Starting phenix.refine on Sat Dec 28 21:06:34 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_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } 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 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 2.22, per 1000 atoms: 0.66 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: 0.57 Conformation dependent library (CDL) restraints added in 261.9 milliseconds Time building geometry restraints manager: 0.77 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 2.450 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 2.450 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 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_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 = 24.273092 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 0.1208 0.1463 0.0254 0.007 0.9 1.3 0.5 0.0 0 12.137 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 14.63 2.54 3.013 19.059 2020.232 0.017 12.44 15.39 2.95 3.414 19.676 2020.232 0.016 Individual atomic B min max mean iso aniso Overall: 8.67 118.47 21.25 2.92 0 1785 Protein: 8.67 118.47 18.06 2.92 0 1519 Water: 11.02 114.50 39.77 N/A 0 258 Other: 23.64 38.43 30.33 N/A 0 8 Chain A: 8.67 118.47 21.25 N/A 0 1785 Histogram: Values Number of atoms 8.67 - 19.65 1204 19.65 - 30.63 231 30.63 - 41.61 156 41.61 - 52.59 102 52.59 - 63.57 57 63.57 - 74.55 19 74.55 - 85.53 9 85.53 - 96.51 2 96.51 - 107.49 2 107.49 - 118.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1244 r_free=0.1539 r_work=0.1249 r_free=0.1544 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1249 r_free = 0.1544 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1248 r_free = 0.1546 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 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= 0.1248 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.015456 | | target function (ls_wunit_k1) not normalized (work): 1287.382550 | | target function (ls_wunit_k1) not normalized (free): 113.183675 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1248 0.1546 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1708 0.1708 0.1771 n_refl.: 87592 remove outliers: r(all,work,free)=0.1708 0.1708 0.1771 n_refl.: 87592 overall B=0.12 to atoms: r(all,work,free)=0.1728 0.1728 0.1785 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1259 0.1245 0.1537 n_refl.: 87592 remove outliers: r(all,work,free)=0.1259 0.1245 0.1537 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 0.3604 294.671 274.960 0.625 1.003 0.380 11.894-9.307 99.02 97 4 0.1620 477.497 465.612 0.907 1.003 0.380 9.237-7.194 100.00 213 7 0.1803 390.534 385.018 0.947 1.003 0.350 7.162-5.571 100.00 427 22 0.1717 293.074 287.553 0.923 1.003 0.263 5.546-4.326 100.00 867 58 0.0913 402.318 399.799 0.950 1.003 0.230 4.315-3.360 100.00 1859 96 0.0770 382.608 381.539 0.995 1.003 0.180 3.356-2.611 100.00 3867 181 0.1026 251.353 250.597 0.998 1.002 0.100 2.608-2.026 99.99 8198 413 0.0982 166.624 165.978 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1215 81.371 81.546 1.018 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1651 36.083 35.547 1.007 0.998 0.000 1.221-1.150 99.97 13689 708 0.2359 22.735 21.255 0.971 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0461 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1245 r_free=0.1537 