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_2731660.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" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2731660.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2731660.pdb" } 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 1 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: 1.63, per 1000 atoms: 0.48 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: 0.54 Conformation dependent library (CDL) restraints added in 194.9 milliseconds Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 420 0.89 - 1.15: 1201 1.15 - 1.41: 598 1.41 - 1.66: 895 1.66 - 1.92: 39 Bond restraints: 3153 Sorted by residual: bond pdb=" N ATYR A 67 " pdb=" CA ATYR A 67 " ideal model delta sigma weight residual 1.455 1.217 0.238 1.21e-02 6.83e+03 3.86e+02 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.524 1.762 -0.238 1.27e-02 6.20e+03 3.52e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.237 1.032 0.205 1.14e-02 7.69e+03 3.24e+02 bond pdb=" C BGLU A 90 " pdb=" O BGLU A 90 " ideal model delta sigma weight residual 1.237 1.026 0.210 1.17e-02 7.31e+03 3.23e+02 bond pdb=" N LEU A 166 " pdb=" CA LEU A 166 " ideal model delta sigma weight residual 1.459 1.245 0.214 1.28e-02 6.10e+03 2.80e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 2852 4.20 - 8.39: 1891 8.39 - 12.58: 799 12.58 - 16.78: 204 16.78 - 20.97: 31 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.30 106.14 15.16 1.03e+00 9.43e-01 2.17e+02 angle pdb=" CA ILE A 9 " pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 120.53 135.60 -15.07 1.07e+00 8.73e-01 1.98e+02 angle pdb=" CA THR A 19 " pdb=" C THR A 19 " pdb=" O THR A 19 " ideal model delta sigma weight residual 120.56 137.52 -16.96 1.21e+00 6.83e-01 1.96e+02 angle pdb=" O GLU A 176 " pdb=" C GLU A 176 " pdb=" N VAL A 177 " ideal model delta sigma weight residual 122.07 136.33 -14.26 1.03e+00 9.43e-01 1.92e+02 angle pdb=" O SER A 155 " pdb=" C SER A 155 " pdb=" N ARG A 156 " ideal model delta sigma weight residual 123.26 108.99 14.27 1.05e+00 9.07e-01 1.85e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 943 17.51 - 35.02: 119 35.02 - 52.53: 31 52.53 - 70.04: 16 70.04 - 87.55: 2 Dihedral angle restraints: 1111 sinusoidal: 852 harmonic: 259 Sorted by residual: dihedral pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" N MET A 134 " pdb=" CA MET A 134 " ideal model delta harmonic sigma weight residual -180.00 -157.77 -22.23 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CG PHE A 119 " pdb=" CD1 PHE A 119 " pdb=" CE1 PHE A 119 " pdb=" HE1 PHE A 119 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+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 -160.48 -19.52 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 1108 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.217: 92 0.217 - 0.432: 85 0.432 - 0.647: 36 0.647 - 0.862: 23 0.862 - 1.077: 7 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 33 " pdb=" CA VAL A 33 " pdb=" CG1 VAL A 33 " pdb=" CG2 VAL A 33 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -1.71 -0.92 2.00e-01 2.50e+01 2.12e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " 0.107 2.00e-02 2.50e+03 7.43e-02 1.66e+02 pdb=" CG TYR A 141 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.098 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.081 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.133 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " -0.027 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.042 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.016 9.50e-02 1.11e+02 7.27e-02 1.18e+02 pdb=" NE ARG A 5 " -0.075 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.149 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.104 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.057 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.016 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.014 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.032 2.00e-02 2.50e+03 5.88e-02 1.04e+02 pdb=" CG PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.054 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.088 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.052 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.077 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.078 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.115 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1314 2.36 - 2.92: 8268 2.92 - 3.48: 10480 3.48 - 4.04: 15127 4.04 - 4.60: 21440 Nonbonded interactions: 56629 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.794 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.836 2.100 nonbonded pdb=" HG2 LYS A 12 " pdb=" HZ2 LYS A 12 " model vdw 1.838 2.270 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.842 2.100 nonbonded pdb=" H ALA A 104 " pdb=" O ALEU A 153 " model vdw 1.846 1.850 ... (remaining 56624 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_2731660_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= 0.2610 r_free= 0.1920 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788486 | | target function (ml) not normalized (work): 232297.590165 | | target function (ml) not normalized (free): 11803.691513 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3022 0.2050 7.1285 4.9389| | 2: 3.57 - 2.84 1.00 2876 122 0.2441 0.1764 4.3388 4.3345| | 3: 2.84 - 2.48 1.00 2833 165 0.2370 0.1675 4.1222 4.1577| | 4: 2.47 - 2.25 1.00 2825 136 0.2355 0.1469 3.8284 3.8534| | 5: 2.25 - 2.09 1.00 2756 127 0.2479 0.1508 3.7943 3.8169| | 6: 2.09 - 1.97 1.00 2846 113 0.2547 0.1702 3.4511 