Starting phenix.refine on Sat Dec 28 21:06:32 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4872201.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4872201.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4872201.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 } 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: 2.26, per 1000 atoms: 0.67 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: 0.73 Conformation dependent library (CDL) restraints added in 280.5 milliseconds Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 524 0.91 - 1.17: 1127 1.17 - 1.44: 671 1.44 - 1.70: 811 1.70 - 1.96: 20 Bond restraints: 3153 Sorted by residual: bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.235 1.482 -0.246 1.14e-02 7.69e+03 4.67e+02 bond pdb=" N ALYS A 132 " pdb=" CA ALYS A 132 " ideal model delta sigma weight residual 1.459 1.674 -0.215 1.19e-02 7.06e+03 3.26e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.337 1.524 -0.188 1.11e-02 8.12e+03 2.86e+02 bond pdb=" CA TYR A 139 " pdb=" C TYR A 139 " ideal model delta sigma weight residual 1.522 1.315 0.207 1.23e-02 6.61e+03 2.84e+02 bond pdb=" C ASP A 68 " pdb=" N VAL A 69 " ideal model delta sigma weight residual 1.332 1.135 0.197 1.20e-02 6.94e+03 2.70e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.36: 3002 4.36 - 8.72: 1849 8.72 - 13.08: 738 13.08 - 17.43: 165 17.43 - 21.79: 23 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 78 " pdb=" C GLY A 78 " pdb=" N ALA A 79 " ideal model delta sigma weight residual 122.18 135.54 -13.36 9.60e-01 1.09e+00 1.94e+02 angle pdb=" N VAL A 88 " pdb=" CA VAL A 88 " pdb=" C VAL A 88 " ideal model delta sigma weight residual 110.62 125.63 -15.01 1.14e+00 7.69e-01 1.73e+02 angle pdb=" CA ALA A 171 " pdb=" C ALA A 171 " pdb=" N LEU A 172 " ideal model delta sigma weight residual 117.30 102.54 14.76 1.16e+00 7.43e-01 1.62e+02 angle pdb=" N ALA A 179 " pdb=" CA ALA A 179 " pdb=" C ALA A 179 " ideal model delta sigma weight residual 111.28 124.70 -13.42 1.09e+00 8.42e-01 1.52e+02 angle pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 109.00 121.29 -12.29 1.00e+00 1.00e+00 1.51e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 940 16.97 - 33.93: 114 33.93 - 50.89: 40 50.89 - 67.86: 14 67.86 - 84.82: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA AGLY A 65 " pdb=" C AGLY A 65 " pdb=" N APRO A 66 " pdb=" CA APRO A 66 " ideal model delta harmonic sigma weight residual 0.00 26.56 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA THR A 125 " pdb=" C THR A 125 " pdb=" N HIS A 126 " pdb=" CA HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" ND1 HIS A 115 " pdb=" CG HIS A 115 " pdb=" CD2 HIS A 115 " pdb=" HD2 HIS A 115 " ideal model delta harmonic sigma weight residual -180.00 -158.09 -21.91 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.210: 100 0.210 - 0.420: 65 0.420 - 0.629: 47 0.629 - 0.838: 24 0.838 - 1.047: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLEU A 153 " pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CB BLEU A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.56 -1.05 2.00e-01 2.50e+01 2.74e+01 chirality pdb=" CA PHE A 119 " pdb=" N PHE A 119 " pdb=" C PHE A 119 " pdb=" CB PHE A 119 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CA LEU A 82 " pdb=" N LEU A 82 " pdb=" C LEU A 82 " pdb=" CB LEU A 82 " both_signs ideal model delta sigma weight residual False 2.51 3.48 -0.97 2.00e-01 2.50e+01 2.37e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 28 " 0.236 9.50e-02 1.11e+02 1.05e-01 1.14e+02 pdb=" NE ARG A 28 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 28 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 28 " 0.070 2.00e-02 2.50e+03 pdb=" NH2 ARG A 28 " -0.133 2.00e-02 2.50e+03 pdb="HH11 ARG A 28 " -0.026 2.00e-02 2.50e+03 pdb="HH12 ARG A 28 " 0.028 2.00e-02 2.50e+03 pdb="HH21 ARG A 28 " 0.127 2.00e-02 2.50e+03 pdb="HH22 ARG A 28 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " -0.006 2.00e-02 2.50e+03 7.02e-02 1.11e+02 pdb=" CG HIS A 126 " 0.071 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.100 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.059 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.108 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.104 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 48 " -0.074 9.50e-02 1.11e+02 7.15e-02 1.02e+02 pdb=" NE ARG A 48 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG A 48 " -0.092 2.00e-02 2.50e+03 pdb=" NH1 ARG A 48 " 0.127 2.00e-02 2.50e+03 pdb=" NH2 ARG A 48 " -0.036 2.00e-02 2.50e+03 pdb="HH11 ARG A 48 " -0.084 2.00e-02 2.50e+03 pdb="HH12 ARG A 48 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 48 " -0.021 2.00e-02 2.50e+03 pdb="HH22 ARG A 48 " 0.046 