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_4735076.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4735076.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } 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: 1.36, per 1000 atoms: 0.40 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: 0.40 Conformation dependent library (CDL) restraints added in 211.0 milliseconds Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 390 0.89 - 1.15: 1214 1.15 - 1.40: 614 1.40 - 1.66: 889 1.66 - 1.92: 46 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.456 1.690 -0.233 1.23e-02 6.61e+03 3.60e+02 bond pdb=" C GLN A 180 " pdb=" O GLN A 180 " ideal model delta sigma weight residual 1.236 0.997 0.239 1.29e-02 6.01e+03 3.42e+02 bond pdb=" C GLY A 78 " pdb=" O GLY A 78 " ideal model delta sigma weight residual 1.234 1.455 -0.222 1.21e-02 6.83e+03 3.36e+02 bond pdb=" C LYS A 12 " pdb=" O LYS A 12 " ideal model delta sigma weight residual 1.234 1.016 0.219 1.20e-02 6.94e+03 3.33e+02 bond pdb=" C GLY A 157 " pdb=" O GLY A 157 " ideal model delta sigma weight residual 1.235 1.479 -0.244 1.35e-02 5.49e+03 3.26e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.47: 3088 4.47 - 8.94: 1853 8.94 - 13.41: 670 13.41 - 17.88: 152 17.88 - 22.35: 14 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.83 109.48 11.35 5.90e-01 2.87e+00 3.70e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 130.43 -10.01 6.40e-01 2.44e+00 2.45e+02 angle pdb=" CA GLU A 116 " pdb=" C GLU A 116 " pdb=" O GLU A 116 " ideal model delta sigma weight residual 120.98 104.33 16.65 1.24e+00 6.50e-01 1.80e+02 angle pdb=" O ALEU A 153 " pdb=" C ALEU A 153 " pdb=" N THR A 154 " ideal model delta sigma weight residual 123.12 140.58 -17.46 1.32e+00 5.74e-01 1.75e+02 angle pdb=" CG HIS A 115 " pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 107.20 94.55 12.65 1.00e+00 1.00e+00 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 942 16.87 - 33.74: 114 33.74 - 50.61: 35 50.61 - 67.47: 17 67.47 - 84.34: 3 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: 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 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " ideal model delta harmonic sigma weight residual 180.00 -153.25 -26.75 0 5.00e+00 4.00e-02 2.86e+01 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 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.198: 89 0.198 - 0.393: 77 0.393 - 0.588: 43 0.588 - 0.783: 25 0.783 - 0.978: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA ALA A 183 " pdb=" N ALA A 183 " pdb=" C ALA A 183 " pdb=" CB ALA A 183 " both_signs ideal model delta sigma weight residual False 2.48 1.52 0.97 2.00e-01 2.50e+01 2.34e+01 chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.018 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG PHE A 119 " -0.170 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.102 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.066 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.083 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.013 2.00e-02 2.50e+03 6.68e-02 1.34e+02 pdb=" CG TYR A 139 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.080 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.071 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.065 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.099 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.020 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.108 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.035 9.50e-02 1.11e+02 7.54e-02 1.25e+02 pdb=" NE ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.022 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.072 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.096 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.154 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.053 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.28: 759 2.28 - 2.86: 7804 2.86 - 3.44: 10629 3.44 - 4.02: 15316 4.02 - 4.60: 22095 Nonbonded interactions: 56603 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.695 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.721 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.781 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.801 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.835 1.850 ... (remaining 56598 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_4735076_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= 0.2608 r_free= 0.1920 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790287 | | target function (ml) not normalized (work): 232447.646542 | | target function (ml) not normalized (free): 11735.341920 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3042 0.2068 7.0128 4.9413| | 2: 3.57 - 2.84 1.00 2876 122 0.2423 0.1854 4.3531 4.341| | 3: 2.84 - 2.48 1.00 2833 165 0.2365 0.1630 4.1352 4.1709| | 4: 2.47 - 2.25 1.00 2825 136 0.2334 0.1412 3.8359 3.8346| | 5: 2.25 - 2.09 1.00 2756 127 0.2490 0.1650 3.8002 3.8362| | 6: 2.09 - 1.97 1.00 2846 113 0.2521 0.1749 3.4681 3.5208| | 7: 1.97 - 1.87 1.00 2787 165 0.2487 0.1767 3.1149 3.1669| | 8: 1.87 - 1.79 1.00 2789 144 0.2470 0.1826 3.052 3.0976| | 9: 1.79 - 1.72 1.00 2745 138 0.2427 0.1947 2.903 2.9901| | 10: 1.72 - 1.66 1.00 2789 158 0.2392 0.1895 2.794 2.8488| | 11: 1.66 - 1.61 1.00 2740 147 0.2479 0.1821 2.7357 2.7609| | 12: 1.61 - 1.56 1.00 2787 146 0.2611 0.1851 2.6384 2.6146| | 13: 1.56 - 1.52 1.00 2745 130 0.2626 0.1905 2.5588 2.5998| | 