Starting phenix.refine on Fri Dec 27 17:58:27 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6727304.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_6727304.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6727304.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } pdb_interpretation { nonbonded_weight = 16 const_shrink_donor_acceptor = 0.6 } ordered_solvent { mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.46, per 1000 atoms: 0.43 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 208.5 milliseconds Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.60 - 0.87: 330 0.87 - 1.15: 1271 1.15 - 1.42: 675 1.42 - 1.69: 851 1.69 - 1.96: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.540 1.756 -0.217 1.11e-02 8.12e+03 3.80e+02 bond pdb=" C ALA A 61 " pdb=" O ALA A 61 " ideal model delta sigma weight residual 1.237 1.459 -0.223 1.19e-02 7.06e+03 3.51e+02 bond pdb=" CA VAL A 177 " pdb=" C VAL A 177 " ideal model delta sigma weight residual 1.523 1.744 -0.221 1.27e-02 6.20e+03 3.03e+02 bond pdb=" CA ILE A 117 " pdb=" CB ILE A 117 " ideal model delta sigma weight residual 1.537 1.336 0.202 1.17e-02 7.31e+03 2.97e+02 bond pdb=" N LYS A 130 " pdb=" CA LYS A 130 " ideal model delta sigma weight residual 1.459 1.261 0.198 1.16e-02 7.43e+03 2.91e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.00: 3270 5.00 - 9.99: 1905 9.99 - 14.98: 523 14.98 - 19.98: 74 19.98 - 24.97: 5 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 106.55 15.22 1.00e+00 1.00e+00 2.32e+02 angle pdb=" CA PHE A 164 " pdb=" CB PHE A 164 " pdb=" CG PHE A 164 " ideal model delta sigma weight residual 113.80 127.87 -14.07 1.00e+00 1.00e+00 1.98e+02 angle pdb=" O ALA A 104 " pdb=" C ALA A 104 " pdb=" N ILE A 105 " ideal model delta sigma weight residual 123.31 108.07 15.24 1.17e+00 7.31e-01 1.70e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.80 107.45 14.35 1.13e+00 7.83e-01 1.61e+02 angle pdb=" CA LYS A 89 " pdb=" C LYS A 89 " pdb=" O LYS A 89 " ideal model delta sigma weight residual 120.20 106.35 13.85 1.12e+00 7.97e-01 1.53e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.96: 945 17.96 - 35.91: 117 35.91 - 53.86: 36 53.86 - 71.81: 10 71.81 - 89.76: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " pdb=" CA THR A 124 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ARG A 48 " pdb=" C ARG A 48 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta harmonic sigma weight residual 180.00 156.53 23.47 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA CYS A 46 " pdb=" C CYS A 46 " pdb=" N SER A 47 " pdb=" CA SER A 47 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.214: 99 0.214 - 0.428: 81 0.428 - 0.641: 46 0.641 - 0.855: 13 0.855 - 1.068: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" C3 ADTT A 201 " pdb=" C2 ADTT A 201 " pdb=" C4 ADTT A 201 " pdb=" O3 ADTT A 201 " both_signs ideal model delta sigma weight residual False 2.56 3.62 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" CA LEU A 185 " pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CB LEU A 185 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA LEU A 112 " pdb=" N LEU A 112 " pdb=" C LEU A 112 " pdb=" CB LEU A 112 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.18e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.064 2.00e-02 2.50e+03 6.92e-02 1.44e+02 pdb=" CG PHE A 119 " -0.145 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.101 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.060 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.069 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.033 2.00e-02 2.50e+03 5.55e-02 9.25e+01 pdb=" CG TYR A 139 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.067 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.083 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.120 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.010 2.00e-02 2.50e+03 5.50e-02 9.07e+01 pdb=" CG PHE A 164 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.081 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.030 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.039 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.071 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 990 2.31 - 2.88: 7948 2.88 - 3.45: 10630 3.45 - 4.03: 15219 4.03 - 4.60: 21827 Nonbonded interactions: 56614 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.737 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.796 1.850 nonbonded pdb=" H LYS A 122 " pdb=" OD2 ASP A 149 " model vdw 1.810 1.850 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.825 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.840 1.850 ... (remaining 56609 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_6727304_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= 0.1951 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789777 | | target function (ml) not normalized (work): 232405.150905 | | target function (ml) not normalized (free): 11828.986722 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3038 0.2083 6.993 4.9387| | 2: 3.57 - 2.84 1.00 2876 122 0.2450 0.1985 4.3599 4.3825| | 3: 2.84 - 2.48 1.00 2833 165 0.2319 0.1609 4.1377 4.1638| | 4: 2.47 - 2.25 1.00 2825 136 0.2361 0.1487 3.8498 3.8401| | 5: 2.25 - 2.09 1.00 2756 127 0.2430 0.1604 3.8071 3.8484| | 6: 2.09 - 1.97 1.00 2846 113 0.2574 0.1637 3.4659 3.5521| | 7: 1.97 - 1.87 1.00 2787 165 0.2588 0.1821 3.1459 3.193| | 8: 1.87 - 1.79 1.00 2789 144 0.2512 0.2063 3.062 3.1827| | 9: 1.79 - 1.72 1.00 2745 138 