Starting phenix.refine on Wed Dec 11 09:10:41 2024 by pafonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 5SY6_modified.updated.pdb Found miller_array, 5SY6.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- ordered_solvent=true main.number_of_mac=5 ordered_solvent.mode=every_macro_cycle miller_array.labels.name=IOBS,SIGIOBS overwrite=true Found labels in command-line ---------------------------- Combined labels PHIL -------------------- data_manager { miller_array { labels { name = IOBS,SIGIOBS } } } No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "5SY6_modified.updated.pdb" } default_model = "5SY6_modified.updated.pdb" miller_array { file = "5SY6.mtz" labels { name = "IOBS,SIGIOBS" array_type = unknown amplitude bool complex hendrickson_lattman \ integer *intensity nonsense } user_selected_labels = "IOBS,SIGIOBS" } default_miller_array = "5SY6.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 } } main { ordered_solvent = true number_of_macro_cycles = 5 } ordered_solvent { mode = second_half filter_only *every_macro_cycle \ every_macro_cycle_after_first } } output { overwrite = true } Starting job =============================================================================== Monomer Library directory: "/Users/pafonine/Desktop/all/phenix/modules/chem_data/mon_lib" Total number of atoms: 3079 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 2805 Classifications: {'peptide': 187} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 274 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 256} Link IDs: {None: 256} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N LYS A 41 " occ=0.52 ... (20 atoms not shown) pdb=" HZ3 LYS A 41 " occ=0.52 residue: pdb=" N CYS A 53 " occ=0.70 ... (9 atoms not shown) pdb=" HG CYS A 53 " occ=0.70 residue: pdb=" N GLU A 64 " occ=0.53 ... (13 atoms not shown) pdb=" HG3 GLU A 64 " occ=0.53 residue: pdb=" N GLY A 65 " occ=0.53 ... (5 atoms not shown) pdb=" HA3 GLY A 65 " occ=0.53 residue: pdb=" N PRO A 66 " occ=0.53 ... (12 atoms not shown) pdb=" HD3 PRO A 66 " occ=0.53 residue: pdb=" N TYR A 67 " occ=0.53 ... (19 atoms not shown) pdb=" HH TYR A 67 " occ=0.53 residue: pdb=" N ASN A 76 " occ=0.75 ... (12 atoms not shown) pdb="HD22 ASN A 76 " occ=0.75 residue: pdb=" N GLN A 80 " occ=0.54 ... (15 atoms not shown) pdb="HE22 GLN A 80 " occ=0.54 residue: pdb=" N GLU A 90 " occ=0.59 ... (13 atoms not shown) pdb=" HG3 GLU A 90 " occ=0.59 residue: pdb=" N LYS A 93 " occ=0.57 ... (20 atoms not shown) pdb=" HZ3 LYS A 93 " occ=0.57 residue: pdb=" N GLU A 94 " occ=0.52 ... (13 atoms not shown) pdb=" HG3 GLU A 94 " occ=0.52 residue: pdb=" N GLU A 96 " occ=0.57 ... (13 atoms not shown) pdb=" HG3 GLU A 96 " occ=0.57 ... (remaining 20 not shown) Time building chain proxies: 0.55, per 1000 atoms: 0.18 Number of scatterers: 3079 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 520 8.00 N 240 7.00 C 869 6.00 H 1441 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.20 Conformation dependent library (CDL) restraints added in 33.3 milliseconds Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 1436 1.03 - 1.22: 53 1.22 - 1.42: 474 1.42 - 1.61: 863 1.61 - 1.81: 13 Bond restraints: 2839 Sorted by residual: bond pdb=" C LYS A 93 " pdb=" N GLU A 94 " ideal model delta sigma weight residual 1.335 1.530 -0.195 1.31e-02 5.83e+03 2.22e+02 bond pdb=" C GLU A 96 " pdb=" N ASN A 97 " ideal model delta sigma weight residual 1.335 1.421 -0.086 1.31e-02 5.83e+03 4.29e+01 bond pdb=" CD GLN A 45 " pdb=" NE2 GLN A 45 " ideal model delta sigma weight residual 1.328 1.246 0.082 2.10e-02 2.27e+03 1.53e+01 bond pdb=" CB LEU A 77 " pdb=" CG LEU A 77 " ideal model delta sigma weight residual 1.530 1.601 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CD GLU A 96 " pdb=" OE2 GLU A 96 " ideal model delta sigma weight residual 1.249 1.187 0.062 1.90e-02 2.77e+03 1.08e+01 ... (remaining 2834 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 4995 2.68 - 5.35: 179 5.35 - 8.03: 9 8.03 - 10.71: 1 10.71 - 13.38: 1 Bond angle restraints: 5185 Sorted by residual: angle pdb=" C2 DTT A 201 " pdb=" C3 DTT A 201 " pdb=" O3 DTT A 201 " ideal model delta sigma weight residual 104.38 117.76 -13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" C ARG A 156 " ideal model delta sigma weight residual 113.12 118.19 -5.07 1.25e+00 6.40e-01 1.64e+01 angle pdb=" C CYS A 106 " pdb=" CA CYS A 106 " pdb=" CB CYS A 106 " ideal model delta sigma weight residual 110.42 118.19 -7.77 1.99e+00 2.53e-01 1.52e+01 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 117.69 -3.89 1.00e+00 1.00e+00 1.52e+01 angle pdb=" N SER A 47 " pdb=" CA SER A 47 " pdb=" C SER A 47 " ideal model delta sigma weight residual 111.28 115.46 -4.18 1.09e+00 8.42e-01 1.47e+01 ... (remaining 5180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 870 17.36 - 34.71: 72 34.71 - 52.06: 32 52.06 - 69.42: 11 69.42 - 86.77: 2 Dihedral angle restraints: 987 sinusoidal: 762 harmonic: 225 Sorted by residual: dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual -180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" N GLY A 75 " pdb=" CA GLY A 75 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 163.79 16.21 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 178 0.145 - 0.290: 44 0.290 - 0.435: 3 0.435 - 0.580: 0 0.580 - 0.724: 1 Chirality restraints: 226 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.98e+00 ... (remaining 223 not shown) Planarity restraints: 421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.047 2.00e-02 2.50e+03 2.15e-02 1.38e+01 pdb=" CG PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.000 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.045 2.00e-02 2.50e+03 2.10e-02 1.33e+01 pdb=" CG PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.028 2.00e-02 2.50e+03 1.64e-02 6.05e+00 pdb=" CG HIS A 126 " -0.034 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.016 