Starting phenix.refine on Fri Dec 27 17:58:26 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.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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_4872201.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4872201.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.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 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.90, per 1000 atoms: 0.56 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: 0.50 Conformation dependent library (CDL) restraints added in 212.9 milliseconds Time building geometry restraints manager: 0.71 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 1.850 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 1.850 ... (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 nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "shake_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 = 25.171519 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 0.1727 0.1833 0.0106 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1570 0.1704 0.0134 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1446 0.1611 0.0164 0.001 0.4 4.2 0.0 0.0 0 0.500 0.1365 0.1554 0.0189 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1351 0.1553 0.0202 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1349 0.1546 0.0197 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1295 0.1512 0.0217 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1268 0.1488 0.0220 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1259 0.1488 0.0229 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1248 0.1474 0.0226 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1246 0.1478 0.0232 0.004 0.7 3.5 0.5 0.0 0 6.000 0.1240 0.1472 0.0231 0.005 0.8 3.5 0.5 0.0 0 7.000 0.1237 0.1471 0.0234 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1233 0.1467 0.0234 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1231 0.1469 0.0238 0.006 0.9 3.8 0.5 0.0 0 10.000 0.1229 0.1472 0.0243 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1226 0.1476 0.0250 0.007 0.9 4.2 0.5 0.0 0 12.586 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1233 0.1467 0.0234 0.006 0.8 3.5 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.33 14.67 2.34 3.013 19.057 1988.054 0.018 12.33 14.66 2.33 2.989 19.057 59.642 0.018 12.40 14.64 2.24 2.665 19.056 248.507 0.017 12.72 15.26 2.54 2.734 19.212 994.027 0.017 12.58 15.43 2.84 3.163 19.525 1988.054 0.016 12.47 15.42 2.94 3.263 19.601 2982.081 0.015 12.40 15.45 3.05 3.413 19.675 3976.108 0.015 12.34 15.53 3.19 3.340 19.640 4970.135 0.015 12.24 15.35 3.11 3.342 19.622 5964.161 0.015 12.24 15.36 3.12 3.181 19.513 6958.188 0.015 12.25 15.43 3.18 3.303 19.575 7952.215 0.015 12.24 15.47 3.23 3.469 19.656 8946.242 0.015 12.22 15.45 3.22 3.347 19.574 9940.269 0.015 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 248.507 Accepted refinement result: 12.40 14.64 2.24 2.665 19.056 248.507 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.45 20.08 3.30 0 1785 Protein: 9.07 114.96 16.99 3.31 0 1519 Water: 11.45 119.45 38.23 N/A 0 258 Other: 19.72 26.61 22.06 N/A 0 8 Chain A: 9.07 119.45 20.08 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.33 7 86.33 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1240 r_free=0.1464 r_work=0.1242 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1242 r_free = 0.1467 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1234 r_free = 0.1458 target_work(ls_wunit_k1) = 0.017 | | 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.