0.2392 0.1985 2.912 2.9608| | 10: 1.72 - 1.66 1.00 2789 158 0.2386 0.1983 2.8056 2.8609| | 11: 1.66 - 1.61 1.00 2740 147 0.2511 0.1684 2.7501 2.7025| | 12: 1.61 - 1.56 1.00 2787 146 0.2527 0.1999 2.6301 2.6688| | 13: 1.56 - 1.52 1.00 2745 130 0.2555 0.1790 2.561 2.5974| | 14: 1.52 - 1.48 1.00 2803 134 0.2582 0.1796 2.513 2.5138| | 15: 1.48 - 1.45 1.00 2738 128 0.2587 0.1860 2.4338 2.39| | 16: 1.45 - 1.42 1.00 2756 161 0.2612 0.2264 2.3761 2.481| | 17: 1.42 - 1.39 1.00 2785 139 0.2694 0.2237 2.3415 2.474| | 18: 1.39 - 1.36 1.00 2741 179 0.2678 0.2188 2.283 2.3077| | 19: 1.36 - 1.34 1.00 2807 134 0.2585 0.2321 2.2393 2.3083| | 20: 1.34 - 1.32 1.00 2696 147 0.2608 0.2292 2.1863 2.2284| | 21: 1.32 - 1.30 1.00 2785 112 0.2670 0.2106 2.1427 2.1581| | 22: 1.29 - 1.27 1.00 2704 152 0.2726 0.2471 2.1346 2.1477| | 23: 1.27 - 1.26 1.00 2802 156 0.2723 0.2593 2.0882 2.2308| | 24: 1.26 - 1.24 1.00 2744 132 0.2766 0.2426 2.0722 2.1208| | 25: 1.24 - 1.22 1.00 2734 148 0.2850 0.2531 2.0288 2.0588| | 26: 1.22 - 1.21 1.00 2727 135 0.2870 0.2381 2.0136 2.1311| | 27: 1.21 - 1.19 1.00 2814 148 0.2954 0.2372 2.0073 1.992| | 28: 1.19 - 1.18 1.00 2671 147 0.2984 0.2876 1.9899 2.0173| | 29: 1.18 - 1.16 1.00 2800 134 0.2920 0.2816 1.9659 2.0491| | 30: 1.16 - 1.15 1.00 2740 148 0.3096 0.2849 1.9443 1.9564| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.20 0.76 0.23 1525.90| | 2: 3.57 - 2.84 2876 122 0.80 26.50 1.28 0.23 1525.90| | 3: 2.84 - 2.48 2833 165 0.74 32.34 1.24 0.24 1265.17| | 4: 2.47 - 2.25 2825 136 0.81 25.90 1.26 0.25 588.52| | 5: 2.25 - 2.09 2756 127 0.77 29.64 1.28 0.25 588.52| | 6: 2.09 - 1.97 2846 113 0.83 23.11 1.30 0.25 321.30| | 7: 1.97 - 1.87 2787 165 0.90 16.92 1.29 0.26 93.40| | 8: 1.87 - 1.79 2789 144 0.85 21.61 1.26 0.26 93.40| | 9: 1.79 - 1.72 2745 138 0.88 18.81 1.23 0.26 56.38| | 10: 1.72 - 1.66 2789 158 0.86 20.24 1.22 0.26 48.96| | 11: 1.66 - 1.61 2740 147 0.85 21.52 1.25 0.26 47.12| | 12: 1.61 - 1.56 2787 146 0.89 17.98 1.23 0.25 28.49| | 13: 1.56 - 1.52 2745 130 0.87 19.83 1.24 0.25 28.49| | 14: 1.52 - 1.48 2803 134 0.87 19.99 1.24 0.25 25.48| | 15: 1.48 - 1.45 2738 128 0.88 19.56 1.23 0.25 19.96| | 16: 1.45 - 1.42 2756 161 0.86 21.02 1.23 0.25 19.96| | 17: 1.42 - 1.39 2785 139 0.87 20.35 1.23 0.25 17.20| | 18: 1.39 - 1.36 2741 179 0.87 20.89 1.22 0.25 15.60| | 19: 1.36 - 1.34 2807 134 0.86 21.59 1.21 0.25 15.60| | 20: 1.34 - 1.32 2696 147 0.87 20.70 1.20 0.25 12.97| | 21: 1.32 - 1.30 2785 112 0.86 21.86 1.20 0.25 12.78| | 22: 1.29 - 1.27 2704 152 0.85 22.31 1.21 0.25 12.51| | 23: 1.27 - 1.26 2802 156 0.86 21.89 1.21 0.24 11.14| | 24: 1.26 - 1.24 2744 132 0.85 22.75 1.20 0.24 11.14| | 25: 1.24 - 1.22 2734 148 0.84 23.80 1.22 0.24 10.63| | 26: 1.22 - 1.21 2727 135 0.84 24.40 1.20 0.23 10.06| | 27: 1.21 - 1.19 2814 148 0.83 24.66 1.20 0.23 10.06| | 28: 1.19 - 1.18 2671 147 0.82 25.87 1.18 0.23 9.63| | 29: 1.18 - 1.16 2800 134 0.82 26.11 1.15 0.22 9.47| | 30: 1.16 - 1.15 2740 148 0.80 28.09 1.14 0.22 9.47| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 9.47 max = 1525.90 mean = 220.91| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.96 mean = 22.65| |phase err.(test): min = 0.00 max = 89.47 mean = 22.43| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.275 1557 Z= 5.356 Angle : 5.237 16.778 2118 Z= 3.690 Chirality : 0.368 1.068 243 Planarity : 0.032 0.087 284 Dihedral : 14.189 89.760 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 30.27 % 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: -3.64 (0.43), residues: 224 helix: -3.42 (0.30), residues: 109 sheet: -2.32 (0.88), residues: 28 loop : -0.61 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.057 0.019 ARG A 98 TYR 0.061 0.031 TYR A 141 PHE 0.123 0.036 PHE A 119 HIS 0.033 0.016 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= 0.2606 r_free= 0.1951 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.789777 | | target function (ml) not normalized (work): 232405.150905 | | target function (ml) not normalized (free): 11828.986722 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2607 0.1952 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2607 0.1952 n_refl.: 87602 remove outliers: r(all,work,free)=0.1980 0.1984 0.1952 n_refl.: 87594 overall B=0.23 to atoms: r(all,work,free)=0.2009 0.2013 0.1969 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1647 0.1640 0.1774 n_refl.: 87594 remove outliers: r(all,work,free)=0.1646 0.1640 0.1774 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 0.3759 386.187 358.160 0.668 1.004 0.397 11.894-9.307 99.02 97 4 0.1800 613.439 592.167 0.923 1.004 0.380 9.237-7.194 100.00 213 7 0.2208 501.717 489.001 0.954 1.005 0.380 7.162-5.571 100.00 427 22 0.2191 376.511 364.315 0.928 1.004 0.329 5.546-4.326 100.00 867 58 0.1274 516.857 511.066 0.962 1.004 0.249 4.315-3.360 100.00 1859 96 0.1151 491.534 487.260 1.002 1.004 0.189 3.356-2.611 100.00 3867 181 0.1449 322.913 319.769 0.996 1.003 0.089 2.608-2.026 99.99 8198 413 0.1354 214.062 211.924 1.004 1.001 0.000 2.025-1.573 100.00 17313 902 0.1660 104.537 103.782 1.015 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2053 46.356 45.052 1.005 0.994 0.000 1.221-1.150 99.97 13689 708 0.2594 29.207 26.928 0.975 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0533 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1640 r_free=0.1774 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** A 144 ASN Total number of N/Q/H flips: 2 r_work=0.1643 r_free=0.1772 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.978982 