14: 1.52 - 1.48 1.00 2803 134 0.2574 0.1790 2.5179 2.4982| | 15: 1.48 - 1.45 1.00 2738 128 0.2578 0.2180 2.4305 2.5064| | 16: 1.45 - 1.42 1.00 2756 161 0.2675 0.2169 2.4179 2.438| | 17: 1.42 - 1.39 1.00 2785 139 0.2691 0.2143 2.3516 2.3693| | 18: 1.39 - 1.36 1.00 2741 179 0.2597 0.2291 2.2686 2.3646| | 19: 1.36 - 1.34 1.00 2807 134 0.2620 0.2234 2.2443 2.2483| | 20: 1.34 - 1.32 1.00 2696 147 0.2689 0.1959 2.1932 2.0844| | 21: 1.32 - 1.30 1.00 2785 112 0.2668 0.2273 2.1568 2.1266| | 22: 1.29 - 1.27 1.00 2704 152 0.2759 0.2191 2.141 2.0797| | 23: 1.27 - 1.26 1.00 2802 156 0.2811 0.2367 2.0987 2.1628| | 24: 1.26 - 1.24 1.00 2744 132 0.2832 0.2427 2.0825 2.1294| | 25: 1.24 - 1.22 1.00 2734 148 0.2869 0.2486 2.0489 2.0579| | 26: 1.22 - 1.21 1.00 2727 135 0.2852 0.2300 2.0208 2.0622| | 27: 1.21 - 1.19 1.00 2814 148 0.2965 0.2584 2.0073 1.9852| | 28: 1.19 - 1.18 1.00 2671 147 0.2952 0.2933 1.9805 2.006| | 29: 1.18 - 1.16 1.00 2800 134 0.3006 0.2677 1.9649 2.0113| | 30: 1.16 - 1.15 1.00 2740 148 0.3070 0.2803 1.9277 1.9378| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.02 0.76 0.23 1503.85| | 2: 3.57 - 2.84 2876 122 0.80 26.37 1.27 0.23 1503.85| | 3: 2.84 - 2.48 2833 165 0.74 32.12 1.24 0.23 1245.98| | 4: 2.47 - 2.25 2825 136 0.81 25.62 1.26 0.25 576.77| | 5: 2.25 - 2.09 2756 127 0.77 29.46 1.28 0.25 576.77| | 6: 2.09 - 1.97 2846 113 0.83 22.57 1.29 0.25 313.29| | 7: 1.97 - 1.87 2787 165 0.90 16.29 1.28 0.26 88.58| | 8: 1.87 - 1.79 2789 144 0.86 20.80 1.25 0.26 88.58| | 9: 1.79 - 1.72 2745 138 0.88 18.33 1.23 0.25 54.20| | 10: 1.72 - 1.66 2789 158 0.87 19.89 1.22 0.25 47.31| | 11: 1.66 - 1.61 2740 147 0.86 20.96 1.24 0.25 45.62| | 12: 1.61 - 1.56 2787 146 0.89 18.33 1.25 0.25 28.47| | 13: 1.56 - 1.52 2745 130 0.87 20.19 1.25 0.25 28.47| | 14: 1.52 - 1.48 2803 134 0.87 20.33 1.23 0.25 25.51| | 15: 1.48 - 1.45 2738 128 0.87 19.86 1.23 0.25 20.09| | 16: 1.45 - 1.42 2756 161 0.86 21.00 1.23 0.25 20.09| | 17: 1.42 - 1.39 2785 139 0.87 20.18 1.23 0.25 16.90| | 18: 1.39 - 1.36 2741 179 0.87 20.36 1.21 0.25 15.06| | 19: 1.36 - 1.34 2807 134 0.86 21.33 1.21 0.25 15.06| | 20: 1.34 - 1.32 2696 147 0.88 19.84 1.21 0.25 11.96| | 21: 1.32 - 1.30 2785 112 0.87 20.60 1.20 0.25 11.74| | 22: 1.29 - 1.27 2704 152 0.87 21.03 1.21 0.25 11.47| | 23: 1.27 - 1.26 2802 156 0.87 20.84 1.22 0.24 10.11| | 24: 1.26 - 1.24 2744 132 0.86 21.61 1.20 0.24 10.11| | 25: 1.24 - 1.22 2734 148 0.85 22.55 1.20 0.24 9.69| | 26: 1.22 - 1.21 2727 135 0.85 22.82 1.19 0.24 9.22| | 27: 1.21 - 1.19 2814 148 0.84 23.63 1.20 0.24 9.22| | 28: 1.19 - 1.18 2671 147 0.83 24.87 1.17 0.23 8.91| | 29: 1.18 - 1.16 2800 134 0.83 25.49 1.16 0.22 8.80| | 30: 1.16 - 1.15 2740 148 0.81 27.02 1.15 0.22 8.80| |alpha: min = 0.22 max = 0.26 mean = 0.24| |beta: min = 8.80 max = 1503.85 mean = 216.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 90.00 mean = 22.12| |phase err.(test): min = 0.00 max = 88.87 mean = 22.11| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.244 1557 Z= 5.545 Angle : 5.417 18.814 2118 Z= 3.858 Chirality : 0.388 0.978 243 Planarity : 0.031 0.133 284 Dihedral : 14.032 84.343 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % 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: -1.98 (0.49), residues: 224 helix: -2.23 (0.41), residues: 109 sheet: 0.06 (0.95), residues: 28 loop : -0.17 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.066 0.020 ARG A 48 TYR 0.077 0.042 TYR A 139 PHE 0.142 0.046 PHE A 119 HIS 0.057 0.028 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= 0.2608 r_free= 0.1920 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.790287 | | target function (ml) not normalized (work): 232447.646542 | | target function (ml) not normalized (free): 11735.341920 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2566 0.2609 0.1921 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2566 0.2609 0.1921 n_refl.: 87602 remove outliers: r(all,work,free)=0.1979 0.1984 0.1921 n_refl.: 87594 overall B=0.22 to atoms: r(all,work,free)=0.2005 0.2011 0.1938 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1643 0.1637 0.1754 n_refl.: 87594 remove outliers: r(all,work,free)=0.1643 0.1637 0.1754 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 0.3883 386.248 356.542 0.721 0.931 0.402 11.894-9.307 99.02 97 4 0.1829 613.536 594.060 0.994 0.932 0.390 9.237-7.194 100.00 213 7 0.2154 501.797 490.488 1.032 0.932 0.359 7.162-5.571 100.00 427 22 0.2190 376.571 365.241 1.012 0.932 0.340 5.546-4.326 100.00 867 58 0.1304 516.939 510.771 1.035 0.932 0.214 4.315-3.360 100.00 1859 96 0.1152 491.612 488.028 1.083 0.932 0.189 3.356-2.611 100.00 3867 181 0.1431 322.964 319.384 1.069 0.931 0.109 2.608-2.026 99.99 8198 413 0.1347 214.096 212.154 1.083 0.931 0.000 2.025-1.573 100.00 17313 902 0.1628 104.553 103.826 1.085 0.930 0.000 1.573-1.221 100.00 36679 1900 0.2084 46.363 45.049 1.077 0.928 0.000 1.221-1.150 99.97 13689 708 0.2596 29.212 26.972 1.046 0.927 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0501 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1637 r_free=0.1754 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1644 r_free=0.1766 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.404084 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2005.753629 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 0.1622 0.1752 0.0130 0.002 0.5 4.5 0.0 0.0 0 0.125 0.1564 0.1705 0.0141 0.002 0.5 4.2 0.0 0.0 0 0.250 0.1419 0.1586 0.0167 0.001 0.5 3.8 0.0 0.0 0 0.500 0.1390 