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_4047050.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif Found restraint, /net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" restraint_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/GLX.cif" default_restraint = "/net/anaconda/raid1/afonine/work/ANI/5SY6/ASX.cif" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4047050.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY4/shaken/shake_4047050.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY4/params_unrestrained.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY4/5SY4.mtz" } 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 2 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: 2.57, per 1000 atoms: 0.38 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: 2.783 distance_ideal: 2.720 ideal - model: -0.063 slack: 0.000 delta_slack: -0.063 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: 2.760 distance_ideal: 2.710 ideal - model: -0.050 slack: 0.000 delta_slack: -0.050 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: 0.91 Conformation dependent library (CDL) restraints added in 130.4 milliseconds Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.03: 795 1.03 - 1.27: 2563 1.27 - 1.51: 1619 1.51 - 1.75: 942 1.75 - 1.98: 15 Bond restraints: 5934 Sorted by residual: bond pdb=" CA VAL A 114 " pdb=" CB VAL A 114 " ideal model delta sigma weight residual 1.539 1.683 -0.144 5.40e-03 3.43e+04 7.12e+02 bond pdb=" C ALA B 10 " pdb=" O ALA B 10 " ideal model delta sigma weight residual 1.236 1.453 -0.217 8.90e-03 1.26e+04 5.96e+02 bond pdb=" CA ILE B 134 " pdb=" C ILE B 134 " ideal model delta sigma weight residual 1.523 1.710 -0.187 8.80e-03 1.29e+04 4.51e+02 bond pdb=" N VAL B 181 " pdb=" H VAL B 181 " ideal model delta sigma weight residual 0.860 1.234 -0.374 2.00e-02 2.50e+03 3.49e+02 bond pdb=" N ASP A 68 " pdb=" H ASP A 68 " ideal model delta sigma weight residual 0.860 1.227 -0.367 2.00e-02 2.50e+03 3.36e+02 ... (remaining 5929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 5750 4.30 - 8.61: 3581 8.61 - 12.91: 1270 12.91 - 17.21: 194 17.21 - 21.51: 15 Bond angle restraints: 10810 Sorted by residual: angle pdb=" NE ARG B 27 " pdb=" CZ ARG B 27 " pdb=" NH2 ARG B 27 " ideal model delta sigma weight residual 119.20 137.10 -17.90 9.00e-01 1.23e+00 3.96e+02 angle pdb=" O ILE B 70 " pdb=" C ILE B 70 " pdb=" N VAL B 71 " ideal model delta sigma weight residual 123.14 142.50 -19.36 1.02e+00 9.61e-01 3.60e+02 angle pdb=" CA THR A 91 " pdb=" C THR A 91 " pdb=" O THR A 91 " ideal model delta sigma weight residual 120.92 136.98 -16.06 1.12e+00 7.97e-01 2.06e+02 angle pdb=" O VAL A 62 " pdb=" C VAL A 62 " pdb=" N ALA A 63 " ideal model delta sigma weight residual 122.06 136.21 -14.15 9.90e-01 1.02e+00 2.04e+02 angle pdb=" CA ASP A 68 " pdb=" C ASP A 68 " pdb=" O ASP A 68 " ideal model delta sigma weight residual 119.27 103.21 16.06 1.17e+00 7.31e-01 1.88e+02 ... (remaining 10805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.53: 1827 16.53 - 33.05: 147 33.05 - 49.58: 46 49.58 - 66.10: 25 66.10 - 82.62: 5 Dihedral angle restraints: 2050 sinusoidal: 1530 harmonic: 520 Sorted by residual: dihedral pdb=" CA TRP A 139 " pdb=" C TRP A 139 " pdb=" N LEU A 140 " pdb=" CA LEU A 140 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLN B 184 " pdb=" C GLN B 184 " pdb=" N LEU B 185 " pdb=" CA LEU B 185 " ideal model delta harmonic sigma weight residual 180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.30e+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 -156.43 -23.57 0 5.00e+00 4.00e-02 2.22e+01 ... (remaining 2047 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.225: 199 0.225 - 0.450: 165 0.450 - 0.675: 93 0.675 - 0.899: 31 0.899 - 1.124: 4 Chirality restraints: 492 Sorted by residual: chirality pdb=" CA THR A 91 " pdb=" N THR A 91 " pdb=" C THR A 91 " pdb=" CB THR A 91 " both_signs ideal model delta sigma weight residual False 2.53 1.40 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CA GLN B 156 " pdb=" N GLN B 156 " pdb=" C GLN B 156 " pdb=" CB GLN B 156 " both_signs ideal model delta sigma weight residual False 2.51 1.41 1.10 2.00e-01 2.50e+01 3.04e+01 chirality pdb=" CA VAL B 114 " pdb=" N VAL B 114 " pdb=" C VAL B 114 " pdb=" CB VAL B 114 " both_signs ideal model delta sigma weight residual False 2.44 1.50 0.94 2.00e-01 2.50e+01 2.23e+01 ... (remaining 489 not shown) Planarity restraints: 882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 194 " -0.049 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG TYR A 194 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 194 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 TYR A 194 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 TYR A 194 " 0.098 2.00e-02 2.50e+03 pdb=" CE2 TYR A 194 " -0.070 2.00e-02 2.50e+03 pdb=" CZ TYR A 194 " 0.031 2.00e-02 2.50e+03 pdb=" OH TYR A 194 " -0.101 2.00e-02 2.50e+03 pdb=" HD1 TYR A 194 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR A 194 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TYR A 194 " -0.041 2.00e-02 2.50e+03 pdb=" HE2 TYR A 194 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.127 2.00e-02 2.50e+03 6.19e-02 1.15e+02 pdb=" CG PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.055 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.030 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 164 " 0.106 2.00e-02 2.50e+03 6.06e-02 1.10e+02 pdb=" CG PHE B 164 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE B 164 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 164 " -0.093 2.00e-02 2.50e+03 pdb=" CE1 PHE B 164 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE B 164 " -0.037 2.00e-02 2.50e+03 pdb=" CZ PHE B 164 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE B 164 " 0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE B 164 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE B 164 " -0.082 2.00e-02 2.50e+03 pdb=" HE2 PHE B 164 " 0.027 2.00e-02 2.50e+03 pdb=" HZ PHE B 164 " 0.114 2.00e-02 2.50e+03 ... (remaining 879 not shown) Histogram of nonbonded interaction distances: 0.86 - 1.60: 24 1.60 - 2.35: 2305 2.35 - 3.10: 22264 3.10 - 3.85: 32937 3.85 - 4.60: 52781 Warning: very small nonbonded interaction distances. Nonbonded interactions: 110311 Sorted by model distance: nonbonded pdb=" HB2 CYS B 81 " pdb=" O HOH S1417 " model vdw 0.856 2.620 nonbonded pdb=" HB2 GLN A 94 " pdb=" O HOH S1428 " model vdw 0.966 2.620 nonbonded pdb=" HB3 ASP B 64 " pdb=" O HOH S1496 " model vdw 1.007 2.620 nonbonded pdb=" HB3 ASP A 64 " pdb=" O HOH S1565 " model vdw 1.037 2.620 nonbonded pdb=" HB2 ARG A 49 " pdb=" O HOH S1498 " model vdw 1.187 2.620 ... (remaining 110306 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_4047050_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= 0.2035 r_free= 0.2013 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.300049 | | target function (ml) not normalized (work): 805455.073327 | | target function (ml) not normalized (free): 16549.068709 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2136 0.1987 6.6811 6.3056| | 2: 2.94 - 2.33 1.00 7339 128 0.1625 0.1761 5.5478 5.6146| | 3: 2.33 - 2.04 0.96 6939 150 0.1623 0.1713 5.1499 5.2327| | 4: 2.04 - 1.85 1.00 7170 155 0.1747 0.1709 4.9596 5.0886| | 5: 1.85 - 1.72 0.99 7113 159 0.1927 0.1616 4.7965 4.7558| | 6: 1.72 - 1.62 0.99 7102 142 0.1960 0.2073 4.6656 4.7241| | 7: 1.62 - 1.54 0.99 7104 148 0.2030 0.1740 4.5683 4.5391| | 8: 1.54 - 1.47 0.96 6798 152 0.2044 0.2425 4.4795 4.5861| | 9: 1.47 - 1.41 0.98 6938 155 0.2126 0.2270 4.4045 4.5195| | 10: 1.41 - 1.36 0.99 7022 150 0.2101 0.2228 4.308 4.3567| | 11: 1.36 - 1.32 0.99 6997 151 0.2097 0.1904 4.2342 4.2309| | 12: 1.32 - 1.28 0.98 6976 149 0.2090 0.1959 4.1787 4.2069| | 13: 1.28 - 1.25 0.98 6907 166 0.2057 0.2081 4.1265 4.1381| | 14: 1.25 - 1.22 0.98 7015 113 0.2093 0.2259 4.0776 4.2268| | 15: 1.22 - 1.19 0.98 6957 137 0.2085 0.2045 