Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1446411.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.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 } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.38, per 1000 atoms: 0.41 Number of scatterers: 3381 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: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 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: 0.43 Conformation dependent library (CDL) restraints added in 163.1 milliseconds Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.88: 324 0.88 - 1.14: 1275 1.14 - 1.40: 599 1.40 - 1.65: 899 1.65 - 1.91: 56 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.243 1.053 0.190 9.50e-03 1.11e+04 4.02e+02 bond pdb=" C SER A 161 " pdb=" N PHE A 162 " ideal model delta sigma weight residual 1.335 1.079 0.256 1.31e-02 5.83e+03 3.81e+02 bond pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.374 1.564 -0.190 1.10e-02 8.26e+03 2.98e+02 bond pdb=" CA THR A 125 " pdb=" C THR A 125 " ideal model delta sigma weight residual 1.523 1.736 -0.212 1.24e-02 6.50e+03 2.93e+02 bond pdb=" C ALA A 165 " pdb=" O ALA A 165 " ideal model delta sigma weight residual 1.237 1.043 0.193 1.17e-02 7.31e+03 2.73e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 2961 4.31 - 8.63: 1896 8.63 - 12.94: 732 12.94 - 17.26: 168 17.26 - 21.57: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OD1BASN A 76 " pdb=" CG BASN A 76 " pdb=" ND2BASN A 76 " ideal model delta sigma weight residual 122.60 136.71 -14.11 1.00e+00 1.00e+00 1.99e+02 angle pdb=" O SER A 3 " pdb=" C SER A 3 " pdb=" N LYS A 4 " ideal model delta sigma weight residual 123.03 107.17 15.86 1.13e+00 7.83e-01 1.97e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 106.99 12.21 9.00e-01 1.23e+00 1.84e+02 angle pdb=" C LYS A 89 " pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " ideal model delta sigma weight residual 120.54 138.79 -18.25 1.35e+00 5.49e-01 1.83e+02 angle pdb=" N LYS A 182 " pdb=" CA LYS A 182 " pdb=" C LYS A 182 " ideal model delta sigma weight residual 111.71 127.15 -15.44 1.15e+00 7.56e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.03 - 17.86: 945 17.86 - 35.69: 114 35.69 - 53.52: 38 53.52 - 71.35: 11 71.35 - 89.19: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 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 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LEU A 172 " pdb=" C LEU A 172 " pdb=" N ASN A 173 " pdb=" CA ASN A 173 " ideal model delta harmonic sigma weight residual 180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA LYS A 4 " pdb=" C LYS A 4 " pdb=" N ARG A 5 " pdb=" CA ARG A 5 " ideal model delta harmonic sigma weight residual -180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.248: 110 0.248 - 0.496: 85 0.496 - 0.743: 36 0.743 - 0.991: 10 0.991 - 1.238: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.39 -1.24 2.00e-01 2.50e+01 3.83e+01 chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.57 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA ASP A 131 " pdb=" N ASP A 131 " pdb=" C ASP A 131 " pdb=" CB ASP A 131 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 145 " -0.170 9.50e-02 1.11e+02 9.09e-02 1.17e+02 pdb=" NE ARG A 145 " -0.068 2.00e-02 2.50e+03 pdb=" CZ ARG A 145 " 0.089 2.00e-02 2.50e+03 pdb=" NH1 ARG A 145 " -0.111 2.00e-02 2.50e+03 pdb=" NH2 ARG A 145 " 0.021 2.00e-02 2.50e+03 pdb="HH11 ARG A 145 " 0.126 2.00e-02 2.50e+03 pdb="HH12 ARG A 145 " -0.065 2.00e-02 2.50e+03 pdb="HH21 ARG A 145 " 0.008 2.00e-02 2.50e+03 pdb="HH22 ARG A 145 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.057 2.00e-02 2.50e+03 6.23e-02 1.17e+02 pdb=" CG PHE A 164 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.094 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.130 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.022 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 119 " -0.111 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.068 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.061 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1266 2.35 - 2.92: 8275 2.92 - 3.48: 10535 3.48 - 4.04: 15103 4.04 - 4.60: 21473 Nonbonded interactions: 56652 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.792 2.100 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.830 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.836 2.100 nonbonded pdb=" HA AASN A 76 " pdb="HD22AASN A 76 " model vdw 1.847 2.270 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.870 1.850 x-y,-y,-z-4/3 ... (remaining 56647 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 10 15.96 2 O1- 2 8.97 3 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 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 = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 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 = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 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 occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } pdb_interpretation { c_beta_restraints = False nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } 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 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_1446411_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794514 | | target function (ml) not normalized (work): 232799.803617 | | target function (ml) not normalized (free): 11856.861459 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3030 0.2001 7.138 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2416 0.1803 4.3378 