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_3074067.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/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_3074067.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_3074067.pdb" } 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: 2.61, per 1000 atoms: 0.39 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: 2.689 distance_ideal: 2.720 ideal - model: 0.031 slack: 0.000 delta_slack: 0.031 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: 2.645 distance_ideal: 2.710 ideal - model: 0.065 slack: 0.000 delta_slack: 0.065 sigma: 10.0000 Total number of added/changed bonds: 4 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 117.8 milliseconds Time building geometry restraints manager: 0.93 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: 872 1.03 - 1.26: 2436 1.26 - 1.48: 1462 1.48 - 1.71: 1141 1.71 - 1.93: 23 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL B 114 " pdb=" CB VAL B 114 " ideal model delta sigma weight residual 1.539 1.666 -0.127 5.40e-03 3.43e+04 5.49e+02 bond pdb=" C VAL B 114 " pdb=" O VAL B 114 " ideal model delta sigma weight residual 1.242 1.047 0.195 8.60e-03 1.35e+04 5.13e+02 bond pdb=" N LEU A 171 " pdb=" H LEU A 171 " ideal model delta sigma weight residual 0.860 1.246 -0.386 2.00e-02 2.50e+03 3.73e+02 bond pdb=" C LEU A 25 " pdb=" O LEU A 25 " ideal model delta sigma weight residual 1.236 1.458 -0.222 1.15e-02 7.56e+03 3.73e+02 bond pdb=" N SER A 85 " pdb=" CA SER A 85 " ideal model delta sigma weight residual 1.458 1.689 -0.232 1.22e-02 6.72e+03 3.61e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.42: 5846 4.42 - 8.84: 3555 8.84 - 13.26: 1205 13.26 - 17.68: 190 17.68 - 22.10: 14 Bond angle restraints: 10810 Sorted by residual: angle pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " ideal model delta sigma weight residual 120.83 109.53 11.30 6.10e-01 2.69e+00 3.43e+02 angle pdb=" O LYS B 177 " pdb=" C LYS B 177 " pdb=" N ALA B 178 " ideal model delta sigma weight residual 122.09 103.97 18.12 1.08e+00 8.57e-01 2.82e+02 angle pdb=" NE ARG B 27 " pdb=" CZ ARG B 27 " pdb=" NH1 ARG B 27 " ideal model delta sigma weight residual 121.50 107.45 14.05 1.00e+00 1.00e+00 1.97e+02 angle pdb=" CA PHE B 127 " pdb=" C PHE B 127 " pdb=" O PHE B 127 " ideal model delta sigma weight residual 119.71 107.97 11.74 8.40e-01 1.42e+00 1.95e+02 angle pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta sigma weight residual 119.64 105.60 14.04 1.01e+00 9.80e-01 1.93e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.63: 1861 17.63 - 35.26: 126 35.26 - 52.89: 41 52.89 - 70.52: 17 70.52 - 88.15: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA ILE B 105 " pdb=" C ILE B 105 " pdb=" N CYS B 106 " pdb=" CA CYS B 106 " ideal model delta harmonic sigma weight residual 180.00 154.89 25.11 0 5.00e+00 4.00e-02 2.52e+01 dihedral pdb=" CA GLN A 184 " pdb=" C GLN A 184 " pdb=" N LEU A 185 " pdb=" CA LEU A 185 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+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 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.226: 191 0.226 - 0.450: 156 0.450 - 0.673: 105 0.673 - 0.897: 29 0.897 - 1.121: 11 Chirality restraints: 492 Sorted by residual: chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 3.77 -1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CA LYS B 133 " pdb=" N LYS B 133 " pdb=" C LYS B 133 " pdb=" CB LYS B 133 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.98e+01 chirality pdb=" CA GLN A 156 " pdb=" N GLN A 156 " pdb=" C GLN A 156 " pdb=" CB GLN A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.47 1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.157 2.00e-02 2.50e+03 7.78e-02 1.82e+02 pdb=" CG PHE B 164 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.057 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.112 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.093 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.060 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.078 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 139 " -0.033 2.00e-02 2.50e+03 6.18e-02 1.53e+02 pdb=" CG TRP B 139 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TRP B 139 " 0.062 2.00e-02 2.50e+03 pdb=" CD2 TRP B 139 " 0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 139 " 0.126 2.00e-02 2.50e+03 pdb=" CE2 TRP B 139 " -0.112 2.00e-02 2.50e+03 pdb=" CE3 TRP B 139 " -0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 139 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 139 " -0.073 2.00e-02 2.50e+03 pdb=" CH2 TRP B 139 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 TRP B 139 " -0.102 2.00e-02 2.50e+03 pdb=" HE1 TRP B 139 " 0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP B 139 " 0.049 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 139 " -0.031 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 139 " 0.023 2.00e-02 2.50e+03 pdb=" HH2 TRP B 139 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 179 " 0.055 2.00e-02 2.50e+03 7.78e-02 1.36e+02 pdb=" CG HIS A 179 " -0.165 2.00e-02 2.50e+03 pdb=" ND1 HIS A 179 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 HIS A 179 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS A 179 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 179 " 0.132 2.00e-02 2.50e+03 pdb=" HD2 HIS A 179 " -0.007 2.00e-02 2.50e+03 pdb=" HE1 HIS A 179 " -0.027 2.00e-02 2.50e+03 pdb=" HE2 HIS A 179 " -0.046 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.62: 26 1.62 - 2.36: 2410 2.36 - 3.11: 22378 3.11 - 3.85: 32836 3.85 - 4.60: 52714 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110364 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.874 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.975 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 0.979 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.140 2.620 nonbonded pdb=" HD3 ARG A 97 " pdb=" O HOH S1635 " model vdw 1.189 2.620 ... (remaining 110359 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_3074067_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= 0.2034 r_free= 0.2001 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.301325 | | target function (ml) not normalized (work): 805694.152369 | | target function (ml) not normalized (free): 16560.261927 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2133 0.1977 6.6763 6.3202| | 2: 2.94 - 2.33 1.00 7339 128 0.1618 0.1677 5.5449 5.5949| | 3: 2.33 - 2.04 0.96 6939 150 0.1636 0.1570 5.1515 5.1429| | 4: 2.04 - 1.85 1.00 7170 155 0.1744 0.1722 4.9673 5.0926| | 5: 1.85 - 1.72 0.99 7113 159 0.1920 0.1791 4.7986 4.8319| | 6: 1.72 - 1.62 0.99 7102 142 0.1960 0.1893 4.6691 4.6602| | 7: 1.62 - 1.54 0.99 7104 148 0.2046 0.1858 4.5709 4.5643| | 8: 1.54 - 1.47 0.96 6798 152 0.2041 0.2269 4.4718 4.5485| | 9: 1.47 - 1.41 0.98 6938 155 0.2114 0.2244 4.4084 4.5238| | 10: 1.41 - 1.36 0.99 7022 150 0.2125 0.2144 4.3046 4.3591| | 11: 1.36 - 1.32 0.99 6997 151 0.2086 0.2112 4.2245 4.2467| | 12: 1.32 - 1.28 0.98 6976 149 0.2104 0.1878 4.1735 4.1745| | 13: 1.28 - 1.25 0.98 6907 166 0.2045 0.2100 4.1234 4.1859| | 14: 1.25 - 1.22 0.98 7015 113 0.2072 0.2302 4.0845 4.2699| | 15: 1.22 - 1.19 0.98 6957 137 0.2102 0.2188 4.0518 4.087| | 16: 1.19 - 1.17 0.93 6604 132 0.2161 0.2288 4.0214 4.0992| | 17: 1.17 - 1.14 0.98 6941 135 0.2196 0.1984 3.9661 4.0322| | 18: 1.14 - 1.12 0.98 6875 142 0.2232 0.2235 3.9241 3.8919| | 19: 1.12 - 1.10 0.97 6949 106 0.2264 0.2251 3.8655 3.9623| | 20: 1.10 - 1.08 0.97 6884 147 0.2310 0.2382 3.8178 3.8858| | 21: 1.08 - 1.07 0.97 6852 152 0.2428 0.2735 3.7855 3.8269| | 22: 1.07 - 1.05 0.97 6838 135 0.2529 0.2309 3.7428 3.6708| | 23: 1.05 - 1.03 0.97 6829 159 0.2723 0.2671 3.7269 3.8| | 24: 1.03 - 1.02 0.96 6785 133 0.2866 0.2864 3.6977 3.7933| | 25: 1.02 - 1.01 0.93 6552 130 0.3077 0.2722 3.684 3.6809| | 26: 1.01 - 0.99 0.96 6767 158 0.3154 0.3180 3.6174 3.6037| | 27: 0.99 - 0.98 0.94 6648 131 0.3406 0.2949 3.6534 3.5497| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.85 20.69 0.91 0.97 36300.04| | 2: 2.94 - 2.33 7339 128 0.85 21.53 1.09 1.02 15488.03| | 3: 2.33 - 2.04 6939 150 0.93 12.83 1.11 1.05 4311.74| | 4: 2.04 - 1.85 7170 155 0.92 13.77 1.11 1.06 2880.88| | 5: 1.85 - 1.72 7113 159 0.91 15.81 1.11 1.07 2094.29| | 6: 1.72 - 1.62 7102 142 0.90 16.50 1.11 1.08 1619.06| | 7: 1.62 - 1.54 7104 148 0.89 17.68 1.11 1.08 1351.68| | 8: 1.54 - 1.47 6798 152 0.88 18.67 1.11 1.07 1196.97| | 9: 1.47 - 1.41 6938 155 0.88 19.62 1.10 1.06 1046.20| | 10: 1.41 - 1.36 7022 150 0.87 20.53 1.10 1.04 881.71| | 11: 1.36 - 1.32 6997 151 0.87 20.18 1.08 1.04 738.36| | 12: 1.32 - 1.28 6976 149 0.88 19.61 1.08 1.03 629.80| | 13: 1.28 - 1.25 6907 166 0.88 19.73 1.07 1.04 601.22| | 14: 1.25 - 1.22 7015 113 0.86 21.19 1.08 1.04 599.27| | 15: 1.22 - 1.19 6957 137 0.86 21.78 1.07 1.05 582.52| | 16: 1.19 - 1.17 6604 132 0.86 21.32 1.07 1.03 523.19| | 17: 1.17 - 1.14 6941 135 0.86 21.40 1.09 1.01 453.81| | 18: 1.14 - 1.12 6875 142 0.86 21.49 1.09 1.00 406.04| | 19: 1.12 - 1.10 6949 106 0.86 22.09 1.07 1.00 380.63| | 20: 1.10 - 1.08 6884 147 0.85 22.82 1.07 0.98 349.33| | 21: 1.08 - 1.07 6852 152 0.84 23.52 1.06 0.98 325.26| | 22: 1.07 - 1.05 6838 135 0.83 24.74 1.05 0.96 306.21| | 23: 1.05 - 1.03 6829 159 0.81 26.73 1.05 0.98 312.80| | 24: 1.03 - 1.02 6785 133 0.79 28.60 1.05 1.00 316.90| | 25: 1.02 - 1.01 6552 130 0.78 29.33 1.03 0.98 298.26| | 26: 1.01 - 0.99 6767 158 0.78 29.72 1.03 0.96 265.26| | 27: 0.99 - 0.98 6648 131 0.79 28.89 1.04 0.93 228.83| |alpha: min = 0.93 max = 1.08 mean = 1.02| |beta: min = 228.83 max = 36300.04 mean = 2889.16| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.95 mean = 21.44| |phase err.(test): min = 0.00 max = 88.82 mean = 21.46| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.248 2950 Z= 5.514 Angle : 5.269 18.121 4018 Z= 3.767 Chirality : 0.404 1.121 492 Planarity : 0.033 0.167 512 Dihedral : 12.979 88.151 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.34 % Rotamer: Outliers : 0.32 % Allowed : 4.19 % Favored : 95.48 % Cbeta Deviations : 32.87 % 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: -2.10 (0.39), residues: 386 helix: -2.23 (0.33), residues: 144 sheet: -0.57 (0.50), residues: 86 loop : -0.75 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.021 ARG A 83 TYR 0.079 0.035 TYR B 67 PHE 0.105 0.033 PHE B 164 TRP 0.140 0.034 TRP B 139 HIS 0.096 0.039 HIS A 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2034 r_free= 0.2001 coordinate error (max.-lik. estimate): 0.03 A | | | | normalized target function (ml) (work): 4.301325 | | target function (ml) not normalized (work): 805694.152369 | | target function (ml) not normalized (free): 16560.261927 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2034 0.2001 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2034 0.2001 n_refl.: 191155 remove outliers: r(all,work,free)=0.2033 0.2034 0.2001 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2033 0.2034 0.2001 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1803 0.1800 0.1937 n_refl.: 191145 remove outliers: r(all,work,free)=0.1801 0.1798 0.1935 n_refl.: 191138 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4215 400.535 296.516 0.434 0.914 0.301 13.296-10.522 99.01 99 1 0.2485 528.187 520.415 0.786 0.915 0.255 10.503-8.327 98.90 177 3 0.2482 564.205 559.392 0.969 0.915 0.233 8.318-6.595 100.00 360 8 0.2432 414.736 404.500 0.973 0.915 0.180 6.588-5.215 100.00 711 7 0.2242 381.101 365.535 0.959 0.915 0.170 5.214-4.128 98.38 1367 28 0.1471 557.435 550.723 1.075 0.915 0.090 4.126-3.266 94.74 2603 46 0.1337 508.132 499.188 1.145 0.915 0.019 3.266-2.585 99.86 5447 97 0.1426 342.774 338.144 1.119 0.914 0.000 2.585-2.046 97.45 10613 204 0.1400 258.603 254.250 1.125 0.914 0.000 2.046-1.619 99.39 21536 464 0.1623 153.054 149.789 1.140 0.912 0.000 1.619-1.281 98.00 42464 925 0.1928 82.395 80.209 1.130 0.910 0.000 1.281-0.980 96.53 101826 2055 0.2320 44.202 41.665 1.113 0.906 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0059 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1798 r_free=0.1935 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 r_work=0.1806 r_free=0.1938 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.771015 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 564.605326 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 0.1270 0.1494 0.0223 0.037 1.2 11.0 0.0 0.3 0 12.386 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.70 14.94 2.23 1.117 13.109 564.605 0.018 12.97 15.55 2.58 1.277 13.374 564.605 0.017 Individual atomic B min max mean iso aniso Overall: 5.22 73.04 15.08 1.41 435 3274 Protein: 5.22 40.43 11.03 1.41 0 2902 Water: 6.34 73.04 29.65 N/A 435 370 Other: 15.91 30.20 23.05 N/A 0 2 Chain A: 5.25 60.92 13.11 N/A 0 1626 Chain B: 5.22 73.04 12.83 N/A 0 1648 Chain S: 11.18 63.96 30.95 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.00 2170 12.00 - 18.78 632 18.78 - 25.56 315 25.56 - 32.35 258 32.35 - 39.13 156 39.13 - 45.91 111 45.91 - 52.69 42 52.69 - 59.48 21 59.48 - 66.26 3 66.26 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1297 r_free=0.1555 r_work=0.1296 r_free=0.1550 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1296 r_free = 0.1550 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1281 r_free = 0.1538 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191138 (all), 2.01 % free)-----------| | | | r_work= 0.1281 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015585 | | target function (ls_wunit_k1) not normalized (work): 2919.058936 | | target function (ls_wunit_k1) not normalized (free): 113.794377 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1286 0.1281 0.1538 n_refl.: 191138 re-set all scales: r(all,work,free)=0.1474 0.1472 0.1611 n_refl.: 191138 remove outliers: r(all,work,free)=0.1474 0.1472 0.1611 n_refl.: 191138 overall B=0.16 to atoms: r(all,work,free)=0.1498 0.1496 0.1623 n_refl.: 191138 bulk-solvent and scaling: r(all,work,free)=0.1278 0.1273 0.1529 n_refl.: 191138 remove outliers: r(all,work,free)=0.1278 0.1273 0.1529 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 0.3583 402.814 375.305 0.461 1.001 0.275 13.296-10.522 99.01 99 1 0.2082 528.187 521.290 0.712 1.003 0.250 10.503-8.327 98.90 177 3 0.1721 564.205 561.985 0.851 1.003 0.208 8.318-6.595 100.00 360 8 0.1727 414.736 412.206 0.874 1.002 0.165 6.588-5.215 100.00 711 7 0.1547 381.101 373.530 0.854 1.003 0.160 5.214-4.128 98.38 1367 28 0.0909 557.435 554.227 0.939 1.003 0.080 4.126-3.266 94.74 2603 46 0.0836 508.132 504.382 1.003 1.004 0.014 3.266-2.585 99.86 5447 97 0.0921 342.774 340.352 0.986 1.003 0.000 2.585-2.046 97.45 10613 204 0.0949 258.603 256.460 0.997 1.004 0.000 2.046-1.619 99.39 21536 464 0.1085 153.054 151.401 1.014 1.004 0.000 1.619-1.281 98.00 42464 925 0.1274 82.395 81.420 1.008 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1871 44.202 42.165 0.985 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0374 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1529 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN Total number of N/Q/H flips: 1 r_work=0.1276 r_free=0.1537 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1537 | n_water=805 | time (s): 2.690 (total time: 2.690) Filter (dist) r_work=0.1280 r_free=0.1545 | n_water=796 | time (s): 101.310 (total time: 104.000) Filter (q & B) r_work=0.1281 r_free=0.1543 | n_water=792 | time (s): 4.860 (total time: 108.860) Compute maps r_work=0.1281 r_free=0.1543 | n_water=792 | time (s): 2.260 (total time: 111.120) Filter (map) r_work=0.1304 r_free=0.1523 | n_water=664 | time (s): 4.390 (total time: 115.510) Find peaks r_work=0.1304 r_free=0.1523 | n_water=664 | time (s): 0.860 (total time: 116.370) Add new water r_work=0.1328 r_free=0.1556 | n_water=970 | time (s): 5.000 (total time: 121.370) Refine new water occ: r_work=0.1287 r_free=0.1510 adp: r_work=0.1274 r_free=0.1504 occ: r_work=0.1277 r_free=0.1502 adp: r_work=0.1270 r_free=0.1499 occ: r_work=0.1272 r_free=0.1498 adp: r_work=0.1268 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1498 r_work=0.1268 r_free=0.1498 | n_water=970 | time (s): 77.580 (total time: 198.950) Filter (q & B) r_work=0.1272 r_free=0.1501 | n_water=893 | time (s): 5.380 (total time: 204.330) Filter (dist only) r_work=0.1273 r_free=0.1499 | n_water=891 | time (s): 114.940 (total time: 319.270) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.424847 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 583.272106 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 0.1259 0.1520 0.0261 0.041 1.1 17.0 0.0 0.3 0 11.212 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.59 15.20 2.61 2.055 15.220 583.272 0.015 12.35 15.06 2.71 2.425 15.269 583.272 0.014 Individual atomic B min max mean iso aniso Overall: 5.46 68.21 16.36 1.21 523 3272 Protein: 5.46 40.55 11.02 1.21 0 2902 Water: 6.65 68.21 33.73 N/A 523 368 Other: 16.40 33.49 24.94 N/A 0 2 Chain A: 5.50 57.14 13.05 N/A 0 1624 Chain B: 5.46 68.21 12.88 N/A 0 1648 Chain S: 13.38 67.04 37.58 N/A 523 0 Histogram: Values Number of atoms 5.46 - 11.74 2072 11.74 - 18.01 691 18.01 - 24.29 273 24.29 - 30.56 213 30.56 - 36.83 177 36.83 - 43.11 172 43.11 - 49.38 98 49.38 - 55.66 55 55.66 - 61.93 28 61.93 - 68.21 16 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1506 r_work=0.1236 r_free=0.1507 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1236 r_free = 0.1507 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 = 0.1229 r_free = 0.1504 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1229 r_free= 0.1504 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013435 | | target function (ls_wunit_k1) not normalized (work): 2516.322576 | | target function (ls_wunit_k1) not normalized (free): 99.097855 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1229 0.1504 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1438 0.1435 0.1594 n_refl.: 191137 remove outliers: r(all,work,free)=0.1438 0.1435 0.1594 n_refl.: 191137 overall B=-0.02 to atoms: r(all,work,free)=0.1435 0.1432 0.1592 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1241 0.1236 0.1512 n_refl.: 191137 remove outliers: r(all,work,free)=0.1241 0.1236 0.1512 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 0.3305 402.814 377.178 0.483 0.963 0.267 13.296-10.522 99.01 99 1 0.1884 528.187 519.079 0.759 0.964 0.229 10.503-8.327 98.90 177 3 0.1383 564.205 567.464 0.920 0.964 0.179 8.318-6.595 100.00 360 8 0.1531 414.736 414.715 0.935 0.963 0.150 6.588-5.215 100.00 711 7 0.1323 381.101 376.926 0.915 0.963 0.150 5.214-4.128 98.38 1367 28 0.0831 557.435 556.229 0.994 0.963 0.100 4.126-3.266 94.74 2603 46 0.0759 508.132 505.216 1.059 0.963 0.009 3.266-2.585 99.86 5447 97 0.0859 342.774 341.342 1.046 0.962 0.000 2.585-2.046 97.45 10613 204 0.0903 258.603 256.781 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1050 153.054 151.601 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1260 82.395 81.340 1.074 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1877 44.202 42.209 1.060 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0555 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1236 r_free=0.1512 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1236 r_free=0.1512 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1236 r_free=0.1512 | n_water=891 | time (s): 2.780 (total time: 2.780) Filter (dist) r_work=0.1238 r_free=0.1512 | n_water=885 | time (s): 128.810 (total time: 131.590) Filter (q & B) r_work=0.1238 r_free=0.1513 | n_water=882 | time (s): 5.400 (total time: 136.990) Compute maps r_work=0.1238 r_free=0.1513 | n_water=882 | time (s): 1.640 (total time: 138.630) Filter (map) r_work=0.1279 r_free=0.1524 | n_water=686 | time (s): 5.420 (total time: 144.050) Find peaks r_work=0.1279 r_free=0.1524 | n_water=686 | time (s): 0.900 (total time: 144.950) Add new water r_work=0.1303 r_free=0.1554 | n_water=1005 | time (s): 4.770 (total time: 149.720) Refine new water occ: r_work=0.1258 r_free=0.1510 adp: r_work=0.1258 r_free=0.1512 occ: r_work=0.1254 r_free=0.1506 adp: r_work=0.1254 r_free=0.1508 occ: r_work=0.1251 r_free=0.1503 adp: r_work=0.1250 r_free=0.1505 ADP+occupancy (water only), MIN, final r_work=0.1250 r_free=0.1505 r_work=0.1250 r_free=0.1505 | n_water=1005 | time (s): 213.150 (total time: 362.870) Filter (q & B) r_work=0.1255 r_free=0.1507 | n_water=868 | time (s): 4.550 (total time: 367.420) Filter (dist only) r_work=0.1255 r_free=0.1506 | n_water=867 | time (s): 123.970 (total time: 491.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.737561 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.659736 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1241 0.1428 0.0188 0.036 1.1 8.0 0.0 0.0 0 0.869 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.41 14.28 1.88 1.941 14.607 15.660 3.941 12.39 13.88 1.49 2.280 14.499 15.660 3.899 Individual atomic B min max mean iso aniso Overall: 5.56 67.74 15.25 1.05 504 3267 Protein: 5.56 36.54 10.75 1.05 0 2902 Water: 6.71 67.74 30.29 N/A 504 363 Other: 13.86 28.87 21.36 N/A 0 2 Chain A: 5.58 56.19 12.77 N/A 0 1623 Chain B: 5.56 67.74 12.50 N/A 0 1644 Chain S: 13.98 63.38 32.19 N/A 504 0 Histogram: Values Number of atoms 5.56 - 11.78 2132 11.78 - 17.99 684 17.99 - 24.21 303 24.21 - 30.43 221 30.43 - 36.65 179 36.65 - 42.87 141 42.87 - 49.08 74 49.08 - 55.30 27 55.30 - 61.52 7 61.52 - 67.74 3 =========================== Idealize ADP of riding H ========================== r_work=0.1239 r_free=0.1389 r_work=0.1240 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1240 r_free = 0.1389 target_work(ml) = 3.899 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1233 r_free = 0.1379 target_work(ml) = 3.893 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191137 (all), 2.01 % free)-----------| | | | r_work= 0.1233 r_free= 0.1379 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.892750 | | target function (ml) not normalized (work): 729096.504493 | | target function (ml) not normalized (free): 15228.030599 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1233 0.1378 n_refl.: 191137 re-set all scales: r(all,work,free)=0.1448 0.1447 0.1478 n_refl.: 191137 remove outliers: r(all,work,free)=0.1448 0.1447 0.1478 n_refl.: 191137 overall B=-0.03 to atoms: r(all,work,free)=0.1441 0.1440 0.1473 n_refl.: 191137 bulk-solvent and scaling: r(all,work,free)=0.1232 0.1229 0.1371 n_refl.: 191137 remove outliers: r(all,work,free)=0.1231 0.1228 0.1371 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 92.08 90 3 0.3778 393.895 353.249 0.399 0.946 0.220 13.296-10.522 98.02 98 1 0.2413 528.900 502.966 0.707 0.947 0.209 10.503-8.327 98.35 176 3 0.1974 562.248 562.855 0.883 0.947 0.174 8.318-6.595 100.00 360 8 0.2072 414.736 410.842 0.901 0.947 0.129 6.588-5.215 100.00 711 7 0.1832 381.101 370.833 0.887 0.947 0.110 5.214-4.128 98.38 1367 28 0.1153 557.435 552.347 0.973 0.947 0.080 4.126-3.266 94.74 2603 46 0.1104 508.132 500.909 1.034 0.947 0.014 3.266-2.585 99.86 5447 97 0.1094 342.774 339.113 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0971 258.603 255.820 1.035 