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_6824987.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_6824987.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6824987.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 =============================================================================== 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: 1.38, per 1000 atoms: 0.41 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: 0.38 Conformation dependent library (CDL) restraints added in 172.0 milliseconds Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 585 0.92 - 1.18: 1063 1.18 - 1.44: 702 1.44 - 1.70: 781 1.70 - 1.96: 22 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 9 " pdb=" C ILE A 9 " ideal model delta sigma weight residual 1.526 1.308 0.217 1.13e-02 7.83e+03 3.70e+02 bond pdb=" C VAL A 20 " pdb=" N ILE A 21 " ideal model delta sigma weight residual 1.329 1.527 -0.198 1.13e-02 7.83e+03 3.06e+02 bond pdb=" CA PHE A 164 " pdb=" C PHE A 164 " ideal model delta sigma weight residual 1.524 1.748 -0.224 1.29e-02 6.01e+03 3.02e+02 bond pdb=" N ARG A 27 " pdb=" CA ARG A 27 " ideal model delta sigma weight residual 1.459 1.671 -0.213 1.28e-02 6.10e+03 2.76e+02 bond pdb=" C ALA A 29 " pdb=" N GLY A 30 " ideal model delta sigma weight residual 1.330 1.131 0.199 1.23e-02 6.61e+03 2.63e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.29: 2984 4.29 - 8.57: 1820 8.57 - 12.86: 780 12.86 - 17.14: 180 17.14 - 21.42: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA LEU A 187 " pdb=" C LEU A 187 " pdb=" O LEU A 187 " ideal model delta sigma weight residual 121.47 106.45 15.02 1.15e+00 7.56e-01 1.71e+02 angle pdb=" CA BLYS A 132 " pdb=" C BLYS A 132 " pdb=" O BLYS A 132 " ideal model delta sigma weight residual 120.42 106.68 13.74 1.06e+00 8.90e-01 1.68e+02 angle pdb=" O GLY A 100 " pdb=" C GLY A 100 " pdb=" N LEU A 101 " ideal model delta sigma weight residual 123.21 107.82 15.39 1.20e+00 6.94e-01 1.65e+02 angle pdb=" CA BASN A 76 " pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 120.90 134.44 -13.54 1.07e+00 8.73e-01 1.60e+02 angle pdb=" C ILE A 9 " pdb=" CA ILE A 9 " pdb=" CB ILE A 9 " ideal model delta sigma weight residual 111.23 124.79 -13.56 1.08e+00 8.57e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.85: 944 17.85 - 35.69: 120 35.69 - 53.53: 35 53.53 - 71.37: 10 71.37 - 89.21: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ARG A 145 " pdb=" C ARG A 145 " pdb=" N VAL A 146 " pdb=" CA VAL A 146 " ideal model delta harmonic sigma weight residual 180.00 157.24 22.76 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CD2 TYR A 139 " pdb=" CG TYR A 139 " pdb=" CD1 TYR A 139 " pdb=" HD1 TYR A 139 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.286: 132 0.286 - 0.571: 69 0.571 - 0.856: 36 0.856 - 1.141: 5 1.141 - 1.426: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 184 " pdb=" N PRO A 184 " pdb=" C PRO A 184 " pdb=" CB PRO A 184 " both_signs ideal model delta sigma weight residual False 2.72 1.29 1.43 2.00e-01 2.50e+01 5.08e+01 chirality pdb=" CA SER A 3 " pdb=" N SER A 3 " pdb=" C SER A 3 " pdb=" CB SER A 3 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CA GLU A 163 " pdb=" N GLU A 163 " pdb=" C GLU A 163 " pdb=" CB GLU A 163 " both_signs ideal model delta sigma weight residual False 2.51 3.44 -0.93 2.00e-01 2.50e+01 2.15e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.012 2.00e-02 2.50e+03 6.63e-02 1.32e+02 pdb=" CG BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.086 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.120 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.088 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.001 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.032 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.060 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.130 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG PHE A 164 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.034 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.069 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.036 2.00e-02 2.50e+03 6.23e-02 1.17e+02 pdb=" CG PHE A 119 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.132 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.044 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.059 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.060 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.085 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 903 2.30 - 2.88: 8054 2.88 - 3.45: 10531 3.45 - 4.03: 15257 4.03 - 4.60: 21875 Nonbonded interactions: 56620 Sorted by model distance: nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.728 1.850 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.750 1.850 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.776 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.819 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.821 2.100 ... (remaining 56615 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_6824987_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= 0.2599 r_free= 0.1925 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781996 | | target function (ml) not normalized (work): 231756.974713 | | target function (ml) not normalized (free): 11769.389710 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3024 0.2085 7.0086 4.9316| | 2: 3.57 - 2.84 1.00 2876 122 0.2437 0.1888 4.3568 4.3708| | 3: 2.84 - 2.48 1.00 2833 165 0.2359 0.1606 4.1312 4.1524| | 4: 2.47 - 2.25 1.00 2825 136 0.2345 0.1458 3.8347 3.8329| | 5: 2.25 - 2.09 1.00 2756 127 0.2457 0.1576 3.7972 