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.003 2.00e-02 2.50e+03 ... (remaining 418 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 453 2.25 - 2.84: 7138 2.84 - 3.43: 9251 3.43 - 4.01: 13784 4.01 - 4.60: 19744 Nonbonded interactions: 50370 Sorted by model distance: nonbonded pdb=" HZ3 LYS A 93 " pdb=" O HOH A 382 " model vdw 1.663 2.450 nonbonded pdb=" HZ2 LYS A 93 " pdb=" O HOH A 382 " model vdw 1.684 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.747 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.876 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.877 2.450 ... (remaining 50365 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: 5 Type Number sf(0) Gaussians S 9 15.96 2 O 520 7.97 2 N 240 6.97 2 C 869 5.97 2 H 1441 1.00 2 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 = 3079 n_use_u_iso = 1441 n_use_u_aniso = 1638 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 = 3079 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3079 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1441 aniso = 1638) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (561 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" } } main { ordered_solvent = True number_of_macro_cycles = 5 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False } ordered_solvent { mode = second_half filter_only *every_macro_cycle \ every_macro_cycle_after_first } } output { prefix = "5SY6_modified.updated_refine" serial = 1 target_output_format = None *pdb mmcif overwrite = True } #phil __OFF__ ================================== Hydrogens ================================== TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. Total: count: 1441 occupancy sum: 1376.65 (% of total atoms 46.76) Rotatable: count: 465 occupancy sum: 454.20 (% of total atoms 15.43) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2477 r_free= 0.1707 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.535709 | | target function (ml) not normalized (work): 211239.760976 | | target function (ml) not normalized (free): 10888.318004 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.58 1.00 2941 171 0.3114 0.2198 7.0332 4.9628| | 2: 3.57 - 2.84 1.00 2876 122 0.2433 0.1843 4.3628 4.3688| | 3: 2.84 - 2.48 1.00 2833 165 0.2308 0.1692 4.1261 4.1599| | 4: 2.47 - 2.25 1.00 2825 136 0.2278 0.1249 3.807 3.8178| | 5: 2.25 - 2.09 1.00 2756 127 0.2397 0.1367 3.7684 3.7992| | 6: 2.09 - 1.97 1.00 2846 113 0.2429 0.1537 3.3031 3.4364| | 7: 1.97 - 1.87 1.00 2787 165 0.2405 0.1433 2.848 2.9538| | 8: 1.87 - 1.79 1.00 2789 144 0.2245 0.1430 2.768 2.8306| | 9: 1.79 - 1.72 1.00 2745 138 0.2155 0.1410 2.5184 2.6706| | 10: 1.72 - 1.66 1.00 2789 158 0.2112 0.1291 2.3985 2.4977| | 11: 1.66 - 1.61 1.00 2740 147 0.2197 0.1288 2.3402 2.3879| | 12: 1.61 - 1.56 1.00 2787 146 0.2221 0.1421 2.1601 2.3107| | 13: 1.56 - 1.52 1.00 2745 130 0.2265 0.1373 2.1193 2.2233| | 14: 1.52 - 1.48 1.00 2803 134 0.2258 0.1284 2.0459 2.1556| | 15: 1.48 - 1.45 1.00 2738 128 0.2258 0.1527 1.9668 2.1123| | 16: 1.45 - 1.42 1.00 2756 161 0.2318 0.1477 1.9408 2.0291| | 17: 1.42 - 1.39 1.00 2785 139 0.2331 0.1504 1.9112 2.0268| | 18: 1.39 - 1.36 1.00 2741 179 0.2337 0.1627 1.8815 2.0543| | 19: 1.36 - 1.34 1.00 2807 134 0.2296 0.1715 1.8778 2.0142| | 20: 1.34 - 1.32 1.00 2696 147 0.2315 0.1700 1.8813 1.947| | 21: 1.32 - 1.30 1.00 2785 112 0.2333 0.1688 1.8646 1.8522| | 22: 1.29 - 1.27 1.00 2704 152 0.2398 0.1927 1.8567 1.9659| | 23: 1.27 - 1.26 1.00 2802 156 0.2451 0.2002 1.86 1.9639| | 24: 1.26 - 1.24 1.00 2744 132 0.2424 0.1999 1.8455 1.9533| | 25: 1.24 - 1.22 1.00 2734 148 0.2500 0.2287 1.8459 1.9716| | 26: 1.22 - 1.21 1.00 2727 135 0.2521 0.1878 1.8329 1.8853| | 27: 1.21 - 1.19 1.00 2814 148 0.2674 0.2190 1.8619 1.8609| | 28: 1.19 - 1.18 1.00 2671 147 0.2689 0.2380 1.8649 1.8673| | 29: 1.18 - 1.16 1.00 2800 134 0.2672 0.2427 1.8504 1.9208| | 30: 1.16 - 1.15 1.00 2740 148 0.2786 0.2602 1.8396 1.8863| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 49.25 - 3.58 2941 171 0.87 19.19 0.75 0.23 1547.21| | 2: 3.57 - 2.84 2876 122 0.80 26.58 1.27 0.23 1547.21| | 3: 2.84 - 2.48 2833 165 0.73 32.41 1.25 0.24 1274.16| | 4: 2.47 - 2.25 2825 136 0.82 25.20 1.26 0.26 565.54| | 5: 2.25 - 2.09 2756 127 0.78 28.99 1.29 0.26 565.54| | 6: 2.09 - 1.97 2846 113 0.85 20.45 1.30 0.26 290.67| | 7: 1.97 - 1.87 2787 165 0.93 12.50 1.29 0.26 56.24| | 8: 1.87 - 1.79 2789 144 0.90 16.41 1.26 0.26 56.24| | 9: 1.79 - 1.72 2745 138 0.92 12.83 1.25 0.26 29.79| | 10: 1.72 - 1.66 2789 158 0.92 13.82 1.24 0.26 24.49| | 11: 1.66 - 1.61 2740 147 0.91 14.54 1.26 0.26 23.49| | 12: 1.61 - 1.56 2787 146 0.94 11.35 1.26 0.26 13.33| | 13: 1.56 - 1.52 2745 130 0.93 12.82 1.26 0.26 13.33| | 14: 1.52 - 1.48 2803 134 0.93 13.19 1.26 0.26 11.92| | 15: 1.48 - 1.45 2738 128 0.94 12.30 1.26 0.26 9.33| | 16: 1.45 - 1.42 2756 161 0.93 13.53 1.26 0.26 9.33| | 17: 1.42 - 1.39 2785 139 0.93 13.25 1.25 0.26 8.26| | 18: 1.39 - 1.36 2741 179 0.93 13.77 1.25 0.26 7.64| | 19: 1.36 - 1.34 2807 134 0.92 14.26 1.24 0.26 7.64| | 20: 1.34 - 1.32 2696 147 0.93 14.00 1.23 0.26 6.95| | 21: 1.32 - 1.30 2785 112 0.92 15.06 1.22 0.26 6.90| | 22: 1.29 - 1.27 2704 152 0.92 15.62 1.22 0.26 6.87| | 23: 1.27 - 1.26 2802 156 0.91 16.46 1.22 0.25 6.71| | 24: 1.26 - 1.24 2744 132 0.91 16.71 1.21 0.25 6.71| | 25: 1.24 - 1.22 2734 148 0.90 18.02 1.21 0.25 6.74| | 26: 1.22 - 1.21 2727 135 0.89 19.16 1.20 0.24 6.79| | 27: 1.21 - 1.19 2814 148 0.88 19.77 1.20 0.24 6.79| | 28: 1.19 - 1.18 2671 147 0.87 21.38 1.18 0.23 6.96| | 29: 1.18 - 1.16 2800 134 0.86 21.85 1.16 0.23 7.02| | 30: 1.16 - 1.15 2740 148 0.85 23.41 1.15 0.23 7.02| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 6.71 max = 1547.21 mean = 210.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.89| |phase err.(work): min = 0.00 max = 90.00 mean = 17.66| |phase err.