4.33| | 3: 2.84 - 2.48 1.00 2833 165 0.2338 0.1684 4.1182 4.1429| | 4: 2.47 - 2.25 1.00 2825 136 0.2330 0.1438 3.8271 3.8306| | 5: 2.25 - 2.09 1.00 2756 127 0.2466 0.1664 3.7834 3.834| | 6: 2.09 - 1.97 1.00 2846 113 0.2551 0.1701 3.4621 3.5111| | 7: 1.97 - 1.87 1.00 2787 165 0.2590 0.2051 3.155 3.2704| | 8: 1.87 - 1.79 1.00 2789 144 0.2485 0.1873 3.0705 3.121| | 9: 1.79 - 1.72 1.00 2745 138 0.2423 0.2037 2.8987 2.9902| | 10: 1.72 - 1.66 1.00 2789 158 0.2389 0.1929 2.7963 2.8938| | 11: 1.66 - 1.61 1.00 2740 147 0.2470 0.1778 2.7426 2.7605| | 12: 1.61 - 1.56 1.00 2787 146 0.2496 0.1930 2.6107 2.6984| | 13: 1.56 - 1.52 1.00 2745 130 0.2554 0.1780 2.5749 2.6091| | 14: 1.52 - 1.48 1.00 2803 134 0.2586 0.1923 2.5194 2.5399| | 15: 1.48 - 1.45 1.00 2738 128 0.2622 0.2185 2.4281 2.5224| | 16: 1.45 - 1.42 1.00 2756 161 0.2711 0.2084 2.3921 2.3984| | 17: 1.42 - 1.39 1.00 2785 139 0.2713 0.2054 2.3418 2.3525| | 18: 1.39 - 1.36 1.00 2741 179 0.2746 0.2248 2.2927 2.3885| | 19: 1.36 - 1.34 1.00 2807 134 0.2664 0.2240 2.2509 2.3003| | 20: 1.34 - 1.32 1.00 2696 147 0.2662 0.2258 2.1832 2.2669| | 21: 1.32 - 1.30 1.00 2785 112 0.2678 0.2243 2.1613 2.123| | 22: 1.29 - 1.27 1.00 2704 152 0.2762 0.2414 2.1424 2.1703| | 23: 1.27 - 1.26 1.00 2802 156 0.2688 0.2346 2.091 2.1932| | 24: 1.26 - 1.24 1.00 2744 132 0.2796 0.2499 2.0736 2.1148| | 25: 1.24 - 1.22 1.00 2734 148 0.2829 0.2541 2.0395 2.0769| | 26: 1.22 - 1.21 1.00 2727 135 0.2865 0.2286 2.0162 2.0812| | 27: 1.21 - 1.19 1.00 2814 148 0.2987 0.3032 2.011 2.0684| | 28: 1.19 - 1.18 1.00 2671 147 0.3024 0.2851 2.0056 2.0435| | 29: 1.18 - 1.16 1.00 2800 134 0.3005 0.2870 1.9751 2.0578| | 30: 1.16 - 1.15 1.00 2740 148 0.3073 0.2951 1.9367 1.9805| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.55 0.76 0.23 1436.60| | 2: 3.57 - 2.84 2876 122 0.81 25.65 1.27 0.23 1436.60| | 3: 2.84 - 2.48 2833 165 0.74 31.54 1.24 0.24 1192.81| | 4: 2.47 - 2.25 2825 136 0.81 25.31 1.26 0.25 560.12| | 5: 2.25 - 2.09 2756 127 0.77 29.14 1.28 0.25 560.12| | 6: 2.09 - 1.97 2846 113 0.83 22.77 1.29 0.25 309.28| | 7: 1.97 - 1.87 2787 165 0.90 16.96 1.29 0.26 95.35| | 8: 1.87 - 1.79 2789 144 0.85 21.65 1.25 0.26 95.35| | 9: 1.79 - 1.72 2745 138 0.88 18.99 1.23 0.25 57.26| | 10: 1.72 - 1.66 2789 158 0.86 20.55 1.23 0.25 49.63| | 11: 1.66 - 1.61 2740 147 0.85 21.63 1.24 0.25 47.82| | 12: 1.61 - 1.56 2787 146 0.89 18.38 1.24 0.25 29.54| | 13: 1.56 - 1.52 2745 130 0.86 20.52 1.24 0.25 29.54| | 14: 1.52 - 1.48 2803 134 0.86 20.67 1.23 0.25 26.36| | 15: 1.48 - 1.45 2738 128 0.87 20.44 1.23 0.25 20.55| | 16: 1.45 - 1.42 2756 161 0.86 21.70 1.25 0.25 20.55| | 17: 1.42 - 1.39 2785 139 0.86 21.19 1.23 0.25 17.52| | 18: 1.39 - 1.36 2741 179 0.86 21.20 1.23 0.25 15.76| | 19: 1.36 - 1.34 2807 134 0.85 22.03 1.22 0.25 15.76| | 20: 1.34 - 1.32 2696 147 0.87 20.99 1.22 0.24 13.13| | 21: 1.32 - 1.30 2785 112 0.86 21.91 1.20 0.24 12.95| | 22: 1.29 - 1.27 2704 152 0.85 22.57 1.21 0.24 12.66| | 23: 1.27 - 1.26 2802 156 0.86 22.04 1.20 0.24 11.21| | 24: 1.26 - 1.24 2744 132 0.85 23.03 1.21 0.24 11.21| | 25: 1.24 - 1.22 2734 148 0.84 24.07 1.20 0.24 10.82| | 26: 1.22 - 1.21 2727 135 0.83 24.56 1.20 0.23 10.38| | 27: 1.21 - 1.19 2814 148 0.82 25.59 1.20 0.23 10.38| | 28: 1.19 - 1.18 2671 147 0.82 26.38 1.19 0.23 10.04| | 29: 1.18 - 1.16 2800 134 0.81 27.08 1.16 0.22 9.91| | 30: 1.16 - 1.15 2740 148 0.79 28.82 1.15 0.22 9.91| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.91 max = 1436.60 mean = 210.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.86| |phase err.(test): min = 0.00 max = 89.25 mean = 22.61| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.261 1557 Z= 5.495 Angle : 5.249 18.248 2118 Z= 3.703 Chirality : 0.391 1.238 243 Planarity : 0.030 0.076 284 Dihedral : 14.342 89.186 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % Cbeta Deviations : 23.24 % Peptide Plane: Cis-proline : 18.18 % 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: -2.68 (0.46), residues: 224 helix: -2.53 (0.35), residues: 109 sheet: -1.11 (0.93), residues: 28 loop : -0.59 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.035 ARG A 156 TYR 0.032 0.017 TYR A 141 PHE 0.088 0.033 PHE A 119 HIS 0.083 0.030 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 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 = 0.25 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= 0.2606 r_free= 0.1939 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.794514 | | target function (ml) not normalized (work): 232799.803617 | | target function (ml) not normalized (free): 11856.861459 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2565 0.2607 0.1940 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2565 0.2607 0.1940 n_refl.: 87602 remove outliers: r(all,work,free)=0.1977 0.1981 0.1940 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.2001 0.2005 0.1952 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1636 0.1767 n_refl.: 87594 remove outliers: r(all,work,free)=0.1642 0.1635 0.1767 n_refl.: 87592 ======================== 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 32.574-12.150 97.87 87 5 0.3803 382.311 357.807 0.668 1.003 0.401 11.894-9.307 99.02 97 4 0.1840 614.101 595.351 0.928 1.004 0.380 9.237-7.194 100.00 213 7 0.2156 502.259 490.699 0.956 1.004 0.370 7.162-5.571 100.00 427 22 0.2200 376.918 364.291 0.933 1.004 0.336 5.546-4.326 100.00 867 58 0.1279 517.415 511.131 0.964 1.004 0.239 4.315-3.360 100.00 1859 96 0.1128 492.065 488.721 1.003 1.003 0.169 3.356-2.611 100.00 3867 181 0.1436 323.261 319.965 0.994 1.003 0.089 2.608-2.026 99.99 8198 413 0.1346 