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_7718462.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 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: 1.41, per 1000 atoms: 0.42 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: 0.31 Conformation dependent library (CDL) restraints added in 109.7 milliseconds Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 489 0.91 - 1.18: 1179 1.18 - 1.45: 695 1.45 - 1.72: 774 1.72 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ASP A 42 " pdb=" C ASP A 42 " ideal model delta sigma weight residual 1.528 1.310 0.218 1.11e-02 8.12e+03 3.86e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.590 -0.212 1.10e-02 8.26e+03 3.72e+02 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.524 1.766 -0.242 1.26e-02 6.30e+03 3.69e+02 bond pdb=" C ALA A 114 " pdb=" O ALA A 114 " ideal model delta sigma weight residual 1.237 1.009 0.228 1.19e-02 7.06e+03 3.66e+02 bond pdb=" N BLEU A 153 " pdb=" CA BLEU A 153 " ideal model delta sigma weight residual 1.458 1.677 -0.219 1.19e-02 7.06e+03 3.37e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 3153 4.70 - 9.40: 1878 9.40 - 14.10: 621 14.10 - 18.80: 117 18.80 - 23.50: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.06 106.41 16.65 9.50e-01 1.11e+00 3.07e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 140.11 -16.84 1.18e+00 7.18e-01 2.04e+02 angle pdb=" CA BASN A 76 " pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 120.92 135.99 -15.07 1.12e+00 7.97e-01 1.81e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.75 127.20 -12.45 9.90e-01 1.02e+00 1.58e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 135.42 -13.30 1.06e+00 8.90e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 952 17.76 - 35.53: 114 35.53 - 53.29: 30 53.29 - 71.06: 13 71.06 - 88.82: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ASP A 49 " pdb=" C ASP A 49 " pdb=" N VAL A 50 " pdb=" CA VAL A 50 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual 180.00 -156.61 -23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " pdb=" HD2 HIS A 126 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 107 0.224 - 0.447: 82 0.447 - 0.671: 34 0.671 - 0.894: 17 0.894 - 1.117: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.47 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" CB VAL A 181 " pdb=" CA VAL A 181 " pdb=" CG1 VAL A 181 " pdb=" CG2 VAL A 181 " both_signs ideal model delta sigma weight residual False -2.63 -3.56 0.93 2.00e-01 2.50e+01 2.17e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.010 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG PHE A 119 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.123 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.083 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.030 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.090 2.00e-02 2.50e+03 6.71e-02 1.01e+02 pdb=" CG HIS A 138 " -0.066 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.084 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.083 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.024 2.00e-02 2.50e+03 6.36e-02 9.10e+01 pdb=" CG HIS A 126 " -0.111 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.103 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.001 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1226 2.35 - 2.91: 8308 2.91 - 3.47: 10369 3.47 - 4.04: 15199 4.04 - 4.60: 21558 Nonbonded interactions: 56660 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.784 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.816 1.850 x-y,-y,-z-4/3 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.827 1.850 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.832 2.100 ... (remaining 56655 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_7718462_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1944 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791261 | | target function (ml) not normalized (work): 232528.758867 | | target function (ml) not normalized (free): 11808.326958 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3035 0.2158 6.988 4.9563| | 2: 3.57 - 2.84 1.00 2876 122 0.2453 0.1779 4.3605 4.3436| | 3: 2.84 - 2.48 1.00 2833 165 0.2321 0.1689 4.138 4.1809| | 4: 2.47 - 2.25 1.00 2825 136 0.2337 0.1330 3.844 3.8279| | 5: 2.25 - 2.09 1.00 2756 127 0.2483 0.1605 3.8063 3.8349| | 6: 2.09 - 1.97 1.00 2846 113 0.2531 0.1782 3.4719 3.4987| | 7: 1.97 - 1.87 1.00 2787 165 0.2509 0.1762 3.1401 3.2056| | 8: 1.87 - 1.79 1.00 2789 144 0.2412 0.1878 3.0447 3.1174| | 9: 1.79 - 1.72 1.00 2745 138 0.2461 0.1968 2.9058 2.9837| | 10: 1.72 - 1.66 1.00 2789 158 0.2428 0.1891 2.7991 2.8369| | 11: 1.66 - 1.61 1.00 2740 147 0.2472 0.1620 2.7412 2.6834| | 12: 1.61 - 1.56 1.00 2787 146 0.2509 0.2053 2.6355 2.6229| | 13: 1.56 - 1.52 1.00 2745 130 0.2573 0.1823 2.5767 2.5933| | 14: 1.52 - 1.48 1.00 2803 134 0.2639 0.1772 2.5103 2.4709| | 15: 1.48 - 1.45 1.00 2738 128 0.2608 0.2208 2.4341 2.5274| | 16: 1.45 - 1.42 1.00 2756 161 0.2642 0.2059 2.3973 2.4163| | 17: 1.42 - 1.39 1.00 2785 139 0.2651 0.1918 2.3309 2.293| | 18: 1.39 - 1.36 1.00 2741 179 0.2701 0.2263 2.2792 2.3686| | 19: 1.36 - 1.34 1.00 2807 134 0.2677 0.2295 2.2449 2.2671| | 20: 1.34 - 1.32 1.00 2696 147 0.2658 0.2184 2.1849 2.2147| | 21: 1.32 - 1.30 1.00 2785 112 0.2717 0.2313 2.1495 2.2005| | 22: 1.29 - 1.27 1.00 2704 152 0.2753 0.2690 2.1314 2.2395| | 23: 1.27 - 1.26 1.00 2802 156 0.2773 0.2486 