0.946 0.000 2.046-1.619 99.39 21536 464 0.0983 153.054 151.409 1.058 0.945 0.000 1.619-1.281 98.00 42464 925 0.1056 82.395 81.485 1.055 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1687 44.202 42.320 1.042 0.939 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1148 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1228 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1228 r_free=0.1371 | n_water=867 | time (s): 3.170 (total time: 3.170) Filter (dist) r_work=0.1228 r_free=0.1371 | n_water=867 | time (s): 110.640 (total time: 113.810) Filter (q & B) r_work=0.1229 r_free=0.1371 | n_water=858 | time (s): 4.610 (total time: 118.420) Compute maps r_work=0.1229 r_free=0.1371 | n_water=858 | time (s): 1.550 (total time: 119.970) Filter (map) r_work=0.1249 r_free=0.1370 | n_water=726 | time (s): 4.790 (total time: 124.760) Find peaks r_work=0.1249 r_free=0.1370 | n_water=726 | time (s): 0.600 (total time: 125.360) Add new water r_work=0.1263 r_free=0.1391 | n_water=952 | time (s): 4.100 (total time: 129.460) Refine new water occ: r_work=0.1217 r_free=0.1361 adp: r_work=0.1209 r_free=0.1357 occ: r_work=0.1207 r_free=0.1359 adp: r_work=0.1207 r_free=0.1358 occ: r_work=0.1205 r_free=0.1359 adp: r_work=0.1205 r_free=0.1358 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1358 r_work=0.1205 r_free=0.1358 | n_water=952 | time (s): 339.830 (total time: 469.290) Filter (q & B) r_work=0.1209 r_free=0.1366 | n_water=866 | time (s): 5.380 (total time: 474.670) Filter (dist only) r_work=0.1209 r_free=0.1364 | n_water=865 | time (s): 114.500 (total time: 589.170) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.587892 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.688123 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 0.1208 0.1361 0.0153 0.036 1.1 6.1 0.0 0.0 0 0.794 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 13.61 1.53 1.828 14.219 15.688 3.875 11.96 13.58 1.62 1.921 14.190 15.688 3.865 Individual atomic B min max mean iso aniso Overall: 5.52 67.29 15.01 1.01 502 3267 Protein: 5.52 33.43 10.68 1.01 0 2902 Water: 5.84 67.29 29.53 N/A 502 363 Other: 14.00 27.90 20.95 N/A 0 2 Chain A: 5.56 55.14 12.64 N/A 0 1623 Chain B: 5.52 67.29 12.42 N/A 0 1644 Chain S: 5.84 63.41 31.18 N/A 502 0 Histogram: Values Number of atoms 5.52 - 11.70 2110 11.70 - 17.88 732 17.88 - 24.05 290 24.05 - 30.23 224 30.23 - 36.41 188 36.41 - 42.59 128 42.59 - 48.76 69 48.76 - 54.94 20 54.94 - 61.12 6 61.12 - 67.29 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1358 r_work=0.1196 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1358 target_work(ml) = 3.865 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1357 target_work(ml) = 3.863 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.863426 | | target function (ml) not normalized (work): 723584.884817 | | target function (ml) not normalized (free): 15133.052240 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1198 0.1195 0.1357 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1401 0.1400 0.1455 n_refl.: 191132 remove outliers: r(all,work,free)=0.1401 0.1400 0.1455 n_refl.: 191132 overall B=-0.03 to atoms: r(all,work,free)=0.1394 0.1393 0.1450 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1358 n_refl.: 191132 remove outliers: r(all,work,free)=0.1195 0.1192 0.1358 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 0.3806 356.787 320.334 0.408 0.953 0.244 13.296-10.522 96.04 96 1 0.2415 480.584 452.115 0.710 0.954 0.229 10.503-8.327 97.80 175 3 0.1983 502.068 502.499 0.872 0.954 0.182 8.318-6.595 100.00 360 8 0.2086 375.665 371.232 0.893 0.953 0.121 6.588-5.215 100.00 711 7 0.1855 345.198 335.616 0.879 0.953 0.097 5.214-4.128 98.38 1367 28 0.1162 504.920 500.130 0.966 0.954 0.070 4.126-3.266 94.74 2603 46 0.1112 460.262 453.694 1.026 0.953 0.005 3.266-2.585 99.86 5447 97 0.1077 310.482 307.213 1.015 0.952 0.000 2.585-2.046 97.45 10613 204 0.0935 234.241 231.779 1.028 0.952 0.000 2.046-1.619 99.39 21536 464 0.0919 138.635 137.263 1.052 0.950 0.000 1.619-1.281 98.00 42464 925 0.0987 74.633 73.887 1.051 0.947 0.000 1.281-0.980 96.53 101826 2055 0.1663 40.037 38.353 1.040 0.942 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1183 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1359 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1359 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1359 | n_water=865 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1192 r_free=0.1359 | n_water=865 | time (s): 103.230 (total time: 105.780) Filter (q & B) r_work=0.1193 r_free=0.1359 | n_water=856 | time (s): 5.390 (total time: 111.170) Compute maps r_work=0.1193 r_free=0.1359 | n_water=856 | time (s): 1.650 (total time: 112.820) Filter (map) r_work=0.1214 r_free=0.1358 | n_water=756 | time (s): 4.520 (total time: 117.340) Find peaks r_work=0.1214 r_free=0.1358 | n_water=756 | time (s): 0.770 (total time: 118.110) Add new water r_work=0.1224 r_free=0.1366 | n_water=981 | time (s): 4.710 (total time: 122.820) Refine new water occ: r_work=0.1189 r_free=0.1341 adp: r_work=0.1189 r_free=0.1341 occ: r_work=0.1186 r_free=0.1342 adp: r_work=0.1186 r_free=0.1342 occ: r_work=0.1185 r_free=0.1344 adp: r_work=0.1184 r_free=0.1343 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1343 r_work=0.1184 r_free=0.1343 | n_water=981 | time (s): 292.210 (total time: 415.030) Filter (q & B) r_work=0.1189 r_free=0.1357 | n_water=897 | time (s): 4.600 (total time: 419.630) Filter (dist only) r_work=0.1190 r_free=0.1357 | n_water=895 | time (s): 119.160 (total time: 538.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.543308 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.554703 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 0.1362 0.0168 0.036 1.1 5.8 0.0 0.3 0 0.772 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.62 1.68 1.798 14.206 15.555 3.764 11.98 13.67 1.69 1.876 14.173 15.555 3.761 Individual atomic B min max mean iso aniso Overall: 5.58 66.89 15.05 0.96 532 3267 Protein: 5.58 31.95 10.60 0.96 0 2902 Water: 5.95 66.89 29.43 N/A 532 363 Other: 13.84 26.43 20.13 N/A 0 2 Chain A: 5.58 54.16 12.54 N/A 0 1623 Chain B: 5.58 66.89 12.32 N/A 0 1644 Chain S: 5.95 63.40 31.11 N/A 532 0 Histogram: Values Number of atoms 5.58 - 11.71 2135 11.71 - 17.84 722 17.84 - 23.98 296 23.98 - 30.11 226 30.11 - 36.24 182 36.24 - 42.37 131 42.37 - 48.50 74 48.50 - 54.63 26 54.63 - 60.76 5 60.76 - 66.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1367 r_work=0.1199 r_free=0.1367 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1367 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1373 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760887 | | target function (ml) not normalized (work): 704369.059138 | | target function (ml) not normalized (free): 14747.367786 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1197 0.1373 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1401 0.1399 0.1485 n_refl.: 191129 remove outliers: r(all,work,free)=0.1401 0.1399 0.1485 n_refl.: 191129 overall B=-0.04 to atoms: r(all,work,free)=0.1393 0.1391 0.1480 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1196 0.1367 n_refl.: 191129 remove outliers: r(all,work,free)=0.1200 0.1196 0.1367 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 0.3721 356.787 321.632 0.395 0.953 0.221 13.296-10.522 96.04 96 1 0.2412 480.584 460.376 0.701 0.955 0.173 10.503-8.327 97.80 175 3 0.2091 502.068 496.751 0.863 0.955 0.150 8.318-6.595 100.00 360 8 0.2120 375.665 371.074 0.890 0.955 0.114 6.588-5.215 100.00 711 7 0.1891 345.198 335.526 0.880 0.955 0.093 5.214-4.128 98.38 1367 28 0.1203 504.920 499.761 0.966 0.955 0.070 4.126-3.266 94.74 2603 46 0.1140 460.262 453.491 