4.0314 4.0406| | 16: 1.19 - 1.17 0.93 6604 132 0.2122 0.2185 4.0036 4.074| | 17: 1.17 - 1.14 0.98 6941 135 0.2171 0.1773 3.9501 3.9409| | 18: 1.14 - 1.12 0.98 6875 142 0.2249 0.2271 3.9239 3.881| | 19: 1.12 - 1.10 0.97 6949 106 0.2260 0.2527 3.8615 4.0219| | 20: 1.10 - 1.08 0.97 6884 147 0.2302 0.2189 3.8202 3.8677| | 21: 1.08 - 1.07 0.97 6852 152 0.2421 0.2779 3.7812 3.8251| | 22: 1.07 - 1.05 0.97 6838 135 0.2567 0.2605 3.7561 3.7884| | 23: 1.05 - 1.03 0.97 6829 159 0.2743 0.2455 3.7323 3.7428| | 24: 1.03 - 1.02 0.96 6785 133 0.2863 0.2504 3.6983 3.6864| | 25: 1.02 - 1.01 0.93 6552 130 0.3068 0.3201 3.6766 3.7899| | 26: 1.01 - 0.99 0.96 6767 158 0.3207 0.3137 3.6283 3.5993| | 27: 0.99 - 0.98 0.94 6648 131 0.3410 0.3098 3.647 3.5639| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 38.28 - 2.94 7412 127 0.86 20.50 0.91 0.96 35315.33| | 2: 2.94 - 2.33 7339 128 0.85 21.48 1.08 1.02 15456.19| | 3: 2.33 - 2.04 6939 150 0.93 13.16 1.11 1.05 4543.79| | 4: 2.04 - 1.85 7170 155 0.92 13.78 1.11 1.06 2855.89| | 5: 1.85 - 1.72 7113 159 0.91 15.09 1.12 1.08 1984.66| | 6: 1.72 - 1.62 7102 142 0.91 16.09 1.11 1.09 1574.84| | 7: 1.62 - 1.54 7104 148 0.89 17.41 1.11 1.08 1322.76| | 8: 1.54 - 1.47 6798 152 0.88 18.91 1.10 1.06 1209.56| | 9: 1.47 - 1.41 6938 155 0.87 19.93 1.11 1.05 1051.76| | 10: 1.41 - 1.36 7022 150 0.86 20.66 1.09 1.05 888.41| | 11: 1.36 - 1.32 6997 151 0.87 19.98 1.07 1.04 728.73| | 12: 1.32 - 1.28 6976 149 0.88 19.15 1.07 1.03 613.74| | 13: 1.28 - 1.25 6907 166 0.88 19.00 1.07 1.03 556.40| | 14: 1.25 - 1.22 7015 113 0.87 20.01 1.07 1.03 538.01| | 15: 1.22 - 1.19 6957 137 0.87 20.52 1.08 1.03 519.53| | 16: 1.19 - 1.17 6604 132 0.87 20.10 1.07 1.02 467.26| | 17: 1.17 - 1.14 6941 135 0.87 20.23 1.09 1.02 413.27| | 18: 1.14 - 1.12 6875 142 0.87 20.31 1.08 1.01 369.75| | 19: 1.12 - 1.10 6949 106 0.86 21.76 1.07 1.01 373.21| | 20: 1.10 - 1.08 6884 147 0.85 22.72 1.06 0.98 350.04| | 21: 1.08 - 1.07 6852 152 0.84 24.15 1.06 0.98 340.35| | 22: 1.07 - 1.05 6838 135 0.83 24.87 1.06 0.98 312.21| | 23: 1.05 - 1.03 6829 159 0.81 26.39 1.05 0.99 309.16| | 24: 1.03 - 1.02 6785 133 0.80 27.94 1.05 0.98 303.84| | 25: 1.02 - 1.01 6552 130 0.78 29.58 1.03 0.95 295.50| | 26: 1.01 - 0.99 6767 158 0.77 30.84 1.03 0.93 275.24| | 27: 0.99 - 0.98 6648 131 0.77 30.39 1.04 0.92 248.62| |alpha: min = 0.92 max = 1.09 mean = 1.02| |beta: min = 248.62 max = 35315.33 mean = 2839.39| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.98 mean = 21.22| |phase err.(test): min = 0.00 max = 89.74 mean = 21.26| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.083 0.262 2950 Z= 5.456 Angle : 5.164 19.356 4018 Z= 3.689 Chirality : 0.380 1.124 492 Planarity : 0.034 0.171 512 Dihedral : 13.319 82.621 1062 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.66 % Favored : 95.08 % Rotamer: Outliers : 0.65 % Allowed : 4.84 % Favored : 94.52 % Cbeta Deviations : 32.02 % 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: -2.52 (0.38), residues: 386 helix: -2.56 (0.32), residues: 146 sheet: -0.79 (0.54), residues: 86 loop : -0.98 (0.46), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.098 0.019 ARG B 100 TYR 0.094 0.035 TYR B 192 PHE 0.098 0.037 PHE B 95 TRP 0.098 0.031 TRP B 139 HIS 0.103 0.034 HIS B 179 Individual atomic B min max mean iso aniso Overall: 5.22 78.04 14.60 1.58 435 3274 Protein: 5.22 45.32 10.88 1.58 0 2902 Water: 6.72 78.04 28.00 N/A 435 370 Other: 13.80 22.32 18.06 N/A 0 2 Chain A: 5.22 64.48 12.79 N/A 0 1626 Chain B: 5.47 78.04 12.54 N/A 0 1648 Chain S: 12.81 59.76 29.18 N/A 435 0 Histogram: Values Number of atoms 5.22 - 12.51 2262 12.51 - 19.79 633 19.79 - 27.07 368 27.07 - 34.35 233 34.35 - 41.63 129 41.63 - 48.92 51 48.92 - 56.20 22 56.20 - 63.48 9 63.48 - 70.76 1 70.76 - 78.04 1 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191155 (all), 2.01 % free)-----------| | | | r_work= 0.2035 r_free= 0.2013 coordinate error (max.-lik. estimate): 0.04 A | | | | normalized target function (ml) (work): 4.300049 | | target function (ml) not normalized (work): 805455.073327 | | target function (ml) not normalized (free): 16549.068709 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2033 0.2035 0.2013 n_refl.: 191155 re-set all scales: r(all,work,free)=0.2033 0.2035 0.2013 n_refl.: 191155 remove outliers: r(all,work,free)=0.2033 0.2035 0.2013 n_refl.: 191145 overall B=-0.00 to atoms: r(all,work,free)=0.2033 0.2034 0.2013 n_refl.: 191145 bulk-solvent and scaling: r(all,work,free)=0.1806 0.1803 0.1949 n_refl.: 191145 remove outliers: r(all,work,free)=0.1804 0.1801 0.1949 n_refl.: 191141 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 96.04 94 3 0.4236 400.535 295.404 0.435 0.913 0.301 13.296-10.522 100.00 100 1 0.2557 534.497 522.161 0.787 0.914 0.257 10.503-8.327 99.45 178 3 0.2513 565.118 556.788 0.970 0.914 0.237 8.318-6.595 100.00 360 8 0.2468 414.736 403.868 0.978 0.914 0.179 6.588-5.215 100.00 711 7 0.2275 381.101 366.444 0.960 0.914 0.160 5.214-4.128 98.38 1367 28 0.1501 557.435 550.405 1.075 0.914 0.070 4.126-3.266 94.74 2603 46 0.1347 508.132 499.757 1.146 0.915 0.024 3.266-2.585 99.86 5447 97 0.1444 342.774 337.410 1.119 0.914 0.010 2.585-2.046 97.45 10613 204 0.1396 258.603 254.340 1.124 0.913 0.000 2.046-1.619 99.39 21536 464 0.1614 153.054 149.946 1.144 0.912 0.000 1.619-1.281 98.00 42464 925 0.1929 82.395 80.174 1.128 0.910 0.000 1.281-0.980 96.53 101826 2056 0.2320 44.203 41.682 1.114 0.905 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0089 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1801 r_free=0.1949 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN Total number of N/Q/H flips: 1 r_work=0.1804 r_free=0.1950 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.684150 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 567.786390 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1272 0.1493 0.0221 0.037 1.2 11.0 0.0 0.0 0 11.842 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.72 14.93 2.21 1.119 13.108 567.786 0.019 12.97 15.62 2.64 1.237 13.318 567.786 0.018 Individual atomic B min max mean iso aniso Overall: 5.17 73.04 14.98 1.40 435 3274 Protein: 5.17 40.32 10.99 1.40 0 2902 Water: 6.31 73.04 29.35 N/A 435 370 Other: 15.96 30.12 23.04 N/A 0 2 Chain A: 5.38 59.78 13.02 N/A 0 1626 Chain B: 5.17 73.04 12.75 N/A 0 1648 Chain S: 11.01 64.95 30.70 N/A 435 0 Histogram: Values Number of atoms 5.17 - 11.96 2163 11.96 - 18.74 644 18.74 - 25.53 316 25.53 - 32.32 263 32.32 - 39.11 157 39.11 - 45.89 102 45.89 - 52.68 40 52.68 - 59.47 20 59.47 - 66.25 3 66.25 - 73.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.1298 r_free=0.1562 r_work=0.1297 r_free=0.1557 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1297 r_free = 0.1557 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 = 0.1282 r_free = 0.1548 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.