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1995.955070 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 0.1636 0.1762 0.0126 0.002 0.5 4.5 0.0 0.0 0 0.125 0.1551 0.1691 0.0140 0.002 0.5 4.2 0.0 0.0 0 0.250 0.1414 0.1578 0.0164 0.002 0.5 4.2 0.0 0.0 0 0.500 0.1380 0.1558 0.0179 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1348 0.1539 0.0191 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1334 0.1528 0.0194 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1289 0.1506 0.0217 0.002 0.6 2.9 0.5 0.0 0 2.000 0.1265 0.1490 0.0225 0.003 0.7 2.9 0.5 0.0 0 3.000 0.1265 0.1500 0.0235 0.003 0.7 3.8 0.5 0.0 0 4.000 0.1247 0.1480 0.0234 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1247 0.1483 0.0236 0.005 0.8 3.8 0.5 0.0 0 6.000 0.1242 0.1480 0.0239 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1240 0.1479 0.0240 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1231 0.1471 0.0241 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1232 0.1476 0.0244 0.006 0.9 3.2 0.5 0.0 0 10.000 0.1231 0.1474 0.0243 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1232 0.1477 0.0246 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1226 0.1472 0.0246 0.008 1.0 4.2 0.5 0.6 0 13.989 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1231 0.1471 0.0241 0.006 0.9 3.8 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.31 14.71 2.41 3.013 19.091 1995.955 0.018 12.31 14.71 2.41 3.013 19.091 59.879 0.018 12.38 14.68 2.30 2.664 19.090 249.494 0.018 12.76 15.43 2.67 2.928 19.367 997.978 0.017 12.64 15.58 2.93 3.256 19.604 1995.955 0.016 12.47 15.51 3.04 3.225 19.602 2993.933 0.016 12.36 15.42 3.07 3.278 19.617 3991.910 0.015 12.27 15.34 3.08 3.232 19.581 4989.888 0.015 12.27 15.46 3.20 3.369 19.651 5987.865 0.015 12.23 15.42 3.19 3.296 19.597 6985.843 0.015 12.23 15.47 3.24 3.444 19.667 7983.820 0.015 12.17 15.38 3.21 3.288 19.565 8981.798 0.015 12.17 15.45 3.28 3.431 19.637 9979.775 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: 249.494 Accepted refinement result: 12.38 14.68 2.30 2.664 19.090 249.494 0.018 Individual atomic B min max mean iso aniso Overall: 9.10 119.46 20.12 3.30 0 1785 Protein: 9.10 114.98 17.02 3.31 0 1519 Water: 11.49 119.46 38.26 N/A 0 258 Other: 19.73 26.64 22.09 N/A 0 8 Chain A: 9.10 119.46 20.12 N/A 0 1785 Histogram: Values Number of atoms 9.10 - 20.13 1272 20.13 - 31.17 227 31.17 - 42.21 125 42.21 - 53.24 94 53.24 - 64.28 42 64.28 - 75.32 11 75.32 - 86.35 7 86.35 - 97.39 4 97.39 - 108.43 1 108.43 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1238 r_free=0.1468 r_work=0.1239 r_free=0.1471 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1239 r_free = 0.1471 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1232 r_free = 0.1464 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= 0.1232 r_free= 0.1464 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.017066 | | target function (ls_wunit_k1) not normalized (work): 1421.553078 | | target function (ls_wunit_k1) not normalized (free): 108.846423 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1464 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1681 0.1682 0.1696 n_refl.: 87593 remove outliers: r(all,work,free)=0.1681 0.1682 0.1696 n_refl.: 87593 overall B=0.02 to atoms: r(all,work,free)=0.1685 0.1687 0.1699 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1239 0.1228 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1228 0.1454 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 0.3641 303.305 280.319 0.662 1.002 0.391 11.894-9.307 99.02 97 4 0.1663 481.786 469.498 0.922 1.003 0.367 9.237-7.194 100.00 213 7 0.1956 394.041 386.856 0.960 1.003 0.350 7.162-5.571 100.00 427 22 0.1839 295.706 289.612 0.934 1.003 0.264 5.546-4.326 100.00 867 58 0.1004 405.931 402.827 0.966 1.003 0.240 4.315-3.360 100.00 1859 96 0.0876 386.044 384.989 1.008 1.003 0.180 3.356-2.611 100.00 3867 181 0.1174 253.611 252.476 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1022 168.121 167.394 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1108 82.101 82.304 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.407 35.913 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2253 22.939 21.429 0.984 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0149 b_overall=0.0373 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1228 r_free=0.1454 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** A 144 ASN Total number of N/Q/H flips: 1 r_work=0.1227 r_free=0.1452 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1227 r_free=0.1452 | n_water=258 | time (s): 1.710 (total time: 1.710) Filter (dist) r_work=0.1238 r_free=0.1449 | n_water=250 | time (s): 21.810 (total time: 23.520) Filter (q & B) r_work=0.1240 r_free=0.1448 | n_water=247 | time (s): 2.650 (total time: 26.170) Compute maps r_work=0.1240 r_free=0.1448 | n_water=247 | time (s): 1.250 (total time: 27.420) Filter (map) r_work=0.1258 r_free=0.1457 | n_water=223 | time (s): 2.640 (total time: 30.060) Find peaks r_work=0.1258 r_free=0.1457 | n_water=223 | time (s): 0.460 (total time: 30.520) Add new water r_work=0.1408 r_free=0.1627 | n_water=422 | time (s): 2.370 (total time: 32.890) Refine new water occ: r_work=0.1315 r_free=0.1483 adp: r_work=0.1232 r_free=0.1428 occ: r_work=0.1245 r_free=0.1412 adp: r_work=0.1210 r_free=0.1401 occ: r_work=0.1213 r_free=0.1391 adp: r_work=0.1203 r_free=0.1391 ADP+occupancy (water only), MIN, final r_work=0.1203 r_free=0.1391 r_work=0.1203 r_free=0.1391 | n_water=422 | time (s): 63.990 (total time: 96.880) Filter (q & B) r_work=0.1207 r_free=0.1392 | n_water=409 | time (s): 2.940 (total time: 99.820) Filter (dist only) r_work=0.1207 r_free=0.1390 | n_water=408 | time (s): 33.220 (total time: 133.040) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.157336 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1491.870511 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 0.1695 0.1806 0.0111 0.001 0.4 7.4 0.0 0.0 0 0.125 0.1558 0.1684 0.0126 0.001 0.4 6.7 0.0 0.0 0 0.250 0.1394 0.1553 0.0159 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1348 0.1519 0.0171 0.002 0.5 4.8 0.0 0.0 0 0.750 0.1330 0.1507 0.0177 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1350 0.1525 0.0175 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1266 0.1468 0.0202 0.002 0.5 4.8 0.5 0.0 0 2.000 0.1236 0.1447 0.0212 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1216 0.1428 0.0212 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1209 0.1430 0.0221 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1204 0.1423 0.0219 0.004 0.7 4.8 0.5 0.0 0 6.000 0.1202 0.1420 0.0218 0.005 0.8 4.8 0.5 0.0 0 7.000 0.1199 0.1418 0.0219 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1196 0.1415 0.0219 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1193 0.1412 0.0218 0.006 0.9 4.8 0.5 0.0 0 10.000 0.1190 0.1414 0.0224 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1188 0.1415 0.0227 0.007 0.9 5.4 0.5 0.0 0 12.000 0.1187 0.1413 0.0226 0.008 0.9 4.8 0.5 0.0 0 13.579 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1193 0.1412 0.0218 0.006 0.9 4.8 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.93 14.12 2.18 3.774 21.749 1491.871 0.016 11.93 14.12 2.18 3.774 21.749 44.756 0.016 11.93 14.12 2.18 3.774 21.749 186.484 0.016 12.14 14.58 2.44 3.616 21.763 745.935 0.015 12.11 14.93 2.82 3.452 22.009 1491.871 0.015 12.00 14.93 2.93 3.452 22.098 2237.806 0.014 11.87 14.85 2.98 3.472 21.963 2983.741 0.014 11.80 14.79 2.99 3.477 22.069 3729.676 0.014 11.80 14.83 3.03 3.500 22.099 4475.612 0.014 11.78 14.85 3.08 3.513 22.086 5221.547 0.014 11.78 14.92 3.14 3.544 22.117 5967.482 0.014 11.73 14.94 3.21 3.562 22.162 6713.417 0.014 11.69 14.87 3.18 3.556 22.089 7459.353 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: 44.756 Accepted refinement result: 11.93 14.12 2.18 3.774 21.749 44.756 0.016 Individual atomic B min max mean iso aniso Overall: 9.12 115.01 22.11 3.30 185 1750 Protein: 9.12 115.01 17.05 3.31 0 1519 Water: 11.02 76.71 40.96 N/A 185 223 Other: 19.75 26.66 22.11 N/A 0 8 Chain A: 9.12 115.01 19.43 N/A 0 1750 Chain S: 11.02 60.00 47.49 N/A 185 0 Histogram: Values Number of atoms 9.12 - 19.71 1258 19.71 - 30.30 246 30.30 - 40.89 159 40.89 - 51.47 130 51.47 - 62.06 119 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1412 r_work=0.1193 r_free=0.1412 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1412 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1409 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.21 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= 0.1192 r_free= 0.1409 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015084 | | target function (ls_wunit_k1) not normalized (work): 1256.490280 | | target function (ls_wunit_k1) not normalized (free): 100.780054 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1192 0.1409 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1591 0.1589 0.1649 n_refl.: 87593 remove outliers: r(all,work,free)=0.1591 0.1589 0.1649 n_refl.: 87593 overall B=0.00 to atoms: r(all,work,free)=0.1591 0.1590 0.1649 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1199 0.1189 0.1404 n_refl.: 87593 remove outliers: r(all,work,free)=0.1198 0.1188 0.1404 n_refl.: 87590 ======================== 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 93.75 85 5 0.3355 299.302 277.078 0.611 1.002 0.360 11.894-9.307 99.02 97 4 0.1657 481.786 474.914 0.926 1.003 0.350 9.237-7.194 100.00 213 7 0.1697 394.041 393.357 0.981 1.003 0.290 7.162-5.571 100.00 427 22 0.1539 295.706 291.378 0.938 1.003 0.230 5.546-4.326 100.00 867 58 0.0896 405.931 403.109 0.962 1.003 0.210 4.315-3.360 100.00 1859 96 0.0791 386.044 385.053 1.005 1.003 0.200 3.356-2.611 100.00 3867 181 0.1089 253.611 252.717 1.010 1.002 0.130 2.608-2.026 99.99 8198 413 0.1017 168.121 167.585 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1102 82.101 82.304 1.031 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.407 35.944 1.025 0.997 0.000 1.221-1.150 99.97 13689 708 0.2249 22.939 21.461 0.990 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0051 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1404 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1404 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1404 | n_water=408 | time (s): 1.660 (total time: 1.660) Filter (dist) r_work=0.1188 r_free=0.1404 | n_water=405 | time (s): 36.110 (total time: 37.770) Filter (q & B) r_work=0.1188 r_free=0.1404 | n_water=405 | time (s): 0.910 (total time: 38.680) Compute maps r_work=0.1188 r_free=0.1404 | n_water=405 | time (s): 1.450 (total time: 40.130) Filter (map) r_work=0.1231 r_free=0.1406 | n_water=279 | time (s): 2.520 (total time: 42.650) Find peaks r_work=0.1231 r_free=0.1406 | n_water=279 | time (s): 0.550 (total time: 43.200) Add new water r_work=0.1351 r_free=0.1559 | n_water=466 | time (s): 2.660 (total time: 45.860) Refine new water occ: r_work=0.1254 r_free=0.1468 adp: r_work=0.1256 r_free=0.1469 occ: r_work=0.1231 r_free=0.1443 adp: r_work=0.1231 r_free=0.1443 occ: r_work=0.1211 r_free=0.1419 adp: r_work=0.1208 r_free=0.1417 ADP+occupancy (water only), MIN, final r_work=0.1208 r_free=0.1417 r_work=0.1208 r_free=0.1417 | n_water=466 | time (s): 159.890 (total time: 205.750) Filter (q & B) r_work=0.1213 r_free=0.1423 | n_water=432 | time (s): 2.580 (total time: 208.330) Filter (dist only) r_work=0.1213 r_free=0.1421 | n_water=431 | time (s): 34.430 (total time: 242.