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=0.1246 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1538 | n_water=258 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1255 r_free=0.1538 | n_water=252 | time (s): 26.410 (total time: 28.970) Filter (q & B) r_work=0.1259 r_free=0.1538 | n_water=249 | time (s): 3.660 (total time: 32.630) Compute maps r_work=0.1259 r_free=0.1538 | n_water=249 | time (s): 1.940 (total time: 34.570) Filter (map) r_work=0.1277 r_free=0.1545 | n_water=235 | time (s): 3.860 (total time: 38.430) Find peaks r_work=0.1277 r_free=0.1545 | n_water=235 | time (s): 0.720 (total time: 39.150) Add new water r_work=0.1434 r_free=0.1691 | n_water=452 | time (s): 3.820 (total time: 42.970) Refine new water occ: r_work=0.1344 r_free=0.1562 adp: r_work=0.1264 r_free=0.1513 occ: r_work=0.1276 r_free=0.1507 adp: r_work=0.1241 r_free=0.1494 occ: r_work=0.1244 r_free=0.1487 adp: r_work=0.1234 r_free=0.1486 ADP+occupancy (water only), MIN, final r_work=0.1234 r_free=0.1486 r_work=0.1234 r_free=0.1486 | n_water=452 | time (s): 79.890 (total time: 122.860) Filter (q & B) r_work=0.1240 r_free=0.1489 | n_water=428 | time (s): 3.810 (total time: 126.670) Filter (dist only) r_work=0.1240 r_free=0.1489 | n_water=428 | time (s): 42.020 (total time: 168.690) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.067921 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1627.572660 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 0.1235 0.1503 0.0269 0.007 0.9 1.6 0.5 0.0 0 12.534 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.35 15.03 2.69 3.840 23.376 1627.573 0.015 12.06 14.87 2.82 4.222 23.184 1627.573 0.015 Individual atomic B min max mean iso aniso Overall: 8.72 113.59 23.37 2.64 193 1762 Protein: 8.72 113.59 17.84 2.65 0 1519 Water: 10.98 71.64 42.87 N/A 193 235 Other: 23.97 35.62 29.08 N/A 0 8 Chain A: 8.72 113.59 20.57 N/A 0 1762 Chain S: 18.46 70.13 48.94 N/A 193 0 Histogram: Values Number of atoms 8.72 - 19.21 1202 19.21 - 29.69 246 29.69 - 40.18 187 40.18 - 50.67 135 50.67 - 61.16 118 61.16 - 71.64 55 71.64 - 82.13 5 82.13 - 92.62 3 92.62 - 103.10 2 103.10 - 113.59 2 =========================== Idealize ADP of riding H ========================== r_work=0.1206 r_free=0.1487 r_work=0.1206 r_free=0.1487 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1206 r_free = 0.1487 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1206 r_free = 0.1482 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.28 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= 0.1206 r_free= 0.1482 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.013947 | | target function (ls_wunit_k1) not normalized (work): 1161.705163 | | target function (ls_wunit_k1) not normalized (free): 100.989101 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1219 0.1206 0.1482 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1620 0.1617 0.1719 n_refl.: 87591 remove outliers: r(all,work,free)=0.1620 0.1617 0.1719 n_refl.: 87591 overall B=0.03 to atoms: r(all,work,free)=0.1625 0.1622 0.1722 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1202 0.1472 n_refl.: 87591 remove outliers: r(all,work,free)=0.1214 0.1201 0.1472 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 32.574-12.150 91.67 83 5 0.3328 290.792 267.800 0.612 0.938 0.350 11.894-9.307 99.02 97 4 0.1551 477.497 475.819 0.977 0.938 0.331 9.237-7.194 