3.8188| | 6: 2.09 - 1.97 1.00 2846 113 0.2519 0.1581 3.4616 3.4973| | 7: 1.97 - 1.87 1.00 2787 165 0.2554 0.1805 3.1231 3.1853| | 8: 1.87 - 1.79 1.00 2789 144 0.2453 0.1962 3.0507 3.1307| | 9: 1.79 - 1.72 1.00 2745 138 0.2416 0.1862 2.8834 2.9787| | 10: 1.72 - 1.66 1.00 2789 158 0.2397 0.2070 2.7919 2.885| | 11: 1.66 - 1.61 1.00 2740 147 0.2506 0.1729 2.7233 2.7134| | 12: 1.61 - 1.56 1.00 2787 146 0.2525 0.1763 2.6159 2.5907| | 13: 1.56 - 1.52 1.00 2745 130 0.2517 0.1723 2.547 2.5274| | 14: 1.52 - 1.48 1.00 2803 134 0.2582 0.2029 2.5147 2.5825| | 15: 1.48 - 1.45 1.00 2738 128 0.2554 0.1854 2.4198 2.3986| | 16: 1.45 - 1.42 1.00 2756 161 0.2606 0.2180 2.3795 2.4597| | 17: 1.42 - 1.39 1.00 2785 139 0.2648 0.2270 2.3247 2.4418| | 18: 1.39 - 1.36 1.00 2741 179 0.2661 0.2002 2.2632 2.2718| | 19: 1.36 - 1.34 1.00 2807 134 0.2639 0.2351 2.2361 2.2893| | 20: 1.34 - 1.32 1.00 2696 147 0.2634 0.2243 2.1838 2.1951| | 21: 1.32 - 1.30 1.00 2785 112 0.2728 0.2164 2.1618 2.1331| | 22: 1.29 - 1.27 1.00 2704 152 0.2688 0.2612 2.1103 2.2213| | 23: 1.27 - 1.26 1.00 2802 156 0.2827 0.2544 2.1162 2.1747| | 24: 1.26 - 1.24 1.00 2744 132 0.2794 0.2549 2.0652 2.1514| | 25: 1.24 - 1.22 1.00 2734 148 0.2793 0.2388 2.0375 2.0224| | 26: 1.22 - 1.21 1.00 2727 135 0.2830 0.2367 2.0036 2.1124| | 27: 1.21 - 1.19 1.00 2814 148 0.2961 0.2545 2.0008 1.9944| | 28: 1.19 - 1.18 1.00 2671 147 0.2970 0.2934 1.9841 2.0234| | 29: 1.18 - 1.16 1.00 2800 134 0.2923 0.2537 1.9447 2.0112| | 30: 1.16 - 1.15 1.00 2740 148 0.3048 0.2789 1.9333 1.9346| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 19.01 0.76 0.23 1505.99| | 2: 3.57 - 2.84 2876 122 0.80 26.33 1.27 0.23 1505.99| | 3: 2.84 - 2.48 2833 165 0.74 32.23 1.24 0.24 1247.12| | 4: 2.47 - 2.25 2825 136 0.81 25.57 1.26 0.25 575.30| | 5: 2.25 - 2.09 2756 127 0.77 29.32 1.28 0.25 575.30| | 6: 2.09 - 1.97 2846 113 0.84 22.18 1.29 0.25 311.00| | 7: 1.97 - 1.87 2787 165 0.90 16.13 1.28 0.26 85.59| | 8: 1.87 - 1.79 2789 144 0.86 20.38 1.24 0.26 85.59| | 9: 1.79 - 1.72 2745 138 0.89 17.85 1.23 0.26 51.84| | 10: 1.72 - 1.66 2789 158 0.87 19.37 1.22 0.26 45.08| | 11: 1.66 - 1.61 2740 147 0.86 20.56 1.25 0.25 43.46| | 12: 1.61 - 1.56 2787 146 0.89 17.83 1.24 0.25 27.04| | 13: 1.56 - 1.52 2745 130 0.87 19.44 1.24 0.25 27.04| | 14: 1.52 - 1.48 2803 134 0.87 19.83 1.23 0.25 24.48| | 15: 1.48 - 1.45 2738 128 0.87 19.81 1.23 0.25 19.80| | 16: 1.45 - 1.42 2756 161 0.86 20.94 1.23 0.25 19.80| | 17: 1.42 - 1.39 2785 139 0.87 20.59 1.22 0.25 17.18| | 18: 1.39 - 1.36 2741 179 0.86 21.17 1.22 0.25 15.66| | 19: 1.36 - 1.34 2807 134 0.86 21.76 1.21 0.25 15.66| | 20: 1.34 - 1.32 2696 147 0.87 20.87 1.21 0.24 13.18| | 21: 1.32 - 1.30 2785 112 0.85 22.27 1.21 0.24 13.00| | 22: 1.29 - 1.27 2704 152 0.85 22.40 1.22 0.24 12.71| | 23: 1.27 - 1.26 2802 156 0.85 22.42 1.22 0.24 11.23| | 24: 1.26 - 1.24 2744 132 0.85 22.85 1.22 0.24 11.23| | 25: 1.24 - 1.22 2734 148 0.84 23.67 1.20 0.24 10.62| | 26: 1.22 - 1.21 2727 135 0.84 23.72 1.20 0.23 9.93| | 27: 1.21 - 1.19 2814 148 0.83 24.81 1.21 0.23 9.93| | 28: 1.19 - 1.18 2671 147 0.83 25.08 1.18 0.23 9.26| | 29: 1.18 - 1.16 2800 134 0.83 25.57 1.16 0.23 9.01| | 30: 1.16 - 1.15 2740 148 0.81 26.79 1.14 0.23 9.01| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.01 max = 1505.99 mean = 216.58| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.99 mean = 22.36| |phase err.(test): min = 0.00 max = 89.60 mean = 22.26| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.241 1557 Z= 5.406 Angle : 5.285 16.769 2118 Z= 3.659 Chirality : 0.394 1.426 243 Planarity : 0.033 0.126 284 Dihedral : 14.106 89.210 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 30.81 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.45), residues: 224 helix: -2.54 (0.38), residues: 101 sheet: -0.64 (0.92), residues: 28 loop : -0.37 (0.50), residues: 95 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.015 ARG A 98 TYR 0.072 0.026 TYR A 139 PHE 0.125 0.045 PHE A 164 HIS 0.042 0.025 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 0 1785 Protein: 8.85 115.78 16.79 3.90 0 1519 Water: 11.36 119.30 38.03 N/A 0 258 Other: 19.04 26.29 21.71 N/A 0 8 Chain A: 8.85 119.30 19.89 N/A 0 1785 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 1.15 - 49.25 A, n_refl.=87602 (all), 4.90 % free)------------| | | | r_work= 0.2599 r_free= 0.1925 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.781996 | | target function (ml) not normalized (work): 231756.974713 | | target function (ml) not normalized (free): 11769.389710 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2558 0.2600 0.1924 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2558 0.2600 0.1924 n_refl.: 87602 remove outliers: r(all,work,free)=0.1969 0.1973 0.1924 n_refl.: 87594 overall B=0.21 to atoms: r(all,work,free)=0.1994 0.1999 0.1940 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1633 0.1628 0.1740 n_refl.: 87594 remove outliers: r(all,work,free)=0.1633 0.1628 0.1740 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 0.3864 386.208 357.795 0.683 1.003 0.412 11.894-9.307 99.02 97 4 0.1821 613.473 595.061 0.929 1.004 0.400 9.237-7.194 100.00 213 7 0.2182 501.745 490.757 0.955 1.004 0.380 7.162-5.571 100.00 427 22 0.2221 376.532 363.088 0.929 1.004 0.310 5.546-4.326 100.00 867 58 0.1283 516.885 512.086 0.961 1.003 0.224 4.315-3.360 100.00 1859 96 0.1129 491.561 488.104 1.006 1.003 0.199 3.356-2.611 100.00 3867 181 0.1447 322.930 319.776 0.997 1.002 0.129 2.608-2.026 99.99 8198 413 0.1335 214.073 211.885 1.006 1.001 0.000 2.025-1.573 100.00 17313 902 0.1634 104.542 103.915 1.012 0.999 0.000 1.573-1.221 100.00 36679 1900 0.2051 