=191141 (all), 2.01 % free)-----------| | | | r_work= 0.1282 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015689 | | target function (ls_wunit_k1) not normalized (work): 2938.476754 | | target function (ls_wunit_k1) not normalized (free): 116.374106 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1287 0.1282 0.1548 n_refl.: 191141 re-set all scales: r(all,work,free)=0.1472 0.1469 0.1623 n_refl.: 191141 remove outliers: r(all,work,free)=0.1472 0.1469 0.1623 n_refl.: 191141 overall B=0.17 to atoms: r(all,work,free)=0.1496 0.1494 0.1633 n_refl.: 191141 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1274 0.1541 n_refl.: 191141 remove outliers: r(all,work,free)=0.1279 0.1274 0.1540 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3629 402.814 371.737 0.462 1.000 0.281 13.296-10.522 100.00 100 1 0.2104 534.497 530.552 0.723 1.002 0.249 10.503-8.327 99.45 178 3 0.1782 565.118 561.433 0.856 1.002 0.198 8.318-6.595 100.00 360 8 0.1729 414.736 412.055 0.877 1.001 0.155 6.588-5.215 100.00 711 7 0.1541 381.101 373.834 0.855 1.002 0.150 5.214-4.128 98.38 1367 28 0.0912 557.435 554.337 0.940 1.002 0.060 4.126-3.266 94.74 2603 46 0.0841 508.132 504.217 1.005 1.003 0.019 3.266-2.585 99.86 5447 97 0.0926 342.774 340.334 0.987 1.002 0.010 2.585-2.046 97.45 10613 204 0.0947 258.603 256.428 0.998 1.003 0.000 2.046-1.619 99.39 21536 464 0.1082 153.054 151.408 1.016 1.003 0.000 1.619-1.281 98.00 42464 925 0.1276 82.395 81.420 1.008 1.003 0.000 1.281-0.980 96.53 101826 2055 0.1875 44.202 42.158 0.986 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0386 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1540 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1540 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1540 | n_water=805 | time (s): 2.670 (total time: 2.670) Filter (dist) r_work=0.1279 r_free=0.1542 | n_water=796 | time (s): 98.650 (total time: 101.320) Filter (q & B) r_work=0.1279 r_free=0.1542 | n_water=790 | time (s): 4.790 (total time: 106.110) Compute maps r_work=0.1279 r_free=0.1542 | n_water=790 | time (s): 1.640 (total time: 107.750) Filter (map) r_work=0.1304 r_free=0.1534 | n_water=653 | time (s): 5.120 (total time: 112.870) Find peaks r_work=0.1304 r_free=0.1534 | n_water=653 | time (s): 0.870 (total time: 113.740) Add new water r_work=0.1327 r_free=0.1556 | n_water=949 | time (s): 4.820 (total time: 118.560) Refine new water occ: r_work=0.1285 r_free=0.1512 adp: r_work=0.1273 r_free=0.1506 occ: r_work=0.1276 r_free=0.1505 adp: r_work=0.1269 r_free=0.1504 occ: r_work=0.1270 r_free=0.1502 adp: r_work=0.1268 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1268 r_free=0.1501 r_work=0.1268 r_free=0.1501 | n_water=949 | time (s): 84.810 (total time: 203.370) Filter (q & B) r_work=0.1271 r_free=0.1507 | n_water=886 | time (s): 4.310 (total time: 207.680) Filter (dist only) r_work=0.1271 r_free=0.1505 | n_water=884 | time (s): 116.610 (total time: 324.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.647812 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 586.215372 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 0.1256 0.1533 0.0276 0.041 1.1 15.1 0.0 0.3 0 11.824 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.56 15.33 2.76 2.040 15.104 586.215 0.015 12.33 15.18 2.86 2.414 15.222 586.215 0.014 Individual atomic B min max mean iso aniso Overall: 5.33 71.67 16.32 1.21 517 3271 Protein: 5.33 40.38 10.97 1.21 0 2902 Water: 6.60 71.67 33.85 N/A 517 367 Other: 16.30 32.84 24.57 N/A 0 2 Chain A: 5.54 55.94 13.01 N/A 0 1624 Chain B: 5.33 68.21 12.80 N/A 0 1647 Chain S: 12.59 71.67 37.91 N/A 517 0 Histogram: Values Number of atoms 5.33 - 11.96 2130 11.96 - 18.60 678 18.60 - 25.23 265 25.23 - 31.87 209 31.87 - 38.50 177 38.50 - 45.14 163 45.14 - 51.77 94 51.77 - 58.40 48 58.40 - 65.04 18 65.04 - 71.67 6 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1518 r_work=0.1233 r_free=0.1519 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1233 r_free = 0.1519 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 = 0.1227 r_free = 0.1515 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1227 r_free= 0.1515 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.013507 | | target function (ls_wunit_k1) not normalized (work): 2529.856689 | | target function (ls_wunit_k1) not normalized (free): 102.214212 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1232 0.1227 0.1515 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1436 0.1433 0.1623 n_refl.: 191139 remove outliers: r(all,work,free)=0.1436 0.1433 0.1623 n_refl.: 191139 overall B=-0.02 to atoms: r(all,work,free)=0.1433 0.1430 0.1621 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1233 0.1523 n_refl.: 191139 remove outliers: r(all,work,free)=0.1239 0.1233 0.1523 n_refl.: 191139 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 95.05 93 3 0.3273 402.814 379.146 0.494 0.962 0.277 13.296-10.522 100.00 100 1 0.1920 534.497 526.864 0.769 0.963 0.233 10.503-8.327 99.45 178 3 0.1413 565.118 567.644 0.921 0.963 0.184 8.318-6.595 100.00 360 8 0.1552 414.736 414.239 0.939 0.963 0.160 6.588-5.215 100.00 711 7 0.1349 381.101 376.618 0.915 0.963 0.150 5.214-4.128 98.38 1367 28 0.0828 557.435 556.624 0.994 0.963 0.080 4.126-3.266 94.74 2603 46 0.0764 508.132 505.496 1.060 0.963 0.019 3.266-2.585 99.86 5447 97 0.0858 342.774 341.222 1.047 0.962 0.010 2.585-2.046 97.45 10613 204 0.0904 258.603 256.725 1.059 0.961 0.000 2.046-1.619 99.39 21536 464 0.1045 153.054 151.584 1.080 0.959 0.000 1.619-1.281 98.00 42464 925 0.1255 82.395 81.346 1.073 0.956 0.000 1.281-0.980 96.53 101826 2055 0.1870 44.202 42.215 1.059 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0520 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1523 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1233 r_free=0.1523 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1523 | n_water=884 | time (s): 3.420 (total time: 3.420) Filter (dist) r_work=0.1235 r_free=0.1525 | n_water=880 | time (s): 118.770 (total time: 122.190) Filter (q & B) r_work=0.1236 r_free=0.1526 | n_water=877 | time (s): 5.880 (total time: 128.070) Compute maps r_work=0.1236 r_free=0.1526 | n_water=877 | time (s): 2.500 (total time: 130.570) Filter (map) r_work=0.1274 r_free=0.1521 | n_water=698 | time (s): 5.340 (total time: 135.910) Find peaks r_work=0.1274 r_free=0.1521 | n_water=698 | time (s): 0.600 (total time: 136.510) Add new water r_work=0.1298 r_free=0.1563 | n_water=1009 | time (s): 4.810 (total time: 141.320) Refine new water occ: r_work=0.1251 r_free=0.1514 adp: r_work=0.1252 r_free=0.1515 occ: r_work=0.1248 r_free=0.1513 adp: r_work=0.1248 r_free=0.1514 occ: r_work=0.1245 r_free=0.1511 adp: r_work=0.1244 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1244 r_free=0.1512 r_work=0.1244 r_free=0.1512 | n_water=1009 | time (s): 302.510 (total time: 443.830) Filter (q & B) r_work=0.1249 r_free=0.1513 | n_water=871 | time (s): 4.310 (total time: 448.140) Filter (dist only) r_work=0.1250 r_free=0.1513 | n_water=870 | time (s): 108.590 (total time: 556.730) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.686819 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.196880 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1239 0.1428 0.0188 0.035 1.1 7.8 0.0 0.0 0 0.843 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.39 14.28 1.88 1.931 14.598 16.197 3.939 12.37 13.88 1.51 2.277 14.489 16.197 3.898 Individual atomic B min max mean iso aniso Overall: 5.52 67.70 15.27 1.04 505 3269 Protein: 5.52 35.98 10.70 1.04 0 2902 Water: 6.70 67.70 30.50 N/A 505 365 Other: 13.91 28.79 21.35 N/A 0 2 Chain A: 5.57 54.85 12.74 N/A 0 1624 Chain B: 5.52 67.70 12.47 N/A 0 1645 Chain S: 13.83 61.89 32.55 N/A 505 0 Histogram: Values Number of atoms 5.52 - 11.74 2127 11.74 - 17.96 695 17.96 - 24.18 291 24.18 - 30.39 231 30.39 - 36.61 174 36.61 - 42.83 137 42.83 - 49.05 75 49.05 - 55.26 33 55.26 - 61.48 9 61.48 - 67.70 2 =========================== Idealize ADP of riding H ========================== r_work=0.1237 r_free=0.1388 r_work=0.1238 r_free=0.1389 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1238 r_free = 0.1389 target_work(ml) = 3.898 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1381 target_work(ml) = 3.892 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191139 (all), 2.01 % free)-----------| | | | r_work= 0.1232 r_free= 0.1381 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.891740 | | target function (ml) not normalized (work): 728915.185419 | | target function (ml) not normalized (free): 15223.032322 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1234 0.1232 0.1381 n_refl.: 191139 re-set all scales: r(all,work,free)=0.1445 0.1445 0.1485 n_refl.: 191139 remove outliers: r(all,work,free)=0.1445 0.1445 0.1485 n_refl.: 191139 overall B=-0.03 to atoms: r(all,work,free)=0.1439 0.1439 0.1480 n_refl.: 191139 bulk-solvent and scaling: r(all,work,free)=0.1230 0.1228 0.1370 n_refl.: 191139 remove outliers: r(all,work,free)=0.1230 0.1227 0.1370 n_refl.: 191135 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 