(all,work,free)=0.1389 0.1388 0.1471 n_refl.: 191131 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1338 n_refl.: 191131 remove outliers: r(all,work,free)=0.1193 0.1190 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 92.08 90 3 0.4057 356.910 319.350 0.323 1.014 0.128 13.296-10.522 95.05 95 1 0.2256 479.852 454.533 0.656 1.015 0.121 10.503-8.327 98.35 176 3 0.2246 503.127 493.387 0.822 1.016 0.117 8.318-6.595 100.00 360 8 0.2130 375.794 369.613 0.843 1.015 0.096 6.588-5.215 100.00 711 7 0.1905 345.317 335.473 0.842 1.015 0.083 5.214-4.128 98.38 1367 28 0.1241 505.094 498.573 0.928 1.015 0.044 4.126-3.266 94.74 2603 46 0.1156 460.420 452.527 0.988 1.015 0.009 3.266-2.585 99.86 5447 97 0.1119 310.588 306.924 0.974 1.014 0.000 2.585-2.046 97.45 10613 204 0.0958 234.321 231.701 0.986 1.013 0.000 2.046-1.619 99.39 21536 464 0.0910 138.683 137.305 1.007 1.012 0.000 1.619-1.281 98.00 42464 925 0.0946 74.659 74.006 1.006 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.051 38.357 0.988 1.004 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0264 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1190 r_free=0.1338 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1190 r_free=0.1338 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1338 | n_water=899 | time (s): 3.170 (total time: 3.170) Filter (dist) r_work=0.1190 r_free=0.1338 | n_water=899 | time (s): 116.320 (total time: 119.490) Filter (q & B) r_work=0.1190 r_free=0.1338 | n_water=897 | time (s): 5.000 (total time: 124.490) Compute maps r_work=0.1190 r_free=0.1338 | n_water=897 | time (s): 1.830 (total time: 126.320) Filter (map) r_work=0.1210 r_free=0.1348 | n_water=787 | time (s): 5.210 (total time: 131.530) Find peaks r_work=0.1210 r_free=0.1348 | n_water=787 | time (s): 0.740 (total time: 132.270) Add new water r_work=0.1218 r_free=0.1357 | n_water=982 | time (s): 4.510 (total time: 136.780) Refine new water occ: r_work=0.1189 r_free=0.1333 adp: r_work=0.1189 r_free=0.1333 occ: r_work=0.1187 r_free=0.1334 adp: r_work=0.1187 r_free=0.1334 occ: r_work=0.1186 r_free=0.1334 adp: r_work=0.1186 r_free=0.1334 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1334 r_work=0.1186 r_free=0.1334 | n_water=982 | time (s): 281.510 (total time: 418.290) Filter (q & B) r_work=0.1189 r_free=0.1341 | n_water=914 | time (s): 4.280 (total time: 422.570) Filter (dist only) r_work=0.1189 r_free=0.1340 | n_water=913 | time (s): 116.040 (total time: 538.610) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.525518 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.272449 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 0.1347 0.0153 0.037 1.1 6.1 0.0 0.3 0 0.763 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.47 1.53 1.672 13.803 13.272 3.756 11.95 13.51 1.55 1.677 13.798 13.272 3.756 Individual atomic B min max mean iso aniso Overall: 5.51 64.10 14.74 0.86 546 3271 