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 784 2.28 - 2.86: 7835 2.86 - 3.44: 10609 3.44 - 4.02: 15298 4.02 - 4.60: 22050 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.698 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.701 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.802 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.808 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.825 2.450 ... (remaining 56571 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_4872201_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= 0.2601 r_free= 0.1928 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787314 | | target function (ml) not normalized (work): 232199.965389 | | target function (ml) not normalized (free): 11799.046986 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3033 0.2073 6.982 4.9554| | 2: 3.57 - 2.84 1.00 2876 122 0.2426 0.1841 4.3556 4.3456| | 3: 2.84 - 2.48 1.00 2833 165 0.2389 0.1608 4.1358 4.1654| | 4: 2.47 - 2.25 1.00 2825 136 0.2322 0.1455 3.8388 3.8426| | 5: 2.25 - 2.09 1.00 2756 127 0.2477 0.1532 3.8088 3.8198| | 6: 2.09 - 1.97 1.00 2846 113 0.2515 0.1905 3.4697 3.6351| | 7: 1.97 - 1.87 1.00 2787 165 0.2549 0.1773 3.1224 3.1871| | 8: 1.87 - 1.79 1.00 2789 144 0.2449 0.1939 3.0625 3.1441| | 9: 1.79 - 1.72 1.00 2745 138 0.2331 0.1744 2.887 2.8906| | 10: 1.72 - 1.66 1.00 2789 158 0.2387 0.1911 2.7955 2.8864| | 11: 1.66 - 1.61 1.00 2740 147 0.2501 0.1903 2.7573 2.7783| | 12: 1.61 - 1.56 1.00 2787 146 0.2522 0.1828 2.6224 2.5748| | 13: 1.56 - 1.52 1.00 2745 130 0.2586 0.2023 2.5642 2.6408| | 14: 1.52 - 1.48 1.00 2803 134 0.2569 0.1982 2.5119 2.58| | 15: 1.48 - 1.45 1.00 2738 128 0.2632 0.1943 2.4359 2.4391| | 16: 1.45 - 1.42 1.00 2756 161 0.2642 0.2250 2.3847 2.4666| | 17: 1.42 - 1.39 1.00 2785 139 0.2708 0.2044 2.3444 2.3426| | 18: 1.39 - 1.36 1.00 2741 179 0.2664 0.2284 2.2743 2.3542| | 19: 1.36 - 1.34 1.00 2807 134 0.2632 0.2399 2.2351 2.3225| | 20: 1.34 - 1.32 1.00 2696 147 0.2619 0.2130 2.2078 2.1523| | 21: 1.32 - 1.30 1.00 2785 112 0.2686 0.2247 2.1571 2.2077| | 22: 1.29 - 1.27 1.00 2704 152 0.2690 0.2428 2.1258 2.1598| | 23: 1.27 - 1.26 1.00 2802 156 0.2755 0.2540 2.0921 2.2004| | 24: 1.26 - 1.24 1.00 2744 132 0.2753 0.2414 2.0708 2.082| | 25: 1.24 - 1.22 1.00 2734 148 0.2843 0.2457 2.0376 2.0405| | 26: 1.22 - 1.21 1.00 2727 135 0.2877 0.2215 2.012 2.07| | 27: 1.21 - 1.19 1.00 2814 148 0.3004 0.2611 2.0127 2.0168| | 28: 1.19 - 1.18 1.00 2671 147 0.2932 0.2563 1.9741 1.946| | 29: 1.18 - 1.16 1.00 2800 134 0.2928 0.2593 1.9575 2.007| | 30: 1.16 - 1.15 1.00 2740 148 0.3031 0.2950 1.9314 2.0021| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.58 2941 171 0.87 19.07 0.76 0.23 1516.97| | 2: 3.57 - 2.84 2876 122 0.80 26.51 1.27 0.23 1516.97| | 3: 2.84 - 2.48 2833 165 0.73 32.46 1.25 0.23 1257.67| | 4: 2.47 - 2.25 2825 136 0.81 25.84 1.25 0.25 584.75| | 5: 2.25 - 2.09 2756 127 0.77 29.58 1.28 0.25 584.75| | 6: 2.09 - 1.97 2846 113 0.83 22.80 1.29 0.25 319.07| | 7: 1.97 - 1.87 2787 165 0.90 16.75 1.29 0.26 92.48| | 8: 1.87 - 1.79 2789 144 0.86 21.24 1.25 0.26 92.48| | 9: 1.79 - 1.72 2745 138 0.88 18.30 1.22 0.25 54.79| | 10: 1.72 - 1.66 2789 158 0.87 19.92 1.22 0.25 47.25| | 11: 1.66 - 1.61 2740 147 0.86 20.97 1.24 0.25 45.58| | 12: 1.61 - 1.56 2787 146 0.88 18.36 1.23 0.25 28.68| | 13: 1.56 - 1.52 2745 130 0.87 20.29 1.25 0.25 28.68| | 14: 1.52 - 1.48 2803 134 0.87 20.49 1.24 0.25 25.71| | 15: 1.48 - 1.45 2738 128 0.87 19.85 1.24 0.25 20.28| | 16: 1.45 - 1.42 2756 161 0.86 21.21 1.23 0.25 20.28| | 17: 1.42 - 1.39 2785 139 0.87 20.48 1.24 0.25 17.37| | 18: 1.39 - 1.36 2741 179 0.86 21.12 1.23 0.25 15.68| | 19: 1.36 - 1.34 2807 134 0.85 22.02 1.21 0.25 15.68| | 20: 1.34 - 1.32 2696 147 0.87 20.32 1.20 0.25 12.93| | 21: 1.32 - 1.30 2785 112 0.86 21.79 1.20 0.25 12.73| | 22: 1.29 - 1.27 2704 152 0.86 21.97 1.20 0.25 12.43| | 23: 1.27 - 1.26 2802 156 0.86 21.76 1.21 0.24 10.89| | 24: 1.26 - 1.24 2744 132 0.85 22.50 1.20 0.24 10.89| | 25: 1.24 - 1.22 2734 148 0.85 23.07 1.21 0.24 10.28| | 26: 1.22 - 1.21 2727 135 0.85 23.25 1.20 0.24 9.61| | 27: 1.21 - 1.19 2814 148 0.84 24.24 1.21 0.24 9.61| | 28: 1.19 - 1.18 2671 147 0.84 24.44 1.18 0.23 8.97| | 29: 1.18 - 1.16 2800 134 0.83 24.78 1.15 0.23 8.73| | 30: 1.16 - 1.15 2740 148 0.82 26.45 1.15 0.23 8.73| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 8.73 max = 1516.97 mean = 219.40| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.91 mean = 22.40| |phase err.