1.027 0.955 0.005 3.266-2.585 99.86 5447 97 0.1104 310.482 307.117 1.014 0.954 0.000 2.585-2.046 97.45 10613 204 0.0946 234.241 231.792 1.027 0.954 0.000 2.046-1.619 99.39 21536 464 0.0916 138.635 137.300 1.051 0.952 0.000 1.619-1.281 98.00 42464 925 0.0976 74.633 73.911 1.050 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1653 40.037 38.361 1.039 0.946 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1345 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1367 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1367 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1367 | n_water=895 | time (s): 2.600 (total time: 2.600) Filter (dist) r_work=0.1196 r_free=0.1367 | n_water=895 | time (s): 106.810 (total time: 109.410) Filter (q & B) r_work=0.1196 r_free=0.1366 | n_water=886 | time (s): 4.770 (total time: 114.180) Compute maps r_work=0.1196 r_free=0.1366 | n_water=886 | time (s): 1.880 (total time: 116.060) Filter (map) r_work=0.1219 r_free=0.1361 | n_water=756 | time (s): 5.460 (total time: 121.520) Find peaks r_work=0.1219 r_free=0.1361 | n_water=756 | time (s): 0.660 (total time: 122.180) Add new water r_work=0.1231 r_free=0.1370 | n_water=967 | time (s): 4.120 (total time: 126.300) Refine new water occ: r_work=0.1197 r_free=0.1337 adp: r_work=0.1197 r_free=0.1337 occ: r_work=0.1194 r_free=0.1335 adp: r_work=0.1194 r_free=0.1336 occ: r_work=0.1193 r_free=0.1335 adp: r_work=0.1192 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1335 r_work=0.1192 r_free=0.1335 | n_water=967 | time (s): 249.320 (total time: 375.620) Filter (q & B) r_work=0.1196 r_free=0.1349 | n_water=887 | time (s): 5.020 (total time: 380.640) Filter (dist only) r_work=0.1196 r_free=0.1348 | n_water=886 | time (s): 111.460 (total time: 492.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.636301 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.565675 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 0.1354 0.0156 0.038 1.1 5.8 0.0 0.3 0 0.818 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.54 1.56 1.764 14.043 14.566 3.760 12.00 13.57 1.57 1.897 13.997 14.566 3.758 Individual atomic B min max mean iso aniso Overall: 5.59 65.80 14.83 0.90 523 3267 Protein: 5.59 29.33 10.50 0.90 0 2902 Water: 6.02 65.80 29.02 N/A 523 363 Other: 13.86 23.53 18.69 N/A 0 2 Chain A: 5.65 52.37 12.40 N/A 0 1623 Chain B: 5.59 65.80 12.19 N/A 0 1644 Chain S: 6.02 63.53 30.70 N/A 523 0 Histogram: Values Number of atoms 5.59 - 11.61 2115 11.61 - 17.63 766 17.63 - 23.65 282 23.65 - 29.67 214 29.67 - 35.69 178 35.69 - 41.71 127 41.71 - 47.74 72 47.74 - 53.76 29 53.76 - 59.78 5 59.78 - 65.80 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1357 r_work=0.1200 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1358 target_work(ml) = 3.758 | | 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) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191129 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.757548 | | target function (ml) not normalized (work): 703743.667024 | | target function (ml) not normalized (free): 14730.197442 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1357 n_refl.: 191129 re-set all scales: r(all,work,free)=0.1402 0.1401 0.1466 n_refl.: 191129 remove outliers: r(all,work,free)=0.1402 0.1401 0.1466 n_refl.: 191129 overall B=-0.23 to atoms: r(all,work,free)=0.1365 0.1364 0.1444 n_refl.: 191129 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1355 n_refl.: 191129 remove outliers: r(all,work,free)=0.1200 0.1196 0.1355 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3801 356.787 320.562 0.400 0.952 0.215 13.296-10.522 95.05 95 1 0.2287 479.686 455.325 0.722 0.954 0.167 10.503-8.327 97.80 175 3 0.2138 502.068 496.570 0.882 0.954 0.143 8.318-6.595 100.00 360 8 0.2113 375.665 371.647 0.909 0.954 0.104 6.588-5.215 100.00 711 7 0.1921 345.198 335.886 0.902 0.954 0.080 5.214-4.128 98.38 1367 28 0.1203 504.920 499.863 0.991 0.954 0.035 4.126-3.266 94.74 2603 46 0.1144 460.262 453.355 1.054 0.954 0.009 3.266-2.585 99.86 5447 97 0.1115 310.482 307.065 1.038 0.954 0.000 2.585-2.046 97.45 10613 204 0.0950 234.241 231.836 1.046 0.953 0.000 2.046-1.619 99.39 21536 464 0.0914 138.635 137.331 1.064 0.952 0.000 1.619-1.281 98.00 42464 925 0.0970 74.633 73.933 1.053 0.951 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.037 38.369 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=0.0516 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1355 | n_water=886 | time (s): 2.550 (total time: 2.550) Filter (dist) r_work=0.1197 r_free=0.1355 | n_water=886 | time (s): 103.720 (total time: 106.270) Filter (q & B) r_work=0.1197 r_free=0.1355 | n_water=877 | time (s): 4.900 (total time: 111.170) Compute maps r_work=0.1197 r_free=0.1355 | n_water=877 | time (s): 1.880 (total time: 113.050) Filter (map) r_work=0.1219 r_free=0.1356 | n_water=766 | time (s): 5.180 (total time: 118.230) Find peaks r_work=0.1219 r_free=0.1356 | n_water=766 | time (s): 0.900 (total time: 119.130) Add new water r_work=0.1227 r_free=0.1365 | n_water=982 | time (s): 5.160 (total time: 124.290) Refine new water occ: r_work=0.1194 r_free=0.1335 adp: r_work=0.1194 r_free=0.1335 occ: r_work=0.1192 r_free=0.1335 adp: r_work=0.1192 r_free=0.1335 occ: r_work=0.1190 r_free=0.1335 adp: r_work=0.1190 r_free=0.1335 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1335 r_work=0.1190 r_free=0.1335 | n_water=982 | time (s): 209.820 (total time: 334.110) Filter (q & B) r_work=0.1195 r_free=0.1344 | n_water=894 | time (s): 4.710 (total time: 338.820) Filter (dist only) r_work=0.1195 r_free=0.1343 | n_water=893 | time (s): 117.420 (total time: 456.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.590917 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.433835 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1199 0.1351 0.0152 0.038 1.1 5.3 0.0 0.3 0 0.795 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.51 1.52 1.721 13.738 13.434 3.759 12.02 13.55 1.53 1.776 13.715 13.434 3.759 Individual atomic B min max mean iso aniso Overall: 5.40 64.64 14.60 0.87 530 3267 Protein: 5.40 28.23 10.24 0.87 0 2902 Water: 5.82 64.64 28.78 N/A 530 363 Other: 13.70 22.10 17.90 N/A 0 2 Chain A: 5.49 51.84 12.10 N/A 0 1623 Chain B: 5.40 64.64 11.91 N/A 0 1644 Chain S: 5.82 63.34 30.65 N/A 530 0 Histogram: Values Number of atoms 5.40 - 11.33 2100 11.33 - 17.25 787 17.25 - 23.17 272 23.17 - 29.10 201 29.10 - 35.02 189 35.02 - 40.94 125 40.94 - 46.87 85 46.87 - 52.79 30 52.79 - 58.71 5 58.71 - 64.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1202 r_free=0.1356 r_work=0.1203 r_free=0.1356 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1356 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1355 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1201 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758122 | | target function (ml) not normalized (work): 703847.317772 | | target function (ml) not normalized (free): 14731.293252 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1201 0.1355 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1372 0.1370 0.1450 n_refl.: 191128 remove outliers: r(all,work,free)=0.1372 0.1370 0.1450 n_refl.: 191128 overall B=0.05 to atoms: r(all,work,free)=0.1378 0.1377 0.1453 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1195 0.1192 0.1338 n_refl.: 191128 remove outliers: r(all,work,free)=0.1195 0.1192 0.1338 n_refl.: 191128 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 92.08 90 3 0.3947 356.787 321.647 0.318 0.996 0.090 13.296-10.522 95.05 95 1 0.2312 479.686 463.045 0.689 0.997 0.110 10.503-8.327 97.80 175 3 0.2157 502.068 495.610 0.853 0.998 0.120 8.318-6.595 100.00 360 8 0.2108 375.665 371.063 0.874 