214.293 211.971 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1643 104.649 104.041 1.014 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2073 46.406 45.101 1.005 0.995 0.000 1.221-1.150 99.97 13689 708 0.2618 29.239 26.919 0.977 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0017 b_overall=0.0460 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1635 r_free=0.1767 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1636 r_free=0.1766 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.523391 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2020.232138 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 0.1759 0.1882 0.0123 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1616 0.1754 0.0139 0.001 0.4 5.1 0.0 0.0 0 0.250 0.1444 0.1615 0.0172 0.002 0.4 3.8 0.0 0.0 0 0.500 0.1402 0.1598 0.0196 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1370 0.1575 0.0205 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1363 0.1569 0.0206 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1295 0.1517 0.0222 0.002 0.6 3.8 0.5 0.0 0 2.000 0.1268 0.1500 0.0232 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1255 0.1486 0.0231 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1245 0.1478 0.0233 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1238 0.1475 0.0236 0.004 0.7 3.8 0.5 0.0 0 6.000 0.1235 0.1471 0.0236 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1228 0.1465 0.0237 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1227 0.1468 0.0241 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1226 0.1470 0.0244 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1225 0.1471 0.0246 0.007 0.9 4.2 0.5 0.0 0 11.000 0.1223 0.1472 0.0249 0.007 0.9 4.5 0.5 0.6 0 12.000 0.1223 0.1474 0.0251 0.007 0.9 4.5 0.5 0.6 0 13.262 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1465 0.0237 0.005 0.8 3.8 0.5 0.0 0 8.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.65 2.37 3.013 19.059 2020.232 0.017 12.28 14.65 2.36 2.989 19.059 60.607 0.017 12.35 14.64 2.28 2.668 19.058 252.529 0.017 12.72 15.37 2.65 2.752 19.229 1010.116 0.017 12.57 15.52 2.95 3.215 19.558 2020.232 0.016 12.45 15.47 3.02 3.257 19.598 3030.348 0.015 12.33 15.38 3.05 3.311 19.610 4040.464 0.015 12.34 15.48 3.14 3.390 19.639 5050.580 0.015 12.32 15.53 3.21 3.422 19.654 6060.696 0.015 12.26 15.47 3.22 3.246 19.551 7070.812 0.015 12.21 15.43 3.23 3.382 19.622 8080.929 0.015 12.20 15.50 3.30 3.438 19.641 9091.045 0.015 12.22 15.57 3.34 3.581 19.699 10101.161 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 252.529 Accepted refinement result: 12.35 14.64 2.28 2.668 19.058 252.529 0.017 Individual atomic B min max mean iso aniso Overall: 9.06 119.44 20.08 3.31 0 1785 Protein: 9.06 115.00 16.99 3.32 0 1519 Water: 11.45 119.44 38.22 N/A 0 258 Other: 19.70 26.62 22.06 N/A 0 8 Chain A: 9.06 119.44 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.06 - 20.09 1272 20.09 - 31.13 227 31.13 - 42.17 125 42.17 - 53.21 94 53.21 - 64.25 42 64.25 - 75.29 11 75.29 - 86.33 7 86.33 - 97.37 4 97.37 - 108.40 1 108.40 - 119.44 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1464 r_work=0.1237 r_free=0.1468 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1468 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1231 r_free = 0.1461 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1231 r_free= 0.1461 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016939 | | target function (ls_wunit_k1) not normalized (work): 1410.934165 | | target function (ls_wunit_k1) not normalized (free): 108.068290 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1242 0.1231 0.1461 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1690 n_refl.: 87592 remove outliers: r(all,work,free)=0.1676 0.1677 0.1690 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1682 0.1684 0.1694 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1454 n_refl.: 87592 remove outliers: r(all,work,free)=0.1239 0.1228 0.1454 n_refl.: 87591 ======================== 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 32.574-12.150 94.79 86 5 0.3503 297.893 278.742 0.645 1.003 0.380 11.894-9.307 99.02 97 4 0.1657 482.718 470.053 0.923 1.003 0.360 9.237-7.194 100.00 213 7 0.1933 394.804 388.341 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1842 296.279 290.413 0.938 1.003 0.269 5.546-4.326 100.00 867 58 0.1010 406.717 403.744 0.966 1.003 0.240 4.315-3.360 100.00 1859 96 0.0876 386.791 385.633 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1172 254.102 252.983 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1021 168.446 167.733 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1112 82.260 82.456 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.478 35.985 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.983 21.466 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0530 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1454 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1229 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1229 r_free=0.1455 | n_water=258 | time (s): 2.040 (total time: 2.040) Filter (dist) r_work=0.1238 r_free=0.1457 | n_water=250 | time (s): 21.700 (total time: 23.740) Filter (q & B) r_work=0.1240 r_free=0.1456 | n_water=247 | time (s): 3.310 (total time: 27.050) Compute maps r_work=0.1240 r_free=0.1456 | n_water=247 | time (s): 1.720 (total time: 28.770) Filter (map) r_work=0.1262 r_free=0.1463 | n_water=224 | time (s): 3.000 (total time: 31.770) Find peaks r_work=0.1262 r_free=0.1463 | n_water=224 | time (s): 0.680 (total time: 32.450) Add new water r_work=0.1412 r_free=0.1621 | n_water=432 | time (s): 2.670 (total time: 35.120) Refine new water occ: r_work=0.1316 r_free=0.1493 adp: r_work=0.1232 r_free=0.1437 occ: r_work=0.1245 r_free=0.1426 adp: r_work=0.1210 r_free=0.1411 occ: r_work=0.1212 r_free=0.1408 adp: r_work=0.1203 r_free=0.1404 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1404 r_work=0.1203 r_free=0.1404 | n_water=432 | time (s): 52.850 (total time: 87.970) Filter (q & B) r_work=0.1208 r_free=0.1404 | n_water=416 | time (s): 3.090 (total time: 91.060) Filter (dist only) r_work=0.1208 r_free=0.1402 | n_water=414 | time (s): 35.310 (total time: 126.