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_8555406.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_8555406.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8555406.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: 2.13, per 1000 atoms: 0.63 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: 0.49 Conformation dependent library (CDL) restraints added in 131.7 milliseconds Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.90: 449 0.90 - 1.18: 1237 1.18 - 1.47: 788 1.47 - 1.75: 667 1.75 - 2.03: 12 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLY A 136 " pdb=" N GLY A 137 " ideal model delta sigma weight residual 1.329 1.512 -0.183 1.00e-02 1.00e+04 3.34e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.186 0.192 1.10e-02 8.26e+03 3.04e+02 bond pdb=" C LYS A 62 " pdb=" O LYS A 62 " ideal model delta sigma weight residual 1.236 1.458 -0.222 1.29e-02 6.01e+03 2.97e+02 bond pdb=" C GLU A 143 " pdb=" N ASN A 144 " ideal model delta sigma weight residual 1.329 1.562 -0.232 1.36e-02 5.41e+03 2.92e+02 bond pdb=" CZ ARG A 5 " pdb=" NH2 ARG A 5 " ideal model delta sigma weight residual 1.330 1.551 -0.221 1.30e-02 5.92e+03 2.88e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.39: 3122 4.39 - 8.78: 1743 8.78 - 13.17: 714 13.17 - 17.56: 173 17.56 - 21.95: 25 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 137.65 -14.98 1.09e+00 8.42e-01 1.89e+02 angle pdb=" CA ASN A 144 " pdb=" C ASN A 144 " pdb=" O ASN A 144 " ideal model delta sigma weight residual 121.47 136.75 -15.28 1.15e+00 7.56e-01 1.76e+02 angle pdb=" CA ASP A 42 " pdb=" C ASP A 42 " pdb=" O ASP A 42 " ideal model delta sigma weight residual 120.96 134.69 -13.73 1.09e+00 8.42e-01 1.59e+02 angle pdb=" CA VAL A 44 " pdb=" C VAL A 44 " pdb=" O VAL A 44 " ideal model delta sigma weight residual 120.39 133.57 -13.18 1.05e+00 9.07e-01 1.58e+02 angle pdb=" O ALYS A 132 " pdb=" C ALYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 122.12 109.26 12.86 1.06e+00 8.90e-01 1.47e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 913 15.93 - 31.86: 140 31.86 - 47.79: 35 47.79 - 63.71: 20 63.71 - 79.64: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA CYS A 106 " pdb=" C CYS A 106 " pdb=" N ALA A 107 " pdb=" CA ALA A 107 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" N SER A 57 " pdb=" CA SER A 57 " ideal model delta harmonic sigma weight residual 180.00 154.93 25.07 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CG BTYR A 67 " pdb=" CD1BTYR A 67 " pdb=" CE1BTYR A 67 " pdb=" HE1BTYR A 67 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.173: 85 0.173 - 0.345: 59 0.345 - 0.517: 53 0.517 - 0.688: 32 0.688 - 0.860: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BGLN A 80 " pdb=" N BGLN A 80 " pdb=" C BGLN A 80 " pdb=" CB BGLN A 80 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.79 0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" CA PHE A 164 " pdb=" N PHE A 164 " pdb=" C PHE A 164 " pdb=" CB PHE A 164 " both_signs ideal model delta sigma weight residual False 2.51 3.36 -0.84 2.00e-01 2.50e+01 1.78e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.074 2.00e-02 2.50e+03 7.08e-02 1.50e+02 pdb=" CG PHE A 164 " 0.171 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.090 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.036 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.043 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG BTYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.113 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.111 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.046 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.043 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.034 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.005 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.051 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.043 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.083 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.068 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " 0.089 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.067 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.070 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " 0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " 0.036 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 783 2.28 - 2.86: 7873 2.86 - 3.44: 10542 3.44 - 4.02: 15323 4.02 - 4.60: 22055 Nonbonded interactions: 56576 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.698 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.750 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.776 2.100 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.794 1.850 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.798 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_8555406_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= 0.2605 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791195 | | target function (ml) not normalized (work): 232523.290880 | | target function (ml) not normalized (free): 11856.192874 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3027 0.2132 6.9997 4.9525| | 2: 3.57 - 2.84 1.00 2876 122 0.2430 0.1892 4.3542 4.3533| | 3: 2.84 - 2.48 1.00 2833 165 0.2356 0.1796 4.1422 4.1745| | 4: 2.47 - 2.25 1.00 2825 136 0.2353 0.1496 3.8488 3.8493| | 5: 2.25 - 2.09 1.00 2756 127 0.2466 0.1644 3.8135 3.8493| | 6: 2.09 - 1.97 1.00 2846 113 0.2549 0.1945 3.4667 3.5887| | 7: 1.97 - 1.87 1.00 2787 165 0.2542 0.1866 