94.06 92 3 0.3725 398.008 364.053 0.428 0.945 0.244 13.296-10.522 99.01 99 1 0.2423 528.187 511.845 0.705 0.946 0.189 10.503-8.327 98.35 176 3 0.1996 555.265 557.591 0.886 0.946 0.156 8.318-6.595 100.00 360 8 0.2102 414.736 410.227 0.902 0.946 0.130 6.588-5.215 100.00 711 7 0.1862 381.101 370.107 0.887 0.946 0.117 5.214-4.128 98.38 1367 28 0.1171 557.435 552.814 0.973 0.946 0.090 4.126-3.266 94.74 2603 46 0.1087 508.132 501.090 1.035 0.947 0.014 3.266-2.585 99.86 5447 97 0.1092 342.774 339.013 1.021 0.946 0.000 2.585-2.046 97.45 10613 204 0.0975 258.603 255.667 1.034 0.945 0.000 2.046-1.619 99.39 21536 464 0.0979 153.054 151.363 1.057 0.944 0.000 1.619-1.281 98.00 42464 925 0.1053 82.395 81.477 1.054 0.943 0.000 1.281-0.980 96.53 101826 2055 0.1685 44.202 42.312 1.039 0.940 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9646 b_overall=-0.1057 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1227 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1227 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1371 | n_water=870 | time (s): 2.800 (total time: 2.800) Filter (dist) r_work=0.1227 r_free=0.1371 | n_water=869 | time (s): 106.850 (total time: 109.650) Filter (q & B) r_work=0.1227 r_free=0.1371 | n_water=863 | time (s): 4.420 (total time: 114.070) Compute maps r_work=0.1227 r_free=0.1371 | n_water=863 | time (s): 1.670 (total time: 115.740) Filter (map) r_work=0.1250 r_free=0.1384 | n_water=731 | time (s): 4.080 (total time: 119.820) Find peaks r_work=0.1250 r_free=0.1384 | n_water=731 | time (s): 0.640 (total time: 120.460) Add new water r_work=0.1264 r_free=0.1395 | n_water=965 | time (s): 3.950 (total time: 124.410) Refine new water occ: r_work=0.1216 r_free=0.1360 adp: r_work=0.1208 r_free=0.1356 occ: r_work=0.1206 r_free=0.1357 adp: r_work=0.1206 r_free=0.1356 occ: r_work=0.1204 r_free=0.1358 adp: r_work=0.1204 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1357 r_work=0.1204 r_free=0.1357 | n_water=965 | time (s): 290.520 (total time: 414.930) Filter (q & B) r_work=0.1207 r_free=0.1360 | n_water=880 | time (s): 4.230 (total time: 419.160) Filter (dist only) r_work=0.1208 r_free=0.1360 | n_water=878 | time (s): 115.200 (total time: 534.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.621269 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 16.372883 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 0.1206 0.1359 0.0153 0.035 1.1 7.3 0.0 0.0 0 0.811 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.06 13.59 1.53 1.815 14.222 16.373 3.874 11.96 13.55 1.59 1.930 14.186 16.373 3.864 Individual atomic B min max mean iso aniso Overall: 5.49 67.06 15.05 1.00 513 3269 Protein: 5.49 32.76 10.63 1.00 0 2902 Water: 5.84 67.06 29.66 N/A 513 365 Other: 13.88 26.88 20.38 N/A 0 2 Chain A: 5.57 53.27 12.60 N/A 0 1624 Chain B: 5.49 67.06 12.37 N/A 0 1645 Chain S: 5.84 61.57 31.41 N/A 513 0 Histogram: Values Number of atoms 5.49 - 11.65 2095 11.65 - 17.81 747 17.81 - 23.96 296 23.96 - 30.12 232 30.12 - 36.27 178 36.27 - 42.43 131 42.43 - 48.59 66 48.59 - 54.74 28 54.74 - 60.90 5 60.90 - 67.06 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1355 r_work=0.1196 r_free=0.1355 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1355 target_work(ml) = 3.864 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1355 target_work(ml) = 3.862 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191135 (all), 2.01 % free)-----------| | | | r_work= 0.1194 r_free= 0.1355 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.861797 | | target function (ml) not normalized (work): 723291.431770 | | target function (ml) not normalized (free): 15132.838755 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1194 0.1355 n_refl.: 191135 re-set all scales: r(all,work,free)=0.1418 0.1418 0.1467 n_refl.: 191135 remove outliers: r(all,work,free)=0.1418 0.1418 0.1467 n_refl.: 191135 overall B=-0.03 to atoms: r(all,work,free)=0.1411 0.1410 0.1462 n_refl.: 191135 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1193 0.1353 n_refl.: 191135 remove outliers: r(all,work,free)=0.1195 0.1192 0.1353 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3774 361.388 319.972 0.408 0.946 0.235 13.296-10.522 98.02 98 1 0.2445 480.768 454.835 0.692 0.947 0.183 10.503-8.327 98.35 176 3 0.2070 503.054 496.692 0.868 0.947 0.143 8.318-6.595 100.00 360 8 0.2189 375.739 371.025 0.895 0.947 0.113 6.588-5.215 100.00 711 7 0.1922 345.267 334.739 0.885 0.947 0.100 5.214-4.128 98.38 1367 28 0.1184 505.020 500.155 0.974 0.948 0.080 4.126-3.266 94.74 2603 46 0.1098 460.353 453.940 1.035 0.948 0.009 3.266-2.585 99.86 5447 97 0.1071 310.543 307.380 1.021 0.947 0.000 2.585-2.046 97.45 10613 204 0.0936 234.287 231.870 1.033 0.947 0.000 2.046-1.619 99.39 21536 464 0.0916 138.663 137.338 1.057 0.947 0.000 1.619-1.281 98.00 42464 925 0.0985 74.648 73.934 1.052 0.946 0.000 1.281-0.980 96.53 101826 2055 0.1658 40.045 38.389 1.038 0.944 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1218 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1192 r_free=0.1353 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1192 r_free=0.1353 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1192 r_free=0.1353 | n_water=878 | time (s): 2.490 (total time: 2.490) Filter (dist) r_work=0.1192 r_free=0.1353 | n_water=878 | time (s): 103.690 (total time: 106.180) Filter (q & B) r_work=0.1193 r_free=0.1356 | n_water=866 | time (s): 4.930 (total time: 111.110) Compute maps r_work=0.1193 r_free=0.1356 | n_water=866 | time (s): 2.370 (total time: 113.480) Filter (map) r_work=0.1210 r_free=0.1359 | n_water=768 | time (s): 4.180 (total time: 117.660) Find peaks r_work=0.1210 r_free=0.1359 | n_water=768 | time (s): 0.710 (total time: 118.370) Add new water r_work=0.1219 r_free=0.1374 | n_water=967 | time (s): 4.130 (total time: 122.500) Refine new water occ: r_work=0.1190 r_free=0.1346 adp: r_work=0.1190 r_free=0.1346 occ: r_work=0.1188 r_free=0.1346 adp: r_work=0.1188 r_free=0.1346 occ: r_work=0.1186 r_free=0.1345 adp: r_work=0.1186 r_free=0.1345 ADP+occupancy (water only), MIN, final r_work=0.1186 r_free=0.1345 r_work=0.1186 r_free=0.1345 | n_water=967 | time (s): 166.710 (total time: 289.210) Filter (q & B) r_work=0.1191 r_free=0.1351 | n_water=885 | time (s): 5.230 (total time: 294.440) Filter (dist only) r_work=0.1191 r_free=0.1350 | n_water=883 | time (s): 110.980 (total time: 405.420) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.636992 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.302700 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 0.1356 0.0162 0.036 1.1 5.3 0.0 0.3 0 0.818 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.56 1.62 1.781 14.086 15.303 3.762 11.99 13.61 1.61 1.824 14.066 15.303 3.762 Individual atomic B min max mean iso aniso Overall: 5.57 66.81 14.92 0.95 518 3269 Protein: 5.57 31.49 10.57 0.95 0 2902 Water: 5.92 66.81 29.18 N/A 518 365 Other: 13.78 26.22 20.00 N/A 0 2 Chain A: 5.58 52.67 12.52 N/A 0 1624 Chain B: 5.57 66.81 12.29 N/A 0 1645 Chain S: 5.92 61.61 30.75 N/A 518 0 Histogram: Values Number of atoms 5.57 - 11.70 2132 11.70 - 17.82 727 17.82 - 23.94 302 23.94 - 30.07 227 30.07 - 36.19 179 36.19 - 42.31 123 42.31 - 48.44 61 48.44 - 54.56 29 54.56 - 60.68 4 60.68 - 66.