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.471953 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1488.530106 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 0.1713 0.1815 0.0102 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1570 0.1696 0.0127 0.001 0.4 8.0 0.0 0.0 0 0.250 0.1418 0.1578 0.0160 0.001 0.4 7.0 0.0 0.0 0 0.500 0.1365 0.1538 0.0172 0.001 0.4 5.8 0.0 0.0 0 0.750 0.1335 0.1523 0.0188 0.002 0.5 6.4 0.0 0.0 0 1.000 0.1314 0.1489 0.0175 0.002 0.5 6.7 0.0 0.0 0 1.000 0.1257 0.1466 0.0210 0.002 0.5 5.8 0.5 0.0 0 2.000 0.1235 0.1451 0.0216 0.003 0.6 5.8 0.5 0.0 0 3.000 0.1218 0.1441 0.0223 0.003 0.6 5.8 0.5 0.0 0 4.000 0.1209 0.1431 0.0222 0.004 0.7 5.4 0.5 0.0 0 5.000 0.1202 0.1424 0.0222 0.004 0.7 6.1 0.5 0.0 0 6.000 0.1202 0.1430 0.0228 0.005 0.8 5.8 0.5 0.0 0 7.000 0.1197 0.1424 0.0227 0.005 0.8 6.4 0.5 0.0 0 8.000 0.1194 0.1426 0.0232 0.006 0.8 6.1 0.5 0.0 0 9.000 0.1192 0.1426 0.0233 0.006 0.9 7.0 0.5 0.0 0 10.000 0.1189 0.1425 0.0235 0.007 0.9 6.7 0.5 0.0 0 11.000 0.1192 0.1423 0.0231 0.007 0.9 6.1 0.5 0.0 0 12.000 0.1188 0.1427 0.0240 0.008 0.9 6.7 0.5 0.6 0 13.736 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1192 0.1423 0.0231 0.007 0.9 6.1 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.92 14.23 2.31 3.775 21.745 1488.530 0.016 11.92 14.23 2.31 3.775 21.745 44.656 0.016 11.92 14.23 2.31 3.775 21.745 186.066 0.016 12.12 14.71 2.60 3.619 21.756 744.265 0.015 12.09 15.00 2.91 3.463 21.974 1488.530 0.015 11.96 15.03 3.07 3.517 21.881 2232.795 0.014 11.88 15.01 3.13 3.516 21.904 2977.060 0.014 11.80 14.87 3.07 3.495 22.068 3721.325 0.014 11.75 14.85 3.10 3.513 22.073 4465.590 0.014 11.73 14.89 3.16 3.525 22.082 5209.855 0.014 11.74 14.96 3.22 3.556 22.120 5954.120 0.014 11.73 14.97 3.24 3.571 22.124 6698.385 0.014 11.70 14.98 3.29 3.588 22.114 7442.651 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 186.066 Accepted refinement result: 11.92 14.23 2.31 3.775 21.745 186.066 0.016 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 22.13 3.31 190 1751 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.49 76.69 40.83 N/A 190 224 Other: 19.74 26.65 22.09 N/A 0 8 Chain A: 9.09 115.03 19.44 N/A 0 1751 Chain S: 12.45 60.00 46.87 N/A 190 0 Histogram: Values Number of atoms 9.09 - 19.68 1257 19.68 - 30.28 248 30.28 - 40.87 162 40.87 - 51.47 132 51.47 - 62.06 119 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1423 r_work=0.1192 r_free=0.1423 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1192 r_free = 0.1423 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1420 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1189 r_free= 0.1420 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014914 | | target function (ls_wunit_k1) not normalized (work): 1242.288951 | | target function (ls_wunit_k1) not normalized (free): 106.968834 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1189 0.1420 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1592 0.1591 0.1642 n_refl.: 87591 remove outliers: r(all,work,free)=0.1592 0.1591 0.1642 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1594 0.1593 0.1644 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1196 0.1186 0.1412 n_refl.: 87591 remove outliers: r(all,work,free)=0.1196 0.1185 0.1412 n_refl.: 87590 ======================== 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 32.574-12.150 93.75 85 5 0.3472 299.881 275.090 0.643 0.937 0.370 11.894-9.307 99.02 97 4 0.1555 482.718 475.692 0.981 0.937 0.350 9.237-7.194 100.00 213 7 0.1652 394.804 396.393 1.054 0.937 0.280 7.162-5.571 100.00 427 22 0.1594 296.279 291.287 1.002 0.937 0.240 5.546-4.326 100.00 867 58 0.0882 406.717 403.488 1.027 0.938 0.220 4.315-3.360 100.00 1859 96 0.0777 386.791 386.105 1.074 0.938 0.190 3.356-2.611 100.00 3867 181 0.1083 254.102 253.435 1.078 0.939 0.100 2.608-2.026 99.99 8198 413 0.1018 168.446 167.839 1.086 0.940 0.000 2.025-1.573 100.00 17313 902 0.1105 82.260 82.498 1.092 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.478 36.019 1.078 0.947 0.000 1.221-1.150 99.97 13689 708 0.2248 22.983 21.504 1.034 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0154 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1412 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1412 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1412 | n_water=414 | time (s): 1.910 (total time: 1.910) Filter (dist) r_work=0.1185 r_free=0.1410 | n_water=410 | time (s): 36.480 (total time: 38.390) Filter (q & B) r_work=0.1185 r_free=0.1410 | n_water=410 | time (s): 0.780 (total time: 39.170) Compute maps r_work=0.1185 r_free=0.1410 | n_water=410 | time (s): 1.260 (total time: 40.430) Filter (map) r_work=0.1220 r_free=0.1400 | n_water=280 | time (s): 2.950 (total time: 43.380) Find peaks r_work=0.1220 r_free=0.1400 | n_water=280 | time (s): 0.530 (total time: 43.910) Add new water r_work=0.1348 r_free=0.1535 | n_water=472 | time (s): 3.020 (total time: 46.930) Refine new water occ: r_work=0.1255 r_free=0.1441 adp: r_work=0.1257 r_free=0.1444 occ: r_work=0.1230 r_free=0.1410 adp: r_work=0.1229 r_free=0.1415 occ: r_work=0.1209 r_free=0.1389 adp: r_work=0.1204 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1391 r_work=0.1204 r_free=0.1391 | n_water=472 | time (s): 191.670 (total time: 238.600) Filter (q & B) r_work=0.1208 r_free=0.1402 | n_water=445 | time (s): 3.000 (total time: 241.600) Filter (dist only) r_work=0.1208 r_free=0.1401 | n_water=443 | time (s): 37.830 (total time: 279.