46.358 45.067 1.004 0.996 0.000 1.221-1.150 99.97 13689 708 0.2565 29.209 27.005 0.975 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0016 b_overall=0.0470 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1628 r_free=0.1740 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1629 r_free=0.1739 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.580605 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2003.687976 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 0.1767 0.1878 0.0111 0.001 0.4 4.5 0.0 0.0 0 0.125 0.1594 0.1731 0.0137 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1474 0.1644 0.0170 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1391 0.1585 0.0194 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1367 0.1570 0.0202 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1363 0.1567 0.0204 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1299 0.1521 0.0222 0.002 0.6 3.5 0.5 0.0 0 2.000 0.1268 0.1494 0.0226 0.003 0.6 3.5 0.5 0.0 0 3.000 0.1256 0.1489 0.0233 0.003 0.7 3.2 0.5 0.0 0 4.000 0.1248 0.1480 0.0232 0.004 0.7 3.8 0.5 0.0 0 5.000 0.1241 0.1479 0.0237 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1238 0.1474 0.0235 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1235 0.1474 0.0239 0.005 0.8 3.8 0.5 0.0 0 8.000 0.1232 0.1471 0.0240 0.006 0.9 4.5 0.5 0.0 0 9.000 0.1228 0.1470 0.0242 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1227 0.1474 0.0247 0.007 0.9 3.8 0.5 0.0 0 11.000 0.1226 0.1482 0.0256 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1226 0.1486 0.0259 0.008 1.0 4.2 0.5 0.6 0 13.290 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1228 0.1470 0.0242 0.006 0.9 4.2 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.28 14.70 2.42 3.013 19.064 2003.688 0.017 12.28 14.70 2.42 2.994 19.064 60.111 0.017 12.35 14.67 2.32 2.669 19.062 250.461 0.017 12.70 15.29 2.59 2.746 19.224 1001.844 0.017 12.59 15.52 2.92 3.254 19.579 2003.688 0.016 12.45 15.45 3.01 3.328 19.636 3005.532 0.015 12.36 15.47 3.11 3.363 19.640 4007.376 0.015 12.33 15.50 3.17 3.388 19.639 5009.220 0.015 12.28 15.48 3.20 3.379 19.636 6011.064 0.015 12.24 15.45 3.21 3.329 19.596 7012.908 0.015 12.25 15.58 3.33 3.539 19.697 8014.752 0.015 12.18 15.52 3.34 3.441 19.629 9016.596 0.015 12.24 15.65 3.40 3.630 19.719 10018.440 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: 250.461 Accepted refinement result: 12.35 14.67 2.32 2.669 19.062 250.461 0.017 Individual atomic B min max mean iso aniso Overall: 9.07 119.45 20.09 3.31 0 1785 Protein: 9.07 115.00 17.00 3.32 0 1519 Water: 11.48 119.45 38.23 N/A 0 258 Other: 19.72 26.62 22.06 N/A 0 8 Chain A: 9.07 119.45 20.09 N/A 0 1785 Histogram: Values Number of atoms 9.07 - 20.11 1272 20.11 - 31.15 227 31.15 - 42.18 125 42.18 - 53.22 94 53.22 - 64.26 42 64.26 - 75.30 11 75.30 - 86.34 7 86.34 - 97.37 4 97.37 - 108.41 1 108.41 - 119.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.1235 r_free=0.1467 r_work=0.1237 r_free=0.1472 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1237 r_free = 0.1472 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 = 0.1232 r_free = 0.1466 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= 0.1232 r_free= 0.1466 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.017026 | | target function (ls_wunit_k1) not normalized (work): 1418.205437 | | target function (ls_wunit_k1) not normalized (free): 112.469119 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1243 0.1232 0.1466 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1677 0.1679 0.1688 n_refl.: 87593 remove outliers: r(all,work,free)=0.1677 0.1679 0.1688 n_refl.: 87593 overall B=0.03 to atoms: r(all,work,free)=0.1683 0.1685 0.1692 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1240 0.1229 0.1454 n_refl.: 87593 remove outliers: r(all,work,free)=0.1239 0.1228 0.1454 n_refl.: 87591 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3583 297.827 282.191 0.642 1.002 0.376 11.894-9.307 99.02 97 4 0.1726 482.610 469.470 0.918 1.003 0.373 9.237-7.194 100.00 213 7 0.1896 394.716 389.172 0.963 1.003 0.350 7.162-5.571 100.00 427 22 0.1865 296.212 289.912 0.934 1.003 0.259 5.546-4.326 100.00 867 58 0.1021 406.626 403.230 0.961 1.003 0.209 4.315-3.360 100.00 1859 96 0.0870 386.705 385.669 1.010 1.003 0.190 3.356-2.611 100.00 3867 181 0.1174 254.045 252.946 1.010 1.002 0.110 2.608-2.026 99.99 8198 413 0.1022 168.409 167.688 1.018 1.001 0.000 2.025-1.573 100.00 17313 902 0.1109 82.242 82.427 1.027 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1450 36.469 35.972 1.019 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.978 21.457 0.981 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0508 ============================ 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 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1230 r_free=0.1455 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1230 r_free=0.1455 | n_water=258 | time (s): 2.160 (total time: 2.160) Filter (dist) r_work=0.1238 r_free=0.1454 | n_water=252 | time (s): 21.370 (total time: 23.530) Filter (q & B) r_work=0.1240 r_free=0.1454 | n_water=249 | time (s): 2.220 (total time: 25.750) Compute maps r_work=0.1240 r_free=0.1454 | n_water=249 | time (s): 1.290 (total time: 27.040) Filter (map) r_work=0.1257 r_free=0.1457 | n_water=224 | time (s): 3.200 (total time: 30.240) Find peaks r_work=0.1257 r_free=0.1457 | n_water=224 | time (s): 0.520 (total time: 30.760) Add new water r_work=0.1404 r_free=0.1620 | n_water=431 | time (s): 2.430 (total time: 33.190) Refine new water occ: r_work=0.1307 r_free=0.1494 adp: r_work=0.1227 r_free=0.1435 occ: r_work=0.1241 r_free=0.1428 adp: r_work=0.1205 r_free=0.1409 occ: r_work=0.1208 r_free=0.1402 adp: r_work=0.1198 r_free=0.1400 ADP+occupancy (water only), MIN, final r_work=0.1198 r_free=0.1400 r_work=0.1198 r_free=0.1400 | n_water=431 | time (s): 55.810 (total time: 89.000) Filter (q & B) r_work=0.1202 r_free=0.1405 | n_water=414 | time (s): 2.750 (total time: 91.750) Filter (dist only) r_work=0.1203 r_free=0.1403 | n_water=413 | time (s): 33.650 (total time: 125.