0.997 0.096 6.588-5.215 100.00 711 7 0.1924 345.198 335.447 0.872 0.998 0.077 5.214-4.128 98.38 1367 28 0.1212 504.920 499.259 0.958 0.999 0.045 4.126-3.266 94.74 2603 46 0.1152 460.262 452.706 1.019 1.000 0.014 3.266-2.585 99.86 5447 97 0.1124 310.482 306.783 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0957 234.241 231.702 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0911 138.635 137.251 1.026 1.005 0.000 1.619-1.281 98.00 42464 925 0.0953 74.633 73.966 1.014 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1632 40.037 38.340 0.980 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0638 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1338 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1338 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1338 | n_water=893 | time (s): 3.400 (total time: 3.400) Filter (dist) r_work=0.1192 r_free=0.1338 | n_water=893 | time (s): 108.950 (total time: 112.350) Filter (q & B) r_work=0.1192 r_free=0.1339 | n_water=881 | time (s): 5.500 (total time: 117.850) Compute maps r_work=0.1192 r_free=0.1339 | n_water=881 | time (s): 2.120 (total time: 119.970) Filter (map) r_work=0.1214 r_free=0.1337 | n_water=774 | time (s): 4.960 (total time: 124.930) Find peaks r_work=0.1214 r_free=0.1337 | n_water=774 | time (s): 0.580 (total time: 125.510) Add new water r_work=0.1221 r_free=0.1344 | n_water=972 | time (s): 3.930 (total time: 129.440) Refine new water occ: r_work=0.1190 r_free=0.1322 adp: r_work=0.1190 r_free=0.1322 occ: r_work=0.1188 r_free=0.1321 adp: r_work=0.1188 r_free=0.1322 occ: r_work=0.1187 r_free=0.1322 adp: r_work=0.1186 r_free=0.1322 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1322 r_work=0.1186 r_free=0.1322 | n_water=972 | time (s): 239.800 (total time: 369.240) Filter (q & B) r_work=0.1191 r_free=0.1330 | n_water=899 | time (s): 4.860 (total time: 374.100) Filter (dist only) r_work=0.1191 r_free=0.1329 | n_water=898 | time (s): 115.380 (total time: 489.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.528966 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.008996 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1338 0.0146 0.038 1.1 7.5 0.0 0.3 0 0.764 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 13.38 1.46 1.672 13.728 14.009 3.757 11.91 13.37 1.46 1.683 13.721 14.009 3.754 Individual atomic B min max mean iso aniso Overall: 5.48 63.81 14.65 0.87 535 3267 Protein: 5.48 28.20 10.31 0.87 0 2902 Water: 5.92 63.81 28.67 N/A 535 363 Other: 13.78 22.12 17.95 N/A 0 2 Chain A: 5.58 51.64 12.13 N/A 0 1623 Chain B: 5.48 63.81 11.95 N/A 0 1644 Chain S: 5.92 63.47 30.59 N/A 535 0 Histogram: Values Number of atoms 5.48 - 11.31 2072 11.31 - 17.15 811 17.15 - 22.98 265 22.98 - 28.81 205 28.81 - 34.64 194 34.64 - 40.48 129 40.48 - 46.31 87 46.31 - 52.14 31 52.14 - 57.97 5 57.97 - 63.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1337 r_work=0.1191 r_free=0.1337 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1337 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1336 target_work(ml) = 3.753 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191128 (all), 2.01 % free)-----------| | | | r_work= 0.1190 r_free= 0.1336 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.753381 | | target function (ml) not normalized (work): 702959.404860 | | target function (ml) not normalized (free): 14719.086606 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1190 0.1336 n_refl.: 191128 re-set all scales: r(all,work,free)=0.1384 0.1383 0.1456 n_refl.: 191128 remove outliers: r(all,work,free)=0.1384 0.1383 0.1456 n_refl.: 191128 overall B=0.01 to atoms: r(all,work,free)=0.1386 0.1385 0.1457 n_refl.: 191128 bulk-solvent and scaling: r(all,work,free)=0.1191 0.1188 0.1334 n_refl.: 191128 remove outliers: r(all,work,free)=0.1191 0.1188 0.1334 n_refl.: 191127 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 91.09 89 3 0.3795 356.462 315.886 0.310 0.986 0.070 13.296-10.522 95.05 95 1 0.2328 479.686 463.062 0.690 0.987 0.100 10.503-8.327 97.80 175 3 0.2155 502.068 495.569 0.858 0.987 0.110 8.318-6.595 100.00 360 8 0.2100 375.665 370.492 0.880 0.987 0.091 6.588-5.215 100.00 711 7 0.1925 345.198 335.736 0.879 0.988 0.073 5.214-4.128 98.38 1367 28 0.1219 504.920 499.219 0.966 0.989 0.035 4.126-3.266 94.74 2603 46 0.1157 460.262 452.772 1.030 0.990 0.009 3.266-2.585 99.86 5447 97 0.1119 310.482 306.921 1.013 0.991 0.000 2.585-2.046 97.45 10613 204 0.0956 234.241 231.748 1.021 0.992 0.000 2.046-1.619 99.39 21536 464 0.0909 138.635 137.273 1.038 0.996 0.000 1.619-1.281 98.00 42464 925 0.0945 74.633 73.988 1.028 1.001 0.000 1.281-0.980 96.53 101826 2055 0.1627 40.037 38.332 0.996 1.010 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0209 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1334 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1334 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1334 | n_water=898 | time (s): 2.680 (total time: 2.680) Filter (dist) r_work=0.1188 r_free=0.1334 | n_water=898 | time (s): 107.280 (total time: 109.960) Filter (q & B) r_work=0.1189 r_free=0.1335 | n_water=890 | time (s): 5.570 (total time: 115.530) Compute maps r_work=0.1189 r_free=0.1335 | n_water=890 | time (s): 1.990 (total time: 117.520) Filter (map) r_work=0.1211 r_free=0.1342 | n_water=782 | time (s): 4.590 (total time: 122.110) Find peaks r_work=0.1211 r_free=0.1342 | n_water=782 | time (s): 0.710 (total time: 122.820) Add new water r_work=0.1217 r_free=0.1347 | n_water=978 | time (s): 5.270 (total time: 128.090) Refine new water occ: r_work=0.1187 r_free=0.1325 adp: r_work=0.1187 r_free=0.1324 occ: r_work=0.1185 r_free=0.1325 adp: r_work=0.1185 r_free=0.1325 occ: r_work=0.1184 r_free=0.1325 adp: r_work=0.1184 r_free=0.1325 ADP+occupancy (water only), MIN, final r_work=0.1184 r_free=0.1325 r_work=0.1184 r_free=0.1325 | n_water=978 | time (s): 231.340 (total time: 359.430) Filter (q & B) r_work=0.1188 r_free=0.1333 | n_water=906 | time (s): 3.960 (total time: 363.390) Filter (dist only) r_work=0.1188 r_free=0.1332 | n_water=905 | time (s): 118.430 (total time: 481.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.524372 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.202903 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1338 0.0147 0.038 1.1 6.1 0.0 0.3 0 0.762 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 13.38 1.47 1.677 13.734 13.203 3.754 11.93 13.42 1.49 1.675 13.734 13.203 3.754 Individual atomic B min max mean iso aniso Overall: 5.53 63.64 14.64 0.86 542 3267 Protein: 5.53 28.09 10.34 0.86 0 2902 Water: 5.91 63.64 28.44 N/A 542 363 Other: 13.80 22.15 17.98 N/A 0 2 Chain A: 5.61 51.61 12.13 N/A 0 1623 Chain B: 5.53 63.64 11.96 N/A 0 1644 Chain S: 5.91 63.50 30.27 N/A 542 0 Histogram: Values Number of atoms 5.53 - 11.34 2070 11.34 - 17.16 823 17.16 - 22.97 265 22.97 - 28.78 207 28.78 - 34.59 204 34.59 - 40.40 119 40.40 - 46.21 84 46.21 - 52.02 29 52.02 - 57.83 5 57.83 - 63.