3.1371 3.2476| | 8: 1.87 - 1.79 1.00 2789 144 0.2448 0.2003 3.0778 3.1247| | 9: 1.79 - 1.72 1.00 2745 138 0.2451 0.1909 2.9232 2.946| | 10: 1.72 - 1.66 1.00 2789 158 0.2395 0.1775 2.8199 2.8223| | 11: 1.66 - 1.61 1.00 2740 147 0.2455 0.1865 2.7552 2.7757| | 12: 1.61 - 1.56 1.00 2787 146 0.2516 0.2127 2.6416 2.6955| | 13: 1.56 - 1.52 1.00 2745 130 0.2578 0.1798 2.5727 2.5536| | 14: 1.52 - 1.48 1.00 2803 134 0.2624 0.2076 2.4995 2.5895| | 15: 1.48 - 1.45 1.00 2738 128 0.2631 0.2176 2.4184 2.5369| | 16: 1.45 - 1.42 1.00 2756 161 0.2624 0.1990 2.3769 2.3775| | 17: 1.42 - 1.39 1.00 2785 139 0.2631 0.1869 2.314 2.3006| | 18: 1.39 - 1.36 1.00 2741 179 0.2663 0.2207 2.2622 2.3405| | 19: 1.36 - 1.34 1.00 2807 134 0.2641 0.2528 2.2248 2.3406| | 20: 1.34 - 1.32 1.00 2696 147 0.2728 0.2197 2.2178 2.2372| | 21: 1.32 - 1.30 1.00 2785 112 0.2719 0.2245 2.1658 2.1439| | 22: 1.29 - 1.27 1.00 2704 152 0.2752 0.2782 2.1294 2.2742| | 23: 1.27 - 1.26 1.00 2802 156 0.2760 0.2750 2.0963 2.3019| | 24: 1.26 - 1.24 1.00 2744 132 0.2741 0.2584 2.0755 2.1645| | 25: 1.24 - 1.22 1.00 2734 148 0.2814 0.2400 2.0323 2.0412| | 26: 1.22 - 1.21 1.00 2727 135 0.2864 0.2114 2.0193 2.0407| | 27: 1.21 - 1.19 1.00 2814 148 0.2953 0.2313 2.0054 1.9489| | 28: 1.19 - 1.18 1.00 2671 147 0.2959 0.2685 1.984 2.0153| | 29: 1.18 - 1.16 1.00 2800 134 0.2979 0.2857 1.9714 2.0937| | 30: 1.16 - 1.15 1.00 2740 148 0.3004 0.2772 1.9376 1.9629| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.10 0.76 0.23 1524.45| | 2: 3.57 - 2.84 2876 122 0.80 26.41 1.27 0.23 1524.45| | 3: 2.84 - 2.48 2833 165 0.74 32.24 1.24 0.24 1265.33| | 4: 2.47 - 2.25 2825 136 0.81 25.96 1.26 0.25 592.87| | 5: 2.25 - 2.09 2756 127 0.77 29.69 1.28 0.25 592.87| | 6: 2.09 - 1.97 2846 113 0.83 23.40 1.29 0.25 326.08| | 7: 1.97 - 1.87 2787 165 0.89 17.37 1.28 0.26 98.55| | 8: 1.87 - 1.79 2789 144 0.85 21.92 1.24 0.26 98.55| | 9: 1.79 - 1.72 2745 138 0.88 18.94 1.23 0.26 57.67| | 10: 1.72 - 1.66 2789 158 0.86 20.35 1.22 0.26 49.49| | 11: 1.66 - 1.61 2740 147 0.86 21.35 1.24 0.25 47.67| | 12: 1.61 - 1.56 2787 146 0.88 18.38 1.23 0.25 29.29| | 13: 1.56 - 1.52 2745 130 0.87 20.43 1.24 0.25 29.29| | 14: 1.52 - 1.48 2803 134 0.86 20.71 1.25 0.25 26.18| | 15: 1.48 - 1.45 2738 128 0.87 19.99 1.24 0.25 20.47| | 16: 1.45 - 1.42 2756 161 0.86 21.40 1.23 0.25 20.47| | 17: 1.42 - 1.39 2785 139 0.87 20.71 1.23 0.25 17.55| | 18: 1.39 - 1.36 2741 179 0.86 21.30 1.22 0.25 15.86| | 19: 1.36 - 1.34 2807 134 0.85 22.02 1.23 0.25 15.86| | 20: 1.34 - 1.32 2696 147 0.87 21.03 1.21 0.25 13.34| | 21: 1.32 - 1.30 2785 112 0.86 22.13 1.20 0.25 13.16| | 22: 1.29 - 1.27 2704 152 0.85 22.45 1.22 0.25 12.89| | 23: 1.27 - 1.26 2802 156 0.85 22.50 1.21 0.24 11.49| | 24: 1.26 - 1.24 2744 132 0.85 22.86 1.20 0.24 11.49| | 25: 1.24 - 1.22 2734 148 0.84 24.23 1.20 0.24 10.90| | 26: 1.22 - 1.21 2727 135 0.84 24.31 1.19 0.23 10.25| | 27: 1.21 - 1.19 2814 148 0.83 25.29 1.20 0.23 10.25| | 28: 1.19 - 1.18 2671 147 0.81 26.52 1.18 0.22 9.89| | 29: 1.18 - 1.16 2800 134 0.81 26.85 1.15 0.22 9.76| | 30: 1.16 - 1.15 2740 148 0.80 28.16 1.14 0.22 9.76| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.76 max = 1524.45 mean = 221.94| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.99 mean = 22.94| |phase err.(test): min = 0.00 max = 89.96 mean = 22.75| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.232 1557 Z= 5.531 Angle : 5.263 16.495 2118 Z= 3.759 Chirality : 0.374 0.860 243 Planarity : 0.033 0.105 284 Dihedral : 13.785 79.642 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 34.05 % 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: -2.11 (0.48), residues: 224 helix: -2.32 (0.40), residues: 103 sheet: -0.82 (0.75), residues: 28 loop : -0.13 (0.58), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.014 ARG A 48 TYR 0.090 0.055 TYR A 141 PHE 0.147 0.050 PHE A 164 HIS 0.077 0.033 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= 0.2605 r_free= 0.1988 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.791195 | | target function (ml) not normalized (work): 232523.290880 | | target function (ml) not normalized (free): 11856.192874 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2606 0.1989 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2606 0.1989 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1982 0.1989 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.2005 0.2008 0.2005 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1642 0.1634 0.1806 n_refl.: 87594 remove outliers: r(all,work,free)=0.1641 0.1633 0.1806 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 98.94 88 5 0.3877 386.375 358.573 0.732 0.913 0.407 11.894-9.307 98.04 96 4 0.1698 616.229 588.682 1.017 0.914 0.374 9.237-7.194 100.00 213 7 0.2157 501.963 491.969 1.050 0.915 0.360 7.162-5.571 100.00 427 22 0.2182 376.695 365.110 1.019 0.915 0.320 5.546-4.326 100.00 867 58 0.1293 517.109 511.043 1.050 0.916 0.233 4.315-3.360 100.00 1859 96 0.1124 491.775 488.169 1.100 0.917 0.217 3.356-2.611 100.00 3867 181 0.1437 323.070 319.877 1.085 0.919 0.043 2.608-2.026 99.99 8198 413 0.1359 214.166 212.291 1.093 0.922 0.000 2.025-1.573 100.00 17313 902 0.1649 104.588 103.914 1.088 0.927 0.000 1.573-1.221 100.00 36679 1900 0.2048 46.378 45.128 1.072 0.935 0.000 1.221-1.150 99.97 13689 708 0.2591 29.222 26.999 1.027 0.941 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0476 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1633 r_free=0.1806 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=0.1633 r_free=0.1806 