(test): min = 0.00 max = 89.43 mean = 17.48| |-----------------------------------------------------------------------------| ----------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 : 0.015 0.195 1398 Z= 0.908 Angle : 1.471 13.385 1887 Z= 0.874 Chirality : 0.122 0.724 226 Planarity : 0.010 0.063 244 Dihedral : 12.826 86.770 533 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.54 % Allowed : 0.54 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.00 (0.57), residues: 185 helix: 0.19 (0.54), residues: 86 sheet: -0.14 (0.81), residues: 36 loop : 0.14 (0.68), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.004 ARG A 48 TYR 0.024 0.008 TYR A 139 PHE 0.053 0.016 PHE A 119 HIS 0.007 0.004 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.48 3.80 0 1638 Protein: 8.85 115.78 16.01 3.81 0 1374 Water: 11.36 119.30 38.02 N/A 0 256 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.48 N/A 0 1638 Histogram: Values Number of atoms 8.85 - 19.89 1202 19.89 - 30.94 194 30.94 - 41.98 96 41.98 - 53.03 83 53.03 - 64.07 39 64.07 - 75.12 10 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2477 r_free= 0.1707 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.535709 | | target function (ml) not normalized (work): 211239.760976 | | target function (ml) not normalized (free): 10888.318004 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2430 0.2478 0.1708 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2430 0.2478 0.1708 n_refl.: 87602 remove outliers: r(all,work,free)=0.1716 0.1719 0.1708 n_refl.: 87594 overall B=0.18 to atoms: r(all,work,free)=0.1748 0.1751 0.1725 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1365 0.1356 0.1552 n_refl.: 87594 remove outliers: r(all,work,free)=0.1362 0.1352 0.1552 n_refl.: 87588 ======================== 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 32.574-11.894 94.79 86 5 0.4998 370.983 307.608 0.513 1.000 0.320 11.894-9.307 98.02 95 4 0.2192 606.706 573.631 0.934 1.003 0.336 9.237-7.194 99.55 212 7 0.2597 494.929 475.575 0.937 1.004 0.332 7.162-5.571 100.00 427 22 0.2570 370.383 356.624 0.913 1.004 0.278 5.546-4.326 100.00 867 58 0.1454 508.444 502.291 0.957 1.004 0.214 4.315-3.360 100.00 1859 96 0.1251 483.534 478.553 1.001 1.003 0.189 3.356-2.611 100.00 3867 181 0.1380 317.657 315.034 0.993 1.003 0.043 2.608-2.026 99.99 8198 413 0.1139 210.577 209.373 1.003 1.001 0.000 2.025-1.573 100.00 17313 902 0.1080 102.835 103.139 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1372 45.601 45.047 1.012 0.995 0.000 1.221-1.150 99.97 13689 708 0.2216 28.732 26.814 0.966 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0018 b_overall=0.0425 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1352 r_free=0.1552 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1352 r_free=0.1552 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1352 r_free=0.1552 | n_water=256 | time (s): 1.000 (total time: 1.000) Filter (dist) r_work=0.1362 r_free=0.1549 | n_water=249 | time (s): 7.900 (total time: 8.900) Filter (q & B) r_work=0.1363 r_free=0.1548 | n_water=246 | time (s): 1.490 (total time: 10.390) Compute maps r_work=0.1363 r_free=0.1548 | n_water=246 | time (s): 0.730 (total time: 11.120) Filter (map) r_work=0.1406 r_free=0.1555 | n_water=204 | time (s): 1.460 (total time: 12.580) Find peaks r_work=0.1406 r_free=0.1555 | n_water=204 | time (s): 0.190 (total time: 12.770) Add new water r_work=0.1483 r_free=0.1639 | n_water=332 | time (s): 1.390 (total time: 14.160) Refine new water occ: r_work=0.1394 r_free=0.1557 adp: r_work=0.1344 r_free=0.1517 occ: r_work=0.1352 r_free=0.1530 adp: r_work=0.1334 r_free=0.1514 occ: r_work=0.1335 r_free=0.1517 adp: r_work=0.1331 r_free=0.1513 ADP+occupancy (water only), MIN, final r_work=0.1331 r_free=0.1513 r_work=0.1331 r_free=0.1513 | n_water=332 | time (s): 40.970 (total time: 55.130) Filter (q & B) r_work=0.1331 r_free=0.1514 | n_water=330 | time (s): 1.440 (total time: 56.570) Filter (dist only) r_work=0.1332 r_free=0.1514 | n_water=329 | time (s): 10.290 (total time: 66.860) ========================= Local real-space refinement ========================= Before: r_work=0.1332 r_free=0.1514 29 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.339 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.9581 time to fit residues: 28.4102 After: r_work=0.1358 r_free=0.1547 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.830394 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2007.588489 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 0.1380 0.1611 0.0231 0.008 1.0 4.6 0.5 0.0 0 11.415 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1380 r_free=0.1611 30 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.345 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2045 After: r_work=0.1380 r_free=0.1611 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.80 16.11 2.31 2.669 18.644 2007.588 0.024 13.59 16.64 3.05 3.038 19.132 2007.588 0.020 Individual atomic B min max mean iso aniso Overall: 5.48 118.16 20.94 2.99 125 1586 Protein: 5.48 118.16 17.05 3.00 0 1374 Water: 11.38 77.27 37.04 N/A 125 204 Other: 22.82 34.64 28.24 N/A 0 8 Chain A: 5.48 118.16 19.47 N/A 0 1586 Chain S: 14.84 74.74 39.66 N/A 125 0 Histogram: Values Number of atoms 5.48 - 16.74 1025 16.74 - 28.01 305 28.01 - 39.28 178 39.28 - 50.55 126 50.55 - 61.82 46 61.82 - 73.09 19 73.09 - 84.36 6 84.36 - 95.62 3 95.62 - 106.89 1 106.89 - 118.