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.808627 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.279869 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 0.1238 0.1387 0.0149 0.002 0.6 4.5 0.5 0.0 0 0.090 0.1195 0.1350 0.0155 0.003 0.7 3.5 0.5 0.0 0 0.271 0.1180 0.1336 0.0156 0.004 0.8 3.2 0.5 0.0 0 0.543 0.1172 0.1332 0.0160 0.005 0.9 3.5 0.5 0.0 0 0.814 0.1168 0.1332 0.0163 0.006 1.0 3.2 0.5 0.0 0 1.085 0.1166 0.1330 0.0165 0.007 1.0 3.5 0.5 0.0 0 1.356 0.1164 0.1329 0.0165 0.007 1.1 3.2 0.5 0.0 0 1.628 0.1160 0.1330 0.0169 0.008 1.1 3.8 0.5 0.0 0 1.899 0.1171 0.1332 0.0161 0.005 0.9 3.2 0.5 0.0 0 0.904 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1164 0.1329 0.0165 0.007 1.1 3.2 0.5 0.0 0 1.628 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 13.29 1.65 3.777 21.233 38.280 3.622 11.64 13.29 1.65 3.777 21.233 1.148 3.622 11.64 13.29 1.65 3.777 21.233 4.785 3.622 11.69 13.34 1.65 3.709 21.224 19.140 3.617 11.79 13.49 1.70 3.724 21.192 38.280 3.621 11.71 13.47 1.76 3.743 21.177 57.420 3.614 11.63 13.42 1.79 3.764 21.172 76.560 3.609 11.62 13.43 1.81 3.771 21.166 95.700 3.607 11.57 13.40 1.83 3.785 21.160 114.840 3.603 11.56 13.39 1.84 3.795 21.157 133.980 3.602 11.55 13.41 1.86 3.808 21.148 153.119 3.602 11.53 13.40 1.87 3.817 21.143 172.259 3.600 11.53 13.40 1.86 3.828 21.134 191.399 3.600 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.148 Accepted refinement result: 11.64 13.29 1.65 3.777 21.233 1.148 3.622 Individual atomic B min max mean iso aniso Overall: 9.12 115.01 21.16 3.30 212 1746 Protein: 9.12 115.01 17.05 3.31 0 1519 Water: 11.03 76.72 35.65 N/A 212 219 Other: 19.75 26.66 22.12 N/A 0 8 Chain A: 9.12 115.01 19.37 N/A 0 1746 Chain S: 11.03 60.00 35.93 N/A 212 0 Histogram: Values Number of atoms 9.12 - 19.71 1262 19.71 - 30.30 292 30.30 - 40.89 205 40.89 - 51.48 121 51.48 - 62.07 55 62.07 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1164 r_free=0.1329 r_work=0.1164 r_free=0.1329 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1164 r_free = 0.1329 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1155 r_free = 0.1323 target_work(ml) = 3.615 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1155 r_free= 0.1323 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.615328 | | target function (ml) not normalized (work): 301135.169465 | | target function (ml) not normalized (free): 15856.303401 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1155 0.1323 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1500 0.1501 0.1518 n_refl.: 87590 remove outliers: r(all,work,free)=0.1500 0.1501 0.1518 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1498 0.1499 0.1517 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1150 0.1310 n_refl.: 87590 remove outliers: r(all,work,free)=0.1155 0.1147 0.1310 n_refl.: 87582 ======================== 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 0.3998 291.226 265.555 0.496 1.000 0.320 11.894-9.307 97.06 95 4 0.2258 482.009 462.936 0.875 1.001 0.283 9.237-7.194 98.18 209 7 0.2275 385.534 385.681 0.943 1.002 0.210 7.162-5.571 100.00 427 22 0.2086 295.706 284.620 0.912 1.002 0.180 5.546-4.326 100.00 867 58 0.1134 405.931 400.966 0.954 1.002 0.155 4.315-3.360 100.00 1859 96 0.0932 386.044 383.650 0.993 1.002 0.143 3.356-2.611 100.00 3867 181 0.1144 253.611 251.581 0.998 1.002 0.062 2.608-2.026 99.99 8198 413 0.0940 168.121 167.344 1.014 1.001 0.000 2.025-1.573 100.00 17313 902 0.0902 82.101 82.383 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1255 36.407 35.992 1.019 0.998 0.000 1.221-1.150 99.97 13689 708 0.2166 22.939 21.482 0.981 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0255 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1310 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=0.1147 r_free=0.1310 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1147 r_free=0.1310 | n_water=431 | time (s): 2.480 (total time: 2.480) Filter (dist) r_work=0.1146 r_free=0.1310 | n_water=429 | time (s): 44.150 (total time: 46.630) Filter (q & B) r_work=0.1147 r_free=0.1312 | n_water=427 | time (s): 3.990 (total time: 50.620) Compute maps r_work=0.1147 r_free=0.1312 | n_water=427 | time (s): 1.860 (total time: 52.480) Filter (map) r_work=0.1178 r_free=0.1311 | n_water=322 | time (s): 3.820 (total time: 56.300) Find peaks r_work=0.1178 r_free=0.1311 | n_water=322 | time (s): 0.700 (total time: 57.000) Add new water r_work=0.1248 r_free=0.1383 | n_water=475 | time (s): 3.610 (total time: 60.610) Refine new water occ: r_work=0.1168 r_free=0.1314 adp: r_work=0.1169 r_free=0.1316 occ: r_work=0.1154 r_free=0.1303 adp: r_work=0.1153 r_free=0.1303 occ: r_work=0.1143 r_free=0.1297 adp: r_work=0.1140 r_free=0.1296 ADP+occupancy (water only), MIN, final r_work=0.1140 r_free=0.1296 r_work=0.1140 r_free=0.1296 | n_water=475 | time (s): 227.270 (total time: 287.880) Filter (q & B) r_work=0.1145 r_free=0.1301 | n_water=444 | time (s): 4.120 (total time: 292.000) Filter (dist only) r_work=0.1145 r_free=0.1300 | n_water=443 | time (s): 44.920 (total time: 336.920) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.805466 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.606923 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 0.1207 0.1332 0.0125 0.002 0.6 5.4 0.5 0.0 0 0.090 0.1169 0.1310 0.0141 0.003 0.8 4.2 0.5 0.0 0 0.271 0.1155 0.1305 0.0150 0.005 0.9 4.5 0.5 0.0 0 0.542 0.1148 0.1301 0.0153 0.006 1.0 4.5 0.5 0.0 0 0.812 0.1144 0.1301 0.0157 0.006 1.0 4.2 0.5 0.0 0 1.083 0.1141 0.1301 0.0160 0.007 1.1 4.5 0.5 0.0 0 1.354 0.1139 0.1301 0.0161 0.008 1.1 4.5 0.5 0.0 0 1.625 0.1137 0.1301 0.0163 0.009 1.1 4.5 0.5 0.0 0 1.896 0.1146 0.1301 0.0154 0.006 1.0 4.5 0.5 0.0 0 0.903 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1137 0.1301 0.0163 0.009 1.1 4.5 0.5 0.0 0 1.