(test): min = 0.00 max = 89.82 mean = 22.36| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.246 1557 Z= 5.439 Angle : 5.305 18.369 2118 Z= 3.695 Chirality : 0.396 1.047 243 Planarity : 0.032 0.102 284 Dihedral : 13.954 84.819 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.11 % Favored : 96.27 % Cbeta Deviations : 35.14 % 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: -2.31 (0.48), residues: 224 helix: -2.10 (0.39), residues: 109 sheet: -0.17 (1.02), residues: 28 loop : -0.93 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.109 0.023 ARG A 48 TYR 0.093 0.034 TYR A 141 PHE 0.108 0.039 PHE A 119 HIS 0.058 0.027 HIS A 126 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= 0.2601 r_free= 0.1928 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.787314 | | target function (ml) not normalized (work): 232199.965389 | | target function (ml) not normalized (free): 11799.046986 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2560 0.2602 0.1929 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2560 0.2602 0.1929 n_refl.: 87602 remove outliers: r(all,work,free)=0.1972 0.1976 0.1929 n_refl.: 87594 overall B=0.20 to atoms: r(all,work,free)=0.1996 0.2001 0.1942 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1632 0.1765 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1631 0.1765 n_refl.: 87593 ======================== 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 98.94 88 5 0.3837 386.175 358.452 0.738 0.915 0.408 11.894-9.307 99.02 97 4 0.1824 613.421 593.951 1.019 0.916 0.390 9.237-7.194 100.00 213 7 0.2165 501.703 489.851 1.051 0.917 0.370 7.162-5.571 100.00 427 22 0.2184 376.500 366.172 1.013 0.918 0.278 5.546-4.326 100.00 867 58 0.1267 516.842 511.658 1.050 0.919 0.219 4.315-3.360 100.00 1859 96 0.1166 491.520 487.481 1.097 0.920 0.199 3.356-2.611 100.00 3867 181 0.1427 322.903 319.333 1.086 0.922 0.048 2.608-2.026 99.99 8198 413 0.1345 214.055 212.086 1.089 0.926 0.000 2.025-1.573 100.00 17313 902 0.1631 104.533 103.967 1.083 0.932 0.000 1.573-1.221 100.00 36679 1900 0.2063 46.354 45.112 1.062 0.942 0.000 1.221-1.150 99.97 13689 708 0.2586 29.207 26.995 1.021 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0455 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1631 r_free=0.1765 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=0.1632 r_free=0.1766 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.754275 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1988.053815 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 0.1212 0.1456 0.0244 0.007 0.9 1.0 0.5 0.0 0 11.377 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.12 14.56 2.44 3.013 19.057 1988.054 0.017 12.43 15.31 2.88 3.225 19.553 1988.054 0.016 Individual atomic B min max mean iso aniso Overall: 8.43 118.85 21.02 2.87 0 1785 Protein: 8.43 118.85 17.89 2.87 0 1519 Water: 11.05 114.78 39.19 N/A 0 258 Other: 22.60 36.23 29.19 N/A 0 8 Chain A: 8.43 118.85 21.02 N/A 0 1785 Histogram: Values Number of atoms 8.43 - 19.47 1204 19.47 - 30.51 232 30.51 - 41.55 165 41.55 - 52.60 102 52.60 - 63.64 52 63.64 - 74.68 17 74.68 - 85.72 6 85.72 - 96.76 4 96.76 - 107.80 0 107.80 - 118.85 3 =========================== Idealize ADP of riding H ========================== r_work=0.1243 r_free=0.1531 r_work=0.1248 r_free=0.1535 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1248 r_free = 0.1535 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 = 0.1247 r_free = 0.1538 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1247 r_free= 0.1538 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.015483 | | target function (ls_wunit_k1) not normalized (work): 1289.677938 | | target function (ls_wunit_k1) not normalized (free): 113.136280 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1262 0.1247 0.1538 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1700 0.1698 0.1765 n_refl.: 87593 remove outliers: r(all,work,free)=0.1700 0.1698 0.1765 n_refl.: 87593 overall B=0.14 to atoms: r(all,work,free)=0.1722 0.1721 0.1781 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1261 0.1247 0.1532 n_refl.: 87593 remove outliers: r(all,work,free)=0.1260 0.1246 0.1532 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 95.83 87 5 0.3607 299.127 277.877 0.632 1.002 0.375 11.894-9.307 99.02 97 4 0.1624 479.185 468.519 0.908 1.003 0.372 9.237-7.194 100.00 213 7 0.1820 391.914 386.331 0.949 1.003 0.350 7.162-5.571 100.00 427 22 0.1734 294.110 288.837 0.925 1.003 0.254 5.546-4.326 100.00 867 58 0.0908 403.740 401.287 0.950 1.003 0.214 4.315-3.360 100.00 1859 96 0.0776 383.960 382.956 0.996 1.003 0.200 3.356-2.611 100.00 3867 181 0.1025 252.242 251.564 0.999 1.002 0.110 2.608-2.026 99.99 8198 413 0.0981 167.213 166.625 1.010 1.001 0.000 2.025-1.573 100.00 17313 902 0.1215 81.658 81.832 1.017 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1654 36.211 35.664 1.006 0.998 0.000 1.221-1.150 99.97 13689 708 0.2364 22.815 21.314 0.970 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1246 r_free=0.1532 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1246 