100.00 213 7 0.1678 390.534 389.839 1.043 0.939 0.290 7.162-5.571 100.00 427 22 0.1481 293.074 289.924 1.003 0.939 0.240 5.546-4.326 100.00 867 58 0.0837 402.318 399.669 1.022 0.939 0.220 4.315-3.360 100.00 1859 96 0.0709 382.608 381.532 1.068 0.940 0.200 3.356-2.611 100.00 3867 181 0.0953 251.353 250.695 1.075 0.940 0.160 2.608-2.026 99.99 8198 413 0.0956 166.624 166.194 1.083 0.941 0.000 2.025-1.573 100.00 17313 902 0.1189 81.371 81.568 1.090 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1628 36.083 35.586 1.074 0.946 0.000 1.221-1.150 99.97 13689 708 0.2352 22.735 21.297 1.030 0.948 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0471 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1201 r_free=0.1472 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=0.1203 r_free=0.1470 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1203 r_free=0.1470 | n_water=428 | time (s): 1.900 (total time: 1.900) Filter (dist) r_work=0.1203 r_free=0.1468 | n_water=427 | time (s): 39.820 (total time: 41.720) Filter (q & B) r_work=0.1203 r_free=0.1468 | n_water=427 | time (s): 1.140 (total time: 42.860) Compute maps r_work=0.1203 r_free=0.1468 | n_water=427 | time (s): 1.820 (total time: 44.680) Filter (map) r_work=0.1245 r_free=0.1482 | n_water=295 | time (s): 3.620 (total time: 48.300) Find peaks r_work=0.1245 r_free=0.1482 | n_water=295 | time (s): 0.690 (total time: 48.990) Add new water r_work=0.1368 r_free=0.1579 | n_water=473 | time (s): 3.630 (total time: 52.620) Refine new water occ: r_work=0.1265 r_free=0.1502 adp: r_work=0.1266 r_free=0.1502 occ: r_work=0.1244 r_free=0.1490 adp: r_work=0.1241 r_free=0.1485 occ: r_work=0.1232 r_free=0.1484 adp: r_work=0.1224 r_free=0.1475 ADP+occupancy (water only), MIN, final r_work=0.1224 r_free=0.1475 r_work=0.1224 r_free=0.1475 | n_water=473 | time (s): 205.040 (total time: 257.660) Filter (q & B) r_work=0.1228 r_free=0.1470 | n_water=440 | time (s): 4.220 (total time: 261.880) Filter (dist only) r_work=0.1228 r_free=0.1470 | n_water=440 | time (s): 35.970 (total time: 297.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.086041 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.913269 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 0.1229 0.1430 0.0201 0.006 0.9 1.6 0.5 0.0 0 1.043 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 14.30 2.01 3.670 22.341 51.913 3.724 12.08 13.87 1.79 4.256 22.132 51.913 3.647 Individual atomic B min max mean iso aniso Overall: 9.32 108.62 21.87 2.37 208 1759 Protein: 9.32 108.62 17.35 2.37 0 1519 Water: 11.55 70.37 37.39 N/A 208 232 Other: 19.41 31.86 25.81 N/A 0 8 Chain A: 9.32 108.62 20.03 N/A 0 1759 Chain S: 16.16 65.87 37.39 N/A 208 0 Histogram: Values Number of atoms 9.32 - 19.25 1230 19.25 - 29.18 259 29.18 - 39.11 218 39.11 - 49.04 134 49.04 - 58.97 87 58.97 - 68.90 25 68.90 - 78.83 7 78.83 - 88.76 3 88.76 - 98.69 2 98.69 - 108.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.1208 r_free=0.1387 r_work=0.1209 r_free=0.1388 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1209 r_free = 0.1388 target_work(ml) = 3.647 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1387 target_work(ml) = 3.645 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1204 r_free= 0.1387 coordinate error (max.