3.5287| | 7: 1.97 - 1.87 1.00 2787 165 0.2505 0.1887 3.1238 3.2213| | 8: 1.87 - 1.79 1.00 2789 144 0.2469 0.1784 3.064 3.1068| | 9: 1.79 - 1.72 1.00 2745 138 0.2442 0.1751 2.8863 2.9113| | 10: 1.72 - 1.66 1.00 2789 158 0.2430 0.2172 2.8045 2.9639| | 11: 1.66 - 1.61 1.00 2740 147 0.2490 0.1680 2.7498 2.7047| | 12: 1.61 - 1.56 1.00 2787 146 0.2529 0.2024 2.6222 2.6696| | 13: 1.56 - 1.52 1.00 2745 130 0.2535 0.1811 2.5635 2.5734| | 14: 1.52 - 1.48 1.00 2803 134 0.2569 0.1943 2.4984 2.5026| | 15: 1.48 - 1.45 1.00 2738 128 0.2624 0.2203 2.4279 2.5398| | 16: 1.45 - 1.42 1.00 2756 161 0.2688 0.2196 2.3747 2.4101| | 17: 1.42 - 1.39 1.00 2785 139 0.2697 0.2038 2.3196 2.3739| | 18: 1.39 - 1.36 1.00 2741 179 0.2697 0.2092 2.2665 2.3127| | 19: 1.36 - 1.34 1.00 2807 134 0.2648 0.2125 2.2193 2.2324| | 20: 1.34 - 1.32 1.00 2696 147 0.2711 0.2254 2.1853 2.2159| | 21: 1.32 - 1.30 1.00 2785 112 0.2723 0.2267 2.1731 2.2076| | 22: 1.29 - 1.27 1.00 2704 152 0.2684 0.2570 2.1291 2.2044| | 23: 1.27 - 1.26 1.00 2802 156 0.2770 0.2391 2.1097 2.1372| | 24: 1.26 - 1.24 1.00 2744 132 0.2749 0.2599 2.0698 2.184| | 25: 1.24 - 1.22 1.00 2734 148 0.2859 0.2485 2.0441 2.0775| | 26: 1.22 - 1.21 1.00 2727 135 0.2902 0.2296 2.0255 2.0497| | 27: 1.21 - 1.19 1.00 2814 148 0.2971 0.2632 2.0028 2.0375| | 28: 1.19 - 1.18 1.00 2671 147 0.2958 0.2683 1.975 1.9699| | 29: 1.18 - 1.16 1.00 2800 134 0.3005 0.2905 1.9614 2.0769| | 30: 1.16 - 1.15 1.00 2740 148 0.3084 0.2852 1.935 1.9665| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 18.64 0.76 0.23 1452.67| | 2: 3.57 - 2.84 2876 122 0.81 25.75 1.27 0.23 1452.67| | 3: 2.84 - 2.48 2833 165 0.74 31.68 1.24 0.24 1204.89| | 4: 2.47 - 2.25 2825 136 0.81 25.28 1.26 0.25 561.85| | 5: 2.25 - 2.09 2756 127 0.77 29.08 1.28 0.25 561.85| | 6: 2.09 - 1.97 2846 113 0.84 22.42 1.29 0.25 307.65| | 7: 1.97 - 1.87 2787 165 0.90 16.42 1.28 0.26 90.85| | 8: 1.87 - 1.79 2789 144 0.86 21.06 1.25 0.26 90.85| | 9: 1.79 - 1.72 2745 138 0.88 18.62 1.24 0.26 54.56| | 10: 1.72 - 1.66 2789 158 0.87 19.83 1.22 0.26 47.29| | 11: 1.66 - 1.61 2740 147 0.86 20.81 1.24 0.26 45.57| | 12: 1.61 - 1.56 2787 146 0.89 17.97 1.23 0.25 28.12| | 13: 1.56 - 1.52 2745 130 0.87 19.88 1.23 0.25 28.12| | 14: 1.52 - 1.48 2803 134 0.87 20.09 1.24 0.25 25.17| | 15: 1.48 - 1.45 2738 128 0.87 19.66 1.24 0.25 19.76| | 16: 1.45 - 1.42 2756 161 0.86 20.96 1.25 0.25 19.76| | 17: 1.42 - 1.39 2785 139 0.87 20.08 1.25 0.25 16.83| | 18: 1.39 - 1.36 2741 179 0.87 20.56 1.24 0.25 15.13| | 19: 1.36 - 1.34 2807 134 0.86 21.47 1.22 0.25 15.13| | 20: 1.34 - 1.32 2696 147 0.87 20.68 1.22 0.25 12.75| | 21: 1.32 - 1.30 2785 112 0.86 21.65 1.20 0.25 12.58| | 22: 1.29 - 1.27 2704 152 0.86 21.83 1.21 0.24 12.33| | 23: 1.27 - 1.26 2802 156 0.86 21.97 1.21 0.24 11.05| | 24: 1.26 - 1.24 2744 132 0.85 22.89 1.20 0.24 11.05| | 25: 1.24 - 1.22 2734 148 0.84 23.89 1.20 0.24 10.62| | 26: 1.22 - 1.21 2727 135 0.84 24.14 1.21 0.23 10.15| | 27: 1.21 - 1.19 2814 148 0.83 25.23 1.21 0.23 10.15| | 28: 1.19 - 1.18 2671 147 0.82 25.80 1.18 0.23 9.70| | 29: 1.18 - 1.16 2800 134 0.81 26.54 1.17 0.23 9.53| | 30: 1.16 - 1.15 2740 148 0.80 28.01 1.16 0.23 9.53| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 9.53 max = 1452.67 mean = 211.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.98 mean = 22.43| |phase err.(test): min = 0.00 max = 89.96 mean = 22.30| |-----------------------------------------------------------------------------| ----------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 0.238 1557 Z= 5.523 Angle : 5.295 17.793 2118 Z= 3.754 Chirality : 0.405 1.077 243 Planarity : 0.033 0.101 284 Dihedral : 13.758 87.555 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 38.92 % 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: -2.42 (0.47), residues: 224 helix: -2.39 (0.38), residues: 109 sheet: -0.53 (0.97), residues: 28 loop : -0.54 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.142 0.025 ARG A 5 TYR 0.109 0.052 TYR A 141 PHE 0.088 0.033 PHE A 119 HIS 0.058 0.025 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= 0.2610 r_free= 0.1920 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 2.788486 | | target function (ml) not normalized (work): 232297.590165 | | target function (ml) not normalized (free): 11803.691513 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2567 0.2611 0.1921 n_refl.: 87602 re-set all scales: r(all,work,free)=0.2567 0.2611 0.1921 n_refl.: 87602 remove outliers: r(all,work,free)=0.1976 0.1981 0.1921 n_refl.: 87594 overall B=0.14 to atoms: r(all,work,free)=0.1993 0.1998 0.1930 n_refl.: 87594 bulk-solvent and scaling: r(all,work,free)=0.1639 0.1633 0.1748 n_refl.: 87594 remove outliers: r(all,work,free)=0.1638 0.1632 0.1748 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 0.3850 386.571 356.797 0.667 1.002 0.401 11.894-9.307 99.02 97 4 0.1764 614.050 595.842 0.934 1.003 0.380 9.237-7.194 100.00 213 7 0.2139 502.217 492.264 0.969 1.003 0.352 7.162-5.571 100.00 427 22 0.2255 376.886 364.096 0.931 1.003 0.290 5.546-4.326 100.00 867 58 0.1271 517.371 511.482 0.967 1.003 0.229 4.315-3.360 100.00 1859 96 0.1130 492.024 487.748 1.008 1.003 0.209 3.356-2.611 100.00 3867 181 0.1442 323.234 319.929 1.002 1.003 0.100 2.608-2.026 99.99 8198 413 0.1359 214.275 211.917 1.010 1.002 0.000 2.025-1.573 100.00 17313 902 0.1641 104.641 103.928 1.012 1.000 0.000 1.573-1.221 100.00 36679 1900 0.2051 46.402 45.145 1.005 0.997 0.000 1.221-1.150 99.97 13689 708 0.2571 29.236 27.053 0.978 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.0531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1632 r_free=0.1748 