Protein: 5.51 28.04 10.36 0.86 0 2902 Water: 5.97 64.10 28.67 N/A 546 367 Other: 13.78 22.12 17.95 N/A 0 2 Chain A: 5.61 51.44 12.18 N/A 0 1624 Chain B: 5.51 64.10 12.04 N/A 0 1647 Chain S: 5.97 59.94 30.50 N/A 546 0 Histogram: Values Number of atoms 5.51 - 11.37 2072 11.37 - 17.23 809 17.23 - 23.09 278 23.09 - 28.95 219 28.95 - 34.80 189 34.80 - 40.66 128 40.66 - 46.52 80 46.52 - 52.38 28 52.38 - 58.24 10 58.24 - 64.10 4 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1351 r_work=0.1195 r_free=0.1351 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1351 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1351 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1351 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755772 | | target function (ml) not normalized (work): 703411.072614 | | target function (ml) not normalized (free): 14735.253578 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1351 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1396 0.1395 0.1488 n_refl.: 191129 remove outliers: r(all,work,free)=0.1396 0.1395 0.1488 n_refl.: 191129 overall B=-0.00 to atoms: r(all,work,free)=0.1396 0.1394 0.1487 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1193 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1193 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 92.08 90 3 0.4041 356.910 317.041 0.326 0.982 0.110 13.296-10.522 95.05 95 1 0.2251 479.852 464.016 0.694 0.983 0.108 10.503-8.327 98.35 176 3 0.2268 503.127 492.924 0.859 0.984 0.107 8.318-6.595 100.00 360 8 0.2132 375.794 369.522 0.881 0.984 0.089 6.588-5.215 100.00 711 7 0.1936 345.317 335.341 0.882 0.984 0.080 5.214-4.128 98.38 1367 28 0.1252 505.094 498.547 0.970 0.985 0.039 4.126-3.266 94.74 2603 46 0.1168 460.420 452.557 1.033 0.986 0.005 3.266-2.585 99.86 5447 97 0.1131 310.588 306.812 1.016 0.987 0.000 2.585-2.046 97.45 10613 204 0.0958 234.321 231.727 1.026 0.989 0.000 2.046-1.619 99.39 21536 464 0.0911 138.683 137.329 1.043 0.993 0.000 1.619-1.281 98.00 42464 925 0.0946 74.659 74.003 1.035 0.998 0.000 1.281-0.980 96.53 101826 2055 0.1626 40.051 38.338 1.006 1.007 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=-0.0127 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1350 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 ASN Total number of N/Q/H flips: 1 r_work=0.1194 r_free=0.1352 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1194 r_free=0.1352 | n_water=913 | time (s): 2.240 (total time: 2.240) Filter (dist) r_work=0.1194 r_free=0.1352 | n_water=913 | time (s): 122.930 (total time: 125.170) Filter (q & B) r_work=0.1195 r_free=0.1353 | n_water=901 | time (s): 4.190 (total time: 129.360) Compute maps r_work=0.1195 r_free=0.1353 | n_water=901 | time (s): 2.020 (total time: 131.380) Filter (map) r_work=0.1219 r_free=0.1358 | n_water=781 | time (s): 4.970 (total time: 136.350) Find peaks r_work=0.1219 r_free=0.1358 | n_water=781 | time (s): 0.560 (total time: 136.910) Add new water r_work=0.1226 r_free=0.1365 | n_water=974 | time (s): 3.820 (total time: 140.730) Refine new water occ: r_work=0.1193 r_free=0.1341 adp: r_work=0.1194 r_free=0.1342 occ: r_work=0.1192 r_free=0.1341 adp: r_work=0.1192 r_free=0.1342 occ: r_work=0.1190 r_free=0.1342 adp: r_work=0.1190 r_free=0.1342 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1342 r_work=0.1190 r_free=0.1342 | n_water=974 | time (s): 364.980 (total time: 505.710) Filter (q & B) r_work=0.1193 r_free=0.1348 | n_water=914 | time (s): 5.530 (total time: 511.240) Filter (dist only) r_work=0.1193 r_free=0.1347 | n_water=913 | time (s): 116.070 (total time: 627.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.534546 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.698675 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1353 0.0156 0.037 1.1 6.1 0.0 0.3 0 0.767 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.53 1.56 1.680 13.803 13.699 3.758 11.96 13.55 1.58 1.689 13.796 13.699 3.755 Individual atomic B min max mean iso aniso Overall: 5.59 63.30 14.72 0.85 546 3271 Protein: 5.59 27.85 10.36 0.85 0 2902 Water: 5.98 63.30 28.56 N/A 546 367 Other: 13.82 22.08 17.95 N/A 0 2 Chain A: 5.65 51.28 12.16 N/A 0 1624 Chain B: 5.59 63.30 12.02 N/A 0 1647 Chain S: 5.98 59.95 30.45 N/A 546 0 Histogram: Values Number of atoms 5.59 - 11.36 2067 11.36 - 17.13 820 17.13 - 22.90 273 22.90 - 28.67 208 28.67 - 34.44 197 34.44 - 40.22 129 40.22 - 45.99 76 45.99 - 51.76 29 51.76 - 57.53 14 57.53 - 63.30 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1355 r_work=0.1196 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | 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: 15 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1353 target_work(ml) = 3.755 | | 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= 0.1195 r_free= 0.1353 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755277 | | target function (ml) not normalized (work): 703318.281464 | | target function (ml) not normalized (free): 14739.276773 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1353 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1406 0.1404 0.1503 n_refl.: 191129 remove outliers: r(all,work,free)=0.1406 0.1404 0.1503 n_refl.: 191129 overall B=-0.01 to atoms: r(all,work,free)=0.1403 0.1401 0.1501 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1194 0.1350 n_refl.: 191129 remove outliers: r(all,work,free)=0.1197 0.1194 0.1350 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3899 356.585 311.439 0.300 0.986 0.060 13.296-10.522 95.05 95 1 0.2276 479.852 463.119 0.675 0.987 0.086 10.503-8.327 98.35 176 3 0.2272 503.127 492.949 0.846 0.988 0.097 8.318-6.595 100.00 360 8 0.2135 375.794 369.869 0.868 0.988 0.086 6.588-5.215 100.00 711 7 0.1943 345.317 335.526 0.868 0.988 0.077 5.214-4.128 98.38 1367 28 0.1254 505.094 