-lik. estimate): 0.06 A | | | | normalized target function (ml) (work): 3.644755 | | target function (ml) not normalized (work): 303578.927890 | | target function (ml) not normalized (free): 16046.151030 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1204 0.1387 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1549 0.1549 0.1581 n_refl.: 87588 remove outliers: r(all,work,free)=0.1549 0.1549 0.1581 n_refl.: 87588 overall B=-0.02 to atoms: r(all,work,free)=0.1546 0.1546 0.1579 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1203 0.1194 0.1368 n_refl.: 87588 remove outliers: r(all,work,free)=0.1200 0.1191 0.1368 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 0.4068 282.851 260.604 0.476 0.999 0.324 11.894-9.307 97.06 95 4 0.2295 470.877 455.181 0.857 1.001 0.254 9.237-7.194 98.18 209 7 0.2208 382.103 385.774 0.945 1.001 0.190 7.162-5.571 100.00 427 22 0.1955 293.074 284.530 0.914 1.002 0.183 5.546-4.326 100.00 867 58 0.1088 402.318 397.848 0.948 1.002 0.173 4.315-3.360 100.00 1859 96 0.0918 382.608 379.941 0.991 1.002 0.170 3.356-2.611 100.00 3867 181 0.1156 251.353 249.559 0.999 1.002 0.081 2.608-2.026 99.99 8198 413 0.1039 166.624 165.674 1.011 1.002 0.000 2.025-1.573 100.00 17313 902 0.1012 81.371 81.522 1.026 1.002 0.000 1.573-1.221 100.00 36679 1900 0.1297 36.083 35.621 1.020 1.001 0.000 1.221-1.150 99.97 13689 708 0.2128 22.735 21.262 0.975 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0435 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1368 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1368 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1368 | n_water=440 | time (s): 1.750 (total time: 1.750) Filter (dist) r_work=0.1191 r_free=0.1368 | n_water=440 | time (s): 38.990 (total time: 40.740) Filter (q & B) r_work=0.1191 r_free=0.1368 | n_water=440 | time (s): 0.980 (total time: 41.720) Compute maps r_work=0.1191 r_free=0.1368 | n_water=440 | time (s): 1.200 (total time: 42.920) Filter (map) r_work=0.1214 r_free=0.1376 | n_water=312 | time (s): 2.960 (total time: 45.880) Find peaks r_work=0.1214 r_free=0.1376 | n_water=312 | time (s): 0.470 (total time: 46.350) Add new water r_work=0.1284 r_free=0.1436 | n_water=476 | time (s): 2.790 (total time: 49.140) Refine new water occ: r_work=0.1211 r_free=0.1366 adp: r_work=0.1212 r_free=0.1368 occ: r_work=0.1196 r_free=0.1357 adp: r_work=0.1194 r_free=0.1356 occ: r_work=0.1184 r_free=0.1353 adp: r_work=0.1180 r_free=0.1349 ADP+occupancy (water only), MIN, final r_work=0.1180 r_free=0.1349 r_work=0.1180 r_free=0.1349 | n_water=476 | time (s): 202.540 (total time: 251.680) Filter (q & B) r_work=0.1187 r_free=0.1351 | n_water=441 | time (s): 3.070 (total time: 254.750) Filter (dist only) r_work=0.1187 r_free=0.1350 | n_water=440 | time (s): 38.660 (total time: 293.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.947022 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 53.823119 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1194 0.1364 0.0170 0.006 0.9 2.2 0.5 0.0 0 0.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.94 13.64 1.70 3.464 21.643 53.823 3.636 11.79 13.59 1.80 3.916 21.513 53.823 3.619 Individual atomic B min max mean iso aniso Overall: 9.28 104.32 21.37 2.21 210 1757 Protein: 9.28 104.32 17.03 2.21 0 1519 Water: 11.57 68.56 36.33 N/A 210 230 Other: 18.83 28.56 23.46 N/A 0 8 Chain A: 9.28 104.32 19.62 N/A 0 1757 Chain S: 15.44 60.01 36.02 N/A 210 0 Histogram: Values Number of atoms 9.28 - 18.79 1223 18.79 - 28.29 272 28.29 - 37.80 207 37.80 - 47.30 148 47.30 - 56.80 76 56.80 - 66.31 27 66.31 - 75.81 9 75.81 - 85.31 1 85.31 - 94.82 2 94.82 - 104.