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.787069 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.466805 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 0.1238 0.1377 0.0138 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1188 0.1338 0.0150 0.003 0.7 4.5 0.5 0.0 0 0.268 0.1173 0.1329 0.0156 0.004 0.8 3.5 0.5 0.0 0 0.536 0.1167 0.1328 0.0161 0.005 0.9 4.5 0.5 0.0 0 0.804 0.1162 0.1327 0.0166 0.006 1.0 3.5 0.5 0.0 0 1.072 0.1160 0.1326 0.0167 0.007 1.0 3.5 0.5 0.0 0 1.340 0.1157 0.1324 0.0167 0.007 1.0 4.2 0.5 0.0 0 1.608 0.1156 0.1326 0.0170 0.008 1.1 4.2 0.5 0.0 0 1.876 0.1164 0.1328 0.0164 0.005 0.9 3.8 0.5 0.0 0 0.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1157 0.1324 0.0167 0.007 1.0 4.2 0.5 0.0 0 1.608 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 13.24 1.67 3.779 21.293 36.467 3.622 11.57 13.24 1.67 3.779 21.293 1.094 3.622 11.57 13.24 1.67 3.779 21.293 4.558 3.622 11.62 13.29 1.67 3.708 21.286 18.233 3.616 11.64 13.38 1.74 3.730 21.266 36.467 3.616 11.61 13.40 1.79 3.750 21.243 54.700 3.614 11.57 13.38 1.81 3.765 21.233 72.934 3.610 11.54 13.37 1.83 3.776 21.227 91.167 3.607 11.52 13.36 1.84 3.788 21.220 109.400 3.605 11.52 13.39 1.88 3.803 21.207 127.634 3.604 11.49 13.38 1.88 3.814 21.203 145.867 3.602 11.49 13.37 1.89 3.825 21.197 164.101 3.601 11.47 13.35 1.89 3.832 21.197 182.334 3.599 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.094 Accepted refinement result: 11.57 13.24 1.67 3.779 21.293 1.094 3.622 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.29 3.31 224 1746 Protein: 9.10 115.04 17.04 3.32 0 1519 Water: 11.50 76.70 35.85 N/A 224 219 Other: 19.75 26.66 22.10 N/A 0 8 Chain A: 9.10 115.04 19.35 N/A 0 1746 Chain S: 12.46 60.01 36.36 N/A 224 0 Histogram: Values Number of atoms 9.10 - 19.69 1263 19.69 - 30.29 289 30.29 - 40.88 210 40.88 - 51.48 126 51.48 - 62.07 59 62.07 - 72.66 12 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1324 r_work=0.1157 r_free=0.1324 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1157 r_free = 0.1324 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1316 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1147 r_free= 0.1316 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.614585 | | target function (ml) not normalized (work): 301073.281574 | | target function (ml) not normalized (free): 15855.870578 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1147 0.1316 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1494 0.1493 0.1533 n_refl.: 87590 remove outliers: r(all,work,free)=0.1494 0.1493 0.1533 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1493 0.1492 0.1533 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1141 0.1301 n_refl.: 87590 remove outliers: r(all,work,free)=0.1145 0.1137 0.1301 n_refl.: 87580 ======================== 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 32.574-12.150 89.58 81 5 0.3593 290.995 270.579 0.513 1.000 0.330 11.894-9.307 97.06 95 4 0.2180 483.446 467.742 0.879 1.002 0.297 9.237-7.194 98.18 209 7 0.2222 386.280 388.464 0.955 1.002 0.215 7.162-5.571 100.00 427 22 0.2003 296.279 286.398 0.922 1.002 0.210 5.546-4.326 100.00 867 58 0.1108 406.717 401.738 0.965 1.002 0.160 4.315-3.360 100.00 1859 96 0.0927 386.791 384.342 1.006 1.002 0.160 3.356-2.611 100.00 3867 181 0.1135 254.102 252.046 1.007 1.002 0.070 2.608-2.026 99.99 8198 413 0.0934 168.446 167.604 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0897 82.260 82.546 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1256 36.478 36.061 1.028 0.998 0.000 1.221-1.150 99.97 13689 708 0.2164 22.983 21.529 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0155 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1137 r_free=0.1301 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1141 r_free=0.1304 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1141 r_free=0.1304 | n_water=443 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1141 r_free=0.1304 | n_water=443 | time (s): 41.130 (total time: 43.530) Filter (q & B) r_work=0.1141 r_free=0.1305 | n_water=442 | time (s): 3.700 (total time: 47.230) Compute maps r_work=0.1141 r_free=0.1305 | n_water=442 | time (s): 1.660 (total time: 48.890) Filter (map) r_work=0.1163 r_free=0.1306 | n_water=333 | time (s): 3.760 (total time: 52.650) Find peaks r_work=0.1163 r_free=0.1306 | n_water=333 | time (s): 0.700 (total time: 53.350) Add new water r_work=0.1234 r_free=0.1377 | n_water=495 | time (s): 3.660 (total time: 57.010) Refine new water occ: r_work=0.1163 r_free=0.1307 adp: r_work=0.1163 r_free=0.1310 occ: r_work=0.1147 r_free=0.1290 adp: r_work=0.1146 r_free=0.1293 occ: r_work=0.1136 r_free=0.1279 adp: r_work=0.1132 r_free=0.1279 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1279 r_work=0.1132 r_free=0.1279 | n_water=495 | time (s): 194.540 (total time: 251.550) Filter (q & B) r_work=0.1139 r_free=0.1286 | n_water=458 | time (s): 3.960 (total time: 255.510) Filter (dist only) r_work=0.1142 r_free=0.1286 | n_water=456 | time (s): 47.480 (total time: 302.990) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.781833 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.332076 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 0.1328 0.0129 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1160 0.1301 0.0141 0.003 0.7 3.5 0.5 0.0 0 0.267 0.1147 0.1294 0.0147 0.005 0.9 3.8 0.5 0.0 0 0.535 0.1141 0.1291 0.0150 0.006 0.9 3.5 0.5 0.0 0 0.802 0.1137 0.1287 0.0149 0.007 1.0 4.2 0.5 0.0 0 1.069 0.1134 0.1291 0.0157 0.007 1.0 3.8 0.5 0.0 0 1.336 0.1133 0.1289 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.604 0.1130 0.1292 0.0161 0.009 1.1 3.8 0.5 0.0 0 1.871 0.1140 0.1291 0.0152 0.006 1.0 3.5 0.5 0.0 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1287 0.0149 0.007 1.0 4.2 0.5 0.0 0 1.069 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 12.87 1.49 3.780 21.268 41.332 3.607 11.37 12.87 1.49 3.780 21.268 1.240 3.607 11.37 12.87 1.49 3.780 21.268 5.167 3.607 11.41 12.94 1.53 3.711 21.262 20.666 3.602 11.49 13.11 1.62 3.728 21.236 41.332 3.606 11.41 13.06 1.66 3.752 21.225 61.998 3.600 11.35 13.02 1.67 3.767 21.222 82.664 3.595 11.30 12.97 1.67 3.774 21.223 103.330 3.592 11.28 12.97 1.69 3.784 21.220 123.996 3.590 11.30 13.06 1.75 3.806 21.203 144.662 3.591 11.27 13.02 1.75 3.813 21.204 165.328 3.589 11.27 13.02 1.75 3.823 21.199 185.994 3.589 11.26 13.00 1.74 3.828 21.199 206.660 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.240 Accepted refinement result: 11.37 12.87 1.49 3.780 21.268 1.240 3.607 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.25 3.31 239 1744 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.49 76.70 35.28 N/A 239 217 Other: 19.74 26.66 22.10 N/A 0 8 Chain A: 9.09 115.03 19.34 N/A 0 1744 Chain S: 12.45 60.00 35.16 N/A 239 0 Histogram: Values Number of atoms 9.09 - 19.69 1264 19.69 - 30.28 294 30.28 - 40.88 221 40.88 - 51.47 131 51.47 - 62.06 50 62.06 - 72.66 12 72.66 - 83.25 5 83.25 - 93.85 4 93.85 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1287 r_work=0.1137 r_free=0.1287 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1287 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1132 r_free = 0.1284 target_work(ml) = 3.605 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1132 r_free= 0.1284 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.604658 | | target function (ml) not normalized (work): 300210.312315 | | target function (ml) not normalized (free): 15805.832015 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1139 0.1132 0.1284 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1468 0.1467 0.1512 n_refl.: 87580 remove outliers: r(all,work,free)=0.1468 0.1467 0.1512 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1467 0.1466 0.1511 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1138 0.1131 0.1283 n_refl.: 87580 remove outliers: r(all,work,free)=0.1137 0.1129 0.1283 n_refl.: 87577 ======================== 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 32.574-12.150 88.54 80 5 0.3712 293.210 256.480 0.467 1.001 0.314 11.894-9.307 95.10 93 4 0.2200 476.630 466.670 0.876 1.002 0.310 9.237-7.194 98.18 209 7 0.2311 386.280 380.779 0.927 1.002 0.195 7.162-5.571 100.00 427 22 0.2049 296.279 286.812 0.912 1.003 0.167 5.546-4.326 100.00 867 58 0.1104 406.717 402.157 0.964 1.003 0.130 4.315-3.360 100.00 1859 96 0.0907 386.791 384.861 1.005 1.002 0.130 3.356-2.611 100.00 3867 181 0.1107 254.102 252.299 1.009 1.002 0.034 2.608-2.026 99.99 8198 413 0.0915 168.446 167.831 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.260 82.610 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1258 36.478 36.092 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.983 21.537 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0155 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1129 r_free=0.1283 After: r_work=0.1130 r_free=0.1283 ================================== NQH flips ================================== r_work=0.1130 r_free=0.1283 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1130 r_free=0.1283 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1130 r_free=0.1283 | n_water=456 | time (s): 2.350 (total time: 2.350) Filter (dist) r_work=0.1130 r_free=0.1281 | n_water=454 | time (s): 46.980 (total time: 49.330) Filter (q & B) r_work=0.1130 r_free=0.1280 | n_water=453 | time (s): 4.080 (total time: 53.410) Compute maps r_work=0.1130 r_free=0.1280 | n_water=453 | time (s): 1.760 (total time: 55.170) Filter (map) r_work=0.1153 r_free=0.1292 | n_water=359 | time (s): 3.880 (total time: 59.050) Find peaks r_work=0.1153 r_free=0.1292 | n_water=359 | time (s): 0.710 (total time: 59.760) Add new water r_work=0.1205 r_free=0.1352 | n_water=501 | time (s): 3.660 (total time: 63.420) Refine new water occ: r_work=0.1149 r_free=0.1294 adp: r_work=0.1149 r_free=0.1297 occ: r_work=0.1137 r_free=0.1281 adp: r_work=0.1136 r_free=0.1284 occ: r_work=0.1128 r_free=0.1270 adp: r_work=0.1125 r_free=0.1273 ADP+occupancy (water only), MIN, final r_work=0.1125 r_free=0.1273 r_work=0.1125 r_free=0.1273 | n_water=501 | time (s): 198.960 (total time: 262.380) Filter (q & B) r_work=0.1131 r_free=0.1280 | n_water=463 | time (s): 3.990 (total time: 266.370) Filter (dist only) r_work=0.1132 r_free=0.1278 | n_water=462 | time (s): 48.270 (total time: 314.640) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.705133 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.593092 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 0.1214 0.1336 0.0122 0.004 0.7 6.1 0.0 0.0 0 0.085 0.1168 0.1307 0.0139 0.004 0.8 6.1 0.0 0.0 0 