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1234 r_free= 0.1458 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016954 | | target function (ls_wunit_k1) not normalized (work): 1412.255288 | | target function (ls_wunit_k1) not normalized (free): 109.611613 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1245 0.1234 0.1458 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1678 0.1689 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1678 0.1689 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1683 0.1684 0.1693 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1244 0.1233 0.1450 n_refl.: 87593 remove outliers: r(all,work,free)=0.1243 0.1233 0.1450 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 0.3533 301.666 281.395 0.646 1.003 0.376 11.894-9.307 99.02 97 4 0.1664 483.252 471.448 0.923 1.003 0.373 9.237-7.194 100.00 213 7 0.1895 395.241 388.993 0.965 1.003 0.350 7.162-5.571 100.00 427 22 0.1814 296.606 291.157 0.938 1.003 0.259 5.546-4.326 100.00 867 58 0.0998 407.167 404.554 0.963 1.003 0.209 4.315-3.360 100.00 1859 96 0.0874 387.219 386.171 1.009 1.003 0.190 3.356-2.611 100.00 3867 181 0.1180 254.383 253.237 1.010 1.002 0.053 2.608-2.026 99.99 8198 413 0.1030 168.633 167.876 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1121 82.351 82.520 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1458 36.518 36.016 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2255 23.009 21.488 0.981 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0540 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1233 r_free=0.1450 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=0.1233 r_free=0.1450 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1233 r_free=0.1450 | n_water=258 | time (s): 1.560 (total time: 1.560) Filter (dist) r_work=0.1240 r_free=0.1448 | n_water=252 | time (s): 22.050 (total time: 23.610) Filter (q & B) r_work=0.1243 r_free=0.1449 | n_water=249 | time (s): 2.250 (total time: 25.860) Compute maps r_work=0.1243 r_free=0.1449 | n_water=249 | time (s): 1.350 (total time: 27.210) Filter (map) r_work=0.1265 r_free=0.1450 | n_water=221 | time (s): 2.570 (total time: 29.780) Find peaks r_work=0.1265 r_free=0.1450 | n_water=221 | time (s): 0.500 (total time: 30.280) Add new water r_work=0.1413 r_free=0.1624 | n_water=424 | time (s): 2.830 (total time: 33.110) Refine new water occ: r_work=0.1314 r_free=0.1490 adp: r_work=0.1234 r_free=0.1434 occ: r_work=0.1246 r_free=0.1419 adp: r_work=0.1213 r_free=0.1405 occ: r_work=0.1215 r_free=0.1399 adp: r_work=0.1205 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1205 r_free=0.1394 r_work=0.1205 r_free=0.1394 | n_water=424 | time (s): 51.440 (total time: 84.550) Filter (q & B) r_work=0.1207 r_free=0.1398 | n_water=410 | time (s): 2.510 (total time: 87.060) Filter (dist only) r_work=0.1207 r_free=0.1396 | n_water=409 | time (s): 33.040 (total time: 120.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.385594 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1481.939802 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 0.1681 0.1788 0.0107 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1522 0.1651 0.0130 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1428 0.1577 0.0149 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1373 0.1537 0.0164 0.001 0.4 4.8 0.0 0.0 0 0.750 0.1321 0.1497 0.0176 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1321 0.1495 0.0173 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1255 0.1446 0.0191 0.002 0.5 3.8 0.5 0.0 0 2.000 0.1229 0.1427 0.0198 0.003 0.6 4.2 0.5 0.0 0 3.000 0.1213 0.1419 0.0206 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1209 0.1416 0.0207 0.004 0.7 4.2 0.5 0.0 0 5.000 0.1206 0.1415 0.0209 0.004 0.7 4.5 0.5 0.0 0 6.000 0.1203 0.1415 0.0212 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1198 0.1413 0.0215 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1198 0.1416 0.0218 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1193 0.1416 0.0222 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1191 0.1411 0.0220 0.007 0.9 4.8 0.5 0.0 0 11.000 0.1191 0.1417 0.0226 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1190 0.1416 0.0226 0.008 0.9 5.4 0.5 0.0 0 13.693 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1411 0.0220 0.007 0.9 4.8 0.5 0.0 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 14.11 2.20 3.772 21.680 1481.940 0.016 11.91 14.11 2.20 3.772 21.680 44.458 0.016 11.91 14.11 2.20 3.771 21.680 185.242 0.016 12.11 14.58 2.48 3.617 21.691 740.970 0.015 12.09 14.86 2.77 3.555 21.747 1481.940 0.015 12.02 14.95 2.93 3.503 21.841 2222.910 0.015 11.83 14.67 2.83 3.464 21.985 2963.880 0.014 11.77 14.76 3.00 3.537 21.809 3704.850 0.014 11.71 14.71 3.00 3.527 21.840 4445.819 0.014 11.77 14.77 3.00 3.527 22.049 