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1361 r_work=0.1199 r_free=0.1361 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1361 target_work(ml) = 3.762 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1365 target_work(ml) = 3.761 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1198 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.760967 | | target function (ml) not normalized (work): 704398.988824 | | target function (ml) not normalized (free): 14754.404246 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1201 0.1198 0.1365 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1407 0.1406 0.1489 n_refl.: 191133 remove outliers: r(all,work,free)=0.1407 0.1406 0.1489 n_refl.: 191133 overall B=-0.04 to atoms: r(all,work,free)=0.1400 0.1398 0.1484 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191133 remove outliers: r(all,work,free)=0.1200 0.1197 0.1363 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3752 361.388 321.592 0.400 0.950 0.221 13.296-10.522 98.02 98 1 0.2475 480.768 457.585 0.683 0.952 0.154 10.503-8.327 98.35 176 3 0.2169 503.054 495.577 0.863 0.952 0.128 8.318-6.595 100.00 360 8 0.2220 375.739 370.798 0.884 0.952 0.095 6.588-5.215 100.00 711 7 0.1945 345.267 334.534 0.879 0.952 0.085 5.214-4.128 98.38 1367 28 0.1212 505.020 499.627 0.970 0.952 0.080 4.126-3.266 94.74 2603 46 0.1138 460.353 453.707 1.031 0.952 0.000 3.266-2.585 99.86 5447 97 0.1098 310.543 307.243 1.017 0.951 0.000 2.585-2.046 97.45 10613 204 0.0945 234.287 231.791 1.029 0.951 0.000 2.046-1.619 99.39 21536 464 0.0914 138.663 137.341 1.053 0.950 0.000 1.619-1.281 98.00 42464 925 0.0974 74.648 73.939 1.051 0.948 0.000 1.281-0.980 96.53 101826 2055 0.1650 40.045 38.382 1.039 0.945 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=-0.1293 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1197 r_free=0.1363 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1197 r_free=0.1363 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1363 | n_water=883 | time (s): 2.780 (total time: 2.780) Filter (dist) r_work=0.1197 r_free=0.1363 | n_water=882 | time (s): 113.610 (total time: 116.390) Filter (q & B) r_work=0.1197 r_free=0.1363 | n_water=873 | time (s): 5.320 (total time: 121.710) Compute maps r_work=0.1197 r_free=0.1363 | n_water=873 | time (s): 2.300 (total time: 124.010) Filter (map) r_work=0.1218 r_free=0.1375 | n_water=760 | time (s): 4.810 (total time: 128.820) Find peaks r_work=0.1218 r_free=0.1375 | n_water=760 | time (s): 0.670 (total time: 129.490) Add new water r_work=0.1227 r_free=0.1388 | n_water=969 | time (s): 4.280 (total time: 133.770) Refine new water occ: r_work=0.1194 r_free=0.1354 adp: r_work=0.1194 r_free=0.1354 occ: r_work=0.1192 r_free=0.1353 adp: r_work=0.1192 r_free=0.1353 occ: r_work=0.1191 r_free=0.1353 adp: r_work=0.1191 r_free=0.1353 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1353 r_work=0.1191 r_free=0.1353 | n_water=969 | time (s): 224.720 (total time: 358.490) Filter (q & B) r_work=0.1195 r_free=0.1362 | n_water=899 | time (s): 5.060 (total time: 363.550) Filter (dist only) r_work=0.1195 r_free=0.1361 | n_water=898 | time (s): 121.040 (total time: 484.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.582310 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 15.530447 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 0.1371 0.0171 0.037 1.1 8.0 0.0 0.3 0 0.791 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.99 13.71 1.71 1.754 14.000 15.530 3.762 12.01 13.71 1.69 1.834 13.972 15.530 3.759 Individual atomic B min max mean iso aniso Overall: 5.55 66.06 14.82 0.92 533 3269 Protein: 5.55 29.92 10.50 0.92 0 2902 Water: 5.93 66.06 28.78 N/A 533 365 Other: 13.86 24.19 19.02 N/A 0 2 Chain A: 5.62 52.07 12.41 N/A 0 1624 Chain B: 5.55 66.06 12.20 N/A 0 1645 Chain S: 5.93 61.75 30.26 N/A 533 0 Histogram: Values Number of atoms 5.55 - 11.60 2118 11.60 - 17.65 765 17.65 - 23.70 295 23.70 - 29.76 229 29.76 - 35.81 174 35.81 - 41.86 119 41.86 - 47.91 65 47.91 - 53.96 28 53.96 - 60.01 6 60.01 - 66.06 3 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1371 r_work=0.1202 r_free=0.1371 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1202 r_free = 0.1371 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1200 r_free = 0.1373 target_work(ml) = 3.759 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1200 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.758993 | | target function (ml) not normalized (work): 704029.342484 | | target function (ml) not normalized (free): 14750.019378 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1204 0.1200 0.1373 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1407 0.1405 0.1512 n_refl.: 191133 remove outliers: r(all,work,free)=0.1407 0.1405 0.1512 n_refl.: 191133 overall B=-0.22 to atoms: r(all,work,free)=0.1372 0.1370 0.1487 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1200 0.1372 n_refl.: 191133 remove outliers: r(all,work,free)=0.1203 0.1200 0.1372 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3864 361.388 319.422 0.400 0.950 0.218 13.296-10.522 98.02 98 1 0.2512 480.768 458.748 0.697 0.952 0.156 10.503-8.327 98.35 176 3 0.2176 503.054 494.949 0.882 0.952 0.130 8.318-6.595 100.00 360 8 0.2227 375.739 371.240 0.904 0.952 0.090 6.588-5.215 100.00 711 7 0.1968 345.267 334.186 0.901 0.952 0.080 5.214-4.128 98.38 1367 28 0.1227 505.020 499.348 0.995 0.952 0.070 4.126-3.266 94.74 2603 46 0.1149 460.353 453.331 1.057 0.953 0.005 3.266-2.585 99.86 5447 97 0.1118 310.543 307.177 1.040 0.952 0.000 2.585-2.046 97.45 10613 204 0.0953 234.287 231.781 1.048 0.952 0.000 2.046-1.619 99.39 21536 464 0.0911 138.663 137.343 1.066 0.951 0.000 1.619-1.281 98.00 42464 925 0.0968 74.648 73.943 1.054 0.950 0.000 1.281-0.980 96.53 101826 2055 0.1646 40.045 38.378 1.025 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=0.0484 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1200 r_free=0.1372 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1200 r_free=0.1372 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1200 r_free=0.1372 | n_water=898 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1200 r_free=0.1371 | n_water=897 | time (s): 115.050 (total time: 118.060) Filter (q & B) r_work=0.1201 r_free=0.1368 | n_water=884 | time (s): 5.390 (total time: 123.450) Compute maps r_work=0.1201 r_free=0.1368 | n_water=884 | time (s): 1.860 (total time: 125.310) Filter (map) r_work=0.1219 r_free=0.1373 | n_water=773 | time (s): 4.680 (total time: 129.990) Find peaks r_work=0.1219 r_free=0.1373 | n_water=773 | time (s): 0.760 (total time: 130.750) Add new water r_work=0.1228 r_free=0.1386 | n_water=981 | time (s): 3.920 (total time: 134.670) Refine new water occ: r_work=0.1197 r_free=0.1361 adp: r_work=0.1197 r_free=0.1361 occ: r_work=0.1195 r_free=0.1360 adp: r_work=0.1195 r_free=0.1360 occ: r_work=0.1193 r_free=0.1360 adp: r_work=0.1193 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1360 r_work=0.1193 r_free=0.1360 | n_water=981 | time (s): 221.940 (total time: 356.610) Filter (q & B) r_work=0.1197 r_free=0.1368 | n_water=911 | time (s): 4.350 (total time: 360.960) Filter (dist only) r_work=0.1197 r_free=0.1367 | n_water=910 | time (s): 117.380 (total time: 478.340) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.493467 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.383931 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 0.1202 0.1372 0.0170 0.038 1.1 6.8 0.0 0.3 0 0.747 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.02 13.72 1.70 1.726 13.768 14.384 3.760 12.05 13.78 1.73 1.784 13.743 14.384 3.760 Individual atomic B min max mean iso aniso Overall: 5.41 65.03 14.64 0.88 545 3269 Protein: 5.41 28.65 10.25 0.88 0 2902 Water: 5.77 65.03 28.62 N/A 545 365 Other: 13.66 22.47 18.06 N/A 0 2 Chain A: 5.45 51.42 12.13 N/A 0 1624 Chain B: 5.41 65.03 11.93 N/A 0 1645 Chain S: 5.77 61.64 30.30 N/A 545 0 Histogram: Values Number of atoms 5.41 - 11.37 2109 11.37 - 17.33 779 17.33 - 23.29 282 23.29 - 29.26 224 29.26 - 35.22 180 35.22 - 41.18 131 41.18 - 47.14 70 47.14 - 53.10 30 53.10 - 59.06 6 59.06 - 65.03 3 =========================== Idealize ADP of riding H ========================== r_work=0.1205 r_free=0.1378 r_work=0.1205 r_free=0.1378 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1205 r_free = 0.1378 target_work(ml) = 3.760 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1379 target_work(ml) = 3.760 | | 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.