0.256 0.1148 0.1292 0.0143 0.005 0.9 5.4 0.5 0.0 0 0.512 0.1135 0.1280 0.0145 0.006 1.0 5.1 0.5 0.0 0 0.767 0.1132 0.1278 0.0146 0.006 1.0 4.8 0.5 0.0 0 1.023 0.1131 0.1278 0.0147 0.007 1.0 4.8 0.5 0.0 0 1.279 0.1130 0.1277 0.0147 0.007 1.0 4.8 0.5 0.0 0 1.535 0.1129 0.1277 0.0148 0.008 1.1 4.8 0.5 0.0 0 1.790 0.1134 0.1279 0.0145 0.006 1.0 5.1 0.5 0.0 0 0.853 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1129 0.1277 0.0148 0.008 1.1 4.8 0.5 0.0 0 1.790 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 12.77 1.48 3.779 21.282 44.593 3.603 11.29 12.77 1.48 3.779 21.282 1.338 3.603 11.29 12.77 1.48 3.768 21.282 5.574 3.603 11.31 12.82 1.51 3.714 21.276 22.297 3.597 11.34 12.92 1.58 3.738 21.252 44.593 3.598 11.32 12.96 1.65 3.751 21.237 66.890 3.595 11.26 12.91 1.65 3.770 21.234 89.186 3.590 11.22 12.89 1.67 3.781 21.232 111.483 3.587 11.19 12.87 1.68 3.790 21.232 133.779 3.585 11.19 12.91 1.72 3.810 21.219 156.076 3.584 11.19 12.91 1.72 3.821 21.215 178.372 3.584 11.17 12.90 1.73 3.829 21.215 200.669 3.583 11.17 12.89 1.73 3.837 21.214 222.965 3.582 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.338 Accepted refinement result: 11.29 12.77 1.48 3.779 21.282 1.338 3.603 Individual atomic B min max mean iso aniso Overall: 9.09 115.03 21.28 3.31 245 1744 Protein: 9.09 115.03 17.03 3.32 0 1519 Water: 11.49 76.69 35.24 N/A 245 217 Other: 19.74 26.65 22.09 N/A 0 8 Chain A: 9.09 115.03 19.34 N/A 0 1744 Chain S: 12.44 60.00 35.10 N/A 245 0 Histogram: Values Number of atoms 9.09 - 19.68 1266 19.68 - 30.28 301 30.28 - 40.87 216 40.87 - 51.47 134 51.47 - 62.06 49 62.06 - 72.65 12 72.65 - 83.25 5 83.25 - 93.84 4 93.84 - 104.44 0 104.44 - 115.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.1129 r_free=0.1277 r_work=0.1129 r_free=0.1277 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1129 r_free = 0.1277 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1126 r_free = 0.1275 target_work(ml) = 3.602 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1126 r_free= 0.1275 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601542 | | target function (ml) not normalized (work): 299939.980891 | | target function (ml) not normalized (free): 15801.688580 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1299 0.1274 5.6205 5.5771| | 2: 3.57 - 2.84 1.00 2888 124 0.1053 0.1398 5.1455 5.2077| | 3: 2.83 - 2.48 1.00 2820 163 0.1095 0.1222 4.9287 4.9794| | 4: 2.47 - 2.25 1.00 2825 136 0.0895 0.0948 4.6179 4.634| | 5: 2.25 - 2.09 1.00 2756 127 0.0872 0.0981 4.5656 4.6229| | 6: 2.09 - 1.97 1.00 2846 113 0.0859 0.1032 4.262 4.3777| | 7: 1.97 - 1.87 1.00 2787 165 0.0888 0.1123 3.9791 4.1016| | 8: 1.87 - 1.79 1.00 2789 144 0.0915 0.1072 3.8925 3.9816| | 9: 1.79 - 1.72 1.00 2745 138 0.0876 0.1205 3.6508 3.8311| | 10: 1.72 - 1.66 1.00 2831 160 0.0915 0.1182 3.5638 3.7099| | 11: 1.66 - 1.61 1.00 2712 147 0.0875 0.1015 3.5004 3.5692| | 12: 1.61 - 1.56 1.00 2773 144 0.0910 0.1158 3.3321 3.4727| | 13: 1.56 - 1.52 1.00 2745 130 0.0952 0.1012 3.3093 3.3842| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1080 3.2389 3.3358| | 15: 1.48 - 1.45 1.00 2738 128 0.1003 0.1220 3.1545 3.266| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1236 3.1359 3.2408| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1287 3.1184 3.229| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1335 3.1025 3.2448| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1555 3.1126 3.2711| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1466 3.1146 3.1555| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1482 3.1133 3.0954| | 22: 1.29 - 1.27 1.00 2704 152 0.1564 0.1996 3.1247 3.2994| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1772 3.1333 3.1968| | 24: 1.26 - 1.24 1.00 2744 132 0.1710 0.1842 3.1286 3.2297| | 25: 1.24 - 1.22 1.00 2733 148 0.1884 0.2142 3.1437 3.2615| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1759 3.1472 3.1979| | 27: 1.21 - 1.19 1.00 2814 148 0.2075 0.2162 3.1715 3.1616| | 28: 1.19 - 1.18 1.00 2671 147 0.2201 0.2279 3.1652 3.1686| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2384 3.1479 3.2303| | 30: 1.16 - 1.15 1.00 2739 148 0.2446 0.2450 3.1436 3.1668| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2919 171 0.95 8.31 1.00 0.97 5492.06| | 2: 3.57 - 2.84 2888 124 0.93 12.25 1.01 0.97 5492.06| | 3: 2.83 - 2.48 2820 163 0.90 16.12 0.99 0.97 4594.67| | 4: 2.47 - 2.25 2825 136 0.92 13.14 1.00 0.98 2280.59| | 5: 2.25 - 2.09 2756 127 0.91 15.29 1.01 0.98 2280.59| | 6: 2.09 - 1.97 2846 113 0.93 12.23 1.02 0.98 1328.60| | 7: 1.97 - 1.87 2787 165 0.95 9.38 1.02 0.98 516.68| | 8: 1.87 - 1.79 2789 144 0.93 12.69 1.00 0.98 516.68| | 9: 1.79 - 1.72 2745 138 0.94 10.08 0.98 0.98 291.18| | 10: 1.72 - 1.66 2831 160 0.94 11.18 0.98 0.98 246.02| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.97 235.68| | 12: 1.61 - 1.56 2773 144 0.95 8.94 0.99 0.97 138.19| | 13: 1.56 - 1.52 2745 130 0.95 10.47 1.03 0.97 138.19| | 14: 1.52 - 1.48 2803 134 0.94 10.79 1.02 0.98 123.98| | 15: 1.48 - 1.45 2738 128 0.95 9.88 1.02 0.98 97.96| | 16: 1.45 - 1.42 2756 161 0.94 11.11 1.02 0.98 97.96| | 17: 1.42 - 1.39 2785 139 0.95 10.95 1.01 0.98 89.19| | 18: 1.39 - 1.36 2741 179 0.94 11.59 1.01 0.98 84.11| | 19: 1.36 - 1.34 2807 134 0.94 11.91 1.00 0.98 84.11| | 20: 1.34 - 1.32 2696 147 0.94 12.10 0.98 0.96 79.96| | 21: 1.32 - 1.30 2785 112 0.94 13.08 0.98 0.96 79.66| | 22: 1.29 - 1.27 2704 152 0.93 13.64 0.98 0.96 80.06| | 23: 1.27 - 1.26 2802 156 0.92 14.83 0.97 0.94 82.08| | 24: 1.26 - 1.24 2744 132 0.92 14.86 0.96 0.94 82.08| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 84.01| | 26: 1.22 - 1.21 2727 135 0.90 18.06 1.03 0.93 86.15| | 27: 1.21 - 1.19 2814 148 0.89 18.73 1.02 0.93 86.15| | 28: 1.19 - 1.18 2671 147 0.88 20.36 1.01 0.93 89.83| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.93 91.22| | 30: 1.16 - 1.15 2739 148 0.86 21.98 0.98 0.93 91.22| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.66 max = 5492.06 mean = 856.