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1246 r_free=0.1532 | n_water=258 | time (s): 2.400 (total time: 2.400) Filter (dist) r_work=0.1256 r_free=0.1531 | n_water=251 | time (s): 25.670 (total time: 28.070) Filter (q & B) r_work=0.1259 r_free=0.1531 | n_water=248 | time (s): 3.570 (total time: 31.640) Compute maps r_work=0.1259 r_free=0.1531 | n_water=248 | time (s): 1.760 (total time: 33.400) Filter (map) r_work=0.1276 r_free=0.1538 | n_water=235 | time (s): 3.710 (total time: 37.110) Find peaks r_work=0.1276 r_free=0.1538 | n_water=235 | time (s): 0.710 (total time: 37.820) Add new water r_work=0.1431 r_free=0.1691 | n_water=449 | time (s): 3.800 (total time: 41.620) Refine new water occ: r_work=0.1340 r_free=0.1574 adp: r_work=0.1257 r_free=0.1515 occ: r_work=0.1269 r_free=0.1520 adp: r_work=0.1235 r_free=0.1499 occ: r_work=0.1237 r_free=0.1503 adp: r_work=0.1229 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1229 r_free=0.1501 r_work=0.1229 r_free=0.1501 | n_water=449 | time (s): 151.620 (total time: 193.240) Filter (q & B) r_work=0.1234 r_free=0.1506 | n_water=428 | time (s): 3.730 (total time: 196.970) Filter (dist only) r_work=0.1234 r_free=0.1506 | n_water=428 | time (s): 40.040 (total time: 237.010) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.796162 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1435.288602 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 0.1513 0.0285 0.007 0.9 1.9 0.5 0.0 0 12.898 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.29 15.13 2.85 3.795 23.167 1435.289 0.015 12.03 14.90 2.87 4.182 22.975 1435.289 0.015 Individual atomic B min max mean iso aniso Overall: 8.77 115.12 23.11 2.59 193 1762 Protein: 8.77 115.12 17.69 2.59 0 1519 Water: 11.09 73.13 42.22 N/A 193 235 Other: 25.77 37.00 30.83 N/A 0 8 Chain A: 8.77 115.12 20.36 N/A 0 1762 Chain S: 17.68 69.01 48.18 N/A 193 0 Histogram: Values Number of atoms 8.77 - 19.40 1211 19.40 - 30.04 254 30.04 - 40.67 189 40.67 - 51.31 140 51.31 - 61.94 99 61.94 - 72.58 50 72.58 - 83.22 6 83.22 - 93.85 3 93.85 - 104.49 1 104.49 - 115.12 2 =========================== Idealize ADP of riding H ========================== r_work=0.1203 r_free=0.1490 r_work=0.1203 r_free=0.1490 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1490 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1204 r_free = 0.1487 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1204 r_free= 0.1487 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.014147 | | target function (ls_wunit_k1) not normalized (work): 1178.371456 | | target function (ls_wunit_k1) not normalized (free): 103.620785 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1204 0.1487 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1609 0.1605 0.1724 n_refl.: 87592 remove outliers: r(all,work,free)=0.1609 0.1605 0.1724 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1615 0.1611 0.1727 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1201 0.1486 n_refl.: 87592 remove outliers: r(all,work,free)=0.1213 0.1199 0.1486 n_refl.: 87589 ======================== 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 92.71 84 5 0.3364 295.062 272.910 0.634 0.938 0.364 11.894-9.307 99.02 97 4 0.1521 479.185 477.240 0.979 0.939 0.360 9.237-7.194 100.00 213 7 0.1725 391.914 391.340 1.041 0.939 0.310 7.162-5.571 100.00 427 22 0.1496 294.110 290.980 1.000 0.939 0.223 5.546-4.326 100.00 867 58 0.0850 403.740 400.945 1.020 0.940 0.201 4.315-3.360 100.00 1859 96 0.0725 383.960 382.793 1.067 0.940 0.187 3.356-2.611 100.00 3867 181 0.0967 252.242 251.391 1.075 0.941 0.140 2.608-2.026 99.99 8198 413 0.0953 167.213 166.814 1.082 0.942 0.000 2.025-1.573 100.00 17313 902 0.1177 81.658 81.845 1.088 0.944 0.000 1.573-1.221 100.00 36679 1900 0.1613 36.211 35.715 1.072 0.948 0.000 1.221-1.150 99.97 13689 708 0.2340 22.815 21.362 1.026 0.950 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0538 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1199 r_free=0.1486 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1199 r_free=0.1486 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1199 r_free=0.1486 | n_water=428 | time (s): 2.130 (total time: 2.130) Filter (dist) r_work=0.1199 r_free=0.1483 | n_water=426 | time (s): 39.620 (total time: 41.750) Filter (q & B) r_work=0.1199 r_free=0.1483 | n_water=426 | time (s): 1.080 (total time: 42.830) Compute maps r_work=0.1199 r_free=0.1483 | n_water=426 | time (s): 1.540 (total time: 44.370) Filter (map) r_work=0.1238 r_free=0.1476 | n_water=293 | time (s): 3.380 (total time: 47.750) Find peaks r_work=0.1238 r_free=0.1476 | n_water=293 | time (s): 0.560 (total time: 48.310) Add new water r_work=0.1365 r_free=0.1601 | n_water=485 | time (s): 2.550 (total time: 50.860) Refine new water occ: r_work=0.1266 r_free=0.1512 adp: r_work=0.1267 r_free=0.1514 occ: r_work=0.1243 r_free=0.1497 adp: r_work=0.1240 r_free=0.1495 occ: r_work=0.1228 r_free=0.1490 adp: r_work=0.1221 r_free=0.1483 ADP+occupancy (water only), MIN, final r_work=0.1221 r_free=0.1483 r_work=0.1221 r_free=0.1483 | n_water=485 | time (s): 172.180 (total time: 223.040) Filter (q & B) r_work=0.1225 r_free=0.1483 | n_water=453 | time (s): 3.380 (total time: 226.420) Filter (dist only) r_work=0.1225 r_free=0.1483 | n_water=453 | time (s): 37.380 (total time: 263.