2.109 2.1772| | 24: 1.26 - 1.24 1.00 2744 132 0.2769 0.2241 2.0745 2.0929| | 25: 1.24 - 1.22 1.00 2734 148 0.2884 0.2586 2.0619 2.0798| | 26: 1.22 - 1.21 1.00 2727 135 0.2904 0.2409 2.0267 2.0756| | 27: 1.21 - 1.19 1.00 2814 148 0.2984 0.3013 2.0121 2.065| | 28: 1.19 - 1.18 1.00 2671 147 0.2990 0.3103 1.9887 2.0582| | 29: 1.18 - 1.16 1.00 2800 134 0.2934 0.2822 1.9649 2.053| | 30: 1.16 - 1.15 1.00 2740 148 0.3002 0.2990 1.9334 1.9998| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.06 0.76 0.23 1523.04| | 2: 3.57 - 2.84 2876 122 0.80 26.39 1.27 0.23 1523.04| | 3: 2.84 - 2.48 2833 165 0.74 32.30 1.24 0.23 1262.65| | 4: 2.47 - 2.25 2825 136 0.81 25.81 1.25 0.25 586.88| | 5: 2.25 - 2.09 2756 127 0.77 29.65 1.28 0.25 586.88| | 6: 2.09 - 1.97 2846 113 0.83 22.99 1.29 0.25 320.02| | 7: 1.97 - 1.87 2787 165 0.90 16.61 1.28 0.26 92.43| | 8: 1.87 - 1.79 2789 144 0.86 21.29 1.25 0.26 92.43| | 9: 1.79 - 1.72 2745 138 0.88 18.31 1.24 0.26 54.77| | 10: 1.72 - 1.66 2789 158 0.87 20.01 1.23 0.26 47.23| | 11: 1.66 - 1.61 2740 147 0.86 21.01 1.24 0.26 45.48| | 12: 1.61 - 1.56 2787 146 0.89 17.74 1.23 0.25 27.71| | 13: 1.56 - 1.52 2745 130 0.87 19.49 1.24 0.25 27.71| | 14: 1.52 - 1.48 2803 134 0.87 20.25 1.24 0.25 24.79| | 15: 1.48 - 1.45 2738 128 0.88 19.18 1.23 0.25 19.44| | 16: 1.45 - 1.42 2756 161 0.87 20.51 1.23 0.25 19.44| | 17: 1.42 - 1.39 2785 139 0.87 20.11 1.23 0.25 16.84| | 18: 1.39 - 1.36 2741 179 0.87 20.62 1.23 0.25 15.33| | 19: 1.36 - 1.34 2807 134 0.86 21.53 1.23 0.25 15.33| | 20: 1.34 - 1.32 2696 147 0.87 20.74 1.21 0.25 12.99| | 21: 1.32 - 1.30 2785 112 0.86 22.03 1.21 0.25 12.82| | 22: 1.29 - 1.27 2704 152 0.85 22.40 1.22 0.25 12.58| | 23: 1.27 - 1.26 2802 156 0.85 22.36 1.21 0.24 11.32| | 24: 1.26 - 1.24 2744 132 0.85 22.93 1.21 0.24 11.32| | 25: 1.24 - 1.22 2734 148 0.84 24.14 1.21 0.24 10.97| | 26: 1.22 - 1.21 2727 135 0.83 24.73 1.21 0.23 10.59| | 27: 1.21 - 1.19 2814 148 0.82 25.77 1.20 0.23 10.59| | 28: 1.19 - 1.18 2671 147 0.80 27.30 1.18 0.22 10.41| | 29: 1.18 - 1.16 2800 134 0.80 27.75 1.17 0.22 10.35| | 30: 1.16 - 1.15 2740 148 0.78 29.30 1.15 0.22 10.35| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 10.35 max = 1523.04 mean = 220.24| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.74| |phase err.(test): min = 0.00 max = 89.75 mean = 22.89| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.258 1557 Z= 5.613 Angle : 5.190 17.692 2118 Z= 3.674 Chirality : 0.371 1.117 243 Planarity : 0.029 0.127 284 Dihedral : 13.817 88.820 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 28.65 % 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: -1.78 (0.49), residues: 224 helix: -2.06 (0.41), residues: 102 sheet: -1.01 (0.66), residues: 40 loop : 0.38 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.012 ARG A 98 TYR 0.073 0.030 TYR A 141 PHE 0.097 0.045 PHE A 162 HIS 0.061 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2606 r_free= 0.1944 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791261 | | target function (ml) not normalized (work): 232528.758867 | | target function (ml) not normalized (free): 11808.326958 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1944 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1944 n_refl.: 87602 remove outliers: r(all,work,free)=0.1982 0.1986 0.1944 n_refl.: 87594 overall B=0.19 to atoms: r(all,work,free)=0.2004 0.2009 0.1956 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1644 0.1637 0.1783 n_refl.: 87594 remove outliers: r(all,work,free)=0.1644 0.1636 0.1783 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 0.3823 386.712 359.539 0.680 1.003 0.415 11.894-9.307 99.02 97 4 0.1797 614.272 595.813 0.933 1.003 0.404 9.237-7.194 100.00 213 7 0.2094 502.399 493.521 0.955 1.004 0.344 7.162-5.571 100.00 427 22 0.2170 377.023 366.114 0.935 1.004 0.330 5.546-4.326 100.00 867 58 0.1290 517.559 511.789 0.962 1.004 0.219 4.315-3.360 100.00 1859 96 0.1147 492.202 487.995 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1445 323.351 320.284 0.998 1.003 0.090 2.608-2.026 99.99 8198 413 0.1350 214.352 212.384 1.007 1.001 0.000 2.025-1.573 100.00 17313 902 0.1638 104.679 103.981 1.011 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2075 46.419 45.096 1.005 0.996 0.000 1.221-1.150 99.97 13689 708 0.2581 29.247 27.055 0.977 0.993 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0425 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1636 r_free=0.1783 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=0.1636 r_free=0.1783 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.334259 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2034.187299 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 0.1628 0.1761 0.0133 0.002 0.5 4.8 0.0 0.0 0 0.125 0.1528 0.1673 0.0145 0.002 0.5 4.2 0.0 0.0 0 0.250 0.1447 0.1612 0.0165 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1396 0.1577 0.0180 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1332 0.1524 0.0192 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1359 0.1550 0.0191 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1283 0.1499 0.0216 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1275 0.1498 0.0223 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1261 0.1495 0.0235 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1249 0.1489 0.0240 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1242 0.1481 0.0239 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1235 0.1472 0.0237 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1235 0.1477 0.0242 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1233 0.1474 0.0241 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1230 0.1471 0.0241 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1226 0.1464 0.0238 0.007 0.9 3.5 0.5 0.6 0 11.000 0.1226 0.1470 0.0244 0.007 0.9 3.2 0.5 0.6 0 12.000 0.1225 0.1470 0.0244 0.007 0.9 4.5 0.5 0.6 0 13.000 0.1222 0.1468 0.0245 0.008 1.0 3.8 0.5 0.6 0 14.167 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1226 0.1464 0.0238 0.007 0.9 3.5 0.5 0.6 0 11.