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.1179 r_free=0.1359 r_work=0.1179 r_free=0.1358 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1179 r_free = 0.1358 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1175 r_free = 0.1357 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.17 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= 0.1175 r_free= 0.1357 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617367 | | target function (ml) not normalized (work): 301268.778994 | | target function (ml) not normalized (free): 15926.580877 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1184 0.1175 0.1357 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1528 0.1529 0.1560 n_refl.: 87580 remove outliers: r(all,work,free)=0.1528 0.1529 0.1560 n_refl.: 87580 overall B=-0.03 to atoms: r(all,work,free)=0.1524 0.1524 0.1556 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1183 0.1174 0.1355 n_refl.: 87580 remove outliers: r(all,work,free)=0.1180 0.1171 0.1355 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 86.46 78 5 0.4084 282.778 241.009 0.429 1.000 0.308 11.894-9.307 94.12 92 4 0.2350 476.792 450.155 0.840 1.002 0.250 9.237-7.194 98.18 209 7 0.2420 382.103 376.096 0.912 1.002 0.175 7.162-5.571 100.00 427 22 0.2161 293.074 282.737 0.902 1.002 0.150 5.546-4.326 100.00 867 58 0.1125 402.318 398.383 0.952 1.002 0.140 4.315-3.360 100.00 1859 96 0.0933 382.608 380.173 0.994 1.002 0.140 3.356-2.611 100.00 3867 181 0.1141 251.353 249.733 1.002 1.002 0.110 2.608-2.026 99.99 8198 413 0.1015 166.624 165.937 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0957 81.371 81.689 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1241 36.083 35.728 1.027 0.998 0.000 1.221-1.150 99.97 13689 708 0.2128 22.735 21.377 0.986 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0049 b_overall=-0.0688 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1171 r_free=0.1355 After: r_work=0.1172 r_free=0.1355 ================================== NQH flips ================================== r_work=0.1172 r_free=0.1355 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1172 r_free=0.1355 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1172 r_free=0.1355 | n_water=440 | time (s): 2.030 (total time: 2.030) Filter (dist) r_work=0.1172 r_free=0.1355 | n_water=440 | time (s): 44.160 (total time: 46.190) Filter (q & B) r_work=0.1172 r_free=0.1354 | n_water=438 | time (s): 3.350 (total time: 49.540) Compute maps r_work=0.1172 r_free=0.1354 | n_water=438 | time (s): 1.720 (total time: 51.260) Filter (map) r_work=0.1197 r_free=0.1358 | n_water=330 | time (s): 3.500 (total time: 54.760) Find peaks r_work=0.1197 r_free=0.1358 | n_water=330 | time (s): 0.610 (total time: 55.370) Add new water r_work=0.1251 r_free=0.1398 | n_water=492 | time (s): 3.490 (total time: 58.860) Refine new water occ: r_work=0.1182 r_free=0.1337 adp: r_work=0.1182 r_free=0.1340 occ: r_work=0.1170 r_free=0.1330 adp: r_work=0.1168 r_free=0.1331 occ: r_work=0.1161 r_free=0.1327 adp: r_work=0.1157 r_free=0.1327 ADP+occupancy (water only), MIN, final r_work=0.1157 r_free=0.1327 r_work=0.1157 r_free=0.1327 | n_water=492 | time (s): 202.620 (total time: 