5186.789 0.014 11.74 14.77 3.03 3.548 22.066 5927.759 0.014 11.73 14.79 3.06 3.563 22.051 6668.729 0.014 11.72 14.80 3.09 3.581 22.062 7409.699 0.014 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 185.242 Accepted refinement result: 11.91 14.11 2.20 3.771 21.680 185.242 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 114.99 22.01 3.30 188 1748 Protein: 9.11 114.99 17.03 3.31 0 1519 Water: 11.48 76.69 40.53 N/A 188 221 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.11 114.99 19.36 N/A 0 1748 Chain S: 16.81 60.00 46.65 N/A 188 0 Histogram: Values Number of atoms 9.11 - 19.69 1260 19.69 - 30.28 245 30.28 - 40.87 165 40.87 - 51.46 125 51.46 - 62.05 119 62.05 - 72.63 11 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1411 r_work=0.1191 r_free=0.1411 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1411 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1190 r_free = 0.1408 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.27 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= 0.1190 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015044 | | target function (ls_wunit_k1) not normalized (work): 1253.134032 | | target function (ls_wunit_k1) not normalized (free): 101.957696 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1200 0.1190 0.1408 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1593 0.1594 0.1608 n_refl.: 87592 remove outliers: r(all,work,free)=0.1593 0.1594 0.1608 n_refl.: 87592 overall B=0.01 to atoms: r(all,work,free)=0.1595 0.1596 0.1610 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1186 0.1401 n_refl.: 87592 remove outliers: r(all,work,free)=0.1196 0.1185 0.1401 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 0.3435 297.567 276.412 0.599 1.003 0.360 11.894-9.307 99.02 97 4 0.1629 483.252 475.815 0.918 1.003 0.350 9.237-7.194 100.00 213 7 0.1662 395.241 395.864 0.987 1.003 0.280 7.162-5.571 100.00 427 22 0.1559 296.606 292.055 0.938 1.003 0.234 5.546-4.326 100.00 867 58 0.0898 407.167 403.987 0.961 1.003 0.210 4.315-3.360 100.00 1859 96 0.0778 387.219 386.375 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1086 254.383 253.756 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1013 168.633 168.074 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1101 82.351 82.574 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1445 36.518 36.051 1.023 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 23.009 21.521 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0172 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1185 r_free=0.1401 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1185 r_free=0.1401 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1185 r_free=0.1401 | n_water=409 | time (s): 2.060 (total time: 2.060) Filter (dist) r_work=0.1185 r_free=0.1403 | n_water=407 | time (s): 34.390 (total time: 36.450) Filter (q & B) r_work=0.1185 r_free=0.1403 | n_water=407 | time (s): 0.780 (total time: 37.230) Compute maps r_work=0.1185 r_free=0.1403 | n_water=407 | time (s): 1.350 (total time: 38.580) Filter (map) r_work=0.1221 r_free=0.1394 | n_water=289 | time (s): 3.000 (total time: 41.580) Find peaks r_work=0.1221 r_free=0.1394 | n_water=289 | time (s): 0.610 (total time: 42.190) Add new water r_work=0.1340 r_free=0.1521 | n_water=470 | time (s): 2.480 (total time: 44.670) Refine new water occ: r_work=0.1245 r_free=0.1441 adp: r_work=0.1246 r_free=0.1442 occ: r_work=0.1224 r_free=0.1421 adp: r_work=0.1223 r_free=0.1420 occ: r_work=0.1208 r_free=0.1402 adp: r_work=0.1203 r_free=0.1398 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1398 r_work=0.1203 r_free=0.1398 | n_water=470 | time (s): 192.600 (total time: 237.270) Filter (q & B) r_work=0.1208 r_free=0.1402 | n_water=438 | time (s): 2.450 (total time: 239.720) Filter (dist only) r_work=0.1207 r_free=0.1400 | n_water=436 | time (s): 37.690 (total time: 277.