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.26 14.64 2.38 3.013 19.044 2034.187 0.017 12.26 14.63 2.38 2.991 19.044 61.026 0.017 12.33 14.62 2.29 2.666 19.043 254.273 0.017 12.68 15.28 2.60 2.741 19.206 1017.094 0.016 12.55 15.49 2.94 3.352 19.633 2034.187 0.016 12.42 15.43 3.01 3.250 19.574 3051.281 0.015 12.31 15.38 3.07 3.347 19.619 4068.375 0.015 12.24 15.39 3.15 3.292 19.581 5085.468 0.015 12.19 15.36 3.17 3.347 19.603 6102.562 0.015 12.19 15.39 3.20 3.371 19.602 7119.656 0.015 12.30 15.69 3.38 3.641 19.729 8136.749 0.015 12.25 15.62 3.38 3.561 19.682 9153.843 0.015 12.16 15.51 3.35 3.489 19.637 10170.936 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: 254.273 Accepted refinement result: 12.33 14.62 2.29 2.666 19.043 254.273 0.017 Individual atomic B min max mean iso aniso Overall: 9.04 119.42 20.07 3.31 0 1785 Protein: 9.04 114.96 16.98 3.31 0 1519 Water: 11.48 119.42 38.21 N/A 0 258 Other: 19.71 26.59 22.04 N/A 0 8 Chain A: 9.04 119.42 20.07 N/A 0 1785 Histogram: Values Number of atoms 9.04 - 20.08 1272 20.08 - 31.12 227 31.12 - 42.16 125 42.16 - 53.19 94 53.19 - 64.23 42 64.23 - 75.27 11 75.27 - 86.31 7 86.31 - 97.35 4 97.35 - 108.39 1 108.39 - 119.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1233 r_free=0.1462 r_work=0.1234 r_free=0.1464 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1234 r_free = 0.1464 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 = 0.1228 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 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= 0.1228 r_free= 0.1462 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016808 | | target function (ls_wunit_k1) not normalized (work): 1400.069765 | | target function (ls_wunit_k1) not normalized (free): 110.190262 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1239 0.1228 0.1462 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1670 0.1671 0.1690 n_refl.: 87593 remove outliers: r(all,work,free)=0.1670 0.1671 0.1690 n_refl.: 87593 overall B=0.04 to atoms: r(all,work,free)=0.1677 0.1678 0.1695 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1236 0.1225 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1236 0.1225 0.1453 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 96.88 88 5 0.3542 304.494 281.151 0.666 1.002 0.392 11.894-9.307 99.02 97 4 0.1631 483.674 470.284 0.927 1.003 0.367 9.237-7.194 100.00 213 7 0.1846 395.586 391.653 0.965 1.003 0.324 7.162-5.571 100.00 427 22 0.1820 296.865 291.039 0.936 1.003 0.263 5.546-4.326 100.00 867 58 0.1004 407.522 404.425 0.964 1.003 0.204 4.315-3.360 100.00 1859 96 0.0875 387.557 386.597 1.008 1.002 0.180 3.356-2.611 100.00 3867 181 0.1171 254.605 253.483 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1022 168.780 168.059 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1107 82.423 82.631 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1449 36.550 36.053 1.018 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 23.029 21.505 0.980 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0586 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1453 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=0.1225 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1453 | n_water=258 | time (s): 1.760 (total time: 1.760) Filter (dist) r_work=0.1233 r_free=0.1450 | n_water=251 | time (s): 22.950 (total time: 24.710) Filter (q & B) r_work=0.1235 r_free=0.1450 | n_water=248 | time (s): 2.760 (total time: 27.470) Compute maps r_work=0.1235 r_free=0.1450 | n_water=248 | time (s): 1.260 (total time: 28.730) Filter (map) r_work=0.1257 r_free=0.1462 | n_water=223 | time (s): 3.180 (total time: 31.910) Find peaks r_work=0.1257 r_free=0.1462 | n_water=223 | time (s): 0.690 (total time: 32.600) Add new water r_work=0.1411 r_free=0.1631 | n_water=431 | time (s): 3.290 (total time: 35.890) Refine new water occ: r_work=0.1311 r_free=0.1501 adp: r_work=0.1227 r_free=0.1435 occ: r_work=0.1239 r_free=0.1424 adp: r_work=0.1204 r_free=0.1407 occ: r_work=0.1206 r_free=0.1396 adp: r_work=0.1197 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1394 r_work=0.1197 r_free=0.1394 | n_water=431 | time (s): 56.500 (total time: 92.390) Filter (q & B) r_work=0.1201 r_free=0.1397 | n_water=418 | time (s): 3.370 (total time: 95.760) Filter (dist only) r_work=0.1201 r_free=0.1396 | n_water=417 | time (s): 34.060 (total time: 129.