0.1569 0.0179 0.002 0.5 3.8 0.0 0.0 0 0.750 0.1347 0.1539 0.0192 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1361 0.1550 0.0189 0.002 0.5 3.2 0.0 0.0 0 1.000 0.1281 0.1497 0.0216 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1266 0.1493 0.0227 0.003 0.7 2.6 0.5 0.0 0 3.000 0.1261 0.1493 0.0233 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1250 0.1489 0.0239 0.004 0.7 2.9 0.5 0.0 0 5.000 0.1238 0.1477 0.0239 0.005 0.8 3.2 0.5 0.0 0 6.000 0.1234 0.1474 0.0239 0.005 0.8 3.2 0.5 0.0 0 7.000 0.1233 0.1478 0.0245 0.005 0.8 3.5 0.5 0.0 0 8.000 0.1230 0.1473 0.0243 0.006 0.9 3.8 0.5 0.0 0 9.000 0.1225 0.1469 0.0244 0.006 0.9 2.9 0.5 0.0 0 10.000 0.1224 0.1471 0.0247 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1227 0.1475 0.0248 0.007 0.9 3.5 0.5 0.0 0 12.000 0.1220 0.1469 0.0249 0.008 1.0 3.2 0.5 0.6 0 13.702 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1220 0.1469 0.0249 0.008 1.0 3.2 0.5 0.6 0 13.702 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.20 14.69 2.49 3.012 19.077 2005.754 0.017 12.20 14.68 2.49 2.994 19.077 60.173 0.017 12.27 14.65 2.38 2.668 19.075 250.719 0.017 12.65 15.31 2.66 2.836 19.297 1002.877 0.016 12.47 15.41 2.93 3.096 19.485 2005.754 0.016 12.43 15.52 3.09 3.398 19.688 3008.630 0.015 12.25 15.34 3.09 3.284 19.608 4011.507 0.015 12.19 15.32 3.12 3.197 19.531 5014.384 0.015 12.14 15.33 3.19 3.221 19.560 6017.261 0.015 12.21 15.45 3.24 3.376 19.636 7020.138 0.015 12.15 15.38 3.24 3.326 19.600 8023.015 0.015 12.13 15.44 3.30 3.454 19.661 9025.891 0.015 12.13 15.50 3.37 3.483 19.652 10028.768 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: 250.719 Accepted refinement result: 12.27 14.65 2.38 2.668 19.075 250.719 0.017 Individual atomic B min max mean iso aniso Overall: 9.08 119.46 20.10 3.31 0 1785 Protein: 9.08 115.02 17.01 3.32 0 1519 Water: 11.49 119.46 38.24 N/A 0 258 Other: 19.71 26.61 22.07 N/A 0 8 Chain A: 9.08 119.46 20.10 N/A 0 1785 Histogram: Values Number of atoms 9.08 - 20.12 1272 20.12 - 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 - 86.35 7 86.35 - 97.39 4 97.39 - 108.42 1 108.42 - 119.46 2 =========================== Idealize ADP of riding H ========================== r_work=0.1227 r_free=0.1465 r_work=0.1228 r_free=0.1467 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1228 r_free = 0.1467 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1223 r_free = 0.1468 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 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= 0.1223 r_free= 0.1468 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.016836 | | target function (ls_wunit_k1) not normalized (work): 1402.352469 | | target function (ls_wunit_k1) not normalized (free): 110.308063 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1235 0.1223 0.1468 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1676 0.1677 0.1700 n_refl.: 87593 remove outliers: r(all,work,free)=0.1676 0.1677 0.1700 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1681 0.1682 0.1703 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1233 0.1222 0.1458 n_refl.: 87593 remove outliers: r(all,work,free)=0.1233 0.1221 0.1458 n_refl.: 87592 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3546 300.201 279.859 0.652 1.002 0.383 11.894-9.307 99.02 97 4 0.1645 482.208 470.183 0.920 1.002 0.355 9.237-7.194 100.00 213 7 0.1873 394.387 389.104 0.965 1.003 0.340 7.162-5.571 100.00 427 22 0.1823 295.966 290.161 0.934 1.003 0.268 5.546-4.326 100.00 867 58 0.1016 406.288 402.872 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0870 386.382 385.240 1.009 1.002 0.180 3.356-2.611 100.00 3867 181 0.1168 253.833 252.679 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1016 168.268 167.574 1.019 1.001 0.000 2.025-1.573 100.00 17313 902 0.1103 82.173 82.370 1.027 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1442 36.439 35.939 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2248 22.959 21.449 0.982 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0425 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1221 r_free=0.1458 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 180 GLN Total number of N/Q/H flips: 2 r_work=0.1221 r_free=0.1456 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1221 r_free=0.1456 | n_water=258 | time (s): 2.000 (total time: 2.000) Filter (dist) r_work=0.1230 r_free=0.1456 | n_water=250 | time (s): 22.460 (total time: 24.460) Filter (q & B) r_work=0.1233 r_free=0.1456 | n_water=247 | time (s): 2.550 (total time: 27.010) Compute maps r_work=0.1233 r_free=0.1456 | n_water=247 | time (s): 1.530 (total time: 28.540) Filter (map) r_work=0.1255 r_free=0.1463 | n_water=221 | time (s): 2.920 (total time: 31.460) Find peaks r_work=0.1255 r_free=0.1463 | n_water=221 | time (s): 0.490 (total time: 31.950) Add new water r_work=0.1405 r_free=0.1620 | n_water=428 | time (s): 2.460 (total time: 34.410) Refine new water occ: r_work=0.1308 r_free=0.1490 adp: r_work=0.1224 r_free=0.1434 occ: r_work=0.1236 r_free=0.1423 adp: r_work=0.1203 r_free=0.1409 occ: r_work=0.1205 r_free=0.1401 adp: r_work=0.1197 r_free=0.1399 ADP+occupancy (water only), MIN, final r_work=0.1197 r_free=0.1399 r_work=0.1197 r_free=0.1399 | n_water=428 | time (s): 60.960 (total time: 95.370) Filter (q & B) r_work=0.1199 r_free=0.1402 | n_water=415 | time (s): 3.400 (total time: 98.770) Filter (dist only) r_work=0.1199 r_free=0.1401 | n_water=414 | time (s): 35.670 (total time: 