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.087902 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 50.550988 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 0.1237 0.1455 0.0217 0.006 0.9 3.8 0.5 0.0 0 1.044 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.37 14.55 2.17 3.623 22.154 50.551 3.728 12.19 14.12 1.94 4.251 21.937 50.551 3.655 Individual atomic B min max mean iso aniso Overall: 9.26 110.16 21.66 2.33 221 1759 Protein: 9.26 110.16 17.15 2.33 0 1519 Water: 11.71 71.57 36.70 N/A 221 232 Other: 21.16 32.63 26.86 N/A 0 8 Chain A: 9.26 110.16 19.78 N/A 0 1759 Chain S: 15.80 65.25 36.62 N/A 221 0 Histogram: Values Number of atoms 9.26 - 19.35 1238 19.35 - 29.44 287 29.44 - 39.53 212 39.53 - 49.62 132 49.62 - 59.71 75 59.71 - 69.80 23 69.80 - 79.89 7 79.89 - 89.98 3 89.98 - 100.07 1 100.07 - 110.16 2 =========================== Idealize ADP of riding H ========================== r_work=0.1219 r_free=0.1412 r_work=0.1220 r_free=0.1413 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1220 r_free = 0.1413 target_work(ml) = 3.655 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1215 r_free = 0.1406 target_work(ml) = 3.652 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1215 r_free= 0.1406 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.652280 | | target function (ml) not normalized (work): 304209.349266 | | target function (ml) not normalized (free): 16066.246482 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1224 0.1215 0.1406 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1539 0.1537 0.1598 n_refl.: 87589 remove outliers: r(all,work,free)=0.1539 0.1537 0.1598 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1536 0.1535 0.1596 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1214 0.1206 0.1374 n_refl.: 87589 remove outliers: r(all,work,free)=0.1212 0.1204 0.1374 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3965 291.811 260.068 0.468 1.000 0.304 11.894-9.307 99.02 97 4 0.2583 479.185 462.731 0.847 1.002 0.293 9.237-7.194 98.18 209 7 0.2435 383.453 384.513 0.938 1.002 0.200 7.162-5.571 100.00 427 22 0.2126 294.110 282.907 0.908 1.002 0.155 5.546-4.326 100.00 867 58 0.1120 403.740 398.765 0.950 1.002 0.147 4.315-3.360 100.00 1859 96 0.0935 383.960 381.644 0.993 1.002 0.143 3.356-2.611 100.00 3867 181 0.1155 252.242 250.347 1.001 1.002 0.120 2.608-2.026 99.99 8198 413 0.1052 167.213 166.218 1.012 1.001 0.000 2.025-1.573 100.00 17313 902 0.1011 81.658 81.831 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1290 36.211 35.779 1.021 0.998 0.000 1.221-1.150 99.97 13689 708 0.2124 22.815 21.429 0.980 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0382 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1204 r_free=0.1374 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=0.1204 r_free=0.1376 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1204 r_free=0.1376 | n_water=453 | time (s): 1.780 (total time: 1.780) Filter (dist) r_work=0.1204 r_free=0.1376 | n_water=451 | time (s): 40.340 (total time: 42.120) Filter (q & B) r_work=0.1204 r_free=0.1376 | n_water=450 | time (s): 2.730 (total time: 44.850) Compute maps r_work=0.1204 r_free=0.1376 | n_water=450 | time (s): 1.340 (total time: 46.190) Filter (map) r_work=0.1223 r_free=0.1383 | n_water=318 | time (s): 2.820 (total time: 49.010) Find peaks r_work=0.1223 r_free=0.1383 | n_water=318 | time (s): 0.520 (total time: 49.530) Add new water r_work=0.1289 r_free=0.1444 | n_water=481 | time (s): 2.630 (total time: 52.160) Refine new water occ: r_work=0.1218 r_free=0.1373 adp: r_work=0.1218 r_free=0.1373 occ: r_work=0.1203 r_free=0.1367 adp: r_work=0.1202 r_free=0.1364 occ: r_work=0.1194 r_free=0.1365 adp: r_work=0.1190 r_free=0.1360 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1360 r_work=0.1190 r_free=0.1360 | n_water=481 | time (s): 181.310 (total time: 233.470) Filter (q & B) r_work=0.1196 r_free=0.1359 | n_water=449 | time (s): 3.080 (total time: 236.550) Filter (dist only) r_work=0.1196 r_free=0.1358 | n_water=447 | time (s): 37.290 (total time: 273.