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.759759 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2000.946103 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 0.1722 0.1843 0.0121 0.002 0.4 4.8 0.0 0.0 0 0.125 0.1500 0.1649 0.0148 0.001 0.4 3.2 0.0 0.0 0 0.250 0.1444 0.1612 0.0168 0.002 0.5 3.5 0.0 0.0 0 0.500 0.1388 0.1577 0.0189 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1361 0.1566 0.0205 0.002 0.5 2.9 0.0 0.0 0 1.000 0.1354 0.1552 0.0199 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1295 0.1511 0.0216 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1266 0.1490 0.0224 0.003 0.6 2.9 0.5 0.0 0 3.000 0.1253 0.1485 0.0232 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1245 0.1477 0.0232 0.004 0.7 3.5 0.5 0.0 0 5.000 0.1239 0.1474 0.0235 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1236 0.1468 0.0232 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1234 0.1464 0.0230 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1227 0.1461 0.0235 0.006 0.9 3.5 0.5 0.0 0 9.000 0.1225 0.1456 0.0232 0.006 0.9 3.5 0.5 0.0 0 10.000 0.1223 0.1455 0.0232 0.007 0.9 3.2 0.5 0.0 0 11.000 0.1222 0.1453 0.0231 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1218 0.1456 0.0238 0.008 1.0 3.5 0.5 0.0 0 13.880 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1222 0.1453 0.0231 0.007 0.9 3.5 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 14.53 2.31 3.013 19.066 2000.946 0.017 12.22 14.53 2.31 3.013 19.066 60.028 0.017 12.29 14.50 2.21 2.669 19.065 250.118 0.017 12.64 15.16 2.52 2.733 19.227 1000.473 0.016 12.47 15.33 2.86 3.270 19.612 2000.946 0.016 12.42 15.37 2.94 3.318 19.637 3001.419 0.015 12.28 15.26 2.98 3.305 19.622 4001.892 0.015 12.23 15.27 3.04 3.297 19.606 5002.365 0.015 12.20 15.32 3.12 3.397 19.655 6002.838 0.015 12.21 15.39 3.17 3.273 19.573 7003.311 0.015 12.07 15.19 3.12 3.315 19.597 8003.784 0.015 12.08 15.22 3.14 3.308 19.578 9004.257 0.015 12.10 15.29 3.19 3.421 19.636 10004.731 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: 250.118 Accepted refinement result: 12.29 14.50 2.21 2.669 19.065 250.118 0.017 Individual atomic B min max mean iso aniso Overall: 9.09 119.45 20.09 3.31 0 1785 Protein: 9.09 115.01 17.00 3.32 0 1519 Water: 11.47 119.45 38.23 N/A 0 258 Other: 19.74 26.60 22.07 N/A 0 8 Chain A: 9.09 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.09 - 20.13 1272 20.13 - 31.16 227 31.16 - 42.20 125 42.20 - 53.23 94 53.23 - 64.27 42 64.27 - 75.31 11 75.31 - 86.34 7 86.34 - 97.38 4 97.38 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1229 r_free=0.1450 r_work=0.1231 r_free=0.1454 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1454 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 = 0.1226 r_free = 0.1450 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1226 r_free= 0.1450 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016775 | | target function (ls_wunit_k1) not normalized (work): 1397.286792 | | target function (ls_wunit_k1) not normalized (free): 108.747938 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1236 0.1226 0.1450 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1675 0.1677 0.1688 n_refl.: 87592 remove outliers: r(all,work,free)=0.1675 0.1677 0.1688 n_refl.: 87592 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1683 0.1692 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1235 0.1224 0.1442 n_refl.: 87592 remove outliers: r(all,work,free)=0.1234 0.1224 0.1442 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 95.83 87 5 0.3588 300.853 282.462 0.635 1.003 0.376 11.894-9.307 98.04 96 4 0.1641 483.906 470.201 0.928 1.003 0.361 9.237-7.194 100.00 213 7 0.1928 394.176 387.188 0.959 1.003 0.350 7.162-5.571 100.00 427 22 0.1816 295.807 289.906 0.938 1.003 0.269 5.546-4.326 100.00 867 58 0.1000 406.070 402.975 0.962 1.003 0.214 4.315-3.360 100.00 1859 96 0.0863 386.176 385.141 1.010 1.003 0.190 3.356-2.611 100.00 3867 181 0.1169 253.697 252.591 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1017 168.178 167.516 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.129 82.318 1.026 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.420 35.930 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.947 21.431 0.982 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0479 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1224 r_free=0.1442 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1225 r_free=0.1443 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1443 | n_water=258 | time (s): 1.550 (total time: 1.550) Filter (dist) r_work=0.1233 r_free=0.1442 | n_water=252 | time (s): 19.770 (total time: 21.320) Filter (q & B) r_work=0.1236 r_free=0.1441 | n_water=249 | time (s): 2.430 (total time: 23.750) Compute maps r_work=0.1236 r_free=0.1441 | n_water=249 | time (s): 1.600 (total time: 25.350) Filter (map) r_work=0.1250 r_free=0.1455 | n_water=228 | time (s): 2.890 (total time: 28.240) Find peaks r_work=0.1250 r_free=0.1455 | n_water=228 | time (s): 0.510 (total time: 28.750) Add new water r_work=0.1390 r_free=0.1630 | n_water=437 | time (s): 2.600 (total time: 31.350) Refine new water occ: r_work=0.1293 r_free=0.1485 adp: r_work=0.1220 r_free=0.1436 occ: r_work=0.1232 r_free=0.1418 adp: r_work=0.1201 r_free=0.1404 occ: r_work=0.1204 r_free=0.1396 adp: r_work=0.1193 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1394 r_work=0.1193 r_free=0.1394 | n_water=437 | time (s): 56.510 (total time: 87.860) Filter (q & B) r_work=0.1199 r_free=0.1401 | n_water=421 | time (s): 3.570 (total time: 91.430) Filter (dist only) r_work=0.1199 r_free=0.1400 | n_water=420 | time (s): 32.800 (total time: 124.