134.440) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 27.685901 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1485.121833 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 0.1657 0.1769 0.0111 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1511 0.1641 0.0130 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1403 0.1554 0.0151 0.002 0.5 6.1 0.0 0.0 0 0.500 0.1354 0.1515 0.0161 0.002 0.5 5.4 0.0 0.0 0 0.750 0.1308 0.1481 0.0173 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1324 0.1496 0.0173 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1260 0.1455 0.0195 0.002 0.5 5.4 0.5 0.0 0 2.000 0.1231 0.1438 0.0207 0.003 0.6 5.1 0.5 0.0 0 3.000 0.1218 0.1433 0.0216 0.003 0.7 4.8 0.5 0.0 0 4.000 0.1212 0.1428 0.0216 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1208 0.1427 0.0219 0.005 0.7 4.5 0.5 0.0 0 6.000 0.1202 0.1419 0.0217 0.005 0.8 4.5 0.5 0.0 0 7.000 0.1200 0.1430 0.0229 0.005 0.8 5.4 0.5 0.0 0 8.000 0.1196 0.1417 0.0221 0.006 0.8 5.1 0.5 0.0 0 9.000 0.1195 0.1422 0.0227 0.006 0.9 4.5 0.5 0.0 0 10.000 0.1193 0.1426 0.0232 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1190 0.1423 0.0232 0.007 0.9 5.1 0.5 0.0 0 12.000 0.1188 0.1420 0.0233 0.008 0.9 5.4 0.5 0.6 0 13.843 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1196 0.1417 0.0221 0.006 0.8 5.1 0.5 0.0 0 9.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.96 14.17 2.21 3.777 21.741 1485.122 0.016 11.96 14.17 2.21 3.777 21.741 44.554 0.016 11.96 14.17 2.21 3.777 21.741 185.640 0.016 12.13 14.55 2.41 3.633 21.739 742.561 0.016 12.18 14.91 2.73 3.437 21.995 1485.122 0.015 12.05 14.88 2.82 3.440 22.011 2227.683 0.015 11.96 14.82 2.86 3.459 22.122 2970.244 0.014 11.94 14.86 2.92 3.485 22.147 3712.805 0.014 11.88 14.83 2.95 3.502 22.157 4455.365 0.014 11.82 14.76 2.94 3.513 22.124 5197.926 0.014 11.80 14.79 3.00 3.536 22.138 5940.487 0.014 11.75 14.82 3.07 3.561 22.178 6683.048 0.014 11.74 14.81 3.07 3.573 22.170 7425.609 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: 44.554 Accepted refinement result: 11.96 14.17 2.21 3.777 21.741 44.554 0.016 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 22.11 3.31 193 1748 Protein: 9.11 115.05 17.04 3.32 0 1519 Water: 11.52 76.71 40.72 N/A 193 221 Other: 19.74 26.64 22.09 N/A 0 8 Chain A: 9.11 115.05 19.38 N/A 0 1748 Chain S: 15.67 60.00 46.84 N/A 193 0 Histogram: Values Number of atoms 9.11 - 19.70 1258 19.70 - 30.30 248 30.30 - 40.89 166 40.89 - 51.48 123 51.48 - 62.08 123 62.08 - 72.67 12 72.67 - 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=0.1196 r_free=0.1417 r_work=0.1196 r_free=0.1417 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1417 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 = 0.1415 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1192 r_free= 0.1415 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015194 | | target function (ls_wunit_k1) not normalized (work): 1265.607718 | | target function (ls_wunit_k1) not normalized (free): 102.400567 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1203 0.1192 0.1415 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1593 0.1592 0.1653 n_refl.: 87592 remove outliers: r(all,work,free)=0.1593 0.1592 0.1653 n_refl.: 87592 overall B=0.00 to atoms: r(all,work,free)=0.1594 0.1592 0.1653 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1200 0.1189 0.1415 n_refl.: 87592 remove outliers: r(all,work,free)=0.1199 0.1188 0.1415 n_refl.: 87589 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 92.71 84 5 0.3352 296.924 274.242 0.634 0.937 0.350 11.894-9.307 99.02 97 4 0.1598 482.208 476.666 0.982 0.938 0.333 9.237-7.194 100.00 213 7 0.1710 394.387 396.157 1.054 0.938 0.280 7.162-5.571 100.00 427 22 0.1666 295.966 290.349 0.995 0.938 0.227 5.546-4.326 100.00 867 58 0.0904 406.288 402.891 1.023 0.938 0.197 4.315-3.360 100.00 1859 96 0.0800 386.382 385.381 1.073 0.939 0.180 3.356-2.611 100.00 3867 181 0.1095 253.833 252.903 1.078 0.940 0.110 2.608-2.026 99.99 8198 413 0.1002 168.268 167.760 1.086 0.941 0.000 2.025-1.573 100.00 17313 902 0.1100 82.173 82.417 1.093 0.943 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.439 35.977 1.080 0.946 0.000 1.221-1.150 99.97 13689 708 0.2254 22.959 21.480 1.036 0.949 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=0.0066 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1415 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1188 r_free=0.1415 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1415 | n_water=414 | time (s): 1.790 (total time: 1.790) Filter (dist) r_work=0.1188 r_free=0.1415 | n_water=413 | time (s): 36.520 (total time: 38.310) Filter (q & B) r_work=0.1188 r_free=0.1415 | n_water=413 | time (s): 0.970 (total time: 39.280) Compute maps r_work=0.1188 r_free=0.1415 | n_water=413 | time (s): 1.650 (total time: 40.930) Filter (map) r_work=0.1231 r_free=0.1402 | n_water=285 | time (s): 2.580 (total time: 43.510) Find peaks r_work=0.1231 r_free=0.1402 | n_water=285 | time (s): 0.450 (total time: 43.960) Add new water r_work=0.1340 r_free=0.1520 | n_water=462 | time (s): 2.710 (total time: 46.670) Refine new water occ: r_work=0.1245 r_free=0.1436 adp: r_work=0.1246 r_free=0.1437 occ: r_work=0.1223 r_free=0.1413 adp: r_work=0.1222 r_free=0.1412 occ: r_work=0.1206 r_free=0.1398 adp: r_work=0.1201 r_free=0.1394 ADP+occupancy (water only), MIN, final r_work=0.1201 r_free=0.1394 r_work=0.1201 r_free=0.1394 | n_water=462 | time (s): 214.780 (total time: 261.450) Filter (q & B) r_work=0.1206 r_free=0.1397 | n_water=435 | time (s): 3.240 (total time: 264.690) Filter (dist only) r_work=0.1206 r_free=0.1398 | n_water=433 | time (s): 36.410 (total time: 301.