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 r_work=0.1637 r_free=0.1755 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 26.308952 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2030.578479 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 0.1785 0.0128 0.001 0.4 4.8 0.0 0.0 0 0.125 0.1591 0.1732 0.0142 0.001 0.4 4.5 0.0 0.0 0 0.250 0.1425 0.1595 0.0170 0.002 0.5 3.8 0.0 0.0 0 0.500 0.1389 0.1574 0.0185 0.002 0.5 3.5 0.0 0.0 0 0.750 0.1352 0.1552 0.0201 0.002 0.5 3.5 0.0 0.0 0 1.000 0.1357 0.1553 0.0197 0.002 0.5 3.8 0.0 0.0 0 1.000 0.1290 0.1499 0.0209 0.002 0.6 3.2 0.5 0.0 0 2.000 0.1275 0.1497 0.0222 0.003 0.6 3.2 0.5 0.0 0 3.000 0.1254 0.1483 0.0229 0.003 0.7 3.5 0.5 0.0 0 4.000 0.1243 0.1471 0.0228 0.004 0.7 3.2 0.5 0.0 0 5.000 0.1241 0.1474 0.0233 0.004 0.8 3.5 0.5 0.0 0 6.000 0.1236 0.1470 0.0234 0.005 0.8 3.8 0.5 0.0 0 7.000 0.1233 0.1470 0.0237 0.005 0.8 4.2 0.5 0.0 0 8.000 0.1231 0.1467 0.0236 0.006 0.8 3.5 0.5 0.0 0 9.000 0.1226 0.1463 0.0237 0.006 0.9 4.2 0.5 0.0 0 10.000 0.1227 0.1469 0.0243 0.007 0.9 3.5 0.5 0.0 0 11.000 0.1222 0.1462 0.0240 0.007 0.9 3.8 0.5 0.0 0 12.000 0.1222 0.1470 0.0249 0.007 0.9 4.2 0.5 0.0 0 13.154 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1222 0.1462 0.0240 0.007 0.9 3.8 0.5 0.0 0 12.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.22 14.62 2.40 3.013 18.995 2030.578 0.017 12.22 14.61 2.39 2.979 18.995 60.917 0.017 12.30 14.59 2.29 2.669 18.995 253.822 0.017 12.66 15.26 2.60 2.787 19.209 1015.289 0.016 12.52 15.42 2.90 3.240 19.509 2030.578 0.016 12.37 15.40 3.03 3.365 19.596 3045.868 0.015 12.35 15.46 3.11 3.496 19.652 4061.157 0.015 12.29 15.43 3.14 3.415 19.593 5076.446 0.015 12.11 15.29 3.18 3.381 19.587 6091.735 0.015 12.12 15.29 3.16 3.377 19.565 7107.025 0.015 12.12 15.34 3.22 3.458 19.604 8122.314 0.015 12.12 15.33 3.21 3.406 19.556 9137.603 0.015 12.12 15.41 3.29 3.441 19.566 10152.892 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: 253.822 Accepted refinement result: 12.30 14.59 2.29 2.669 18.995 253.822 0.017 Individual atomic B min max mean iso aniso Overall: 9.03 119.38 20.02 3.31 0 1785 Protein: 9.03 114.94 16.93 3.32 0 1519 Water: 11.41 119.38 38.16 N/A 0 258 Other: 19.66 26.53 21.99 N/A 0 8 Chain A: 9.03 119.38 20.02 N/A 0 1785 Histogram: Values Number of atoms 9.03 - 20.06 1272 20.06 - 31.10 227 31.10 - 42.13 125 42.13 - 53.17 94 53.17 - 64.20 42 64.20 - 75.24 11 75.24 - 86.28 7 86.28 - 97.31 4 97.31 - 108.35 1 108.35 - 119.38 2 =========================== Idealize ADP of riding H ========================== r_work=0.1230 r_free=0.1459 r_work=0.1231 r_free=0.1462 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1231 r_free = 0.1462 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1226 r_free = 0.1458 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87593 (all), 4.90 % free)------------| | | | r_work= 0.1226 r_free= 0.1458 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ls_wunit_k1) (work): 0.016826 | | target function (ls_wunit_k1) not normalized (work): 1401.581845 | | target function (ls_wunit_k1) not normalized (free): 110.767076 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1237 0.1226 0.1458 n_refl.: 87593 re-set all scales: r(all,work,free)=0.1661 0.1662 0.1686 n_refl.: 87593 remove outliers: r(all,work,free)=0.1661 0.1662 0.1686 n_refl.: 87593 overall B=0.05 to atoms: r(all,work,free)=0.1670 0.1671 0.1692 n_refl.: 87593 bulk-solvent and scaling: r(all,work,free)=0.1237 0.1226 0.1453 n_refl.: 87593 remove outliers: r(all,work,free)=0.1236 0.1225 0.1453 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 0.3605 303.108 284.290 0.643 1.003 0.379 11.894-9.307 99.02 97 4 0.1712 485.562 471.237 0.920 1.003 0.379 9.237-7.194 100.00 213 7 0.1896 397.130 391.484 0.964 1.003 0.342 7.162-5.571 100.00 427 22 0.1850 298.024 291.728 0.936 1.003 0.259 5.546-4.326 100.00 867 58 0.1009 409.114 406.004 0.962 1.003 0.204 4.315-3.360 100.00 1859 96 0.0873 389.070 387.967 1.007 1.003 0.180 3.356-2.611 100.00 3867 181 0.1168 255.599 254.500 1.009 1.002 0.100 2.608-2.026 99.99 8198 413 0.1019 169.439 168.758 1.017 1.001 0.000 2.025-1.573 100.00 17313 902 0.1106 82.745 82.936 1.024 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1447 36.693 36.199 1.015 0.996 0.000 1.221-1.150 99.97 13689 708 0.2251 23.119 21.587 0.976 0.994 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0839 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1225 r_free=0.1453 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1225 r_free=0.1453 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1225 r_free=0.1453 | n_water=258 | time (s): 1.910 (total time: 1.910) Filter (dist) r_work=0.1234 r_free=0.1452 | n_water=252 | time (s): 24.340 (total time: 26.250) Filter (q & B) r_work=0.1236 r_free=0.1452 | n_water=249 | time (s): 2.430 (total time: 28.680) Compute maps r_work=0.1236 r_free=0.1452 | n_water=249 | time (s): 1.390 (total time: 30.070) Filter (map) r_work=0.1250 r_free=0.1456 | n_water=227 | time (s): 2.540 (total time: 32.610) Find peaks r_work=0.1250 r_free=0.1456 | n_water=227 | time (s): 0.590 (total time: 33.200) Add new water r_work=0.1397 r_free=0.1633 | n_water=439 | time (s): 2.700 (total time: 35.900) Refine new water occ: r_work=0.1298 r_free=0.1486 adp: r_work=0.1219 r_free=0.1428 occ: r_work=0.1229 r_free=0.1421 adp: r_work=0.1198 r_free=0.1400 occ: r_work=0.1200 r_free=0.1391 adp: r_work=0.1190 r_free=0.1389 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1389 r_work=0.1190 r_free=0.1389 | n_water=439 | time (s): 58.460 (total time: 94.360) Filter (q & B) r_work=0.1194 r_free=0.1395 | n_water=422 | time (s): 2.590 (total time: 96.950) Filter (dist only) r_work=0.1194 r_free=0.1394 | n_water=421 | time (s): 36.640 (total time: 133.590) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 28.535963 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1491.920838 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 0.1684 0.1798 0.0114 0.001 0.4 7.7 0.0 0.0 0 0.125 0.1515 0.1653 0.0137 0.001 0.4 7.0 0.0 0.0 0 0.250 0.1399 0.1557 0.0158 0.001 0.4 5.8 0.0 0.0 0 0.500 0.1348 0.1519 0.0171 0.002 0.5 5.8 0.0 0.0 0 0.750 0.1321 0.1502 0.0180 0.002 0.5 5.1 0.0 0.0 0 1.000 0.1321 0.1501 0.0180 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 0.1230 0.1444 0.0214 0.003 0.6 4.5 0.5 0.0 0 3.000 0.1212 0.1424 0.0212 0.003 0.7 4.2 0.5 0.0 0 4.000 0.1209 0.1433 0.0224 0.004 0.7 4.5 0.5 0.0 0 5.000 0.1201 0.1419 0.0217 0.004 0.7 4.2 0.5 0.0 0 6.000 0.1197 0.1424 0.0227 0.005 0.8 4.2 0.5 0.0 0 7.000 0.1197 0.1428 0.0231 0.005 0.8 4.8 0.5 0.0 0 8.000 0.1193 0.1421 0.0229 0.006 0.8 4.5 0.5 0.0 0 9.000 0.1192 0.1423 0.0232 0.006 0.8 5.4 0.5 0.0 0 10.000 0.1189 0.1424 0.0236 0.007 0.9 5.1 0.5 0.0 0 11.000 0.1185 0.1421 0.0236 0.007 0.9 4.8 0.5 0.0 0 12.000 0.1185 0.1418 0.0233 0.007 0.9 4.8 0.5 0.0 0 13.000 0.1183 0.1417 0.0234 0.008 0.9 5.1 0.5 0.6 0 14.268 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1183 0.1417 0.0234 0.008 0.9 5.1 0.5 0.6 0 14.268 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.83 14.17 2.34 3.770 21.742 1491.921 0.016 11.83 14.17 2.34 3.770 21.742 44.758 0.016 11.83 14.17 2.34 3.770 21.742 186.490 0.016 11.97 14.54 2.57 3.635 21.742 745.960 0.015 12.00 14.90 2.90 3.552 21.809 1491.921 0.015 11.79 14.64 2.85 3.463 22.096 2237.881 0.014 11.77 14.75 2.98 3.493 22.082 2983.842 0.014 11.66 14.64 2.98 3.477 22.031 3729.802 0.014 11.70 14.77 3.06 3.506 22.137 4475.763 0.014 11.65 14.71 3.07 3.511 22.095 5221.723 0.014 11.64 14.77 3.13 3.525 22.045 5967.683 0.014 11.61 14.76 3.15 3.536 22.086 6713.644 0.014 11.60 14.78 3.19 3.573 22.175 7459.604 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: 186.490 Accepted refinement result: 11.83 14.17 2.34 3.770 21.742 186.490 0.016 Individual atomic B min max mean iso aniso Overall: 9.08 114.99 22.16 3.31 194 1754 Protein: 9.08 114.99 16.99 3.32 0 1519 Water: 11.46 76.65 40.85 N/A 194 227 Other: 19.72 26.59 22.05 N/A 0 8 Chain A: 9.08 114.99 19.44 N/A 0 1754 Chain S: 16.88 60.00 46.79 N/A 194 0 Histogram: Values Number of atoms 9.08 - 19.67 1261 19.67 - 30.26 245 30.26 - 40.85 162 40.85 - 51.45 137 51.45 - 62.04 120 62.04 - 72.63 12 72.63 - 83.22 5 83.22 - 93.81 4 93.81 - 104.40 0 104.40 - 114.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1183 r_free=0.1417 r_work=0.1183 r_free=0.1417 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1183 r_free = 0.1417 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 = 0.1183 r_free = 0.1406 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87592 (all), 4.90 % free)------------| | | | r_work= 0.1183 r_free= 0.1406 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ls_wunit_k1) (work): 0.014897 | | target function (ls_wunit_k1) not normalized (work): 1240.857025 | | target function (ls_wunit_k1) not normalized (free): 100.798930 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1193 0.1183 0.1406 n_refl.: 87592 re-set all scales: r(all,work,free)=0.1576 0.1576 0.1612 n_refl.: 87592 remove outliers: r(all,work,free)=0.1576 0.1576 0.1612 n_refl.: 87592 overall B=0.02 to atoms: r(all,work,free)=0.1580 0.1580 0.1615 n_refl.: 87592 bulk-solvent and scaling: r(all,work,free)=0.1190 0.1179 0.1402 n_refl.: 87592 remove outliers: r(all,work,free)=0.1189 0.1178 0.1402 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 0.3350 301.648 277.751 0.593 1.002 0.360 11.894-9.307 99.02 97 4 0.1703 485.562 476.311 0.915 1.003 0.337 9.237-7.194 100.00 213 7 0.1666 397.130 395.588 0.984 1.003 0.280 7.162-5.571 100.00 427 22 0.1590 298.024 293.109 0.941 1.003 0.250 5.546-4.326 100.00 867 58 0.0873 409.114 406.238 0.960 1.003 0.220 4.315-3.360 100.00 1859 96 0.0778 389.070 388.376 1.006 1.003 0.190 3.356-2.611 100.00 3867 181 0.1068 255.599 254.790 1.009 1.002 0.110 2.608-2.026 99.99 8198 413 0.1006 169.439 168.894 1.020 1.001 0.000 2.025-1.573 100.00 17313 902 0.1094 82.745 82.956 1.028 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1441 36.693 36.230 1.021 0.997 0.000 1.221-1.150 99.97 13689 708 0.2250 23.119 21.617 0.983 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0150 b_overall=0.0372 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1178 r_free=0.1402 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1178 r_free=0.1402 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1178 r_free=0.1402 | n_water=421 | time (s): 2.230 (total time: 2.230) Filter (dist) r_work=0.1178 r_free=0.1402 | n_water=417 | time (s): 37.030 (total time: 39.260) Filter (q & B) r_work=0.1178 r_free=0.1402 | n_water=417 | time (s): 1.000 (total time: 40.260) Compute maps r_work=0.1178 r_free=0.1402 | n_water=417 | time (s): 1.470 (total time: 41.730) Filter (map) r_work=0.1215 r_free=0.1396 | n_water=288 | time (s): 2.750 (total time: 44.480) Find peaks r_work=0.1215 r_free=0.1396 | n_water=288 | time (s): 0.510 (total time: 44.990) Add new water r_work=0.1330 r_free=0.1516 | n_water=462 | time (s): 3.110 (total time: 48.100) Refine new water occ: r_work=0.1242 r_free=0.1434 adp: r_work=0.1243 r_free=0.1433 occ: r_work=0.1222 r_free=0.1417 adp: r_work=0.1220 r_free=0.1415 occ: r_work=0.1206 r_free=0.1407 adp: r_work=0.1200 r_free=0.1402 ADP+occupancy (water only), MIN, final r_work=0.1200 