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.295862 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 52.127490 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 0.1366 0.0172 0.007 1.0 5.8 0.5 0.0 0 1.148 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.95 13.66 1.72 3.415 21.457 52.127 3.637 11.81 13.59 1.78 3.784 21.340 52.127 3.620 Individual atomic B min max mean iso aniso Overall: 9.25 105.67 21.25 2.17 216 1758 Protein: 9.25 105.67 16.89 2.17 0 1519 Water: 11.67 70.00 35.98 N/A 216 231 Other: 20.74 30.18 25.43 N/A 0 8 Chain A: 9.25 105.67 19.46 N/A 0 1758 Chain S: 14.33 63.47 35.76 N/A 216 0 Histogram: Values Number of atoms 9.25 - 18.89 1229 18.89 - 28.53 285 28.53 - 38.17 211 38.17 - 47.81 140 47.81 - 57.46 67 57.46 - 67.10 28 67.10 - 76.74 9 76.74 - 86.38 2 86.38 - 96.02 1 96.02 - 105.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.1181 r_free=0.1359 r_work=0.1181 r_free=0.1359 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1181 r_free = 0.1359 target_work(ml) = 3.620 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1178 r_free = 0.1358 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1178 r_free= 0.1358 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.618770 | | target function (ml) not normalized (work): 301396.487025 | | target function (ml) not normalized (free): 15926.098179 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1187 0.1178 0.1358 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1494 0.1491 0.1581 n_refl.: 87583 remove outliers: r(all,work,free)=0.1494 0.1491 0.1581 n_refl.: 87583 overall B=-0.02 to atoms: r(all,work,free)=0.1491 0.1487 0.1579 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1186 0.1177 0.1365 n_refl.: 87583 remove outliers: r(all,work,free)=0.1183 0.1174 0.1365 n_refl.: 87576 ======================== 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 0.4263 287.194 256.638 0.450 0.956 0.269 11.894-9.307 93.14 91 4 0.2320 470.885 454.841 0.872 0.957 0.247 9.237-7.194 98.18 209 7 0.2467 383.453 378.404 0.955 0.957 0.124 7.162-5.571 100.00 427 22 0.2210 294.110 283.258 0.943 0.957 0.118 5.546-4.326 100.00 867 58 0.1141 403.740 399.049 0.996 0.957 0.108 4.315-3.360 100.00 1859 96 0.0950 383.960 381.663 1.040 0.957 0.107 3.356-2.611 100.00 3867 181 0.1151 252.242 250.381 1.048 0.957 0.043 2.608-2.026 99.99 8198 413 0.1012 167.213 166.305 1.061 0.956 0.000 2.025-1.573 100.00 17313 902 0.0951 81.658 81.924 1.076 0.956 0.000 1.573-1.221 100.00 36679 1900 0.1234 36.211 35.845 1.070 0.954 0.000 1.221-1.150 99.97 13689 708 0.2115 22.815 21.456 1.026 0.953 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0478 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1174 r_free=0.1365 After: r_work=0.1174 r_free=0.1366 ================================== NQH flips ================================== r_work=0.1174 r_free=0.1366 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=0.1174 r_free=0.1366 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1174 r_free=0.1366 | n_water=447 | time (s): 1.620 (total time: 1.620) Filter (dist) r_work=0.1174 r_free=0.1366 | n_water=447 | time (s): 36.280 (total time: 37.900) Filter (q & B) r_work=0.1174 r_free=0.1367 | n_water=445 | time (s): 2.750 (total time: 40.650) Compute maps r_work=0.1174 r_free=0.1367 | n_water=445 | time (s): 1.280 (total time: 41.930) Filter (map) r_work=0.1204 r_free=0.1383 | n_water=331 | time (s): 2.730 (total time: 44.660) Find peaks r_work=0.1204 r_free=0.1383 | n_water=331 | time (s): 0.630 (total time: 45.290) Add new water r_work=0.1248 r_free=0.1433 | n_water=505 | time (s): 3.070 (total time: 48.360) Refine new water occ: r_work=0.1183 r_free=0.1367 adp: r_work=0.1183 r_free=0.1368 occ: r_work=0.1173 r_free=0.1361 adp: r_work=0.1172 r_free=0.1362 occ: r_work=0.1164 r_free=0.1357 adp: r_work=0.1162 r_free=0.1357 ADP+occupancy (water only), MIN, final r_work=0.1162 r_free=0.1357 r_work=0.1162 r_free=0.1357 | n_water=505 | time (s): 177.290 (total time: 225.650) Filter (q & B) r_work=0.1173 r_free=0.1368 | n_water=452 | time (s): 2.600 (total time: 228.250) Filter (dist only) r_work=0.1173 r_free=0.1368 | n_water=451 | time (s): 38.490 (total time: 266.740) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.028306 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 33.642300 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 0.1201 0.1395 0.0194 0.007 1.0 5.8 0.5 0.0 0 1.014 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.01 13.95 1.94 3.286 21.112 33.642 3.630 12.01 13.95 1.94 3.299 21.103 33.642 3.629 Individual atomic B min max mean iso aniso Overall: 9.24 105.08 21.13 2.13 221 1757 Protein: 9.24 105.08 16.85 2.13 0 1519 Water: 11.70 69.94 35.48 N/A 221 230 Other: 20.72 29.98 25.38 N/A 0 8 Chain A: 9.24 105.08 19.40 N/A 0 1757 Chain S: 14.29 60.60 34.86 N/A 221 0 Histogram: Values Number of atoms 9.24 - 18.83 1229 18.83 - 