498.927 0.956 0.989 0.039 4.126-3.266 94.74 2603 46 0.1174 460.420 452.478 1.019 0.991 0.005 3.266-2.585 99.86 5447 97 0.1137 310.588 306.833 1.002 0.992 0.000 2.585-2.046 97.45 10613 204 0.0959 234.321 231.759 1.012 0.994 0.000 2.046-1.619 99.39 21536 464 0.0912 138.683 137.335 1.029 0.998 0.000 1.619-1.281 98.00 42464 925 0.0945 74.659 74.012 1.022 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.051 38.338 0.994 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0372 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1194 r_free=0.1351 After: r_work=0.1195 r_free=0.1351 ================================== NQH flips ================================== r_work=0.1195 r_free=0.1351 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1351 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1351 | n_water=913 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1195 r_free=0.1351 | n_water=913 | time (s): 116.420 (total time: 119.010) Filter (q & B) r_work=0.1195 r_free=0.1350 | n_water=901 | time (s): 4.480 (total time: 123.490) Compute maps r_work=0.1195 r_free=0.1350 | n_water=901 | time (s): 1.950 (total time: 125.440) Filter (map) r_work=0.1218 r_free=0.1358 | n_water=783 | time (s): 4.590 (total time: 130.030) Find peaks r_work=0.1218 r_free=0.1358 | n_water=783 | time (s): 0.680 (total time: 130.710) Add new water r_work=0.1225 r_free=0.1363 | n_water=977 | time (s): 4.460 (total time: 135.170) Refine new water occ: r_work=0.1195 r_free=0.1341 adp: r_work=0.1195 r_free=0.1342 occ: r_work=0.1193 r_free=0.1341 adp: r_work=0.1193 r_free=0.1341 occ: r_work=0.1191 r_free=0.1341 adp: r_work=0.1191 r_free=0.1341 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1341 r_work=0.1191 r_free=0.1341 | n_water=977 | time (s): 252.860 (total time: 388.030) Filter (q & B) r_work=0.1194 r_free=0.1349 | n_water=915 | time (s): 5.270 (total time: 393.300) Filter (dist only) r_work=0.1194 r_free=0.1349 | n_water=914 | time (s): 117.680 (total time: 510.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.508129 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.221531 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1197 0.1353 0.0155 0.037 1.2 8.2 0.0 0.3 0 0.754 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.53 1.55 1.677 13.777 14.222 3.758 11.97 13.54 1.58 1.673 13.779 14.222 3.756 Individual atomic B min max mean iso aniso Overall: 5.60 62.21 14.69 0.86 548 3270 Protein: 5.60 27.91 10.37 0.86 0 2902 Water: 6.03 62.21 28.41 N/A 548 366 Other: 13.85 22.09 17.97 N/A 0 2 Chain A: 5.66 49.73 12.12 N/A 0 1623 Chain B: 5.60 62.21 12.01 N/A 0 1647 Chain S: 6.03 60.03 30.36 N/A 548 0 Histogram: Values Number of atoms 5.60 - 11.26 2038 11.26 - 16.92 837 16.92 - 22.58 278 22.58 - 28.24 198 28.24 - 33.90 203 33.90 - 39.56 129 39.56 - 45.23 83 45.23 - 50.89 32 50.89 - 56.55 16 56.55 - 62.21 4 =========================== 