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 29.765309 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1483.628309 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 0.1654 0.1770 0.0116 0.001 0.4 8.0 0.0 0.0 0 0.125 0.1566 0.1693 0.0127 0.001 0.4 7.4 0.0 0.0 0 0.250 0.1440 0.1590 0.0150 0.001 0.4 4.8 0.0 0.0 0 0.500 0.1341 0.1512 0.0171 0.002 0.5 4.5 0.0 0.0 0 0.750 0.1321 0.1498 0.0176 0.002 0.5 4.5 0.0 0.0 0 1.000 0.1327 0.1504 0.0176 0.002 0.5 4.8 0.0 0.0 0 1.000 0.1259 0.1455 0.0196 0.002 0.5 4.5 0.5 0.0 0 2.000 0.1227 0.1441 0.0214 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1216 0.1437 0.0221 0.004 0.7 4.8 0.5 0.0 0 4.000 0.1212 0.1430 0.0218 0.004 0.7 4.8 0.5 0.0 0 5.000 0.1208 0.1428 0.0220 0.005 0.7 4.8 0.5 0.0 0 6.000 0.1201 0.1420 0.0218 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1200 0.1417 0.0217 0.005 0.8 4.5 0.5 0.0 0 8.000 0.1197 0.1415 0.0219 0.006 0.8 3.8 0.5 0.0 0 9.000 0.1191 0.1407 0.0216 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1191 0.1416 0.0225 0.007 0.9 4.5 0.5 0.0 0 11.000 0.1190 0.1414 0.0224 0.007 0.9 4.5 0.5 0.0 0 12.000 0.1188 0.1415 0.0226 0.007 0.9 4.8 0.5 0.0 0 13.000 0.1185 0.1417 0.0231 0.008 1.0 4.8 0.5 0.0 0 14.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1191 0.1407 0.0216 0.006 0.9 4.2 0.5 0.0 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.91 14.07 2.16 3.776 21.746 1483.628 0.016 11.91 14.07 2.16 3.776 21.746 44.509 0.016 11.91 14.07 2.16 3.776 21.746 185.454 0.016 12.06 14.49 2.43 3.639 21.748 741.814 0.015 12.10 14.86 2.75 3.464 22.001 1483.628 0.015 11.98 14.92 2.93 3.516 21.886 2225.442 0.014 11.86 14.78 2.92 3.489 22.115 2967.257 0.014 11.77 14.69 2.92 3.487 22.052 3709.071 0.014 11.85 14.90 3.05 3.544 22.156 4450.885 0.014 11.79 14.85 3.06 3.545 22.102 5192.699 0.014 11.70 14.78 3.08 3.558 22.144 5934.513 0.014 11.72 14.84 3.12 3.562 22.071 6676.327 0.014 11.69 14.80 3.11 3.588 22.132 7418.142 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: 44.509 Accepted refinement result: 11.91 14.07 2.16 3.776 21.746 44.509 0.016 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 22.13 3.31 189 1751 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.52 76.69 40.87 N/A 189 224 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.10 115.04 19.43 N/A 0 1751 Chain S: 13.31 60.00 47.15 N/A 189 0 Histogram: Values Number of atoms 9.10 - 19.70 1261 19.70 - 30.29 243 30.29 - 40.88 159 40.88 - 51.48 131 51.48 - 62.07 124 62.07 - 72.66 11 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1191 r_free=0.1407 r_work=0.1191 r_free=0.1407 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1191 r_free = 0.1407 target_work(ls_wunit_k1) = 0.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1189 r_free = 0.1403 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87591 (all), 4.90 % free)------------| | | | r_work= 0.1189 r_free= 0.1403 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.015023 | | target function (ls_wunit_k1) not normalized (work): 1251.354229 | | target function (ls_wunit_k1) not normalized (free): 100.960554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1199 0.1189 0.1403 n_refl.: 87591 re-set all scales: r(all,work,free)=0.1589 0.1589 0.1622 n_refl.: 87591 remove outliers: r(all,work,free)=0.1589 0.1589 0.1622 n_refl.: 87591 overall B=0.01 to atoms: r(all,work,free)=0.1591 0.1591 0.1623 n_refl.: 87591 bulk-solvent and scaling: r(all,work,free)=0.1197 0.1187 0.1400 n_refl.: 87591 remove outliers: r(all,work,free)=0.1196 0.1186 0.1400 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 0.3390 299.814 272.245 0.583 1.003 0.350 11.894-9.307 99.02 97 4 0.1625 482.610 475.763 0.914 1.003 0.333 9.237-7.194 100.00 213 7 0.1670 394.716 395.124 0.984 1.003 0.290 7.162-5.571 100.00 427 22 0.1602 296.212 291.577 0.933 1.003 0.230 5.546-4.326 100.00 867 58 0.0900 406.626 403.552 0.960 1.003 0.220 4.315-3.360 100.00 1859 96 0.0795 386.705 385.872 1.006 1.003 0.190 3.356-2.611 100.00 3867 181 0.1081 254.045 253.188 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1008 168.409 167.852 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1101 82.242 82.466 1.030 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1444 36.469 36.006 1.024 0.997 0.000 1.221-1.150 99.97 13689 708 0.2254 22.978 21.495 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0148 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1186 r_free=0.1400 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=0.1186 r_free=0.1400 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1186 r_free=0.1400 | n_water=413 | time (s): 1.800 (total time: 1.800) Filter (dist) r_work=0.1186 r_free=0.1397 | n_water=409 | time (s): 33.900 (total time: 35.700) Filter (q & B) r_work=0.1186 r_free=0.1397 | n_water=409 | time (s): 0.950 (total time: 36.650) Compute maps r_work=0.1186 r_free=0.1397 | n_water=409 | time (s): 1.250 (total time: 37.900) Filter (map) r_work=0.1222 r_free=0.1388 | n_water=292 | time (s): 2.820 (total time: 40.720) Find peaks r_work=0.1222 r_free=0.1388 | n_water=292 | time (s): 0.590 (total time: 41.310) Add new water r_work=0.1336 r_free=0.1496 | n_water=460 | time (s): 2.490 (total time: 43.800) Refine new water occ: r_work=0.1248 r_free=0.1420 adp: r_work=0.1249 r_free=0.1420 occ: r_work=0.1226 r_free=0.1403 adp: r_work=0.1225 r_free=0.1401 occ: r_work=0.1210 r_free=0.1396 adp: r_work=0.1204 r_free=0.1390 ADP+occupancy (water only), MIN, final r_work=0.1204 r_free=0.1390 r_work=0.1204 r_free=0.1390 | n_water=460 | time (s): 188.110 (total time: 231.910) Filter (q & B) r_work=0.1208 r_free=0.1393 | n_water=434 | time (s): 3.290 (total time: 235.200) Filter (dist only) r_work=0.1208 r_free=0.1392 | n_water=433 | time (s): 37.580 (total time: 272.