r_free=0.1402 r_work=0.1200 r_free=0.1402 | n_water=462 | time (s): 212.250 (total time: 260.350) Filter (q & B) r_work=0.1205 r_free=0.1405 | n_water=431 | time (s): 3.190 (total time: 263.540) Filter (dist only) r_work=0.1205 r_free=0.1403 | n_water=430 | time (s): 35.580 (total time: 299.120) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.766933 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 47.927015 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 0.1230 0.1375 0.0144 0.002 0.6 4.8 0.5 0.0 0 0.088 0.1194 0.1342 0.0148 0.003 0.7 4.2 0.5 0.0 0 0.265 0.1176 0.1331 0.0155 0.004 0.8 3.2 0.5 0.0 0 0.530 0.1169 0.1330 0.0161 0.005 0.9 3.2 0.5 0.0 0 0.795 0.1164 0.1327 0.0162 0.006 1.0 3.2 0.5 0.0 0 1.060 0.1162 0.1326 0.0164 0.007 1.0 3.2 0.5 0.0 0 1.325 0.1160 0.1327 0.0166 0.007 1.1 3.2 0.5 0.0 0 1.590 0.1158 0.1328 0.0170 0.008 1.1 3.5 0.5 0.0 0 1.855 0.1167 0.1330 0.0162 0.005 0.9 2.9 0.5 0.0 0 0.883 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1162 0.1326 0.0164 0.007 1.0 3.2 0.5 0.0 0 1.325 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 13.26 1.64 3.775 21.215 47.927 3.628 11.62 13.26 1.64 3.775 21.215 1.438 3.628 11.63 13.27 1.64 3.764 21.215 5.991 3.628 11.68 13.37 1.69 3.708 21.202 23.964 3.622 11.69 13.45 1.76 3.726 21.169 47.927 3.621 11.62 13.42 1.79 3.753 21.158 71.891 3.616 11.56 13.38 1.82 3.769 21.153 95.854 3.611 11.52 13.36 1.83 3.781 21.150 119.818 3.608 11.52 13.38 1.86 3.796 21.133 143.781 3.607 11.49 13.37 1.87 3.806 21.136 167.745 3.606 11.48 13.36 1.88 3.816 21.126 191.708 3.604 11.48 13.36 1.89 3.826 21.118 215.672 3.603 11.46 13.35 1.89 3.829 21.123 239.635 3.602 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.438 Accepted refinement result: 11.62 13.26 1.64 3.775 21.215 1.438 3.628 Individual atomic B min max mean iso aniso Overall: 9.11 115.02 21.18 3.31 205 1752 Protein: 9.11 115.02 17.01 3.32 0 1519 Water: 11.48 76.67 35.88 N/A 205 225 Other: 19.74 26.61 22.07 N/A 0 8 Chain A: 9.11 115.02 19.43 N/A 0 1752 Chain S: 16.02 60.02 36.13 N/A 205 0 Histogram: Values Number of atoms 9.11 - 19.70 1266 19.70 - 30.29 285 30.29 - 40.88 199 40.88 - 51.47 131 51.47 - 62.06 53 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.02 2 =========================== Idealize ADP of riding H ========================== r_work=0.1162 r_free=0.1326 r_work=0.1162 r_free=0.1326 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1162 r_free = 0.1326 target_work(ml) = 3.628 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1154 r_free = 0.1324 target_work(ml) = 3.622 | | occupancies: max = 1.00 min = 0.20 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= 0.1154 r_free= 0.1324 coordinate error (max.-lik. estimate): 0.07 A | | | | normalized target function (ml) (work): 3.621919 | | target function (ml) not normalized (work): 301684.111032 | | target function (ml) not normalized (free): 15882.472196 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1154 0.1324 n_refl.: 87590 re-set all scales: r(all,work,free)=0.1505 0.1504 0.1561 n_refl.: 87590 remove outliers: r(all,work,free)=0.1505 0.1504 0.1561 n_refl.: 87590 overall B=-0.00 to atoms: r(all,work,free)=0.1505 0.1504 0.1561 n_refl.: 87590 bulk-solvent and scaling: r(all,work,free)=0.1158 0.1151 0.1314 n_refl.: 87590 remove outliers: r(all,work,free)=0.1155 0.1147 0.1314 n_refl.: 87582 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 91.67 83 5 0.3736 295.704 276.192 0.504 1.000 0.304 11.894-9.307 97.06 95 4 0.2299 478.858 463.334 0.881 1.002 0.256 9.237-7.194 98.18 209 7 0.2240 388.556 388.721 0.960 1.002 0.220 7.162-5.571 100.00 427 22 0.2079 298.024 289.036 0.930 1.002 0.220 5.546-4.326 100.00 867 58 0.1106 409.114 404.186 0.965 1.002 0.175 4.315-3.360 100.00 1859 96 0.0956 389.070 386.472 1.005 1.002 0.170 3.356-2.611 100.00 3867 181 0.1143 255.599 253.457 1.006 1.002 0.043 2.608-2.026 99.99 8198 413 0.0939 169.439 168.567 1.023 1.001 0.000 2.025-1.573 100.00 17313 902 0.0901 82.745 83.019 1.034 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1260 36.693 36.268 1.026 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.119 21.647 0.987 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0002 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1147 r_free=0.1314 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1147 r_free=0.1314 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1147 r_free=0.1314 | n_water=430 | time (s): 2.580 (total time: 2.580) Filter (dist) r_work=0.1147 r_free=0.1315 | n_water=427 | time (s): 45.330 (total time: 47.910) Filter (q & B) r_work=0.1147 r_free=0.1315 | n_water=427 | time (s): 1.330 (total time: 49.240) Compute maps r_work=0.1147 r_free=0.1315 | n_water=427 | time (s): 1.890 (total time: 51.130) Filter (map) r_work=0.1168 r_free=0.1310 | n_water=316 | time (s): 3.870 (total time: 55.000) Find peaks r_work=0.1168 r_free=0.1310 | n_water=316 | time (s): 0.700 (total time: 55.700) Add new water r_work=0.1247 r_free=0.1398 | n_water=482 | time (s): 3.750 (total time: 59.450) Refine new water occ: r_work=0.1174 r_free=0.1335 adp: r_work=0.1175 r_free=0.1337 occ: r_work=0.1158 r_free=0.1318 adp: r_work=0.1158 r_free=0.1319 occ: r_work=0.1145 r_free=0.1306 adp: r_work=0.1142 r_free=0.1305 ADP+occupancy (water only), MIN, final r_work=0.1142 r_free=0.1305 r_work=0.1142 r_free=0.1305 | n_water=482 | time (s): 270.680 (total time: 330.130) Filter (q & B) r_work=0.1149 r_free=0.1309 | n_water=446 | time (s): 3.990 (total time: 334.120) Filter (dist only) r_work=0.1155 r_free=0.1308 | n_water=444 | time (s): 47.250 (total time: 381.