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1359 r_free=0.1664 r_work=0.1359 r_free=0.1661 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1359 r_free = 0.1661 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1345 r_free = 0.1629 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1345 r_free= 0.1629 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.017716 | | target function (ls_wunit_k1) not normalized (work): 1475.602528 | | target function (ls_wunit_k1) not normalized (free): 125.278128 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1359 0.1345 0.1629 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1735 0.1732 0.1829 n_refl.: 87588 remove outliers: r(all,work,free)=0.1735 0.1732 0.1829 n_refl.: 87588 overall B=0.04 to atoms: r(all,work,free)=0.1741 0.1738 0.1832 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1355 0.1341 0.1627 n_refl.: 87588 remove outliers: r(all,work,free)=0.1355 0.1341 0.1627 n_refl.: 87587 ======================== 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 32.574-11.894 93.75 85 5 0.3813 284.756 259.662 0.591 1.000 0.339 11.894-9.307 98.02 95 4 0.1546 469.721 464.412 0.936 1.002 0.338 9.237-7.194 99.55 212 7 0.1787 383.182 381.012 0.965 1.002 0.328 7.162-5.571 100.00 427 22 0.1843 286.756 281.073 0.928 1.002 0.270 5.546-4.326 100.00 867 58 0.1003 393.645 391.699 0.957 1.003 0.220 4.315-3.360 100.00 1859 96 0.0870 374.359 372.378 1.003 1.003 0.210 3.356-2.611 100.00 3867 181 0.1109 245.935 244.459 1.007 1.002 0.048 2.608-2.026 99.99 8198 413 0.1036 163.032 162.387 1.019 1.002 0.000 2.025-1.573 100.00 17313 902 0.1299 79.616 79.623 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1808 35.305 34.663 1.015 0.999 0.000 1.221-1.150 99.97 13689 708 0.2517 22.245 20.712 0.977 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0577 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1341 r_free=0.1627 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1341 r_free=0.1628 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1341 r_free=0.1628 | n_water=329 | time (s): 0.960 (total time: 0.960) Filter (dist) r_work=0.1341 r_free=0.1628 | n_water=329 | time (s): 8.750 (total time: 9.710) Filter (q & B) r_work=0.1342 r_free=0.1628 | n_water=328 | time (s): 1.510 (total time: 11.220) Compute maps r_work=0.1342 r_free=0.1628 | n_water=328 | time (s): 0.810 (total time: 12.030) Filter (map) r_work=0.1386 r_free=0.1634 | n_water=248 | time (s): 1.480 (total time: 13.510) Find peaks r_work=0.1386 r_free=0.1634 | n_water=248 | time (s): 0.230 (total time: 13.740) Add new water r_work=0.1493 r_free=0.1764 | n_water=382 | time (s): 1.420 (total time: 15.160) Refine new water occ: r_work=0.1402 r_free=0.1643 adp: r_work=0.1348 r_free=0.1616 occ: r_work=0.1356 r_free=0.1602 adp: r_work=0.1332 r_free=0.1596 occ: r_work=0.1334 r_free=0.1585 adp: r_work=0.1327 r_free=0.1588 ADP+occupancy (water only), MIN, final r_work=0.1327 r_free=0.1588 r_work=0.1327 r_free=0.1588 | n_water=382 | time (s): 26.310 (total time: 41.470) Filter (q & B) r_work=0.1331 r_free=0.1592 | n_water=375 | time (s): 1.550 (total time: 43.020) Filter (dist only) r_work=0.1331 r_free=0.1593 | n_water=373 | time (s): 11.420 (total time: 54.440) ========================= Local real-space refinement ========================= Before: r_work=0.1331 r_free=0.1593 22 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.353 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.8533 time to fit residues: 19.3611 After: r_work=0.1346 r_free=0.1607 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.563443 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1607.101059 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 0.1330 0.1616 0.0286 0.008 1.0 5.3 0.5 0.0 0 12.782 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1330 r_free=0.1616 23 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.340 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1938 After: r_work=0.1330 r_free=0.1616 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.30 16.16 2.86 3.736 21.729 1607.101 0.017 12.69 15.59 2.90 4.075 21.605 1607.101 0.016 Individual atomic B min max mean iso aniso Overall: 7.00 113.34 21.45 2.69 172 1583 Protein: 7.00 113.34 16.82 2.69 0 1374 Water: 11.06 74.05 38.39 N/A 172 201 Other: 22.77 34.43 27.31 N/A 0 8 Chain A: 7.00 113.34 19.12 N/A 0 1583 Chain S: 14.14 65.46 42.91 N/A 172 0 Histogram: Values Number of atoms 7.00 - 17.63 1083 17.63 - 28.27 251 28.27 - 38.90 178 38.90 - 49.54 142 49.54 - 60.17 65 60.17 - 70.81 23 70.81 - 81.44 7 81.44 - 92.07 3 92.07 - 102.71 1 102.71 - 113.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1269 r_free=0.1559 r_work=0.1269 r_free=0.1559 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1269 r_free = 0.1559 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1268 r_free = 0.1542 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87587 (all), 4.90 % free)------------| | | | r_work= 0.1268 r_free= 0.1542 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.015690 | | target function (ls_wunit_k1) not normalized (work): 1306.859507 | | target function (ls_wunit_k1) not normalized (free): 114.543197 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1282 0.1268 0.1542 n_refl.: 87587 re-set all scales: r(all,work,free)=0.1660 0.1658 0.1739 n_refl.: 87587 remove outliers: r(all,work,free)=0.1660 0.1658 0.1739 n_refl.: 87587 overall B=0.02 to atoms: r(all,work,free)=0.1663 0.1661 0.1741 n_refl.: 87587 bulk-solvent and scaling: r(all,work,free)=0.1280 0.1267 0.1541 n_refl.: 87587 remove outliers: r(all,work,free)=0.1280 0.1266 0.1541 n_refl.: 87586 ======================== 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 32.574-11.894 92.71 84 5 0.3508 282.090 264.429 0.612 1.002 0.350 11.894-9.307 98.02 95 4 0.1442 469.721 465.923 0.950 1.003 0.347 9.237-7.194 99.55 212 7 0.1675 383.182 382.446 0.983 1.003 0.294 7.162-5.571 100.00 427 22 0.1703 286.756 282.429 0.935 1.003 0.270 5.546-4.326 100.00 867 58 0.0945 393.645 391.060 0.959 1.003 0.230 4.315-3.360 100.00 1859 96 0.0830 374.359 372.872 1.002 1.003 0.230 3.356-2.611 100.00 3867 181 0.1063 245.935 244.777 1.009 1.003 0.072 2.608-2.026 99.99 8198 413 0.0984 163.032 162.572 1.020 1.002 0.000 2.025-1.573 100.00 17313 902 0.1226 79.616 79.761 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1684 35.305 34.760 1.019 0.999 0.000 1.221-1.150 99.97 13689 708 0.2416 22.245 20.777 0.984 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0283 