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.766907 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 48.524268 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 0.1358 0.0120 0.002 0.6 5.4 0.5 0.0 0 0.088 0.1188 0.1321 0.0133 0.003 0.7 4.5 0.5 0.0 0 0.265 0.1173 0.1313 0.0140 0.004 0.8 3.5 0.5 0.0 0 0.530 0.1164 0.1310 0.0146 0.005 0.9 3.2 0.5 0.0 0 0.795 0.1160 0.1307 0.0147 0.006 1.0 3.5 0.5 0.0 0 1.060 0.1158 0.1306 0.0148 0.007 1.0 3.5 0.5 0.0 0 1.325 0.1156 0.1306 0.0150 0.007 1.1 3.5 0.5 0.0 0 1.590 0.1154 0.1306 0.0152 0.008 1.1 4.2 0.5 0.0 0 1.855 0.1163 0.1308 0.0145 0.005 0.9 3.2 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1158 0.1306 0.0148 0.007 1.0 3.5 0.5 0.0 0 1.325 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 13.06 1.48 3.779 21.287 48.524 3.619 11.58 13.06 1.48 3.779 21.287 1.456 3.619 11.58 13.06 1.48 3.764 21.287 6.066 3.619 11.64 13.15 1.51 3.711 21.274 24.262 3.614 11.63 13.21 1.58 3.732 21.245 48.524 3.612 11.56 13.17 1.61 3.756 21.236 72.786 3.606 11.50 13.12 1.62 3.768 21.233 97.049 3.602 11.47 13.12 1.65 3.780 21.228 121.311 3.600 11.47 13.14 1.67 3.797 21.216 145.573 3.599 11.45 13.14 1.69 3.811 21.206 169.835 3.598 11.43 13.13 1.70 3.818 21.207 194.097 3.597 11.42 13.11 1.68 3.826 21.203 218.359 3.595 11.43 13.12 1.69 3.838 21.196 242.621 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: 1.456 Accepted refinement result: 11.58 13.06 1.48 3.779 21.287 1.456 3.619 Individual atomic B min max mean iso aniso Overall: 9.11 115.05 21.28 3.31 211 1749 Protein: 9.11 115.05 17.04 3.32 0 1519 Water: 11.53 76.70 36.12 N/A 211 222 Other: 19.76 26.66 22.10 N/A 0 8 Chain A: 9.11 115.05 19.41 N/A 0 1749 Chain S: 13.32 60.01 36.71 N/A 211 0 Histogram: Values Number of atoms 9.11 - 19.71 1264 19.71 - 30.30 282 30.30 - 40.89 208 40.89 - 51.49 122 51.49 - 62.08 62 62.08 - 72.67 11 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=0.1158 r_free=0.1306 r_work=0.1158 r_free=0.1306 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1306 target_work(ml) = 3.619 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1149 r_free = 0.1316 target_work(ml) = 3.614 | | 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.=87590 (all), 4.90 % free)------------| | | | r_work= 0.1149 r_free= 0.1316 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.613738 | | target function (ml) not normalized (work): 301002.690589 | | target function (ml) not normalized (free): 15845.605186 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1149 0.1316 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1499 0.1498 0.1546 n_refl.: 87590 remove outliers: r(all,work,free)=0.1499 0.1498 0.1546 n_refl.: 87590 overall B=-0.01 to atoms: r(all,work,free)=0.1498 0.1497 0.1545 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1154 0.1145 0.1312 n_refl.: 87590 remove outliers: r(all,work,free)=0.1151 0.1143 0.1312 n_refl.: 87583 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3801 291.724 272.003 0.521 1.002 0.330 11.894-9.307 98.04 96 4 0.2129 482.735 465.552 0.895 1.002 0.330 9.237-7.194 98.18 209 7 0.2194 386.194 388.307 0.959 1.003 0.209 7.162-5.571 100.00 427 22 0.2023 296.212 285.987 0.921 1.003 0.190 5.546-4.326 100.00 867 58 0.1092 406.626 401.742 0.965 1.003 0.185 4.315-3.360 100.00 1859 96 0.0935 386.705 384.268 1.006 1.002 0.180 3.356-2.611 100.00 3867 181 0.1143 254.045 251.915 1.006 1.002 0.100 2.608-2.026 99.99 8198 413 0.0940 168.409 167.611 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0905 82.242 82.517 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.469 36.048 1.029 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 22.978 21.519 0.991 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0160 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1312 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1143 r_free=0.1312 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1312 | n_water=433 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1143 r_free=0.1312 | n_water=429 | time (s): 46.390 (total time: 48.820) Filter (q & B) r_work=0.1144 r_free=0.1311 | n_water=427 | time (s): 3.720 (total time: 52.540) Compute maps r_work=0.1144 r_free=0.1311 | n_water=427 | time (s): 1.830 (total time: 54.370) Filter (map) r_work=0.1162 r_free=0.1305 | n_water=326 | time (s): 3.780 (total time: 58.150) Find peaks r_work=0.1162 r_free=0.1305 | n_water=326 | time (s): 0.690 (total time: 58.840) Add new water r_work=0.1239 r_free=0.1391 | n_water=486 | time (s): 3.660 (total time: 62.500) Refine new water occ: r_work=0.1167 r_free=0.1329 adp: r_work=0.1167 r_free=0.1332 occ: r_work=0.1152 r_free=0.1313 adp: r_work=0.1151 r_free=0.1317 occ: r_work=0.1139 r_free=0.1299 adp: r_work=0.1136 r_free=0.1300 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1300 r_work=0.1136 r_free=0.1300 | n_water=486 | time (s): 257.990 (total time: 320.490) Filter (q & B) r_work=0.1142 r_free=0.1303 | n_water=444 | time (s): 3.890 (total time: 324.380) Filter (dist only) r_work=0.1142 r_free=0.1301 | n_water=442 | time (s): 45.750 (total time: 370.