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.758067 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 46.210854 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 0.1339 0.0127 0.002 0.6 4.2 0.5 0.0 0 0.088 0.1180 0.1320 0.0140 0.003 0.7 3.2 0.5 0.0 0 0.264 0.1165 0.1311 0.0147 0.005 0.9 4.8 0.5 0.0 0 0.527 0.1159 0.1310 0.0151 0.006 0.9 4.2 0.5 0.0 0 0.791 0.1155 0.1309 0.0154 0.006 1.0 3.8 0.5 0.0 0 1.055 0.1152 0.1306 0.0154 0.007 1.1 4.8 0.5 0.0 0 1.319 0.1150 0.1311 0.0161 0.008 1.1 3.8 0.5 0.0 0 1.582 0.1149 0.1306 0.0157 0.009 1.1 4.8 0.5 0.0 0 1.846 0.1157 0.1309 0.0152 0.006 1.0 3.8 0.5 0.0 0 0.879 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1149 0.1306 0.0157 0.009 1.1 4.8 0.5 0.0 0 1.846 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.49 13.06 1.57 3.777 21.179 46.211 3.616 11.49 13.06 1.57 3.777 21.179 1.386 3.616 11.49 13.06 1.57 3.774 21.179 5.776 3.616 11.52 13.12 1.60 3.711 21.170 23.105 3.610 11.58 13.25 1.68 3.731 21.139 46.211 3.612 11.49 13.22 1.73 3.754 21.132 69.316 3.606 11.46 13.19 1.74 3.766 21.126 92.422 3.603 11.43 13.19 1.76 3.777 21.122 115.527 3.600 11.42 13.21 1.79 3.791 21.110 138.633 3.599 11.40 13.20 1.80 3.804 21.107 161.738 3.598 11.39 13.19 1.80 3.814 21.102 184.843 3.597 11.37 13.18 1.80 3.821 21.103 207.949 3.596 11.37 13.19 1.82 3.828 21.098 231.054 3.594 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.386 Accepted refinement result: 11.49 13.06 1.57 3.777 21.179 1.386 3.616 Individual atomic B min max mean iso aniso Overall: 9.11 115.01 21.11 3.31 221 1750 Protein: 9.11 115.01 17.01 3.32 0 1519 Water: 11.48 76.67 35.12 N/A 221 223 Other: 19.74 26.61 22.07 N/A 0 8 Chain A: 9.11 115.01 19.42 N/A 0 1750 Chain S: 16.13 60.02 34.50 N/A 221 0 Histogram: Values Number of atoms 9.11 - 19.70 1269 19.70 - 30.29 292 30.29 - 40.88 218 40.88 - 51.47 119 51.47 - 62.06 50 62.06 - 72.65 12 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1149 r_free=0.1306 r_work=0.1149 r_free=0.1306 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1149 r_free = 0.1306 target_work(ml) = 3.616 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1303 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 1.15 - 32.57 A, n_refl.=87582 (all), 4.91 % free)------------| | | | r_work= 0.1143 r_free= 0.1303 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.612765 | | target function (ml) not normalized (work): 300892.753061 | | target function (ml) not normalized (free): 15846.056300 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1151 0.1143 0.1303 n_refl.: 87582 re-set all scales: r(all,work,free)=0.1481 0.1481 0.1519 n_refl.: 87582 remove outliers: r(all,work,free)=0.1481 0.1481 0.1519 n_refl.: 87582 overall B=-0.00 to atoms: r(all,work,free)=0.1481 0.1481 0.1519 n_refl.: 87582 bulk-solvent and scaling: r(all,work,free)=0.1148 0.1140 0.1301 n_refl.: 87582 remove outliers: r(all,work,free)=0.1147 0.1139 0.1301 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 90.62 82 5 0.4039 290.122 258.954 0.457 1.001 0.314 11.894-9.307 95.10 93 4 0.2278 479.412 465.614 0.855 1.002 0.310 9.237-7.194 98.18 209 7 0.2420 388.556 380.394 0.921 1.003 0.210 7.162-5.571 100.00 427 22 0.2219 298.024 286.515 0.916 1.003 0.160 5.546-4.326 100.00 867 58 0.1142 409.114 403.838 0.964 1.003 0.130 4.315-3.360 100.00 1859 96 0.0938 389.070 386.879 1.004 1.002 0.130 3.356-2.611 100.00 3867 181 0.1118 255.599 253.647 1.010 1.002 0.040 2.608-2.026 99.99 8198 413 0.0918 169.439 168.829 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0886 82.745 83.083 1.034 0.999 0.000 1.573-1.221 100.00 36679 1900 0.1249 36.693 36.291 1.027 0.997 0.000 1.221-1.150 99.97 13689 708 0.2166 23.119 21.651 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=-0.0006 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1139 r_free=0.1301 After: r_work=0.1140 r_free=0.1301 ================================== NQH flips ================================== r_work=0.1140 r_free=0.1301 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=0.1301 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1140 r_free=0.1301 | n_water=444 | time (s): 2.560 (total time: 2.560) Filter (dist) r_work=0.1140 r_free=0.1303 | n_water=442 | time (s): 46.820 (total time: 49.380) Filter (q & B) r_work=0.1140 r_free=0.1303 | n_water=442 | time (s): 1.330 (total time: 50.710) Compute maps r_work=0.1140 r_free=0.1303 | n_water=442 | time (s): 1.920 (total time: 52.630) Filter (map) r_work=0.1165 r_free=0.1321 | n_water=335 | time (s): 4.040 (total time: 56.670) Find peaks r_work=0.1165 r_free=0.1321 | n_water=335 | time (s): 0.700 (total time: 57.370) Add new water r_work=0.1217 r_free=0.1382 | n_water=477 | time (s): 3.710 (total time: 61.080) Refine new water occ: r_work=0.1161 r_free=0.1327 adp: r_work=0.1162 r_free=0.1330 occ: r_work=0.1151 r_free=0.1308 adp: r_work=0.1150 r_free=0.1312 occ: r_work=0.1142 r_free=0.1293 adp: r_work=0.1139 r_free=0.1296 ADP+occupancy (water only), MIN, final r_work=0.1139 r_free=0.1296 r_work=0.1139 r_free=0.1296 | n_water=477 | time (s): 292.540 (total time: 353.620) Filter (q & B) r_work=0.1147 r_free=0.1300 | n_water=437 | time (s): 3.970 (total time: 357.590) Filter (dist only) r_work=0.1147 r_free=0.1299 | n_water=436 | time (s): 45.390 (total time: 402.980) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.838400 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 36.201938 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 0.1220 0.1342 0.0122 0.004 0.7 5.8 0.0 0.0 0 0.092 0.1178 0.1315 0.0137 0.004 0.8 4.5 0.0 0.0 0 0.276 0.1161 0.1304 0.0143 0.005 1.0 4.5 0.5 0.0 0 0.552 0.1154 