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.550252 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1489.799275 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 0.1676 0.1789 0.0113 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1468 0.1613 0.0146 0.001 0.4 6.4 0.0 0.0 0 0.250 0.1392 0.1546 0.0154 0.001 0.4 6.4 0.0 0.0 0 0.500 0.1354 0.1518 0.0164 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1321 0.1493 0.0172 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1310 0.1485 0.0175 0.002 0.5 5.4 0.0 0.0 0 1.000 0.1257 0.1453 0.0197 0.002 0.5 5.4 0.5 0.0 0 2.000 0.1228 0.1435 0.0207 0.003 0.6 5.8 0.5 0.0 0 3.000 0.1220 0.1433 0.0213 0.003 0.6 4.8 0.5 0.0 0 4.000 0.1204 0.1415 0.0211 0.004 0.7 5.4 0.5 0.0 0 5.000 0.1203 0.1417 0.0215 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1198 0.1417 0.0219 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1194 0.1415 0.0220 0.005 0.8 5.1 0.5 0.0 0 8.000 0.1192 0.1419 0.0227 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1188 0.1410 0.0221 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1189 0.1410 0.0221 0.007 0.9 6.4 0.5 0.0 0 11.000 0.1189 0.1415 0.0226 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1187 0.1408 0.0221 0.007 0.9 5.1 0.5 0.0 0 13.000 0.1186 0.1410 0.0224 0.008 0.9 5.1 0.5 0.0 0 14.275 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1187 0.1408 0.0221 0.007 0.9 5.1 0.5 0.0 0 13.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.87 14.08 2.21 3.777 21.777 1489.799 0.016 11.87 14.08 2.21 3.777 21.777 44.694 0.016 11.87 14.08 2.21 3.777 21.777 186.225 0.016 12.01 14.45 2.44 3.645 21.775 744.900 0.015 12.05 14.79 2.75 3.475 22.036 1489.799 0.015 11.93 14.87 2.95 3.543 21.882 2234.699 0.014 11.79 14.74 2.95 3.518 21.927 2979.599 0.014 11.71 14.66 2.96 3.516 21.953 3724.498 0.014 11.68 14.66 2.97 3.525 22.042 4469.398 0.014 11.67 14.73 3.06 3.536 22.013 5214.297 0.014 11.71 14.89 3.19 3.577 22.108 5959.197 0.014 11.67 14.87 3.20 3.585 22.099 6704.097 0.014 11.61 14.79 3.18 3.597 22.149 7448.996 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: 44.694 Accepted refinement result: 11.87 14.08 2.21 3.777 21.777 44.694 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.04 22.18 3.31 192 1755 Protein: 9.12 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 40.80 N/A 192 228 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.12 115.04 19.50 N/A 0 1755 Chain S: 19.28 60.00 46.64 N/A 192 0 Histogram: Values Number of atoms 9.12 - 19.71 1259 19.71 - 30.31 248 30.31 - 40.90 164 40.90 - 51.49 135 51.49 - 62.08 118 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1187 r_free=0.1408 r_work=0.1187 r_free=0.1408 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1187 r_free = 0.1408 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1187 r_free = 0.1405 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1187 r_free= 0.1405 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014958 | | target function (ls_wunit_k1) not normalized (work): 1245.937027 | | target function (ls_wunit_k1) not normalized (free): 102.764006 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1197 0.1187 0.1405 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1588 0.1588 0.1614 n_refl.: 87591 remove outliers: r(all,work,free)=0.1588 0.1588 0.1614 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1589 0.1590 0.1615 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1194 0.1184 0.1396 n_refl.: 87591 remove outliers: r(all,work,free)=0.1193 0.1182 0.1396 n_refl.: 87588 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3391 296.765 277.353 0.600 1.003 0.370 11.894-9.307 98.04 96 4 0.1691 483.906 475.043 0.922 1.003 0.311 9.237-7.194 100.00 213 7 0.1657 394.176 392.214 0.981 1.003 0.280 7.162-5.571 100.00 427 22 0.1595 295.807 291.382 0.942 1.003 0.224 5.546-4.326 100.00 867 58 0.0880 406.070 403.267 0.960 1.003 0.205 4.315-3.360 100.00 1859 96 0.0773 386.176 385.450 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1070 253.697 253.133 1.009 1.002 0.120 2.608-2.026 99.99 8198 413 0.1017 168.178 167.617 1.021 1.001 0.000 2.025-1.573 100.00 17313 902 0.1102 82.129 82.318 1.030 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.420 35.952 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2251 22.947 21.452 0.988 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0139 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1182 r_free=0.1396 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1182 r_free=0.1396 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1182 r_free=0.1396 | n_water=420 | time (s): 1.730 (total time: 1.730) Filter (dist) r_work=0.1183 r_free=0.1400 | n_water=416 | time (s): 34.550 (total time: 36.280) Filter (q & B) r_work=0.1183 r_free=0.1400 | n_water=416 | time (s): 0.820 (total time: 37.100) Compute maps r_work=0.1183 r_free=0.1400 | n_water=416 | time (s): 1.120 (total time: 38.220) Filter (map) r_work=0.1228 r_free=0.1413 | n_water=280 | time (s): 2.610 (total time: 40.830) Find peaks r_work=0.1228 r_free=0.1413 | n_water=280 | time (s): 0.450 (total time: 41.280) Add new water r_work=0.1341 r_free=0.1531 | n_water=466 | time (s): 2.470 (total time: 43.750) Refine new water occ: r_work=0.1242 r_free=0.1431 adp: r_work=0.1244 r_free=0.1433 occ: r_work=0.1219 r_free=0.1411 adp: r_work=0.1218 r_free=0.1411 occ: r_work=0.1200 