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.875530 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.407332 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 0.1236 0.1376 0.0140 0.002 0.6 5.1 0.5 0.0 0 0.094 0.1192 0.1340 0.0148 0.003 0.7 3.8 0.5 0.0 0 0.281 0.1175 0.1330 0.0155 0.004 0.8 3.5 0.5 0.0 0 0.563 0.1168 0.1328 0.0160 0.005 0.9 3.2 0.5 0.0 0 0.844 0.1164 0.1327 0.0163 0.006 1.0 3.5 0.5 0.0 0 1.125 0.1162 0.1330 0.0168 0.007 1.0 3.5 0.5 0.0 0 1.407 0.1159 0.1326 0.0167 0.007 1.1 3.5 0.5 0.0 0 1.688 0.1158 0.1328 0.0170 0.008 1.1 3.5 0.5 0.0 0 1.969 0.1168 0.1329 0.0161 0.006 0.9 3.2 0.5 0.0 0 0.938 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1159 0.1326 0.0167 0.007 1.1 3.5 0.5 0.0 0 1.688 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 13.26 1.67 3.775 21.216 43.407 3.623 11.59 13.26 1.67 3.775 21.216 1.302 3.623 11.60 13.26 1.66 3.759 21.216 5.426 3.623 11.63 13.31 1.69 3.709 21.210 21.704 3.616 11.69 13.45 1.76 3.732 21.174 43.407 3.618 11.61 13.43 1.82 3.755 21.159 65.111 3.611 11.56 13.40 1.84 3.772 21.153 86.815 3.607 11.53 13.39 1.86 3.784 21.146 108.518 3.604 11.49 13.37 1.87 3.793 21.146 130.222 3.602 11.50 13.40 1.90 3.815 21.129 151.926 3.601 11.49 13.40 1.91 3.825 21.128 173.629 3.600 11.47 13.38 1.91 3.833 21.126 195.333 3.599 11.48 13.39 1.91 3.845 21.119 217.037 3.598 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.302 Accepted refinement result: 11.59 13.26 1.67 3.775 21.216 1.302 3.623 Individual atomic B min max mean iso aniso Overall: 9.12 115.00 21.15 3.30 218 1745 Protein: 9.12 115.00 17.04 3.31 0 1519 Water: 11.49 76.70 35.47 N/A 218 218 Other: 19.76 26.66 22.11 N/A 0 8 Chain A: 9.12 115.00 19.33 N/A 0 1745 Chain S: 16.02 60.01 35.71 N/A 218 0 Histogram: Values Number of atoms 9.12 - 19.70 1261 19.70 - 30.29 297 30.29 - 40.88 206 40.88 - 51.47 121 51.47 - 62.06 56 62.06 - 72.65 11 72.65 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1159 r_free=0.1326 r_work=0.1159 r_free=0.1326 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1159 r_free = 0.1326 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1152 r_free = 0.1319 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.14 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= 0.1152 r_free= 0.1319 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615602 | | target function (ml) not normalized (work): 301154.303802 | | target function (ml) not normalized (free): 15858.979189 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1160 0.1152 0.1319 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1501 0.1501 0.1538 n_refl.: 87589 remove outliers: r(all,work,free)=0.1501 0.1501 0.1538 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1500 0.1500 0.1537 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1147 0.1312 n_refl.: 87589 remove outliers: r(all,work,free)=0.1154 0.1146 0.1312 n_refl.: 87585 ======================== 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 0.3853 297.567 270.046 0.508 1.001 0.330 11.894-9.307 98.04 96 4 0.2236 483.377 463.720 0.877 1.002 0.272 9.237-7.194 98.64 210 7 0.2186 387.716 389.075 0.966 1.002 0.220 7.162-5.571 100.00 427 22 0.2068 296.606 286.268 0.924 1.003 0.220 5.546-4.326 100.00 867 58 0.1108 407.167 402.086 0.966 1.003 0.170 4.315-3.360 100.00 1859 96 0.0938 387.219 384.808 1.003 1.002 0.150 3.356-2.611 100.00 3867 181 0.1148 254.383 252.401 1.007 1.002 0.043 2.608-2.026 99.99 8198 413 0.0941 168.633 167.857 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0899 82.351 82.648 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1259 36.518 36.103 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.009 21.553 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0158 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1146 r_free=0.1312 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=0.1146 r_free=0.1312 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1146 r_free=0.1312 | n_water=436 | time (s): 2.320 (total time: 2.320) Filter (dist) r_work=0.1146 r_free=0.1312 | n_water=436 | time (s): 40.320 (total time: 42.640) Filter (q & B) r_work=0.1146 r_free=0.1313 | n_water=435 | time (s): 3.910 (total time: 46.550) Compute maps r_work=0.1146 r_free=0.1313 | n_water=435 | time (s): 1.870 (total time: 48.420) Filter (map) r_work=0.1173 r_free=0.1303 | n_water=322 | time (s): 3.870 (total time: 52.290) Find peaks r_work=0.1173 r_free=0.1303 | n_water=322 | time (s): 0.690 (total time: 52.980) Add new water r_work=0.1250 r_free=0.1385 | n_water=485 | time (s): 3.680 (total time: 56.660) Refine new water occ: r_work=0.1171 r_free=0.1325 adp: r_work=0.1171 r_free=0.1326 occ: r_work=0.1154 r_free=0.1307 adp: r_work=0.1152 r_free=0.1307 occ: r_work=0.1141 r_free=0.1293 adp: r_work=0.1136 r_free=0.1291 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1291 r_work=0.1136 r_free=0.1291 | n_water=485 | time (s): 223.470 (total time: 280.130) Filter (q & B) r_work=0.1142 r_free=0.1298 | n_water=448 | time (s): 3.850 (total time: 283.980) Filter (dist only) r_work=0.1142 r_free=0.1297 | n_water=446 | time (s): 46.410 (total time: 330.