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: 16 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1352 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1352 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756042 | | target function (ml) not normalized (work): 703457.869240 | | target function (ml) not normalized (free): 14739.515346 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7396 127 0.1371 0.1462 5.6928 5.7834| | 2: 2.94 - 2.33 1.00 7339 128 0.1072 0.1343 5.0825 5.1751| | 3: 2.33 - 2.04 0.96 6939 150 0.0905 0.1147 4.6597 4.7466| | 4: 2.04 - 1.85 1.00 7170 155 0.0903 0.1067 4.3969 4.5856| | 5: 1.85 - 1.72 0.99 7113 159 0.0937 0.0989 4.1537 4.2363| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1080 3.9487 4.0841| | 7: 1.62 - 1.54 0.99 7104 148 0.0894 0.0959 3.8036 3.9288| | 8: 1.54 - 1.47 0.96 6798 152 0.0893 0.1327 3.7047 3.9206| | 9: 1.47 - 1.41 0.98 6938 155 0.0927 0.1127 3.6243 3.7598| | 10: 1.41 - 1.36 0.99 7022 150 0.0978 0.1186 3.5573 3.6712| | 11: 1.36 - 1.32 0.99 6997 151 0.0995 0.1127 3.488 3.5858| | 12: 1.32 - 1.28 0.98 6975 149 0.1030 0.1124 3.4588 3.5838| | 13: 1.28 - 1.25 0.98 6907 166 0.1039 0.1241 3.4369 3.5667| | 14: 1.25 - 1.22 0.98 7015 112 0.1103 0.1593 3.4339 3.6879| | 15: 1.22 - 1.19 0.98 6956 137 0.1169 0.1249 3.4508 3.4957| | 16: 1.19 - 1.17 0.93 6604 132 0.1250 0.1556 3.4668 3.6629| | 17: 1.17 - 1.14 0.98 6940 135 0.1298 0.1225 3.4333 3.4385| | 18: 1.14 - 1.12 0.98 6875 142 0.1385 0.1705 3.4389 3.5339| | 19: 1.12 - 1.10 0.97 6948 106 0.1470 0.1756 3.4204 3.5969| | 20: 1.10 - 1.08 0.97 6884 147 0.1584 0.1578 3.4114 3.438| | 21: 1.08 - 1.07 0.97 6852 152 0.1727 0.2140 3.4186 3.5048| | 22: 1.07 - 1.05 0.97 6836 135 0.1903 0.1954 3.4137 3.4162| | 23: 1.05 - 1.03 0.97 6827 159 0.2120 0.2026 3.4337 3.489| | 24: 1.03 - 1.02 0.96 6784 133 0.2331 0.2245 3.4365 3.5081| | 25: 1.02 - 1.01 0.93 6552 130 0.2614 0.2518 3.4503 3.5255| | 26: 1.01 - 0.99 0.96 6767 158 0.2757 0.2864 3.4165 3.4263| | 27: 0.99 - 0.98 0.94 6647 131 0.3040 0.2807 3.4692 3.3962| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7396 127 0.93 11.85 1.00 0.96 11404.64| | 2: 2.94 - 2.33 7339 128 0.92 12.96 0.99 0.96 5212.31| | 3: 2.33 - 2.04 6939 150 0.96 7.68 1.01 0.96 1717.20| | 4: 2.04 - 1.85 7170 155 0.96 7.77 1.00 0.96 1023.83| | 5: 1.85 - 1.72 7113 159 0.96 8.11 1.00 0.97 638.57| | 6: 1.72 - 1.62 7102 142 0.96 8.05 1.00 0.97 447.21| | 7: 1.62 - 1.54 7104 148 0.96 8.20 1.01 0.98 340.05| | 8: 1.54 - 1.47 6798 152 0.96 8.36 1.01 0.98 283.44| | 9: 1.47 - 1.41 6938 155 0.96 8.54 1.00 0.99 233.69| | 10: 1.41 - 1.36 7022 150 0.96 8.95 1.00 0.98 203.48| | 11: 1.36 - 1.32 6997 151 0.96 8.92 0.99 0.97 174.89| | 12: 1.32 - 1.28 6975 149 0.96 8.97 0.98 0.96 160.88| | 13: 1.28 - 1.25 6907 166 0.96 9.54 1.01 0.97 159.05| | 14: 1.25 - 1.22 7015 112 0.95 10.76 1.01 0.98 164.58| | 15: 1.22 - 1.19 6956 137 0.95 11.31 1.01 0.99 168.12| | 16: 1.19 - 1.17 6604 