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1266 r_free=0.1541 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1266 r_free=0.1541 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1266 r_free=0.1541 | n_water=373 | time (s): 1.000 (total time: 1.000) Filter (dist) r_work=0.1266 r_free=0.1541 | n_water=373 | time (s): 10.150 (total time: 11.150) Filter (q & B) r_work=0.1266 r_free=0.1541 | n_water=373 | time (s): 0.500 (total time: 11.650) Compute maps r_work=0.1266 r_free=0.1541 | n_water=373 | time (s): 0.830 (total time: 12.480) Filter (map) r_work=0.1320 r_free=0.1570 | n_water=265 | time (s): 1.530 (total time: 14.010) Find peaks r_work=0.1320 r_free=0.1570 | n_water=265 | time (s): 0.220 (total time: 14.230) Add new water r_work=0.1437 r_free=0.1687 | n_water=411 | time (s): 1.440 (total time: 15.670) Refine new water occ: r_work=0.1329 r_free=0.1586 adp: r_work=0.1331 r_free=0.1588 occ: r_work=0.1307 r_free=0.1572 adp: r_work=0.1307 r_free=0.1572 occ: r_work=0.1291 r_free=0.1564 adp: r_work=0.1287 r_free=0.1560 ADP+occupancy (water only), MIN, final r_work=0.1287 r_free=0.1560 r_work=0.1287 r_free=0.1560 | n_water=411 | time (s): 77.930 (total time: 93.600) Filter (q & B) r_work=0.1291 r_free=0.1561 | n_water=398 | time (s): 1.520 (total time: 95.120) Filter (dist only) r_work=0.1291 r_free=0.1561 | n_water=397 | time (s): 13.080 (total time: 108.200) ========================= Local real-space refinement ========================= Before: r_work=0.1291 r_free=0.1561 24 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.351 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.8807 time to fit residues: 21.7902 After: r_work=0.1303 r_free=0.1570 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.119825 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.768812 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 0.1300 0.1530 0.0231 0.007 1.0 6.4 0.5 0.0 0 1.060 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1300 r_free=0.1530 24 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.325 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2131 After: r_work=0.1300 r_free=0.1530 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.00 15.30 2.31 3.560 20.967 46.769 3.748 12.86 14.83 1.96 4.050 20.835 46.769 3.665 Individual atomic B min max mean iso aniso Overall: 9.28 108.61 20.45 2.31 199 1580 Protein: 9.28 108.61 16.45 2.32 0 1374 Water: 11.78 68.94 34.19 N/A 199 198 Other: 19.28 30.53 25.14 N/A 0 8 Chain A: 9.28 108.61 18.70 N/A 0 1580 Chain S: 13.98 57.14 34.37 N/A 199 0 Histogram: Values Number of atoms 9.28 - 19.21 1168 19.21 - 29.15 241 29.15 - 39.08 186 39.08 - 49.01 121 49.01 - 58.95 41 58.95 - 68.88 10 68.88 - 78.81 6 78.81 - 88.75 3 88.75 - 98.68 1 98.68 - 108.61 2 =========================== Idealize ADP of riding H ========================== r_work=0.1286 r_free=0.1483 r_work=0.1288 r_free=0.1483 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1288 r_free = 0.1483 target_work(ml) = 3.665 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1275 r_free = 0.1468 target_work(ml) = 3.659 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87586 (all), 4.90 % free)------------| | | | r_work= 0.1275 r_free= 0.1468 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.658846 | | target function (ml) not normalized (work): 304745.257597 | | target function (ml) not normalized (free): 16067.842671 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1285 0.1275 0.1468 n_refl.: 87586 re-set all scales: r(all,work,free)=0.1646 0.1646 0.1682 n_refl.: 87586 remove outliers: r(all,work,free)=0.1646 0.1646 0.1682 n_refl.: 87586 overall B=-0.03 to atoms: r(all,work,free)=0.1640 0.1639 0.1678 n_refl.: 87586 bulk-solvent and scaling: r(all,work,free)=0.1279 0.1270 0.1446 n_refl.: 87586 remove outliers: r(all,work,free)=0.1278 0.1269 0.1446 n_refl.: 87584 ======================== 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 32.574-11.894 91.67 83 5 0.3957 279.410 253.374 0.517 1.000 0.321 11.894-9.307 98.02 95 4 0.2067 469.721 459.817 0.917 1.001 0.313 9.237-7.194 99.09 211 7 0.2225 381.270 377.990 0.971 1.002 0.250 7.162-5.571 100.00 427 22 0.2112 286.756 280.116 0.918 1.002 0.250 5.546-4.326 100.00 867 58 0.1214 393.645 388.787 0.951 1.002 0.195 4.315-3.360 100.00 1859 96 0.1033 374.359 371.259 0.995 1.002 0.190 3.356-2.611 100.00 3867 181 0.1269 245.935 243.469 1.000 1.002 0.062 2.608-2.026 99.99 8198 413 0.1129 163.032 161.880 1.013 1.002 0.000 2.025-1.573 100.00 17313 902 0.1083 79.616 79.694 1.028 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1332 35.305 34.885 1.026 1.001 0.000 1.221-1.150 99.97 13689 708 0.2155 22.245 20.890 0.988 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0904 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1269 r_free=0.1446 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1269 r_free=0.1446 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1269 r_free=0.1446 | n_water=397 | time (s): 0.980 (total time: 0.980) Filter (dist) r_work=0.1269 r_free=0.1446 | n_water=397 | time (s): 10.940 (total time: 11.920) Filter (q & B) r_work=0.1270 r_free=0.1450 | n_water=391 | time (s): 1.500 (total time: 13.420) Compute maps r_work=0.1270 r_free=0.1450 | n_water=391 | time (s): 0.770 (total time: 14.190) Filter (map) r_work=0.1303 r_free=0.1465 | n_water=277 | time (s): 1.500 (total time: 15.690) Find peaks r_work=0.1303 r_free=0.1465 | n_water=277 | time (s): 0.200 (total time: 15.890) Add new water r_work=0.1384 r_free=0.1554 | n_water=402 | time (s): 1.480 (total time: 17.370) Refine new water occ: r_work=0.1297 r_free=0.1473 adp: r_work=0.1298 r_free=0.1475 occ: r_work=0.1279 r_free=0.1455 adp: r_work=0.1279 r_free=0.1456 occ: r_work=0.1264 r_free=0.1434 adp: r_work=0.1262 r_free=0.1435 ADP+occupancy (water only), MIN, final r_work=0.1262 r_free=0.1435 r_work=0.1262 r_free=0.1435 | n_water=402 | time (s): 103.920 (total time: 121.290) Filter (q & B) r_work=0.1265 r_free=0.1437 | n_water=391 | time (s): 1.590 (total time: 122.880) Filter (dist only) r_work=0.1265 r_free=0.1437 | n_water=390 | time (s): 12.400 (total time: 135.280) ========================= Local real-space refinement ========================= Before: r_work=0.1265 r_free=0.1437 44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.337 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.8219 time to fit residues: 37.0727 After: r_work=0.1297 r_free=0.1453 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.009510 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.519312 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 0.1282 0.1444 0.0163 0.007 1.0 5.7 0.5 0.0 0 1.005 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1282 r_free=0.1444 44 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.329 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.1932 After: r_work=0.1282 r_free=0.1444 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.82 14.44 1.63 3.328 20.392 53.519 3.655 12.53 14.31 1.77 3.696 20.325 53.519 3.633 Individual atomic B min max mean iso aniso Overall: 9.33 104.09 20.03 2.20 194 1578 Protein: 9.33 104.09 16.20 2.20 0 1374 Water: 11.71 68.17 33.44 N/A 194 196 Other: 19.03 27.21 22.94 N/A 0 8 Chain A: 9.33 104.09 18.36 N/A 0 1578 Chain S: 14.10 52.63 33.56 N/A 194 0 Histogram: Values Number of atoms 9.33 - 18.80 1160 18.80 - 28.28 238 28.28 - 37.75 195 37.75 - 47.23 114 47.23 - 56.71 44 56.71 - 66.18 9 66.18 - 75.66 7 75.66 - 85.13 2 85.13 - 94.61 1 94.61 - 104.09 2 =========================== Idealize ADP of riding H ========================== r_work=0.1253 r_free=0.1431 r_work=0.1254 r_free=0.1431 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1254 r_free = 0.1431 target_work(ml) = 3.633 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1245 r_free = 0.1414 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1245 r_free= 0.1414 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.628197 | | target function (ml) not normalized (work): 302185.312247 | | target function (ml) not normalized (free): 15935.381329 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1254 0.1245 0.1414 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1618 0.1619 0.1627 n_refl.: 87584 remove outliers: r(all,work,free)=0.1618 0.1619 0.1627 n_refl.: 87584 overall B=-0.03 to atoms: r(all,work,free)=0.1613 0.1614 0.1623 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1254 0.1246 0.1413 n_refl.: 87584 remove outliers: r(all,work,free)=0.1253 0.1245 0.1413 n_refl.: 87583 ======================== 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 32.574-11.894 91.67 83 5 0.3945 279.410 251.208 0.512 1.001 0.327 11.894-9.307 97.03 94 4 0.2050 463.107 458.447 0.904 1.002 0.317 9.237-7.194 99.09 211 7 0.2271 381.270 375.081 0.967 1.002 0.250 7.162-5.571 100.00 427 22 0.2163 286.756 279.903 0.910 1.002 0.250 5.546-4.326 100.00 867 58 0.1220 393.645 389.123 0.951 1.002 0.190 4.315-3.360 100.00 1859 96 0.1053 374.359 371.036 0.996 1.002 0.190 3.356-2.611 100.00 3867 181 0.1266 245.935 243.597 1.002 1.002 0.072 2.608-2.026 99.99 8198 413 0.1114 163.032 161.911 1.012 1.002 0.000 2.025-1.573 100.00 17313 902 0.1030 79.616 79.792 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1271 35.305 34.939 1.025 1.000 0.000 1.221-1.150 99.97 13689 708 0.2129 22.245 20.918 0.987 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0796 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1245 r_free=0.1413 After: r_work=0.1245 r_free=0.1412 ================================== NQH flips ================================== r_work=0.1245 r_free=0.1412 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1245 r_free=0.1412 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1245 r_free=0.1412 | n_water=390 | time (s): 1.010 (total time: 1.010) Filter (dist) r_work=0.1245 r_free=0.1412 | n_water=390 | time (s): 10.420 (total time: 11.430) Filter (q & B) r_work=0.1245 r_free=0.1413 | n_water=387 | time (s): 1.490 (total time: 12.920) Compute maps r_work=0.1245 r_free=0.1413 | n_water=387 | time (s): 0.750 (total time: 13.670) Filter (map) r_work=0.1273 r_free=0.1441 | n_water=289 | time (s): 1.500 (total time: 15.170) Find peaks r_work=0.1273 r_free=0.1441 | n_water=289 | time (s): 0.200 (total time: 15.370) Add new water r_work=0.1348 r_free=0.1505 | n_water=412 | time (s): 1.450 (total time: 16.820) Refine new water occ: r_work=0.1268 r_free=0.1430 adp: r_work=0.1269 r_free=0.1432 occ: r_work=0.1252 r_free=0.1417 adp: r_work=0.1251 r_free=0.1418 occ: r_work=0.1238 r_free=0.1407 adp: r_work=0.1235 r_free=0.1406 ADP+occupancy (water only), MIN, final r_work=0.1235 r_free=0.1406 r_work=0.1235 r_free=0.1406 | n_water=412 | time (s): 90.350 (total time: 107.170) Filter (q & B) r_work=0.1239 r_free=0.1410 | n_water=401 | time (s): 1.510 (total time: 108.680) Filter (dist only) r_work=0.1239 r_free=0.1409 | n_water=399 | time (s): 12.230 (total time: 120.910) ========================= Local real-space refinement ========================= Before: r_work=0.1239 r_free=0.1409 43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.322 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.8853 time to fit residues: 38.9669 After: r_work=0.1270 r_free=0.1429 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.965625 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.379737 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 0.1277 0.1440 0.0163 0.007 1.1 6.4 0.5 0.0 0 0.983 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1277 r_free=0.1440 43 residues out of total 145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.327 TARDY: cannot create tardy model for: "LYS A 188 " (corrupted residue). Skipping it. outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2020 After: r_work=0.1277 r_free=0.1440 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.77 14.40 1.63 3.214 20.109 51.380 3.642 12.75 14.37 1.63 3.359 20.087 51.380 3.632 Individual atomic B min max mean iso aniso Overall: 9.33 100.38 19.90 2.06 203 1578 Protein: 9.33 100.38 16.07 2.07 0 1374 Water: 11.65 67.80 33.04 N/A 203 196 Other: 18.73 26.25 22.96 N/A 0 8 Chain A: 9.33 100.38 18.22 N/A 0 1578 Chain S: 13.93 54.37 32.95 N/A 203 0 Histogram: Values Number of atoms 9.33 - 18.43 1153 18.43 - 27.54 242 27.54 - 36.64 195 36.64 - 45.75 119 45.75 - 54.86 49 54.86 - 63.96 9 63.96 - 73.07 10 73.07 - 82.17 1 82.17 - 91.28 1 91.28 - 100.