r_free=0.1395 adp: r_work=0.1196 r_free=0.1393 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1393 r_work=0.1196 r_free=0.1393 | n_water=466 | time (s): 141.010 (total time: 184.760) Filter (q & B) r_work=0.1202 r_free=0.1399 | n_water=435 | time (s): 3.220 (total time: 187.980) Filter (dist only) r_work=0.1201 r_free=0.1399 | n_water=434 | time (s): 36.250 (total time: 224.230) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.789683 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 41.200197 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 0.1233 0.1372 0.0139 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1191 0.1341 0.0149 0.003 0.7 4.2 0.5 0.0 0 0.268 0.1174 0.1327 0.0153 0.004 0.8 3.5 0.5 0.0 0 0.537 0.1169 0.1324 0.0156 0.005 0.9 3.5 0.5 0.0 0 0.805 0.1164 0.1321 0.0157 0.006 1.0 3.5 0.5 0.0 0 1.074 0.1161 0.1322 0.0161 0.007 1.0 4.2 0.5 0.0 0 1.342 0.1160 0.1321 0.0161 0.007 1.1 3.8 0.5 0.0 0 1.611 0.1158 0.1320 0.0162 0.008 1.1 4.2 0.5 0.0 0 1.879 0.1167 0.1324 0.0157 0.005 0.9 3.5 0.5 0.0 0 0.895 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1158 0.1320 0.0162 0.008 1.1 4.2 0.5 0.0 0 1.879 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 13.20 1.62 3.780 21.221 41.200 3.619 11.58 13.20 1.62 3.780 21.221 1.236 3.619 11.58 13.20 1.62 3.779 21.221 5.150 3.619 11.60 13.25 1.66 3.711 21.211 20.600 3.612 11.66 13.40 1.73 3.730 21.177 41.200 3.615 11.57 13.35 1.78 3.755 21.164 61.800 3.608 11.53 13.35 1.81 3.771 21.157 82.400 3.604 11.48 13.30 1.82 3.781 21.155 103.000 3.600 11.49 13.34 1.85 3.795 21.141 123.601 3.599 11.45 13.31 1.86 3.807 21.140 144.201 3.597 11.44 13.29 1.85 3.817 21.131 164.801 3.595 11.44 13.29 1.85 3.828 21.122 185.401 3.595 11.43 13.27 1.83 3.833 21.120 206.001 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: 5.150 Accepted refinement result: 11.58 13.20 1.62 3.779 21.221 5.150 3.619 Individual atomic B min max mean iso aniso Overall: 9.13 115.05 21.16 3.31 212 1749 Protein: 9.13 115.05 17.04 3.32 0 1519 Water: 11.51 76.70 35.54 N/A 212 222 Other: 19.78 26.64 22.11 N/A 0 8 Chain A: 9.13 115.05 19.41 N/A 0 1749 Chain S: 16.51 60.01 35.56 N/A 212 0 Histogram: Values Number of atoms 9.13 - 19.72 1264 19.72 - 30.31 296 30.31 - 40.91 194 40.91 - 51.50 132 51.50 - 62.09 52 62.09 - 72.68 12 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.45 0 104.45 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1158 r_free=0.1320 r_work=0.1158 r_free=0.1320 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1320 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1147 r_free = 0.1317 target_work(ml) = 3.610 | | 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.=87588 (all), 4.90 % free)------------| | | | r_work= 0.1147 r_free= 0.1317 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610316 | | target function (ml) not normalized (work): 300710.411144 | | target function (ml) not normalized (free): 15836.565075 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1155 0.1147 0.1317 n_refl.: 87588 re-set all scales: r(all,work,free)=0.1495 0.1495 0.1523 n_refl.: 87588 remove outliers: r(all,work,free)=0.1495 0.1495 0.1523 n_refl.: 87588 overall B=-0.00 to atoms: r(all,work,free)=0.1495 0.1495 0.1523 n_refl.: 87588 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1143 0.1305 n_refl.: 87588 remove outliers: r(all,work,free)=0.1147 0.1138 0.1305 n_refl.: 87578 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3834 288.851 264.170 0.486 1.000 0.309 11.894-9.307 96.08 94 4 0.2242 477.224 463.160 0.880 1.001 0.293 9.237-7.194 97.73 208 7 0.2291 386.748 385.615 0.949 1.001 0.190 7.162-5.571 100.00 427 22 0.2153 295.807 285.574 0.924 1.001 0.180 5.546-4.326 100.00 867 58 0.1088 406.070 401.254 0.964 1.001 0.165 4.315-3.360 100.00 1859 96 0.0920 386.176 383.431 1.004 1.001 0.160 3.356-2.611 100.00 3867 181 0.1145 253.697 251.528 1.008 1.001 0.038 2.608-2.026 99.99 8198 413 0.0926 168.178 167.402 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.129 82.427 1.032 1.001 0.000 1.573-1.221 100.00 36679 1900 0.1252 36.420 36.004 1.023 1.002 0.000 1.221-1.150 99.97 13689 708 0.2166 22.947 21.414 0.980 1.002 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0050 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1305 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=0.1138 r_free=0.1305 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1305 | n_water=434 | time (s): 2.590 (total time: 2.590) Filter (dist) r_work=0.1138 r_free=0.1305 | n_water=432 | time (s): 44.560 (total time: 47.150) Filter (q & B) r_work=0.1140 r_free=0.1302 | n_water=429 | time (s): 3.790 (total time: 50.940) Compute maps r_work=0.1140 r_free=0.1302 | n_water=429 | time (s): 1.830 (total time: 52.770) Filter (map) r_work=0.1159 r_free=0.1296 | n_water=327 | time (s): 3.950 (total time: 56.720) Find peaks r_work=0.1159 r_free=0.1296 | n_water=327 | time (s): 0.720 (total time: 57.440) Add new water r_work=0.1229 r_free=0.1379 | n_water=488 | time (s): 3.870 (total time: 61.310) Refine new water occ: r_work=0.1161 r_free=0.1319 adp: r_work=0.1162 r_free=0.1320 occ: r_work=0.1147 r_free=0.1303 adp: r_work=0.1146 r_free=0.1305 occ: r_work=0.1134 r_free=0.1290 adp: r_work=0.1131 r_free=0.1290 ADP+occupancy (water only), MIN, final r_work=0.1131 r_free=0.1290 r_work=0.1131 r_free=0.1290 | n_water=488 | time (s): 248.970 (total time: 310.280) Filter (q & B) r_work=0.1137 r_free=0.1296 | n_water=453 | time (s): 4.080 (total time: 314.360) Filter (dist only) r_work=0.1137 r_free=0.1295 | n_water=452 | time (s): 46.730 (total time: 361.