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.37 13.01 1.63 3.777 21.164 46.607 3.606 11.37 13.01 1.63 3.777 21.164 1.398 3.606 11.37 13.01 1.63 3.777 21.164 5.826 3.606 11.40 13.04 1.64 3.716 21.155 23.303 3.600 11.41 13.12 1.71 3.741 21.131 46.607 3.600 11.40 13.14 1.74 3.758 21.112 69.910 3.596 11.33 13.08 1.75 3.775 21.112 93.214 3.592 11.32 13.10 1.78 3.787 21.105 116.517 3.590 11.29 13.08 1.79 3.799 21.101 139.821 3.588 11.30 13.12 1.82 3.817 21.090 163.124 3.588 11.27 13.09 1.82 3.823 21.090 186.428 3.585 11.26 13.08 1.81 3.832 21.088 209.731 3.585 11.24 13.06 1.82 3.832 21.091 233.035 3.584 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.398 Accepted refinement result: 11.37 13.01 1.63 3.777 21.164 1.398 3.606 Individual atomic B min max mean iso aniso Overall: 9.11 115.00 21.05 3.30 226 1744 Protein: 9.11 115.00 17.04 3.31 0 1519 Water: 11.02 76.71 34.77 N/A 226 217 Other: 19.74 26.65 22.11 N/A 0 8 Chain A: 9.11 115.00 19.36 N/A 0 1744 Chain S: 11.02 60.00 34.11 N/A 226 0 Histogram: Values Number of atoms 9.11 - 19.70 1265 19.70 - 30.29 303 30.29 - 40.88 215 40.88 - 51.47 118 51.47 - 62.06 46 62.06 - 72.64 12 72.64 - 83.23 5 83.23 - 93.82 4 93.82 - 104.41 0 104.41 - 115.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.1137 r_free=0.1301 r_work=0.1137 r_free=0.1301 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1137 r_free = 0.1301 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1129 r_free = 0.1294 target_work(ml) = 3.601 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1129 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.601070 | | target function (ml) not normalized (work): 299918.721758 | | target function (ml) not normalized (free): 15806.142034 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1137 0.1129 0.1294 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1469 0.1467 0.1526 n_refl.: 87582 remove outliers: r(all,work,free)=0.1469 0.1467 0.1526 n_refl.: 87582 overall B=-0.01 to atoms: r(all,work,free)=0.1467 0.1466 0.1525 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1137 0.1129 0.1298 n_refl.: 87582 remove outliers: r(all,work,free)=0.1135 0.1127 0.1298 n_refl.: 87579 ======================== 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 0.4003 290.433 251.227 0.448 1.000 0.314 11.894-9.307 96.08 94 4 0.2388 475.164 467.188 0.869 1.002 0.252 9.237-7.194 98.18 209 7 0.2329 385.534 379.803 0.922 1.002 0.197 7.162-5.571 100.00 427 22 0.2054 295.706 286.028 0.907 1.003 0.151 5.546-4.326 100.00 867 58 0.1096 405.931 401.386 0.955 1.003 0.143 4.315-3.360 100.00 1859 96 0.0895 386.044 384.053 0.993 1.002 0.110 3.356-2.611 100.00 3867 181 0.1116 253.611 251.763 0.999 1.002 0.060 2.608-2.026 99.99 8198 413 0.0916 168.121 167.448 1.015 1.001 0.000 2.025-1.573 100.00 17313 902 0.0885 82.101 82.435 1.025 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1246 36.407 36.006 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2167 22.939 21.486 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0048 b_overall=-0.0194 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1127 r_free=0.1298 After: r_work=0.1128 r_free=0.1297 ================================== NQH flips ================================== r_work=0.1128 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=0.1128 r_free=0.1297 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1128 r_free=0.1297 | n_water=443 | time (s): 2.540 (total time: 2.540) Filter (dist) r_work=0.1129 r_free=0.1299 | n_water=442 | time (s): 46.010 (total time: 48.550) Filter (q & B) r_work=0.1129 r_free=0.1299 | n_water=441 | time (s): 3.750 (total time: 52.300) Compute maps r_work=0.1129 r_free=0.1299 | n_water=441 | time (s): 1.920 (total time: 54.220) Filter (map) r_work=0.1151 r_free=0.1299 | n_water=353 | time (s): 4.290 (total time: 58.510) Find peaks r_work=0.1151 r_free=0.1299 | n_water=353 | time (s): 0.690 (total time: 59.200) Add new water r_work=0.1203 r_free=0.1346 | n_water=499 | time (s): 3.860 (total time: 63.060) Refine new water occ: r_work=0.1147 r_free=0.1299 adp: r_work=0.1147 r_free=0.1300 occ: r_work=0.1136 r_free=0.1285 adp: r_work=0.1134 r_free=0.1286 occ: r_work=0.1127 r_free=0.1278 adp: r_work=0.1124 r_free=0.1277 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1277 r_work=0.1124 r_free=0.1277 | n_water=499 | time (s): 224.620 (total time: 287.680) Filter (q & B) r_work=0.1130 r_free=0.1281 | n_water=466 | time (s): 3.900 (total time: 291.580) Filter (dist only) r_work=0.1130 r_free=0.1282 | n_water=464 | time (s): 49.090 (total time: 340.