28.41 288 28.41 - 37.99 221 37.99 - 47.58 129 47.58 - 57.16 72 57.16 - 66.75 25 66.75 - 76.33 9 76.33 - 85.91 2 85.91 - 95.50 1 95.50 - 105.08 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1395 r_work=0.1201 r_free=0.1395 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1395 target_work(ml) = 3.629 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1197 r_free = 0.1397 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87576 (all), 4.91 % free)------------| | | | r_work= 0.1197 r_free= 0.1397 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.627670 | | target function (ml) not normalized (work): 302112.379526 | | target function (ml) not normalized (free): 15966.935059 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2918 171 0.1430 0.1533 5.6743 5.7145| | 2: 3.57 - 2.84 1.00 2888 124 0.1123 0.1499 5.2321 5.3046| | 3: 2.83 - 2.48 1.00 2820 163 0.1208 0.1282 5.039 5.0584| | 4: 2.47 - 2.25 1.00 2825 136 0.1014 0.1178 4.7361 4.7932| | 5: 2.25 - 2.09 1.00 2756 127 0.0989 0.1079 4.6833 4.7374| | 6: 2.09 - 1.97 1.00 2846 113 0.0974 0.1234 4.3706 4.5175| | 7: 1.97 - 1.87 1.00 2787 165 0.0988 0.1209 4.0755 4.1655| | 8: 1.87 - 1.79 1.00 2789 144 0.1010 0.1250 3.9858 4.0794| | 9: 1.79 - 1.72 1.00 2745 138 0.0951 0.1270 3.7122 3.8864| | 10: 1.72 - 1.66 1.00 2831 160 0.0995 0.1245 3.628 3.7458| | 11: 1.66 - 1.61 1.00 2712 147 0.0961 0.1127 3.5648 3.6054| | 12: 1.61 - 1.56 1.00 2773 144 0.0918 0.1168 3.346 3.4668| | 13: 1.56 - 1.52 1.00 2745 130 0.0984 0.1022 3.3389 3.4156| | 14: 1.52 - 1.48 1.00 2803 134 0.0993 0.1104 3.2637 3.357| | 15: 1.48 - 1.45 1.00 2738 128 0.1021 0.1313 3.1712 3.3152| | 16: 1.45 - 1.42 1.00 2756 161 0.1075 0.1246 3.1532 3.2431| | 17: 1.42 - 1.39 1.00 2785 139 0.1119 0.1240 3.1165 3.2153| | 18: 1.39 - 1.36 1.00 2741 179 0.1156 0.1411 3.0889 3.2917| | 19: 1.36 - 1.34 1.00 2807 134 0.1222 0.1567 3.0961 3.2739| | 20: 1.34 - 1.32 1.00 2696 147 0.1321 0.1464 3.0888 3.1384| | 21: 1.32 - 1.30 1.00 2785 112 0.1421 0.1641 3.0915 3.1685| | 22: 1.29 - 1.27 1.00 2704 152 0.1487 0.1941 3.0917 3.2841| | 23: 1.27 - 1.26 1.00 2802 156 0.1593 0.1854 3.1126 3.2097| | 24: 1.26 - 1.24 1.00 2744 132 0.1635 0.1811 3.0997 3.2024| | 25: 1.24 - 1.22 1.00 2733 148 0.1810 0.2343 3.1157 3.2937| | 26: 1.22 - 1.21 1.00 2727 135 0.1865 0.1787 3.1248 3.1969| | 27: 1.21 - 1.19 1.00 2814 148 0.2017 0.2104 3.144 3.1473| | 28: 1.19 - 1.18 1.00 2671 147 0.2140 0.2316 3.1398 3.1623| | 29: 1.18 - 1.16 1.00 2800 134 0.2224 0.2370 3.1301 3.2203| | 30: 1.16 - 1.15 1.00 2739 148 0.2382 0.2496 3.1199 3.1661| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2918 171 0.94 9.90 1.00 0.97 7115.35| | 2: 3.57 - 2.84 2888 124 0.91 14.37 1.01 0.97 7115.35| | 3: 2.83 - 2.48 2820 163 0.88 18.59 0.99 0.97 5944.92| | 4: 2.47 - 2.25 2825 136 0.90 15.45 1.00 0.98 2926.74| | 5: 2.25 - 2.09 2756 127 0.89 17.80 1.01 0.98 2926.74| | 6: 2.09 - 1.97 2846 113 0.91 14.09 1.02 0.97 1685.74| | 7: 1.97 - 1.87 2787 165 0.94 10.80 1.02 0.97 627.34| | 8: 1.87 - 1.79 2789 144 0.91 14.38 1.00 0.97 627.34| | 9: 1.79 - 1.72 2745 138 0.93 11.39 0.98 0.97 336.36| | 10: 1.72 - 1.66 2831 160 0.93 12.13 0.98 0.97 278.09| | 11: 1.66 - 1.61 2712 147 0.93 12.79 0.98 0.97 265.52| | 12: 1.61 - 1.56 2773 144 0.95 9.52 0.99 0.97 146.98| | 13: 1.56 - 1.52 2745 130 0.94 11.10 1.02 0.97 146.98| | 14: 1.52 - 1.48 2803 134 0.94 11.14 1.02 0.97 131.26| | 15: 1.48 - 1.45 2738 128 0.95 10.37 1.01 0.98 102.46| | 16: 1.45 - 1.42 2756 161 0.94 11.49 1.01 0.98 102.46| | 17: 1.42 - 1.39 2785 139 0.95 11.34 1.01 0.98 93.00| | 18: 1.39 - 1.36 2741 179 0.94 11.74 1.01 0.98 87.53| | 19: 1.36 - 1.34 2807 134 0.94 12.28 1.00 0.98 87.53| | 20: 1.34 - 1.32 2696 147 0.94 12.48 0.99 0.97 82.74| | 21: 1.32 - 1.30 2785 112 0.94 13.36 0.98 0.96 82.41| | 22: 1.29 - 1.27 2704 152 0.93 13.89 0.98 0.96 82.59| | 23: 1.27 - 1.26 2802 156 0.92 14.93 0.98 0.95 83.53| | 24: 1.26 - 1.24 2744 132 0.92 15.04 0.97 0.95 83.53| | 25: 1.24 - 1.22 2733 148 0.91 16.44 0.96 0.94 84.97| | 26: 1.22 - 1.21 2727 135 0.90 18.13 1.02 0.93 86.56| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.56| | 28: 1.19 - 1.18 2671 147 0.88 20.22 1.01 0.93 89.60| | 29: 1.18 - 1.16 2800 134 0.88 20.51 0.99 0.93 90.74| | 30: 1.16 - 1.15 2739 148 0.86 21.90 0.98 0.93 90.74| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 82.41 max = 7115.35 mean = 1083.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.95 mean = 14.20| |phase err.