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.787573 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.379090 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 0.1203 0.1337 0.0134 0.002 0.6 4.5 0.5 0.0 0 0.089 0.1164 0.1312 0.0148 0.003 0.7 3.5 0.5 0.0 0 0.268 0.1149 0.1306 0.0157 0.005 0.9 3.8 0.5 0.0 0 0.536 0.1143 0.1303 0.0160 0.006 0.9 3.8 0.5 0.0 0 0.804 0.1139 0.1306 0.0167 0.006 1.0 4.2 0.5 0.0 0 1.073 0.1136 0.1302 0.0166 0.007 1.0 4.2 0.5 0.0 0 1.341 0.1134 0.1300 0.0166 0.008 1.1 4.2 0.5 0.0 0 1.609 0.1133 0.1296 0.0163 0.009 1.1 4.8 0.5 0.0 0 1.877 0.1141 0.1300 0.0159 0.006 1.0 4.2 0.5 0.0 0 0.894 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1296 0.0163 0.009 1.1 4.8 0.5 0.0 0 1.877 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 12.96 1.63 3.780 21.240 36.379 3.604 11.33 12.96 1.63 3.780 21.240 1.091 3.604 11.33 12.96 1.63 3.780 21.240 4.547 3.604 11.38 13.00 1.63 3.710 21.232 18.190 3.600 11.37 13.07 1.69 3.729 21.218 36.379 3.598 11.40 13.16 1.76 3.744 21.190 54.569 3.598 11.33 13.12 1.78 3.767 21.187 72.758 3.594 11.32 13.12 1.80 3.777 21.181 90.948 3.592 11.30 13.12 1.82 3.787 21.175 109.137 3.590 11.27 13.09 1.83 3.794 21.176 127.327 3.587 11.25 13.10 1.84 3.804 21.173 145.516 3.586 11.27 13.11 1.84 3.817 21.157 163.706 3.586 11.25 13.09 1.85 3.825 21.157 181.895 3.585 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.547 Accepted refinement result: 11.33 12.96 1.63 3.780 21.240 4.547 3.604 Individual atomic B min max mean iso aniso Overall: 9.13 115.04 21.19 3.31 230 1749 Protein: 9.13 115.04 17.04 3.32 0 1519 Water: 11.50 76.70 35.13 N/A 230 222 Other: 19.78 26.64 22.11 N/A 0 8 Chain A: 9.13 115.04 19.41 N/A 0 1749 Chain S: 16.47 60.01 34.76 N/A 230 0 Histogram: Values Number of atoms 9.13 - 19.72 1264 19.72 - 30.31 304 30.31 - 40.90 210 40.90 - 51.49 128 51.49 - 62.09 50 62.09 - 72.68 12 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1133 r_free=0.1296 r_work=0.1133 r_free=0.1296 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1133 r_free = 0.1296 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1127 r_free = 0.1290 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87578 (all), 4.91 % free)------------| | | | r_work= 0.1127 r_free= 0.1290 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601177 | | target function (ml) not normalized (work): 299913.210245 | | target function (ml) not normalized (free): 15806.884395 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1127 0.1290 n_refl.: 87578 re-set all scales: r(all,work,free)=0.1453 0.1452 0.1501 n_refl.: 87578 remove outliers: r(all,work,free)=0.1453 0.1452 0.1501 n_refl.: 87578 overall B=-0.01 to atoms: r(all,work,free)=0.1452 0.1451 0.1500 n_refl.: 87578 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1125 0.1286 n_refl.: 87578 remove outliers: r(all,work,free)=0.1133 0.1125 0.1286 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 89.58 81 5 0.4158 288.851 253.478 0.448 1.002 0.293 11.894-9.307 95.10 93 4 0.2384 477.275 461.808 0.860 1.002 0.273 9.237-7.194 97.73 208 7 0.2343 386.748 380.655 0.930 1.003 0.160 7.162-5.571 100.00 427 22 0.2145 295.807 286.455 0.918 1.003 0.160 5.546-4.326 100.00 867 58 0.1090 406.070 401.303 0.964 1.002 0.130 4.315-3.360 100.00 1859 96 0.0900 386.176 383.947 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1108 253.697 251.752 1.009 1.002 0.019 2.608-2.026 99.99 8198 413 0.0903 168.178 167.583 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0881 82.129 82.471 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.420 36.032 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.947 21.502 0.990 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0190 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1125 r_free=0.1286 After: r_work=0.1126 r_free=0.1287 ================================== NQH flips ================================== r_work=0.1126 r_free=0.1287 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=0.1126 r_free=0.1287 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1126 r_free=0.1287 | n_water=452 | time (s): 2.410 (total time: 2.410) Filter (dist) r_work=0.1126 r_free=0.1288 | n_water=451 | time (s): 50.000 (total time: 52.410) Filter (q & B) r_work=0.1126 r_free=0.1288 | n_water=451 | time (s): 1.330 (total time: 53.740) Compute maps r_work=0.1126 r_free=0.1288 | n_water=451 | time (s): 1.830 (total time: 55.570) Filter (map) r_work=0.1154 r_free=0.1294 | n_water=349 | time (s): 3.800 (total time: 59.370) Find peaks r_work=0.1154 r_free=0.1294 | n_water=349 | time (s): 0.650 (total time: 60.020) Add new water r_work=0.1206 r_free=0.1351 | n_water=497 | time (s): 3.480 (total time: 63.500) Refine new water occ: r_work=0.1148 r_free=0.1297 adp: r_work=0.1148 r_free=0.1299 occ: r_work=0.1136 r_free=0.1285 adp: r_work=0.1135 r_free=0.1286 occ: r_work=0.1126 r_free=0.1272 adp: r_work=0.1123 r_free=0.1272 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1272 r_work=0.1123 r_free=0.1272 | n_water=497 | time (s): 257.700 (total time: 321.200) Filter (q & B) r_work=0.1130 r_free=0.1281 | n_water=459 | time (s): 4.070 (total time: 325.270) Filter (dist only) r_work=0.1131 r_free=0.1280 | n_water=458 | time (s): 48.590 (total time: 373.