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.778902 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 38.395466 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 0.0000 R_free-R_work gap: 4.0000 Bond RMSD: 0.0250 Angle RMSD: 3.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1206 0.1338 0.0132 0.002 0.6 4.8 0.5 0.0 0 0.089 0.1168 0.1313 0.0145 0.003 0.7 3.8 0.5 0.0 0 0.267 0.1153 0.1306 0.0154 0.005 0.9 4.2 0.5 0.0 0 0.534 0.1146 0.1304 0.0158 0.006 0.9 4.2 0.5 0.0 0 0.801 0.1143 0.1305 0.0163 0.006 1.0 4.2 0.5 0.0 0 1.067 0.1140 0.1309 0.0169 0.007 1.0 4.2 0.5 0.0 0 1.334 0.1137 0.1305 0.0168 0.008 1.1 4.2 0.5 0.0 0 1.601 0.1135 0.1306 0.0170 0.008 1.1 4.2 0.5 0.0 0 1.868 0.1144 0.1309 0.0165 0.006 1.0 3.8 0.5 0.0 0 0.889 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1146 0.1304 0.0158 0.006 0.9 4.2 0.5 0.0 0 0.801 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.46 13.04 1.58 3.780 21.253 38.395 3.612 11.46 13.04 1.58 3.780 21.253 1.152 3.612 11.46 13.04 1.58 3.780 21.253 4.799 3.612 11.49 13.07 1.58 3.711 21.248 19.198 3.607 11.58 13.23 1.64 3.726 21.225 38.395 3.613 11.51 13.23 1.72 3.743 21.214 57.593 3.606 11.44 13.19 1.75 3.760 21.209 76.791 3.601 11.43 13.19 1.76 3.768 21.205 95.989 3.599 11.38 13.16 1.78 3.780 21.202 115.186 3.596 11.35 13.13 1.78 3.786 21.204 134.384 3.594 11.37 13.20 1.83 3.804 21.189 153.582 3.595 11.35 13.17 1.82 3.810 21.186 172.780 3.593 11.34 13.17 1.83 3.820 21.185 191.977 3.593 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.152 Accepted refinement result: 11.46 13.04 1.58 3.780 21.253 1.152 3.612 Individual atomic B min max mean iso aniso Overall: 9.11 115.04 21.22 3.31 221 1748 Protein: 9.11 115.04 17.03 3.32 0 1519 Water: 11.52 76.69 35.58 N/A 221 221 Other: 19.76 26.65 22.10 N/A 0 8 Chain A: 9.11 115.04 19.40 N/A 0 1748 Chain S: 13.31 60.00 35.57 N/A 221 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.29 289 30.29 - 40.89 207 40.89 - 51.48 132 51.48 - 62.07 53 62.07 - 72.67 11 72.67 - 83.26 5 83.26 - 93.85 4 93.85 - 104.45 0 104.45 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1304 r_work=0.1146 r_free=0.1304 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1304 target_work(ml) = 3.612 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1140 r_free = 0.1300 target_work(ml) = 3.609 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87583 (all), 4.91 % free)------------| | | | r_work= 0.1140 r_free= 0.1300 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.609381 | | target function (ml) not normalized (work): 300614.505561 | | target function (ml) not normalized (free): 15823.649430 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1148 0.1140 0.1300 n_refl.: 87583 re-set all scales: r(all,work,free)=0.1480 0.1480 0.1509 n_refl.: 87583 remove outliers: r(all,work,free)=0.1480 0.1480 0.1509 n_refl.: 87583 overall B=-0.00 to atoms: r(all,work,free)=0.1479 0.1479 0.1508 n_refl.: 87583 bulk-solvent and scaling: r(all,work,free)=0.1145 0.1138 0.1298 n_refl.: 87583 remove outliers: r(all,work,free)=0.1144 0.1136 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 0.3944 290.930 259.175 0.467 1.002 0.308 11.894-9.307 96.08 94 4 0.2312 475.978 464.123 0.870 1.003 0.300 9.237-7.194 98.18 209 7 0.2308 386.194 379.879 0.931 1.003 0.188 7.162-5.571 100.00 427 22 0.2076 296.212 285.638 0.913 1.003 0.154 5.546-4.326 100.00 867 58 0.1114 406.626 402.229 0.964 1.003 0.140 4.315-3.360 100.00 1859 96 0.0925 386.705 384.382 1.005 1.002 0.140 3.356-2.611 100.00 3867 181 0.1113 254.045 252.202 1.009 1.002 0.014 2.608-2.026 99.99 8198 413 0.0919 168.409 167.760 1.025 1.000 0.000 2.025-1.573 100.00 17313 902 0.0894 82.242 82.580 1.037 0.998 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.469 36.072 1.032 0.994 0.000 1.221-1.150 99.97 13689 708 0.2173 22.978 21.527 0.995 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0129 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1136 r_free=0.1298 After: r_work=0.1136 r_free=0.1298 ================================== NQH flips ================================== r_work=0.1136 r_free=0.1298 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=0.1136 r_free=0.1298 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1136 r_free=0.1298 | n_water=442 | time (s): 2.430 (total time: 2.430) Filter (dist) r_work=0.1136 r_free=0.1298 | n_water=442 | time (s): 44.430 (total time: 46.860) Filter (q & B) r_work=0.1137 r_free=0.1299 | n_water=440 | time (s): 3.840 (total time: 50.700) Compute maps r_work=0.1137 r_free=0.1299 | n_water=440 | time (s): 1.830 (total time: 52.530) Filter (map) r_work=0.1167 r_free=0.1319 | n_water=354 | time (s): 3.750 (total time: 56.280) Find peaks r_work=0.1167 r_free=0.1319 | n_water=354 | time (s): 0.700 (total time: 56.980) Add new water r_work=0.1220 r_free=0.1373 | n_water=495 | time (s): 3.700 (total time: 60.680) Refine new water occ: r_work=0.1154 r_free=0.1320 adp: r_work=0.1154 r_free=0.1321 occ: r_work=0.1144 r_free=0.1309 adp: r_work=0.1143 r_free=0.1309 occ: r_work=0.1135 r_free=0.1298 adp: r_work=0.1133 r_free=0.1297 ADP+occupancy (water only), MIN, final r_work=0.1133 r_free=0.1297 r_work=0.1133 r_free=0.1297 | n_water=495 | time (s): 228.410 (total time: 289.090) Filter (q & B) r_work=0.1139 r_free=0.1299 | n_water=454 | time (s): 3.660 (total time: 292.750) Filter (dist only) r_work=0.1139 r_free=0.1298 | n_water=453 | time (s): 47.680 (total time: 340.430) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.842664 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 