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.717990 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.320592 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1332 0.0126 0.002 0.6 4.2 0.5 0.0 0 0.086 0.1171 0.1311 0.0140 0.003 0.7 3.5 0.5 0.0 0 0.258 0.1156 0.1305 0.0149 0.005 0.9 3.5 0.5 0.0 0 0.515 0.1150 0.1305 0.0155 0.005 0.9 3.2 0.5 0.0 0 0.773 0.1146 0.1302 0.0156 0.006 1.0 3.2 0.5 0.0 0 1.031 0.1143 0.1302 0.0159 0.007 1.0 3.2 0.5 0.0 0 1.288 0.1141 0.1297 0.0156 0.008 1.1 3.5 0.5 0.0 0 1.546 0.1139 0.1295 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.804 0.1149 0.1304 0.0156 0.006 1.0 3.2 0.5 0.0 0 0.859 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1295 0.0156 0.008 1.1 3.8 0.5 0.0 0 1.804 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 12.95 1.56 3.776 21.223 44.321 3.608 11.39 12.95 1.56 3.776 21.223 1.330 3.608 11.39 12.95 1.56 3.772 21.223 5.540 3.608 11.41 13.00 1.59 3.712 21.216 22.160 3.602 11.43 13.07 1.64 3.738 21.194 44.321 3.604 11.41 13.08 1.67 3.758 21.174 66.481 3.599 11.34 13.03 1.69 3.774 21.172 88.641 3.594 11.32 13.02 1.70 3.785 21.170 110.801 3.592 11.29 13.01 1.72 3.797 21.165 132.962 3.590 11.30 13.04 1.73 3.818 21.151 155.122 3.590 11.30 13.03 1.74 3.830 21.149 177.282 3.589 11.27 13.00 1.73 3.836 21.149 199.443 3.587 11.25 12.99 1.74 3.835 21.153 221.603 3.586 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.330 Accepted refinement result: 11.39 12.95 1.56 3.776 21.223 1.330 3.608 Individual atomic B min max mean iso aniso Overall: 9.11 114.99 21.17 3.30 230 1743 Protein: 9.11 114.99 17.03 3.31 0 1519 Water: 11.49 76.69 35.24 N/A 230 216 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.11 114.99 19.32 N/A 0 1743 Chain S: 16.82 60.01 35.16 N/A 230 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 297 30.29 - 40.88 211 40.88 - 51.46 126 51.46 - 62.05 53 62.05 - 72.64 11 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1139 r_free=0.1295 r_work=0.1139 r_free=0.1295 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1295 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1135 r_free = 0.1291 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87585 (all), 4.90 % free)------------| | | | r_work= 0.1135 r_free= 0.1291 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605601 | | target function (ml) not normalized (work): 300306.910477 | | target function (ml) not normalized (free): 15813.338202 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1142 0.1135 0.1291 n_refl.: 87585 re-set all scales: r(all,work,free)=0.1478 0.1478 0.1507 n_refl.: 87585 remove outliers: r(all,work,free)=0.1478 0.1478 0.1507 n_refl.: 87585 overall B=0.00 to atoms: r(all,work,free)=0.1478 0.1478 0.1507 n_refl.: 87585 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1134 0.1290 n_refl.: 87585 remove outliers: r(all,work,free)=0.1139 0.1132 0.1290 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 90.62 82 5 0.3925 294.696 258.519 0.468 0.999 0.320 11.894-9.307 95.10 93 4 0.2299 479.682 463.305 0.866 1.001 0.273 9.237-7.194 98.64 210 7 0.2327 387.716 382.078 0.935 1.001 0.170 7.162-5.571 100.00 427 22 0.2110 296.606 285.923 0.912 1.001 0.160 5.546-4.326 100.00 867 58 0.1133 407.167 402.319 0.964 1.001 0.140 4.315-3.360 100.00 1859 96 0.0918 387.219 385.241 1.004 1.002 0.140 3.356-2.611 100.00 3867 181 0.1109 254.383 252.735 1.009 1.002 0.050 2.608-2.026 99.99 8198 413 0.0912 168.633 168.035 1.024 1.002 0.000 2.025-1.573 100.00 17313 902 0.0888 82.351 82.714 1.033 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.518 36.104 