0.1302 0.0148 0.006 1.0 4.2 0.5 0.0 0 0.827 0.1151 0.1301 0.0149 0.007 1.1 4.2 0.5 0.0 0 1.103 0.1148 0.1299 0.0152 0.008 1.1 4.2 0.5 0.0 0 1.379 0.1147 0.1299 0.0152 0.008 1.1 4.2 0.5 0.0 0 1.655 0.1147 0.1299 0.0153 0.009 1.1 4.2 0.5 0.0 0 1.930 0.1153 0.1301 0.0148 0.006 1.1 4.2 0.5 0.0 0 0.919 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1147 0.1299 0.0152 0.008 1.1 4.2 0.5 0.0 0 1.655 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.47 12.99 1.52 3.777 21.130 36.202 3.614 11.47 12.99 1.52 3.777 21.130 1.086 3.614 11.47 12.99 1.52 3.777 21.130 4.525 3.614 11.51 13.03 1.52 3.706 21.122 18.101 3.610 11.52 13.11 1.59 3.725 21.106 36.202 3.610 11.50 13.14 1.64 3.745 21.086 54.303 3.608 11.46 13.14 1.68 3.759 21.080 72.404 3.604 11.44 13.13 1.69 3.767 21.077 90.505 3.602 11.42 13.12 1.70 3.776 21.074 108.606 3.600 11.41 13.14 1.73 3.787 21.069 126.707 3.599 11.38 13.11 1.73 3.795 21.067 144.808 3.597 11.39 13.15 1.75 3.810 21.058 162.909 3.598 11.38 13.12 1.75 3.817 21.056 181.010 3.596 max suggested for this run: 10.00 max allowed Rfree-Rwork gap: 4.0 range of equivalent Rfree: 0.0 Best ADP weight: 1.086 Accepted refinement result: 11.47 12.99 1.52 3.777 21.130 1.086 3.614 Individual atomic B min max mean iso aniso Overall: 9.10 115.01 21.02 3.31 215 1748 Protein: 9.10 115.01 17.01 3.32 0 1519 Water: 11.48 76.67 34.97 N/A 215 221 Other: 19.74 26.61 22.07 N/A 0 8 Chain A: 9.10 115.01 19.37 N/A 0 1748 Chain S: 16.13 60.02 34.42 N/A 215 0 Histogram: Values Number of atoms 9.10 - 19.70 1269 19.70 - 30.29 291 30.29 - 40.88 214 40.88 - 51.47 119 51.47 - 62.06 48 62.06 - 72.65 11 72.65 - 83.24 5 83.24 - 93.83 4 93.83 - 104.42 0 104.42 - 115.01 2 =========================== Idealize ADP of riding H ========================== r_work=0.1147 r_free=0.1299 r_work=0.1147 r_free=0.1299 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1147 r_free = 0.1299 target_work(ml) = 3.614 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1143 r_free = 0.1295 target_work(ml) = 3.613 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 1.15 - 32.57 A, n_refl.=87579 (all), 4.91 % free)------------| | | | r_work= 0.1143 r_free= 0.1295 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 3.612802 | | target function (ml) not normalized (work): 300884.968556 | | target function (ml) not normalized (free): 15835.131164 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1360 0.1361 5.6764 5.6127| | 2: 3.57 - 2.84 1.00 2888 124 0.1094 0.1439 5.1838 5.2595| | 3: 2.83 - 2.48 1.00 2820 163 0.1102 0.1214 4.9582 4.9898| | 4: 2.47 - 2.25 1.00 2825 136 0.0912 0.1015 4.6439 4.69| | 5: 2.25 - 2.09 1.00 2756 127 0.0869 0.0933 4.5886 4.6335| | 6: 2.09 - 1.97 1.00 2846 113 0.0865 0.0987 4.2809 4.3654| | 7: 1.97 - 1.87 1.00 2787 165 0.0891 0.1085 3.9893 4.0823| | 8: 1.87 - 1.79 1.00 2789 144 0.0918 0.1113 3.8959 3.9981| | 9: 1.79 - 1.72 1.00 2745 138 0.0878 0.1174 3.653 3.8215| | 10: 1.72 - 1.66 1.00 2831 160 0.0922 0.1203 3.5712 3.7191| | 11: 1.66 - 1.61 1.00 2712 147 0.0871 0.1037 3.5022 3.5756| | 12: 1.61 - 1.56 1.00 2773 144 0.0909 0.1139 3.3367 3.4679| | 13: 1.56 - 1.52 1.00 2745 130 0.0950 0.1074 3.3174 3.4187| | 14: 1.52 - 1.48 1.00 2803 134 0.0988 0.1020 3.2502 3.3186| | 15: 1.48 - 1.45 1.00 2738 128 0.1005 0.1200 3.1602 3.258| | 16: 1.45 - 1.42 1.00 2756 161 0.1052 0.1256 3.1417 3.2525| | 17: 1.42 - 1.39 1.00 2785 139 0.1143 0.1313 3.1273 3.2469| | 18: 1.39 - 1.36 1.00 2741 179 0.1201 0.1317 3.1113 3.2352| | 19: 1.36 - 1.34 1.00 2807 134 0.1256 0.1560 3.1156 3.2634| | 20: 1.34 - 1.32 1.00 2696 147 0.1367 0.1456 3.1166 3.1537| | 21: 1.32 - 1.30 1.00 2785 112 0.1473 0.1516 3.1194 3.1168| | 22: 1.29 - 1.27 1.00 2704 152 0.1563 0.1968 3.1295 3.296| | 23: 1.27 - 1.26 1.00 2802 156 0.1649 0.1791 3.1384 3.2059| | 24: 1.26 - 1.24 1.00 2744 132 0.1713 0.1833 3.1338 3.2336| | 25: 1.24 - 1.22 1.00 2733 148 0.1886 0.2167 3.1492 3.2673| | 26: 1.22 - 1.21 1.00 2727 135 0.1905 0.1766 3.1535 3.2083| | 27: 1.21 - 1.19 1.00 2814 148 0.2076 0.2166 3.1777 3.1692| | 28: 1.19 - 1.18 1.00 2671 147 0.2203 0.2278 3.1724 3.1754| | 29: 1.18 - 1.16 1.00 2800 134 0.2264 0.2383 3.153 3.2335| | 30: 1.16 - 1.15 1.00 2739 148 0.2445 0.2447 3.1487 3.1729| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.64 1.00 0.97 5925.73| | 2: 3.57 - 2.84 2888 124 0.92 12.74 1.01 0.97 5925.73| | 3: 2.83 - 2.48 2820 163 0.89 16.70 0.99 0.98 4946.94| | 4: 2.47 - 2.25 2825 136 0.92 13.61 1.00 0.98 2422.96| | 5: 2.25 - 2.09 2756 127 0.90 15.73 1.01 0.98 2422.96| | 6: 2.09 - 1.97 2846 113 0.92 12.43 1.02 0.98 1393.49| | 7: 1.97 - 1.87 2787 165 0.95 9.26 1.02 0.98 515.50| | 8: 1.87 - 1.79 2789 144 0.93 12.62 1.00 0.98 515.50| | 9: 1.79 - 1.72 2745 138 0.94 10.07 0.98 0.98 292.71| | 10: 1.72 - 1.66 2831 160 0.94 11.15 0.98 0.98 248.09| | 11: 1.66 - 1.61 2712 147 0.93 11.76 0.98 0.98 237.73| | 12: 1.61 - 1.56 2773 144 0.95 8.94 0.99 0.98 139.96| | 13: 1.56 - 1.52 2745 130 0.95 10.44 1.03 0.98 139.96| | 14: 1.52 - 1.48 2803 134 0.94 10.80 1.02 0.98 125.47| | 15: 1.48 - 1.45 2738 128 0.95 9.96 1.02 0.99 98.92| | 16: 1.45 - 1.42 2756 161 0.94 11.06 1.02 0.99 98.92| | 17: 1.42 - 1.39 2785 139 0.95 10.91 1.01 0.99 89.96| | 18: 1.39 - 1.36 2741 179 0.94 11.52 1.01 0.99 84.77| | 19: 1.36 - 1.34 2807 134 0.94 11.86 0.99 0.99 84.77| | 20: 1.34 - 1.32 2696 147 0.94 12.10 0.98 0.97 80.64| | 21: 1.32 - 1.30 2785 112 0.94 13.09 0.98 0.97 80.35| | 22: 1.29 - 1.27 2704 152 0.93 13.62 0.98 0.97 80.77| | 23: 1.27 - 1.26 2802 156 0.92 14.81 0.97 0.95 82.91| | 24: 1.26 - 1.24 2744 132 0.92 14.85 0.96 0.95 82.91| | 25: 1.24 - 1.22 2733 148 0.91 16.32 0.96 0.94 84.91| | 26: 1.22 - 1.21 2727 135 0.90 18.08 1.02 0.94 87.13| | 27: 1.21 - 1.19 2814 148 0.89 18.77 1.02 0.94 87.13| | 28: 1.19 - 1.18 2671 147 0.88 20.38 1.01 0.93 90.80| | 29: 1.18 - 1.16 2800 134 0.88 20.46 0.99 0.93 92.17| | 30: 1.16 - 1.15 2739 148 0.86 22.00 0.98 0.93 92.17| |alpha: min = 0.93 max = 0.99 mean = 0.97| |beta: min = 80.35 max = 5925.73 mean = 910.