42.507401 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 0.1217 0.1348 0.0131 0.003 0.7 6.1 0.0 0.0 0 0.092 0.1165 0.1312 0.0148 0.004 0.8 6.4 0.0 0.0 0 0.276 0.1146 0.1301 0.0156 0.005 0.9 6.1 0.5 0.0 0 0.553 0.1138 0.1298 0.0159 0.006 1.0 5.8 0.5 0.0 0 0.829 0.1136 0.1297 0.0161 0.006 1.0 5.8 0.5 0.0 0 1.106 0.1134 0.1296 0.0162 0.007 1.0 5.8 0.5 0.0 0 1.382 0.1132 0.1296 0.0163 0.008 1.1 5.8 0.5 0.0 0 1.658 0.1132 0.1296 0.0164 0.009 1.1 5.8 0.5 0.0 0 1.935 0.1138 0.1298 0.0160 0.006 1.0 5.8 0.5 0.0 0 0.921 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1132 0.1296 0.0164 0.009 1.1 5.8 0.5 0.0 0 1.935 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.32 12.96 1.64 3.780 21.261 42.507 3.604 11.32 12.96 1.64 3.780 21.261 1.275 3.604 11.32 12.96 1.64 3.777 21.261 5.313 3.604 11.35 13.01 1.66 3.712 21.255 21.254 3.599 11.39 13.11 1.72 3.736 21.233 42.507 3.602 11.35 13.13 1.78 3.752 21.218 63.761 3.597 11.27 13.07 1.80 3.765 21.219 85.015 3.592 11.28 13.10 1.83 3.776 21.208 106.269 3.591 11.24 13.07 1.83 3.787 21.210 127.522 3.588 11.25 13.13 1.88 3.807 21.199 148.776 3.590 11.23 13.10 1.88 3.815 21.197 170.030 3.588 11.21 13.09 1.88 3.820 21.196 191.283 3.586 11.19 13.08 1.88 3.825 21.198 212.537 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: 1.275 Accepted refinement result: 11.32 12.96 1.64 3.780 21.261 1.275 3.604 Individual atomic B min max mean iso aniso Overall: 9.10 115.04 21.24 3.31 233 1747 Protein: 9.10 115.04 17.03 3.32 0 1519 Water: 11.52 76.69 35.33 N/A 233 220 Other: 19.75 26.65 22.09 N/A 0 8 Chain A: 9.10 115.04 19.40 N/A 0 1747 Chain S: 13.31 60.00 35.01 N/A 233 0 Histogram: Values Number of atoms 9.10 - 19.70 1267 19.70 - 30.29 296 30.29 - 40.88 213 40.88 - 51.48 133 51.48 - 62.07 49 62.07 - 72.66 11 72.66 - 83.26 5 83.26 - 93.85 4 93.85 - 104.44 0 104.44 - 115.04 2 =========================== Idealize ADP of riding H ========================== r_work=0.1132 r_free=0.1296 r_work=0.1132 r_free=0.1296 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1132 r_free = 0.1296 target_work(ml) = 3.604 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1128 r_free = 0.1294 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.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1128 r_free= 0.1294 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.603254 | | target function (ml) not normalized (work): 300089.839507 | | target function (ml) not normalized (free): 15818.181899 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1321 0.1338 5.6333 5.6137| | 2: 3.57 - 2.84 1.00 2888 124 0.1063 0.1347 5.1565 5.221| | 3: 2.83 - 2.48 1.00 2820 163 0.1095 0.1293 4.9418 4.9943| | 4: 2.47 - 2.25 1.00 2825 136 0.0895 0.1004 4.6279 4.6686| | 5: 2.25 - 2.09 1.00 2756 127 0.0862 0.0966 4.5773 4.6334| | 6: 2.09 - 1.97 1.00 2846 113 0.0856 0.1004 4.267 4.3573| | 7: 1.97 - 1.87 1.00 2787 165 0.0885 0.1131 3.9834 4.1024| | 8: 1.87 - 1.79 1.00 2789 144 0.0913 0.1141 3.8964 4.0134| | 9: 1.79 - 1.72 1.00 2745 138 0.0870 0.1184 3.6522 3.8278| | 10: 1.72 - 1.66 1.00 2831 160 0.0913 0.1170 3.5683 3.7081| | 11: 1.66 - 1.61 1.00 2712 147 0.0866 0.1013 3.499 3.5656| | 12: 1.61 - 1.56 1.00 2773 144 0.0902 0.1149 3.3289 3.4669| | 13: 1.56 - 1.52 1.00 2745 130 0.0948 0.1060 3.3088 3.4081| | 14: 1.52 - 1.48 1.00 2803 134 0.0982 0.1075 3.2392 3.3341| | 15: 1.48 - 1.45 1.00 2738 128 0.1004 0.1203 3.156 3.2523| | 16: 1.45 - 1.42 1.00 2756 161 0.1047 0.1243 3.132 3.2441| | 17: 1.42 - 1.39 1.00 2785 139 0.1141 0.1294 3.119 3.2283| | 18: 1.39 - 1.36 1.00 2741 179 0.1192 0.1318 3.1005 3.2309| | 19: 1.36 - 1.34 1.00 2807 134 0.1258 0.1568 3.1101 3.2663| | 20: 1.34 - 1.32 1.00 2696 147 0.1364 0.1460 3.1107 3.1474| | 21: 1.32 - 1.30 1.00 2785 112 0.1466 0.1532 3.1122 3.1133| | 22: 1.29 - 1.27 1.00 2704 152 0.1556 0.1983 3.1201 3.293| | 23: 1.27 - 1.26 1.00 2802 156 0.1642 0.1814 3.1327 3.206| | 24: 1.26 - 1.24 1.00 2744 132 0.1699 0.1840 3.1251 3.2229| | 25: 1.24 - 1.22 1.00 2733 148 0.1875 0.2136 3.1415 3.2641| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1765 3.1461 3.1999| | 27: 1.21 - 1.19 1.00 2814 148 0.2072 0.2157 3.1697 3.164| | 28: 1.19 - 1.18 1.00 2671 147 0.2205 0.2295 3.1664 3.1695| | 29: 1.18 - 1.16 1.00 2800 134 0.2269 0.2377 3.1485 3.2286| | 30: 1.16 - 1.15 1.00 2739 148 0.2441 0.2446 3.1421 3.1675| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.36 1.00 0.97 5716.10| | 2: 3.57 - 2.84 2888 124 0.93 12.60 1.01 0.97 5716.10| | 3: 2.83 - 2.48 2820 163 0.89 16.51 0.99 0.97 4779.41| | 4: 2.47 - 2.25 2825 136 0.92 13.48 1.00 0.98 2363.96| | 5: 2.25 - 2.09 2756 127 0.90 15.62 1.01 0.98 2363.96| | 6: 2.09 - 1.97 2846 113 0.92 12.47 1.02 0.98 1371.84| | 7: 1.97 - 1.87 2787 165 0.95 9.47 1.02 0.97 525.70| | 8: 1.87 - 1.79 2789 144 0.92 12.83 1.00 0.97 525.70| | 9: 1.79 - 1.72 2745 138 0.94 10.20 0.98 0.97 295.71| | 10: 1.72 - 1.66 2831 160 0.94 11.28 0.98 0.97 249.65| | 11: 1.66 - 1.61 2712 147 0.93 11.87 0.98 0.97 239.02| | 12: 1.61 - 1.56 2773 144 0.95 8.94 0.99 0.97 138.74| | 13: 1.56 - 1.52 2745 130 0.95 10.47 1.03 0.97 138.74| | 14: 1.52 - 1.48 2803 134 0.94 10.79 1.02 0.98 124.41| | 15: 1.48 - 1.45 2738 128 0.95 9.95 1.02 0.98 98.18| | 16: 1.45 - 1.42 2756 161 0.94 11.10 1.02 0.98 98.18| | 17: 1.42 - 1.39 2785 139 0.95 10.93 1.01 0.98 89.19| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.98 83.98| | 19: 1.36 - 1.34 2807 134 0.94 11.85 1.00 0.98 83.98| | 20: 1.34 - 1.32 2696 147 0.94 12.12 0.99 0.97 80.04| | 21: 1.32 - 1.30 2785 112 0.94 13.10 0.98 0.96 79.77| | 22: 1.29 - 1.27 2704 152 0.93 13.65 0.98 0.96 80.18| | 23: 1.27 - 1.26 2802 156 0.92 14.85 0.97 0.95 82.28| | 24: 1.26 - 1.24 2744 132 0.92 14.87 0.96 0.95 82.28| | 25: 1.24 - 1.22 2733 148 0.91 16.35 0.96 0.94 84.23| | 26: 1.22 - 1.21 2727 135 0.90 18.09 1.03 0.93 86.39| | 27: 1.21 - 1.19 2814 148 0.89 18.75 1.02 0.93 86.39| | 28: 1.19 - 1.18 2671 147 0.88 20.39 1.01 0.93 89.89| | 29: 1.18 - 1.16 2800 134 0.88 20.48 0.99 0.93 91.20| | 30: 1.16 - 1.15 2739 148 0.86 22.00 0.98 0.93 91.20| |alpha: min = 0.93 max = 0.98 mean = 0.96| |beta: min = 79.77 max = 5716.10 mean = 886.