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.768555 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.278968 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 0.1231 0.1360 0.0129 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1188 0.1326 0.0138 0.003 0.7 3.8 0.5 0.0 0 0.265 0.1172 0.1320 0.0148 0.004 0.8 3.2 0.5 0.0 0 0.531 0.1165 0.1315 0.0150 0.005 0.9 3.5 0.5 0.0 0 0.796 0.1160 0.1312 0.0152 0.006 1.0 3.8 0.5 0.0 0 1.061 0.1158 0.1311 0.0153 0.007 1.0 3.8 0.5 0.0 0 1.326 0.1156 0.1309 0.0154 0.007 1.1 3.8 0.5 0.0 0 1.592 0.1153 0.1308 0.0155 0.008 1.1 3.8 0.5 0.0 0 1.857 0.1163 0.1314 0.0150 0.005 0.9 3.5 0.5 0.0 0 0.884 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1153 0.1308 0.0155 0.008 1.1 3.8 0.5 0.0 0 1.857 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.53 13.08 1.55 3.780 21.236 43.279 3.616 11.53 13.08 1.55 3.780 21.236 1.298 3.616 11.53 13.08 1.55 3.780 21.236 5.410 3.616 11.60 13.18 1.58 3.709 21.224 21.639 3.612 11.60 13.25 1.65 3.734 21.200 43.279 3.612 11.57 13.29 1.72 3.748 21.180 64.918 3.608 11.49 13.23 1.74 3.766 21.180 86.558 3.603 11.48 13.24 1.76 3.774 21.168 108.197 3.601 11.44 13.20 1.76 3.786 21.167 129.837 3.598 11.45 13.24 1.78 3.803 21.145 151.476 3.598 11.43 13.22 1.79 3.812 21.144 173.116 3.596 11.41 13.21 1.80 3.819 21.146 194.755 3.595 11.41 13.20 1.79 3.828 21.140 216.395 3.595 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.298 Accepted refinement result: 11.53 13.08 1.55 3.780 21.236 1.298 3.616 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 21.18 3.31 216 1744 Protein: 9.11 115.05 17.04 3.32 0 1519 Water: 11.52 76.71 35.69 N/A 216 217 Other: 19.74 26.64 22.10 N/A 0 8 Chain A: 9.11 115.05 19.32 N/A 0 1744 Chain S: 15.67 60.00 36.23 N/A 216 0 Histogram: Values Number of atoms 9.11 - 19.71 1261 19.71 - 30.30 290 30.30 - 40.89 209 40.89 - 51.49 119 51.49 - 62.08 58 62.08 - 72.68 12 72.68 - 83.27 5 83.27 - 93.86 4 93.86 - 104.46 0 104.46 - 115.05 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1308 r_work=0.1153 r_free=0.1308 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1308 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1303 target_work(ml) = 3.611 | | 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.=87589 (all), 4.90 % free)------------| | | | r_work= 0.1146 r_free= 0.1303 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.610521 | | target function (ml) not normalized (work): 300731.147126 | | target function (ml) not normalized (free): 15845.279363 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1153 0.1146 0.1303 n_refl.: 87589 re-set all scales: r(all,work,free)=0.1492 0.1491 0.1534 n_refl.: 87589 remove outliers: r(all,work,free)=0.1492 0.1491 0.1534 n_refl.: 87589 overall B=-0.01 to atoms: r(all,work,free)=0.1491 0.1490 0.1534 n_refl.: 87589 bulk-solvent and scaling: r(all,work,free)=0.1149 0.1142 0.1294 n_refl.: 87589 remove outliers: r(all,work,free)=0.1147 0.1140 0.1294 n_refl.: 87584 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 90.62 82 5 0.3756 297.218 265.543 0.508 1.001 0.340 11.894-9.307 99.02 97 4 0.2327 482.208 468.416 0.880 1.002 0.274 9.237-7.194 98.64 210 7 0.2271 387.899 388.265 0.958 1.003 0.220 7.162-5.571 100.00 427 22 0.2091 295.966 285.609 0.917 1.003 0.190 5.546-4.326 100.00 867 58 0.1095 406.288 401.829 0.963 1.003 0.165 4.315-3.360 100.00 1859 96 0.0927 386.382 384.174 1.005 1.002 0.160 3.356-2.611 100.00 3867 181 0.1140 253.833 251.790 1.008 1.002 0.038 2.608-2.026 99.99 8198 413 0.0935 168.268 167.497 1.024 1.001 0.000 2.025-1.573 100.00 17313 902 0.0894 82.173 82.470 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.439 36.026 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2163 22.959 21.507 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=-0.0156 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1140 r_free=0.1294 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=0.1140 r_free=0.1294 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1294 | n_water=433 | time (s): 2.390 (total time: 2.390) Filter (dist) r_work=0.1140 r_free=0.1295 | n_water=432 | time (s): 43.990 (total time: 46.380) Filter (q & B) r_work=0.1140 r_free=0.1295 | n_water=431 | time (s): 3.870 (total time: 50.250) Compute maps r_work=0.1140 r_free=0.1295 | n_water=431 | time (s): 1.860 (total time: 52.110) Filter (map) r_work=0.1172 r_free=0.1317 | n_water=333 | time (s): 3.800 (total time: 55.910) Find peaks r_work=0.1172 r_free=0.1317 | n_water=333 | time (s): 0.680 (total time: 56.590) Add new water r_work=0.1245 r_free=0.1405 | n_water=494 | time (s): 3.840 (total time: 60.430) Refine new water occ: r_work=0.1168 r_free=0.1311 adp: r_work=0.1168 r_free=0.1313 occ: r_work=0.1151 r_free=0.1292 adp: r_work=0.1151 r_free=0.1293 occ: r_work=0.1139 r_free=0.1281 adp: r_work=0.1135 r_free=0.1278 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1278 r_work=0.1135 r_free=0.1278 | n_water=494 | time (s): 290.610 (total time: 351.040) Filter (q & B) r_work=0.1142 r_free=0.1283 | n_water=457 | time (s): 3.950 (total time: 354.990) Filter (dist only) r_work=0.1142 r_free=0.1282 | n_water=456 | time (s): 45.640 (total time: 400.