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1204 r_free= 0.1379 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.759698 | | target function (ml) not normalized (work): 704161.441629 | | target function (ml) not normalized (free): 14754.250336 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1204 0.1379 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1380 0.1378 0.1497 n_refl.: 191133 remove outliers: r(all,work,free)=0.1380 0.1378 0.1497 n_refl.: 191133 overall B=0.06 to atoms: r(all,work,free)=0.1389 0.1387 0.1503 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1368 n_refl.: 191133 remove outliers: r(all,work,free)=0.1198 0.1195 0.1368 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3913 361.388 318.758 0.375 0.995 0.200 13.296-10.522 98.02 98 1 0.2532 480.768 458.118 0.669 0.997 0.150 10.503-8.327 98.35 176 3 0.2151 503.054 494.413 0.848 0.998 0.132 8.318-6.595 100.00 360 8 0.2213 375.739 370.506 0.870 0.998 0.086 6.588-5.215 100.00 711 7 0.1975 345.267 333.533 0.868 0.998 0.073 5.214-4.128 98.38 1367 28 0.1229 505.020 498.985 0.960 0.999 0.060 4.126-3.266 94.74 2603 46 0.1158 460.353 452.769 1.019 1.000 0.005 3.266-2.585 99.86 5447 97 0.1128 310.543 306.848 1.002 1.000 0.000 2.585-2.046 97.45 10613 204 0.0962 234.287 231.631 1.010 1.002 0.000 2.046-1.619 99.39 21536 464 0.0910 138.663 137.274 1.026 1.005 0.000 1.619-1.281 98.00 42464 925 0.0951 74.648 73.981 1.015 1.009 0.000 1.281-0.980 96.53 101826 2055 0.1629 40.045 38.348 0.982 1.016 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0577 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1195 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1195 r_free=0.1368 | n_water=910 | time (s): 2.660 (total time: 2.660) Filter (dist) r_work=0.1195 r_free=0.1368 | n_water=909 | time (s): 115.290 (total time: 117.950) Filter (q & B) r_work=0.1196 r_free=0.1369 | n_water=898 | time (s): 4.440 (total time: 122.390) Compute maps r_work=0.1196 r_free=0.1369 | n_water=898 | time (s): 2.440 (total time: 124.830) Filter (map) r_work=0.1217 r_free=0.1364 | n_water=779 | time (s): 5.200 (total time: 130.030) Find peaks r_work=0.1217 r_free=0.1364 | n_water=779 | time (s): 0.670 (total time: 130.700) Add new water r_work=0.1224 r_free=0.1374 | n_water=959 | time (s): 4.070 (total time: 134.770) Refine new water occ: r_work=0.1196 r_free=0.1356 adp: r_work=0.1196 r_free=0.1357 occ: r_work=0.1194 r_free=0.1355 adp: r_work=0.1194 r_free=0.1356 occ: r_work=0.1193 r_free=0.1355 adp: r_work=0.1192 r_free=0.1356 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1356 r_work=0.1192 r_free=0.1356 | n_water=959 | time (s): 239.030 (total time: 373.800) Filter (q & B) r_work=0.1195 r_free=0.1362 | n_water=906 | time (s): 4.410 (total time: 378.210) Filter (dist only) r_work=0.1195 r_free=0.1361 | n_water=905 | time (s): 115.560 (total time: 493.770) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.575447 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.134968 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 0.1365 0.0168 0.038 1.1 5.5 0.0 0.3 0 0.788 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.65 1.68 1.679 13.735 14.135 3.758 11.98 13.68 1.70 1.709 13.722 14.135 3.756 Individual atomic B min max mean iso aniso Overall: 5.50 64.12 14.63 0.87 540 3269 Protein: 5.50 28.15 10.31 0.87 0 2902 Water: 5.90 64.12 28.48 N/A 540 365 Other: 13.75 22.17 17.96 N/A 0 2 Chain A: 5.54 50.96 12.15 N/A 0 1624 Chain B: 5.50 64.12 11.96 N/A 0 1645 Chain S: 5.90 61.78 30.22 N/A 540 0 Histogram: Values Number of atoms 5.50 - 11.36 2076 11.36 - 17.22 810 17.22 - 23.09 277 23.09 - 28.95 224 28.95 - 34.81 181 34.81 - 40.67 118 40.67 - 46.54 82 46.54 - 52.40 29 52.40 - 58.26 9 58.26 - 64.12 3 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1368 r_work=0.1198 r_free=0.1368 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1368 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1369 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1197 r_free= 0.1369 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.756026 | | target function (ml) not normalized (work): 703473.611490 | | target function (ml) not normalized (free): 14737.255356 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1197 0.1369 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1397 0.1395 0.1510 n_refl.: 191133 remove outliers: r(all,work,free)=0.1397 0.1395 0.1510 n_refl.: 191133 overall B=0.01 to atoms: r(all,work,free)=0.1399 0.1397 0.1512 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1196 0.1366 n_refl.: 191133 remove outliers: r(all,work,free)=0.1199 0.1196 0.1366 n_refl.: 191133 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3908 361.388 318.447 0.366 0.995 0.188 13.296-10.522 98.02 98 1 0.2488 480.768 459.492 0.660 0.997 0.128 10.503-8.327 98.35 176 3 0.2217 503.054 494.182 0.845 0.997 0.103 8.318-6.595 100.00 360 8 0.2222 375.739 370.577 0.868 0.997 0.086 6.588-5.215 100.00 711 7 0.1984 345.267 333.664 0.866 0.998 0.073 5.214-4.128 98.38 1367 28 0.1248 505.020 498.679 0.960 0.998 0.070 4.126-3.266 94.74 2603 46 0.1171 460.353 452.561 1.020 1.000 0.005 3.266-2.585 99.86 5447 97 0.1132 310.543 306.843 1.003 1.000 0.000 2.585-2.046 97.45 10613 204 0.0967 234.287 231.617 1.011 1.002 0.000 2.046-1.619 99.39 21536 464 0.0909 138.663 137.290 1.028 1.006 0.000 1.619-1.281 98.00 42464 925 0.0946 74.648 73.989 1.018 1.011 0.000 1.281-0.980 96.53 101826 2055 0.1625 40.045 38.334 0.987 1.020 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0196 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1196 r_free=0.1366 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1366 | n_water=905 | time (s): 3.010 (total time: 3.010) Filter (dist) r_work=0.1196 r_free=0.1366 | n_water=905 | time (s): 109.180 (total time: 112.190) Filter (q & B) r_work=0.1196 r_free=0.1366 | n_water=897 | time (s): 5.690 (total time: 117.880) Compute maps r_work=0.1196 r_free=0.1366 | n_water=897 | time (s): 2.450 (total time: 120.330) Filter (map) r_work=0.1214 r_free=0.1362 | n_water=791 | time (s): 4.570 (total time: 124.900) Find peaks r_work=0.1214 r_free=0.1362 | n_water=791 | time (s): 0.680 (total time: 125.580) Add new water r_work=0.1222 r_free=0.1372 | n_water=978 | time (s): 4.220 (total time: 129.800) Refine new water occ: r_work=0.1192 r_free=0.1353 adp: r_work=0.1193 r_free=0.1353 occ: r_work=0.1191 r_free=0.1353 adp: r_work=0.1191 r_free=0.1352 occ: r_work=0.1189 r_free=0.1352 adp: r_work=0.1189 r_free=0.1351 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1351 r_work=0.1189 r_free=0.1351 | n_water=978 | time (s): 229.010 (total time: 358.810) Filter (q & B) r_work=0.1193 r_free=0.1361 | n_water=916 | time (s): 5.850 (total time: 364.660) Filter (dist only) r_work=0.1193 r_free=0.1360 | n_water=914 | time (s): 113.130 (total time: 477.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.464520 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.453347 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 0.1370 0.0173 0.039 1.1 7.3 0.0 0.3 0 0.732 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 13.70 1.73 1.677 13.726 14.453 3.757 11.97 13.72 1.75 1.684 13.720 14.453 3.755 Individual atomic B min max mean iso aniso Overall: 5.54 63.12 14.62 0.87 549 3269 Protein: 5.54 28.04 10.33 0.87 0 2902 Water: 5.92 63.12 28.21 N/A 549 365 Other: 13.81 22.08 17.95 N/A 0 2 Chain A: 5.59 50.61 12.14 N/A 0 1624 Chain B: 5.54 63.12 11.96 N/A 0 1645 Chain S: 5.92 61.84 29.88 N/A 549 0 Histogram: Values Number of atoms 5.54 - 11.30 2056 11.30 - 17.06 828 17.06 - 22.81 286 22.81 - 28.57 211 28.57 - 34.33 189 34.33 - 40.09 122 40.09 - 45.85 82 45.85 - 51.60 32 51.60 - 57.36 9 57.36 - 63.12 3 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1372 r_work=0.1197 r_free=0.1373 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1373 target_work(ml) = 3.756 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1373 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ |--(resolution: 0.98 - 38.28 A, n_refl.