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.40| |phase err.(test): min = 0.00 max = 89.69 mean = 13.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1133 0.1126 0.1275 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1449 0.1448 0.1484 n_refl.: 87577 remove outliers: r(all,work,free)=0.1449 0.1448 0.1484 n_refl.: 87577 overall B=-0.00 to atoms: r(all,work,free)=0.1448 0.1447 0.1483 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1126 0.1274 n_refl.: 87577 remove outliers: r(all,work,free)=0.1132 0.1125 0.1274 n_refl.: 87574 ======================== 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 32.574-12.150 87.50 79 5 0.3954 288.439 260.720 0.443 0.999 0.269 11.894-9.307 93.14 91 4 0.2260 474.002 462.875 0.865 1.001 0.253 9.237-7.194 98.18 209 7 0.2302 386.280 381.210 0.926 1.002 0.160 7.162-5.571 100.00 427 22 0.2021 296.279 287.322 0.911 1.002 0.160 5.546-4.326 100.00 867 58 0.1112 406.717 401.625 0.962 1.002 0.113 4.315-3.360 100.00 1859 96 0.0904 386.791 384.726 1.002 1.002 0.097 3.356-2.611 100.00 3867 181 0.1102 254.102 252.153 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0910 168.446 167.843 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0890 82.260 82.601 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.478 36.082 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.983 21.530 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0140 ================= 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 : 0.2606 0.1939 0.082 5.249 8.8 119.3 19.9 258 0.000 1_bss: 0.1635 0.1767 0.082 5.249 9.0 119.5 20.1 258 0.000 1_settarget: 0.1635 0.1767 0.082 5.249 9.0 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1766 0.082 5.249 9.0 119.5 20.1 258 0.003 1_weight: 0.1636 0.1766 0.082 5.249 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1228 0.1465 0.005 0.813 9.0 119.5 20.1 258 0.133 1_adp: 0.1235 0.1464 0.005 0.813 9.1 119.4 20.1 258 0.133 1_regHadp: 0.1237 0.1468 0.005 0.813 9.1 119.4 20.1 258 0.133 1_occ: 0.1231 0.1461 0.005 0.813 9.1 119.4 20.1 258 0.133 2_bss: 0.1228 0.1454 0.005 0.813 9.1 119.5 20.1 258 0.133 2_settarget: 0.1228 0.1454 0.005 0.813 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1228 0.1454 0.005 0.835 9.1 119.5 20.1 258 0.133 2_nqh: 0.1229 0.1455 0.005 0.835 9.1 119.5 20.1 258 0.136 2_sol: 0.1208 0.1402 0.005 0.835 9.1 115.0 22.1 414 n/a 2_weight: 0.1208 0.1402 0.005 0.835 9.1 115.0 22.1 414 n/a 2_xyzrec: 0.1192 0.1423 0.007 0.904 9.1 115.0 22.1 414 n/a 2_adp: 0.1192 0.1423 0.007 0.904 9.1 115.0 22.1 414 n/a 2_regHadp: 0.1192 0.1423 0.007 0.904 9.1 115.0 22.1 414 n/a 2_occ: 0.1189 0.1420 0.007 0.904 9.1 115.0 22.1 414 n/a 3_bss: 0.1185 0.1412 0.007 0.904 9.1 115.0 22.1 414 n/a 3_settarget: 0.1185 0.1412 0.007 0.904 9.1 115.0 22.1 414 n/a 3_updatecdl: 0.1185 0.1412 0.007 0.905 9.1 115.0 22.1 414 n/a 3_nqh: 0.1185 0.1412 0.007 0.905 9.1 115.0 22.1 414 n/a 3_sol: 0.1208 0.1401 0.007 0.905 9.1 115.0 21.3 443 n/a 3_weight: 0.1208 0.1401 0.007 0.905 9.1 115.0 21.3 443 n/a 3_xyzrec: 0.1157 0.1324 0.007 1.049 9.1 115.0 21.3 443 n/a 3_adp: 0.1157 0.1324 0.007 1.049 9.1 115.0 21.3 443 n/a 3_regHadp: 0.1157 0.1324 0.007 1.049 9.1 115.0 21.3 443 n/a 3_occ: 0.1147 0.1316 0.007 1.049 9.1 115.0 21.3 443 n/a 4_bss: 0.1137 0.1301 0.007 1.049 9.1 115.0 21.3 443 n/a 4_settarget: 0.1137 0.1301 0.007 1.049 9.1 115.0 21.3 443 n/a 4_updatecdl: 0.1137 0.1301 0.007 1.051 9.1 115.0 21.3 443 n/a 4_nqh: 0.1141 0.1304 0.007 1.051 9.1 115.0 21.3 443 n/a 4_sol: 0.1142 0.1286 0.007 1.051 9.1 115.0 21.2 456 n/a 4_weight: 0.1142 0.1286 0.007 1.051 9.1 115.0 21.2 456 n/a 4_xyzrec: 0.1137 0.1287 0.007 1.006 9.1 115.0 21.2 456 n/a 4_adp: 0.1137 0.1287 0.007 1.006 9.1 115.0 21.2 456 n/a 4_regHadp: 0.1137 0.1287 0.007 1.006 9.1 115.0 21.2 456 n/a 4_occ: 0.1132 0.1284 0.007 1.006 9.1 115.0 21.2 456 n/a 5_bss: 0.1129 0.1283 0.007 1.006 9.1 115.0 21.2 456 n/a 5_settarget: 0.1129 0.1283 0.007 1.006 9.1 115.0 21.2 456 n/a 5_updatecdl: 0.1129 0.1283 0.007 1.008 9.1 115.0 21.2 456 n/a 5_setrh: 0.1130 0.1283 0.007 1.008 9.1 115.0 21.2 456 n/a 5_nqh: 0.1130 0.1283 0.007 1.008 9.1 115.0 21.2 456 n/a 5_sol: 0.1132 0.1278 0.007 1.008 9.1 115.0 21.3 462 n/a 5_weight: 0.1132 0.1278 0.007 1.008 9.1 115.0 21.3 462 n/a 5_xyzrec: 0.1129 0.1277 0.008 1.081 9.1 115.0 21.3 462 n/a 5_adp: 0.1129 0.1277 0.008 1.081 9.1 115.0 21.3 462 n/a 5_regHadp: 0.1129 0.1277 0.008 1.081 9.1 115.0 21.3 462 n/a 5_occ: 0.1126 0.1275 0.008 1.081 9.1 115.0 21.3 462 n/a end: 0.1125 0.1274 0.008 1.081 9.1 115.0 21.3 462 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1446411_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_1446411_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2000 Refinement macro-cycles (run) : 13314.1000 Write final files (write_after_run_outputs) : 95.8900 Total : 13413.1900 Total CPU time: 3.73 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:01:45 PST -0800 (1735365705.08 s) Start R-work = 0.1635, R-free = 0.1767 Final R-work = 0.1125, R-free = 0.1274 =============================================================================== Job complete usr+sys time: 13598.03 seconds wall clock time: 246 minutes 16.96 seconds (14776.96 seconds total)