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.95 mean = 13.48| |phase err.(test): min = 0.00 max = 89.24 mean = 13.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1136 0.1128 0.1294 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1465 0.1465 0.1488 n_refl.: 87579 remove outliers: r(all,work,free)=0.1465 0.1465 0.1488 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1464 0.1464 0.1488 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1137 0.1129 0.1295 n_refl.: 87579 remove outliers: r(all,work,free)=0.1135 0.1127 0.1295 n_refl.: 87576 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 87.50 79 5 0.3801 288.374 252.293 0.452 1.001 0.308 11.894-9.307 95.10 93 4 0.2312 476.524 461.661 0.858 1.002 0.300 9.237-7.194 98.18 209 7 0.2352 386.194 380.086 0.924 1.002 0.180 7.162-5.571 100.00 427 22 0.2100 296.212 285.579 0.911 1.003 0.133 5.546-4.326 100.00 867 58 0.1092 406.626 402.144 0.962 1.003 0.120 4.315-3.360 100.00 1859 96 0.0930 386.705 384.626 1.003 1.002 0.120 3.356-2.611 100.00 3867 181 0.1101 254.045 252.182 1.010 1.002 0.024 2.608-2.026 99.99 8198 413 0.0907 168.409 167.760 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.242 82.585 1.035 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1250 36.469 36.074 1.028 0.997 0.000 1.221-1.150 99.97 13689 708 0.2170 22.978 21.517 0.989 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0120 ================= 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 : 0.2599 0.1925 0.082 5.285 8.8 119.3 19.9 258 0.000 1_bss: 0.1628 0.1740 0.082 5.285 9.1 119.5 20.1 258 0.000 1_settarget: 0.1628 0.1740 0.082 5.285 9.1 119.5 20.1 258 0.000 1_nqh: 0.1629 0.1739 0.082 5.285 9.1 119.5 20.1 258 0.003 1_weight: 0.1629 0.1739 0.082 5.285 9.1 119.5 20.1 258 0.003 1_xyzrec: 0.1228 0.1470 0.006 0.882 9.1 119.5 20.1 258 0.135 1_adp: 0.1235 0.1467 0.006 0.882 9.1 119.5 20.1 258 0.135 1_regHadp: 0.1237 0.1472 0.006 0.882 9.1 119.5 20.1 258 0.135 1_occ: 0.1232 0.1466 0.006 0.882 9.1 119.5 20.1 258 0.135 2_bss: 0.1228 0.1454 0.006 0.882 9.1 119.5 20.1 258 0.135 2_settarget: 0.1228 0.1454 0.006 0.882 9.1 119.5 20.1 258 0.135 2_updatecdl: 0.1228 0.1454 0.006 0.893 9.1 119.5 20.1 258 0.135 2_nqh: 0.1230 0.1455 0.006 0.893 9.1 119.5 20.1 258 0.135 2_sol: 0.1203 0.1403 0.006 0.893 9.1 115.0 22.1 413 n/a 2_weight: 0.1203 0.1403 0.006 0.893 9.1 115.0 22.1 413 n/a 2_xyzrec: 0.1191 0.1407 0.006 0.853 9.1 115.0 22.1 413 n/a 2_adp: 0.1191 0.1407 0.006 0.853 9.1 115.0 22.1 413 n/a 2_regHadp: 0.1191 0.1407 0.006 0.853 9.1 115.0 22.1 413 n/a 2_occ: 0.1189 0.1403 0.006 0.853 9.1 115.0 22.1 413 n/a 3_bss: 0.1186 0.1400 0.006 0.853 9.1 115.0 22.1 413 n/a 3_settarget: 0.1186 0.1400 0.006 0.853 9.1 115.0 22.1 413 n/a 3_updatecdl: 0.1186 0.1400 0.006 0.854 9.1 115.0 22.1 413 n/a 3_nqh: 0.1186 0.1400 0.006 0.854 9.1 115.0 22.1 413 n/a 3_sol: 0.1208 0.1392 0.006 0.854 9.1 115.0 21.3 433 n/a 3_weight: 0.1208 0.1392 0.006 0.854 9.1 115.0 21.3 433 n/a 3_xyzrec: 0.1158 0.1306 0.007 1.019 9.1 115.0 21.3 433 n/a 3_adp: 0.1158 0.1306 0.007 1.019 9.1 115.0 21.3 433 n/a 3_regHadp: 0.1158 0.1306 0.007 1.019 9.1 115.0 21.3 433 n/a 3_occ: 0.1149 0.1316 0.007 1.019 9.1 115.0 21.3 433 n/a 4_bss: 0.1143 0.1312 0.007 1.019 9.1 115.0 21.3 433 n/a 4_settarget: 0.1143 0.1312 0.007 1.019 9.1 115.0 21.3 433 n/a 4_updatecdl: 0.1143 0.1312 0.007 1.020 9.1 115.0 21.3 433 n/a 4_nqh: 0.1143 0.1312 0.007 1.020 9.1 115.0 21.3 433 n/a 4_sol: 0.1142 0.1301 0.007 1.020 9.1 115.0 21.2 442 n/a 4_weight: 0.1142 0.1301 0.007 1.020 9.1 115.0 21.2 442 n/a 4_xyzrec: 0.1146 0.1304 0.006 0.945 9.1 115.0 21.2 442 n/a 4_adp: 0.1146 0.1304 0.006 0.945 9.1 115.0 21.2 442 n/a 4_regHadp: 0.1146 0.1304 0.006 0.945 9.1 115.0 21.2 442 n/a 4_occ: 0.1140 0.1300 0.006 0.945 9.1 115.0 21.2 442 n/a 5_bss: 0.1136 0.1298 0.006 0.945 9.1 115.0 21.2 442 n/a 5_settarget: 0.1136 0.1298 0.006 0.945 9.1 115.0 21.2 442 n/a 5_updatecdl: 0.1136 0.1298 0.006 0.947 9.1 115.0 21.2 442 n/a 5_setrh: 0.1136 0.1298 0.006 0.947 9.1 115.0 21.2 442 n/a 5_nqh: 0.1136 0.1298 0.006 0.947 9.1 115.0 21.2 442 n/a 5_sol: 0.1139 0.1298 0.006 0.947 9.1 115.0 21.2 453 n/a 5_weight: 0.1139 0.1298 0.006 0.947 9.1 115.0 21.2 453 n/a 5_xyzrec: 0.1132 0.1296 0.009 1.123 9.1 115.0 21.2 453 n/a 5_adp: 0.1132 0.1296 0.009 1.123 9.1 115.0 21.2 453 n/a 5_regHadp: 0.1132 0.1296 0.009 1.123 9.1 115.0 21.2 453 n/a 5_occ: 0.1128 0.1294 0.009 1.123 9.1 115.0 21.2 453 n/a end: 0.1127 0.1295 0.009 1.123 9.1 115.0 21.2 453 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6824987_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_6824987_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8500 Refinement macro-cycles (run) : 13500.4300 Write final files (write_after_run_outputs) : 95.0600 Total : 13599.3400 Total CPU time: 3.79 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:04:44 PST -0800 (1735365884.82 s) Start R-work = 0.1628, R-free = 0.1740 Final R-work = 0.1127, R-free = 0.1295 =============================================================================== Job complete usr+sys time: 13786.23 seconds wall clock time: 249 minutes 4.85 seconds (14944.85 seconds total)