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.701559 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 43.538813 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 0.1328 0.0115 0.002 0.6 4.5 0.5 0.0 0 0.085 0.1173 0.1302 0.0129 0.003 0.7 3.5 0.5 0.0 0 0.255 0.1158 0.1294 0.0136 0.004 0.9 3.8 0.5 0.0 0 0.510 0.1151 0.1289 0.0139 0.005 0.9 3.8 0.5 0.0 0 0.766 0.1146 0.1286 0.0140 0.006 1.0 4.2 0.5 0.0 0 1.021 0.1144 0.1283 0.0139 0.007 1.1 4.5 0.5 0.0 0 1.276 0.1142 0.1286 0.0144 0.008 1.1 4.2 0.5 0.0 0 1.531 0.1140 0.1288 0.0148 0.008 1.1 4.2 0.5 0.0 0 1.787 0.1149 0.1288 0.0138 0.006 1.0 3.8 0.5 0.0 0 0.851 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1144 0.1283 0.0139 0.007 1.1 4.5 0.5 0.0 0 1.276 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.44 12.83 1.39 3.780 21.259 43.539 3.608 11.44 12.83 1.39 3.780 21.259 1.306 3.608 11.44 12.83 1.39 3.780 21.259 5.442 3.608 11.48 12.88 1.40 3.715 21.252 21.769 3.604 11.51 13.00 1.49 3.739 21.228 43.539 3.605 11.48 13.04 1.56 3.759 21.211 65.308 3.601 11.43 13.02 1.59 3.774 21.206 87.078 3.597 11.39 12.97 1.58 3.782 21.205 108.847 3.593 11.39 13.00 1.62 3.797 21.198 130.616 3.593 11.38 13.02 1.64 3.810 21.188 152.386 3.591 11.37 13.02 1.65 3.821 21.183 174.155 3.590 11.36 13.01 1.65 3.830 21.181 195.925 3.590 11.33 12.98 1.65 3.833 21.185 217.694 3.588 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 5.442 Accepted refinement result: 11.44 12.83 1.39 3.780 21.259 5.442 3.608 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.23 3.31 241 1742 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.52 76.70 35.18 N/A 241 215 Other: 19.74 26.63 22.09 N/A 0 8 Chain A: 9.11 115.04 19.29 N/A 0 1742 Chain S: 15.06 60.00 35.21 N/A 241 0 Histogram: Values Number of atoms 9.11 - 19.70 1261 19.70 - 30.30 298 30.30 - 40.89 226 40.89 - 51.48 127 51.48 - 62.08 48 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=0.1144 r_free=0.1283 r_work=0.1144 r_free=0.1283 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1144 r_free = 0.1283 target_work(ml) = 3.608 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1279 target_work(ml) = 3.606 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87584 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1279 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.605877 | | target function (ml) not normalized (work): 300326.262648 | | target function (ml) not normalized (free): 15809.827294 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1146 0.1140 0.1279 n_refl.: 87584 re-set all scales: r(all,work,free)=0.1478 0.1477 0.1513 n_refl.: 87584 remove outliers: r(all,work,free)=0.1478 0.1477 0.1513 n_refl.: 87584 overall B=-0.00 to atoms: r(all,work,free)=0.1477 0.1476 0.1512 n_refl.: 87584 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1138 0.1286 n_refl.: 87584 remove outliers: r(all,work,free)=0.1144 0.1136 0.1286 n_refl.: 87580 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 89.58 81 5 0.3984 291.652 255.941 0.475 1.001 0.328 11.894-9.307 96.08 94 4 0.2265 479.415 461.966 0.861 1.002 0.247 9.237-7.194 98.64 210 7 0.2402 387.899 383.047 0.928 1.002 0.158 7.162-5.571 100.00 427 22 0.2145 295.966 285.749 0.914 1.003 0.140 5.546-4.326 100.00 867 58 0.1138 406.288 401.797 0.963 1.003 0.120 4.315-3.360 100.00 1859 96 0.0914 386.382 384.574 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1116 253.833 252.050 1.010 1.002 0.019 2.608-2.026 99.99 8198 413 0.0919 168.268 167.588 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.173 82.511 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.439 36.042 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.959 21.506 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=-0.0137 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1136 r_free=0.1286 After: r_work=0.1137 r_free=0.1286 ================================== NQH flips ================================== r_work=0.1137 r_free=0.1286 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=0.1137 r_free=0.1286 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1286 | n_water=456 | time (s): 2.370 (total time: 2.370) Filter (dist) r_work=0.1137 r_free=0.1286 | n_water=456 | time (s): 45.250 (total time: 47.620) Filter (q & B) r_work=0.1137 r_free=0.1286 | n_water=456 | time (s): 1.420 (total time: 49.040) Compute maps r_work=0.1137 r_free=0.1286 | n_water=456 | time (s): 1.730 (total time: 50.770) Filter (map) r_work=0.1165 r_free=0.1311 | n_water=355 | time (s): 3.710 (total time: 54.480) Find peaks r_work=0.1165 r_free=0.1311 | n_water=355 | time (s): 0.700 (total time: 55.180) Add new water r_work=0.1213 r_free=0.1366 | n_water=492 | time (s): 3.650 (total time: 58.830) Refine new water occ: r_work=0.1157 r_free=0.1301 adp: r_work=0.1157 r_free=0.1304 occ: r_work=0.1146 r_free=0.1288 adp: r_work=0.1145 r_free=0.1289 occ: r_work=0.1138 r_free=0.1277 adp: r_work=0.1135 r_free=0.1276 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1276 r_work=0.1135 r_free=0.1276 | n_water=492 | time (s): 170.770 (total time: 229.600) Filter (q & B) r_work=0.1139 r_free=0.1279 | n_water=465 | time (s): 3.830 (total time: 233.430) Filter (dist only) r_work=0.1139 r_free=0.1278 | n_water=464 | time (s): 50.570 (total time: 284.