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.347686 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1484.672362 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 0.1693 0.1788 0.0095 0.001 0.4 8.3 0.0 0.0 0 0.125 0.1533 0.1656 0.0123 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1419 0.1562 0.0143 0.001 0.4 6.7 0.0 0.0 0 0.500 0.1345 0.1508 0.0164 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1326 0.1499 0.0173 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1325 0.1495 0.0171 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1256 0.1456 0.0201 0.002 0.6 5.1 0.5 0.0 0 2.000 0.1233 0.1443 0.0210 0.003 0.6 4.8 0.5 0.0 0 3.000 0.1214 0.1420 0.0207 0.003 0.7 4.5 0.5 0.0 0 4.000 0.1203 0.1413 0.0210 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1200 0.1411 0.0211 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1200 0.1417 0.0218 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1197 0.1414 0.0217 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1195 0.1418 0.0224 0.006 0.8 4.8 0.5 0.0 0 9.000 0.1192 0.1412 0.0219 0.006 0.9 4.8 0.5 0.6 0 10.000 0.1192 0.1417 0.0225 0.007 0.9 4.5 0.5 0.6 0 11.000 0.1190 0.1411 0.0221 0.007 0.9 4.8 0.5 0.6 0 12.000 0.1190 0.1412 0.0222 0.008 0.9 4.2 0.5 0.6 0 13.000 0.1189 0.1414 0.0226 0.008 1.0 4.8 0.5 0.6 0 14.174 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1200 0.1411 0.0211 0.004 0.7 4.2 0.5 0.0 0 6.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.00 14.11 2.11 3.772 21.805 1484.672 0.016 12.00 14.11 2.11 3.772 21.805 44.540 0.016 12.00 14.11 2.11 3.772 21.805 185.584 0.016 12.23 14.56 2.33 3.589 21.831 742.336 0.015 12.18 14.84 2.66 3.437 22.128 1484.672 0.015 12.08 14.88 2.80 3.482 21.965 2227.009 0.014 11.91 14.65 2.74 3.469 22.177 2969.345 0.014 11.89 14.74 2.85 3.481 22.169 3711.681 0.014 11.88 14.73 2.85 3.511 22.214 4454.017 0.014 11.87 14.83 2.96 3.520 22.148 5196.353 0.014 11.79 14.73 2.94 3.534 22.202 5938.689 0.014 11.80 14.87 3.06 3.547 22.103 6681.026 0.014 11.81 14.89 3.08 3.564 22.138 7423.362 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: 44.540 Accepted refinement result: 12.00 14.11 2.11 3.772 21.805 44.540 0.016 Individual atomic B min max mean iso aniso Overall: 9.08 115.00 22.25 3.31 194 1750 Protein: 9.08 115.00 17.02 3.31 0 1519 Water: 11.52 76.67 41.30 N/A 194 223 Other: 19.75 26.63 22.08 N/A 0 8 Chain A: 9.08 115.00 19.39 N/A 0 1750 Chain S: 15.03 60.00 47.98 N/A 194 0 Histogram: Values Number of atoms 9.08 - 19.67 1257 19.67 - 30.26 243 30.26 - 40.86 168 40.86 - 51.45 121 51.45 - 62.04 132 62.04 - 72.63 12 72.63 - 83.22 5 83.22 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1200 r_free=0.1411 r_work=0.1200 r_free=0.1411 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 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 = 0.1198 r_free = 0.1408 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1198 r_free= 0.1408 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015180 | | target function (ls_wunit_k1) not normalized (work): 1264.459211 | | target function (ls_wunit_k1) not normalized (free): 96.782029 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1208 0.1198 0.1408 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1599 0.1599 0.1646 n_refl.: 87593 remove outliers: r(all,work,free)=0.1599 0.1599 0.1646 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1602 0.1601 0.1648 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1206 0.1196 0.1403 n_refl.: 87593 remove outliers: r(all,work,free)=0.1205 0.1195 0.1403 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3311 303.937 278.619 0.615 1.003 0.360 11.894-9.307 99.02 97 4 0.1633 483.674 476.862 0.924 1.003 0.340 9.237-7.194 100.00 213 7 0.1758 395.586 396.532 0.983 1.003 0.290 7.162-5.571 100.00 427 22 0.1655 296.865 292.176 0.937 1.003 0.250 5.546-4.326 100.00 867 58 0.0896 407.522 404.647 0.958 1.003 0.200 4.315-3.360 100.00 1859 96 0.0796 387.557 386.655 1.004 1.003 0.200 3.356-2.611 100.00 3867 181 0.1093 254.605 253.631 1.010 1.002 0.120 2.608-2.026 99.99 8198 413 0.1011 168.780 168.225 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1113 82.423 82.614 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1456 36.550 36.065 1.023 0.996 0.000 1.221-1.150 99.97 13689 708 0.2262 23.029 21.523 0.987 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0248 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1195 r_free=0.1403 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.1197 r_free=0.1406 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1197 r_free=0.1406 | n_water=417 | time (s): 1.870 (total time: 1.870) Filter (dist) r_work=0.1198 r_free=0.1406 | n_water=413 | time (s): 37.410 (total time: 39.280) Filter (q & B) r_work=0.1198 r_free=0.1406 | n_water=413 | time (s): 1.260 (total time: 40.540) Compute maps r_work=0.1198 r_free=0.1406 | n_water=413 | time (s): 1.320 (total time: 41.860) Filter (map) r_work=0.1236 r_free=0.1405 | n_water=289 | time (s): 2.430 (total time: 44.290) Find peaks r_work=0.1236 r_free=0.1405 | n_water=289 | time (s): 0.470 (total time: 44.760) Add new water r_work=0.1362 r_free=0.1539 | n_water=468 | time (s): 2.400 (total time: 47.160) Refine new water occ: r_work=0.1273 r_free=0.1457 adp: r_work=0.1274 r_free=0.1459 occ: r_work=0.1251 r_free=0.1428 adp: r_work=0.1250 r_free=0.1430 occ: r_work=0.1233 r_free=0.1400 adp: r_work=0.1227 r_free=0.1401 ADP+occupancy (water only), MIN, final r_work=0.1227 r_free=0.1401 r_work=0.1227 r_free=0.1401 | n_water=468 | time (s): 182.250 (total time: 229.410) Filter (q & B) r_work=0.1230 r_free=0.1406 | n_water=443 | time (s): 2.530 (total time: 231.940) Filter (dist only) r_work=0.1230 r_free=0.1404 | n_water=442 | time (s): 37.510 (total time: 269.