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.739905 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.948081 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 0.1222 0.1336 0.0115 0.004 0.7 7.0 0.0 0.0 0 0.087 0.1169 0.1304 0.0136 0.004 0.8 7.7 0.0 0.0 0 0.261 0.1151 0.1293 0.0142 0.005 0.9 7.0 0.5 0.0 0 0.522 0.1142 0.1287 0.0145 0.006 1.0 7.0 0.5 0.0 0 0.783 0.1136 0.1284 0.0148 0.006 1.1 7.4 0.5 0.0 0 1.044 0.1133 0.1283 0.0150 0.007 1.1 7.7 0.5 0.0 0 1.305 0.1130 0.1282 0.0152 0.008 1.1 7.7 0.5 0.0 0 1.566 0.1130 0.1282 0.0153 0.009 1.1 7.4 0.5 0.0 0 1.827 0.1139 0.1286 0.0146 0.006 1.0 7.7 0.5 0.0 0 0.870 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1130 0.1282 0.0152 0.008 1.1 7.7 0.5 0.0 0 1.566 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 12.82 1.52 3.776 21.264 38.948 3.600 11.30 12.82 1.52 3.776 21.264 1.168 3.600 11.30 12.82 1.52 3.776 21.264 4.869 3.600 11.33 12.83 1.50 3.711 21.256 19.474 3.595 11.42 12.99 1.58 3.724 21.227 38.948 3.599 11.30 12.92 1.62 3.753 21.220 58.422 3.592 11.28 12.92 1.64 3.765 21.213 77.896 3.589 11.26 12.91 1.65 3.776 21.211 97.370 3.587 11.21 12.86 1.65 3.781 21.213 116.844 3.583 11.21 12.89 1.68 3.795 21.205 136.318 3.582 11.21 12.91 1.70 3.810 21.197 155.792 3.582 11.19 12.89 1.70 3.815 21.197 175.266 3.581 11.19 12.91 1.72 3.828 21.193 194.740 3.581 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 4.869 Accepted refinement result: 11.30 12.82 1.52 3.776 21.264 4.869 3.600 Individual atomic B min max mean iso aniso Overall: 9.11 114.99 21.24 3.30 247 1744 Protein: 9.11 114.99 17.03 3.31 0 1519 Water: 11.01 76.70 34.98 N/A 247 217 Other: 19.74 26.65 22.10 N/A 0 8 Chain A: 9.11 114.99 19.35 N/A 0 1744 Chain S: 11.01 59.99 34.56 N/A 247 0 Histogram: Values Number of atoms 9.11 - 19.69 1265 19.69 - 30.28 308 30.28 - 40.87 217 40.87 - 51.46 131 51.46 - 62.05 47 62.05 - 72.64 12 72.64 - 83.23 5 83.23 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1130 r_free=0.1282 r_work=0.1130 r_free=0.1282 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1130 r_free = 0.1282 target_work(ml) = 3.600 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1127 r_free = 0.1277 target_work(ml) = 3.598 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1127 r_free= 0.1277 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.597669 | | target function (ml) not normalized (work): 299624.641122 | | target function (ml) not normalized (free): 15778.735088 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2921 171 0.1303 0.1265 5.6354 5.5405| | 2: 3.57 - 2.84 1.00 2888 124 0.1060 0.1413 5.1357 5.2094| | 3: 2.83 - 2.48 1.00 2820 163 0.1095 0.1242 4.917 4.959| | 4: 2.47 - 2.25 1.00 2825 136 0.0898 0.0949 4.6069 4.6193| | 5: 2.25 - 2.09 1.00 2756 127 0.0866 0.0988 4.5499 4.6079| | 6: 2.09 - 1.97 1.00 2846 113 0.0850 0.0997 4.2473 4.3631| | 7: 1.97 - 1.87 1.00 2787 165 0.0889 0.1111 3.9749 4.0779| | 8: 1.87 - 1.79 1.00 2789 144 0.0927 0.1074 3.8868 3.978| | 9: 1.79 - 1.72 1.00 2745 138 0.0877 0.1220 3.6475 3.8406| | 10: 1.72 - 1.66 1.00 2831 160 0.0921 0.1203 3.5632 3.7157| | 11: 1.66 - 1.61 1.00 2712 147 0.0865 0.1028 3.4914 3.5584| | 12: 1.61 - 1.56 1.00 2773 144 0.0909 0.1129 3.3306 3.4566| | 13: 1.56 - 1.52 1.00 2745 130 0.0945 0.1046 3.3059 3.4068| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1054 3.2367 3.3196| | 15: 1.48 - 1.45 1.00 2738 128 0.0993 0.1244 3.149 3.2664| | 16: 1.45 - 1.42 1.00 2756 161 0.1054 0.1217 3.1329 3.2255| | 17: 1.42 - 1.39 1.00 2785 139 0.1138 0.1325 3.1144 3.238| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1322 3.1004 3.2357| | 19: 1.36 - 1.34 1.00 2807 134 0.1266 0.1563 3.1117 3.267| | 20: 1.34 - 1.32 1.00 2696 147 0.1367 0.1476 3.1109 3.1551| | 21: 1.32 - 1.30 1.00 2785 112 0.1468 0.1506 3.1108 3.1006| | 22: 1.29 - 1.27 1.00 2704 152 0.1558 0.1990 3.1201 3.2946| | 23: 1.27 - 1.26 1.00 2802 156 0.1647 0.1799 3.1309 3.2003| | 24: 1.26 - 1.24 1.00 2744 132 0.1709 0.1836 3.1258 3.2288| | 25: 1.24 - 1.22 1.00 2733 148 0.1883 0.2160 3.1404 3.2587| | 26: 1.22 - 1.21 1.00 2727 135 0.1910 0.1769 3.1474 3.2025| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2171 3.1708 3.1624| | 28: 1.19 - 1.18 1.00 2671 147 0.2202 0.2295 3.1647 3.173| | 29: 1.18 - 1.16 1.00 2800 134 0.2265 0.2381 3.1462 3.2274| | 30: 1.16 - 1.15 1.00 2739 148 0.2447 0.2444 3.1412 3.1658| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2921 171 0.95 8.04 1.00 0.98 5277.51| | 2: 3.57 - 2.84 2888 124 0.93 11.90 1.01 0.98 5277.51| | 3: 2.83 - 2.48 2820 163 0.90 15.82 0.99 0.98 4417.33| | 4: 2.47 - 2.25 2825 136 0.92 12.91 1.00 0.99 2199.19| | 5: 2.25 - 2.09 2756 127 0.91 15.04 1.01 0.99 2199.19| | 6: 2.09 - 1.97 2846 113 0.93 12.01 1.02 0.99 1285.58| | 7: 1.97 - 1.87 2787 165 0.95 9.28 1.02 0.98 506.40| | 8: 1.87 - 1.79 2789 144 0.93 12.56 1.00 0.98 506.40| | 9: 1.79 - 1.72 2745 138 0.94 10.03 0.98 0.98 288.75| | 10: 1.72 - 1.66 2831 160 0.94 11.18 0.98 0.98 245.16| | 11: 1.66 - 1.61 2712 147 0.93 11.81 0.98 0.98 234.82| | 12: 1.61 - 1.56 2773 144 0.95 8.91 0.99 0.98 137.29| | 13: 1.56 - 1.52 2745 130 0.95 10.42 1.02 0.98 137.29| | 14: 1.52 - 1.48 2803 134 0.94 10.78 1.02 0.98 123.17| | 15: 1.48 - 1.45 2738 128 0.95 9.91 1.02 0.99 97.32| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.99 97.32| | 17: 1.42 - 1.39 2785 139 0.95 10.89 1.01 0.99 88.63| | 18: 1.39 - 1.36 2741 179 0.94 11.51 1.01 0.99 83.60| | 19: 1.36 - 1.34 2807 134 0.94 11.88 1.00 0.99 83.60| | 20: 1.34 - 1.32 2696 147 0.94 12.13 0.98 0.97 79.81| | 21: 1.32 - 1.30 2785 112 0.94 13.14 0.98 0.97 79.54| | 22: 1.29 - 1.27 2704 152 0.93 13.67 0.98 0.97 79.98| | 23: 1.27 - 1.26 2802 156 0.92 14.88 0.97 0.95 82.19| | 24: 1.26 - 1.24 2744 132 0.92 14.93 0.96 0.95 82.19| | 25: 1.24 - 1.22 2733 148 0.91 16.40 0.96 0.94 84.17| | 26: 1.22 - 1.21 2727 135 0.90 18.17 1.02 0.94 86.36| | 27: 1.21 - 1.19 2814 148 0.89 18.81 1.02 0.94 86.36| | 28: 1.19 - 1.18 2671 147 0.88 20.41 1.01 0.93 89.88| | 29: 1.18 - 1.16 2800 134 0.88 20.53 0.99 0.93 91.20| | 30: 1.16 - 1.15 2739 148 0.86 22.07 0.98 0.93 91.20| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 79.54 max = 5277.51 mean = 827.