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.765724 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.590161 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 0.1218 0.1324 0.0106 0.004 0.7 5.4 0.0 0.0 0 0.088 0.1168 0.1293 0.0125 0.004 0.8 5.1 0.0 0.0 0 0.265 0.1149 0.1281 0.0133 0.005 1.0 4.5 0.5 0.0 0 0.530 0.1143 0.1279 0.0136 0.006 1.0 4.5 0.5 0.0 0 0.795 0.1139 0.1278 0.0139 0.007 1.1 4.5 0.5 0.0 0 1.059 0.1139 0.1278 0.0139 0.007 1.1 4.5 0.5 0.0 0 1.324 0.1138 0.1278 0.0139 0.007 1.1 4.5 0.5 0.0 0 1.589 0.1137 0.1278 0.0140 0.008 1.1 4.5 0.5 0.0 0 1.854 0.1141 0.1278 0.0137 0.006 1.0 4.5 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1138 0.1278 0.0139 0.007 1.1 4.5 0.5 0.0 0 1.589 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.38 12.78 1.39 3.780 21.218 36.590 3.604 11.38 12.78 1.39 3.780 21.218 1.098 3.604 11.38 12.78 1.39 3.780 21.218 4.574 3.604 11.42 12.83 1.41 3.711 21.211 18.295 3.601 11.53 13.05 1.52 3.718 21.184 36.590 3.606 11.45 13.02 1.57 3.744 21.172 54.885 3.601 11.39 12.99 1.60 3.764 21.166 73.180 3.596 11.35 12.96 1.61 3.776 21.164 91.475 3.592 11.32 12.93 1.61 3.783 21.165 109.770 3.590 11.29 12.91 1.62 3.788 21.165 128.066 3.588 11.31 12.96 1.65 3.808 21.146 146.361 3.588 11.29 12.94 1.65 3.816 21.147 164.656 3.586 11.28 12.93 1.65 3.822 21.145 182.951 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: 4.574 Accepted refinement result: 11.38 12.78 1.39 3.780 21.218 4.574 3.604 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.16 3.31 250 1741 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.51 76.70 34.66 N/A 250 214 Other: 19.73 26.63 22.09 N/A 0 8 Chain A: 9.10 115.04 19.27 N/A 0 1741 Chain S: 15.05 59.99 34.30 N/A 250 0 Histogram: Values Number of atoms 9.10 - 19.70 1263 19.70 - 30.29 312 30.29 - 40.88 225 40.88 - 51.48 122 51.48 - 62.07 46 62.07 - 72.66 12 72.66 - 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=0.1138 r_free=0.1278 r_work=0.1138 r_free=0.1278 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1138 r_free = 0.1278 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1134 r_free = 0.1272 target_work(ml) = 3.603 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87580 (all), 4.91 % free)------------| | | | r_work= 0.1134 r_free= 0.1272 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.602598 | | target function (ml) not normalized (work): 300038.748408 | | target function (ml) not normalized (free): 15794.596294 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.58 0.99 2922 171 0.1347 0.1313 5.6661 5.6105| | 2: 3.57 - 2.84 1.00 2888 124 0.1059 0.1367 5.1573 5.2115| | 3: 2.83 - 2.48 1.00 2820 163 0.1100 0.1185 4.9387 4.9788| | 4: 2.47 - 2.25 1.00 2825 136 0.0899 0.0941 4.624 4.6309| | 5: 2.25 - 2.09 1.00 2756 127 0.0869 0.0944 4.5728 4.6218| | 6: 2.09 - 1.97 1.00 2846 113 0.0856 0.1027 4.264 4.3581| | 7: 1.97 - 1.87 1.00 2787 165 0.0880 0.1108 3.9718 4.0902| | 8: 1.87 - 1.79 1.00 2789 144 0.0911 0.1094 3.8855 3.9841| | 9: 1.79 - 1.72 1.00 2745 138 0.0881 0.1133 3.6499 3.805| | 10: 1.72 - 1.66 1.00 2831 160 0.0917 0.1200 3.5617 3.7183| | 11: 1.66 - 1.61 1.00 2712 147 0.0875 0.1028 3.4961 3.567| | 12: 1.61 - 1.56 1.00 2773 144 0.0902 0.1155 3.3286 3.4732| | 13: 1.56 - 1.52 1.00 2745 130 0.0945 0.1016 3.3076 3.384| | 14: 1.52 - 1.48 1.00 2803 134 0.0980 0.1053 3.2362 3.3162| | 15: 1.48 - 1.45 1.00 2738 128 0.1001 0.1226 3.1524 3.264| | 16: 1.45 - 1.42 1.00 2756 161 0.1054 0.1247 3.1331 3.2428| | 17: 1.42 - 1.39 1.00 2785 139 0.1134 0.1326 3.1157 3.2369| | 18: 1.39 - 1.36 1.00 2741 179 0.1194 0.1324 3.1024 3.2386| | 19: 1.36 - 1.34 1.00 2807 134 0.1256 0.1546 3.108 3.2561| | 20: 1.34 - 1.32 1.00 2696 147 0.1367 0.1456 3.1105 3.1446| | 21: 1.32 - 1.30 1.00 2785 112 0.1469 0.1485 3.1116 3.0996| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1985 3.1207 3.2948| | 23: 1.27 - 1.26 1.00 2802 156 0.1653 0.1814 3.1333 3.2035| | 24: 1.26 - 1.24 1.00 2744 132 0.1714 0.1825 3.1271 3.2225| | 25: 1.24 - 1.22 1.00 2733 148 0.1881 0.2156 3.1414 3.2614| | 26: 1.22 - 1.21 1.00 2727 135 0.1908 0.1763 3.1483 3.1946| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2178 3.1702 3.1641| | 28: 1.19 - 1.18 1.00 2671 147 0.2204 0.2306 3.1664 3.1728| | 29: 1.18 - 1.16 1.00 2800 134 0.2266 0.2390 3.1466 3.2319| | 30: 1.16 - 1.15 1.00 2739 148 0.2452 0.2434 3.1431 3.1615| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.58 2922 171 0.95 8.37 1.00 0.97 5667.43| | 2: 3.57 - 2.84 2888 124 0.93 12.44 1.01 0.97 5667.43| | 3: 2.83 - 2.48 2820 163 0.90 16.41 0.99 0.97 4734.31| | 4: 2.47 - 2.25 2825 136 0.92 13.35 1.00 0.98 2328.09| | 5: 2.25 - 2.09 2756 127 0.90 15.53 1.01 0.98 2328.09| | 6: 2.09 - 1.97 2846 113 0.93 12.31 1.02 0.98 1344.38| | 7: 1.97 - 1.87 2787 165 0.95 9.21 1.02 0.98 505.40| | 8: 1.87 - 1.79 2789 144 0.93 12.51 1.00 0.98 505.40| | 9: 1.79 - 1.72 2745 138 0.94 10.01 0.98 0.97 286.88| | 10: 1.72 - 1.66 2831 160 0.94 11.07 0.98 0.97 243.12| | 11: 1.66 - 1.61 2712 147 0.94 11.67 0.98 0.97 232.99| | 12: 1.61 - 1.56 2773 144 0.95 8.91 0.99 0.97 137.44| | 13: 1.56 - 1.52 2745 130 0.95 10.41 1.03 0.97 137.44| | 14: 1.52 - 1.48 2803 134 0.94 10.80 1.02 0.98 123.28| | 15: 1.48 - 1.45 2738 128 0.95 9.85 1.02 0.98 97.35| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.98 97.35| | 17: 1.42 - 1.39 2785 139 0.95 10.92 1.01 0.98 88.68| | 18: 1.39 - 1.36 2741 179 0.94 11.54 1.01 0.98 83.67| | 19: 1.36 - 1.34 2807 134 0.94 11.86 1.00 0.98 83.67| | 20: 1.34 - 1.32 2696 147 0.94 12.07 0.98 0.96 79.49| | 21: 1.32 - 1.30 2785 112 0.94 13.05 0.98 0.96 79.19| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.96 79.62| | 23: 1.27 - 1.26 2802 156 0.92 14.80 0.97 0.94 81.75| | 24: 1.26 - 1.24 2744 132 0.93 14.83 0.96 0.94 81.75| | 25: 1.24 - 1.22 2733 148 0.91 16.31 0.96 0.94 83.78| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.03 0.93 86.02| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.93 86.02| | 28: 1.19 - 1.18 2671 147 0.88 20.43 1.01 0.92 89.92| | 29: 1.18 - 1.16 2800 134 0.88 20.56 0.99 0.92 91.38| | 30: 1.16 - 1.15 2739 148 0.86 22.08 0.98 0.92 91.38| |alpha: min = 0.92 max = 0.98 mean = 0.96| |beta: min = 79.19 max = 5667.43 mean = 875.66| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.99 mean = 13.41| |phase err.