=191133 (all), 2.01 % free)-----------| | | | r_work= 0.1196 r_free= 0.1373 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.755162 | | target function (ml) not normalized (work): 703311.817564 | | target function (ml) not normalized (free): 14743.671285 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1196 0.1373 n_refl.: 191133 re-set all scales: r(all,work,free)=0.1408 0.1405 0.1520 n_refl.: 191133 remove outliers: r(all,work,free)=0.1408 0.1405 0.1520 n_refl.: 191133 overall B=-0.00 to atoms: r(all,work,free)=0.1407 0.1405 0.1520 n_refl.: 191133 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1195 0.1371 n_refl.: 191133 remove outliers: r(all,work,free)=0.1199 0.1195 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 93.07 91 3 0.3895 361.388 318.307 0.373 0.975 0.192 13.296-10.522 97.03 97 1 0.2409 481.443 456.763 0.671 0.977 0.126 10.503-8.327 98.35 176 3 0.2237 503.054 494.616 0.860 0.977 0.100 8.318-6.595 100.00 360 8 0.2201 375.739 370.916 0.885 0.977 0.090 6.588-5.215 100.00 711 7 0.1993 345.267 333.782 0.883 0.978 0.080 5.214-4.128 98.38 1367 28 0.1245 505.020 498.907 0.979 0.979 0.070 4.126-3.266 94.74 2603 46 0.1176 460.353 452.474 1.040 0.980 0.000 3.266-2.585 99.86 5447 97 0.1137 310.543 306.845 1.023 0.981 0.000 2.585-2.046 97.45 10613 204 0.0967 234.287 231.653 1.031 0.983 0.000 2.046-1.619 99.39 21536 464 0.0909 138.663 137.301 1.049 0.987 0.000 1.619-1.281 98.00 42464 925 0.0942 74.648 74.002 1.040 0.993 0.000 1.281-0.980 96.53 101826 2055 0.1623 40.045 38.328 1.010 1.003 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0093 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1195 r_free=0.1371 After: r_work=0.1196 r_free=0.1371 ================================== NQH flips ================================== r_work=0.1196 r_free=0.1371 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1196 r_free=0.1371 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1196 r_free=0.1371 | n_water=914 | time (s): 3.380 (total time: 3.380) Filter (dist) r_work=0.1197 r_free=0.1372 | n_water=913 | time (s): 126.340 (total time: 129.720) Filter (q & B) r_work=0.1198 r_free=0.1372 | n_water=900 | time (s): 4.850 (total time: 134.570) Compute maps r_work=0.1198 r_free=0.1372 | n_water=900 | time (s): 1.970 (total time: 136.540) Filter (map) r_work=0.1219 r_free=0.1366 | n_water=784 | time (s): 5.250 (total time: 141.790) Find peaks r_work=0.1219 r_free=0.1366 | n_water=784 | time (s): 0.600 (total time: 142.390) Add new water r_work=0.1226 r_free=0.1380 | n_water=987 | time (s): 4.810 (total time: 147.200) Refine new water occ: r_work=0.1195 r_free=0.1360 adp: r_work=0.1196 r_free=0.1360 occ: r_work=0.1194 r_free=0.1357 adp: r_work=0.1194 r_free=0.1358 occ: r_work=0.1192 r_free=0.1354 adp: r_work=0.1192 r_free=0.1355 ADP+occupancy (water only), MIN, final r_work=0.1192 r_free=0.1355 r_work=0.1192 r_free=0.1355 | n_water=987 | time (s): 242.810 (total time: 390.010) Filter (q & B) r_work=0.1196 r_free=0.1366 | n_water=914 | time (s): 4.780 (total time: 394.790) Filter (dist only) r_work=0.1196 r_free=0.1366 | n_water=913 | time (s): 124.200 (total time: 518.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.555223 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 14.360326 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1368 0.0172 0.039 1.2 8.0 0.0 0.3 0 0.778 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 13.68 1.72 1.676 13.717 14.360 3.756 11.96 13.69 1.73 1.673 13.716 14.360 3.755 Individual atomic B min max mean iso aniso Overall: 5.55 62.76 14.60 0.86 548 3269 Protein: 5.55 28.01 10.35 0.86 0 2902 Water: 6.03 62.76 28.11 N/A 548 365 Other: 13.84 22.07 17.95 N/A 0 2 Chain A: 5.60 50.48 12.13 N/A 0 1624 Chain B: 5.55 62.76 11.96 N/A 0 1645 Chain S: 6.03 61.81 29.84 N/A 548 0 Histogram: Values Number of atoms 5.55 - 11.27 2045 11.27 - 16.99 838 16.99 - 22.71 286 22.71 - 28.43 215 28.43 - 34.16 190 34.16 - 39.88 109 39.88 - 45.60 87 45.60 - 51.32 35 51.32 - 57.04 8 57.04 - 62.76 4 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1369 r_work=0.1196 r_free=0.1369 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1369 target_work(ml) = 3.755 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1368 target_work(ml) = 3.754 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 15 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 0.98 - 38.28 A, n_refl.=191132 (all), 2.01 % free)-----------| | | | r_work= 0.1195 r_free= 0.1368 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.754432 | | target function (ml) not normalized (work): 703171.256607 | | target function (ml) not normalized (free): 14736.930089 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 38.28 - 2.94 0.98 7400 127 0.1373 0.1499 5.6996 5.7842| | 2: 2.94 - 2.33 1.00 7339 128 0.1084 0.1387 5.0912 5.1956| | 3: 2.33 - 2.04 0.96 6939 150 0.0910 0.1206 4.6654 4.7718| | 4: 2.04 - 1.85 1.00 7170 155 0.0898 0.1050 4.392 4.5617| | 5: 1.85 - 1.72 0.99 7113 159 0.0931 0.1010 4.149 4.2528| | 6: 1.72 - 1.62 0.99 7102 142 0.0896 0.1087 3.9472 4.0773| | 7: 1.62 - 1.54 0.99 7104 148 0.0888 0.0996 3.8018 3.9524| | 8: 1.54 - 1.47 0.96 6798 152 0.0888 0.1333 3.6997 3.9099| | 9: 1.47 - 1.41 0.98 6938 155 0.0923 0.1105 3.6202 3.7389| | 10: 1.41 - 1.36 0.99 7022 150 0.0972 0.1185 3.553 3.6751| | 11: 1.36 - 1.32 0.99 6997 151 0.0989 0.1130 3.4829 3.5928| | 12: 1.32 - 1.28 0.98 6975 149 0.1031 0.1132 3.4574 3.5818| | 13: 1.28 - 1.25 0.98 6907 166 0.1038 0.1243 3.4357 3.5614| | 14: 1.25 - 1.22 0.98 7015 112 0.1104 0.1597 3.4314 3.683| | 15: 1.22 - 1.19 0.98 6956 137 0.1164 0.1249 3.4461 3.4927| | 16: 1.19 - 1.17 0.93 6604 132 0.1246 0.1541 3.4629 3.6545| | 17: 1.17 - 1.14 0.98 6940 135 0.1297 0.1226 3.4314 3.44| | 18: 1.14 - 1.12 0.98 6875 142 0.1379 0.1696 3.436 3.5319| | 19: 1.12 - 1.10 0.97 6948 106 0.1464 0.1738 3.4164 3.5942| | 20: 1.10 - 1.08 0.97 6884 147 0.1579 0.1561 3.4073 3.4256| | 21: 1.08 - 1.07 0.97 6852 152 0.1725 0.2121 3.4167 3.5039| | 22: 1.07 - 1.05 0.97 6836 135 0.1900 0.1943 3.4118 3.4121| | 23: 1.05 - 1.03 0.97 6827 159 0.2116 0.2030 3.4326 3.4847| | 24: 1.03 - 1.02 0.96 6784 133 0.2328 0.2260 3.4356 3.5109| | 25: 1.02 - 1.01 0.93 6552 130 0.2611 0.2514 3.4491 3.5232| | 26: 1.01 - 0.99 0.96 6767 158 0.2752 0.2855 3.4155 3.4238| | 27: 0.99 - 0.98 0.94 6647 131 0.3036 0.2799 3.4681 3.3952| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 7400 127 0.93 12.01 1.00 0.95 11582.49| | 2: 2.94 - 2.33 7339 128 0.92 13.06 0.99 0.95 5309.80| | 3: 2.33 - 2.04 6939 150 0.96 7.84 1.01 0.95 1755.06| | 4: 2.04 - 1.85 7170 155 0.96 7.71 1.00 0.95 1017.29| | 5: 1.85 - 1.72 7113 159 0.96 8.12 1.00 0.96 638.03| | 6: 1.72 - 1.62 7102 142 0.96 8.11 1.00 0.96 447.77| | 7: 1.62 - 1.54 7104 148 0.96 8.25 1.01 0.97 343.51| | 8: 1.54 - 1.47 6798 152 0.96 8.34 1.01 0.97 282.49| | 9: 1.47 - 1.41 6938 155 0.96 8.48 1.00 0.98 231.60| | 10: 1.41 - 1.36 7022 150 0.96 8.87 1.00 0.97 201.73| | 11: 1.36 - 1.32 6997 151 0.96 8.93 0.99 0.96 174.91| | 12: 1.32 - 1.28 6975 149 0.96 8.99 0.98 0.95 161.08| | 13: 1.28 - 1.25 6907 166 0.96 9.54 1.01 0.96 158.57| | 14: 1.25 - 1.22 7015 112 0.95 10.70 1.01 0.96 163.23| | 15: 1.22 - 1.19 6956 137 0.95 11.22 1.01 0.98 166.52| | 16: 1.19 - 1.17 6604 132 0.95 11.39 1.01 0.96 159.85| | 17: 1.17 - 1.14 6940 135 0.94 12.21 1.01 0.96 153.22| | 18: 1.14 - 1.12 6875 142 0.94 12.67 1.01 0.95 146.45| | 19: 1.12 - 1.10 6948 106 0.93 14.04 1.00 0.95 149.66| | 20: 1.10 - 1.08 6884 147 0.92 15.09 1.00 0.94 148.54| | 21: 1.08 - 1.07 6852 152 0.91 16.53 1.00 0.93 152.01| | 22: 1.07 - 1.05 6836 135 0.90 18.20 0.99 0.93 154.04| | 23: 1.05 - 1.03 6827 159 0.87 20.45 0.99 0.92 164.34| | 24: 1.03 - 1.02 6784 133 0.85 23.12 0.99 0.93 178.80| | 25: 1.02 - 1.01 6552 130 0.83 25.10 0.98 0.90 181.88| | 26: 1.01 - 0.99 6767 158 0.81 26.57 0.98 0.88 176.39| | 27: 0.99 - 0.98 6647 131 0.82 26.26 0.99 0.87 160.89| |alpha: min = 0.87 max = 0.98 mean = 0.95| |beta: min = 146.45 max = 11582.49 mean = 950.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 13.30| |phase err.