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.35| |phase err.(test): min = 0.00 max = 89.11 mean = 13.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1134 0.1127 0.1277 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1464 0.1463 0.1507 n_refl.: 87579 remove outliers: r(all,work,free)=0.1464 0.1463 0.1507 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1463 0.1463 0.1506 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1134 0.1127 0.1276 n_refl.: 87579 remove outliers: r(all,work,free)=0.1131 0.1124 0.1276 n_refl.: 87572 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 86.46 78 5 0.3740 289.999 248.638 0.439 1.000 0.280 11.894-9.307 93.14 91 4 0.2253 476.513 463.078 0.862 1.002 0.260 9.237-7.194 97.73 208 7 0.2344 386.615 379.949 0.924 1.002 0.160 7.162-5.571 100.00 427 22 0.2026 295.706 286.712 0.915 1.003 0.150 5.546-4.326 100.00 867 58 0.1088 405.931 401.756 0.963 1.003 0.120 4.315-3.360 100.00 1859 96 0.0910 386.044 384.097 1.004 1.003 0.110 3.356-2.611 100.00 3867 181 0.1105 253.611 251.734 1.009 1.002 0.029 2.608-2.026 99.99 8198 413 0.0907 168.121 167.547 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0890 82.101 82.470 1.035 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.407 36.015 1.029 0.996 0.000 1.221-1.150 99.97 13689 708 0.2170 22.939 21.485 0.991 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0129 ================= 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 0.1951 0.081 5.237 8.8 119.3 19.9 258 0.000 1_bss: 0.1640 0.1774 0.081 5.237 9.1 119.5 20.1 258 0.000 1_settarget: 0.1640 0.1774 0.081 5.237 9.1 119.5 20.1 258 0.000 1_nqh: 0.1643 0.1772 0.081 5.237 9.1 119.5 20.1 258 0.006 1_weight: 0.1643 0.1772 0.081 5.237 9.1 119.5 20.1 258 0.006 1_xyzrec: 0.1231 0.1471 0.006 0.870 9.1 119.5 20.1 258 0.131 1_adp: 0.1238 0.1468 0.006 0.870 9.1 119.5 20.1 258 0.131 1_regHadp: 0.1239 0.1471 0.006 0.870 9.1 119.5 20.1 258 0.131 1_occ: 0.1232 0.1464 0.006 0.870 9.1 119.5 20.1 258 0.131 2_bss: 0.1228 0.1454 0.006 0.870 9.1 119.5 20.1 258 0.131 2_settarget: 0.1228 0.1454 0.006 0.870 9.1 119.5 20.1 258 0.131 2_updatecdl: 0.1228 0.1454 0.006 0.873 9.1 119.5 20.1 258 0.131 2_nqh: 0.1227 0.1452 0.006 0.873 9.1 119.5 20.1 258 0.128 2_sol: 0.1207 0.1390 0.006 0.873 9.1 115.0 22.1 408 n/a 2_weight: 0.1207 0.1390 0.006 0.873 9.1 115.0 22.1 408 n/a 2_xyzrec: 0.1193 0.1412 0.006 0.862 9.1 115.0 22.1 408 n/a 2_adp: 0.1193 0.1412 0.006 0.862 9.1 115.0 22.1 408 n/a 2_regHadp: 0.1193 0.1412 0.006 0.862 9.1 115.0 22.1 408 n/a 2_occ: 0.1192 0.1409 0.006 0.862 9.1 115.0 22.1 408 n/a 3_bss: 0.1188 0.1404 0.006 0.862 9.1 115.0 22.1 408 n/a 3_settarget: 0.1188 0.1404 0.006 0.862 9.1 115.0 22.1 408 n/a 3_updatecdl: 0.1188 0.1404 0.006 0.864 9.1 115.0 22.1 408 n/a 3_nqh: 0.1188 0.1404 0.006 0.864 9.1 115.0 22.1 408 n/a 3_sol: 0.1213 0.1421 0.006 0.864 9.1 115.0 21.2 431 n/a 3_weight: 0.1213 0.1421 0.006 0.864 9.1 115.0 21.2 431 n/a 3_xyzrec: 0.1164 0.1329 0.007 1.060 9.1 115.0 21.2 431 n/a 3_adp: 0.1164 0.1329 0.007 1.060 9.1 115.0 21.2 431 n/a 3_regHadp: 0.1164 0.1329 0.007 1.060 9.1 115.0 21.2 431 n/a 3_occ: 0.1155 0.1323 0.007 1.060 9.1 115.0 21.2 431 n/a 4_bss: 0.1147 0.1310 0.007 1.060 9.1 115.0 21.2 431 n/a 4_settarget: 0.1147 0.1310 0.007 1.060 9.1 115.0 21.2 431 n/a 4_updatecdl: 0.1147 0.1310 0.007 1.060 9.1 115.0 21.2 431 n/a 4_nqh: 0.1147 0.1310 0.007 1.060 9.1 115.0 21.2 431 n/a 4_sol: 0.1145 0.1300 0.007 1.060 9.1 115.0 21.0 443 n/a 4_weight: 0.1145 0.1300 0.007 1.060 9.1 115.0 21.0 443 n/a 4_xyzrec: 0.1137 0.1301 0.009 1.128 9.1 115.0 21.0 443 n/a 4_adp: 0.1137 0.1301 0.009 1.128 9.1 115.0 21.0 443 n/a 4_regHadp: 0.1137 0.1301 0.009 1.128 9.1 115.0 21.0 443 n/a 4_occ: 0.1129 0.1294 0.009 1.128 9.1 115.0 21.0 443 n/a 5_bss: 0.1127 0.1298 0.009 1.128 9.1 115.0 21.0 443 n/a 5_settarget: 0.1127 0.1298 0.009 1.128 9.1 115.0 21.0 443 n/a 5_updatecdl: 0.1127 0.1298 0.009 1.130 9.1 115.0 21.0 443 n/a 5_setrh: 0.1128 0.1297 0.009 1.130 9.1 115.0 21.0 443 n/a 5_nqh: 0.1128 0.1297 0.009 1.130 9.1 115.0 21.0 443 n/a 5_sol: 0.1130 0.1282 0.009 1.130 9.1 115.0 21.2 464 n/a 5_weight: 0.1130 0.1282 0.009 1.130 9.1 115.0 21.2 464 n/a 5_xyzrec: 0.1130 0.1282 0.008 1.129 9.1 115.0 21.2 464 n/a 5_adp: 0.1130 0.1282 0.008 1.129 9.1 115.0 21.2 464 n/a 5_regHadp: 0.1130 0.1282 0.008 1.129 9.1 115.0 21.2 464 n/a 5_occ: 0.1127 0.1277 0.008 1.129 9.1 115.0 21.2 464 n/a end: 0.1124 0.1276 0.008 1.129 9.1 115.0 21.2 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6727304_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6727304_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3700 Refinement macro-cycles (run) : 13599.9000 Write final files (write_after_run_outputs) : 92.6000 Total : 13695.8700 Total CPU time: 3.81 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:10:33 PST -0800 (1735366233.31 s) Start R-work = 0.1640, R-free = 0.1774 Final R-work = 0.1124, R-free = 0.1276 =============================================================================== Job complete usr+sys time: 13875.02 seconds wall clock time: 254 minutes 43.97 seconds (15283.97 seconds total)