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1275 r_free=0.1437 r_work=0.1275 r_free=0.1437 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1275 r_free = 0.1437 target_work(ml) = 3.632 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1266 r_free = 0.1443 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| ======================= ordered solvent: final clean up ======================= Start r_work=0.1266 r_free=0.1443 | n_water=399 | time (s): 1.110 (total time: 1.110) Filter (dist) r_work=0.1266 r_free=0.1442 | n_water=398 | time (s): 13.170 (total time: 14.280) Filter (q & B) r_work=0.1266 r_free=0.1440 | n_water=392 | time (s): 1.640 (total time: 15.920) Compute maps r_work=0.1266 r_free=0.1440 | n_water=392 | time (s): 0.880 (total time: 16.800) Filter (map) r_work=0.1291 r_free=0.1459 | n_water=285 | time (s): 1.670 (total time: 18.470) Find peaks r_work=0.1291 r_free=0.1459 | n_water=285 | time (s): 0.040 (total time: 18.510) Add new water r_work=0.1291 r_free=0.1459 | n_water=285 | time (s): 0.040 (total time: 18.550) Refine new water r_work=0.1291 r_free=0.1459 | n_water=285 | time (s): 0.030 (total time: 18.580) Filter (q & B) r_work=0.1291 r_free=0.1459 | n_water=285 | time (s): 0.460 (total time: 19.040) Filter (dist only) r_work=0.1291 r_free=0.1459 | n_water=285 | time (s): 7.510 (total time: 26.550) ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1291 r_free= 0.1459 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 3.636892 | | target function (ml) not normalized (work): 302905.830407 | | target function (ml) not normalized (free): 15966.769076 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 1.00 2925 171 0.1479 0.1560 5.671 5.6874| | 2: 3.57 - 2.84 1.00 2888 124 0.1340 0.1595 5.3105 5.3212| | 3: 2.83 - 2.48 1.00 2820 163 0.1355 0.1488 5.0686 5.0911| | 4: 2.47 - 2.25 1.00 2825 136 0.1150 0.1164 4.7757 4.7954| | 5: 2.25 - 2.09 1.00 2756 127 0.1106 0.1268 4.7061 4.7773| | 6: 2.09 - 1.97 1.00 2846 113 0.1065 0.1258 4.4126 4.516| | 7: 1.97 - 1.87 1.00 2787 165 0.1076 0.1270 4.1278 4.1919| | 8: 1.87 - 1.79 1.00 2789 144 0.1143 0.1290 4.044 4.1104| | 9: 1.79 - 1.72 1.00 2745 138 0.1067 0.1301 3.779 3.9183| | 10: 1.72 - 1.66 1.00 2831 160 0.1078 0.1373 3.6708 3.8197| | 11: 1.66 - 1.61 1.00 2712 147 0.1032 0.1164 3.6036 3.6327| | 12: 1.61 - 1.56 1.00 2773 144 0.0994 0.1196 3.3819 3.45| | 13: 1.56 - 1.52 1.00 2745 130 0.1017 0.1074 3.3507 3.4198| | 14: 1.52 - 1.48 1.00 2803 134 0.1040 0.1208 3.2758 3.3865| | 15: 1.48 - 1.45 1.00 2738 128 0.1039 0.1361 3.1776 3.3192| | 16: 1.45 - 1.42 1.00 2756 161 0.1113 0.1289 3.1629 3.2374| | 17: 1.42 - 1.39 1.00 2785 139 0.1150 0.1368 3.1169 3.2347| | 18: 1.39 - 1.36 1.00 2741 179 0.1176 0.1418 3.0804 3.2737| | 19: 1.36 - 1.34 1.00 2807 134 0.1252 0.1636 3.0893 3.2793| | 20: 1.34 - 1.32 1.00 2696 147 0.1334 0.1462 3.072 3.114| | 21: 1.32 - 1.30 1.00 2785 112 0.1440 0.1597 3.0729 3.1298| | 22: 1.29 - 1.27 1.00 2704 152 0.1493 0.1820 3.0729 3.2234| | 23: 1.27 - 1.26 1.00 2802 156 0.1583 0.1820 3.081 3.1772| | 24: 1.26 - 1.24 1.00 2744 132 0.1648 0.1774 3.078 3.1841| | 25: 1.24 - 1.22 1.00 2733 148 0.1787 0.2371 3.0853 3.2792| | 26: 1.22 - 1.21 1.00 2727 135 0.1870 0.1777 3.1027 3.1779| | 27: 1.21 - 1.19 1.00 2814 148 0.2001 0.2116 3.1155 3.1345| | 28: 1.19 - 1.18 1.00 2671 147 0.2142 0.2320 3.1142 3.1515| | 29: 1.18 - 1.16 1.00 2800 134 0.2227 0.2362 3.1053 3.2002| | 30: 1.16 - 1.15 1.00 2739 148 0.2391 0.2509 3.0942 3.1427| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.57 - 3.58 2925 171 0.94 10.37 1.00 0.95 7024.66| | 2: 3.57 - 2.84 2888 124 0.91 14.65 1.01 0.95 7024.66| | 3: 2.83 - 2.48 2820 163 0.87 18.88 0.98 0.96 5886.75| | 4: 2.47 - 2.25 2825 136 0.90 15.96 1.00 0.96 2952.43| | 5: 2.25 - 2.09 2756 127 0.88 18.36 1.01 0.96 2952.43| | 6: 2.09 - 1.97 2846 113 0.91 14.79 1.01 0.96 1729.11| | 7: 1.97 - 1.87 2787 165 0.94 11.74 1.02 0.96 685.77| | 8: 1.87 - 1.79 2789 144 0.90 15.61 0.99 0.96 685.77| | 9: 1.79 - 1.72 2745 138 0.93 12.20 0.98 0.96 364.00| | 10: 1.72 - 1.66 2831 160 0.92 13.13 0.98 0.96 299.56| | 11: 1.66 - 1.61 2712 147 0.92 13.69 0.98 0.96 285.43| | 12: 1.61 - 1.56 2773 144 0.95 10.06 0.99 0.96 152.19| | 13: 1.56 - 1.52 2745 130 0.94 11.74 1.02 0.96 152.19| | 14: 1.52 - 1.48 2803 134 0.94 11.90 1.02 0.96 135.54| | 15: 1.48 - 1.45 2738 128 0.95 10.92 1.01 0.97 105.04| | 16: 1.45 - 1.42 2756 161 0.94 12.15 1.01 0.97 105.04| | 17: 1.42 - 1.39 2785 139 0.94 11.81 1.01 0.97 93.56| | 18: 1.39 - 1.36 2741 179 0.94 12.21 1.01 0.97 86.91| | 19: 1.36 - 1.34 2807 134 0.94 12.71 1.00 0.97 86.91| | 20: 1.34 - 1.32 2696 147 0.94 12.67 0.99 0.95 80.14| | 21: 1.32 - 1.30 2785 112 0.93 13.55 0.98 0.95 79.67| | 22: 1.29 - 1.27 2704 152 0.93 14.03 0.98 0.95 79.61| | 23: 1.27 - 1.26 2802 156 0.92 14.93 0.97 0.93 79.36| | 24: 1.26 - 1.24 2744 132 0.92 15.04 0.97 0.93 79.36| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.93 80.74| | 26: 1.22 - 1.21 2727 135 0.90 18.01 1.02 0.92 82.28| | 27: 1.21 - 1.19 2814 148 0.89 18.69 1.02 0.92 82.28| | 28: 1.19 - 1.18 2671 147 0.88 20.27 1.01 0.91 85.58| | 29: 1.18 - 1.16 2800 134 0.88 20.59 0.99 0.91 86.82| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.91 86.82| |alpha: min = 0.91 max = 0.97 mean = 0.95| |beta: min = 79.36 max = 7024.66 mean = 1084.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.86 mean = 14.62| |phase err.