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.774597 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.460443 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 0.1213 0.1334 0.0121 0.004 0.7 6.4 0.0 0.0 0 0.089 0.1163 0.1302 0.0138 0.004 0.8 6.4 0.0 0.0 0 0.266 0.1147 0.1290 0.0144 0.005 0.9 6.1 0.5 0.0 0 0.532 0.1139 0.1284 0.0145 0.006 1.0 5.8 0.5 0.0 0 0.799 0.1135 0.1282 0.0146 0.007 1.1 5.8 0.5 0.0 0 1.065 0.1132 0.1280 0.0148 0.008 1.1 6.1 0.5 0.0 0 1.331 0.1131 0.1280 0.0149 0.008 1.1 6.1 0.5 0.0 0 1.597 0.1131 0.1280 0.0150 0.009 1.1 6.1 0.5 0.0 0 1.863 0.1138 0.1284 0.0146 0.006 1.0 5.8 0.5 0.0 0 0.887 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1131 0.1280 0.0149 0.008 1.1 6.1 0.5 0.0 0 1.597 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.31 12.80 1.49 3.780 21.237 46.460 3.600 11.31 12.80 1.49 3.780 21.237 1.394 3.600 11.31 12.80 1.49 3.769 21.237 5.808 3.600 11.33 12.84 1.51 3.717 21.228 23.230 3.594 11.40 12.99 1.59 3.734 21.193 46.460 3.596 11.31 12.95 1.64 3.763 21.184 69.691 3.591 11.28 12.94 1.66 3.778 21.180 92.921 3.588 11.23 12.90 1.67 3.786 21.180 116.151 3.584 11.21 12.90 1.68 3.798 21.175 139.381 3.582 11.23 12.95 1.72 3.819 21.159 162.612 3.583 11.21 12.93 1.73 3.827 21.161 185.842 3.582 11.18 12.89 1.71 3.830 21.161 209.072 3.579 11.17 12.88 1.72 3.834 21.162 232.302 3.579 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.394 Accepted refinement result: 11.31 12.80 1.49 3.780 21.237 1.394 3.600 Individual atomic B min max mean iso aniso Overall: 9.12 115.04 21.19 3.31 237 1748 Protein: 9.12 115.04 17.03 3.32 0 1519 Water: 11.50 76.70 34.97 N/A 237 221 Other: 19.77 26.63 22.10 N/A 0 8 Chain A: 9.12 115.04 19.38 N/A 0 1748 Chain S: 16.24 60.00 34.52 N/A 237 0 Histogram: Values Number of atoms 9.12 - 19.71 1263 19.71 - 30.31 308 30.31 - 40.90 214 40.90 - 51.49 128 51.49 - 62.08 49 62.08 - 72.67 12 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1131 r_free=0.1280 r_work=0.1131 r_free=0.1280 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1131 r_free = 0.1280 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1277 target_work(ml) = 3.599 | | 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= 0.1128 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.598686 | | target function (ml) not normalized (work): 299702.192389 | | target function (ml) not normalized (free): 15781.518131 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1338 0.1306 5.6599 5.5806| | 2: 3.57 - 2.84 1.00 2888 124 0.1060 0.1333 5.1461 5.1977| | 3: 2.83 - 2.48 1.00 2820 163 0.1084 0.1242 4.9259 4.9628| | 4: 2.47 - 2.25 1.00 2825 136 0.0890 0.1010 4.6113 4.6543| | 5: 2.25 - 2.09 1.00 2756 127 0.0852 0.0956 4.5595 4.6135| | 6: 2.09 - 1.97 1.00 2846 113 0.0843 0.1011 4.2535 4.3724| | 7: 1.97 - 1.87 1.00 2787 165 0.0879 0.1089 3.9766 4.0765| | 8: 1.87 - 1.79 1.00 2789 144 0.0913 0.1101 3.8828 3.9963| | 9: 1.79 - 1.72 1.00 2745 138 0.0874 0.1159 3.6415 3.8192| | 10: 1.72 - 1.66 1.00 2831 160 0.0909 0.1202 3.5571 3.706| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1010 3.4901 3.5514| | 12: 1.61 - 1.56 1.00 2773 144 0.0900 0.1126 3.3222 3.4527| | 13: 1.56 - 1.52 1.00 2745 130 0.0943 0.1055 3.302 3.3962| | 14: 1.52 - 1.48 1.00 2803 134 0.0979 0.1053 3.2338 3.3145| | 15: 1.48 - 1.45 1.00 2738 128 0.0999 0.1219 3.1486 3.2633| | 16: 1.45 - 1.42 1.00 2756 161 0.1053 0.1242 3.1319 3.2367| | 17: 1.42 - 1.39 1.00 2785 139 0.1137 0.1294 3.1131 3.2168| | 18: 1.39 - 1.36 1.00 2741 179 0.1196 0.1328 3.0994 3.2349| | 19: 1.36 - 1.34 1.00 2807 134 0.1263 0.1583 3.1103 3.2733| | 20: 1.34 - 1.32 1.00 2696 147 0.1366 0.1460 3.1094 3.1502| | 21: 1.32 - 1.30 1.00 2785 112 0.1471 0.1514 3.1117 3.1048| | 22: 1.29 - 1.27 1.00 2704 152 0.1564 0.1978 3.1212 3.289| | 23: 1.27 - 1.26 1.00 2802 156 0.1649 0.1766 3.1308 3.1893| | 24: 1.26 - 1.24 1.00 2744 132 0.1713 0.1854 3.1271 3.2343| | 25: 1.24 - 1.22 1.00 2733 148 0.1885 0.2145 3.1419 3.2584| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1760 3.1471 3.2014| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2169 3.1694 3.1628| | 28: 1.19 - 1.18 1.00 2671 147 0.2200 0.2298 3.1648 3.1699| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2373 3.1461 3.2266| | 30: 1.16 - 1.15 1.00 2739 148 0.2449 0.2444 3.1417 3.163| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.22 1.00 0.97 5477.83| | 2: 3.57 - 2.84 2888 124 0.93 12.22 1.01 0.97 5477.83| | 3: 2.83 - 2.48 2820 163 0.90 16.07 0.99 0.97 4581.05| | 4: 2.47 - 2.25 2825 136 0.92 13.17 1.00 0.98 2268.55| | 5: 2.25 - 2.09 2756 127 0.91 15.27 1.01 0.98 2268.55| | 6: 2.09 - 1.97 2846 113 0.93 12.22 1.02 0.97 1318.46| | 7: 1.97 - 1.87 2787 165 0.95 9.28 1.02 0.97 508.17| | 8: 1.87 - 1.79 2789 144 0.93 12.65 1.00 0.97 508.17| | 9: 1.79 - 1.72 2745 138 0.94 10.06 0.98 0.97 287.74| | 10: 1.72 - 1.66 2831 160 0.94 11.10 0.98 0.97 243.60| | 11: 1.66 - 1.61 2712 147 0.93 11.74 0.98 0.97 233.25| | 12: 1.61 - 1.56 2773 144 0.96 8.83 0.99 0.97 135.64| | 13: 1.56 - 1.52 2745 130 0.95 10.32 1.02 0.97 135.64| | 14: 1.52 - 1.48 2803 134 0.94 10.67 1.02 0.98 121.78| | 15: 1.48 - 1.45 2738 128 0.95 9.84 1.02 0.98 96.39| | 16: 1.45 - 1.42 2756 161 0.94 10.99 1.02 0.98 96.39| | 17: 1.42 - 1.39 2785 139 0.95 10.83 1.01 0.98 87.89| | 18: 1.39 - 1.36 2741 179 0.94 11.47 1.01 0.98 82.97| | 19: 1.36 - 1.34 2807 134 0.94 11.78 0.99 0.98 82.97| | 20: 1.34 - 1.32 2696 147 0.94 12.11 0.98 0.96 79.46| | 21: 1.32 - 1.30 2785 112 0.94 13.07 0.98 0.96 79.21| | 22: 1.29 - 1.27 2704 152 0.93 13.61 0.98 0.96 79.63| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.94 81.77| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.94 81.77| | 25: 1.24 - 1.22 2733 148 0.91 16.34 0.96 0.94 83.74| | 26: 1.22 - 1.21 2727 135 0.90 18.10 1.02 0.93 85.91| | 27: 1.21 - 1.19 2814 148 0.89 18.76 1.02 0.93 85.91| | 28: 1.19 - 1.18 2671 147 0.88 20.35 1.01 0.93 89.38| | 29: 1.18 - 1.16 2800 134 0.88 20.44 0.99 0.92 90.68| | 30: 1.16 - 1.15 2739 148 0.86 21.97 0.98 0.92 90.68| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.21 max = 5477.83 mean = 852.07| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.97 mean = 13.35| |phase err.