1.023 1.001 0.000 1.221-1.150 99.97 13689 708 0.2167 23.009 21.460 0.979 1.001 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0019 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1132 r_free=0.1290 After: r_work=0.1133 r_free=0.1289 ================================== NQH flips ================================== r_work=0.1133 r_free=0.1289 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=0.1133 r_free=0.1289 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1133 r_free=0.1289 | n_water=446 | time (s): 2.310 (total time: 2.310) Filter (dist) r_work=0.1133 r_free=0.1289 | n_water=446 | time (s): 41.750 (total time: 44.060) Filter (q & B) r_work=0.1134 r_free=0.1287 | n_water=443 | time (s): 3.820 (total time: 47.880) Compute maps r_work=0.1134 r_free=0.1287 | n_water=443 | time (s): 1.820 (total time: 49.700) Filter (map) r_work=0.1160 r_free=0.1306 | n_water=339 | time (s): 3.850 (total time: 53.550) Find peaks r_work=0.1160 r_free=0.1306 | n_water=339 | time (s): 0.700 (total time: 54.250) Add new water r_work=0.1213 r_free=0.1363 | n_water=498 | time (s): 3.700 (total time: 57.950) Refine new water occ: r_work=0.1153 r_free=0.1307 adp: r_work=0.1154 r_free=0.1309 occ: r_work=0.1141 r_free=0.1298 adp: r_work=0.1140 r_free=0.1299 occ: r_work=0.1132 r_free=0.1293 adp: r_work=0.1129 r_free=0.1291 ADP+occupancy (water only), MIN, final r_work=0.1129 r_free=0.1291 r_work=0.1129 r_free=0.1291 | n_water=498 | time (s): 285.790 (total time: 343.740) Filter (q & B) r_work=0.1137 r_free=0.1300 | n_water=451 | time (s): 4.060 (total time: 347.800) Filter (dist only) r_work=0.1140 r_free=0.1301 | n_water=449 | time (s): 46.680 (total time: 394.480) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.782818 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.864188 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 0.1219 0.1352 0.0132 0.004 0.7 6.7 0.0 0.0 0 0.089 0.1179 0.1327 0.0148 0.004 0.8 6.4 0.0 0.0 0 0.267 0.1159 0.1313 0.0154 0.005 0.9 5.8 0.5 0.0 0 0.535 0.1152 0.1309 0.0156 0.006 1.0 5.4 0.5 0.0 0 0.802 0.1146 0.1303 0.0157 0.006 1.1 5.4 0.5 0.0 0 1.070 0.1142 0.1301 0.0159 0.008 1.1 5.1 0.5 0.0 0 1.337 0.1140 0.1301 0.0161 0.008 1.1 5.1 0.5 0.0 0 1.605 0.1139 0.1301 0.0161 0.008 1.1 5.1 0.5 0.0 0 1.872 0.1149 0.1305 0.0157 0.006 1.0 5.4 0.5 0.0 0 0.891 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1139 0.1301 0.0161 0.008 1.1 5.1 0.5 0.0 0 1.872 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.39 13.01 1.61 3.775 21.194 46.864 3.609 11.39 13.01 1.61 3.775 21.194 1.406 3.609 11.40 13.01 1.61 3.764 21.195 5.858 3.609 11.46 13.11 1.65 3.711 21.182 23.432 3.605 11.43 13.16 1.73 3.741 21.162 46.864 3.603 11.41 13.19 1.78 3.760 21.143 70.296 3.600 11.34 13.14 1.80 3.779 21.141 93.728 3.595 11.31 13.12 1.81 3.788 21.141 117.160 3.592 11.29 13.10 1.82 3.799 21.138 140.593 3.591 11.29 13.14 1.85 3.820 21.126 164.025 3.590 11.27 13.11 1.84 3.827 21.124 187.457 3.589 11.28 13.12 1.84 3.843 21.118 210.889 3.588 11.26 13.10 1.84 3.846 21.120 234.321 3.587 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.406 Accepted refinement result: 11.39 13.01 1.61 3.775 21.194 1.406 3.609 Individual atomic B min max mean iso aniso Overall: 9.11 114.99 21.12 3.30 234 1742 Protein: 9.11 114.99 17.03 3.31 0 1519 Water: 11.49 76.69 34.92 N/A 234 215 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.11 114.99 19.32 N/A 0 1742 Chain S: 16.00 60.01 34.50 N/A 234 0 Histogram: Values Number of atoms 9.11 - 19.70 1264 19.70 - 30.29 304 30.29 - 40.88 209 40.88 - 51.46 127 51.46 - 62.05 50 62.05 - 72.64 11 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1139 r_free=0.1301 r_work=0.1139 r_free=0.1301 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1139 r_free = 0.1301 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1299 target_work(ml) = 3.607 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1136 r_free= 0.1299 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.607028 | | target function (ml) not normalized (work): 300407.679305 | | target function (ml) not normalized (free): 15815.493324 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1352 0.1349 5.6744 5.6027| | 2: 3.57 - 