261.480) Filter (q & B) r_work=0.1164 r_free=0.1333 | n_water=455 | time (s): 3.190 (total time: 264.670) Filter (dist only) r_work=0.1164 r_free=0.1333 | n_water=454 | time (s): 39.840 (total time: 304.510) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.815231 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.017490 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1195 0.1364 0.0169 0.007 1.0 4.8 0.5 0.0 0 0.908 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.64 1.69 3.318 21.248 52.017 3.626 11.98 13.62 1.64 3.527 21.188 52.017 3.618 Individual atomic B min max mean iso aniso Overall: 9.30 100.07 21.18 2.08 226 1755 Protein: 9.30 100.07 16.83 2.08 0 1519 Water: 11.56 67.68 35.70 N/A 226 228 Other: 18.99 26.55 23.10 N/A 0 8 Chain A: 9.30 100.07 19.37 N/A 0 1755 Chain S: 14.71 57.67 35.21 N/A 226 0 Histogram: Values Number of atoms 9.30 - 18.37 1213 18.37 - 27.45 277 27.45 - 36.53 208 36.53 - 45.61 158 45.61 - 54.68 81 54.68 - 63.76 25 63.76 - 72.84 14 72.84 - 81.92 2 81.92 - 91.00 1 91.00 - 100.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1198 r_free=0.1362 r_work=0.1198 r_free=0.1362 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1362 target_work(ml) = 3.618 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1365 target_work(ml) = 3.617 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87574 (all), 4.91 % free)------------| | | | r_work= 0.1194 r_free= 0.1365 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.617231 | | target function (ml) not normalized (work): 301235.794471 | | target function (ml) not normalized (free): 15932.499057 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2916 171 0.1375 0.1371 5.6361 5.5919| | 2: 3.57 - 2.84 1.00 2888 124 0.1125 0.1427 5.1889 5.2664| | 3: 2.83 - 2.48 1.00 2820 163 0.1236 0.1365 4.9963 5.0317| | 4: 2.47 - 2.25 1.00 2825 136 0.1039 0.1119 4.7041 4.7332| | 5: 2.25 - 2.09 1.00 2756 127 0.1010 0.1082 4.6403 4.6953| | 6: 2.09 - 1.97 1.00 2846 113 0.0979 0.1159 4.3467 4.4485| | 7: 1.97 - 1.87 1.00 2787 165 0.0994 0.1262 4.0762 4.2096| | 8: 1.87 - 1.79 1.00 2789 144 0.1019 0.1258 3.991 4.0821| | 9: 1.79 - 1.72 1.00 2745 138 0.0964 0.1293 3.7203 3.893| | 10: 1.72 - 1.66 1.00 2831 160 0.1002 0.1284 3.6363 3.7966| | 11: 1.66 - 1.61 1.00 2712 147 0.0971 0.1101 3.5732 3.619| | 12: 1.61 - 1.56 1.00 2773 144 0.0922 0.1179 3.3482 3.4824| | 13: 1.56 - 1.52 1.00 2745 130 0.0983 0.1071 3.3381 3.4387| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1095 3.2591 3.3281| | 15: 1.48 - 1.45 1.00 2738 128 0.1010 0.1347 3.1668 3.3228| | 16: 1.45 - 1.42 1.00 2756 161 0.1072 0.1287 3.1533 3.2542| | 17: 1.42 - 1.39 1.00 2785 139 0.1119 0.1314 3.1127 3.238| | 18: 1.39 - 1.36 1.00 2741 179 0.1152 0.1401 3.0826 3.2697| | 19: 1.36 - 1.34 1.00 2807 134 0.1226 0.1591 3.0923 3.2757| | 20: 1.34 - 1.32 1.00 2696 147 0.1314 0.1454 3.0835 3.1259| | 21: 1.32 - 1.30 1.00 2785 112 0.1407 0.1604 3.084 3.1508| | 22: 1.29 - 1.27 1.00 2704 152 0.1471 0.1923 3.0806 3.2843| | 23: 1.27 - 1.26 1.00 2802 156 0.1570 0.1857 3.0972 3.2075| | 24: 1.26 - 1.24 1.00 2744 132 0.1617 0.1782 3.0893 3.1997| | 25: 1.24 - 1.22 1.00 2733 148 0.1778 0.2284 3.1035 3.2835| | 26: 1.22 - 1.21 1.00 2727 135 0.1855 0.1773 3.1182 3.1917| | 27: 1.21 - 1.19 1.00 2814 148 0.2010 0.2131 3.1374 3.1575| | 28: 1.19 - 1.18 1.00 2671 147 0.2144 0.2338 3.1378 3.1664| | 29: 1.18 - 1.16 