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1342 r_work=0.1193 r_free=0.1342 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1342 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1344 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191127 (all), 2.01 % free)-----------| | | | r_work= 0.1192 r_free= 0.1344 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754250 | | target function (ml) not normalized (work): 703118.453143 | | target function (ml) not normalized (free): 14723.075495 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1195 0.1192 0.1344 n_refl.: 191127 re-set all scales: r(all,work,free)=0.1387 0.1385 0.1477 n_refl.: 191127 remove outliers: r(all,work,free)=0.1387 0.1385 0.1477 n_refl.: 191127 overall B=-0.00 to atoms: r(all,work,free)=0.1386 0.1385 0.1477 n_refl.: 191127 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1191 0.1343 n_refl.: 191127 remove outliers: r(all,work,free)=0.1194 0.1191 0.1343 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3702 356.229 321.776 0.315 0.987 0.060 13.296-10.522 95.05 95 1 0.2302 479.686 462.897 0.682 0.988 0.090 10.503-8.327 97.80 175 3 0.2208 502.068 494.176 0.853 0.989 0.100 8.318-6.595 100.00 360 8 0.2103 375.665 370.391 0.876 0.989 0.083 6.588-5.215 100.00 711 7 0.1954 345.198 335.632 0.875 0.989 0.067 5.214-4.128 98.38 1367 28 0.1233 504.920 499.140 0.966 0.990 0.035 4.126-3.266 94.74 2603 46 0.1166 460.262 452.549 1.028 0.991 0.009 3.266-2.585 99.86 5447 97 0.1126 310.482 306.836 1.012 0.992 0.000 2.585-2.046 97.45 10613 204 0.0960 234.241 231.715 1.020 0.995 0.000 2.046-1.619 99.39 21536 464 0.0909 138.635 137.269 1.037 0.999 0.000 1.619-1.281 98.00 42464 925 0.0944 74.633 73.985 1.028 1.004 0.000 1.281-0.980 96.53 101826 2055 0.1628 40.037 38.315 0.997 1.015 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0072 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1191 r_free=0.1343 After: r_work=0.1192 r_free=0.1343 ================================== NQH flips ================================== r_work=0.1192 r_free=0.1343 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1343 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1343 | n_water=905 | time (s): 3.030 (total time: 3.030) Filter (dist) r_work=0.1192 r_free=0.1344 | n_water=904 | time (s): 115.050 (total time: 118.080) Filter (q & B) r_work=0.1192 r_free=0.1343 | n_water=894 | time (s): 4.900 (total time: 122.980) Compute maps r_work=0.1192 r_free=0.1343 | n_water=894 | time (s): 2.440 (total time: 125.420) Filter (map) r_work=0.1214 r_free=0.1346 | n_water=789 | time (s): 4.350 (total time: 129.770) Find peaks r_work=0.1214 r_free=0.1346 | n_water=789 | time (s): 0.700 (total time: 130.470) Add new water r_work=0.1220 r_free=0.1351 | n_water=993 | time (s): 4.790 (total time: 135.260) Refine new water occ: r_work=0.1189 r_free=0.1331 adp: r_work=0.1189 r_free=0.1332 occ: r_work=0.1187 r_free=0.1331 adp: r_work=0.1187 r_free=0.1332 occ: r_work=0.1186 r_free=0.1331 adp: r_work=0.1186 r_free=0.1332 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1332 r_work=0.1186 r_free=0.1332 | n_water=993 | time (s): 197.210 (total time: 332.470) Filter (q & B) r_work=0.1190 r_free=0.1337 | n_water=907 | time (s): 4.790 (total time: 337.260) Filter (dist only) r_work=0.1191 r_free=0.1336 | n_water=906 | time (s): 112.750 (total time: 450.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.569726 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 13.081257 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1344 0.0149 0.039 1.2 8.5 0.0 0.3 0 0.785 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.44 1.49 1.675 13.744 13.081 3.757 11.97 13.47 1.50 1.683 13.741 13.081 3.757 Individual atomic B min max mean iso aniso Overall: 5.56 63.45 14.64 0.85 543 3267 Protein: 5.56 27.80 10.34 0.85 0 2902 Water: 5.94 63.45 28.41 N/A 543 363 Other: 13.85 22.01 17.93 N/A 0 2 Chain A: 5.66 51.35 12.12 N/A 0 1623 Chain B: 5.56 62.86 11.95 N/A 0 1644 Chain S: 5.94 63.45 30.33 N/A 543 0 Histogram: Values Number of atoms 5.56 - 11.35 2066 11.35 - 17.14 832 17.14 - 22.93 267 22.93 - 28.71 208 28.71 - 34.50 194 34.50 - 40.29 117 40.29 - 46.08 86 46.08 - 51.87 30 51.87 - 57.66 7 57.66 - 63.45 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1347 r_work=0.1197 r_free=0.1347 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1347 target_work(ml) = 3.758 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1347 target_work(ml) = 3.757 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191126 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1347 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.757394 | | target function (ml) not normalized (work): 703703.442915 | | target function (ml) not normalized (free): 14732.847884 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.97 7394 127 0.1356 0.1423 5.6829 5.753| | 2: 2.94 - 2.33 1.00 7339 128 0.1076 0.1335 5.0764 5.1744| | 3: 2.33 - 2.04 0.96 6939 150 0.0909 0.1162 4.6588 4.7338| | 4: 2.04 - 1.85 1.00 7170 155 0.0905 0.1064 4.3956 4.5728| | 5: 1.85 - 1.72 0.99 7113 159 0.0935 0.0992 4.1554 4.2459| | 6: 1.72 - 1.62 0.99 7102 142 0.0903 0.1091 3.954 4.0822| | 7: 1.62 - 1.54 0.99 7104 148 0.0895 0.0969 3.8058 3.9384| | 8: 1.54 - 1.47 0.96 6798 152 0.0900 0.1303 3.7089 3.9043| | 9: 1.47 - 1.41 0.98 6938 155 0.0932 0.1123 3.6276 3.7532| | 10: 1.41 - 1.36 0.99 7022 150 0.0981 0.1191 3.5612 3.6779| | 11: 1.36 - 1.32 0.99 6997 151 0.1000 0.1155 3.493 3.5995| | 12: 1.32 - 1.28 0.98 6975 149 0.1040 0.1129 3.4654 3.5847| | 13: 1.28 - 1.25 0.98 6907 166 0.1048 0.1254 3.4434 3.5741| | 14: 1.25 - 1.22 0.98 7015 112 0.1110 0.1600 3.4367 3.6917| | 15: 1.22 - 1.19 0.98 6956 137 0.1172 0.1239 3.4514 3.4871| | 16: 1.19 - 1.17 0.93 6604 132 0.1256 0.1534 3.4676 3.6517| | 17: 1.17 - 1.14 0.98 6940 135 0.1303 0.1223 3.4354 3.4407| | 18: 1.14 - 1.12 0.98 6875 142 0.1389 0.1719 3.441 3.5354| | 19: 1.12 - 1.10 0.97 6948 106 0.1474 0.1763 3.4218 3.5944| | 20: 1.10 - 1.08 0.97 6884 147 0.1589 0.1589 3.4127 3.4386| | 21: 1.08 - 1.07 0.97 6852 152 0.1732 0.2144 3.4204 3.504| | 22: 1.07 - 1.05 0.97 6836 135 0.1909 0.1957 3.4148 3.4144| | 23: 1.05 - 1.03 0.97 6827 159 0.2124 0.2018 3.4348 3.487| | 24: 1.03 - 1.02 0.96 6784 133 0.2338 0.2264 3.4375 3.5149| | 25: 1.02 - 1.01 0.93 6552 130 0.2618 0.2515 3.4505 3.5221| | 26: 1.01 - 0.99 0.96 6767 158 0.2761 0.2863 3.4167 3.4234| | 27: 0.99 - 0.98 0.94 6647 131 0.3048 0.2809 3.4701 3.3975| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7394 127 0.93 11.47 1.00 0.96 10938.49| | 2: 2.94 - 2.33 7339 128 0.93 12.60 0.99 0.95 5032.34| | 3: 2.33 - 2.04 6939 150 0.96 7.56 1.01 0.95 1690.18| | 4: 2.04 - 1.85 7170 155 0.96 7.63 1.00 0.95 1004.00| | 5: 1.85 - 1.72 7113 159 0.96 8.09 1.00 0.96 637.39| | 6: 1.72 - 1.62 7102 142 0.96 8.08 1.00 0.96 448.11| | 7: 1.62 - 1.54 7104 148 0.96 8.18 1.01 0.97 340.39| | 8: 1.54 - 1.47 6798 152 0.96 8.30 1.01 0.97 280.95| | 9: 1.47 - 1.41 6938 155 0.96 8.50 1.00 0.98 232.34| | 10: 1.41 - 1.36 7022 150 0.96 8.99 1.00 0.97 204.58| | 11: 1.36 - 1.32 6997 151 0.96 9.05 0.99 0.96 177.89| | 12: 1.32 - 1.28 6975 149 0.96 9.11 0.98 0.95 163.45| | 13: 1.28 - 1.25 6907 166 0.96 9.64 1.01 0.96 160.66| | 14: 1.25 - 1.22 7015 112 0.95 10.78 1.01 0.96 164.65| | 15: 1.22 - 1.19 6956 137 0.95 11.29 1.01 0.98 167.34| | 16: 1.19 - 1.17 6604 132 0.95 11.43 1.01 0.96 160.18| | 17: 1.17 - 1.14 6940 135 0.94 12.25 1.01 0.96 153.96| | 18: 1.14 - 1.12 6875 142 0.94 12.78 1.01 0.95 148.23| | 19: 1.12 - 1.10 6948 106 0.93 14.21 1.00 0.95 152.08| | 20: 1.10 - 1.08 6884 147 0.92 15.29 1.00 0.94 151.20| | 21: 1.08 - 1.07 6852 152 0.91 16.67 1.00 0.93 153.82| | 22: 1.07 - 1.05 6836 135 0.89 18.32 0.99 0.93 155.23| | 23: 1.05 - 1.03 6827 159 0.87 20.52 0.99 0.92 164.97| | 24: 1.03 - 1.02 6784 133 0.85 23.20 0.99 0.93 179.53| | 25: 1.02 - 1.01 6552 130 0.83 25.19 0.98 0.90 182.56| | 26: 1.01 - 0.99 6767 158 0.81 26.70 0.98 0.88 177.25| | 27: 0.99 - 0.98 6647 131 0.82 26.40 0.99 0.87 161.95| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 148.23 max = 10938.49 mean = 912.08| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.99 mean = 13.32| |phase err.