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.773641 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 51.005585 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 0.1245 0.1359 0.0114 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1199 0.1323 0.0124 0.003 0.7 3.2 0.5 0.0 0 0.266 0.1183 0.1315 0.0132 0.004 0.8 2.9 0.5 0.0 0 0.532 0.1176 0.1313 0.0137 0.005 0.9 2.6 0.5 0.0 0 0.798 0.1171 0.1313 0.0142 0.006 1.0 2.9 0.5 0.0 0 1.064 0.1169 0.1316 0.0147 0.007 1.0 3.2 0.5 0.0 0 1.330 0.1166 0.1314 0.0148 0.007 1.1 3.5 0.5 0.0 0 1.596 0.1164 0.1313 0.0149 0.008 1.1 3.5 0.5 0.0 0 1.862 0.1172 0.1311 0.0139 0.005 0.9 3.2 0.5 0.0 0 0.887 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1172 0.1311 0.0139 0.005 0.9 3.2 0.5 0.0 0 0.887 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.72 13.11 1.39 3.776 21.261 51.006 3.631 11.72 13.11 1.39 3.776 21.261 1.530 3.631 11.73 13.11 1.39 3.766 21.261 6.376 3.630 11.78 13.23 1.44 3.712 21.242 25.503 3.625 11.75 13.27 1.52 3.741 21.218 51.006 3.623 11.71 13.30 1.58 3.754 21.205 76.508 3.618 11.64 13.23 1.59 3.772 21.204 102.011 3.613 11.62 13.23 1.61 3.783 21.197 127.514 3.610 11.62 13.27 1.65 3.802 21.179 153.017 3.610 11.58 13.22 1.64 3.810 21.179 178.520 3.607 11.57 13.22 1.65 3.817 21.180 204.022 3.606 11.57 13.22 1.65 3.825 21.177 229.525 3.606 11.56 13.23 1.66 3.834 21.175 255.028 3.605 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 6.376 Accepted refinement result: 11.73 13.11 1.39 3.766 21.261 6.376 3.630 Individual atomic B min max mean iso aniso Overall: 9.11 114.90 21.24 3.27 222 1747 Protein: 9.11 114.90 17.03 3.28 0 1519 Water: 11.53 76.69 35.67 N/A 222 220 Other: 19.72 26.60 22.09 N/A 0 8 Chain A: 9.11 114.90 19.35 N/A 0 1747 Chain S: 15.06 60.02 36.09 N/A 222 0 Histogram: Values Number of atoms 9.11 - 19.68 1259 19.68 - 30.26 290 30.26 - 40.84 218 40.84 - 51.42 130 51.42 - 62.00 49 62.00 - 72.58 11 72.58 - 83.16 6 83.16 - 93.74 4 93.74 - 104.32 0 104.32 - 114.90 2 =========================== Idealize ADP of riding H ========================== r_work=0.1173 r_free=0.1311 r_work=0.1173 r_free=0.1311 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1173 r_free = 0.1311 target_work(ml) = 3.630 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1165 r_free = 0.1301 target_work(ml) = 3.623 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1165 r_free= 0.1301 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.623042 | | target function (ml) not normalized (work): 301781.313589 | | target function (ml) not normalized (free): 15855.605443 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1172 0.1165 0.1301 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1504 0.1504 0.1535 n_refl.: 87591 remove outliers: r(all,work,free)=0.1504 0.1504 0.1535 n_refl.: 87591 overall B=-0.01 to atoms: r(all,work,free)=0.1503 0.1502 0.1534 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1165 0.1158 0.1297 n_refl.: 87591 remove outliers: r(all,work,free)=0.1162 0.1155 0.1297 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 91.67 83 5 0.3762 300.041 271.152 0.519 1.001 0.330 11.894-9.307 97.06 95 4 0.2318 483.898 465.191 0.876 1.002 0.283 9.237-7.194 98.64 210 7 0.2281 388.054 386.497 0.949 1.002 0.202 7.162-5.571 100.00 427 22 0.2147 296.865 286.110 0.920 1.002 0.173 5.546-4.326 100.00 867 58 0.1124 407.522 402.577 0.965 1.002 0.170 4.315-3.360 100.00 1859 96 0.0939 387.557 385.231 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1141 254.605 252.510 1.008 1.002 0.043 2.608-2.026 99.99 8198 413 0.0945 168.780 167.966 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0918 82.423 82.696 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1268 36.550 36.133 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2171 23.029 21.561 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0156 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1155 r_free=0.1297 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=0.1155 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1155 r_free=0.1297 | n_water=442 | time (s): 2.500 (total time: 2.500) Filter (dist) r_work=0.1158 r_free=0.1298 | n_water=439 | time (s): 45.240 (total time: 47.740) Filter (q & B) r_work=0.1158 r_free=0.1297 | n_water=437 | time (s): 4.310 (total time: 52.050) Compute maps r_work=0.1158 r_free=0.1297 | n_water=437 | time (s): 1.880 (total time: 53.930) Filter (map) r_work=0.1178 r_free=0.1300 | n_water=331 | time (s): 4.060 (total time: 57.990) Find peaks r_work=0.1178 r_free=0.1300 | n_water=331 | time (s): 0.750 (total time: 58.740) Add new water r_work=0.1249 r_free=0.1376 | n_water=483 | time (s): 3.970 (total time: 62.710) Refine new water occ: r_work=0.1178 r_free=0.1320 adp: r_work=0.1179 r_free=0.1321 occ: r_work=0.1164 r_free=0.1308 adp: r_work=0.1162 r_free=0.1308 occ: r_work=0.1153 r_free=0.1303 adp: r_work=0.1149 r_free=0.1300 ADP+occupancy (water only), MIN, final r_work=0.1149 r_free=0.1300 r_work=0.1149 r_free=0.1300 | n_water=483 | time (s): 179.960 (total time: 242.670) Filter (q & B) r_work=0.1155 r_free=0.1305 | n_water=450 | time (s): 3.910 (total time: 246.580) Filter (dist only) r_work=0.1162 r_free=0.1303 | n_water=448 | time (s): 46.950 (total time: 293.