1.00 2800 134 0.2215 0.2372 3.123 3.2212| | 30: 1.16 - 1.15 1.00 2739 148 0.2364 0.2465 3.1106 3.1601| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2916 171 0.95 8.90 1.00 0.97 5980.44| | 2: 3.57 - 2.84 2888 124 0.92 13.08 1.01 0.97 5980.44| | 3: 2.83 - 2.48 2820 163 0.89 17.15 0.98 0.97 5022.19| | 4: 2.47 - 2.25 2825 136 0.91 14.29 1.00 0.98 2551.16| | 5: 2.25 - 2.09 2756 127 0.90 16.58 1.01 0.98 2551.16| | 6: 2.09 - 1.97 2846 113 0.92 13.63 1.02 0.98 1514.56| | 7: 1.97 - 1.87 2787 165 0.94 10.90 1.02 0.97 630.48| | 8: 1.87 - 1.79 2789 144 0.91 14.53 1.00 0.97 630.48| | 9: 1.79 - 1.72 2745 138 0.93 11.52 0.98 0.97 342.63| | 10: 1.72 - 1.66 2831 160 0.93 12.37 0.98 0.97 284.98| | 11: 1.66 - 1.61 2712 147 0.93 12.98 0.98 0.97 271.87| | 12: 1.61 - 1.56 2773 144 0.95 9.64 0.99 0.97 148.19| | 13: 1.56 - 1.52 2745 130 0.94 11.23 1.02 0.97 148.19| | 14: 1.52 - 1.48 2803 134 0.94 11.34 1.02 0.97 132.30| | 15: 1.48 - 1.45 2738 128 0.95 10.45 1.01 0.98 103.21| | 16: 1.45 - 1.42 2756 161 0.94 11.59 1.01 0.98 103.21| | 17: 1.42 - 1.39 2785 139 0.94 11.51 1.01 0.98 93.06| | 18: 1.39 - 1.36 2741 179 0.94 11.74 1.01 0.98 87.19| | 19: 1.36 - 1.34 2807 134 0.94 12.35 1.00 0.98 87.19| | 20: 1.34 - 1.32 2696 147 0.94 12.41 0.99 0.97 81.98| | 21: 1.32 - 1.30 2785 112 0.94 13.31 0.99 0.96 81.62| | 22: 1.29 - 1.27 2704 152 0.93 13.95 0.99 0.96 81.77| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.98 0.95 82.52| | 24: 1.26 - 1.24 2744 132 0.92 14.99 0.97 0.95 82.52| | 25: 1.24 - 1.22 2733 148 0.91 16.39 0.96 0.94 84.11| | 26: 1.22 - 1.21 2727 135 0.90 18.07 1.02 0.93 85.87| | 27: 1.21 - 1.19 2814 148 0.89 18.74 1.02 0.93 85.87| | 28: 1.19 - 1.18 2671 147 0.88 20.27 1.01 0.93 89.37| | 29: 1.18 - 1.16 2800 134 0.88 20.60 0.99 0.93 90.68| | 30: 1.16 - 1.15 2739 148 0.86 21.99 0.98 0.93 90.68| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 81.62 max = 5980.44 mean = 942.55| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.98 mean = 14.03| |phase err.(test): min = 0.00 max = 89.56 mean = 14.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1202 0.1194 0.1365 n_refl.: 87574 re-set all scales: r(all,work,free)=0.1522 0.1521 0.1565 n_refl.: 87574 remove outliers: r(all,work,free)=0.1522 0.1521 0.1565 n_refl.: 87574 overall B=-0.02 to atoms: r(all,work,free)=0.1517 0.1516 0.1562 n_refl.: 87574 bulk-solvent and scaling: r(all,work,free)=0.1202 0.1193 0.1367 n_refl.: 87574 remove outliers: r(all,work,free)=0.1202 0.1193 0.1367 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 86.46 78 5 0.4142 282.778 247.414 0.440 1.000 0.310 11.894-9.307 94.12 92 4 0.2235 476.792 462.145 0.862 1.002 0.256 9.237-7.194 98.18 209 7 0.2491 382.103 376.269 0.908 1.002 0.176 7.162-5.571 100.00 427 22 0.2159 293.074 282.919 0.895 1.002 0.149 5.546-4.326 100.00 867 58 0.1165 402.318 397.980 0.954 1.002 0.140 4.315-3.360 100.00 1859 96 0.0973 382.608 379.941 0.995 1.002 0.124 3.356-2.611 100.00 3867 181 0.1189 251.353 249.274 1.001 1.002 0.110 2.608-2.026 99.99 8198 413 0.1057 166.624 165.628 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0978 81.371 81.625 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1225 36.083 35.717 1.027 0.996 0.000 1.221-1.150 99.97 13689 708 0.2111 22.735 21.378 0.988 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0645 ================= 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: 