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.93| |phase err.(work): min = 0.00 max = 89.98 mean = 13.47| |phase err.(test): min = 0.00 max = 89.88 mean = 13.46| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1151 0.1143 0.1295 n_refl.: 87579 re-set all scales: r(all,work,free)=0.1483 0.1484 0.1493 n_refl.: 87579 remove outliers: r(all,work,free)=0.1483 0.1484 0.1493 n_refl.: 87579 overall B=-0.00 to atoms: r(all,work,free)=0.1483 0.1484 0.1493 n_refl.: 87579 bulk-solvent and scaling: r(all,work,free)=0.1151 0.1144 0.1296 n_refl.: 87579 remove outliers: r(all,work,free)=0.1150 0.1143 0.1296 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 88.54 80 5 0.4038 287.941 252.452 0.433 1.001 0.291 11.894-9.307 94.12 92 4 0.2393 479.450 462.647 0.858 1.002 0.277 9.237-7.194 98.18 209 7 0.2414 388.556 379.420 0.921 1.002 0.190 7.162-5.571 100.00 427 22 0.2209 298.024 286.862 0.914 1.003 0.180 5.546-4.326 100.00 867 58 0.1142 409.114 403.801 0.963 1.003 0.116 4.315-3.360 100.00 1859 96 0.0938 389.070 386.974 1.002 1.002 0.097 3.356-2.611 100.00 3867 181 0.1127 255.599 253.617 1.011 1.002 0.029 2.608-2.026 99.99 8198 413 0.0918 169.439 168.843 1.025 1.001 0.000 2.025-1.573 100.00 17313 902 0.0893 82.745 83.097 1.034 1.000 0.000 1.573-1.221 100.00 36679 1900 0.1253 36.693 36.296 1.026 0.997 0.000 1.221-1.150 99.97 13689 708 0.2168 23.119 21.654 0.987 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0151 b_overall=-0.0011 ================= 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 : 0.2610 0.1920 0.082 5.295 8.8 119.3 19.9 258 0.000 1_bss: 0.1632 0.1748 0.082 5.295 9.0 119.4 20.0 258 0.000 1_settarget: 0.1632 0.1748 0.082 5.295 9.0 119.4 20.0 258 0.000 1_nqh: 0.1637 0.1755 0.082 5.295 9.0 119.4 20.0 258 0.003 1_weight: 0.1637 0.1755 0.082 5.295 9.0 119.4 20.0 258 0.003 1_xyzrec: 0.1222 0.1462 0.007 0.929 9.0 119.4 20.0 258 0.138 1_adp: 0.1230 0.1459 0.007 0.929 9.0 119.4 20.0 258 0.138 1_regHadp: 0.1231 0.1462 0.007 0.929 9.0 119.4 20.0 258 0.138 1_occ: 0.1226 0.1458 0.007 0.929 9.0 119.4 20.0 258 0.138 2_bss: 0.1225 0.1453 0.007 0.929 9.1 119.4 20.1 258 0.138 2_settarget: 0.1225 0.1453 0.007 0.929 9.1 119.4 20.1 258 0.138 2_updatecdl: 0.1225 0.1453 0.007 0.937 9.1 119.4 20.1 258 0.138 2_nqh: 0.1225 0.1453 0.007 0.937 9.1 119.4 20.1 258 0.138 2_sol: 0.1194 0.1394 0.007 0.937 9.1 115.0 22.2 421 n/a 2_weight: 0.1194 0.1394 0.007 0.937 9.1 115.0 22.2 421 n/a 2_xyzrec: 0.1183 0.1417 0.008 0.940 9.1 115.0 22.2 421 n/a 2_adp: 0.1183 0.1417 0.008 0.940 9.1 115.0 22.2 421 n/a 2_regHadp: 0.1183 0.1417 0.008 0.940 9.1 115.0 22.2 421 n/a 2_occ: 0.1183 0.1406 0.008 0.940 9.1 115.0 22.2 421 n/a 3_bss: 0.1178 0.1402 0.008 0.940 9.1 115.0 22.2 421 n/a 3_settarget: 0.1178 0.1402 0.008 0.940 9.1 115.0 22.2 421 n/a 3_updatecdl: 0.1178 0.1402 0.008 0.939 9.1 115.0 22.2 421 n/a 3_nqh: 0.1178 0.1402 0.008 0.939 9.1 115.0 22.2 421 n/a 3_sol: 0.1205 0.1403 0.008 0.939 9.1 115.0 21.2 430 n/a 3_weight: 0.1205 0.1403 0.008 0.939 9.1 115.0 21.2 430 n/a 3_xyzrec: 0.1162 0.1326 0.007 1.012 9.1 115.0 21.2 430 n/a 3_adp: 0.1162 0.1326 0.007 1.012 9.1 115.0 21.2 430 n/a 3_regHadp: 0.1162 0.1326 0.007 1.012 9.1 115.0 21.2 430 n/a 3_occ: 0.1154 0.1324 0.007 1.012 9.1 115.0 21.2 430 n/a 4_bss: 0.1147 0.1314 0.007 1.012 9.1 115.0 21.2 430 n/a 4_settarget: 0.1147 0.1314 0.007 1.012 9.1 115.0 21.2 430 n/a 4_updatecdl: 0.1147 0.1314 0.007 1.014 9.1 115.0 21.2 430 n/a 4_nqh: 0.1147 0.1314 0.007 1.014 9.1 115.0 21.2 430 n/a 4_sol: 0.1155 0.1308 0.007 1.014 9.1 115.0 21.1 444 n/a 4_weight: 0.1155 0.1308 0.007 1.014 9.1 115.0 21.1 444 n/a 4_xyzrec: 0.1149 0.1306 0.009 1.125 9.1 115.0 21.1 444 n/a 4_adp: 0.1149 0.1306 0.009 1.125 9.1 115.0 21.1 444 n/a 4_regHadp: 0.1149 0.1306 0.009 1.125 9.1 115.0 21.1 444 n/a 4_occ: 0.1143 0.1303 0.009 1.125 9.1 115.0 21.1 444 n/a 5_bss: 0.1139 0.1301 0.009 1.125 9.1 115.0 21.1 444 n/a 5_settarget: 0.1139 0.1301 0.009 1.125 9.1 115.0 21.1 444 n/a 5_updatecdl: 0.1139 0.1301 0.009 1.127 9.1 115.0 21.1 444 n/a 5_setrh: 0.1140 0.1301 0.009 1.127 9.1 115.0 21.1 444 n/a 5_nqh: 0.1140 0.1301 0.009 1.127 9.1 115.0 21.1 444 n/a 5_sol: 0.1147 0.1299 0.009 1.127 9.1 115.0 21.0 436 n/a 5_weight: 0.1147 0.1299 0.009 1.127 9.1 115.0 21.0 436 n/a 5_xyzrec: 0.1147 0.1299 0.008 1.127 9.1 115.0 21.0 436 n/a 5_adp: 0.1147 0.1299 0.008 1.127 9.1 115.0 21.0 436 n/a 5_regHadp: 0.1147 0.1299 0.008 1.127 9.1 115.0 21.0 436 n/a 5_occ: 0.1143 0.1295 0.008 1.127 9.1 115.0 21.0 436 n/a end: 0.1143 0.1296 0.008 1.127 9.1 115.0 21.0 436 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2731660_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained/shake_2731660_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1100 Refinement macro-cycles (run) : 14385.3300 Write final files (write_after_run_outputs) : 67.6600 Total : 14457.1000 Total CPU time: 4.02 hours =========================== phenix.refine: finished =========================== # Date 2024-12-27 Time 22:21:12 PST -0800 (1735366872.59 s) Start R-work = 0.1632, R-free = 0.1748 Final R-work = 0.1143, R-free = 0.1296 =============================================================================== Job complete usr+sys time: 14588.92 seconds wall clock time: 264 minutes 33.00 seconds (15873.00 seconds total)