(test): min = 0.00 max = 89.91 mean = 13.45| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1195 0.1368 n_refl.: 191132 re-set all scales: r(all,work,free)=0.1412 0.1410 0.1512 n_refl.: 191132 remove outliers: r(all,work,free)=0.1412 0.1410 0.1512 n_refl.: 191132 overall B=-0.05 to atoms: r(all,work,free)=0.1404 0.1402 0.1505 n_refl.: 191132 bulk-solvent and scaling: r(all,work,free)=0.1198 0.1195 0.1367 n_refl.: 191132 remove outliers: r(all,work,free)=0.1198 0.1195 0.1367 n_refl.: 191132 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 38.277-13.317 93.07 91 3 0.3876 361.388 318.403 0.388 0.913 0.188 13.296-10.522 97.03 97 1 0.2423 481.443 461.589 0.707 0.915 0.129 10.503-8.327 98.35 176 3 0.2204 503.054 494.159 0.897 0.916 0.107 8.318-6.595 100.00 360 8 0.2194 375.739 371.058 0.922 0.915 0.080 6.588-5.215 100.00 711 7 0.1978 345.267 334.111 0.919 0.916 0.080 5.214-4.128 98.38 1367 28 0.1253 505.020 498.699 1.018 0.917 0.039 4.126-3.266 94.74 2603 46 0.1172 460.353 452.467 1.085 0.918 0.005 3.266-2.585 99.86 5447 97 0.1130 310.543 306.904 1.066 0.919 0.000 2.585-2.046 97.45 10613 204 0.0972 234.287 231.626 1.073 0.922 0.000 2.046-1.619 99.39 21536 464 0.0909 138.663 137.287 1.090 0.926 0.000 1.619-1.281 98.00 42464 925 0.0942 74.648 74.000 1.079 0.932 0.000 1.281-0.980 96.53 101826 2055 0.1621 40.045 38.325 1.045 0.943 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 : 0.2035 0.2013 0.083 5.164 5.2 78.0 14.6 805 0.000 1_bss: 0.1801 0.1949 0.083 5.164 5.2 78.0 14.6 805 0.000 1_settarget: 0.1801 0.1949 0.083 5.164 5.2 78.0 14.6 805 0.000 1_nqh: 0.1804 0.1950 0.083 5.164 5.2 78.0 14.6 805 0.002 1_weight: 0.1804 0.1950 0.083 5.164 5.2 78.0 14.6 805 0.002 1_xyzrec: 0.1272 0.1493 0.037 1.164 5.2 78.0 14.6 805 0.152 1_adp: 0.1298 0.1562 0.037 1.164 5.2 73.0 15.0 805 0.152 1_regHadp: 0.1297 0.1557 0.037 1.164 5.2 73.0 15.0 805 0.152 1_occ: 0.1282 0.1548 0.037 1.164 5.2 73.0 15.0 805 0.152 2_bss: 0.1274 0.1540 0.037 1.164 5.3 73.2 15.1 805 0.152 2_settarget: 0.1274 0.1540 0.037 1.164 5.3 73.2 15.1 805 0.152 2_updatecdl: 0.1274 0.1540 0.037 1.185 5.3 73.2 15.1 805 0.152 2_nqh: 0.1274 0.1540 0.037 1.185 5.3 73.2 15.1 805 0.152 2_sol: 0.1271 0.1505 0.037 1.185 5.3 73.2 16.1 884 n/a 2_weight: 0.1271 0.1505 0.037 1.185 5.3 73.2 16.1 884 n/a 2_xyzrec: 0.1256 0.1533 0.041 1.142 5.3 73.2 16.1 884 n/a 2_adp: 0.1233 0.1518 0.041 1.142 5.3 71.7 16.3 884 n/a 2_regHadp: 0.1233 0.1519 0.041 1.142 5.3 71.7 16.3 884 n/a 2_occ: 0.1227 0.1515 0.041 1.142 5.3 71.7 16.3 884 n/a 3_bss: 0.1233 0.1523 0.041 1.142 5.3 71.7 16.3 884 n/a 3_settarget: 0.1233 0.1523 0.041 1.142 5.3 71.7 16.3 884 n/a 3_updatecdl: 0.1233 0.1523 0.041 1.146 5.3 71.7 16.3 884 n/a 3_nqh: 0.1233 0.1523 0.041 1.146 5.3 71.7 16.3 884 n/a 3_sol: 0.1250 0.1513 0.041 1.146 5.3 68.2 15.5 870 n/a 3_weight: 0.1250 0.1513 0.041 1.146 5.3 68.2 15.5 870 n/a 3_xyzrec: 0.1239 0.1428 0.035 1.099 5.3 68.2 15.5 870 n/a 3_adp: 0.1237 0.1388 0.035 1.099 5.5 67.7 15.3 870 n/a 3_regHadp: 0.1238 0.1389 0.035 1.099 5.5 67.7 15.3 870 n/a 3_occ: 0.1232 0.1381 0.035 1.099 5.5 67.7 15.3 870 n/a 4_bss: 0.1227 0.1371 0.035 1.099 5.5 67.7 15.2 870 n/a 4_settarget: 0.1227 0.1371 0.035 1.099 5.5 67.7 15.2 870 n/a 4_updatecdl: 0.1227 0.1371 0.035 1.104 5.5 67.7 15.2 870 n/a 4_nqh: 0.1227 0.1371 0.035 1.104 5.5 67.7 15.2 870 n/a 4_sol: 0.1208 0.1360 0.035 1.104 5.5 67.7 15.1 878 n/a 4_weight: 0.1208 0.1360 0.035 1.104 5.5 67.7 15.1 878 n/a 4_xyzrec: 0.1206 0.1359 0.035 1.143 5.5 67.7 15.1 878 n/a 4_adp: 0.1196 0.1355 0.035 1.143 5.5 67.1 15.1 878 n/a 4_regHadp: 0.1196 0.1355 0.035 1.143 5.5 67.1 15.1 878 n/a 4_occ: 0.1194 0.1355 0.035 1.143 5.5 67.1 15.1 878 n/a 5_bss: 0.1192 0.1353 0.035 1.143 5.5 67.0 15.0 878 n/a 5_settarget: 0.1192 0.1353 0.035 1.143 5.5 67.0 15.0 878 n/a 5_updatecdl: 0.1192 0.1353 0.035 1.143 5.5 67.0 15.0 878 n/a 5_nqh: 0.1192 0.1353 0.035 1.143 5.5 67.0 15.0 878 n/a 5_sol: 0.1191 0.1350 0.035 1.143 5.5 67.0 15.0 883 n/a 5_weight: 0.1191 0.1350 0.035 1.143 5.5 67.0 15.0 883 n/a 5_xyzrec: 0.1194 0.1356 0.036 1.137 5.5 67.0 15.0 883 n/a 5_adp: 0.1199 0.1361 0.036 1.137 5.6 66.8 14.9 883 n/a 5_regHadp: 0.1199 0.1361 0.036 1.137 5.6 66.8 14.9 883 n/a 5_occ: 0.1198 0.1365 0.036 1.137 5.6 66.8 14.9 883 n/a 6_bss: 0.1197 0.1363 0.036 1.137 5.5 66.8 14.9 883 n/a 6_settarget: 0.1197 0.1363 0.036 1.137 5.5 66.8 14.9 883 n/a 6_updatecdl: 0.1197 0.1363 0.036 1.137 5.5 66.8 14.9 883 n/a 6_nqh: 0.1197 0.1363 0.036 1.137 5.5 66.8 14.9 883 n/a 6_sol: 0.1195 0.1361 0.036 1.137 5.5 66.8 14.9 898 n/a 6_weight: 0.1195 0.1361 0.036 1.137 5.5 66.8 14.9 898 n/a 6_xyzrec: 0.1199 0.1371 0.037 1.130 5.5 66.8 14.9 898 n/a 6_adp: 0.1201 0.1371 0.037 1.130 5.6 66.1 14.8 898 n/a 6_regHadp: 0.1202 0.1371 0.037 1.130 5.6 66.1 14.8 898 n/a 6_occ: 0.1200 0.1373 0.037 1.130 5.6 66.1 14.8 898 n/a 7_bss: 0.1200 0.1372 0.037 1.130 5.3 65.8 14.6 898 n/a 7_settarget: 0.1200 0.1372 0.037 1.130 5.3 65.8 14.6 898 n/a 7_updatecdl: 0.1200 0.1372 0.037 1.131 5.3 65.8 14.6 898 n/a 7_nqh: 0.1200 0.1372 0.037 1.131 5.3 65.8 14.6 898 n/a 7_sol: 0.1197 0.1367 0.037 1.131 5.3 65.8 14.7 910 n/a 7_weight: 0.1197 0.1367 0.037 1.131 5.3 65.8 14.7 910 n/a 7_xyzrec: 0.1202 0.1372 0.038 1.122 5.3 65.8 14.7 910 n/a 7_adp: 0.1205 0.1378 0.038 1.122 5.4 65.0 14.6 910 n/a 7_regHadp: 0.1205 0.1378 0.038 1.122 5.4 65.0 14.6 910 n/a 7_occ: 0.1204 0.1379 0.038 1.122 5.4 65.0 14.6 910 n/a 8_bss: 0.1195 0.1368 0.038 1.122 5.5 65.1 14.7 910 n/a 8_settarget: 0.1195 0.1368 0.038 1.122 5.5 65.1 14.7 910 n/a 8_updatecdl: 0.1195 0.1368 0.038 1.122 5.5 65.1 14.7 910 n/a 8_nqh: 0.1195 0.1368 0.038 1.122 5.5 65.1 14.7 910 n/a 8_sol: 0.1195 0.1361 0.038 1.122 5.5 65.1 14.7 905 n/a 8_weight: 0.1195 0.1361 0.038 1.122 5.5 65.1 14.7 905 n/a 8_xyzrec: 0.1197 0.1365 0.038 1.124 5.5 65.1 14.7 905 n/a 8_adp: 0.1198 0.1368 0.038 1.124 5.5 64.1 14.6 905 n/a 8_regHadp: 0.1198 0.1368 0.038 1.124 5.5 64.1 14.6 905 n/a 8_occ: 0.1197 0.1369 0.038 1.124 5.5 64.1 14.6 905 n/a 9_bss: 0.1196 0.1366 0.038 1.124 5.5 64.1 14.6 905 n/a 9_settarget: 0.1196 0.1366 0.038 1.124 5.5 64.1 14.6 905 n/a 9_updatecdl: 0.1196 0.1366 0.038 1.124 5.5 64.1 14.6 905 n/a 9_nqh: 0.1196 0.1366 0.038 1.124 5.5 64.1 14.6 905 n/a 9_sol: 0.1193 0.1360 0.038 1.124 5.5 64.1 14.6 914 n/a 9_weight: 0.1193 0.1360 0.038 1.124 5.5 64.1 14.6 914 n/a 9_xyzrec: 0.1197 0.1370 0.039 1.113 5.5 64.1 14.6 914 n/a 9_adp: 0.1197 0.1372 0.039 1.113 5.5 63.1 14.6 914 n/a 9_regHadp: 0.1197 0.1373 0.039 1.113 5.5 63.1 14.6 914 n/a 9_occ: 0.1196 0.1373 0.039 1.113 5.5 63.1 14.6 914 n/a 10_bss: 0.1195 0.1371 0.039 1.113 5.5 63.1 14.6 914 n/a 10_settarget: 0.1195 0.1371 0.039 1.113 5.5 63.1 14.6 914 n/a 10_updatecdl: 0.1195 0.1371 0.039 1.112 5.5 63.1 14.6 914 n/a 10_setrh: 0.1196 0.1371 0.039 1.112 5.5 63.1 14.6 914 n/a 10_nqh: 0.1196 0.1371 0.039 1.112 5.5 63.1 14.6 914 n/a 10_sol: 0.1196 0.1366 0.039 1.112 5.5 63.1 14.6 913 n/a 10_weight: 0.1196 0.1366 0.039 1.112 5.5 63.1 14.6 913 n/a 10_xyzrec: 0.1196 0.1368 0.039 1.150 5.5 63.1 14.6 913 n/a 10_adp: 0.1196 0.1369 0.039 1.150 5.5 62.8 14.6 913 n/a 10_regHadp: 0.1196 0.1369 0.039 1.150 5.5 62.8 14.6 913 n/a 10_occ: 0.1195 0.1368 0.039 1.150 5.5 62.8 14.6 913 n/a end: 0.1195 0.1368 0.039 1.150 5.5 62.7 14.5 913 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4047050_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY4/unrestrained/shake_4047050_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 7.1700 Refinement macro-cycles (run) : 12037.0200 Write final files (write_after_run_outputs) : 173.1900 Total : 12217.3800 Total CPU time: 3.40 hours =========================== phenix.refine: finished =========================== # Date 2025-01-12 Time 18:40:48 PST -0800 (1736736048.31 s) Start R-work = 0.1801, R-free = 0.1949 Final R-work = 0.1195, R-free = 0.1368 =============================================================================== Job complete usr+sys time: 12520.92 seconds wall clock time: 209 minutes 39.31 seconds (12579.31 seconds total)