132 0.95 11.48 1.01 0.97 161.43| | 17: 1.17 - 1.14 6940 135 0.94 12.26 1.01 0.97 154.49| | 18: 1.14 - 1.12 6875 142 0.94 12.76 1.01 0.96 148.14| | 19: 1.12 - 1.10 6948 106 0.93 14.17 1.00 0.96 151.76| | 20: 1.10 - 1.08 6884 147 0.92 15.27 1.00 0.95 151.10| | 21: 1.08 - 1.07 6852 152 0.91 16.68 1.00 0.94 154.11| | 22: 1.07 - 1.05 6836 135 0.89 18.32 0.99 0.94 155.45| | 23: 1.05 - 1.03 6827 159 0.87 20.51 0.99 0.93 165.17| | 24: 1.03 - 1.02 6784 133 0.85 23.18 0.99 0.94 179.51| | 25: 1.02 - 1.01 6552 130 0.83 25.19 0.98 0.91 182.73| | 26: 1.01 - 0.99 6767 158 0.81 26.65 0.98 0.90 177.14| | 27: 0.99 - 0.98 6647 131 0.82 26.27 0.99 0.88 161.19| |alpha: min = 0.88 max = 0.99 mean = 0.96| |beta: min = 148.14 max = 11404.64 mean = 939.31| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 90.00 mean = 13.34| |phase err.(test): min = 0.00 max = 89.48 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1352 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1403 0.1401 0.1508 n_refl.: 191128 remove outliers: r(all,work,free)=0.1403 0.1401 0.1508 n_refl.: 191128 overall B=-0.09 to atoms: r(all,work,free)=0.1389 0.1387 0.1497 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191128 remove outliers: r(all,work,free)=0.1198 0.1195 0.1351 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3912 356.585 322.692 0.323 0.919 0.050 13.296-10.522 95.05 95 1 0.2298 479.852 462.777 0.714 0.920 0.090 10.503-8.327 98.35 176 3 0.2268 503.127 492.546 0.892 0.921 0.087 8.318-6.595 100.00 360 8 0.2126 375.794 370.312 0.917 0.921 0.077 6.588-5.215 100.00 711 7 0.1934 345.317 335.220 0.916 0.921 0.070 5.214-4.128 98.38 1367 28 0.1254 505.094 498.643 1.010 0.922 0.029 4.126-3.266 94.74 2603 46 0.1179 460.420 452.316 1.077 0.923 0.000 3.266-2.585 99.86 5447 97 0.1133 310.588 306.938 1.060 0.925 0.000 2.585-2.046 97.45 10613 204 0.0961 234.321 231.714 1.067 0.927 0.000 2.046-1.619 99.39 21536 464 0.0913 138.683 137.324 1.083 0.931 0.000 1.619-1.281 98.00 42464 925 0.0947 74.659 73.999 1.072 0.937 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.051 38.321 1.037 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0196 ================= 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 : 0.2031 0.1999 0.081 5.183 5.2 78.0 14.6 805 0.000 1_bss: 0.1794 0.1925 0.081 5.183 5.2 78.0 14.6 805 0.000 1_settarget: 0.1794 0.1925 0.081 5.183 5.2 78.0 14.6 805 0.000 1_nqh: 0.1798 0.1928 0.081 5.183 5.2 78.0 14.6 805 0.004 1_weight: 0.1798 0.1928 0.081 5.183 5.2 78.0 14.6 805 0.004 1_xyzrec: 0.1275 0.1485 0.035 1.170 5.2 78.0 14.6 805 0.145 1_adp: 0.1303 0.1551 0.035 1.170 5.2 73.0 15.0 805 0.145 1_regHadp: 0.1302 0.1546 0.035 1.170 5.2 73.0 15.0 805 0.145 1_occ: 0.1287 0.1536 0.035 1.170 5.2 73.0 15.0 805 0.145 2_bss: 0.1279 0.1531 0.035 1.170 5.3 73.2 15.2 805 0.145 2_settarget: 0.1279 0.1531 0.035 1.170 5.3 73.2 15.2 805 0.145 2_updatecdl: 0.1279 0.1531 0.035 1.192 