2.84 1.00 2888 124 0.1058 0.1397 5.1613 5.2196| | 3: 2.83 - 2.48 1.00 2820 163 0.1110 0.1260 4.9463 4.9873| | 4: 2.47 - 2.25 1.00 2825 136 0.0897 0.1029 4.6303 4.6616| | 5: 2.25 - 2.09 1.00 2756 127 0.0865 0.0992 4.5789 4.6392| | 6: 2.09 - 1.97 1.00 2846 113 0.0849 0.0992 4.2648 4.3677| | 7: 1.97 - 1.87 1.00 2787 165 0.0885 0.1115 3.9818 4.0933| | 8: 1.87 - 1.79 1.00 2789 144 0.0913 0.1100 3.8942 3.9931| | 9: 1.79 - 1.72 1.00 2745 138 0.0882 0.1170 3.6551 3.8221| | 10: 1.72 - 1.66 1.00 2831 160 0.0918 0.1223 3.568 3.7366| | 11: 1.66 - 1.61 1.00 2712 147 0.0870 0.1040 3.5029 3.5763| | 12: 1.61 - 1.56 1.00 2773 144 0.0913 0.1155 3.3353 3.4682| | 13: 1.56 - 1.52 1.00 2745 130 0.0950 0.1019 3.3093 3.3888| | 14: 1.52 - 1.48 1.00 2803 134 0.0985 0.1052 3.2431 3.3234| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1233 3.1565 3.2667| | 16: 1.45 - 1.42 1.00 2756 161 0.1056 0.1252 3.1371 3.2438| | 17: 1.42 - 1.39 1.00 2785 139 0.1140 0.1279 3.1194 3.2159| | 18: 1.39 - 1.36 1.00 2741 179 0.1197 0.1333 3.1049 3.2419| | 19: 1.36 - 1.34 1.00 2807 134 0.1261 0.1550 3.1125 3.2654| | 20: 1.34 - 1.32 1.00 2696 147 0.1371 0.1456 3.114 3.145| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1494 3.114 3.0985| | 22: 1.29 - 1.27 1.00 2704 152 0.1565 0.2005 3.1252 3.3056| | 23: 1.27 - 1.26 1.00 2802 156 0.1648 0.1786 3.1338 3.1999| | 24: 1.26 - 1.24 1.00 2744 132 0.1711 0.1829 3.1296 3.2229| | 25: 1.24 - 1.22 1.00 2733 148 0.1886 0.2129 3.1458 3.2616| | 26: 1.22 - 1.21 1.00 2727 135 0.1913 0.1772 3.1509 3.2043| | 27: 1.21 - 1.19 1.00 2814 148 0.2077 0.2170 3.1735 3.1653| | 28: 1.19 - 1.18 1.00 2671 147 0.2205 0.2289 3.1674 3.1723| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2384 3.1487 3.2313| | 30: 1.16 - 1.15 1.00 2739 148 0.2443 0.2449 3.1445 3.1694| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2922 171 0.95 8.56 1.00 0.97 5734.52| | 2: 3.57 - 2.84 2888 124 0.93 12.50 1.01 0.97 5734.52| | 3: 2.83 - 2.48 2820 163 0.89 16.46 0.99 0.98 4793.21| | 4: 2.47 - 2.25 2825 136 0.92 13.41 1.00 0.98 2365.88| | 5: 2.25 - 2.09 2756 127 0.90 15.58 1.01 0.98 2365.88| | 6: 2.09 - 1.97 2846 113 0.92 12.43 1.02 0.98 1370.70| | 7: 1.97 - 1.87 2787 165 0.95 9.38 1.02 0.98 521.93| | 8: 1.87 - 1.79 2789 144 0.92 12.76 1.00 0.98 521.93| | 9: 1.79 - 1.72 2745 138 0.94 10.18 0.98 0.98 294.69| | 10: 1.72 - 1.66 2831 160 0.94 11.25 0.98 0.98 249.18| | 11: 1.66 - 1.61 2712 147 0.93 11.83 0.98 0.98 238.60| | 12: 1.61 - 1.56 2773 144 0.95 8.94 0.99 0.98 138.82| | 13: 1.56 - 1.52 2745 130 0.95 10.48 1.03 0.98 138.82| | 14: 1.52 - 1.48 2803 134 0.94 10.78 1.03 0.98 124.28| | 15: 1.48 - 1.45 2738 128 0.95 9.86 1.02 0.99 97.65| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.99 97.65| | 17: 1.42 - 1.39 2785 139 0.95 10.87 1.01 0.99 88.83| | 18: 1.39 - 1.36 2741 179 0.94 11.50 1.01 0.99 83.72| | 19: 1.36 - 1.34 2807 134 0.94 11.84 1.00 0.99 83.72| | 20: 1.34 - 1.32 2696 147 0.94 12.07 0.98 0.97 79.77| | 21: 1.32 - 1.30 2785 112 0.94 13.04 0.98 0.97 79.49| | 22: 1.29 - 1.27 2704 152 0.93 13.60 0.98 0.96 79.94| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.95 82.22| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.95 82.22| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.26| | 26: 1.22 - 1.21 2727 135 0.90 18.12 1.03 0.94 86.52| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.03 0.94 86.52| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 90.23| | 29: 1.18 - 1.16 2800 134 0.88 20.50 0.99 0.93 91.63| | 30: 1.16 - 1.15 2739 148 0.86 22.01 0.98 0.93 91.63| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.49 max = 5734.52 mean = 887.82| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.45| |phase err.