(test): min = 0.00 max = 89.64 mean = 14.65| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1299 0.1291 0.1459 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1717 0.1719 0.1711 n_refl.: 87583 remove outliers: r(all,work,free)=0.1717 0.1719 0.1711 n_refl.: 87583 overall B=-0.02 to atoms: r(all,work,free)=0.1714 0.1716 0.1709 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1287 0.1459 n_refl.: 87583 remove outliers: r(all,work,free)=0.1295 0.1287 0.1459 n_refl.: 87583 ======================== 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 32.574-11.894 91.67 83 5 0.3752 279.410 249.973 0.575 0.999 0.350 11.894-9.307 97.03 94 4 0.1807 463.107 452.595 0.909 1.001 0.342 9.237-7.194 99.09 211 7 0.2273 381.270 371.750 0.959 1.001 0.299 7.162-5.571 100.00 427 22 0.2190 286.756 277.541 0.921 1.002 0.280 5.546-4.326 100.00 867 58 0.1304 393.645 388.558 0.955 1.002 0.260 4.315-3.360 100.00 1859 96 0.1145 374.359 371.006 0.998 1.002 0.220 3.356-2.611 100.00 3867 181 0.1376 245.935 243.508 1.001 1.002 0.062 2.608-2.026 99.99 8198 413 0.1152 163.032 161.919 1.011 1.001 0.000 2.025-1.573 100.00 17313 902 0.1073 79.616 79.770 1.023 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1256 35.305 34.949 1.020 1.000 0.000 1.221-1.150 99.97 13689 708 0.2118 22.245 20.936 0.982 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0436 ================= 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 : 0.2477 0.1707 0.015 1.471 8.8 119.3 19.5 256 0.000 1_bss: 0.1352 0.1552 0.015 1.471 9.0 119.5 19.7 256 0.000 1_settarget: 0.1352 0.1552 0.015 1.471 9.0 119.5 19.7 256 0.000 1_nqh: 0.1352 0.1552 0.015 1.471 9.0 119.5 19.7 256 0.000 1_sol: 0.1332 0.1514 0.015 1.471 9.0 116.0 20.0 329 n/a 1_realsrl: 0.1358 0.1547 0.015 1.471 9.0 116.0 20.0 329 n/a 1_weight: 0.1358 0.1547 0.015 1.471 9.0 116.0 20.0 329 n/a 1_xyzrec: 0.1380 0.1611 0.008 1.023 9.0 116.0 20.0 329 n/a 1_realsrl2: 0.1380 0.1611 0.008 1.023 9.0 116.0 20.0 329 n/a 1_adp: 0.1359 0.1664 0.008 1.023 5.5 118.2 20.9 329 n/a 1_regHadp: 0.1359 0.1661 0.008 1.023 5.5 118.2 20.9 329 n/a 1_occ: 0.1345 0.1629 0.008 1.023 5.5 118.2 20.9 329 n/a 2_bss: 0.1341 0.1627 0.008 1.023 5.5 118.2 21.0 329 n/a 2_settarget: 0.1341 0.1627 0.008 1.023 5.5 118.2 21.0 329 n/a 2_updatecdl: 0.1341 0.1627 0.008 1.027 5.5 118.2 21.0 329 n/a 2_nqh: 0.1341 0.1628 0.008 1.027 5.5 118.2 21.0 329 n/a 2_sol: 0.1331 0.1593 0.008 1.027 5.5 118.2 21.7 373 n/a 2_realsrl: 0.1346 0.1607 0.008 1.027 5.5 118.2 21.7 373 n/a 2_weight: 0.1346 0.1607 0.008 1.027 5.5 118.2 21.7 373 n/a 2_xyzrec: 0.1330 0.1616 0.008 0.963 5.5 118.2 21.7 373 n/a 2_realsrl2: 0.1330 0.1616 0.008 0.963 5.5 118.2 21.7 373 n/a 2_adp: 0.1269 0.1559 0.008 0.963 7.0 113.3 21.5 373 n/a 2_regHadp: 0.1269 0.1559 0.008 0.963 7.0 113.3 21.5 373 n/a 2_occ: 0.1268 0.1542 0.008 0.963 7.0 113.3 21.5 373 n/a 3_bss: 0.1266 0.1541 0.008 0.963 7.0 113.4 21.5 373 n/a 3_settarget: 0.1266 0.1541 0.008 0.963 7.0 113.4 21.5 373 n/a 3_updatecdl: 0.1266 0.1541 0.008 0.964 7.0 113.4 21.5 373 n/a 3_nqh: 0.1266 0.1541 0.008 0.964 7.0 113.4 21.5 373 n/a 3_sol: 0.1291 0.1561 0.008 0.964 7.0 113.4 20.7 397 n/a 3_realsrl: 0.1303 0.1570 0.008 0.964 7.0 113.4 20.7 397 n/a 3_weight: 0.1303 0.1570 0.008 0.964 7.0 113.4 20.7 397 n/a 3_xyzrec: 0.1300 0.1530 0.007 1.008 7.0 113.4 20.7 397 n/a 3_realsrl2: 0.1300 0.1530 0.007 1.008 7.0 113.4 20.7 397 n/a 3_adp: 0.1286 0.1483 0.007 1.008 9.3 108.6 20.4 397 n/a 3_regHadp: 0.1288 0.1483 0.007 1.008 9.3 108.6 20.4 397 n/a 3_occ: 0.1275 0.1468 0.007 1.008 9.3 108.6 20.4 397 n/a 4_bss: 0.1269 0.1446 0.007 1.008 9.2 108.6 20.4 397 n/a 4_settarget: 0.1269 0.1446 0.007 1.008 9.2 108.6 20.4 397 n/a 4_updatecdl: 0.1269 0.1446 0.007 1.008 9.2 108.6 20.4 397 n/a 4_nqh: 0.1269 0.1446 0.007 1.008 9.2 108.6 20.4 397 n/a 4_sol: 0.1265 0.1437 0.007 1.008 9.2 108.6 20.1 390 n/a 4_realsrl: 0.1297 0.1453 0.007 1.008 9.2 108.6 20.1 390 n/a 4_weight: 0.1297 0.1453 0.007 1.008 9.2 108.6 20.1 390 n/a 4_xyzrec: 0.1282 0.1444 0.007 0.996 9.2 108.6 20.1 390 n/a 4_realsrl2: 0.1282 0.1444 0.007 0.996 9.2 108.6 20.1 390 n/a 4_adp: 0.1253 0.1431 0.007 0.996 9.3 104.1 20.0 390 n/a 4_regHadp: 0.1254 0.1431 0.007 0.996 9.3 104.1 20.0 390 n/a 4_occ: 0.1245 0.1414 0.007 0.996 9.3 104.1 20.0 390 n/a 5_bss: 0.1245 0.1413 0.007 0.996 9.3 104.1 20.0 390 n/a 5_settarget: 0.1245 0.1413 0.007 0.996 9.3 104.1 20.0 390 n/a 5_updatecdl: 0.1245 0.1413 0.007 0.996 9.3 104.1 20.0 390 n/a 5_setrh: 0.1245 0.1412 0.007 0.996 9.3 104.1 20.0 390 n/a 5_nqh: 0.1245 0.1412 0.007 0.996 9.3 104.1 20.0 390 n/a 5_sol: 0.1239 0.1409 0.007 0.996 9.3 104.1 19.9 399 n/a 5_realsrl: 0.1270 0.1429 0.007 0.995 9.3 104.1 19.9 399 n/a 5_weight: 0.1270 0.1429 0.007 0.995 9.3 104.1 19.9 399 n/a 5_xyzrec: 0.1277 0.1440 0.007 1.125 9.3 104.1 19.9 399 n/a 5_realsrl2: 0.1277 0.1440 0.007 1.125 9.3 104.1 19.9 399 n/a 5_adp: 0.1275 0.1437 0.007 1.125 9.3 100.4 19.9 399 n/a 5_regHadp: 0.1275 0.1437 0.007 1.125 9.3 100.4 19.9 399 n/a 5_occ: 0.1266 0.1443 0.007 1.125 9.3 100.4 19.9 399 n/a end: 0.1287 0.1460 0.007 1.125 9.3 100.4 18.9 285 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /Users/pafonine/Desktop/NCI/examples/pozharski/5SY6/5SY6_modified.updated_refine_001.cif Writing default parameters for subsequent refinement: /Users/pafonine/Desktop/NCI/examples/pozharski/5SY6/5SY6_modified.updated_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 1.4600 Refinement macro-cycles (run) : 1603.6100 Write final files (write_after_run_outputs) : 35.7400 Total : 1640.8100 Total CPU time: 27.60 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-11 Time 09:38:32 PST -0800 (1733938712.84 s) Start R-work = 0.1352, R-free = 0.1552 Final R-work = 0.1287, R-free = 0.1460 =============================================================================== Job complete usr+sys time: 1714.00 seconds wall clock time: 28 minutes 52.30 seconds (1732.30 seconds total)