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.899110 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 44.689020 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 0.1215 0.1343 0.0128 0.002 0.6 4.5 0.5 0.0 0 0.095 0.1179 0.1317 0.0138 0.003 0.8 2.9 0.5 0.0 0 0.285 0.1165 0.1309 0.0145 0.005 0.9 3.2 0.5 0.0 0 0.570 0.1159 0.1304 0.0146 0.006 1.0 2.9 0.5 0.0 0 0.855 0.1155 0.1301 0.0146 0.007 1.0 2.9 0.5 0.0 0 1.139 0.1153 0.1302 0.0149 0.007 1.1 3.2 0.5 0.0 0 1.424 0.1151 0.1300 0.0149 0.008 1.1 3.2 0.5 0.0 0 1.709 0.1149 0.1301 0.0151 0.009 1.1 3.2 0.5 0.0 0 1.994 0.1157 0.1305 0.0148 0.006 1.0 2.9 0.5 0.0 0 0.950 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1151 0.1300 0.0149 0.008 1.1 3.2 0.5 0.0 0 1.709 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 13.00 1.49 3.763 21.254 44.689 3.614 11.51 13.00 1.49 3.763 21.254 1.341 3.614 11.51 13.00 1.49 3.763 21.254 5.586 3.614 11.53 13.05 1.52 3.702 21.245 22.345 3.608 11.58 13.22 1.64 3.732 21.216 44.689 3.612 11.52 13.21 1.69 3.751 21.203 67.034 3.606 11.46 13.16 1.70 3.763 21.202 89.378 3.601 11.43 13.14 1.71 3.773 21.198 111.723 3.598 11.41 13.14 1.73 3.783 21.196 134.067 3.597 11.43 13.22 1.79 3.808 21.178 156.412 3.597 11.42 13.22 1.81 3.818 21.178 178.756 3.597 11.41 13.22 1.82 3.824 21.176 201.101 3.595 11.38 13.17 1.80 3.825 21.178 223.445 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.341 Accepted refinement result: 11.51 13.00 1.49 3.763 21.254 1.341 3.614 Individual atomic B min max mean iso aniso Overall: 9.10 114.89 21.23 3.27 232 1743 Protein: 9.10 114.89 17.03 3.28 0 1519 Water: 11.53 76.68 35.46 N/A 232 216 Other: 19.72 26.59 22.08 N/A 0 8 Chain A: 9.10 114.89 19.31 N/A 0 1743 Chain S: 15.05 60.01 35.60 N/A 232 0 Histogram: Values Number of atoms 9.10 - 19.68 1262 19.68 - 30.26 288 30.26 - 40.84 223 40.84 - 51.42 133 51.42 - 61.99 46 61.99 - 72.57 11 72.57 - 83.15 6 83.15 - 93.73 4 93.73 - 104.31 0 104.31 - 114.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1300 r_work=0.1151 r_free=0.1300 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1300 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1297 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.22 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= 0.1146 r_free= 0.1297 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.611860 | | target function (ml) not normalized (work): 300821.005577 | | target function (ml) not normalized (free): 15838.743250 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1154 0.1146 0.1297 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1466 0.1464 0.1523 n_refl.: 87583 remove outliers: r(all,work,free)=0.1466 0.1464 0.1523 n_refl.: 87583 overall B=-0.01 to atoms: r(all,work,free)=0.1465 0.1463 0.1522 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1152 0.1145 0.1297 n_refl.: 87583 remove outliers: r(all,work,free)=0.1150 0.1142 0.1297 n_refl.: 87577 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 88.54 80 5 0.3891 286.402 264.274 0.476 0.999 0.299 11.894-9.307 94.12 92 4 0.2383 471.897 459.512 0.866 1.001 0.222 9.237-7.194 98.64 210 7 0.2399 388.054 381.092 0.923 1.002 0.170 7.162-5.571 100.00 427 22 0.2202 296.865 285.672 0.913 1.002 0.135 5.546-4.326 100.00 867 58 0.1136 407.522 402.752 0.964 1.002 0.130 4.315-3.360 100.00 1859 96 0.0928 387.557 385.290 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1126 254.605 252.703 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0932 168.780 168.009 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.423 82.698 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.550 36.137 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2165 23.029 21.564 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0162 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1142 r_free=0.1297 After: r_work=0.1143 r_free=0.1297 ================================== NQH flips ================================== r_work=0.1143 r_free=0.1297 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=0.1143 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1297 | n_water=448 | time (s): 2.340 (total time: 2.340) Filter (dist) r_work=0.1144 r_free=0.1298 | n_water=447 | time (s): 47.350 (total time: 49.690) Filter (q & B) r_work=0.1144 r_free=0.1298 | n_water=447 | time (s): 1.390 (total time: 51.080) Compute maps r_work=0.1144 r_free=0.1298 | n_water=447 | time (s): 1.900 (total time: 52.980) Filter (map) r_work=0.1167 r_free=0.1288 | n_water=359 | time (s): 3.950 (total time: 56.930) Find peaks r_work=0.1167 r_free=0.1288 | n_water=359 | time (s): 0.710 (total time: 57.640) Add new water r_work=0.1215 r_free=0.1348 | n_water=508 | time (s): 4.050 (total time: 61.690) Refine new water occ: r_work=0.1161 r_free=0.1303 adp: r_work=0.1161 r_free=0.1303 occ: r_work=0.1151 r_free=0.1292 adp: r_work=0.1149 r_free=0.1291 occ: r_work=0.1143 r_free=0.1283 adp: r_work=0.1139 r_free=0.1280 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1280 r_work=0.1139 r_free=0.1280 | n_water=508 | time (s): 233.810 (total time: 295.500) Filter (q & B) r_work=0.1144 r_free=0.1297 | n_water=472 | time (s): 4.050 (total time: 299.550) Filter (dist only) r_work=0.1145 r_free=0.1296 | n_water=471 | time (s): 50.050 (total time: 349.600) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.857275 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 37.407272 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 0.1210 0.1343 0.0133 0.003 0.7 4.8 0.0 0.0 0 0.093 0.1175 0.1317 0.0142 0.004 0.8 4.2 0.0 0.0 0 0.279 0.1160 0.1306 0.0146 0.005 0.9 3.8 0.5 0.0 0 0.557 0.1152 0.1300 0.0148 0.006 1.0 3.5 0.5 0.0 0 0.836 0.1148 0.1297 0.0149 0.007 1.1 3.5 0.5 0.0 