(test): min = 0.00 max = 88.38 mean = 13.47| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1196 0.1347 n_refl.: 191126 re-set all scales: r(all,work,free)=0.1391 0.1390 0.1484 n_refl.: 191126 remove outliers: r(all,work,free)=0.1391 0.1390 0.1484 n_refl.: 191126 overall B=-0.05 to atoms: r(all,work,free)=0.1384 0.1382 0.1479 n_refl.: 191126 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1346 n_refl.: 191126 remove outliers: r(all,work,free)=0.1198 0.1195 0.1346 n_refl.: 191126 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 90.10 88 3 0.3729 356.229 327.381 0.336 0.919 0.060 13.296-10.522 95.05 95 1 0.2340 479.686 461.834 0.712 0.920 0.084 10.503-8.327 97.80 175 3 0.2198 502.068 494.372 0.894 0.921 0.085 8.318-6.595 100.00 360 8 0.2100 375.665 370.652 0.915 0.920 0.078 6.588-5.215 100.00 711 7 0.1954 345.198 335.432 0.916 0.921 0.070 5.214-4.128 98.38 1367 28 0.1232 504.920 499.120 1.012 0.922 0.030 4.126-3.266 94.74 2603 46 0.1169 460.262 452.592 1.078 0.923 0.005 3.266-2.585 99.86 5447 97 0.1125 310.482 306.898 1.061 0.924 0.000 2.585-2.046 97.45 10613 204 0.0968 234.241 231.686 1.068 0.927 0.000 2.046-1.619 99.39 21536 464 0.0915 138.635 137.263 1.084 0.931 0.000 1.619-1.281 98.00 42464 925 0.0952 74.633 73.972 1.073 0.937 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.037 38.309 1.038 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0117 ================= 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 : 0.2034 0.2001 0.082 5.269 5.2 78.0 14.6 805 0.000 1_bss: 0.1798 0.1935 0.082 5.269 5.2 78.0 14.6 805 0.000 1_settarget: 0.1798 0.1935 0.082 5.269 5.2 78.0 14.6 805 0.000 1_nqh: 0.1806 0.1938 0.082 5.269 5.2 78.0 14.6 805 0.002 1_weight: 0.1806 0.1938 0.082 5.269 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1270 0.1494 0.037 1.182 5.2 78.0 14.6 805 0.151 1_adp: 0.1297 0.1555 0.037 1.182 5.2 73.0 15.1 805 0.151 1_regHadp: 0.1296 0.1550 0.037 1.182 5.2 73.0 15.1 805 0.151 1_occ: 0.1281 0.1538 0.037 1.182 5.2 73.0 15.1 805 0.151 2_bss: 0.1273 0.1529 0.037 1.182 5.4 73.2 15.2 805 0.151 2_settarget: 0.1273 0.1529 0.037 1.182 5.4 73.2 15.2 805 0.151 2_updatecdl: 0.1273 0.1529 0.037 1.194 5.4 73.2 15.2 805 0.151 2_nqh: 0.1276 0.1537 0.037 1.194 5.4 73.2 15.2 805 0.150 2_sol: 0.1273 0.1499 0.037 1.194 5.4 73.2 16.3 891 n/a 2_weight: 0.1273 0.1499 0.037 1.194 5.4 73.2 16.3 891 n/a 2_xyzrec: 0.1259 0.1520 0.041 1.134 5.4 73.2 16.3 891 n/a 2_adp: 0.1235 0.1506 0.041 1.134 5.5 68.2 16.4 891 n/a 2_regHadp: 0.1236 0.1507 0.041 1.134 5.5 68.2 16.4 891 n/a 2_occ: 0.1229 0.1504 0.041 1.134 5.5 68.2 16.4 891 n/a 3_bss: 0.1236 0.1512 0.041 1.134 5.4 68.2 16.3 891 n/a 3_settarget: 0.1236 0.1512 0.041 1.134 5.4 68.2 16.3 891 n/a 3_updatecdl: 0.1236 0.1512 0.041 1.145 5.4 68.2 16.3 891 n/a 3_nqh: 0.1236 0.1512 0.041 1.145 5.4 68.2 16.3 891 n/a 3_sol: 0.1255 0.1506 0.041 1.145 5.4 68.2 15.4 867 n/a 3_weight: 0.1255 0.1506 0.041 1.145 5.4 68.2 15.4 867 n/a 3_xyzrec: 0.1241 0.1428 0.036 1.108 5.4 68.2 15.4 867 n/a 3_adp: 0.1239 0.1389 0.036 1.108 5.6 67.7 15.2 867 n/a 3_regHadp: 0.1240 0.1389 0.036 1.108 5.6 67.7 15.2 867 n/a 3_occ: 0.1233 0.1379 0.036 1.108 5.6 67.7 15.2 867 n/a 4_bss: 0.1228 0.1371 0.036 1.108 5.5 67.7 15.2 867 n/a 4_settarget: 0.1228 0.1371 0.036 1.108 5.5 67.7 15.2 867 n/a 4_updatecdl: 0.1228 0.1371 0.036 1.109 5.5 67.7 15.2 867 n/a 4_nqh: 0.1228 0.1371 0.036 1.109 5.5 67.7 15.2 867 n/a 4_sol: 0.1209 0.1364 0.036 1.109 5.5 67.7 15.1 865 n/a 4_weight: 0.1209 0.1364 0.036 1.109 5.5 67.7 15.1 865 n/a 4_xyzrec: 0.1208 0.1361 0.036 1.132 5.5 67.7 15.1 865 n/a 4_adp: 0.1196 0.1358 0.036 1.132 5.5 67.3 15.0 865 n/a 4_regHadp: 0.1196 0.1358 0.036 1.132 5.5 67.3 15.0 865 n/a 4_occ: 0.1195 0.1357 0.036 1.132 5.5 67.3 15.0 865 n/a 5_bss: 0.1192 0.1359 0.036 1.132 5.5 67.3 15.0 865 n/a 5_settarget: 0.1192 0.1359 0.036 1.132 5.5 67.3 15.0 865 n/a 5_updatecdl: 0.1192 0.1359 0.036 1.133 5.5 67.3 15.0 865 n/a 5_nqh: 0.1192 0.1359 0.036 1.133 5.5 67.3 15.0 865 n/a 5_sol: 0.1190 0.1357 0.036 1.133 5.5 67.3 15.1 895 n/a 5_weight: 0.1190 0.1357 0.036 1.133 5.5 67.3 15.1 895 n/a 5_xyzrec: 0.1194 0.1362 0.036 1.132 5.5 67.3 15.1 895 n/a 5_adp: 0.1198 0.1367 0.036 1.132 5.6 66.9 15.0 895 n/a 5_regHadp: 0.1199 0.1367 0.036 1.132 5.6 66.9 15.0 895 n/a 5_occ: 0.1197 0.1373 0.036 1.132 5.6 66.9 15.0 895 n/a 6_bss: 0.1196 0.1367 0.036 1.132 5.5 66.9 15.0 895 n/a 6_settarget: 0.1196 0.1367 0.036 1.132 5.5 66.9 15.0 895 n/a 6_updatecdl: 0.1196 0.1367 0.036 1.131 5.5 66.9 15.0 895 n/a 6_nqh: 0.1196 0.1367 0.036 1.131 5.5 66.9 15.0 895 n/a 6_sol: 0.1196 0.1348 0.036 1.131 5.5 66.9 14.9 886 n/a 6_weight: 0.1196 0.1348 0.036 1.131 5.5 66.9 14.9 886 n/a 6_xyzrec: 0.1197 0.1354 0.038 1.133 5.5 66.9 14.9 886 n/a 6_adp: 0.1200 0.1357 0.038 1.133 5.6 65.8 14.8 886 n/a 6_regHadp: 0.1200 0.1358 0.038 1.133 5.6 65.8 14.8 886 n/a 6_occ: 0.1198 0.1357 0.038 1.133 5.6 65.8 14.8 886 n/a 7_bss: 0.1197 0.1355 0.038 1.133 5.4 65.6 14.6 886 n/a 7_settarget: 0.1197 0.1355 0.038 1.133 5.4 65.6 14.6 886 n/a 7_updatecdl: 0.1197 0.1355 0.038 1.134 5.4 65.6 14.6 886 n/a 7_nqh: 0.1197 0.1355 0.038 1.134 5.4 65.6 14.6 886 n/a 7_sol: 0.1195 0.1343 0.038 1.134 5.4 65.6 14.6 893 n/a 7_weight: 0.1195 0.1343 0.038 1.134 5.4 65.6 14.6 893 n/a 7_xyzrec: 0.1199 0.1351 0.038 1.134 5.4 65.6 14.6 893 n/a 7_adp: 0.1202 0.1356 0.038 1.134 5.4 64.6 14.6 893 n/a 7_regHadp: 0.1203 0.1356 0.038 1.134 5.4 64.6 14.6 893 n/a 7_occ: 0.1201 0.1355 0.038 1.134 5.4 64.6 14.6 893 n/a 8_bss: 0.1192 0.1338 0.038 1.134 5.5 64.7 14.7 893 n/a 8_settarget: 0.1192 0.1338 0.038 1.134 5.5 64.7 14.7 893 n/a 8_updatecdl: 0.1192 0.1338 0.038 1.133 5.5 64.7 14.7 893 n/a 8_nqh: 0.1192 0.1338 0.038 1.133 5.5 64.7 14.7 893 n/a 8_sol: 0.1191 0.1329 0.038 1.133 5.5 64.7 14.7 898 n/a 8_weight: 0.1191 0.1329 0.038 1.133 5.5 64.7 14.7 898 n/a 8_xyzrec: 0.1192 0.1338 0.038 1.115 5.5 64.7 14.7 898 n/a 8_adp: 0.1191 0.1337 0.038 1.115 5.5 63.8 14.6 898 n/a 8_regHadp: 0.1191 0.1337 0.038 1.115 5.5 63.8 14.6 898 n/a 8_occ: 0.1190 0.1336 0.038 1.115 5.5 63.8 14.6 898 n/a 9_bss: 0.1188 0.1334 0.038 1.115 5.5 63.8 14.7 898 n/a 9_settarget: 0.1188 0.1334 0.038 1.115 5.5 63.8 14.7 898 n/a 9_updatecdl: 0.1188 0.1334 0.038 1.116 5.5 63.8 14.7 898 n/a 9_nqh: 0.1188 0.1334 0.038 1.116 5.5 63.8 14.7 898 n/a 9_sol: 0.1188 0.1332 0.038 1.116 5.5 63.8 14.6 905 n/a 9_weight: 0.1188 0.1332 0.038 1.116 5.5 63.8 14.6 905 n/a 9_xyzrec: 0.1191 0.1338 0.038 1.120 5.5 63.8 14.6 905 n/a 9_adp: 0.1193 0.1342 0.038 1.120 5.5 63.6 14.6 905 n/a 9_regHadp: 0.1193 0.1342 0.038 1.120 5.5 63.6 14.6 905 n/a 9_occ: 0.1192 0.1344 0.038 1.120 5.5 63.6 14.6 905 n/a 10_bss: 0.1191 0.1343 0.038 1.120 5.5 63.6 14.6 905 n/a 10_settarget: 0.1191 0.1343 0.038 1.120 5.5 63.6 14.6 905 n/a 10_updatecdl: 0.1191 0.1343 0.038 1.119 5.5 63.6 14.6 905 n/a 10_setrh: 0.1192 0.1343 0.038 1.119 5.5 63.6 14.6 905 n/a 10_nqh: 0.1192 0.1343 0.038 1.119 5.5 63.6 14.6 905 n/a 10_sol: 0.1191 0.1336 0.038 1.119 5.5 63.6 14.6 906 n/a 10_weight: 0.1191 0.1336 0.038 1.119 5.5 63.6 14.6 906 n/a 10_xyzrec: 0.1195 0.1344 0.039 1.185 5.5 63.6 14.6 906 n/a 10_adp: 0.1197 0.1347 0.039 1.185 5.6 63.4 14.6 906 n/a 10_regHadp: 0.1197 0.1347 0.039 1.185 5.6 63.4 14.6 906 n/a 10_occ: 0.1196 0.1347 0.039 1.185 5.6 63.4 14.6 906 n/a end: 0.1195 0.1346 0.039 1.185 5.5 63.4 14.6 906 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3074067_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_3074067_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.9400 Refinement macro-cycles (run) : 12067.6100 Write final files (write_after_run_outputs) : 163.5300 Total : 12239.0800 Total CPU time: 3.41 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:41:12 PST -0800 (1736736072.11 s) Start R-work = 0.1798, R-free = 0.1935 Final R-work = 0.1195, R-free = 0.1346 =============================================================================== Job complete usr+sys time: 12530.23 seconds wall clock time: 209 minutes 51.10 seconds (12591.10 seconds total)