(test): min = 0.00 max = 88.69 mean = 13.40| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1141 0.1134 0.1272 n_refl.: 87580 re-set all scales: r(all,work,free)=0.1466 0.1468 0.1471 n_refl.: 87580 remove outliers: r(all,work,free)=0.1466 0.1468 0.1471 n_refl.: 87580 overall B=-0.01 to atoms: r(all,work,free)=0.1465 0.1467 0.1470 n_refl.: 87580 bulk-solvent and scaling: r(all,work,free)=0.1141 0.1134 0.1271 n_refl.: 87580 remove outliers: r(all,work,free)=0.1138 0.1131 0.1271 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 0.3918 285.568 247.831 0.443 1.000 0.308 11.894-9.307 92.16 90 4 0.2375 470.530 452.401 0.849 1.002 0.218 9.237-7.194 98.18 209 7 0.2416 385.872 382.049 0.923 1.002 0.150 7.162-5.571 100.00 427 22 0.2154 295.966 286.600 0.910 1.002 0.120 5.546-4.326 100.00 867 58 0.1134 406.288 401.581 0.962 1.002 0.100 4.315-3.360 100.00 1859 96 0.0915 386.382 384.571 1.003 1.002 0.087 3.356-2.611 100.00 3867 181 0.1102 253.833 252.024 1.012 1.002 0.019 2.608-2.026 99.99 8198 413 0.0910 168.268 167.593 1.026 1.001 0.000 2.025-1.573 100.00 17313 902 0.0889 82.173 82.505 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.439 36.038 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2169 22.959 21.504 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0152 b_overall=-0.0138 ================= 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 : 0.2608 0.1920 0.083 5.417 8.8 119.3 19.9 258 0.000 1_bss: 0.1637 0.1754 0.083 5.417 9.1 119.5 20.1 258 0.000 1_settarget: 0.1637 0.1754 0.083 5.417 9.1 119.5 20.1 258 0.000 1_nqh: 0.1644 0.1766 0.083 5.417 9.1 119.5 20.1 258 0.003 1_weight: 0.1644 0.1766 0.083 5.417 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1220 0.1469 0.008 0.982 9.1 119.5 20.1 258 0.133 1_adp: 0.1227 0.1465 0.008 0.982 9.1 119.5 20.1 258 0.133 1_regHadp: 0.1228 0.1467 0.008 0.982 9.1 119.5 20.1 258 0.133 1_occ: 0.1223 0.1468 0.008 0.982 9.1 119.5 20.1 258 0.133 2_bss: 0.1221 0.1458 0.008 0.982 9.1 119.5 20.1 258 0.133 2_settarget: 0.1221 0.1458 0.008 0.982 9.1 119.5 20.1 258 0.133 2_updatecdl: 0.1221 0.1458 0.008 0.976 9.1 119.5 20.1 258 0.133 2_nqh: 0.1221 0.1456 0.008 0.976 9.1 119.5 20.1 258 0.132 2_sol: 0.1199 0.1401 0.008 0.976 9.1 115.0 22.1 414 n/a 2_weight: 0.1199 0.1401 0.008 0.976 9.1 115.0 22.1 414 n/a 2_xyzrec: 0.1196 0.1417 0.006 0.831 9.1 115.0 22.1 414 n/a 2_adp: 0.1196 0.1417 0.006 0.831 9.1 115.0 22.1 414 n/a 2_regHadp: 0.1196 0.1417 0.006 0.831 9.1 115.0 22.1 414 n/a 2_occ: 0.1192 0.1415 0.006 0.831 9.1 115.0 22.1 414 n/a 3_bss: 0.1188 0.1415 0.006 0.831 9.1 115.1 22.1 414 n/a 3_settarget: 0.1188 0.1415 0.006 0.831 9.1 115.1 22.1 414 n/a 3_updatecdl: 0.1188 0.1415 0.006 0.833 9.1 115.1 22.1 414 n/a 3_nqh: 0.1188 0.1415 0.006 0.833 9.1 115.1 22.1 414 n/a 3_sol: 0.1206 0.1398 0.006 0.833 9.1 115.1 21.2 433 n/a 3_weight: 0.1206 0.1398 0.006 0.833 9.1 115.1 21.2 433 n/a 3_xyzrec: 0.1153 0.1308 0.008 1.087 9.1 115.1 21.2 433 n/a 3_adp: 0.1153 0.1308 0.008 1.087 9.1 115.1 21.2 433 n/a 3_regHadp: 0.1153 0.1308 0.008 1.087 9.1 115.1 21.2 433 n/a 3_occ: 0.1146 0.1303 0.008 1.087 9.1 115.1 21.2 433 n/a 4_bss: 0.1140 0.1294 0.008 1.087 9.1 115.0 21.2 433 n/a 4_settarget: 0.1140 0.1294 0.008 1.087 9.1 115.0 21.2 433 n/a 4_updatecdl: 0.1140 0.1294 0.008 1.087 9.1 115.0 21.2 433 n/a 4_nqh: 0.1140 0.1294 0.008 1.087 9.1 115.0 21.2 433 n/a 4_sol: 0.1142 0.1282 0.008 1.087 9.1 115.0 21.2 456 n/a 4_weight: 0.1142 0.1282 0.008 1.087 9.1 115.0 21.2 456 n/a 4_xyzrec: 0.1144 0.1283 0.007 1.052 9.1 115.0 21.2 456 n/a 4_adp: 0.1144 0.1283 0.007 1.052 9.1 115.0 21.2 456 n/a 4_regHadp: 0.1144 0.1283 0.007 1.052 9.1 115.0 21.2 456 n/a 4_occ: 0.1140 0.1279 0.007 1.052 9.1 115.0 21.2 456 n/a 5_bss: 0.1136 0.1286 0.007 1.052 9.1 115.0 21.2 456 n/a 5_settarget: 0.1136 0.1286 0.007 1.052 9.1 115.0 21.2 456 n/a 5_updatecdl: 0.1136 0.1286 0.007 1.053 9.1 115.0 21.2 456 n/a 5_setrh: 0.1137 0.1286 0.007 1.053 9.1 115.0 21.2 456 n/a 5_nqh: 0.1137 0.1286 0.007 1.053 9.1 115.0 21.2 456 n/a 5_sol: 0.1139 0.1278 0.007 1.053 9.1 115.0 21.2 464 n/a 5_weight: 0.1139 0.1278 0.007 1.053 9.1 115.0 21.2 464 n/a 5_xyzrec: 0.1138 0.1278 0.007 1.069 9.1 115.0 21.2 464 n/a 5_adp: 0.1138 0.1278 0.007 1.069 9.1 115.0 21.2 464 n/a 5_regHadp: 0.1138 0.1278 0.007 1.069 9.1 115.0 21.2 464 n/a 5_occ: 0.1134 0.1272 0.007 1.069 9.1 115.0 21.2 464 n/a end: 0.1131 0.1271 0.007 1.069 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_4735076_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_4735076_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7300 Refinement macro-cycles (run) : 13323.3500 Write final files (write_after_run_outputs) : 91.3000 Total : 13418.3800 Total CPU time: 3.73 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:01:49 PST -0800 (1735365709.58 s) Start R-work = 0.1637, R-free = 0.1754 Final R-work = 0.1131, R-free = 0.1271 =============================================================================== Job complete usr+sys time: 13596.23 seconds wall clock time: 246 minutes 9.85 seconds (14769.85 seconds total)