0 1.114 0.1145 0.1296 0.0151 0.008 1.1 3.5 0.5 0.0 0 1.393 0.1145 0.1296 0.0151 0.008 1.1 3.5 0.5 0.0 0 1.672 0.1145 0.1296 0.0151 0.008 1.1 3.5 0.5 0.0 0 1.950 0.1150 0.1298 0.0148 0.006 1.1 3.5 0.5 0.0 0 0.929 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1145 0.1296 0.0151 0.008 1.1 3.5 0.5 0.0 0 1.393 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.45 12.96 1.51 3.762 21.342 37.407 3.611 11.45 12.96 1.51 3.762 21.342 1.122 3.611 11.45 12.96 1.51 3.762 21.342 4.676 3.611 11.48 13.01 1.53 3.697 21.334 18.704 3.606 11.47 13.09 1.61 3.716 21.323 37.407 3.605 11.51 13.23 1.72 3.735 21.298 56.111 3.607 11.43 13.18 1.74 3.755 21.294 74.815 3.601 11.39 13.14 1.75 3.764 21.294 93.518 3.598 11.38 13.15 1.77 3.776 21.289 112.222 3.597 11.37 13.17 1.80 3.788 21.284 130.925 3.595 11.35 13.16 1.81 3.798 21.282 149.629 3.594 11.36 13.20 1.85 3.813 21.274 168.333 3.594 11.35 13.20 1.85 3.818 21.275 187.036 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.676 Accepted refinement result: 11.45 12.96 1.51 3.762 21.342 4.676 3.611 Individual atomic B min max mean iso aniso Overall: 9.09 114.88 21.39 3.27 256 1742 Protein: 9.09 114.88 17.02 3.28 0 1519 Water: 11.52 76.68 35.48 N/A 256 215 Other: 19.71 26.59 22.08 N/A 0 8 Chain A: 9.09 114.88 19.29 N/A 0 1742 Chain S: 15.05 60.00 35.70 N/A 256 0 Histogram: Values Number of atoms 9.09 - 19.67 1263 19.67 - 30.25 297 30.25 - 40.83 231 40.83 - 51.41 133 51.41 - 61.99 51 61.99 - 72.57 11 72.57 - 83.15 6 83.15 - 93.73 4 93.73 - 104.31 0 104.31 - 114.88 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1296 r_work=0.1145 r_free=0.1296 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1296 target_work(ml) = 3.611 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1293 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87577 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1293 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.608622 | | target function (ml) not normalized (work): 300529.612910 | | target function (ml) not normalized (free): 15823.280247 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2919 171 0.1347 0.1331 5.6523 5.5944| | 2: 3.57 - 2.84 1.00 2888 124 0.1070 0.1433 5.1664 5.2412| | 3: 2.83 - 2.48 1.00 2820 163 0.1118 0.1217 4.9534 4.9801| | 4: 2.47 - 2.25 1.00 2825 136 0.0909 0.1013 4.6367 4.6711| | 5: 2.25 - 2.09 1.00 2756 127 0.0877 0.0977 4.5832 4.6456| | 6: 2.09 - 1.97 1.00 2846 113 0.0857 0.1027 4.2744 4.3871| | 7: 1.97 - 1.87 1.00 2787 165 0.0902 0.1105 3.9961 4.0949| | 8: 1.87 - 1.79 1.00 2789 144 0.0920 0.1088 3.9003 3.9929| | 9: 1.79 - 1.72 1.00 2745 138 0.0877 0.1192 3.6542 3.8241| | 10: 1.72 - 1.66 1.00 2831 160 0.0929 0.1203 3.5749 3.7252| | 11: 1.66 - 1.61 1.00 2712 147 0.0878 0.1024 3.5046 3.5769| | 12: 1.61 - 1.56 1.00 2773 144 0.0911 0.1145 3.3375 3.464| | 13: 1.56 - 1.52 1.00 2745 130 0.0948 0.1059 3.3128 3.4209| | 14: 1.52 - 1.48 1.00 2803 134 0.0977 0.1037 3.2439 3.3198| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1229 3.1564 3.2722| | 16: 1.45 - 1.42 1.00 2756 161 0.1055 0.1220 3.1381 3.2269| | 17: 1.42 - 1.39 1.00 2785 139 0.1144 0.1281 3.123 3.2293| | 18: 1.39 - 1.36 1.00 2741 179 0.1202 0.1315 3.1082 3.2391| | 19: 1.36 - 1.34 1.00 2807 134 0.1259 0.1541 3.1143 3.2592| | 20: 1.34 - 1.32 1.00 2696 147 0.1366 0.1461 3.113 3.1561| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1499 3.1151 3.1042| | 22: 1.29 - 1.27 1.00 2704 152 0.1562 0.1983 3.1248 3.3024| | 23: 1.27 - 1.26 1.00 2802 156 0.1646 0.1799 3.1346 3.2064| | 24: 1.26 - 1.24 1.00 2744 132 0.1702 0.1820 3.1273 3.2224| | 25: 1.24 - 1.22 1.00 2733 148 0.1879 0.2157 3.1445 3.2646| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1765 3.1491 3.2009| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2160 3.1729 3.1629| | 28: 1.19 - 1.18 1.00 2671 147 0.2198 0.2290 3.1672 3.175| | 29: 1.18 - 1.16 1.00 2800 134 0.2262 0.2388 3.1492 3.2305| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2462 3.1454 3.1722| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2919 171 0.95 8.59 1.00 0.97 5764.51| | 2: 3.57 - 2.84 2888 124 0.93 12.48 1.01 0.97 5764.51| | 3: 2.83 - 2.48 2820 163 0.90 16.43 0.99 0.97 4818.81| | 4: 2.47 - 2.25 2825 136 0.92 13.53 1.00 0.98 2380.15| | 5: 2.25 - 2.09 2756 127 0.90 15.62 1.01 0.98 2380.15| | 6: 2.09 - 1.97 2846 113 0.92 12.43 1.02 0.98 1379.60| | 7: 1.97 - 1.87 2787 165 0.95 9.45 1.02 0.98 526.26| | 8: 1.87 - 1.79 2789 144 0.92 12.79 1.00 0.98 526.26| | 9: 1.79 - 1.72 2745 138 0.94 10.22 0.98 0.98 295.98| | 10: 1.72 - 1.66 2831 160 0.94 11.26 0.98 0.98 249.86| | 11: 1.66 - 1.61 2712 147 0.93 11.87 0.98 0.97 239.26| | 12: 1.61 - 1.56 2773 144 0.95 8.98 0.99 0.97 139.31| | 13: 1.56 - 1.52 2745 130 0.95 10.47 1.03 0.97 139.31| | 14: 1.52 - 1.48 2803 134 0.94 10.81 1.02 0.98 124.80| | 15: 1.48 - 1.45 2738 128 0.95 9.94 1.02 0.98 98.24| | 16: 1.45 - 1.42 2756 161 0.94 11.14 1.02 0.98 98.24| | 17: 1.42 - 1.39 2785 139 0.95 10.92 1.01 0.98 89.27| | 18: 1.39 - 1.36 2741 179 0.94 11.53 1.01 0.98 84.08| | 19: 1.36 - 1.34 2807 134 0.94 11.84 1.00 0.98 84.08| | 20: 1.34 - 1.32 2696 147 0.94 12.08 0.98 0.97 79.98| | 21: 1.32 - 1.30 2785 112 0.94 13.07 0.98 0.97 79.69| | 22: 1.29 - 1.27 2704 152 0.93 13.60 0.98 0.96 80.13| | 23: 1.27 - 1.26 2802 156 0.92 14.82 0.97 0.95 82.33| | 24: 1.26 - 1.24 2744 132 0.92 14.84 0.96 0.95 82.33| | 25: 1.24 - 1.22 2733 148 0.91 16.33 0.96 0.94 84.40| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.02 0.93 86.69| | 27: 1.21 - 1.19 2814 148 0.89 18.78 1.02 0.93 86.69| | 28: 1.19 - 1.18 2671 147 0.88 20.42 1.01 0.93 90.54| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.93 91.98| | 30: 1.16 - 1.15 2739 148 0.86 22.06 0.98 0.93 91.98| |alpha: min = 0.93 max = 0.98 mean = 0.97| |beta: min = 79.69 max = 5764.51 mean = 892.44| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.48| |phase err.