0.1208 0.1463 0.007 0.932 9.0 119.5 20.1 258 0.128 1_adp: 0.1244 0.1539 0.007 0.932 8.7 118.5 21.3 258 0.128 1_regHadp: 0.1249 0.1544 0.007 0.932 8.7 118.5 21.3 258 0.128 1_occ: 0.1248 0.1546 0.007 0.932 8.7 118.5 21.3 258 0.128 2_bss: 0.1245 0.1537 0.007 0.932 8.8 118.6 21.4 258 0.128 2_settarget: 0.1245 0.1537 0.007 0.932 8.8 118.6 21.4 258 0.128 2_updatecdl: 0.1245 0.1537 0.007 0.948 8.8 118.6 21.4 258 0.128 2_nqh: 0.1246 0.1538 0.007 0.948 8.8 118.6 21.4 258 0.131 2_sol: 0.1240 0.1489 0.007 0.948 8.8 118.6 23.7 428 n/a 2_weight: 0.1240 0.1489 0.007 0.948 8.8 118.6 23.7 428 n/a 2_xyzrec: 0.1235 0.1503 0.007 0.880 8.8 118.6 23.7 428 n/a 2_adp: 0.1206 0.1487 0.007 0.880 8.7 113.6 23.4 428 n/a 2_regHadp: 0.1206 0.1487 0.007 0.880 8.7 113.6 23.4 428 n/a 2_occ: 0.1206 0.1482 0.007 0.880 8.7 113.6 23.4 428 n/a 3_bss: 0.1201 0.1472 0.007 0.880 8.8 113.6 23.4 428 n/a 3_settarget: 0.1201 0.1472 0.007 0.880 8.8 113.6 23.4 428 n/a 3_updatecdl: 0.1201 0.1472 0.007 0.881 8.8 113.6 23.4 428 n/a 3_nqh: 0.1203 0.1470 0.007 0.881 8.8 113.6 23.4 428 n/a 3_sol: 0.1228 0.1470 0.007 0.881 8.8 113.6 22.2 440 n/a 3_weight: 0.1228 0.1470 0.007 0.881 8.8 113.6 22.2 440 n/a 3_xyzrec: 0.1229 0.1430 0.006 0.918 8.8 113.6 22.2 440 n/a 3_adp: 0.1208 0.1387 0.006 0.918 9.3 108.6 21.9 440 n/a 3_regHadp: 0.1209 0.1388 0.006 0.918 9.3 108.6 21.9 440 n/a 3_occ: 0.1204 0.1387 0.006 0.918 9.3 108.6 21.9 440 n/a 4_bss: 0.1191 0.1368 0.006 0.918 9.3 108.6 21.8 440 n/a 4_settarget: 0.1191 0.1368 0.006 0.918 9.3 108.6 21.8 440 n/a 4_updatecdl: 0.1191 0.1368 0.006 0.917 9.3 108.6 21.8 440 n/a 4_nqh: 0.1191 0.1368 0.006 0.917 9.3 108.6 21.8 440 n/a 4_sol: 0.1187 0.1350 0.006 0.917 9.3 108.6 21.6 440 n/a 4_weight: 0.1187 0.1350 0.006 0.917 9.3 108.6 21.6 440 n/a 4_xyzrec: 0.1194 0.1364 0.006 0.949 9.3 108.6 21.6 440 n/a 4_adp: 0.1179 0.1359 0.006 0.949 9.3 104.3 21.4 440 n/a 4_regHadp: 0.1179 0.1358 0.006 0.949 9.3 104.3 21.4 440 n/a 4_occ: 0.1175 0.1357 0.006 0.949 9.3 104.3 21.4 440 n/a 5_bss: 0.1171 0.1355 0.006 0.949 9.3 104.3 21.3 440 n/a 5_settarget: 0.1171 0.1355 0.006 0.949 9.3 104.3 21.3 440 n/a 5_updatecdl: 0.1171 0.1355 0.006 0.950 9.3 104.3 21.3 440 n/a 5_setrh: 0.1172 0.1355 0.006 0.950 9.3 104.3 21.3 440 n/a 5_nqh: 0.1172 0.1355 0.006 0.950 9.3 104.3 21.3 440 n/a 5_sol: 0.1164 0.1333 0.006 0.950 9.3 104.3 21.3 454 n/a 5_weight: 0.1164 0.1333 0.006 0.950 9.3 104.3 21.3 454 n/a 5_xyzrec: 0.1195 0.1364 0.007 1.040 9.3 104.3 21.3 454 n/a 5_adp: 0.1198 0.1362 0.007 1.040 9.3 100.1 21.2 454 n/a 5_regHadp: 0.1198 0.1362 0.007 1.040 9.3 100.1 21.2 454 n/a 5_occ: 0.1194 0.1365 0.007 1.040 9.3 100.1 21.2 454 n/a end: 0.1193 0.1367 0.007 1.040 9.3 100.1 21.2 454 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1446411_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_1446411_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8200 Refinement macro-cycles (run) : 3523.3600 Write final files (write_after_run_outputs) : 64.9900 Total : 3593.1700 Total CPU time: 60.51 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:11:31 PST -0800 (1735452691.33 s) Start R-work = 0.1635, R-free = 0.1767 Final R-work = 0.1193, R-free = 0.1367 =============================================================================== Job complete usr+sys time: 3727.27 seconds wall clock time: 66 minutes 39.37 seconds (3999.37 seconds total)