(test): min = 0.00 max = 89.37 mean = 14.30| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1207 0.1197 0.1397 n_refl.: 87576 re-set all scales: r(all,work,free)=0.1505 0.1502 0.1590 n_refl.: 87576 remove outliers: r(all,work,free)=0.1505 0.1502 0.1590 n_refl.: 87576 overall B=-0.01 to atoms: r(all,work,free)=0.1503 0.1500 0.1589 n_refl.: 87576 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1197 0.1401 n_refl.: 87576 remove outliers: r(all,work,free)=0.1207 0.1197 0.1401 n_refl.: 87575 ======================== 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 0.4215 287.194 257.887 0.430 0.999 0.274 11.894-9.307 92.16 90 4 0.2440 464.492 450.478 0.829 1.000 0.177 9.237-7.194 98.18 209 7 0.2566 383.453 377.632 0.900 1.000 0.115 7.162-5.571 100.00 427 22 0.2284 294.110 281.330 0.892 1.001 0.108 5.546-4.326 100.00 867 58 0.1195 403.740 398.752 0.952 1.001 0.104 4.315-3.360 100.00 1859 96 0.0994 383.960 381.443 0.996 1.001 0.103 3.356-2.611 100.00 3867 181 0.1183 252.242 250.321 1.003 1.001 0.038 2.608-2.026 99.99 8198 413 0.1028 167.213 166.240 1.013 1.001 0.000 2.025-1.573 100.00 17313 902 0.0973 81.658 81.928 1.027 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1235 36.211 35.861 1.019 1.001 0.000 1.221-1.150 99.97 13689 708 0.2121 22.815 21.409 0.974 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0364 ================= 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 : 0.2601 0.1928 0.081 5.305 8.8 119.3 19.9 258 0.000 1_bss: 0.1631 0.1765 0.081 5.305 9.0 119.5 20.1 258 0.000 1_settarget: 0.1631 0.1765 0.081 5.305 9.0 119.5 20.1 258 0.000 1_nqh: 0.1632 0.1766 0.081 5.305 9.0 119.5 20.1 258 0.003 1_weight: 0.1632 0.1766 0.081 5.305 9.0 119.5 20.1 258 0.003 1_xyzrec: 0.1212 0.1456 0.007 0.922 9.0 119.5 20.1 258 0.128 1_adp: 0.1243 0.1531 0.007 0.922 8.4 118.8 21.0 258 0.128 1_regHadp: 0.1248 0.1535 0.007 0.922 8.4 118.8 21.0 258 0.128 1_occ: 0.1247 0.1538 0.007 0.922 8.4 118.8 21.0 258 0.128 2_bss: 0.1246 0.1532 0.007 0.922 8.6 119.0 21.2 258 0.128 2_settarget: 0.1246 0.1532 0.007 0.922 8.6 119.0 21.2 258 0.128 2_updatecdl: 0.1246 0.1532 0.007 0.932 8.6 119.0 21.2 258 0.128 2_nqh: 0.1246 0.1532 0.007 0.932 8.6 119.0 21.2 258 0.128 2_sol: 0.1234 0.1506 0.007 0.932 8.6 119.0 23.5 428 n/a 2_weight: 0.1234 0.1506 0.007 0.932 8.6 119.0 23.5 428 n/a 2_xyzrec: 0.1229 0.1513 0.007 0.874 8.6 119.0 23.5 428 n/a 2_adp: 0.1203 0.1490 0.007 0.874 8.8 115.1 23.1 428 n/a 2_regHadp: 0.1203 0.1490 0.007 0.874 8.8 115.1 23.1 428 n/a 2_occ: 0.1204 0.1487 0.007 0.874 8.8 115.1 23.1 428 n/a 3_bss: 0.1199 0.1486 0.007 0.874 8.8 115.2 23.1 428 n/a 3_settarget: 0.1199 0.1486 0.007 0.874 8.8 115.2 23.1 428 n/a 3_updatecdl: 0.1199 0.1486 0.007 0.875 8.8 115.2 23.1 428 n/a 3_nqh: 0.1199 0.1486 0.007 0.875 8.8 115.2 23.1 428 n/a 3_sol: 0.1225 0.1483 0.007 0.875 8.8 115.2 22.1 453 n/a 3_weight: 0.1225 0.1483 0.007 0.875 8.8 115.2 22.1 453 n/a 3_xyzrec: 0.1237 0.1455 0.006 0.930 8.8 115.2 22.1 453 n/a 3_adp: 0.1219 0.1412 0.006 0.930 9.3 110.2 21.7 453 n/a 3_regHadp: 0.1220 0.1413 0.006 0.930 9.3 110.2 21.7 453 n/a 3_occ: 0.1215 0.1406 0.006 0.930 9.3 110.2 21.7 453 n/a 4_bss: 0.1204 0.1374 0.006 0.930 9.2 110.1 21.6 453 n/a 4_settarget: 0.1204 0.1374 0.006 0.930 9.2 110.1 21.6 453 n/a 4_updatecdl: 0.1204 0.1374 0.006 0.930 9.2 110.1 21.6 453 n/a 4_nqh: 0.1204 0.1376 0.006 0.930 9.2 110.1 21.6 453 n/a 4_sol: 0.1196 0.1358 0.006 0.930 9.2 110.1 21.5 447 n/a 4_weight: 0.1196 0.1358 0.006 0.930 9.2 110.1 21.5 447 n/a 4_xyzrec: 0.1195 0.1366 0.007 0.973 9.2 110.1 21.5 447 n/a 4_adp: 0.1181 0.1359 0.007 0.973 9.2 105.7 21.2 447 n/a 4_regHadp: 0.1181 0.1359 0.007 0.973 9.2 105.7 21.2 447 n/a 4_occ: 0.1178 0.1358 0.007 0.973 9.2 105.7 21.2 447 n/a 5_bss: 0.1174 0.1365 0.007 0.973 9.2 105.6 21.2 447 n/a 5_settarget: 0.1174 0.1365 0.007 0.973 9.2 105.6 21.2 447 n/a 5_updatecdl: 0.1174 0.1365 0.007 0.975 9.2 105.6 21.2 447 n/a 5_setrh: 0.1174 0.1366 0.007 0.975 9.2 105.6 21.2 447 n/a 5_nqh: 0.1174 0.1366 0.007 0.975 9.2 105.6 21.2 447 n/a 5_sol: 0.1173 0.1368 0.007 0.975 9.2 105.6 21.1 451 n/a 5_weight: 0.1173 0.1368 0.007 0.975 9.2 105.6 21.1 451 n/a 5_xyzrec: 0.1201 0.1395 0.007 1.042 9.2 105.6 21.1 451 n/a 5_adp: 0.1201 0.1395 0.007 1.042 9.2 105.1 21.1 451 n/a 5_regHadp: 0.1201 0.1395 0.007 1.042 9.2 105.1 21.1 451 n/a 5_occ: 0.1197 0.1397 0.007 1.042 9.2 105.1 21.1 451 n/a end: 0.1197 0.1401 0.007 1.042 9.2 105.1 21.1 451 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4872201_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_nowopt/shake_4872201_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.8800 Refinement macro-cycles (run) : 3369.5800 Write final files (write_after_run_outputs) : 72.3700 Total : 3446.8300 Total CPU time: 58.06 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-28 Time 22:08:55 PST -0800 (1735452535.03 s) Start R-work = 0.1631, R-free = 0.1765 Final R-work = 0.1197, R-free = 0.1401 =============================================================================== Job complete usr+sys time: 3600.99 seconds wall clock time: 64 minutes 25.29 seconds (3865.29 seconds total)