(test): min = 0.00 max = 89.81 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1147 0.1140 0.1293 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1453 0.1450 0.1513 n_refl.: 87577 remove outliers: r(all,work,free)=0.1453 0.1450 0.1513 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1452 0.1449 0.1512 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1148 0.1140 0.1292 n_refl.: 87577 remove outliers: r(all,work,free)=0.1145 0.1137 0.1292 n_refl.: 87570 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3964 283.828 251.985 0.429 0.999 0.279 11.894-9.307 90.20 88 4 0.2334 466.439 452.864 0.847 1.001 0.196 9.237-7.194 97.73 208 7 0.2302 388.678 381.843 0.921 1.001 0.138 7.162-5.571 100.00 427 22 0.2142 296.865 286.289 0.911 1.002 0.130 5.546-4.326 100.00 867 58 0.1141 407.522 402.593 0.963 1.002 0.120 4.315-3.360 100.00 1859 96 0.0930 387.557 385.143 1.005 1.001 0.120 3.356-2.611 100.00 3867 181 0.1120 254.605 252.918 1.012 1.001 0.019 2.608-2.026 99.99 8198 413 0.0920 168.780 168.103 1.026 1.000 0.000 2.025-1.573 100.00 17313 902 0.0897 82.423 82.741 1.036 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1251 36.550 36.151 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.029 21.573 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=-0.0155 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2606 0.1944 0.084 5.190 8.8 119.3 19.9 258 0.000 1_bss: 0.1636 0.1783 0.084 5.190 9.0 119.5 20.1 258 0.000 1_settarget: 0.1636 0.1783 0.084 5.190 9.0 119.5 20.1 258 0.000 1_nqh: 0.1636 0.1783 0.084 5.190 9.0 119.5 20.1 258 0.000 1_weight: 0.1636 0.1783 0.084 5.190 9.0 119.5 20.1 258 0.000 1_xyzrec: 0.1226 0.1464 0.007 0.902 9.0 119.5 20.1 258 0.127 1_adp: 0.1233 0.1462 0.007 0.902 9.0 119.4 20.1 258 0.127 1_regHadp: 0.1234 0.1464 0.007 0.902 9.0 119.4 20.1 258 0.127 1_occ: 0.1228 0.1462 0.007 0.902 9.0 119.4 20.1 258 0.127 2_bss: 0.1225 0.1453 0.007 0.902 9.1 119.5 20.1 258 0.127 2_settarget: 0.1225 0.1453 0.007 0.902 9.1 119.5 20.1 258 0.127 2_updatecdl: 0.1225 0.1453 0.007 0.910 9.1 119.5 20.1 258 0.127 2_nqh: 0.1225 0.1453 0.007 0.910 9.1 119.5 20.1 258 0.127 2_sol: 0.1201 0.1396 0.007 0.910 9.1 115.0 22.2 417 n/a 2_weight: 0.1201 0.1396 0.007 0.910 9.1 115.0 22.2 417 n/a 2_xyzrec: 0.1200 0.1411 0.004 0.733 9.1 115.0 22.2 417 n/a 2_adp: 0.1200 0.1411 0.004 0.733 9.1 115.0 22.2 417 n/a 2_regHadp: 0.1200 0.1411 0.004 0.733 9.1 115.0 22.2 417 n/a 2_occ: 0.1198 0.1408 0.004 0.733 9.1 115.0 22.2 417 n/a 3_bss: 0.1195 0.1403 0.004 0.733 9.1 115.0 22.3 417 n/a 3_settarget: 0.1195 0.1403 0.004 0.733 9.1 115.0 22.3 417 n/a 3_updatecdl: 0.1195 0.1403 0.004 0.734 9.1 115.0 22.3 417 n/a 3_nqh: 0.1197 0.1406 0.004 0.734 9.1 115.0 22.3 417 n/a 3_sol: 0.1230 0.1404 0.004 0.734 9.1 115.0 21.2 442 n/a 3_weight: 0.1230 0.1404 0.004 0.734 9.1 115.0 21.2 442 n/a 3_xyzrec: 0.1172 0.1311 0.005 0.928 9.1 115.0 21.2 442 n/a 3_adp: 0.1173 0.1311 0.005 0.928 9.1 114.9 21.2 442 n/a 3_regHadp: 0.1173 0.1311 0.005 0.928 9.1 114.9 21.2 442 n/a 3_occ: 0.1165 0.1301 0.005 0.928 9.1 114.9 21.2 442 n/a 4_bss: 0.1155 0.1297 0.005 0.928 9.1 114.9 21.2 442 n/a 4_settarget: 0.1155 0.1297 0.005 0.928 9.1 114.9 21.2 442 n/a 4_updatecdl: 0.1155 0.1297 0.005 0.930 9.1 114.9 21.2 442 n/a 4_nqh: 0.1155 0.1297 0.005 0.930 9.1 114.9 21.2 442 n/a 4_sol: 0.1162 0.1303 0.005 0.930 9.1 114.9 21.2 448 n/a 4_weight: 0.1162 0.1303 0.005 0.930 9.1 114.9 21.2 448 n/a 4_xyzrec: 0.1151 0.1300 0.008 1.111 9.1 114.9 21.2 448 n/a 4_adp: 0.1151 0.1300 0.008 1.111 9.1 114.9 21.2 448 n/a 4_regHadp: 0.1151 0.1300 0.008 1.111 9.1 114.9 21.2 448 n/a 4_occ: 0.1146 0.1297 0.008 1.111 9.1 114.9 21.2 448 n/a 5_bss: 0.1142 0.1297 0.008 1.111 9.1 114.9 21.2 448 n/a 5_settarget: 0.1142 0.1297 0.008 1.111 9.1 114.9 21.2 448 n/a 5_updatecdl: 0.1142 0.1297 0.008 1.113 9.1 114.9 21.2 448 n/a 5_setrh: 0.1143 0.1297 0.008 1.113 9.1 114.9 21.2 448 n/a 5_nqh: 0.1143 0.1297 0.008 1.113 9.1 114.9 21.2 448 n/a 5_sol: 0.1145 0.1296 0.008 1.113 9.1 114.9 21.4 471 n/a 5_weight: 0.1145 0.1296 0.008 1.113 9.1 114.9 21.4 471 n/a 5_xyzrec: 0.1145 0.1296 0.008 1.110 9.1 114.9 21.4 471 n/a 5_adp: 0.1145 0.1296 0.008 1.110 9.1 114.9 21.4 471 n/a 5_regHadp: 0.1145 0.1296 0.008 1.110 9.1 114.9 21.4 471 n/a 5_occ: 0.1140 0.1293 0.008 1.110 9.1 114.9 21.4 471 n/a end: 0.1137 0.1292 0.008 1.110 9.1 114.9 21.4 471 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7718462_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_7718462_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8900 Refinement macro-cycles (run) : 13805.1300 Write final files (write_after_run_outputs) : 85.4400 Total : 13894.4600 Total CPU time: 3.87 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:11:24 PST -0800 (1735366284.64 s) Start R-work = 0.1636, R-free = 0.1783 Final R-work = 0.1137, R-free = 0.1292 =============================================================================== Job complete usr+sys time: 14064.45 seconds wall clock time: 255 minutes 28.41 seconds (15328.41 seconds total)