5.3 73.2 15.2 805 0.145 2_nqh: 0.1279 0.1531 0.035 1.192 5.3 73.2 15.2 805 0.145 2_sol: 0.1268 0.1508 0.035 1.192 5.3 73.2 16.4 909 n/a 2_weight: 0.1268 0.1508 0.035 1.192 5.3 73.2 16.4 909 n/a 2_xyzrec: 0.1252 0.1526 0.039 1.152 5.3 73.2 16.4 909 n/a 2_adp: 0.1228 0.1504 0.039 1.152 5.4 68.3 16.5 909 n/a 2_regHadp: 0.1229 0.1505 0.039 1.152 5.4 68.3 16.5 909 n/a 2_occ: 0.1223 0.1499 0.039 1.152 5.4 68.3 16.5 909 n/a 3_bss: 0.1230 0.1507 0.039 1.152 5.4 68.2 16.5 909 n/a 3_settarget: 0.1230 0.1507 0.039 1.152 5.4 68.2 16.5 909 n/a 3_updatecdl: 0.1230 0.1507 0.039 1.155 5.4 68.2 16.5 909 n/a 3_nqh: 0.1230 0.1507 0.039 1.155 5.4 68.2 16.5 909 n/a 3_sol: 0.1248 0.1501 0.039 1.155 5.4 68.2 15.6 897 n/a 3_weight: 0.1248 0.1501 0.039 1.155 5.4 68.2 15.6 897 n/a 3_xyzrec: 0.1239 0.1431 0.034 1.106 5.4 68.2 15.6 897 n/a 3_adp: 0.1236 0.1393 0.034 1.106 5.6 67.7 15.4 897 n/a 3_regHadp: 0.1237 0.1394 0.034 1.106 5.6 67.7 15.4 897 n/a 3_occ: 0.1231 0.1384 0.034 1.106 5.6 67.7 15.4 897 n/a 4_bss: 0.1226 0.1375 0.034 1.106 5.5 67.7 15.4 897 n/a 4_settarget: 0.1226 0.1375 0.034 1.106 5.5 67.7 15.4 897 n/a 4_updatecdl: 0.1226 0.1375 0.034 1.106 5.5 67.7 15.4 897 n/a 4_nqh: 0.1230 0.1380 0.034 1.106 5.5 67.7 15.4 897 n/a 4_sol: 0.1218 0.1368 0.034 1.106 5.5 67.7 14.9 845 n/a 4_weight: 0.1218 0.1368 0.034 1.106 5.5 67.7 14.9 845 n/a 4_xyzrec: 0.1211 0.1366 0.036 1.123 5.5 67.7 14.9 845 n/a 4_adp: 0.1204 0.1365 0.036 1.123 5.5 67.2 14.8 845 n/a 4_regHadp: 0.1204 0.1366 0.036 1.123 5.5 67.2 14.8 845 n/a 4_occ: 0.1202 0.1360 0.036 1.123 5.5 67.2 14.8 845 n/a 5_bss: 0.1200 0.1357 0.036 1.123 5.5 67.1 14.8 845 n/a 5_settarget: 0.1200 0.1357 0.036 1.123 5.5 67.1 14.8 845 n/a 5_updatecdl: 0.1200 0.1357 0.036 1.123 5.5 67.1 14.8 845 n/a 5_nqh: 0.1200 0.1357 0.036 1.123 5.5 67.1 14.8 845 n/a 5_sol: 0.1194 0.1348 0.036 1.123 5.5 67.1 15.0 889 n/a 5_weight: 0.1194 0.1348 0.036 1.123 5.5 67.1 15.0 889 n/a 5_xyzrec: 0.1197 0.1355 0.036 1.133 5.5 67.1 15.0 889 n/a 5_adp: 0.1200 0.1358 0.036 1.133 5.6 66.8 15.0 889 n/a 5_regHadp: 0.1200 0.1358 0.036 1.133 5.6 66.8 15.0 889 n/a 5_occ: 0.1198 0.1357 0.036 1.133 5.6 66.8 15.0 889 n/a 6_bss: 0.1197 0.1352 0.036 1.133 5.5 66.7 14.9 889 n/a 6_settarget: 0.1197 0.1352 0.036 1.133 5.5 66.7 14.9 889 n/a 6_updatecdl: 0.1197 0.1352 0.036 1.133 5.5 66.7 14.9 889 n/a 6_nqh: 0.1197 0.1352 0.036 1.133 5.5 66.7 14.9 889 n/a 6_sol: 0.1197 0.1343 0.036 1.133 5.5 66.7 14.9 901 n/a 6_weight: 0.1197 0.1343 0.036 1.133 5.5 66.7 14.9 901 n/a 6_xyzrec: 0.1200 0.1355 0.036 1.123 5.5 66.7 14.9 901 n/a 6_adp: 0.1203 0.1360 0.036 1.123 5.6 65.8 14.9 901 n/a 6_regHadp: 0.1203 0.1360 0.036 1.123 5.6 65.8 14.9 901 n/a 6_occ: 0.1201 0.1358 0.036 1.123 5.6 65.8 14.9 901 n/a 7_bss: 0.1201 0.1357 0.036 1.123 5.4 65.6 14.6 901 n/a 7_settarget: 0.1201 0.1357 0.036 1.123 5.4 65.6 14.6 901 n/a 7_updatecdl: 0.1201 0.1357 0.036 1.123 5.4 65.6 14.6 901 n/a 7_nqh: 