(test): min = 0.00 max = 89.39 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1135 0.1128 0.1277 n_refl.: 87577 re-set all scales: r(all,work,free)=0.1449 0.1448 0.1483 n_refl.: 87577 remove outliers: r(all,work,free)=0.1449 0.1448 0.1483 n_refl.: 87577 overall B=-0.01 to atoms: r(all,work,free)=0.1448 0.1447 0.1482 n_refl.: 87577 bulk-solvent and scaling: r(all,work,free)=0.1135 0.1128 0.1280 n_refl.: 87577 remove outliers: r(all,work,free)=0.1134 0.1126 0.1280 n_refl.: 87573 ======================== 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 0.4150 285.382 249.623 0.446 1.001 0.308 11.894-9.307 92.16 90 4 0.2312 476.144 459.670 0.867 1.002 0.222 9.237-7.194 97.73 208 7 0.2367 386.748 380.943 0.923 1.002 0.150 7.162-5.571 100.00 427 22 0.2135 295.807 286.352 0.912 1.003 0.130 5.546-4.326 100.00 867 58 0.1124 406.070 401.252 0.963 1.003 0.120 4.315-3.360 100.00 1859 96 0.0915 386.176 383.756 1.004 1.002 0.110 3.356-2.611 100.00 3867 181 0.1101 253.697 251.863 1.010 1.002 0.030 2.608-2.026 99.99 8198 413 0.0897 168.178 167.616 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0884 82.129 82.472 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.420 36.028 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 22.947 21.498 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=-0.0149 ================= 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 : 0.2605 0.1988 0.082 5.263 8.8 119.3 19.9 258 0.000 1_bss: 0.1633 0.1806 0.082 5.263 9.1 119.5 20.1 258 0.000 1_settarget: 0.1633 0.1806 0.082 5.263 9.1 119.5 20.1 258 0.000 1_nqh: 0.1633 0.1806 0.082 5.263 9.1 119.5 20.1 258 0.000 1_weight: 0.1633 0.1806 0.082 5.263 9.1 119.5 20.1 258 0.000 1_xyzrec: 0.1222 0.1453 0.007 0.925 9.1 119.5 20.1 258 0.133 1_adp: 0.1229 0.1450 0.007 0.925 9.1 119.5 20.1 258 0.133 1_regHadp: 0.1231 0.1454 0.007 0.925 9.1 119.5 20.1 258 0.133 1_occ: 0.1226 0.1450 0.007 0.925 9.1 119.5 20.1 258 0.133 2_bss: 0.1224 0.1442 0.007 0.925 9.1 119.5 20.1 258 0.133 2_settarget: 0.1224 0.1442 0.007 0.925 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1224 0.1442 0.007 0.940 9.1 119.5 20.1 258 0.133 2_nqh: 0.1225 0.1443 0.007 0.940 9.1 119.5 20.1 258 0.136 2_sol: 0.1199 0.1400 0.007 0.940 9.1 115.0 22.2 420 n/a 2_weight: 0.1199 0.1400 0.007 0.940 9.1 115.0 22.2 420 n/a 2_xyzrec: 0.1187 0.1408 0.007 0.918 9.1 115.0 22.2 420 n/a 2_adp: 0.1187 0.1408 0.007 0.918 9.1 115.0 22.2 420 n/a 2_regHadp: 0.1187 0.1408 0.007 0.918 9.1 115.0 22.2 420 n/a 2_occ: 0.1187 0.1405 0.007 0.918 9.1 115.0 22.2 420 n/a 3_bss: 0.1182 0.1396 0.007 0.918 9.1 115.0 22.2 420 n/a 3_settarget: 0.1182 0.1396 0.007 0.918 9.1 115.0 22.2 420 n/a 3_updatecdl: 0.1182 0.1396 0.007 0.919 9.1 115.0 22.2 420 n/a 3_nqh: 0.1182 0.1396 0.007 0.919 9.1 115.0 22.2 420 n/a 3_sol: 0.1201 0.1399 0.007 0.919 9.1 115.0 21.2 434 n/a 3_weight: 0.1201 0.1399 0.007 0.919 9.1 115.0 21.2 434 n/a 3_xyzrec: 0.1158 0.1320 0.008 1.086 9.1 115.0 21.2 434 n/a 3_adp: 0.1158 0.1320 0.008 1.086 9.1 115.0 21.2 434 n/a 3_regHadp: 0.1158 0.1320 0.008 1.086 9.1 115.0 21.2 434 n/a 3_occ: 0.1147 0.1317 0.008 1.086 9.1 115.0 21.2 434 n/a 4_bss: 0.1138 0.1305 0.008 1.086 9.1 115.0 21.2 434 n/a 4_settarget: 0.1138 0.1305 0.008 1.086 9.1 115.0 21.2 434 n/a 4_updatecdl: 0.1138 0.1305 0.008 1.087 9.1 115.0 21.2 434 n/a 4_nqh: 0.1138 0.1305 0.008 1.087 9.1 115.0 21.2 434 n/a 4_sol: 0.1137 0.1295 0.008 1.087 9.1 115.0 21.2 452 n/a 4_weight: 0.1137 0.1295 0.008 1.087 9.1 115.0 21.2 452 n/a 4_xyzrec: 0.1133 0.1296 0.009 1.127 9.1 115.0 21.2 452 n/a 4_adp: 0.1133 0.1296 0.009 1.127 9.1 115.0 21.2 452 n/a 4_regHadp: 0.1133 0.1296 0.009 1.127 9.1 115.0 21.2 452 n/a 4_occ: 0.1127 0.1290 0.009 1.127 9.1 115.0 21.2 452 n/a 5_bss: 0.1125 0.1286 0.009 1.127 9.1 115.0 21.2 452 n/a 5_settarget: 0.1125 0.1286 0.009 1.127 9.1 115.0 21.2 452 n/a 5_updatecdl: 0.1125 0.1286 0.009 1.127 9.1 115.0 21.2 452 n/a 5_setrh: 0.1126 0.1287 0.009 1.127 9.1 115.0 21.2 452 n/a 5_nqh: 0.1126 0.1287 0.009 1.127 9.1 115.0 21.2 452 n/a 5_sol: 0.1131 0.1280 0.009 1.127 9.1 115.0 21.2 458 n/a 5_weight: 0.1131 0.1280 0.009 1.127 9.1 115.0 21.2 458 n/a 5_xyzrec: 0.1131 0.1280 0.008 1.127 9.1 115.0 21.2 458 n/a 5_adp: 0.1131 0.1280 0.008 1.127 9.1 115.0 21.2 458 n/a 5_regHadp: 0.1131 0.1280 0.008 1.127 9.1 115.0 21.2 458 n/a 5_occ: 0.1128 0.1277 0.008 1.127 9.1 115.0 21.2 458 n/a end: 0.1126 0.1280 0.008 1.127 9.1 115.0 21.2 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8555406_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_8555406_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2400 Refinement macro-cycles (run) : 13657.4400 Write final files (write_after_run_outputs) : 95.3500 Total : 13756.0300 Total CPU time: 3.83 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:09:17 PST -0800 (1735366157.06 s) Start R-work = 0.1633, R-free = 0.1806 Final R-work = 0.1126, R-free = 0.1280 =============================================================================== Job complete usr+sys time: 13936.58 seconds wall clock time: 253 minutes 26.33 seconds (15206.33 seconds total)