(test): min = 0.00 max = 89.70 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1144 0.1136 0.1299 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1474 0.1474 0.1504 n_refl.: 87580 remove outliers: r(all,work,free)=0.1474 0.1474 0.1504 n_refl.: 87580 overall B=-0.00 to atoms: r(all,work,free)=0.1474 0.1473 0.1503 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1144 0.1136 0.1300 n_refl.: 87580 remove outliers: r(all,work,free)=0.1142 0.1134 0.1300 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 88.54 80 5 0.3908 292.247 249.570 0.451 1.000 0.309 11.894-9.307 93.14 91 4 0.2325 473.418 455.423 0.858 1.002 0.234 9.237-7.194 98.64 210 7 0.2364 387.716 381.746 0.923 1.002 0.170 7.162-5.571 100.00 427 22 0.2154 296.606 285.376 0.910 1.002 0.140 5.546-4.326 100.00 867 58 0.1143 407.167 402.143 0.962 1.003 0.120 4.315-3.360 100.00 1859 96 0.0931 387.219 385.123 1.004 1.002 0.120 3.356-2.611 100.00 3867 181 0.1105 254.383 252.604 1.011 1.002 0.024 2.608-2.026 99.99 8198 413 0.0911 168.633 168.005 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0887 82.351 82.684 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.518 36.119 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 23.009 21.548 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0103 ================= 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: 0.1233 0.1467 0.006 0.847 9.0 119.5 20.1 258 0.140 1_adp: 0.1240 0.1464 0.006 0.847 9.1 119.4 20.1 258 0.140 1_regHadp: 0.1242 0.1467 0.006 0.847 9.1 119.4 20.1 258 0.140 1_occ: 0.1234 0.1458 0.006 0.847 9.1 119.4 20.1 258 0.140 2_bss: 0.1233 0.1450 0.006 0.847 9.1 119.5 20.1 258 0.140 2_settarget: 0.1233 0.1450 0.006 0.847 9.1 119.5 20.1 258 0.140 2_updatecdl: 0.1233 0.1450 0.006 0.860 9.1 119.5 20.1 258 0.140 2_nqh: 0.1233 0.1450 0.006 0.860 9.1 119.5 20.1 258 0.140 2_sol: 0.1207 0.1396 0.006 0.860 9.1 115.0 22.0 409 n/a 2_weight: 0.1207 0.1396 0.006 0.860 9.1 115.0 22.0 409 n/a 2_xyzrec: 0.1191 0.1411 0.007 0.877 9.1 115.0 22.0 409 n/a 2_adp: 0.1191 0.1411 0.007 0.877 9.1 115.0 22.0 409 n/a 2_regHadp: 0.1191 0.1411 0.007 0.877 9.1 115.0 22.0 409 n/a 2_occ: 0.1190 0.1408 0.007 0.877 9.1 115.0 22.0 409 n/a 3_bss: 0.1185 0.1401 0.007 0.877 9.1 115.0 22.0 409 n/a 3_settarget: 0.1185 0.1401 0.007 0.877 9.1 115.0 22.0 409 n/a 3_updatecdl: 0.1185 0.1401 0.007 0.880 9.1 115.0 22.0 409 n/a 3_nqh: 0.1185 0.1401 0.007 0.880 9.1 115.0 22.0 409 n/a 3_sol: 0.1207 0.1400 0.007 0.880 9.1 115.0 21.2 436 n/a 3_weight: 0.1207 0.1400 0.007 0.880 9.1 115.0 21.2 436 n/a 3_xyzrec: 0.1159 0.1326 0.007 1.066 9.1 115.0 21.2 436 n/a 3_adp: 0.1159 0.1326 0.007 1.066 9.1 115.0 21.2 436 n/a 3_regHadp: 0.1159 0.1326 0.007 1.066 9.1 115.0 21.2 436 n/a 3_occ: 0.1152 0.1319 0.007 1.066 9.1 115.0 21.2 436 n/a 4_bss: 0.1146 0.1312 0.007 1.066 9.1 115.0 21.1 436 n/a 4_settarget: 0.1146 0.1312 0.007 1.066 9.1 115.0 21.1 436 n/a 4_updatecdl: 0.1146 0.1312 0.007 1.066 9.1 115.0 21.1 436 n/a 4_nqh: 0.1146 0.1312 0.007 1.066 9.1 115.0 21.1 436 n/a 4_sol: 0.1142 0.1297 0.007 1.066 9.1 115.0 21.2 446 n/a 4_weight: 0.1142 0.1297 0.007 1.066 9.1 115.0 21.2 446 n/a 4_xyzrec: 0.1139 0.1295 0.008 1.121 9.1 115.0 21.2 446 n/a 4_adp: 0.1139 0.1295 0.008 1.121 9.1 115.0 21.2 446 n/a 4_regHadp: 0.1139 0.1295 0.008 1.121 9.1 115.0 21.2 446 n/a 4_occ: 0.1135 0.1291 0.008 1.121 9.1 115.0 21.2 446 n/a 5_bss: 0.1132 0.1290 0.008 1.121 9.1 115.0 21.2 446 n/a 5_settarget: 0.1132 0.1290 0.008 1.121 9.1 115.0 21.2 446 n/a 5_updatecdl: 0.1132 0.1290 0.008 1.121 9.1 115.0 21.2 446 n/a 5_setrh: 0.1133 0.1289 0.008 1.121 9.1 115.0 21.2 446 n/a 5_nqh: 0.1133 0.1289 0.008 1.121 9.1 115.0 21.2 446 n/a 5_sol: 0.1140 0.1301 0.008 1.121 9.1 115.0 21.1 449 n/a 5_weight: 0.1140 0.1301 0.008 1.121 9.1 115.0 21.1 449 n/a 5_xyzrec: 0.1139 0.1301 0.008 1.130 9.1 115.0 21.1 449 n/a 5_adp: 0.1139 0.1301 0.008 1.130 9.1 115.0 21.1 449 n/a 5_regHadp: 0.1139 0.1301 0.008 1.130 9.1 115.0 21.1 449 n/a 5_occ: 0.1136 0.1299 0.008 1.130 9.1 115.0 21.1 449 n/a end: 0.1134 0.1300 0.008 1.130 9.1 115.0 21.1 449 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4872201_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4872201_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2000 Refinement macro-cycles (run) : 13386.4000 Write final files (write_after_run_outputs) : 100.5100 Total : 13490.1100 Total CPU time: 3.76 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:06:45 PST -0800 (1735366005.30 s) Start R-work = 0.1631, R-free = 0.1765 Final R-work = 0.1134, R-free = 0.1300 =============================================================================== Job complete usr+sys time: 13682.93 seconds wall clock time: 251 minutes 7.34 seconds (15067.34 seconds total)