0.1201 0.1357 0.036 1.123 5.4 65.6 14.6 901 n/a 7_sol: 0.1200 0.1347 0.036 1.123 5.4 65.6 14.6 899 n/a 7_weight: 0.1200 0.1347 0.036 1.123 5.4 65.6 14.6 899 n/a 7_xyzrec: 0.1201 0.1353 0.036 1.148 5.4 65.6 14.6 899 n/a 7_adp: 0.1203 0.1354 0.036 1.148 5.4 64.3 14.6 899 n/a 7_regHadp: 0.1203 0.1354 0.036 1.148 5.4 64.3 14.6 899 n/a 7_occ: 0.1200 0.1352 0.036 1.148 5.4 64.3 14.6 899 n/a 8_bss: 0.1190 0.1338 0.036 1.148 5.5 64.4 14.7 899 n/a 8_settarget: 0.1190 0.1338 0.036 1.148 5.5 64.4 14.7 899 n/a 8_updatecdl: 0.1190 0.1338 0.036 1.149 5.5 64.4 14.7 899 n/a 8_nqh: 0.1190 0.1338 0.036 1.149 5.5 64.4 14.7 899 n/a 8_sol: 0.1189 0.1340 0.036 1.149 5.5 64.4 14.8 913 n/a 8_weight: 0.1189 0.1340 0.036 1.149 5.5 64.4 14.8 913 n/a 8_xyzrec: 0.1194 0.1347 0.037 1.125 5.5 64.4 14.8 913 n/a 8_adp: 0.1195 0.1351 0.037 1.125 5.5 64.1 14.7 913 n/a 8_regHadp: 0.1195 0.1351 0.037 1.125 5.5 64.1 14.7 913 n/a 8_occ: 0.1194 0.1351 0.037 1.125 5.5 64.1 14.7 913 n/a 9_bss: 0.1193 0.1350 0.037 1.125 5.5 64.1 14.7 913 n/a 9_settarget: 0.1193 0.1350 0.037 1.125 5.5 64.1 14.7 913 n/a 9_updatecdl: 0.1193 0.1350 0.037 1.125 5.5 64.1 14.7 913 n/a 9_nqh: 0.1194 0.1352 0.037 1.125 5.5 64.1 14.7 913 n/a 9_sol: 0.1193 0.1347 0.037 1.125 5.5 64.1 14.7 913 n/a 9_weight: 0.1193 0.1347 0.037 1.125 5.5 64.1 14.7 913 n/a 9_xyzrec: 0.1196 0.1353 0.037 1.114 5.5 64.1 14.7 913 n/a 9_adp: 0.1196 0.1355 0.037 1.114 5.6 63.3 14.7 913 n/a 9_regHadp: 0.1196 0.1355 0.037 1.114 5.6 63.3 14.7 913 n/a 9_occ: 0.1195 0.1353 0.037 1.114 5.6 63.3 14.7 913 n/a 10_bss: 0.1194 0.1351 0.037 1.114 5.6 63.3 14.7 913 n/a 10_settarget: 0.1194 0.1351 0.037 1.114 5.6 63.3 14.7 913 n/a 10_updatecdl: 0.1194 0.1351 0.037 1.115 5.6 63.3 14.7 913 n/a 10_setrh: 0.1195 0.1351 0.037 1.115 5.6 63.3 14.7 913 n/a 10_nqh: 0.1195 0.1351 0.037 1.115 5.6 63.3 14.7 913 n/a 10_sol: 0.1194 0.1349 0.037 1.115 5.6 63.3 14.7 914 n/a 10_weight: 0.1194 0.1349 0.037 1.115 5.6 63.3 14.7 914 n/a 10_xyzrec: 0.1197 0.1353 0.037 1.155 5.6 63.3 14.7 914 n/a 10_adp: 0.1197 0.1354 0.037 1.155 5.6 62.2 14.7 914 n/a 10_regHadp: 0.1197 0.1354 0.037 1.155 5.6 62.2 14.7 914 n/a 10_occ: 0.1195 0.1352 0.037 1.155 5.6 62.2 14.7 914 n/a end: 0.1195 0.1351 0.037 1.155 5.5 62.1 14.6 914 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3157372_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3157372_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.8300 Refinement macro-cycles (run) : 12262.8700 Write final files (write_after_run_outputs) : 152.2700 Total : 12422.9700 Total CPU time: 3.46 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:44:18 PST -0800 (1736736258.52 s) Start R-work = 0.1794, R-free = 0.1925 Final R-work = 0.1195, R-free = 0.1351 =============================================================================== Job complete usr+sys time: 12700.73 seconds wall clock time: 212 minutes 38.97 seconds (12758.97 seconds total)